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Journal of Mammalian Evolution, Vol. 5, No. 2, 1998
Phylogenetic Relationships Between the Orders
Artiodactyla and Cetacea: A Combined Assessment of
Morphological and Molecular Evidence
W. Patrick Luckett1,2,4 and Nancy Hong3
A character analysis of selected conservative morphological traits from extant and fossil artio-
dactyls and cetaceans was combined with a similar analysis of conservative nucleotide positions
from the complete mitochondrial cytochrome b sequences of available extant artiodactyls, ceta-
ceans, sirenians, perissodactyls, and other mammals. This combined analysis focuses on the
evidence that supports conflicting hypotheses of artiodactyl monophyly, including the affinities
of hippopotamids and the monophyly or paraphyly of odontocete cetaceans. Highly conserved
morphological traits of the astragalus and deciduous dentition provide strong corroboration of
artiodactyl monophyly, including extant and fossil hippopotamids. In contrast, cytochrome b
gene sequences are incapable of confirming this monophyly, due to excessive homoplasy of
nucleotide and amino acid traits within extant Eutheria. In like manner, highly conserved and
uniquely derived morphological features of the skull and auditory regions provide robust cor-
roboration of Odontoceti monophyly, including extant and fossil physeteroids. Several nucleo-
tide similarities do exist between physeteroids and mysticetes; however, most are either silent
third-position transversions or occur also in two or more odontocete families. We suggest that
increased taxon sampling, combined with functional considerations of amino acids and their
secondary structure in protein-coding genes, are essential requirements for the phylogenetic
interpretations of molecules at higher taxonomic levels, especially when they conflict with well-
supported hypotheses of mammalian phylogeny, corroborated by uniquely derived morpho-
logical traits from extant and fossil taxa.
KEY WORDS: Artiodactyla; hippopotamuses; Cetacea; morphology; cytochrome b; evolu-
tion.
INTRODUCTION
Artiodactyla is the most successful order of large-bodied extant and fossil mammals
in terms of number of genera and families recognized, and there has been little doubt
about its “naturalness” or monophyly since the classifications erected by Owen (1848)
1 Department of Anatomy, University of Puerto Rico Medical Sciences Campus, P.O. Box 365067, San Juan,
Puerto Rico 00936-5067.
2 Department of Mammalogy, American Museum of Natural History, New York, New York 10024.
3Carribean Primate Research Center, University of Puerto Rico Medical Science Campus, P.O. Box 365067,
San Juan, Puerto Rico 00936-5067.
4To whom correspondence should be addressed at Department of Anatomy, University of Puerto Rico Medical
Sciences Campus, PO Box 365067, San Juan, Puerto Rico 00936-5067. Fax: (787) 767-0788; e-mail:
p_luckett@rcmaca.upr.clu.edu
127
1064-7554/98/0600-0127$15.00/0 © 1998 Plenum Publishing Corporation
128 Luckett and Hong
and by Cope (1888–1889). Much of the available cranial, postcranial, dental, and soft
anatomical evidence for artiodactyl monophyly and intraordinal relationships was sum-
marized ably by Weber (1904, 1928); many of these same attributes have been incor-
porated into subsequent cladistic analyses of eutherian and artiodactyl interrelationships
(Novacek, 1992a, 1993; Prothero et al., 1988; Gentry and Hooker, 1988; Prothero,
1993).
In contrast to the unanimous support for artiodactyl monophyly among evolutionary
morphologists, there is a widespread consensus among molecular biologists concerning
the alleged paraphyly of Artiodactyla, based on analyses of amino acid and gene
sequences from a variety of proteins. In many of these molecular evolutionary studies,
the artiodactyl families Hippopotamidae, Suidae, Tayassuidae, and Camelidae do not
cluster with pecorans; instead, cetaceans commonly group with either Pecora or Hip-
popotamidae, rather than with a monophyletic Artiodactyla as a whole (Irwin et al.,
1991; Irwin and Arnason, 1994; Graur and Higgins, 1994; Arnason and Gullberg, 1996;
Lavergne et al., 1996; Smith et al., 1996; Gatesy et al., 1996; Montgelard et al., 1997;
Gatesy, 1997).
Despite this widespread claim by molecular biologists for the nonmonophyly of
Artiodactyla, most researchers have not presented molecular "synapomorphies" to cor-
roborate their alternative phylogenetic hypotheses, nor have they discussed the mor-
phological synapomorphies that have been used for more than 100 years to support
artiodactyl monophyly. Instead, cladograms (or dendrograms) are presented with tree
robustness or strength of support for the maximum-parsimony, neighbor-joining, or
maximum-likelihood analyses indicated by bootstrap percentages or decay indices. No-
table exceptions to this are the recent study by Montgelard et al. (1997) on cytochrome
b (cyt b) and 12S rRNA mitochondrial gene sequences and the analysis by Gatesy (1997)
of the blood-clotting protein gene g-fibrinogen. In addition to the "robust" bootstrap
and decay index support provided by both research groups for a hippopotamid-cetacean
clade, they also identified some probable nucleotide or amino acid synapomorphies to
support this clade. Thus, Gatesy (1997, p. 538) identified five nucleotide synapomor-
phies in the g-fibrinogen sequences that "unambiguously support the Cetacea/Hippo-
potamidae clade," and Montgelard et al. (1997, p. 557) identified one "nearly exclusive
synapomorphic replacement at position 243" in the aligned cyt b amino acid sequences
of 199 mammalian species, representing 11 eutherian orders. In contrast, the latter authors
could find no synapomorphic amino acids to support a monophyletic Artiodactyla
(including Hippopotamidae).
Gatesy (1997) cited some of the morphological traits that have been used to support
the monophyly of Artiodactyla, including the double-trochleated astragalus that is tra-
ditionally listed as the strongest synapomorphy of extant and fossil Artiodactyla (i.e.,
Schaeffer, 1948; Rose, 1996), including the family Hippopotamidae. Nevertheless, his
combined parsimony analysis of four genes (g-fibrinogen, b-casein, k-casein, and cyto-
chrome b) provided seemingly strong support for the alternative hypothesis of a para-
phyletic Artiodactyla, in which Hippopotamidae is the sister group of Cetacea, rather
than clustering with other artiodactyls. Robust statistical support for the hippo-
potamid-cetacean hypothesis was indicated by a high bootstrap percentage (99) and decay
index (15). Consequently, Gatesy (1997, p. 542) stated that 30 unambiguous skeletal
synapomorphies would have to be added to the combined gene sequence data set "to
Evolution of Artiodactyla and Cetacea 129
force the removal of Cetacea from within Artiodactyla." He also asserted that this
"assumes that a single nucleotide substitution carries as much weight in phylogenetic
analysis as the evolution of a stable morphological feature such as the double-pulleyed
astragalus of artiodactyls," although he acknowledged that this assertion might not be
considered "reasonable" by many paleontologists.
Another area of disagreement between morphologists and some molecular biolo-
gists concerns the relationship of sperm whales (physeteroids) to other extant cetaceans.
Following an analysis of partial sequences from two mitochondrial genes (12S and 16S
rRNA) in 16 species of whales and four outgroup species, Milinkovitch et al. (1993)
detected a "surprising outcome" in that one group of odontocetes (sperm whales) was
more closely related to mysticetes (baleen whales) than it was to the other odontocetes
studied. Milinkovitch et al. (1993, p. 346) noted that this hypothesis is at odds with the
traditional systematic division of extant cetaceans into the suborders Odontoceti and
Mysticeti, and they suggested that this apparent paraphyly of Odontoceti "would seem
to call for a reclassification of cetaceans." This paraphyly hypothesis has been disputed
by morphological studies (Fordyce and Barnes,1994; Luo and Marsh, 1996; Heyning,
1997) and by parsimony analyses of another mitochondrial gene (cytochrome b) by
Arnason and Gullberg (1994, 1996), using a more extensive sampling of cetaceans and
artiodactyls. In addition, a recent combined analysis of morphological and molecular
data (Messenger and McGuire, 1998) strongly supports the traditional view of Odonto-
ceti monophyly. The controversy about physeteroid relations to other cetaceans contin-
ues, with differing assumptions about methods of analysis (parsimony versus maximum
likelihood), taxon sampling, and choice of outgroups for the molecular studies (see
Hasegawa and Adachi, 1996; Milinkovitch et al., 1996; Hasegawa et al., 1997; Mes-
senger and McGuire, 1998).
A major difficulty in assessing the apparent conflicts between molecules and mor-
phology for phylogenetic reconstruction is the differing methods used to test support for
nodes or branches of a cladogram. Morphologists routinely list the probable synapo-
morphies that support extant and/or fossil higher taxa, whereas molecular synapomor-
phies are rarely identified explicitly. Instead, relative support for molecular cladograms
is indicated indirectly, commonly by resampling the data (bootstrap proportion) or by
counting the number of additional steps necessary to cause a particular clade to lose its
support (the decay index). Although Gatesy (1997, p. 542) stressed the need for a method
by which "morphological and molecular characters can be scrutinized simultaneously
using widely accepted criteria for homology," he presented no solution for this dilemma.
An obvious solution was suggested originally by Hennig (1966), when he emphasized
that all types of characters, whether morphological or biochemical, can be used in phy-
logenetic analyses, as long as the relatively primitive and derived character states for
each can be identified. Another valuable procedure for the analysis of higher systematic
relationships is the reconstruction of an ancestral character state or "morphotype" for
each trait used in phylogenetic analysis of each higher taxon, such as families, super-
families, or suborders. Given the mosaic nature of both morphological and molecular
evolution, morphotype reconstruction, based on examination of as many species and
genera as possible, is preferable to choosing "exemplars" to represent higher taxa, if
one wishes to reconstruct the pattern of descent with modification of characters and
character complexes during phylogeny.
130 Luckett and Hong
Within Mammalia at least, there is usually minimal controversy concerning the
species content of monophyletic families, when either morphological or molecular data
are assessed with adequate taxon representation (e.g., Arnason et al., 1996). Morpho-
type reconstruction is relatively straightforward for both morphological and molecular
sequence data at the family level, as shown in an earlier assessment of marsupial evo-
lution (Luckett, 1994), when the analysis is limited to a relatively small and conservative
data set. This approach is fundamental similar to the "compartmentalization" method
of analysis for molecular sequence data proposed by Mishler (1994). Morphotype recon-
struction is especially important when analyzing soft anatomical or gene sequence data
for assessment of higher taxon relationships among extant organisms, in the absence of
fossil evidence for these traits. Apparent shared, derived characters that support a sister-
group relationship between two higher taxa (such as Hippopotamidae and Cetacea) may
instead have been derived independently within each group, if it can be shown that both
primitive and derived character states occur within one or both taxa.
Wagele (1995) has analyzed the "information content" of molecular and morpho-
logical characters in terms of its usefulness for phylogenetic reconstruction. He noted
that nucleotide substitutions are the smallest possible characters that can be analyzed as
plesiomorphies or apomorphies in phylogenetic studies, and Wagele (1995, p. 42) con-
cluded that "the genetic and phylogenetic information content of a complex
morphological character is much higher than that of a sequence position." This postu-
lated inverse relationship between a trait's simplicity or complexity and its information
content (in terms of determining the probability of hypotheses for homology versus
homoplasy and for the polarities of transformation series of character states) can be tested
by careful character analyses of both morphological and molecular data.
The present study was designed to test conflicting hypotheses of artiodactyl
monophyly or paraphyly, particularly with regard to the sister-group relationship of the
Miocene-Recent family Hippopotamidae, either with other artiodactyls or with Cetacea.
The second hypothesis to be tested concerns whether the cetacean suborder Odontoceti
is monophyletic, or whether the physeteroids and mysticetes share a sister-group rela-
tionship, to the exclusion of other odontocetes. Both molecular data (from the mito-
chondrial cytochrome b gene) and selected morphological traits were submitted to
character analysis and morphotype reconstruction at the family level to test these alter-
native hypotheses. Emphasis was placed on the search for shared, derived characters
from both data sets to support any of the conflicting hypotheses, and broad sampling of
families from ingroups and multiple outgroups was employed to facilitate the assessment
of homology or homoplasy of putative synapomorphies that support different hypotheses.
Disagreements about the probable homologous or homoplastic nature of shared derived
similarities between taxa lie at the core of most conflicting phylogenetic hypotheses.
Detailed character analyses can provide further insight into the usefulness and "reli-
ability" of different characters for the study of higher-level phylogenetic relationships
among mammals and other organisms.
MATERIALS AND METHODS
Selected morphological traits from the cranium, postcranium, and dentition of extant
and fossil artiodactyls, cetaceans, mesonychians, perissodactyls, "condylarths," siren-
Evolution of Artiodactyla and Cetacea 131
ians, proboscideans, hyracoids, carnivorans, and other eutherian taxa were examined in
museum collections and/or the literature. Emphasis was placed on conservative char-
acters or character complexes that appear to have some diagnostic value for higher taxa,
such as orders or suborders, based on assessments by earlier investigators. These char-
acter complexes from "hard" anatomy can often be traced through the fossil record and
thus provide valuable evidence for the origin and persistence of rare or unique characters
during mammalian evolution. Where appropriate, data from soft anatomical or ontoge-
netic features were used also to test hypotheses of higher taxa monophyly.
Mammal collections from the following museums (with their abbreviations) were
utilized during this study: American Museum of Natural History, Departments of Mam-
malogy and Vertebrate Paleontology, New York (AMNH); Carnegie Museum of Natural
History, Pittsburgh (CM); Museum National d'Histoire Naturelle, Institut de Paleonto-
logie, and Laboratoire d'Anatomie Comparee, Paris (MNHN IP and MNHN LAC);
Forschungsinstitut und Naturmuseum Senckenberg, Frankfurt am Main (SM); and
National Natuurhistorisch Museum, Leiden (NNM).
Sequence data from the mitochondrial cytochrome b (cyt b) gene of artiodactyls,
cetaceans, perissodactyls, tethytheres, and other eutherian mammals were acquired and
analyzed from various sources, including GenBank (see Appendix for taxa studied and
sources of published sequences); the marsupial family Didelphidae and the monotreme
family Ornithorhynchidae were used as additional outgroups. In most cases complete
sequences of the gene were available. Emphasis was placed on examining sequences
from as many genera and species of the ingroups (Artiodactyla and Cetacea) and out-
groups (other eutherian higher taxa,didelphid marsupials, and the platypus) as feasible,
in order to assess the likelihood of homoplasy and back mutations as potential sources
of systematic error. Such extensive taxon sampling within Eutheria facilitates, however
tentatively, morphotype reconstruction of individual nucleotide positions in the gene for
eutherian families or other higher taxa, as well as a preliminary morphotype reconstruc-
tion for the infraclass Eutheria. Comparisons of nucleotide morphotypes across families
provide a greater chance for the reconstruction of character transformations at nucleotide
(and ultimately at amino acid) positions within higher taxa, such as superfamilies, subor-
ders, and orders, during mammalian evolution. In the absence of ontogenetic and fossil
data, extensive sampling of both ingroup and outgroup taxa provides the only method
for assessing the likely polarity (and homology) of transformation series of specific
nucleotides and amino acids for phylogenetic reconstruction.
Because provisional evolutionary analyses of the cyt b gene in various artiodactyls,
cetaceans, and other eutherians have already been conducted for all family-level and
higher taxa used by the investigators listed in the Appendix (although with less taxon
sampling than the present study), the phylogenetic hypotheses generated by these pub-
lished studies provided the starting point for the present analysis. Comparing the results
of these studies with published morphological analyses of the same taxa indicates that
there is little, if any, controversy concerning the monophyly and content of extant eu-
therian families. Disagreements are often evident, however, with regard to the supra-
familial relationships of these taxa, including the artiodactyls and cetaceans that are the
focus of the present study. These published results reinforce the value of morphotype
reconstruction for both molecular and morphological characters at the family level for
the assessment of higher taxon eutherian relationships.
132 Luckett and Hong
Published studies on cyt b evolution clearly indicate that the gene contains a mixture
of highly conservative or invariable nucleotide positions and other positions that are
highly variable, such as many nucleotides in the third position of codons (see Irwin et
al., 1991; Irwin and Arnason, 1994). Neither of these classes of nucleotides is of much
value for assessing suprafamilial relationships among mammals or other organisms,
because of excessive homoplasy. Instead, it is the nucleotide positions that show an
intermediate or moderate degree of variation that provide the major source of character
data ("informative sites") for phylogenetic reconstruction of gene sequences.
We follow the recommendations of Irwin and Arnason (1994) by analyzing only
"conservative nucleotide substitutions" in the cyt b gene; these are all replacement
substitutions at the first and second positions of codons, but only transversions at the
third position. Thus, nucleotides at the third position of codons are coded as either R
(for the purines, A or G) or Y (for the pyrimidines, C or T). In addition, the first position
of leucine amino acid codons is also coded as Y, because of silent transitions at this
position.
The aligned cyt b sequences of Irwin and Arnason (1994), Arnason and Gullberg
(1996), and Randi et al. (1996) were examined by eye for variations at each of the 1140
nucleotide positions, and those relatively conservative positions that provided adequate
evidence for family-level morphotype reconstruction were selected for further analysis.
Ideally, each genus and species within a family would contain an identical base pair at
the selected nucleotide position; this would provide a virtual 100% certainty that a par-
ticular base (=character) occurred in the last common ancestor of the extant members
of that family. In reality, this certainty was obtained for many positions within many
families. In other cases, variation occurs among genera or species within a family, even
for relatively "conservative" positions. Some of these variations may be the result of
back mutations, a condition virtually impossible to corroborate with any degree of cer-
tainty. Other changes may represent forward or derived changes that occurred after the
origin of the family. These can be expected and detected if only one or two such changes
occur within speciose families containing four or more genera. The more back and for-
ward mutations that occur among genera within a family, the more difficult it is to recon-
struct the ancestral morphotype for individual characters for the family. In such cases,
it is more honest to indicate uncertainty (?) for the morphotype of a particular nucleotide
character in these families.
This method of morphotype reconstruction for nucleotide characters was used in an
earlier study (Luckett, 1994) and is basically similar to that used by McKenna (1987)
for reconstructing the plesiomorphic condition for amino acid residues of myoglobin and
a-crystallin lens protein in Mammalia. Another condition imposed on the selection of
nucleotide characters is that they provide potential information on the evolutionary rela-
tionships among the ingroup taxa that form the focus of this study. No bias existed in
the choice of characters that support one or more conflicting hypotheses of relationships
among hippopotamids, artiodactyls, physeteroids, other odontocetes, and mysticetes.
Instead, the "usefulness" of the characters themselves in terms of testing alternative
hypotheses was the basis for their selection from the 1140 possible nucleotide characters
available in the cytochrome b gene of therian mammals. The multiple outgroups used
may also demonstrate certain patterns of evolutionary relationships among some out-
group taxa (i.e., monophyly of tethytheres); this is only a by-product of the focus of our
Evolution of Artiodactyla and Cetacea 133
analysis on artiodactylan–cetacean interrelationships, but it points the way for further
assessments of other suprafamilial eutherian relationships.
RESULTS
Morphological Character Analyses
Published character analyses of eutherian relationships have provided summaries of
some of the morphological evidence that supports the monophyly of the orders Artio-
dactyla and Cetacea (Prothero et al., 1988; Gentry and Hooker, 1988; Prothero, 1993;
Fordyce and Barnes, 1994; Heyning and Mead, 1990; Heyning, 1989, 1997), and only
a few of these traits are analyzed here. Emphasis is given to those conservative characters
whose evolutionary history can be traced in both extant and fossil taxa and that can aid
in the "diagnosis" of higher taxa such as orders.
Artiodactyla Monophyly. The monophyly of extant Artiodactyla and its fossil rep-
resentatives has not been questioned seriously by morphologists since the time of Owen's
(1848) classification of mammals. The postcranial skeleton provides the most derived
or unique traits that support artiodactyl monophyly; many characters of the dentition and
cranium are relatively primitive or generalized features shared with other "ungulate"
orders, as noted by Rose (1996). The diagnostic character complex of the order is its
uniquely derived double-trochleated astragalus (=talus) in the hindfoot (Fig. 1); this
complex trait and its associated pattern of articular facets for the calcaneus, cuboid, and
navicular occur in all species of extant artiodactyls and in all fossil artiodactyls for which
there is relevant evidence, including the oldest known genus, Diacodexis, from the lower
Eocene of North America, Europe, and Asia (see Schaeffer, 1947, 1948; Thewissen and
Hussain, 1990; Rose, 1996). This unique astragalar morphology has not been found in
any other extant or fossil mammalian group, including the various taxa that have devel-
oped a cursorial locomotor pattern independently, such as mesonychids, arctocyonids,
or perissodactyls (Table I). As emphasized by Schaeffer (1947), this derived character
complex is already completely differentiatedin the lower Eocene artiodactyl Diacodexis,
and only a small amount of further evolutionary modification has occurred in the sub-
sequent 55 million years. We have confirmed the presence of a double-trochleated astra-
galus in all extant genera of artiodactyls, as well as in 208 genera from the 27 fossil
artiodactyl families [classification of McKenna and Bell (1997)] which do not contain
living representatives.
Another derived character complex of all known extant and fossil artiodactyls
(including Diacodexis) is their highly specialized paraxonic feet (especially the hind-
feet), in which there has been subequal elongation and thickening of metapodials III and
IV and concomitant subequal reduction in the length and diameter of metapodials II and
V, associated with an extreme reduction or loss of digit I (Fig. 2). Paraxony also char-
acterized mesonychids and Eocene cetaceans, and this has been the main morphological
feature used to support a sister-group relationship between Artiodactyla and Cetacea
among extant orders (Gingerich et al., 1990).
A third derived, complex character that has received less attention in assessments
of ungulate and eutherian interrelationships is the elongate, trilobed lower fourth de-
ciduous premolar ( = dP4) of the juvenile dentition in extant and fossil artiodactyls (Figs.
134 Luckett and Hong
Fig. 1. Camera lucida drawings of the right astragali of artiodactyls (showing the unique double-
trochleated pattern) and other eutherians. (A) Bunophorus, (B) Chriacus, (C) Pachyaena, and
(E) Choeropsis redrawn from O'Leary and Rose (1995). (D) Kenyapotamus redrawn from Pick-
ford (1983). Scale = 5 mm.
3 and 4). This dental character was not included by Prothero et al. (1998) in their anal-
ysis of ungulate relationships, although it was cited as an artiodactyl autapomorphy by
Gentry and Hooker (1988). Because this trait can be detected only in juvenile or subadult
specimens, it is often overlooked by neontologists and paleontologists who study dental
evolution in mammals. Both occlusal and ontogenetic evidence suggests that the anterior
lobe of the trilobed dP4, bearing a mesiobuccal and mesiolingual cusp, is a neomorphic
feature, compared to the three lower molars of artiodactyls (Pearson, 1923; Hooijer,
1942) and to the molariform dP4 of early eutherians. In addition to an anteriorly dis-
placed paraconid, the anterior lobe of the artiodactyl dP4 is characterized by the devel-
Evolution of Artiodactyla and Cetacea 135
Table I. Character Analysis of Selected Eutherian Cyt b Nucleotide and Morphological Traits for Assessing
Intraartiodactylan Relationships
Primitive
1 . Astragalus not double-trochleated
2. Molariform dP4
3. Nucleotide 722— C
4. Nucleotide 639— Y?
5. Nucleotide 476—C
6. Nucleotide 1092—Y
7. Nucleotide 1053—Y
8. Nucleotide 912— Y
9. Nucleotide 228—Y
10. Nucleotide 921— Y
11. Nucleotide 475— A
12. Nucleotide 198— Y
13. Nucleotide 324—Y
14. Nucleotide 777—Y
15. Nucleotide 1026—R
16. No cartilaginous snout disk
17. Nucleotide 381—R
18. Nucleotide 846—R
19. Nucleotide 1107—R
20. Nucleotide 783—Y
21. Nucleotide 831—R
22. Nucleotide 315—Y
23. Nucleotide 180—R
24. Nucleotide 361— T
25. Nucleotide 282— R
26. Cuboid— navicular not fused
27. Nucleotide 192— R
28. Nucleotide 244— Y
29. Nucleotide 288—Y
30. Nucleotide 357—R
Derived
1 . Double-trochleated astragalus
2. Trilobed dP4
3. Nucleotide 722—T
4. Nucleotide 639—R?
5. Nucleotide 476— A
6. Nucleotide 1092— R
7. Nucleotide 1053— R
8. Nucleotide 912—R
9. Nucleotide 228— R
10. Nucleotide 921—R
11. Nucleotide 475— G
12. Nucleotide 198— R
13. Nucleotide 324—R
14. Nucleotide 777— R
15. Nucleotide 1026—Y
16. Cartilaginous snout disk
17. Nucleotide 381—Y
18. Nucleotide 846—Y
19. Nucleotide 1107—Y
20. Nucleotide 783— R
21. Nucleotide 831—Y
22. Nucleotide 315—R
23. Nucleotide 180—Y
24. Nucleotide 361—C
25. Nucleotide 282—Y
26. Cuboid—navicular fused
27. Nucleotide 192—Y
28. Nucleotide 244—A
29. Nucleotide 288—R
30. Nucleotide 357—Y
opment of a neomorphic cusp on the paracristid that runs between the protoconid and
the paraconid; this new cusp provides a "squaring" of the anterior portion of the tooth
(Fig. 5). The elongate, trilobed dP4 occludes above with dP3–4, with the anterior lobe
of dP4 occluding between the paracone and the metacone of the variably elongate dP3
Fig. 2. Camera lucida drawing of the paraxonic right hindfoot of the early Eocene dichobunid artiodactyl
Diacodexis metsiacus, showing the greatly elongated and thickened metatarsals III and IV and the reduced
metatarsals II and V. Redrawn from Rose (1985). Scale = 10 mm.
136 Luckett and Hong
Fig. 3. Camera lucida drawing of a partial right dentary of the anthracotheriid Bothriogenys gorringei, show-
ing the juvenile dentition, with erupted dP2–4 and the apex of the unerupted M1, in buccal view. AMNH 13365
(Fayum, Egypt).
(Fig. 4), as emphasized by Stehlin (1899) and Pearson (1923). The ontogeny of these
functional and occlusional relationships between dP4 and dP3–4 during tooth eruption has
been described and illustrated for "miniature" domestic pigs between the third and the
tenth weeks of postnatal development (McKean et al., 1971).
Our examinations indicate that the specialized structural and occlusal relationships
among dP3–dP4 are found in all families of extant artiodactyls, regardless of the
Fig. 4. Camera lucida drawing of the juvenile left jaws of the pygmy hippopotamus, Choeropsis liberien-
sis, showing the erupting deciduous premolars. In both jaws, dP3 are in an advanced stage of eruption,
whereas dP4 is in a mideruption phase and dP4 is in very early eruption. Note the developing occlusal
relationship between the anterior lobe of the trilobed dP4 and the middle of dP3. AMNH 150011. Scale
= 10 mm.
Evolution of Artiodactyla and Cetacea 137
Fig. 5. Camera lucida drawing of an isolated left
dP4 from Diacodexis cf. varleti (SLP 29PR 2122)
from Premontre, France (lower Eocene). The
obliquely occlusal view from the buccal side shows
an early evolutionary stage of the trilobed tooth,
with a small mesiobuccal cusp (Pc) developed on
the paracristid. Cast provided by Jean Sudre. M,
metaconid; Pa, paraconid. Scale = 1 mm.
bunodont or selenodont nature of cusp morphology on molars and deciduous premolars.
An identical functional pattern can be detected in middle Eocene to Pleistocene fossils
of juvenile artiodactyls, when occluding jaws are found [see Tobien (1985, Figs. 2, 5)
for these derived occlusal relationships in the middle Eocene haplobunodontid Masilla-
bune, Scott (1940, Plate 49, Fig. 1) for the Oligocene anthracotheriid Elomeryx, and
Filhol (1880, Plate 8) for the Miocene suid Hyotherium]. Another attribute of the artio-
dactyl dP4 is that its anterior-posterior length exceeds that of M1 or M2, whereas this is
not true of upper dP4 and M1–2 relationships. Finally, in nearly all Eocene and later artio-
dactyls, the elongate, molariform dP4 is replaced during ontogeny by a more premo-
lariform P4. This complex pattern of structural-functional and ontogenetic relationships
among dP3–4 and M1–2, characteristic of all extant and fossil artiodactyls (when known),
is not found in any other mammalian order (Table I).
The presence of a derived, trilobed dP4 in numerous families of middle Eo-
cene-Pleistocene fossil artiodactyls (Cuvier, 1822; Stehlin, 1910; Zittel, 1925; Scott,
1940; Sudre, 1978; Tobien, 1985) suggests that this character complex (including its
special occlusal relationships) probably occurs in all fossil artiodactyls. Our examina-
tions of this trait in museum collections, supplemented by illustrations of juvenile den-
titions in the literature, demonstrate that the trilobed, elongate dP4 can be identified to
date in at least 36 of the 37 families of extant and fossil Artiodactyla recognized by
McKenna and Bell (1997), including all 10 Recent families; we lack data for the Eocene
Asian family Raoellidae. We have detected a trilobed dP4 in 78 of 81 genera of extant
artiodactyls examined to date (based onthe classification of Wilson and Reeder, 1993);
juvenile dentitions of the South American cervids Blastocerus and Hippocamelus and of
the bovid Pantholops were not available to us. More recently, a trilobed dP4 was found
in the lower Eocene artiodactyl genus Eurodexis by Sudre and Erfurt (1996), and an
early stage in the evolution of this derived deciduous premolar was identified in Euro-
pean and North American species of Diacodexis (Fig. 5), the oldest known artiodactyl
genus (Luckett and Sudre, in preparation). At present, we have observed a trilobed dP4
in 215 fossil genera of artiodactyls.
In addition to the rare or uniquely derived attributes described above, other dental,
138 Luckett and Hong
cranial, and postcranial characters have been postulated (Gentry and Hooker, 1988;
Prothero et al., 1988) to corroborate the monophyly of Artiodactyla. However, the char-
acter states of these derived traits have not been analyzed carefully for most other mam-
malian higher taxa, and for this reason they are not included in the present study. Some,
such as the greatly reduced or absent third trochanter of the femur in artiodactyls, are
derived in different directions in other cursorial mammals, suggesting that they are also
useful characters for supporting artiodactyl monophyly.
The two extant genera of amphibious hippopotamids (Choeropsis and Hippopota-
mus, Fig. 6), as well as the Pliocene–Pleistocene fossil Hexaprotodon, share the three
derived character complexes of all artiodactyls discussed above (Figs. 1 and 4; Table I,
characters 1 and 2). We agree with Pickford (1983) and Harrison (1997) in retaining the
generic distinction of the extant pygmy hippopotamus Choeropsis, rather than including
it within the fossil genus Hexaprotodon. Its inclusion within the latter genus by Co-
ryndon (1977, 1978) seems to reflect its retained plesiomorphous features, rather than
shared derived traits. The oldest unquestioned hippopotamid (Kenyapotamus) from the
middle-late Miocene of Africa (Pickford, 1983, 1990), known mainly from incomplete
dental remains, also possessed a typical double-trochleated astragalus (Fig. 1D), as in
all other fossil and extant artiodactyls. The structure, proportions, and nature of the
articular facets of the astragalus in Kenyapotamus are fundamentally similar to those of
the extant pygmy hippopotamus Choeropsis (cf. Figs. 1D and E). As yet, data are
unavailable concerning the likely occurrence of a paraxonic foot or trilobed dP4 in Ken-
yapotamus.
An analysis of the systematic relationships of hippopotamids within Artiodactyla is
beyond the scope of the present study. Affinities of hippopotamids have been suggested
with Eocene-Miocene anthracotheriids (Colbert, 1935; Black, 1978; Coryndon, 1978)
or with Oligocene–Miocene Old World tayassuids (Pickford, 1983, 1989, 1990). Nei-
ther hypothesis has been tested by a detailed character analysis of extant and fossil sui-
Fig. 6. Drawing of the river hippopotamus, Hippopotamus amphibius, showing its stocky build, short
limbs, and elevated orbits.
Evolution of Artiodactyla and Cetacea 139
forms; indeed, the monophyly of the suborder Suiformes has been questioned in a recent
assessment of the order Artiodactyla (Gentry and Hooker, 1988).
In contrast, there is little doubt concerning the monophyly of the superfamily Suo-
idea (suids and tayassuids), the suborder Tylopoda (camels and their fossil relatives), or
the suborder Ruminantia (tragulids, pecorans, and their fossil relatives) from either mor-
phological or molecular studies. Consequently, only a few morphological traits are
included here to corroborate the monophyly of Suoidea and of Ruminantia. A derived
character shared by extant suids and tayassuids is the occurrence of a disk-like cartilage
in the mobile snout (Table I, character 16); in suids at least, this cartilage is commonly
replaced by bone and can be readily identified in museum specimens (Weber, 1928;
Simpson, 1984). The presence of this trait in fossils is unknown, but it seems likely that
it occurred in the last common ancestor of extant suoids. Other dental, cranial, and
postcranial derived characters shared by Suidae and Tayassuidae are listed by Gentry
and Hooker (1988). Fossil and extant ruminants are more easily diagnosed by shared,
derived postcranial attributes, including the fusion of the cuboid and navicular bones
(Table I, character 26) in the tarsus (Webb and Taylor, 1980; Janis and Scott, 1987;
Gentry and Hooker, 1988).
Monophyly of Cetacea. Because the monophyly of extant Cetacea is strongly cor-
roborated by both morphological and molecular data, only a few morphological traits
that support this monophyly are discussed here (see also Thewissen, 1994; Fordyce and
Barnes, 1994; Arnason and Gullberg, 1996; Heyning, 1997). However, the inclusion of
Eocene archaeocetes within Cetacea makes it more problematic to diagnose the order.
Many derived characters that unite extant cetaceans, such as monophyodonty, hyper-
phalangy in the forelimbs, and the vestigial nature of the hindlimbs, do not occur in
Eocene archaeocetes, which retain greater evidence of their terrestrial and diphyodont
ancestry (Fordyce and Barnes, 1994). Consequently, character analyses of the available
dental, cranial, and postcranial evidence suggest that the middle ear region provides the
most diagnostic features of fossil and extant cetaceans (Thewissen, 1994; Thewissen et
al., 1996; Luo, 1998).
The ectotympanic bulla of all known extant and fossil cetaceans is formed by dense
bone (pachyosteosclerosis), and it is characterized further by a prominent "conch-like"
thickening and involution of its medial margin to form an involucrum and by a peculiarly
developed sigmoid process (Kellogg, 1936; Thewissen, 1994; Fordyce and Barnes, 1994;
Thewissen et al., 1996). The early ontogeny of these derived traits in extant cetaceans
has been reviewed by Luo (1998). As emphasized earlier by Kellogg (1936, p. 307),
these derived attributes of the middle ear region (Table II, characters 31 and 32) "taken
together constitute a functional remodeling . . . that has not as yet been duplicated in
any other mammal." More recent discoveries and analyses of the oldest known archae-
ocete skulls (the early–middle Eocene genera Pakicetus and Ambulocetus) provide fur-
ther evidence for the uniquely derived pattern of these middle ear traits in all fossil and
extant cetaceans (Gingerich and Russell, 1981; Thewissen, 1994; Thewissen et al.,
1996).
Monophyly of the Cetacean Suborders Mysticeti and Odontoceti. Two different pat-
terns of "telescoping" of the bony elements in the roof of the skull occur in extant
cetaceans, and Miller (1923) emphasized that no transitional or intermediate stages are
known between these patterns. In odontocetes, the elongate, ascending processes of the
140 Luckett and Hong
Table II. Character Analysis of Selected Eutherian Cyt b Nucleotide and Morphological Traits for
Assessing Hippopotamid–Cetacean Relationships
Primitive
31. No pachyosterosclerosis of bulla
32. No sigmoid process on ectotympanic
33. Nucleotide 531— R
34. Nucleotide 498— R
35. Nucleotide 522— Y
36. Nucleotide 796— C
37. Nucleotide 1095— Y
38. Nucleotide 1083— Y
39. Nucleotide 729— R
40. Nucleotide 666— R
41. Nucleotide 727— G
42. Nucleotide 378— R
43. Nucleotide 728— T
44. Nucleotide 111— R
45. Nucleotide 573— Y
46. Nucleotide 501— R
47. Nucleotide 693—R
48. Nucleotide 591— R
49. Nucleotide 569— C
50. Nucleotide 240— Y
51. Nucleotide 873— R
52. Nucleotide 287— T
53. Nucleotide 385— A
54. Nucleotide 558— R
55. No overriding of frontals by maxillae
56. No facial asymmetry
57. No premaxillary foramen
58. No melon on face
59. Nucleotide 219— R
60. Nucleotide 905— C
Derived
31. Pachyosteosclerotic bulla with involucrum
32. Sigmoid process on ectotympanic
33. Nucleotide 531—Y
34. Nucleotide 498—Y
35. Nucleotide 522— R
36. Nucleotide 796—R
37. Nucleotide 1095—R
38. Nucleotide 1083— R
39. Nucleotide 729— Y
40. Nucleotide 666— Y
41. Nucleotide 727— A
42. Nucleotide378— Y
43. Nucleotide 728— C
44. Nucleotide 111— Y
45. Nucleotide 573— R
46. Nucleotide 501—Y
47. Nucleotide 693—Y
48. Nucleotide 591— Y
49. Nucleotide 569— T
50. Nucleotide 240— R
51. Nucleotide 873— Y
52. Nucleotide 287— C
53. Nucleotide 385— G
54. Nucleotide 558— Y
55. Expanded supraorbital processes of
maxillae override frontals
56. Asymmetry of facial air sacs
57. Development of premaxillary foramen
58. Hypertrophied fatty melon
59. Nucleotide 219— Y
60. Nucleotide 905— T
maxilla pass dorsally over the frontals and their supraorbital wings, overriding the fron-
tals and extending posteriorly as terminally expanded supraorbital processes (Fig. 7). A
homologous pattern of maxillary "telescoping" over the frontals characterizes all
unquestioned Oligocene to Recent odontocetes for which the skull is known (Table II,
character 55) including fossil and extant physeteroids (Miller, 1923; Kellogg, 1928;
Heyning, 1989, 1997; Barnes, 1990; Fordyce and Barnes, 1994).
In mysticetes, on the other hand, the maxillae interlock with the anterior margins
of the frontals but do not override them (Fig. 7). Instead, a broad inferior process of the
maxilla projects ventral to the supraorbital wing of the frontal, forming a broad, hori-
zontal infraorbital plate of the maxilla (Miller, 1923). An early stage in the development
of the mysticete pattern of infraorbital "telescoping" is detected in the late Oligocene
mysticete Aetiocetus, even though this genus still retained reduced, single-rooted, and
shallowly implanted teeth in both jaws (Emlong, 1966; Barnes and McLeod, 1984).
These differing patterns of cranial telescoping in fossil and extant odontocetes and
mysticetes are not found in Eocene archaeocetes or other mammalian higher taxa. The
precise causative factors that led to such contrasting derived patterns in cetaceans are
Evolution of Artiodactyla and Cetacea 141
142 Luckett and Hong
unclear, but they may result from different biomechanical remodeling trends in response
to compressive forces acting on the anterior and posterior ends of the skull (Miller,
1923).
Numerous other cranial and soft anatomical characters have been identified as syn-
apomorphies to corroborate the monophyly of Odontoceti (Heyning, 1989, 1997; Barnes,
1990; Fordyce and Barnes, 1994), and only a few of these are considered here (Table
II, characters 56–58). The left-right asymmetry of soft structures of the face, including
the complex of air sacs, has been described and analyzed in detail for all families of
extant odontocetes by Heyning (1989, 1997); a comparable structural pattern is unknown
in mysticetes or other extant mammals. Several additional unique or rare morphological
traits also characterize all known extant and fossil odontocetes. The nasal bones are
greatly reduced, so that they do not form a roof for the bony external nares (Fig. 7).
This contrasts sharply with the moderately reduced nasals of all mysticetes, which con-
tinue to form a bony roof for the nares. Another uniquely derived trait in all known
odontocetes is the development of a premaxillary foramen (Fig. 7), as a modification of
the infraorbital foramen complex (Barnes, 1984, 1990; Heyning, 1997). Early stages in
the development of the premaxillary foramen, and of maxillary telescoping, are already
evident in fetuses of the sperm whale Physeter measuring 21.5 and 32 cm in total body
length (Kuzmin, 1976).
An encapsulated, fatty melon, situated just anterior to the nasal passages, has been
considered previously to be a uniquely derived attribute of Odontoceti within Mammalia
(Heyning, 1989). Subsequently, Heyning and Mead (1990, p. 69) suggested that a small
"fatty structure" in the head of mysticetes "appears to be homologous to the melon of
odontocetes," although no illustration was presented for the suggested melon of mys-
ticetes. Recently, Heyning (1997) concluded that a "hypertrophied melon" is a uniquely
derived trait of extant odontocetes, with the small melon of mysticetes representing an
intermediate condition in the transformation from the primitive mammalian condition
(lack of a melon). It is suggested that the hypertrophied melon of odontocetes (including
physeteroids) plays an important role in the transmission and processing of emitted sounds
(Cranford et al., 1996).
A series of elegant studies on the petrosal and inner ear morphology of extant and
fossil whales (Fleischer, 1976; Ketten, 1992; Luo and Marsh, 1996; Geisler and Luo,
1996) has provided additional compelling evidence for the monophyly of the suborder
Odontoceti, including data from extant and fossil physeteroids. Of particular significance
are the size of the spiral ganglion canal and the relative thickness and width of the basilar
membrane, which can be estimated by the laminar gap between the primary and sec-
ondary bony laminae in fossils as well as extant taxa. Not all cetacean families or other
eutherian orders have been studied as yet for inner ear features, so these characters were
not incorporated into our analysis. Nevertheless, the derived nature of these auditory
traits associated with ultrasonic signal reception in Odontoceti, and their absence in
archaeocetes and fossil and extant mysticetes, provides further corroboration for the
monophyly of Odontoceti (including physeteroids).
Extant mysticetes are characterized by the lack of erupted teeth and by the presence
of long, fringe-like plates of keratinized baleen hanging down from their upper jaws.
These baleen plates are used in filtering small organisms, including krill and tiny fish,
from plankton drifting in the ocean [see the excellent photographs and description in
Heyning (1995)]. However, the earliest-known fossil mysticetes retained teeth, and it is
Evolution of Artiodactyla and Cetacea 143
unclear whether they also possessed baleen (Emlong, 1966; Barnes and McLeod, 1984;
Barnes, 1990). Interestingly, at least some extant mysticetes develop rudimentary but
nonerupting teeth; as these teeth undergo regression and resorption in the fetal jaws,
they are "replaced functionally" by the later differentiation of developing baleen plates
(Karlsen, 1962). Additional synapomorphies from the auditory region that support the
monophyly of Odontoceti and Mysticeti are discussed by Luo (1998).
Molecular Character Analyses
During the past decade, published data on the mitochondrial cytochrome b gene
have accumulated for a wide range of artiodactyl, cetacean, perissodactyl, carnivoran,
and other eutherian families, following the pioneering study by Irwin et al. (1991) and
the advent of the polymerase chain reaction (see Appendix). This abundance of cyt b
sequences facilitates the reconstruction of ancestral "morphotypes" for individual
nucleotide characters at the family level (or higher) for many eutherian orders. Following
visual examination of each nucleotide position in the available artiodactyl and cetacean
cyt b sequences, 106 of the 1140 positions (9.3%) in the complete gene were selected
for further analysis. The relatively conservative nature of nucleotide changes in these
positions (in both ingroups and outgroups) suggested that they might be potentially
informative in addressing cladistic relationships among extant families of Artiodactyla
and Cetacea. The criteria for selection of these conservative and informative nucleotides
were elucidated under Materials and Methods.
For the ingroup taxa (Artiodactyla and Cetacea), the ancestral morphotype was
reconstructed for each selected nucleotide position for each constituent family, using all
available genera and multiple species. There is minimal disagreement concerning the
monophyly of the five extant families that comprise the infraorder Pecora (families Antil-
ocapridae, Bovidae, Cervidae, Giraffidae, and Moschidae), and the moderate taxon sam-
pling available for this speciose clade permits a pooling of data from these families to
construct a morphotype for Pecora. Multiple family-level (or higher) outgroups from
other eutherian orders (seeAppendix) were also analyzed in the same way for the same
nucleotide positions (Fig. 8). This facilitated our ability to detect patterns of potential
homoplasies for the nucleotide (and morphological) traits used in the final character
analysis, as well as to polarize the relatively primitive and derived character states of
each selected nucleotide position within Eutheria.
With the continued addition of outgroups, and the accumulation of additional
ingroup species during the course of the study, it became evident that some of the pre-
liminary "informative" nucleotides showed relatively high levels of homoplasy in both
ingroups and outgroups, diminishing their value for phylogenetic reconstruction (see
Fig. 8). For the final combined character analysis of molecular and morphological traits,
50 conservative nucleotide positions were selected for their potential to test alternative
hypotheses of relationships within and among artiodactyls and cetaceans. These nucleo-
tide traits were combined with the 10 conservative morphological features described
above in a character analysis (Figs. 9 and 10, Tables I and II). For all traits used, the
morphotype of the primitive eutherian condition was also reconstructed, using all avail-
able data. In a few cases, the morphotypic condition for some nucleotide positions could
not be determined readily, due to excessive homoplasy; these uncertainties are indicated
by (?) in all analyses.
Inspection of the nucleotide morphotypes aligned in Figs. 9 and 10 shows that few,
144 Luckett and Hong
Evolution of Artiodactyla and Cetacea 145
146 Luckett and Hong
Evolution of Artiodactyla and Cetacea 147
148 Luckett and Hong
Evolution of Artiodactyla and Cetacea 149
150 Luckett and Hong
if any, shared derived nucleotide positions of the cyt b gene uniquely support the mo-
nophyly of the orders Artiodactyla or Cetacea. Two derived nucleotide positions (num-
bers 531 and 796) that corroborate monophyly of Cetacea are relatively rare within the
eutherian higher taxa analyzed (characters 33 and 36 in Table II and Fig. 10). One of
these (character 33) is a silent third-position transversion of an arginine codon. The other
(nucleotide 796) is a first-position transversion, which results in an amino acid substi-
tution (proline to alanine). This substitution is rare in eutherians studied to date; it does
not occur in hippopotamids but is found, however, in sigmodontine rodents. Other prob-
able nucleotide synapomorphies for cetacean monophyly (characters 34, 35, 37, 38, and
41–43 in Table II and Fig. 10) have evolved convergently in two or more additional
eutherian higher taxa.
In contrast, no undoubted nucleotide synapomorphies from the cyt b gene could be
detected to support the monophyly of Artiodactyla; this is consistent with molecular
studies that have argued for a paraphyletic order Artiodactyla. In order to obtain minimal
nucleotide support for artiodactyl monophyly, it would be necessary to allow for a single
reversal at the family level for two nucleotide positions (numbers 476 and 639). How-
ever, the polarity of these two nucleotides (characters 4 and 5 in Table I and Fig. 9) is
questionable. Even if these reversals had occurred, multiple convergences would have
to be accepted in other eutherian taxa. Another seven synapomorphic nucleotide posi-
tions provide potential support for Artiodactyla monophyly (numbers 228, 475, 722,
912, 921, 1053, and 1092). These are relatively rare substitutions among the eutherians
analyzed, but each of these nucleotide positions (characters 3 and 6–11 in Table I and
Fig. 9) requires two reversals to the primitive artiodactyl condition if monophyly of
Artiodactyla is accepted.
Several relatively rare nucleotide substitutions within Eutheria (characters 27–30 in
Table I and Fig. 9) provide support for a monophyletic Ruminantia clade (Pecora plus
Tragulidae). None of these nucleotide characters is uniquely derived, and two of the
four also occur in at least one nonruminant artiodactyl family (Fig. 9). This mono-
phyletic clade is consistent with most previous analyses of molecular and morphological
data. Another clade within Artiodactyla which receives moderate support from nucleo-
tide character analysis is the superfamily Suoidea (families Suidae plus Tayassuidae);
this taxon is supported by characters 17–22 in Fig. 9, although each of these exhibits
varying degrees of homoplasy within Eutheria.
Monophyly of the suborder Suiformes (families Suidae, Tayassuidae, and Hippo-
potamidae) receives only modest support from our nucleotide analysis of the cyt b gene
(characters 6 and 9–15 in Fig. 9). Only two of these traits are uniquely derived within
Artiodactyla, and all of them show variable degrees of homoplasy in other eutherians.
A possible sister-group relationship between Hippopotamidae and Tayassuidae, as sug-
gested by Pickford (1983, 1989), receives even less support from cyt b nucleotide traits
(characters 23–25 in Fig. 9).
Molecular Evidence for a Hippopotamidae–Cetacea Relationship. The alternative,
provocative hypothesis of a monophyletic hippopotamid–cetacean clade receives a mod-
erate degree of support from the nucleotide analysis (characters 37–43 in Table II and
Fig. 10). However, careful character analysis of these shared, derived nucleotides sug-
gests that an alternative hypothesis of convergence is equally probable. Four of the seven
shared, derived hippopotamid–cetacean nucleotides also characterize at least one addi-
tional artiodactylan family (characters 37–40), and four of the seven nucleotides are also
shared by one or more orders of paenungulates (Sirenia, Proboscidea, and Hyracoidea).
Four additional derived nucleotide positions (characters 44–47 in Fig. 10) are shared by
hippopotamids and some but not all families of cetaceans; each of these also occurs in
either Sirenia or Proboscidea. Most of the shared, derived nucleotides of Cetacea and
Hippopotamidae are third position transversions. The only exceptions are transitions at
nucleotide positions 727 and 728 (characters 41 and 43); these result in a single amino
acid change from valine to threonine (at amino acid position 243), shared by all ceta-
ceans and hippopotamids sequenced to date, but also by all Sirenia. The possible evo-
lutionary implications of this amino acid change are discussed below.
Molecular Evidence for a Physeteroid-Mysticete Relationship. Another major con-
troversy regarding Cetacea is the affinities of sperm whales (superfamily Physeteroidea)
to other odontocetes (the traditional view) or with the suborder Mysticeti, as suggested
by the investigations by Milinkovitch et al. (1993) and Hasegawa et al. (1997). Accord-
ingly, we have analyzed the cyt b nucleotide data separately for each odontocete family,
including the physeteroids (Fig. 11), but we pooled the data for the suborder Mysticeti,
because of the lack of controversy about their monophyly. Thus, the clades Physetero-
idea and other "Odontoceti" are treated separately in Figs. 9 and 10.
Our character analysis of the cyt b data shows that there are indeed several derived
nucleotide traits shared by Physeteroidea and Mysticeti. However, among the 11 nucleo-
tide derived traits shared by these two clades (characters 44–54 in Fig. 10), only 1
(character 48) does not occur also in at least two other odontocete families (Fig. 11).
This single, uniquely derived nucleotide substitution (at position 591) within Cetacea,
which might support the monophyly of a physeteroid–mysticete clade, is a silent third-
position transversion in the amino acid leucine.
Concerning the other 10 relatively rare nucleotide substitutions that might support
Fig. 11. Character analysis of conservative cytochrome b nucleotides in cetacean families, selected out-
groups, and the eutherian morphotype. For genera included in each taxon, see the Appendix.
Evolution of Artiodactyla and Cetacea 151
152 Luckett and Hong
a physeteroid–mysticete clade, 7 are third-position transversions.Among the other three
substitutions, one (nucleotide position 569) is a second-position transition, resulting in
an amino acid substitution from threonine to leucine. This same nucleotide and amino
acid substitution is also shared by the odontocete families Ziphiidae and Platanistidae
(Figs. 10 and 11). Nucleotide position 287 is a second-position transition from T to C;
this substitution is also shared with the odontocete families Ziphiidae, Platanistidae,
Monodontidae, and Delphinidae. Moreover, this nucleotide substitution results in dif-
ferent amino acid substitutions in different cetacean families, depending on whether A
or G occurs at the first nucleotide position of the amino acid codon (AA 96). Thus,
mysticetes, kogiids, ziphiids, and delphinids share alanine, whereas physeterids, mo-
nodontids, and delphinids share threonine at this amino acid position. A first-position
transition that occurs at nucleotide position 385 in mysticetes and physeteroids (A to G)
also results in an amino acid change from isoleucine to valine; however, this substitution
is also shared by the odontocete families Ziphiidae, Platanistidae, Monodontidae, and
Delphinidae. Therefore, none of these three nonsynonymous substitutions appears to be
significant in corroborating the proposed mysticete–physeteroid relationship; they can
be interpreted equally as the result of homoplasy.
Careful examination of the eight third-position transversions (characters 44–48, 50,
51, and 54 in Fig. 10) shared by physeteroids and mysticetes in our analysis reveals that
each of these is a synonymous substitution, which results in no change at the amino acid
level.
We identified only two derived nucleotides that support the traditional monophyly
of the suborder Odontoceti, including the Physeteroidea (characters 59 and 60 in Fig.
10). One of these (nucleotide 219) is a silent third-position transversion; the other
(nucleotide 905) is a second-position transition that results in an amino acid substitution.
However, the number of amino acid substitutions that occurred at this site in odontocetes
and other mammals makes it difficult to assign any systematic significance to these
changes.
DISCUSSION
Phylogeny, defined simply as "descent with modification," and the systematic rela-
tionships among organisms that result from phylogeny, cannot be observed directly.
Instead, these relationships must be inferred or reconstructed from paleontological data
(possessing a time dimension) and neontological data (lacking a time dimension). These
simple but essential principles of phylogenetic reconstruction and systematics have been
summarized ably by Simpson (1961). Although phylogenetic taxa are proposed by
hypotheses of their "propinquity of descent," these relations are judged "largely on
similarities among them" (Simpson, 1961, p. 67). All "similarities" do not carry equal
weight, however, for evolutionary reconstruction. Both Simpson (1961) and Hennig
(1966) have emphasized that two fundamental problems of phylogenetic reconstruction
are (1) distinguishing between similarities that arise by homology (reflecting common
ancestry) and those that arise through homoplasy or convergence (not reflecting common
ancestry) and (2) distinguishing between relatively primitive and derived character states
in a transformation series of characters. Additionally, both investigators have empha-
sized that evolutionary analyses can utilize data from virtually all aspects of biology,
Evolution of Artiodactyla and Cetacea 153
encompassing fossils, comparative anatomy, molecules, and everything in between. Such
multidisciplinary data can provide interpretive and explanatory principles applicable to
all aspects of biological diversity, which are the result of descent with modification
(Simpson, 1961). Many molecular biologists clearly accept these fundamental principles
of systematic analysis (Hillis, 1987; Cracraft and Helm-Bychowski, 1991; Miyamoto
and Cracraft, 1991; Honeycutt and Adkins, 1993; Swofford et al., 1996; Mindell and
Thacker, 1996), and they recognize the importance of congruence among analyses of
different types of biological data as "strong evidence that the underlying historical pat-
tern has been discovered" during phylogenetic reconstruction (Hillis, 1987, p. 23).
This brief consideration of the role and value of systematics in the ordering of
complex data is a necessary prerequisite for assessing the complementary and sometimes
conflicting roles played by evolutionary morphologists and molecular biologists in
attempting to resolve phylogenetic hypotheses, such as those involving artiodactyls and
cetaceans. We believe that the major "conflict" between morphological and molecular
analyses of mammalian evolution is attributed to differences in the methods of "char-
acter analyses" concerning hypotheses of homology and synapomorphy. In particular,
we suggest that many studies of molecular evolution at the higher taxonomic level suffer
from three deficiencies that are less likely to occur in morphological analyses: (1) insuf-
ficient sampling at all taxonomic levels, from species, genera, and families to suborders
and orders; (2) minimal effort devoted to the assessment of homology versus homoplasy
among individual shared traits (nucleotides or amino acids) among taxa; and (3) the
limited use of multiple outgroups to polarize more accurately the relatively primitive and
derived character states of shared nucleotide or amino acid positions.
In their recent assessment of various methods of phylogenetic inference employed
in molecular analyses, Swofford et al. (1996) discussed both random and systematic
errors that can introduce bias into statistical analyses of alternative phylogenies, thereby
leading to robust but "positively misleading" support for historically "incorrect" trees.
The authors noted that random error is a consequence of limited taxonomic sampling;
this source of bias can be minimized readily by an increased density of taxon sampling
for both ingroups and outgroups. Systematic errors in statistical analyses are due pri-
marily to "incorrect assumptions" about rates of evolution, including transition versus
transversion ratios, base compositional bias, weighting schemes, and among-site rate
heterogeneity [see Swofford et al. (1996) and Sullivan and Swofford (1997) for extensive
discussion].
As emphasized by Smith (1994) in his thoughtful discussion of the problems
involved in rooting evolutionary trees, three criteria are widely used by morphologists
for rooting: outgroup comparison, ontogenetic data, and the fossil record. These can be
used together, especially in the case of cranioskeletal and dental characters, although
each has its own limitations. A disadvantage for molecular data is that polarity assess-
ment of nucleotide or amino acid characters is restricted almost completely to outgroup
rooting. We agree with Smith (1994, p. 280) that the primary source of error in both
morphological and molecular analyses of evolution is homoplasy; careful attention must
be given to the selection of taxa and to the rooting of trees, so that we can "make an
informed decision about directionality of evolution'' and the polarity of character trans-
formation. Given that evolutionary biology is "uncertain in its very nature" and that
"its results are rarely absolute" (Simpson, 1961, p. 5), we have chosen to emphasize
154 Luckett and Hong
dense taxonomic sampling and morphotype reconstruction of conservative traits at the
family level, in order to increase the probability of correctly distinguishing between
shared, derived synapomorphies and homoplasies within both ingroups and outgroups
for molecular and morphological traits.
Our character analysis of relatively conservative morphological and nucleotide traits
demonstrates that several uniquely derived morphological characters within Eutheria
corrobrate the monophyly of the orders Artiodactyla and Cetacea, including both their
extant and their fossil representatives. In contrast,no uniquely derived nucleotide or
amino acid traits from the mitochondrial cytochrome b gene could be detected in extant
species to support the monophyly of either order. This corroboration of "traditional"
hypotheses presents few surprises for evolutionary morphologists, who have investigated
in detail the comparative aspects of artiodactyl and cetacean systematics for more than
170 years. More unexpected, however, was the general "weakness" or inability of the
cyt b gene sequences to provide convincing synapomorphies for corroborating higher
level hypotheses of mammalian phylogeny, despite the widespread use of this and other
mitochondrial genes for testing (and sometimes disputing) such systematic hypotheses.
Even though 1140 nucleotide bases or characters comprise the cyt b gene of most eu-
therians, the majority of these traits appear to be of minimal value for assessing higher-
level relationships. This is because of the mosaic pattern of variation and homoplasy for
individual nucleotide positions at the species, generic, and familial levels, coupled with
the invariant nature of numerous other positions. As our analysis shows, even those
nucleotide characters that are relatively conservative in their pattern of evolutionary
change also show varying degrees of homoplasy when numerous other eutherian orders
are examined. This makes it difficult to interpret whether shared, derived nucleotide
similarities between two taxa are the result of synapomorphy or homoplasy, when the
sister-group relationship between these taxa is not supported by derived morphological
traits (as in the case of shared hippopotamid-cetacean nucleotide traits).
Our study suggests that a few well-analyzed morphological characters or character
complexes, whose history can be followed by paleontological and/or ontogenetic meth-
ods and whose adaptive and functional significance can be reasonably inferred, are more
reliable for the diagnosis and definition of monophyletic orders and suborders of eu-
therian mammals than are the numerous nucleotides found in mitochondrial genes. Both
fossils and ontogenetic stages provide valuable (but not foolproof) criteria for the assess-
ment of synapomorphy, homoplasy, and transformation hypotheses, in addition to the
outgroup criterion that can be used for both morphological and molecular traits. Fossils
also have the unique ability to provide direct evidence for the minimal age of particular
derived cranioskeletal and dental traits in the geological record. Our analysis provides
further support for the suggestion by Wagele (1995) that there is a relationship between
the complexity of characters and their value for phylogenetic reconstruction.
Monophyly of Artiodactyla
The results of our analyses are in conflict with the conclusions drawn from several
molecular studies (Irwin and Arnason, 1994; Arnason and Gullberg, 1996; Gatesy et
al., 1996; Gatesy, 1997; Montgelard et al., 1997), which suggest that the order Artio-
dactyla is paraphyletic and that one family—the Hippopotamidae—is more closely related
Evolution of Artiodactyla and Cetacea 155
cladistically to Cetacea than it is to other Artiodactyla. Rose (1996) has recently reviewed
the available information concerning the earliest appearance of artiodactyls in the fossil
record and their possible origins from arctocyonid "condylarths," a diverse, para-
phyletic group that was probably close to the origin of several other ungulate and paen-
ungulate orders. The oldest known artiodactyls, allocated to the genus Diacodexis,
appeared suddenly in the early Eocene faunas of Europe, North America, and Asia; as
emphasized by Rose (1996, p. 1705), these early artiodactyls "are instantly recognizable
from their diagnostic double-pulley astragalus, but much of the skeleton also bears the
hallmarks of the order, including strongly paraxonic feet and other specializations for
cursorial locomotion."
The evolutionary development of a uniquely derived double-trochleated astragalus,
which forms subequal articulations with the cuboid and navicular in all known extant
and fossil artiodactyls (Zittel, 1925; Viret, 1961), may be associated with the acquisition
of highly specialized paraxonic hindfeet in their last common ancestor. However,
"incipient" paraxony occurred in at least some Paleocene–Eocene miacids, arctocyo-
nids, and mesonychids, but this was not accompanied by or followed by the formation
of a double-trochleated astragalus in any of their known forms (see Matthew, 1909,
1937; O'Leary and Rose, 1995). Morphologically intermediate transitions from an arc-
tocyonid-like astragalus to the diagnostic double-trochleated astragalus of early Eocene
artiodactyls are unknown; hypothetical intermediate stages in this evolutionary transfor-
mation have been reconstructed by Schaeffer (1947) using the deformed coordinate
method. The derived tarsal pattern of artiodactyls greatly limits or prevents inversion
and eversion at the ankle joint; movement here is restricted essentially to dorsiflexion
and plantar flexion (Schaeffer, 1947, 1948; Rose, 1985). An emphasized by Rose (1985,
1990), these and other derived attributes of the postcranial skeleton of artiodactyls are
all specializations for cursorial and saltatorial locomotion. A different pattern of as-
tragalar and other postcranial specializations for cursorial locomotion is evident in con-
temporaneous (and mesaxonic) early Eocene perissodactyls (Matthew, 1937; Rose,
1990).
The early-middle Eocene archaeocete Ambulocetus was also paraxonic, but the
distal half of its astragalus is missing, rendering it impossible to determine the nature of
the astragalar head in the single known specimen (Thewissen et al., 1996). Nevertheless,
the nature of the metapodials and other postcranial elements in Ambulocetus suggested
to Thewiseen et al. (1996) that this animal was an amphibious plantigrade that probably
functioned as an "ambush predator" in shallow water and near the water's edge, some-
what analogous to the life style of crocodiles. The known postcranial morphology of
Ambulocetus, coupled with its retention of some plesiomorphous eutherian traits, such
as an astragalar foramen (lost in all known artiodactyls), suggests to us that it is unlikely
that the ancestral cetaceans possessed a double-trochleated astragalus or other pedal syn-
apomorphies characteristic of known artiodactyls. Clearly, intact astragali from Ambu-
locetus and Pakicetus are needed to settle this issue. However, Mesonychia, the
postulated sister group of Cetacea (Thewissen, 1994; O'Leary, 1998), also possessed a
paraxonic hindfoot, but a double-trochleated astragalus is clearly lacking in all genera
for which this trait is known (Matthew, 1937; O'Leary and Rose, 1995).
Although Rose (1996) suggested that the skull and bunodont dentition of Eocene
artiodactyls are relatively conservative and exhibit few if any "diagnostic" traits, our
156 Luckett and Hong
analysis provides additional corroboration for the statement by Scott (1940, p. 497) that
an elongate, trilobed dP4 is "common to all known Artiodactyla." Early descriptions
and illustration of this specialized deciduous tooth were provided by Cuvier (1822) and
Blainville (1839–1864) for the Eocene artiodactyl Anoplotherium. In addition, Cuvier
(1822) described the skeleton and dentition of Hippopotamus, demonstrating the trilobed
nature of its dP4 and its double-trochleated astragalus and noting the similarities of these
skeletal and dental traits to those in the pig and cow. Despite this, Cuvier (1822) con-
tinued to classify the hippopotamus with elephants, rhinoceroses, and tapirs as
"Pachydermes," rather than grouping them with ruminants. In contrast, Blainville
(1839–1864, p. 3) emphasized that the "ensemble de caracteres" from the dentition and
postcranial skeleton argued for a closer association of Hippopotamus and Sus with rum-
inants than with other "ungulates." With the identification of isolated trilobed dP4 in
the early Eocene artiodactyls Diacodexis andEurodexis (Sudre et al., 1983; Sudre and
Erfurt, 1996; present study), and in all other fossil and extant artiodactyls for which the
appropriate juvenile dentitions are available, there seems little doubt that this derived
character complex is also a diagnostic feature of Artiodactyla.
The unusual nature of the trilobed dP4 in extant and fossil artiodactyls, including
its occlusal relationships with dP3–4, has received little or no attention in many recent
summaries of artiodactyl evolution, including Viret (1961), Simpson (1984), and Pro-
thero et al. (1988). In contrast, Tobien (1985) emphasized the widespread occurrence
of a trilobed dP4 in Eocene artiodactyls, and Gentry and Hooker (1988) included this
trait in their diagnosis of the order Artiodactyla. We have expanded our study of deci-
duous dentitions to a variety of extant and fossil ungulates, paenungulates, Eocene ceta-
ceans, mesonychids, and other "condylarths," in order to assess the likelihood that the
trilobed dP4 is indeed a trait unique to artiodactyls. In all of these nonartiodactyl taxa
examined to date, dP4 resembles M1, of the same species (a primitive eutherian pattern
shared with the late Cretaceous Kennalestes), rather than the trilobed dP4 of artiodactyls.
Genera examined for this trait include the Paleocene triisodontid Triisodon, the Paleo-
cene arctocyonid Protogonodon, the Paleocene–Eocene phenacodontids Phenacodus,
Meniscotherium, and Tetraclaenodon (see also West, 1971), the Eocene hyopsodontid
Hyopsodus, the Eocene perissodactyls Homogalax and Hyracotherium, the Eocene pro-
boscideans Moeritherium and Numidotherium (see Andrews, 1906; Noubhani, 1988),
and the early Oligocene hyracoids Bunohyrax, Megalohyrax, Titanohyrax, and Saga-
therium.
The deciduous teeth of the Paleocene–Eocene mesonychids Dissacus navajovius
and Pachyaena gigantea were described but not illustrated by Matthew and Granger
(1915). We have reexamined these juvenile specimens at the American Museum of Nat-
ural History, as well as an additional undescribed juvenile dentary of Mesonyx sp. (with
the valuable assistance of Maureen O'Leary). Although the dP4 in each genus bears a
well-developed and anterior-positioned paraconid (this region is broken in Dissacus),
there is no development of a second anterior cusp or other resemblance to dP4 in artio-
dactyls.
The deciduous dentition, especially dP4, is poorly known for Eocene cetaceans.
Fortunately, a juvenile dentary of Pakicetus bearing dP4 and an unerupted M2 was illus-
trated and described by Thewissen and Hussain (1998), and isolated dP4 were also briefly
described and illustrated for the Eocene genera Nalacetus and Ichthyolestes. These spec-
Evolution of Artiodactyla and Cetacea 157
imens provide no evidence for similarity between the dP4 of Eocene cetaceans and
artiodactyls, although no discussion of this point was provided by Thewissen and Hus-
sain. However, Thewissen (personal communication, 1997) agrees with us that dP4
resembles M1, in Pakicetus and that it does not bear any similarity to the highly derived
dP4 of artiodactyls. Thus, the available evidence on the deciduous dentitions of meso-
nychids and Eocene cetaceans is consistent with the hypothesis of O'Leary (1998), based
on character analysis of the adult dentitions, that Mesonychia and Cetacea are sister taxa
within a supraordinal clade, the Mirorder Cete (including Cetacea, Mesonychia, and
Triisodontidae), which is close to, but distinct from, the ancestry of Artiodactyla. Other
morphological traits that aid in the assessment of phylogenetic relationships among
Artiodactyla, Cetacea, Mesonychia, Perissodactyla, and other eutherians are being ana-
lyzed by Geisler and O'Leary (1997, in preparation).
In all extant and fossil artiodactyls studied (including extant hippopotamids), dP3–4
are the earliest cheek teeth to erupt in both jaws; they are erupting during the second to
fourth weeks postnatally in the miniature pig, Sus scrofa (Weaver et al., 1966). Some
solid food is ingested by 2–3 weeks (Hayssen et al., 1993), and dP3–4 have established
a functional occlusal relationship by 7--8 weeks in pigs (McKean et al., 1971). The
elongate, trilobed dP4, occluding with dP3–4, functions to increase the length of the
occlusal surface available to young artiodactyls during the preweaning phase of life,
when plant material is beginning to be consumed. In wild Hippopotamus, the lactation
period may last from 9 to 12 months; however, juveniles 6–8 weeks in estimated age
can be found with a moderate amount of grass in their stomachs (Laws and Clough,
1966). Consistent with this, we have observed dP3_4 in an early eruptive phase in a
Choeropsis infant about 1 month old (AMNH 214182).
The only other eutherian order in which we have found a derived dP4 pattern that
resembles somewhat the artiodactyl condition is the Macroscelidea; our attention was
drawn to this condition by our colleagues Brigitte Senut and Martin Pickford at the
Museum National d'Histoire Naturelle, Paris. Subsequently, we examined ontogenetic
series of dentitions in the four extant genera of macroscelidids (Luckett and Hong,
unpublished) and compared these with the meager evidence of deciduous dentitions sum-
marized by Butler (1969, 1984) for Miocene macroscelidids. In all Recent genera, a
well-developed paraconid is anteriorly positioned on dP4, and there is a small paracristid
cuspule or swelling, separated from the protoconid by a distinct notch in unworn teeth.
In the Miocene macroscelidid Miorhynchocyon, the trigonid of dP4 is tapered anteriorly
and terminates mesiolingually with a well-developed paraconid (Butler, 1969, 1984).
The long paracristid shows no trace of a cusp on the two available specimens illustrated
(Butler, 1969, Figs. 2D and 3D), and thus this tooth differs fundamentally from the
artiodactyl (and Recent macroscelidid) condition. A relatively unworn dP4 from another
Miocene genus, Myohyrax, has a small mesiobuccal cusp on the paracristid, separated
from the protoconid by a buccal groove, similar to the condition in extant macroscelidids
(Butler, 1984, Fig. 4E). In the Miocene genus Hiwegicyon, a relatively unworn dP4 also
shows a slight elevation on the paracristid (Butler, 1969, Fig. 4B), and the anterior end
of the tooth is more rounded or "squared," rather than tapered as in other Miocene
genera.
These differences between Miocene and Recent macroscelidids, coupled with dif-
ferences in the P4–dP4 relationships between artiodactyls and macroscelidids, indicate
158 Luckett and Hong
the probability that similarities of the elongate dP4 in the two orders are the result of
convergent evolution. Unfortunately, dP4 is unknown in Eocene–Oligocene macroscel-
ideans; however, the striking differences in P4 morphology and P4–M1 proportions
between Eocene–Oligocene artiodactyls and macroscelideans (Hartenberger, 1986;
Simons et al., 1991) suggest that it is unlikely that they shared derived similarities in
dP4.
We propose that all early Eocene–Recent Artiodactyla can be distinguished by the
joint possession of three synapomorphic character complexes: (1) a specialized parax-
onic hindfoot, with thickening and subequal elongation of metapodials III and IV and
concomitant reduction subequally of metapodials II and V; (2) a uniquely derived dou-
ble-trochleated astragalus, with specialized articulations for the cuboid, navicular, and
calcaneus, so that movement in the ankle joints is limited to dorsiflexion and plantar
flexion; and (3) an elongate, trilobed dP4, which occludes above with dP3–4 and functions
to increase the masticatory surface of the early-erupting dP3–4. These same character
complexes were included in Weber's (1928) diagnosis of Artiodactyla 70 years ago.
Although the double-trochleated astragalus may have evolved as a consequence of the
highly specialized paraxonic condition of ancestral artiodactyls, there is no evidence to
link the evolutionary origin of the trilobed dP4 occlusal pattern to the postcranial func-
tional complex.This hypothesis is corroborated by comparing the completely different
(nonhomologous) pattern of postcranial and deciduous dental morphology that appeared
at the same time in the early Eocene record (about 55 mya) of the cursorial and herbiv-
orous-omnivorous Artiodactyla and Perissodactyla.
Affinities of the Family Hippopotamidae
Extant Hippopotamus is a "terrestrial," predominantly nocturnal herbivore, which
spends much of its daylight hours in the rivers and lakes of regions of sub-Saharan Africa
or resting along their shores (Laws, 1984; Klingel, 1995). This transitory daytime
"amphibious" habitat serves as a refuge from the debilitating effects of the hot sun for
these large-bodied and relatively thin-skinned mammals, which lack sweat glands in the
adult. In contrast to other amphibious mammals, hippos feed almost exclusively on land
vegetation, and they may travel overland for 3–10 km each night, along well-marked
trails, in search of grazing grounds (Howell, 1930; Laws, 1984; Klingel, 1995). The
common river hippo (Hippopotamus amphibius) usually feeds throughout the night on
its grazing grounds, returning to its water refuge by dawn (Klingel, 1995). As empha-
sized by Howell (1930), the limbs of hippos exhibit few specializations for aquatic life;
instead they remain adapted primarily for progression on land, as do those of other
artiodactyls. Indeed, underwater observations and photography of Hippopotamus show
that they also use "terrestrial" walking and running along the river or lake bottoms
during their daytime aquatic phase, in addition to swimming or floating (Roosevelt,
1910; Laws, 1984; Estes, 1991; Schwartz, 1996).
Any consideration of the evolutionary relationships of hippopotamuses must take
into account the morphological and behavioral differences between the two extant gen-
era. The large-bodied common or river hippo (Hippopotamus amphibius) is gregarious,
with the group size ranging from 10–15 to 250 individuals (Laws, 1984; Klingel, 1995),
and they are able to produce a variety of sounds, both underwater and out of the water,
including a range of "high-pitched underwater whines," clicks, and grunts (Barklow,
Evolution of Artiodactyla and Cetacea 159
1995). As noted by Barklow (1995, p. 54), however, some of the sounds produced are
"underwater versions of noises hippos make when their heads are out of the water,"
and there is no evidence that hippos can echolocate, contrary to the implications by
Gatesy et al. (1996).
The smaller-bodied pygmy hippo (Choeropsis liberiensis) shows fewer cranial,
postcranial, and behavioral specializations for an amphibious life than does the large
river hippo. Pygmy hippos are more solitary or occur in small groups, and they are
generally confined to lowland forested areas close to rivers in West Africa (Laws, 1984;
Eltringham, 1993); unfortunately, little is known about their habits in the wild, although
they apparently spend more time on land than do river hippos. Their orbits are not
elevated above the frontal bones and the limbs are proportionally more slender when
compared to river hippos (Coryndon, 1977, 1978); these and other morphological fea-
tures of the pygmy hippo are similar to those that occurred in the late Miocene to early
Pliocene fossil hippo Hexaprotodon (Coryndon, 1978; Harrison, 1997).
The metapodials and other limb bones of Hexaprotodon were longer and more
gracile than those of extant hippopotamids; consideration of these and other functional
implications led Harris (1997) to suggest that this fossil genus was more digitigrade,
cursorial, and faster moving than extant Hippopotamus of comparable body size. The
few anatomical similarities shared by hippos and cetaceans are probably the result of
convergent adaptations to an aquatic or amphibious lifestyle, as emphasized by many
earlier investigators (Kukenthal, 1891; Weber, 1904, 1928; Howell, 1930). Traits dis-
cussed by Gatesy et al. (1996) as shared "aquatic" specializations of extant Cetacea
and Hippopotamidae, such as the relatively hairless body, absence of sebaceous glands,
lack of scrotal tests, and nursing offspring in the water, are shared also by sirenians. In
contrast to sirenians and cetaceans, hippos have been observed to give birth to their
young both on land and in the water, and suckling of the young also occurs in both
environments (Laws and Clough, 1966; Laws, 1984).
Fossil and extant hippopotamids share the three synapomorphous character com-
plexes of all artiodactyls, corroborating the monophyly of Artiodactyla. However, the
precise cladistic relationships of Hippopotamidae to other artiodactyls remain contro-
versial. Many authors have held that the middle Eocene–Miocene family Anthraco-
theriidae is the closest relative of hippopotamids and may include their ancestors (Col-
bert, 1935; Coryndon, 1977, 1978). This hypothesis is also supported by the character
analysis of Gentry and Hooker (1988), based predominantly on dental traits in fossil and
extant families. An alternative hypothesis, proposed by Pickford (1983, 1989), suggests
that hippopotamids originated from an Old World tayassuid stock. Although a number
of dental and cranial traits were discussed to support this proposed relationship, an exten-
sive character analysis is needed to test this intriguing hypothesis. Careful analysis of
postcranial, cranial, and dental traits in hippopotamids, tayassuids, anthracotheriids, and
other artiodactyl families (especially nonruminants) is required for further assessment of
the phylogenetic relationships of hippopotamids within the order Artiodactyla.
At present, the major morphological trait that units the families Hippopotamidae,
Tayassuidae, and Suidae in a monophyletic suborder Suiformes is the occurrence of
"amastoidy" in the basicranium (Pearson, 1927; Viret, 1961; Gentry and Hooker, 1988).
This feature is lacking in early–middle Eocene artiodactyls and in Ruminantia and is
undoubtedly a derived condition; however, it has occurred independently within other
160 Luckett and Hong
orders several times during mammalian evolution (Novacek, 1986), including some ceta-
ceans. This makes it unclear whether the derived amastoid condition developed conver-
gently in hippopotamids and suoids. Despite the uncertainty regarding the sister-group
relations of Hippopotamidae within Artiodactyla, the occurrence of the combination of
three derived complex characters of the specialized paraxonic foot, double-trochleated
astragalus, and trilobed dP4 in extant and fossil hippopotamids and all other known
artiodactyls, but in no other mammals, provides robust corroboration of a monophyletic
Artiodactyla. This combination of derived morphological characters can be traced back
for at least 55 million years in the fossil record.
Molecular Evolution Within Artiodactyla and Cetacea
Whatever the disagreements between morphologists and molecular biologists con-
cerning mammalian evolution, there is now universal agreement concerning the mono-
phyly of the order Cetacea from analyses of morphology and molecules. Therefore, this
discussion deals only with the more controversial issues of the possible affinities of
Hippopotamidae to Cetacea and of the sister-group affinities of the Physeteroidea to other
Cetacea.
Careful analysis of individual nucleotide positions of the cytochrome b gene with
Artiodactyla and Cetacea, and within numerous mammalian outgroups, suggests that this
gene (and probably other mitochondrial genes) are of limited value in assessing higher-
level phylogenetic relationships among orders and suborders of mammals. This conclu-
sion is based not on any bias against molecular data but, rather, on the empirical obser-
vation that uniquely derived cyt b nucleotides or amino acids are exceedingly difficult
or impossible to find at the ordinal or subordinal level in speciose orders, due to ho-
moplasy, when adequate taxon sampling is undertaken. In contrast, mitochondrial
nucleotide data are doubtlessly of great value when assessing relationshipsamong eu-
therian species, genera, and families, although character analysis remains essential for
distinguishing between synapomorphies, symplesiomorphies, and homoplasies at any
level of systematic analysis.
Character analysis of the cyt b gene also revealed that the majority (72.6%) of
"conservative" nucleotide positions identified in our study are third-position codon
transversions. The fact that many of these transversions are "silent" or neutral, in that
they result in no change for most amino acids (such as alanine, leucine, proline, threo-
nine, and valine), also diminishes their value for phylogenetic reconstruction. Amino
acids are the smallest "functional" units of proteins, and we agree with the emphasis
placed by Adachi and Hasegawa (1996) on the use of amino acid substitutions, rather
than individual nucleotide substitutions, for the reconstruction of phylogeny. Unfortu-
nately, it is even more difficult to identify shared, derived amino acids among the cyt b
gene sequences of mammalian orders, as noted by Montgelard et al. (1997).
Molecular Evidence for Hippopotamid Affinities
Our character analysis of the cyt b gene corroborated the observation by Montgelard
et al. (1997) that only a single, rare amino acid substitution shared by Cetacea and
Hippopotamidae supports the monophyly of this supposed clade, despite the moderate
bootstrap support (74%) for their majority-rule consensus tree based on parsimony anal-
Evolution of Artiodactyla and Cetacea 161
ysis of DNA nucleotide sequences in 29 species. A lower level of bootstrap support
(53 %) for a hippopotamid–cetacean clade was detected by Arnason and Gullberg (1996)
in their parsimony analysis of a larger number of cetacean species and a single species
of hippopotamus. Montgelard et al. (1997) noted that both extant hippopotamid species
and the 35 cetacean species examined to date share the amino acid threonine at position
243 in the cytochrome b gene (nucleotide positions 727–729). This "nearly exclusive
synapomorphic replacement" was shared by "only 11 distantly related mammals (six
primates, four rodents, and one sirenian) out of 199 comparisons" of species represent-
ing 11 eutherian orders (Montgelard et al., 1997, p. 557).
We conducted a more extensive character analysis of the different amino acids that
occur at position 243 in 219 genera of Mammalia (see Appendix), with emphasis on
assessing whether a rare substitution at this position was a useful and conservative char-
acter for phylogenetic reconstruction at the higher taxonomic level. Our analysis of the
different amino acids that occur at position 243 in mammals suggests that valine codon
GTR represents the plesiomorphic or morphotypic condition in the last common ancestor
of extant Eutheria and of Artiodactyla, based on the commonality of this amino acid.
All substitutions at third codon positions are silent for valine, so that it probably makes
no difference whether a purine or a pyrimidine occurs at this position in Eutheria (see
Fig. 8).
At the higher taxonomic level, a relatively rare substitution of threonine at position
243 characterizes all extant hippopotamids and cetaceans studied to date, as emphasized
by Montgelard et al. (1997). However, the same substitution occurs also in the two
extant genera of Sirenia, as well as in the recently extinct Steller's sea cow (Ozawa et
al., 1997). Thus, this rare substitution characterizes extant members of both orders of
marine Eutheria—Cetacea and Sirenia—as well as the amphibious artiodactyl family
Hippopotamidae. Because there is no molecular or morphological evidence for a clad-
istic relationship between Cetacea and Sirenia, it is evident that convergent evolution
accounts for this shared amino acid similarity between the two marine orders. This amino
acid substitution may be an exception to the generalization by Irwin and Arnason (1994)
that convergent evolution is not evident in the cytochrome b gene of aquatic mammals
(based on their assessment of a smaller number of representatives for each order). It is
also interesting that this amino acid substitution does not occur in the pinnipeds exam-
ined to date.
In addition to the evidence for convergent evolution of threonine at position 243 in
the cyt b gene of Cetacea and Sirenia, we have detected evidence of similar homoplasy
within at least three other eutherian orders, namely, Primates, Rodentia, and Hyra-
coidea. Within Primates, this "rare" amino acid has evolved convergently at least four
to six times: Homo, Pan, Gorilla, and Pongo within Hominoidea (possibly the result of
a single mutation in their last common ancestor); Macaca and Papio within Cercopithe-
cidae; Saimiri within Cebidae; and Daubentonia within Strepsirhini. Among rodents,
threonine occurs independently at position 243 in at least three families: Coendou within
Erethizontidae; Dactylomys, Thrichomys, and Trinomys within Echimyidae; and Akodon
and Microtus within different subfamilies of Muridae. The single genus of Hyracoidea
examined to date, Procavia, also has threonine at AA position 243; it will be interesting
to determine whether a homologous amino acid substitution occurs in the other two
extant genera of this order.
162 Luckett and Hong
It is unclear what, if anything, is the functional significance of the substitution of
threonine for valine at position 243 in the amino acid chain of cytochrome b. Based on
the secondary structural model of the cyt b gene presented by Irwin et al. (1991, Fig.
7), this amino acid position occurs in the "hypervariable" transmembrane portion of the
protein, which consists mainly of hydrophobic residues. In most mammals examined to
date, hydrophobic amino acids occur at position 243 (either valine, alanine, or isoleu-
cine); substitution of threonine, an amino acid with both hydrophobic and hydrophilic
properties, at this position appears to be a more radical change, as pointed out to us by
David Irwin (personal communication, Dec. 1997). Nevertheless, the apparent "rarity"
of this substitution is a relative concept, depending on the number of taxa sampled.
Within akodontin rodents studied by Smith and Patton (1993), valine is also the com-
mon, and presumably primitive, amino acid at this position, as in the majority of eu-
therians examined. However, within the numerous species of Akodon sequenced by Smith
and Patton (1993), three different amino acids could be detected at this position: valine,
alanine, or threonine. Whatever the functional implications (if any) might be for the
unusual substitution of threonine at this transmembrane position, the different species of
Akodon would be an ideal model for assessing this question. The different amino acids
at this position in Akodon also suggest a possible transformation series for the evolu-
tionary change from valine to threonine, through one or two intermediate alanine stages:
GTT (valine) -» GCT (alanine) -» GCC (alanine) -» ACC (threonine). Each of these
"stages" occurs in one or more species of Akodon, and each transformation step would
require only a single transition change.
This documented pattern of intrageneric and intrafamilial variation of amino acids
at transmembrane position 243 in the cytochrome b gene suggests to us that the relatively
"rare" substitution of threonine at this position within Eutheria should not be given
much weight in assessing the ordinal relations of the extant hippopotamids, any more
than it should be used to support a sister-group relationship between Cetacea and Sirenia.
We suspect that greater variation in this amino acid position might be detected within
the Cetacea, Hippopotamidae, and Sirenia if the Eocene–Oligocene cetaceans, the Mio-
cene hippopotamids Kenyapotamus and Hexaprotodon, and the 25 genera (at least) of
fossil sirenians could be analyzed for this trait. The lack of complete cytochrome b
sequences from any species of the eutherian orders Scandentia, Dermoptera, Tubuliden-
tata, Pholidota, and Macroscelidea, as well as from the vast majorityof genera in the
orders Insectivora, Xenarthra, Rodentia, and Chiroptera, makes it difficult to assess the
relative "rarity" of amino acid substitutions at position 243 within Mammalia.
Common sense indicates that the two rare or unique synapomorphic character com-
plexes of the tarsus and deciduous dentition, shared by all known fossil and extant hip-
popotamids and artiodactyls, provide robust corroboration for artiodactyl monophyly,
compared with the observed homoplasy of amino acid 243 in extant genera, families,
and superfamilies of Eutheria. We suggest that this amino acid substitution provides a
good example of an historical signal (Artiodactyla monophyly) being seemingly "over-
turned" by a convergent similarity among distantly related taxa, a condition demon-
strated elegantly by Naylor and Brown (1998) in their analysis of complete mitochondrial
genomes in chordates.
Evolutionary assessment of other mitochondrial and nuclear genes to date has pro-
vided mixed support for a hippopotamid–cetacean clade, although taxon sampling was
Evolution of Artiodactyla and Cetacea 163
sparse in these studies (see Table III). In their parallel study of the mitochondrial 12S
rDNA and cyt b genes, Montgelard et al. (1997) found virtually no corroboration for a
hippo-cetacean clade from separate analysis of the 12S gene. They also noted that the
12S gene showed less variability between the two hippopotamid genera (2%) compared
to the cytochrome b gene (7.5%).
In contrast, Gatesy et al. (1996) found support for the hippopotamid-cetacean clade
in their analyses of nuclear casein genes in a small sample (13 genera) of artiodactyls,
cetaceans, and Hippopotamus, with 8 eutherian outgroup genera. For their combined
K- and B-casein sequences, the bootstrap score for a hippopotamid-cetacean clade (three
species only) was 87 %, and the decay index was 4. Gatesy et al. (1996) stated that seven
“unambiguous character transformations” in the casein genes support the hippo-cetacean
clade. Similar results were obtained by Gatesy (1997) for a small portion (651 bp) of a
nuclear gene for the blood-clotting protein 7-fibrinogen, from 16 genera of eutherians,
including the pygmy hippo Choeropsis, 7 other artiodactyls, and 3 cetaceans. For these
data the hippopotamid-cetacean clustering was supported by a bootstrap of 91 % and a
decay index of 4. The author claimed that five shared derived nucleotides “unambigu-
ously support” this clade. A combined analysis of four genes (7-fibrinogen, two caseins,
and cyt b) by Gatesy (1997) for basically the same taxa resulted in seemingly stronger
support (99% bootstrap) for the hippo-cetacean clade.
The papers by Gatesy et al. (1996) and Gatesy (1997) illustrate several common
shortcomings in many published studies of molecular evolution in mammals. First, tax-
onomic sampling of both ingroups and outgroups is extremely meager (see Table III);
this is especially critical when assessing higher-level hypotheses of phylogeny, such as
the monophyly of Artiodactyla. For most families examined in the studies by Gatesy
and colleagues, only a single genus was sampled; this makes it impossible to evaluate
character variability (whether nucleotides or amino acids) within families. Without such
a knowledge of variability within both ingroups and outgroups, it is premature (and
systematically naive) to claim that “unambiguous” support is provided for any clade
when only 9–11% of the ingroup genera (and even fewer outgroups) are evaluated. In
Table III. Percentage of Extant Mammalian Genera Studied in Molecular Analyses of Hippopotamid/
Artiodactylan/Cetacean Relationshipsa
Irwin and Arnason (1994)
Randi et al. (1996)
Arnason and Gullberg (1996)
Gatesy et al. (1996)
Montgelard et al. (1997)
Gatesy (1997)
Shimamura et al. (1997)
Present study
Ingroups (H, A, C)b
combined
Genera
14/122
29/122
32/122
13/122
17/122
11/122
15/122
75/122
Percentage
11.5
23.8
26.2
10.7
13.9
9.0
12.3
61.5
Outgroups (other
Mammalia)
Genera
12/1013
4/1013
2/1013
8/1013
12/1013
5/1013
6/1013
144/1013
Percentage
1.2
0.4
0.2
0.8
1.2
0.5
0.6
14.2
aTotal numbers of genera in ingroup and outgroup derived from Wilson and Reeder (1993).
bH, Hippopotamidae; A, Artiodactyla; C, Cetacea.
164 Luckett and Hong
contrast, the more extensive taxon sampling used in the present study furnishes ample
evidence for variation and homoplasy, even for relatively conservative nucleotide posi-
tions, in the cytochrome b gene.
In addition to the lack of adequate taxon sampling. Gatesy and colleagues provide
little or no evidence of the functional implications, if any, of the nucleotide substitutions
detected in their assessments of nuclear genes. Gatesy et al. (1996, p. 955) note that
caseins “evolve exceptionally rapidly at the amino acid level,” due apparently to
"relaxed evolutionary constraints on nutritional milk proteins" and that substitutions
“ are evenly distributed over the three codon positions.” Although Gatesy (1997) reported
that g-fibrinogen exhibits a slower overall rate of both nucleotide and amino acid sub-
stitution than do the casein genes, no evidence was presented concerning any possible
amino acid substitutions shared by hippos and cetaceans in either study. It is interesting
to note that three of the five “unambiguous” nucleotide substitutions of the fibrinogen
gene shared by the latter taxa (Gatesy, 1997) are found also in the hyena Crocuta cro-
cuta.
No molecular study that has evaluated the postulated hippopotamid-cetacean rela-
tionship to date has adequately sampled the degree of variation of putative synapomor-
phies of nucleotides or amino acids shared by the two taxa, within either Artiodactyla,
Cetacea, or Eutheria (see Table III). Therefore, we consider these published studies to
provide only "preliminary data" from particular genes; more extensive data collection
is needed (especially from nuclear genes) before one can speculate meaningfully on the
systematic, phylogenetic, or functional implications of variations in these gene patterns,
especially when testing hypotheses of higher-level phylogeny.
The most recent challenge to the monophyly of Artiodactyla comes from two fam-
ilies of short interspersed elements (SINEs) which have been integrated into the genomes
of ruminants, hippopotamids, and cetaceans by retroposition (Shimamura et al., 1997);
these retroposons are apparently absent in the genomes of the single suid and camelid
species examined. Milinkovitch and Thewissen (1997, pp. 622-623) believe that these
new molecular findings “further disrupt phylogenetic dogma” and that they "should
lead morphologists to re-examine what might have mislead them for more than a cen-
tury." Following their analysis of SINE retroposons, Shimamura et al. (1997, p. 669)
concluded that these data provide "unambiguous support" for a cetacean/ruminant/hippo
clade; however, careful inspection of their data suggests an alternative hypothesis.
As noted by Shimamura et al. (1997), it is likely that insertions of SINEs into the
genome of specific evolutionary lineages represent a unique event; as such, they may
serve as useful "molecular markers" for identification of monophyletic clades. It is also
generally accepted (Okada, 1991; Buntjer et al., 1997) that most SINEs have neutral
effects on their host and are not subject to selection. Although there is probably no
specific mechanism for removing SINEs from higher taxa, they can “disappear slowly
by degradation and random deletions” (Buntjer et al., 1997, p. 67). Nine different retro-
positional events of SINEs were evaluated by Shimamura et al. (1997), but only three
of these provided support for a common cetacean-hippo-ruminant clade (=CHR clade;
see their Fig. 4), to the exclusion of suids and camelids. The authors interpreted these
three SINE loci as having been present in the last common ancestor of the CHR clade,
but absent in the camel, pig, and other therian species examined. Not mentioned by
Shimamura et al. (1997), however, is the fact thatfor two of these three SINEs, one or
more of the ingroup species is also lacking the SINE locus.
Evolution of Artiodactyla and Cetacea 165
SINE locus aaa228, while present in the single species of Bovidae, Giraffidae, Hip-
popotamidae, Mysticeti, Physeteridae, Delphinidae, and Phocoenidae examined, is
absent in the single species of Cervidae, Tragulidae, Suidae, and Ziphidae studied.
Therefore, if this locus did occur in the last common ancestor of cetaceans, hippopot-
amids, and ruminants, it must have been lost independently in representatives of at least
three families. Given that two ruminant families (Moschidae and Antilocapridae), seven
or eight cetacean families, and Tayassuidae were not sampled, it is equally likely that
this SINE locus was lost independently also in the pig and camel species investigated.
A second SINE locus (Gm5) is found in most “CHR” species studied, but it is lacking
in the single tragulid examined. Only a single SINE locus (aaa792) is found in all 13
ingroup species studied by Shimamura et al. (1997). Until more extensive taxon sam-
pling is conducted for CHR SINEs in all families of Cetacea and Artiodactyla, it is
premature to speculate about the phylogenetic significance of these retroposons. As an
example, the absence of SINE locus aaa228 in the single cervid examined makes it
impossible to know whether this locus was lost in all 16 extant genera of Cervidae or
only in the single species examined.
Molecular Evidence for a Physeteroid-Mysticete Clade
The molecular support for a physeteroid-mysticete clade within Cetacea appears
relatively strong at first glance (for recent summaries, see Milinkovitch et al., 1996;
Hasegawa et al., 1997), but this support does not withstand careful scrutiny by character
analysis. As described above, most shared derived nucleotide changes in the two taxa
are silent third-position transversions and, thus, of no apparent functional significance
at the amino acid level. Other shared substitutions occur also in one or more additional
odontocete families. Compared to the uniquely derived cranial and auditory traits shared
by all unquestioned extant and fossil odontocetes (including physeteroids), we believe
that little phylogenetic significance can be given to the shared nucleotide similarities
between physeteroids and mysticetes. The mosaic pattern of their distribution in other
cetacean and eutherian families suggests the likelihood that these similarities are the
result of homoplasy, rather than homology.
In the initial molecular assessment of odontocete paraphyly, Milinkovitch et al.
(1993) analyzed two mitochondrial ribosomal genes in 13 of 41 extant genera of ceta-
ceans; this included both genera of physeteroids but only 2 genera of mysticetes. Neither
the single ziphiid genus nor the two physeteroid genera examined clustered with other
odontocetes; instead, the physeteroids grouped with the two mysticetes with moderately
strong bootstrap support (84%) in parsimony analysis. Although the authors acknowl-
edged that the classic cetacean suborders seem well supported by morphological traits,
the only one of these mentioned for odontocetes was the presence of teeth.
In another study of physeterid affinities, based on analysis of cyt b sequences in
seven cetaceans, Arnason and Gullberg (1994) questioned the systematic conclusions of
Milinkovitch et al. (1993). However, in a reassessment of the same cyt b sequences
using transversion-only parsimony, Milinkovitch (1995) found further support for the
physeteroid-mysticete clade, and he discussed the critical problem of tree rooting when
assessing cetacean phylogeny. In particular, Milinkovitch (1995) emphasized the impor-
tance of multiple outgroups in aiding the interpretation of nucleotide character polarity
during phylogenetic reconstruction. We agree with Milinkovitch (1995) concerning the
usage of multiple outgroups and the importance of determining the polarity of nucleotide
166 Luckett and Hong
characters; unfortunately, he presented no explicit hypotheses of nucleotide character
polarity in any of his subsequent analyses of physeteroid-mysticete affinities (see Mil-
inkovitch et al., 1996; Hasegawa et al., 1997).
Despite the sophisticated analysis of cytochrome b data by a variety of parameters
and weighting schemes, including parsimony and maximum-likelihood methods,
Milinkovitch et al. (1996) presented no explicit documentation of putative nucleotide or
amino acid synapomorphies that might corroborate their preferred hypothesis of
physeteroid-mysticete monophyly, and no consistency index (CI) was provided for their
data matrix. The same shortcomings are found in their most recent reexamination of the
then-available cyt b data (Hasegawa et al., 1997). The latter data set was derived almost
entirely from the cyt b matrix of Arnason and Gullberg (1996) on 40 eutherian species
(including 28 cetaceans). The low CI (0.354) found by Arnason and Gullberg (1996)
for their majority-rule consensus tree suggests a high level of homoplasy in their data
set; this is precisely what we found with the addition of more ingroup and outgroup
genera to the cyt b character analysis of the present study. Given the extensive homo-
plasy that occurs in the cyt b gene for most suprafamilial groups of therian mammals
examined by us (with the notable exception of Mysticeti), we endorse the possibility
raised by Milinkovitch et al. (1996, pp. 1830-1831) that, at least in some cases, “cyto-
chrome b might consistently support the wrong hypothesis (i.e., the cytochrome b gene
tree might not correspond to the species tree).” This seems particularly true for the
hypotheses of physeteroid-mysticete and of hippopotamid-cetacean affinities.
Milinkovitch (1995) has further suggested that, if his hypothesis of physete-
roid-mysticete relationships is “correct,” then the morphological data that support mo-
nophyly of Odontoceti need to be reevaluated. He attempted such an analysis by dis-
cussing differences in the occurrence of teeth, baleen, and the number of blowholes in
extant whales, but no mention was made of the most distinct and uniquely derived dif-
ferences between extant and fossil members of the suborders Odontoceti and Mysticeti—
their contrasting patterns of cranial telescoping. These and other morphological attri-
butes of cetaceans have been discussed in great detail and analyzed by Heyning (1997),
who provides strong corroboration for monophyly of the two classical suborders. A
recent combined analysis of morphological (207 characters) and molecular data (three
mitochondrial genes) in mysticetes, odontocetes, physeteroids, and selected artiodactyl
outgroups by Messenger and McGuire (1998) also furnishes strong support for the tra-
ditional view of Odontoceti monophyly.
Systematic Conclusions
The level of homoplasy exhibited by conservative nucleotide positions in the cyt b
gene within and between eutherian orders of mammals diminishes their value for the
reconstruction of cladistic relationships among suprafamilial taxa, particularly when the
parsimony or maximum-likelihood assessments of this gene result in conflicts with well-
established hypotheses of phylogeny, based mainly on rare or uniquely derived mor-
phological attributes shared by both extant and fossil taxa. The main causes of such
phylogenetic conflicts appear to be (1) underestimation of the level of homoplasy within
individual data sets (whether molecular or morphological) and (2) the inadequate taxon
sampling and concomitant imprecise polarity determination that accompany most molec-
Evolution of Artiodactyla and Cetacea 167
ular assessments of higher level mammalian phylogeny. These two problems are inter-
related; homoplasy is more likely to be detected when the majority of species, genera,
and families of mammalian orders are examined for the occurrence of particular char-
acter states, whether morphological or molecular. Indeed, such extensive character anal-
yses provide the only justification for concludingthat particular biological traits are
“uniquely derived” and diagnostic for a particular taxon, whether genus or order. If
taxon sampling is sparse, as in most molecular analyses of mammalian interordinal rela-
tionships, then it is premature to conclude that relatively rare nucleotide or amino acid
substitutions “unambiguously support” (e.g., Gatesy, 1997, p. 537) novel clades, such
as Cetacea/Hippopotamidae.
Many mammalian orders can be diagnosed by the occurrence of one or more
uniquely derived morphological traits or character complexes which have enabled them
to adapt and survive over an extensive period of geological time. Such features are most
readily identified in the dentition or skeleton, because these are the only character com-
plexes whose evolutionary history can be traced in both extant and fossil mammals. This
does not imply that derived soft anatomical or molecular characters cannot be diagnostic
of higher taxa or be of great adaptive significance; it simply means that such features,
when identified, can be attributed only to the last common ancestor of the extant rep-
resentatives of that taxon. In speciose orders, such as Artiodactyla, Cetacea, Rodentia,
and Chiroptera, the earliest fossil representatives of the order commonly exhibit many
morphological differences from, and may be only distantly related to, extant members
of the order. As emphasized by Novacek (1992b), fossils not only increase the number
of taxa that can be sampled for dental and skeletal traits, but also provide additional
insight into the assessment of character polarity and transformation. At present, the
available technology simply cannot provide molecular data from such fossils, which are
key to understanding the evolutionary origins of higher taxa, such as mammalian orders.
For the order Artiodactyla, 27 of its currently recognized 37 families (McKenna and
Bell, 1997) are represented only by fossils.
Given the inability of molecular or soft anatomical data to assess the biological
attributes of the earliest members of mammalian orders, it is essential to sample exten-
sively at the species, generic, and family levels, before using such data for the recon-
struction of higher level relationships among extant members of an order. Just how much
taxon sampling should be considered “adequate” is rarely discussed in molecular assess-
ments of mammalian phylogeny. Montgelard et al. (1997) suggested that it is better to
use two species rather than one when assessing relationships within mammalian orders
or suborders. However, the value and limitations of such an approach are dependent on
the number of species or genera within any specific higher category. For instance, exam-
ining two genera of hippopotamids, as done by Montgelard et al. (1997), effectively
sampled all extant representatives of the family Hippopotamidae. In contrast, their sam-
pling of two genera of Bovidae, Odontoceti, and Carnivora provides insufficient evi-
dence of the nucleotide variation that occurs within these ingroup and outgroup taxa.
For any analysis of systematic relationships, it is essential to collect preliminary molec-
ular or morphological data from a wide range of genera and species, before assessing
the possible use of such data for the reconstruction of higher taxa phylogeny. Unfortu-
nately, this has been done only rarely in molecular analyses of mammalian evolution.
Recent studies by Ruedi and Fumagalli (1996), Ohdachi et al. (1997), and Gatesy et al.
168 Luckett and Hong
(1997) are important contributions to the collection of preliminary data on mitochondrial
gene variation within the insectivoran families Erinaceidae and Soricidae and the artiod-
actyl family Bovidae, respectively. Such extensive taxonomic sampling at the family
level is essential before speculating about the relationships of extant higher taxa to other
eutherians.
It is worthwhile noting that the family Hippopotamidae and the superfamily Phy-
seteroidea, which served as the focus of our study, each contains only two extant genera.
Given the high level of nucleotide homoplasy that occurs in the cytochrome b gene
within Eutheria, the probability is greater that higher taxa with only one or two genera,
as in these cases, are more likely to suffer from the “attraction of long branches” (Fel-
senstein, 1978) than are more speciose taxa, such as Pecora. The distribution of the
unusual amino acid threonine at position 243 in the cyt b gene serves as a useful example
of this. The occurrence of threonine at this position convergently within some genera of
cercopithecid primates and akodontine rodents is not reflected by morphotype recon-
struction of these speciose taxa. In contrast, the presence of this amino acid at position
243 in both extant genera of hippopotamids suggests that it occurred in their last common
ancester, but it is impossible to know whether threonine was found at the same position
in the Miocene-Pliocene hippopotamids Kenyapotamus and Hexaprotodon. Neverthe-
less, the extant hippopotamid branch is “attracted” to the cetacean branch by the shared,
derived homoplastic trait of this amino acid. Such distantly related taxa are particularly
susceptible to “incorrect groupings” due to convergent similarities, as demonstrated by
Naylor and McGuire (1998, p. 61), even when complete mitochondrial genome
sequences are analyzed.
The homology or homoplasy of molecular or morphological traits in hippopotamids
and physeteroids can be judged by assessing the consistency index (CI) of the individual
characters that support conflicting hypotheses, as done by Shoshani et al. (1996) in their
analysis of primate evolution. Thus, the unique double-trochleated astragalar complex,
found in fossil and extant hippopotamids and in all other artiodactyls, has a CI = 1,
compared to all known species of extant and fossil mammals. We do not know the CI
of the amino acid threonine at cyt b position 243 in mammals, because the majority of
genera and species of extant mammals have not been analyzed for this trait; it is clearly
less than 1 within Eutheria. Therefore, the assumption by Gatesy (1997, p. 542) that “a
single nucleotide substitution carries as much weight in phylogenetic analysis as the
evolution of a stable morphological feature” is systematically naive, from either a mor-
phological or a molecular perspective. As we have shown in this study, the majority
of relatively conservative derived nucleotide traits that might support a hippo-
potamid-cetacean clade are silent third-position substitutions; all of these show consid-
erable homoplasy within both the ingroups and the outgroups examined. Even the most
robust amino acid trait identified in our study (and earlier by Montgelard et al., 1997)
for possible support of a hippo-cetacean clade shows moderate variation at the species,
generic, tribal, or familial levels within several mammalian orders.
A general failure to consider the biological and functional significance of the
nucleotide and amino acid substitutions that occur in cytochrome b and other protein-
coding genes also diminishes considerably the value of such data for phylogenetic recon-
struction. We endorse the recommendation by Adachi and Hasegawa (1996, p. 459) that
it "seems preferable to model amino acid substitutions rather than nucleotide substitu-
tions" for protein-coding genes, because "selective constraints are more likely to be
Evolution of Artiodactyla and Cetacea 169
operating at the codon level rather than at the individual nucleotide level.” Virtually all
of the amino acid substitutions that we detected as support for the unorthodox hypotheses
of hippopotamid-cetacean or physeteroid-mysticete affinities occurred in the hyper-
variable transmembrane region of the cyt b model provided by Irwin et al. (1991). More
precise models of the cytochrome bc1 complex of the mitochondrion (which includes cyt
b as one of its components) have recently been constructed (Xia et al., 1997), and Naylor
and Brown (1997, p. 528) have providednew insights from mitochondrial protein-coding
genes that may lead to “a better understanding of the historical and functional constraints
that act on macromolecules and, as a consequence, to more realistic biochemically based
models of change from which to infer evolutionary trees.” The increased incorporation
of such functional considerations into models of molecular phylogenetic inference should
help narrow the gap between molecular and morphological assessments of biological
evolution. We strongly endorse the suggestion by Naylor and Brown (1998, p. 61) that
“accurate phylogenetic estimation may be better served by incorporating knowledge of
molecular structures and processes into inference models and by seeking additional higher
order characters embedded in those sequences.”
In conclusion, cytochrome b gene sequence data cannot corroborate the monophyly
of Artiodactyla, because of extensive homoplasy (and probable back mutations) in this
gene at the higher taxonomic level. Contrary to assertions from many molecular studies
(e.g., Graur and Higgins, 1994; Gatesy et al., 1996; Gatesy, 1997; Montgelard et al.,
1997), however, this inability to corroborate monophyly is not the same thing as falsi-
fying it. Not all data sets are capable of corroborating the monophyly of higher taxa,
due to the mosaic nature of character evolution and differing levels of homoplasy that
are found in different biological character complexes. Indeed, monophyly of a Cetacea
plus Artiodactyla clade was not supported in our study by the occurrence of any rare or
uniquely derived nucleotide traits from the cytochrome b gene (see also Arnason and
Gullberg, 1996). The main morphological trait that supports this superordinal grouping
(paraxony of the hindfeet) also occurs in fossil Mesonychia; moreover, derived aspects
of the dentition (O’Leary, 1998) corroborate a sister-group relationship between Meso-
nychia and Cetacea, to the exclusion of Artiodactyla.
Monophyly of all extant and fossil (where known) Artiodactyla is corroborated by
two derived morphological complexes of the astragalus and deciduous dentition not found
in the morphotype of any other mammalian order. We believe that our character analysis
of both morphological and molecular traits provides a more robust test of artiodactyl
monophyly than do parsimony or maximum-likelihood analyses of a mixture of highly
homoplastic and conservative traits in the cyt b gene. The latter methods are important
first steps in the evaluation of large data sets, such as gene sequences, but restraint on
the part of investigators and careful character analyses of the structural and functional
attributes of genes, with extensive taxon sampling, are needed before rejecting well-
corroborated hypotheses of phylogenetic relationships, such as the monophyly of Artio-
dactyla and of Odontoceti.
ACKNOWLEDGMENTS
Our character analysis of cytochrome b genes was initiated by the gracious coop-
eration of Dr. Ulfur Arnason, University of Lund, Lund, Sweden, in providing us with
his alignment of complete sequences of most cetacean genera and selected artiodactyls,
170 Luckett and Hong
Table AI. Mammals Included in Cytochrome b Sequence Analysis
Order Monotremata
Family Ornithorhynchidae
Ornithorhynchus
Order Didelphimorphia
Family Didelphidae
Caluromys
Didelphis
Glironia
Marmosa
Marmosops
Metachirus
Micoureus
Monodelphis
Philander
Order Artiodactyla
Suborder Suiformes
Family Suidae
Babyrousa
Phacochoerus
Sus
Family Tayassuidae
Catagonus
Pecan
Tayassu
Family Hippopotamidae
Choeropsis
Hippopotamus
Suborder Tylopoda
Family Camelidae
Camelus
Lama
Vicugna
Suborder Ruminantia
Family Tragulidae
Tragulus javanicus
Tragulus napu
Infraorder Pecora
Family Giraffidae
Giraffa
Family Moschidae
Moschus (4 species)
Family Cervidae
Alces
Capreolus
Cervus
Dama
Hydropotes
Mazama
Muntiacus
Odocoileus
Rangifer
Family Antilocapridae
Antilocarpa
Number of genera
studied"
1/1
9/15
51/81
3/5
3/3
2/2
3/3
1/3
1/2
1/1
9/16
1/1
Literature citation or GenBank
accession No.
Janke et al. (1996)
Patton et al. (1996)
"
"
»
»
"
"
"
"
Randi et al. (1996)
"
"
U66291
U66290
Irwin et al. (1991)
Montgelard et al. (1997)
Irwin and Arnason (1994)
Stanley et al. (1994)
"
"
Chikuni et al. (1995)
Irwin et al. (1991)
Irwin et al. (1991)
AF026883-AF026889
Randi et al. (1998)
Y14951, Randi et al. (1998)
Chikuni et al. (1995)
Irwin et al. (1991), Randi et
al. (1998)
Randi et al. (1998)
"
"
Irwin et al. (1991)
Randi et al. (1998)
Irwin et al. (1991)
APPENDIX
Evolution of Artiodactyla and Cetacea 171
Table AI. Continued
Family Bovidae
Addax
Aepyceros
Alcelaphus
Ammotragus
Anoa
Beatragus
Bison
Bos
Bubalus
Budorcas
Capra
Capricornis
Connochaetes
Damaliscus
Gazella
Hemitragus
Hippotragus
Naemorhedus
Oreamnos
Ovibos
Ovis
Pantholops
Pseudois
Rupicapra
Saiga
Sigmoceros
Syncerus
Order Cetacea
Suborder Mysticeti
Family Balaenidae
Balaena
Eubalaena
Family Balaenopteridae
Balaenoptera
Megaptera
Family Eschrichtidae
Eschrichtius
Family Neobalaenidae
Caperea
Suborder Odontoceti
Family Delphinidae
Globiocephala
Lagenorhynchus
Orcaella
Orcinus
Stenella
Tursiops
Family Iniidae
Inia
Pontoporia
Family Monodontidae
Delphinapterus
Monodon
Number of genera
studieda
27/45
24/41
2/2
2/2
1/1
1/1
6/17
2/2
2/2
Literature citation or GenBank
accession No.
Hassanin et al. (1998)
AF034966
AF028822
Hassanin et al. (1998)
Tanaka et al. (1996)
AF034968
Y 15005
Tanaka et al. (1996)
"
Groves and Shields (1996)
Irwin et al. (1991), D84202
Chikuni et al. (1995), Groves
and Shields (1996)
AF034969
AF028821
AF028820
Groves and Shields (1996)
AF047678
Groves and Shields (1996)
Chikuni et al. (1995), Groves
and Shields (1996)
Groves and Shields (1996)
Irwin et al. (1991)
Hassanin et al. (1998)
"
Chikuni et al. (1995)
Groves and Shields (1996)
AF034967
Tanaka et al. (1996)
Arnason and Gullberg (1996)
"
Arnason and Gullberg (1996)
Arnason and Gullberg (1994)
Arnason and Gullberg (1996)
Arnason and Gullberg (1996)
Arnason and Gullberg (1996)
"
"
"
"
"
Arnason and Gullberg (1996)
"
Arnason and Gullberg (1996)
172 Luckett and Hong
Table AI. Continued
Family Phocoenidae
Phocoena
Family Physeteridae
Kogia
Physeter
Family Platanistidae
Platanista
Family Ziphiidae
Berardius
Hyperoodon
Mesoplodon
Ziphius
Order Perissodactyla
Family Equidae
Equus asinus
Equus caballus
Equus grevyi
Family Rhinocerotidae
Ceratotherium
Diceros
Rhinoceros
Family Tapiridae
Tapirus
Order Hyracoidea
Family Procaviidae
Procavia
Order Proboscidea
Family Elephantidae
Elephas
Loxodonta
Mammuthus
Order Sirenia
Family Dugongidae
Dugong
Hydrodamalis
Family Trichechidae
Trichechus
Order Carnivora
Suborder Feliformia
Family Felidae
Felis
Panthera
Family Herpestidae
Herpestes
Suborder Caniformia
Family Ailuridae
Ailurus
Family Canidae
Canis
Vulpes
Family Mustelidae
Enhydra
Gulo
Number of genera
studieda
1/4
2/2
1/2
4/6
1/1
3/4
1/1
1/3
3/3
2/2
1/1
2/18
1/18
1/1
2/14
7/25
Literature citation or GenBank
accession No.
Arnason and Gullberg (1996)
Arnason and Gullberg (1996)
"
Arnason and Gullberg (1996)
Arnason and Gullberg (1996)
"
"
"
Xu et al. (1996)
D82932, D32190
Irwin et al. (1991)
Xu and Arnason (1997)
Irwin et al. (1991)
Xu et al. (1996)
AF056030
Ozawa et al. (1997)
Ozawa et al. (1997), Noro et
al. (1998)
Irwin et al. (1991), Noro et
al. (1998)
Ozawa et al. (1997), Noro et
al. (1998)
Irwin and Arnason (1994)
Ozawa et al. (1997)
Ozawa et al. (1997)
Arnason et al. (1995)
"
Ledje and Arnason (1996)
Ledje and Arnason (1996)
Ledje and Arnason (1996)
"
Ledje and Arnason (1996)
"
Evolution of Artiodactyla and Cetacea 173
Table AI. Continued
Lutra
Meles
Mephitis
Mustela
Spilogale
Family Odobenidae
Odobenus
Family Otariidae
Arctocephalus
Eumetopias
Zalophus
Family Phocidae
Cystophora
Erignathus
Hydrurga
Mirounga
Phoca
Family Procyonidae
Bassaricyon
Procyon
Family Ursidae
Ailuropoda
Helarctos
Melursus
Thalarctos
Tremarctos
Ursus
Order Primates
Suborder StrepsirhiniFamily Cheirogaleidae
Cheirogaleus
Microcebus
Mirza
Family Daubentoniidae
Daubentonia
Family Galagidae
Galago
Family Indridae
Propithecus
Family Lemuridae
Eulemur
Hapalemur
Lemur
Varecia
Family Lorisidae
Loris
Nycticebus
Suborder Haplorhini
Family Cebidae
Saimiri
Family Cercopithecidae
Colobus
Macaca
Nasalis
Papio
Number of genera
studieda
1/1
3/7
5/10
2/6
6/6
3/5
1/1
1/4
1/3
4/4
2/4
1/11
4/18
Literature citation or GenBank
accession No.
"
"
"
"
"
Arnason et al. (1995)
Arnason et al. (1995)
"
"
Arnason et al. (1995)
"
"
"
"
Ledje and Arnason (1996)
"
Ledje and Arnason (1996)
Talbot and Shields (1996)
"
Arnason et al. (1995)
Talbot and Shields (1996)
Arnason et al. (1995)
Yoder et al. (1996)
"
"
Yoder et al. (1996)
Yoder et al. (1996)
Yoder et al. (1996)
Yoder et al. (1996)
"
"
"
Yoder et al. (1996)
"
Yoder et al. (1996)
Collura and Stewart (1995)
"
Collura et al. (1996)
Y 16590
174 Luckett and Hong
Table AI. Continued
Superfamily Hominoidea
Gorilla
Homo
Hylobates
Pan
Pongo
Order Chiroptera
Family Phyllostomidae
Artibeus
Chiroderma
Platyrrhinus
Uroderma
Order Rodentia
Suborder Hystricognathi
Family Bathyergidae
Bathyergus
Cryptomys
Georychus
Heliophobius
Family Caviidae
Cavia
Family Ctenomyidae
Ctenomys
Family Dasyproctidae
Myoprocta
Family Echimyidae
Dactylomys
Echimys
Euryzygomatomys
Isothrix
Makalata
Mesomys
Nelomys
Proechimys
Thrichomys
Trinomys
Family Erethizontidae
Coendou
Family Hystricidae
Hystrix
Family Octodontidae
Octodon
Spalacopus
Tympanoctomys
Family Thryonomyidae
Thryonomys
Suborder Sciurognathi
Family Geomyidae
Cratogeomys
Geomys
Orthogeomys
Pappogeomys
Thomomys
Number of genera
studied"
5/5
4/49
4/5
1/5
1/1
1/2
10/20
1/4
1/3
3/6
1/1
5/6
Literature citation or GenBank
accession No.
Xu and Arnason (1996)
Arnason et al. (1996), Horai
et al. (1995)
Collura and Stewart (1995)
Arnason et al. (1996), Horai
et al. (1995)
Collura and Stewart (1995)
Baker et al. (1994)
"
"
"
Faulkes et al. (1997)
"
"
"
Ma et al. (1993)
Lara et al. (1996), Lessa and
Cook (1998)
Lara et al. (1996)
Lara et al. (1996)
"
"
"
"
"
"
"
"
"
Lara et al. (1996)
Ma et al. (1993)
Lessa and Cook (1998)
"
"
Matthee and Robinson (1997)
Dewalt et al. (1993)
"
Smith (1998)
Dewalt et al. (1993)
Smith (1998)
Evolution of Artiodactyla and Cetacea 175
Table AI. Continued
Family Muridae
Subfamily Arvicolinae
Microtus
Subfamily Murinae
Acomys
Aethomys
Arvicanthis
Lemniscomys
Mus
Rattus
Subfamily Sigmodontinae
Abothrix
Akodon
Aulisomys
Bolomys
Calomys
Chelemys
Geoxus
Irenomys
Lenoxus
Microryzomys
Microxus
Neacomys
Nectomys
Notiomys
Oecomys
Oligoryzomys
Oryzomys
Oxymycterus
Rhipidomys
Scolomys
Thomasomys
Family Pedetidae
Pedetes
Family Sciuridae
Glaucomys
Marmota
Sciurus
Spermophilus
Order Lagomorpha
Family Leporidae
Oryctolagus
Sylvilagus
Order Insectivora
Family Erinaceidae
Erinaceus
Family Soricidae
Sorex
Order Xenarthra
Family Dasypodidae
Dasypus
Number of genera
studieda
28/281
1/26
6/122
21/79
1/1
4/50
2/11
1/7
1/23
1/8
Literature citation or GenBank
accession No.
Baker et al. (1996)
X96996, Z96052, Z96061,
Z96064, Z96065, Z96067,
Z96068
AF004587
AF004566, AF004568,
AF004569, AF004573
AF004586
Irwin et al. (1991)
"
Smith and Patton (1993)
»
"
"
"
"
"
"
"
Patton and da Silva (1995)
Smith and Patton (1993)
Patton and da Silva (1995)
Smith and Patton (1993)
"
Patton and da Silva (1995)
"
"
Smith and Patton (1993)
"
Patton and da Silva (1995)
Smith and Patton (1993)
Matthee and Robinson (1997)
AF030392
Thomas and Martin (1993)
"
Irwin and Arnason (1994)
AF0345256, AF034257
Arnason and Gullberg (1996)
Taberlet et al. (1994),
Ohdachi (pers. commun.)
Arnason et al. (1997)
aTotal number of genera in each higher taxon based on data from Wilson and Reeder (1993).
176 Luckett and Hong
perissodactyls, and other eutherians, prior to their publication (see Arnason and Gull-
berg, 1996). We thank Drs. David Irwin, Claudine Montgelard, and Alexandre Hassanin
for providing additional sequence alignments. Dr. Satoshi Ohdachi kindly sent us the
complete cyt b gene sequence of Sorex unguiculatus to use prior to its publication. The
following museum curators and staff furnished access to specimens and useful discus-
sions: John Alexander, Malcolm McKenna, Richard Tedford, Ross MacPhee, and Dar-
rin Lunde (American Museum of Natural History, New York); Chris Beard, Mary
Dawson, and Zhexi Luo (Carnegie Museum of Natural History, Pittsburgh); Brigitte
Senut, Christian de Muizon, Francoise Jouffroy, and Martin Pickford (Museum National
d’Histoire Naturelle, Paris); Gerhard Storch (Forschungsinstitut und Naturmuseum
Senckenberg, Frankfurt am Main); and Chris Smeenk (Nationaal Natuurhistorisch
Museum, Leiden). Paula Jenkins, Natural History Museum, London, and John de Vos,
Nationaal Natuurhistorisch Museum, Leiden, provided valuable information on the nature
of the astragalus and dP4 in several genera of extant and fossil artiodactyls. We thank
the following colleagues for their comments and constructive criticisms on this paper
(even when they disagree with some of our conclusions): Drs. Richard Cifelli, Jean-
Louis Hartenberger, David Irwin, Zhexi Luo, Malcolm McKenna, Claudine Montge-
lard, and Maureen O’Leary.
REFERENCES
Adachi, J., and Hasegawa, M. (1996). Model of amino acid substitution in proteins encoded by mitochondrial
DNA. J. Mol. Evol. 42: 459-469.
Andrews, C. W. (1906). A Descriptive Catalogue of the Tertiary Vertebrata of the Fayum, Egypt, British
Museum (Natural History), London.
Arnason, U., and Gullberg, A. (1994). Relationship of baleen whales established by cytochrome b gene
sequence comparison. Nature 367: 726-728.
Arnason, U., and Gullberg, A. (1996). Cytochrome b nucleotide sequences and the identification of five
primary lineages of extant cetaceans. Mol. Biol. Evol. 13: 407-417.
Arnason, U., Bodin, K., Gullberg, A., Ledje, C., and Mouchaty, S. (1995). A molecular view of pinniped
relationships with particular emphasis on the true seals. J. Mol. Evol. 40: 78-85.
Arnason, U., Xu, X., and Gullberg, A. (1996). Comparison between the complete mitochondrial DNA
sequences of Homo and the common chimpanzee based on nonchimeric sequences. J. Mol. Evol. 42:
145-152.
Arnason, U., Gullberg, A., and Janke, A. (1997). Phylogenetic analyses of mitochondrial DNA suggest a
sister group relationship between Xenarthra (Edentata) and ferungulates. Mol. Biol. Evol. 14: 762-768.
Baker, R. J., Taddei, V. A., Hudgeons, J. L., and Van den Bussche, R. A. (1994). Systematic relationships
within Chiroderma (Chiroptera: Phyllostomidae) based on cytochrome b sequence variation. J. Mammal.
75: 321-327.
Baker, R. J., Van den Bussche, R. A., Wright, A. J., Wiggins, L. E., Hamilton, M. J., Reat, E. P., Smith,
M. H., Lomakin, M. D., and Chesser, R. K. (1996). High levels of genetic change in rodents of Cher-
nobyl. Nature 380: 707-708.
Barklow, W. (1995). Hippo talk. Nat. Hist. 104(5): 54.
Barnes, L. G. (1984). Whales, dolphins and porpoises: Origin and evolution of the Cetacea. In: Mammals,
Notes for a Short Course, P. D. Gingerich and C. E. Badgley, eds., pp. 139-154, University of Ten-
nessee, Studies in Geology, Vol. 8.
Barnes, L. G. (1990). The fossil record and evolutionary relationships of the genus Tursiops. In: The Bottle-
nose Dolphin, S. Leatherwood and R. R. Reeves, eds., pp. 3-26, Academic Press, San Diego.
Barnes, L. G., and McLeod, S. A. (1984). The fossil record and phyletic relationships of gray whales. In:
The Gray Whale, Eschrichtius robustus, M. L. Jones, S. L. Swartz, and S. Leatherwood, eds., pp. 3-32,
Academic Press, Orlando, FL.
Barnes, L. G., Domning, D. P., and Ray, C. E. (1985). Status of studies on fossil marine mammals. Mar.
Mamm. Sci. 1: 15-53.
Evolution of Artiodactyla and Cetacea 177
Black, C. C. (1978). Anthracotheriidae. In: Evolution of African Mammals, V. J. Maglio and H. B. S. Cooke,
eds., pp. 423-434, Harvard University Press, Cambridge, MA.
Blainville, H. M. D. de (1839-1864).Osteographie ou Description Iconographique Comparee du Squelette
et du Systeme Dentaire des Mammiferes Recents et Fossiles pour Servir de Base a la Zoologie et a la
Geologie, Tome Quatrieme, J. B. Bailliere et Fils, Paris.
Buntjer, J. B., Hoff, I. A., and Lenstra, J. A. (1997). Artiodactyl interspersed DNA repeats in cetacean
genomes. J. Mol. Evol. 45: 66-69.
Butler, P. M. (1969). Insectivores and bats from the Miocene of East Africa: New material. In: Fossil Ver-
tebrates of Africa, L. S. B. Leakey, ed., pp. 1-37, Academic Press, New York.
Butler, P. M. (1984). Macroscelidea, Insectivora, and Chiroptera from the Miocene of East Africa. Palaeo-
vertebrata (Montpellier) 14: 117-200.
Chikuni, K., Mori, Y., Tabata, T., Saito, M., Monma, M., and Kosugiyama, M. (1995). Molecular phy-
logeny based on the k-casein and cytochrome b sequences in the mammalian suborder Ruminantia. J.
Mol. Evol. 41: 859-866.
Colbert, E. H. (1935). Distributional and phylogenetic studies on Indian fossil mammals. IV. The phylogeny
of the Indian Suidae and the origin of the Hippopotamidae. Am. Mus. Novitates 799: 1-24.
Collura, R. V., and Stewart, C. B. (1995). Insertions and duplications of mtDNA in the nuclear genomes of
Old World monkeys and hominoids. Nature 378: 485-489.
Collura, R. V., Auerbach, M. R., and Stewart, C. B. (1996). A quick, direct method that can differentiate
expressed mitochondrial genes from their nuclear pseudogenes. Curr. Biol. 6: 1337-1339.
Cope, E. D. (1888-1889). The Artiodactyla. Am. Nat. 22: 1079-1095; 23: 111-136.
Coryndon, S. (1977). The taxonomy and nomenclature of the Hippopotamidae (Mammalia, Artiodactyla) and
a description of two new fossil species. Proc. Kon. Ned. Akad. von Wetensch. B 80: 61-88.
Coryndon, S. (1978). Hippopotamidae. In: Evolution of African Mammals, V. J. Maglio and H. B. S. Cooke,
eds., pp. 483-495, Harvard University Press, Cambridge, MA.
Cracraft, J., and Helm-Bychowski, K. (1991). Parsimony and phylogenetic inference using DNA sequences:
Some methodological strategies. In: Phylogenetic Analysis of DNA Sequences, M. Miyamoto and J.
Cracraft, eds., pp. 184-220, Oxford University Press, New York.
Cranford, T. W., Amundin, M., and Norris, K. S. (1996). Functional morphology and homology in the
odontocete nasal complex: Implications for sound generation. J. Morphol. 228: 223-285.
Cuvier, G. (1822). Recherches sur les Ossemens Fossiles, ou l'on Retablit Les Caracteres de Plusieurs Ani-
maux dont les Revolutions du Globe ont Detruit les Especes, Nouvelle Edition, Tome Deuxieme, Ire
Partie. G. Dufour et E. D’Ocagne, Libraires, Paris.
Dewalt, T. S., Sudman, P. D., Hafner, M. S., and Davis, S. K. (1993). Phylogenetic relationships of pocket
gophers (Cratogeomys and Pappogeomys) based on mitochondrial DNA cytochrome b sequences. Mol.
Phylogenet. Evol. 2: 193-204.
Eltringham, S. K. (1993). The pygmy hippopotamus (Hexaprotodon liberiensis). In: Pigs. Peccaries, and
Hippos. Status Survey and Conservation Action Plan, W. L. R. Oliver, ed., pp. 55-60, IUCN, Gland,
Switzerland.
Emlong, D. R. (1966). A new archaic cetacean from the Oligocene of northwest Oregon. Bull. Mus. Nat.
Hist., Univ. Oreg. 3: 1-51.
Erfurt, J., and Sudre, J. (1996). Eurodexeinae, eine neue Unterfamilie der Artiodactyla (Mammalia) aus dem
Unter- und Mitteleozan Europas. Palaeovertebrata (Montpellier) 25: 371-390.
Estes, R. D. (1991). The Behavior Guide to African Mammals, University of California Press, Berkeley.
Faulkes, C. G., Bennett, N. C., Bruford, M. W., O’Brien, H. P., Aguilar, G. H., and Jarvis, J. U. M.
(1997). Ecological constraints drive social evolution in the African mole-rats. Proc. Roy. Soc. Lond. B
264: 1619-1627.
Felsenstein, J. (1978). Cases in which parsimony or compatibility methods wll be positively misleading. Syst.
Zool. 27: 401-410.
Filhol, M. H. (1880). Etude des Mammiferes fossiles de Saint-Gerand le Puy (Allier). Bibl. L'Ecole Haut.
Etudes Sci. Nat. 20: 1-86.
Fleischer, G. (1976). Hearing in extinct cetaceans as determined by cochlear structure. J. Paleontol. 50:
133-152.
Fordyce, R. E., and Barnes, L. G. (1994). The evolutionary history of whales and dolphins. Annu. Rev. Earth
Planet. Sci. 22: 419-455.
Gatesy, J. (1997). More DNA support for a Cetacea/Hippopotamidae clade: The blood-clotting protein gene
gamma-fibrinogen. Mol. Biol. Evol. 14: 537-543.
Gatesy, J., Hayashi, C., Cronin, M. A., and Arctander, P. (1996). Evidence from milk casein genes that
cetaceans are close relatives of hippopotamid artiodactyls. Mol. Biol. Evol. 13: 954-963.
Gatesy, J., Amato, G., Vrba, E., Schaller, G., and DeSalle, R. (1997). A cladistic analysis of mitochondrial
ribosomal DNA from the Bovidae. Mol. Phylogenet. Evol. 7: 303-319.
178 Luckett and Hong
Geisler, J. H., and Luo, Z. (1996). The petrosal and inner ear of Herpetocetus sp. (Mammalia: Cetacea) and
their implications for the phylogeny and hearing of archaic mysticetes. J. Paleontol. 70: 1045-1066.
Geisler, J. H., and O’Leary, M. A. (1997). A phylogeny of Cetacea, Artiodactyla, Perissodactyla, and archaic
ungulates: The morphological evidence. J. Vert. Paleontol. 17(3) (Suppl.): 48A.
Gentry, A. W., and Hooker, J. J. (1988). The phylogeny of the Artiodactyla. In: The Phylogeny and Clas-
sification of the Tetrapods, Vol. 2. Mammals, M. J. Benton, ed., pp. 235-272, Clarendon Press, Oxford.
Gingerich, P. D., and Russell, D. E. (1981). Pakicetus inachus, a new archaeocete (Mammalia, Cetacea)
from the early-middle Eocene Kuldana Formation of Kohat (Pakistan). Contrib. Mus. Paleontol. Univ.
Mich. 25: 235-246.
Gingerich, P. D., Smith, B. H., and Simons, E. L. (1990). Hind limbs of Eocene Basilosaurus: Evidence of
feet in whales. Science 249: 154-157.
Graur, D., and Higgins, D. G. (1994). Molecular evidence for the inclusion of cetaceans within the order
Artiodactyla. Mol. Biol. Evol. 11: 357-364.
Groves, P., and Shields, G. F. (1996). Phylogenetics of the Caprinae based on cytochrome b sequence. Mol.
Phylogenet. Evol. 5: 467-476.
Harrison, T. (1997). The anatomy, paleobiology, and phylogenetic relationships of the Hippopotamidae
(Mammalia, Artiodactyla) from the Manonga Valley, Tanzania. In: Neogene Paleontology of the
Manonga Valley, Tanzania, T. Harrison, ed., pp. 137-190, Plenum Press, New York.
Hartenberger, J.-L. (1986). Hypothese paleontologique sur l’origine des Macroscelidea (Mammalia). C.R.
Acad. Sci. Paris 302: 247-249.
Hasegawa, M., and Adachi, J. (1996). Phylogenetic position of cetaceans relative to artiodactyls: Reanalysis
of mitochondrial and nuclear sequences. Mol. Biol. Evol. 13: 710-717.
Hasegawa, M., Adachi, J., and Milinkovitch, M. C. (1997). Novel phylogeny of whales supported by total
molecular evidence. J. Mol. Evol. 44 (Suppl. 1): S117-S120.
Hayssen, V., Van Tienhoven, A., and Van Tienhoven, A. (1993). Asdell's Patterns of Mammalian Repro-
duction, Cornell University Press, Ithaca, NY.
Hennig, W. (1966). Phylogenetic Systematics, University of Illinois Press, Urbana.
Heyning, J. E. (1989). Comparative facial anatomy of beaked whales (Ziphiidae) and a systematic revision
among the families of extant Odontoceti. Contrib. Sci. Nat. Hist. Mus. LA. County 405: 1-64.
Heyning, J. E. (1995). Masters of the Ocean Realm: Whales, Dolphins, and Porpoises, University of Wash-
ington Press, Seattle.
Heyning, J. E. (1997). Sperm whale phylogeny revisited: Analysis of the morphological evidence. Mar.
Mammal Sci. 13: 60-77.
Heyning, J. E., and Mead, J. G. (1990). Evolution of the nasal anatomy of cetaceans. In: Sensory Abilities
of Cetaceans, J. Thomas and R. Kastelein, eds., pp. 67-79, Plenum Press, New York.
Hillis, D. M. (1987). Molecular versus morphological approaches to systematics. Annu. Rev. Ecol. Syst. 18:
23-42.
Honeycutt, R. L., and Adkins, R. M. (1993). Higher level systematics of eutherian mammals: An assessment
of molecular characters and phylogenetic hypotheses. Annu. Rev. Ecol. Syst. 24: 279-305.
Hooijer, D. A. (1942). On the supposed hexaprotodont milk dentition in Hippopotamus amphibiusL. Zool.
Meded. Mus. Leiden 24: 187-196.
Horai, S., Hayasaka, K., Kondo, R., Tsugane, K., and Takahata, N. (1995). Recent African origin of modern
humans revealed by complete sequences of hominoid mitochondrial DNAs. Proc. Natl. Acad. Sci. USA
92: 532-536.
Howell, A. B. (1930). Aquatic Mammals, Charles C Thomas, Springfield, IL.
Irwin, D. M., and Arnason, U. (1994). Cytochrome b gene of marine mammals: Phylogeny and evolution.
J. Mammal. Evol. 2: 37-55.
Irwin, D. M., Kocher, T. D., and Wilson, A. C. (1991). Evolution of the cytochrome b gene of mammals.
J. Mol. Evol. 32: 128-144.
Janis, C. M., and Scott, K. M. (1987). The interrelationships of higher ruminant families with special empha-
sis on the members of the Cervoidea. Am. Mus. Novitates 2893: 1-85.
Janke, A., Gemmell, N. J., Feldmaier-Fuchs, G., von Haeseler, A., and Paabo, S. (1996). The mitochondrial
genome of a monotreme—The playtpus (Ornithorhynchus anatinus). J. Mol. Evol. 42: 153-159.
Karlsen, K. (1962). Development of tooth germs and adjacent structures in the whalebone whale [Balaenop-
tera physalus (L.)]. Hvalradets Skrifter 45: 1-56.
Kellogg, R. (1928). The history of whales—Their adaptation to life in the water. Q. Rev. Biol. 3: 29-76,
174-208.
Kellogg, R. (1934). The Patagonian fossil whalebone whale, Cetotherium moreni (Lydekker). Carnegie Inst.
Wash. Publ. 447:63-81.
Kellogg, R. (1936). A review of the Archaeoceti. Publ. Carnegie Inst. Wash. 482: 1-366.
Ketten, D. R. (1992). The marine mammal ear: Specializations for aquatic audition and echolocation. In: The
Evolutionary Biology of Hearing, D. B. Webster, R. R. Fay, and A. N. Popper, eds., pp. 717-750,
Springer-Verlag, New York.
Evolution of Artiodactyla and Cetacea 179
Klingel, H. (1995). Fluctuating fortunes of the river horse. Nat. Hist. 104(5): 46-56.
Kukenthal, W. (1891). On the adaptation of mammals to aquatic life. Ann. Mag. Nat. Hist. Ser. 6, 7: 153-179.
Kuzmin, A. A. (1976). Embryogenesis of the osseous skull of the sperm whale (Physeter macrocephalus,
Linnaeus, 1758). In: Investigations on Cetacea, Vol. VII, G. Pilleri, ed., pp. 187-202, Institute of Brain
Anatomy, University of Berne, Berne, Switzerland.
Lara, M. C., Patton, J. L., and Da Silva, M. N. F. (1996). The simultaneous diversification of South Amer-
ican echimyid rodents (Hystricognathi) based on complete cytochrome b sequences. Mol. Phylogenet.
Evol. 5: 403-413.
Lavergne, A., Douzery, E., Stichler, T., Catzeflis, F. M., and Springer, M. S. (1996). Interordinal mam-
malian relationships: Evidence for paenungulate monophyly is provided by complete mitochondrial 12S
rRNA sequences. Mol. Phylogenet. Evol. 6: 245-258.
Laws, R. M. (1984). Hippopotamuses. In: The Encyclopedia of Mammals, D. Macdonald, ed., pp. 506-511,
Facts on File, New York.
Laws, R. M., and Clough, G. (1966). Observations on reproduction in the hippopotamus Hippopotamus
amphibius Linn. Symp. Zool. Soc. Lond. 15: 117-140.
Ledje, C., and Arnason, U. (1996). Phylogenetic analyses of complete cytochrome b genes of the order
Carnivora with particular emphasis on the Caniformia. J. Mol. Evol. 42: 135-144.
Lessa, E. P., and Cook, J. A. (1998). The molecular phylogenetics of tuco-tucos (genus Ctenomys, Rodentia:
Octodontidae) suggests an early burst of speciation. Mol. Phylogenet. Evol. 9: 88-99.
Luckett, W. P. (1994). Suprafamilial relationships within Marsupialia: Resolution and discordance from mul-
tidisciplinary data. J. Mammal. Evol. 2: 255-283.
Luo, Z. (1998 in press). Homology and transformation of cetacean ectotympanic structures. In: The Emer-
gence of Whales: Evolutionary Patterns in the Origin of Cetacea, J. G. M. Thewissen, ed., Plenum
Press, New York.
Luo, Z., and Marsh, K. (1996). Petrosal (periotic) and inner ear of a Pliocene kogiine whale (Kogiinae,
Odontoceti): Implications on relationships and hearing evolution of toothed whale. J. Vert. Paleontol.
16: 328-348.
Ma, D.-P., Zharkikh, A., Graur, D., VandeBerg, J. L., and Li, W.-H. (1993). Structure and evolution of
opossum, guinea pig, and porcupine cytochrome b genes. J. Mol. Evol. 36: 327-334.
Matthee, C. A., and Robinson, T. J. (1997). Molecular phylogeny of the springhare, Pedetes capensis, based
on mitochondrial DNA sequences. Mol. Biol. Evol. 14: 20-29.
Matthew, W. D. (1909). The Carnivora and Insectivora of the Bridger Basin, Middle Eocene. Mem. Am.
Mus. Nat. Hist. 9:291-567.
Matthew, W. D. (1937). Paleocene faunas of the San Juan Basin, New Mexico. Trans. Am. Phil. Soc. 30:
1-510.
Matthew, W. D., and Granger, W. (1915). A revision of the Lower Eocene Wasatch and Wind River faunas.
Bull. Am. Mus. Nat. Hist. 34: 1-103.
McKean, C. F., Jump, E. B., and Weaver, M. E. (1971). The calcification pattern of deciduous teeth in
miniature swine. Arch. Oral Biol. 16: 639-648.
McKenna, M. C. (1987). Molecular and morphological analysis of high-level mammalian interrelationships.
In: Molecules and Morphology in Evolution: Conflict or Compromise? C. Patterson, ed., pp. 55-93,
Cambridge University Press, Cambridge.
McKenna, M. C., and Bell, S. K. (1997). Classification of Mammals Above the Species Level, Columbia
University Press, New York.
Messenger, S. L., and McGuire, J. A. (1998). Morphology, molecules, and the phylogenetics of cetaceans.
Syst. Biol. 47: 90-124.
Milinkovitch, M. C. (1995). Molecular phylogeny of cetaceans prompts revision of morphological transfor-
mations. Trends Ecol. Evol. 10: 328-334.
Milinkovitch, M. C., and Thewissen, J. G. M. (1997). Even-toed fingerprints on whale ancestry. Nature 388:
622-624.
Milinkovitch, M. C., Orti, G., and Meyer, A. (1993). Revised phylogeny of whales suggested by mitochon-
drial ribosomal DNA sequences. Nature 361: 346-348.
Milinkovitch, M. C., Meyer, A., and Powell, J. R. (1994). Phylogeny of all major groups of cetaceans based
on DNA sequences from three mitochondrial genes. Mol. Biol. Evol. 11: 939-948.
Milinkovitch, M. C., LeDuc, R. G., Adachi, J., Famir, F., Georges, M., and Hasegawa, M. (1996). Effects
of character weighting and species sampling on phylogeny reconstruction: A case study based on DNA
sequence data in cetaceans. Genetics 144: 1817-1833.
Miller, G. S. (1923). The telescoping of the cetacean skull. Smithson. Misc. Coll. 76: 1-71.
Mindell, D. P., and Thacker, C. E. (1996). Rates of molecular evolution: Phylogenetic issues and applica-
tions. Annu. Rev. Ecol. Syst. 27: 279-303.
Mishler, B. D. (1994). Cladistic analysis of molecular and morphological data. Am. J. Phys. Anthropol. 94:
143-156.
Miyamoto, M. M., and Cracraft, J. (1991). Phylogenetic inference, DNA sequence analysis, and the future
180 Luckett and Hong
of molecular systematics. In: Phylogenetic Analysis of DNA Sequences, M. M. Miyamoto and J. Cra-
craft, eds., pp. 3-17, Oxford University Press, New York.
Montegelard, C., Catzeflis, F. M., and Douzery, E. (1997). Phylogenetic relationships of artiodactyls and
cetaceans as deduced from the comparison of cytochrome b and 12S rRNA mitochondrial sequences.
Mol. Biol. Evol. 14: 550-559.
Naylor, G. J. P., and Brown, W. M. (1997). Structural biology and phylogenetic estimation. Nature 388:
527-528.
Naylor, G. J. P., and Brown, W. M. (1998). Amphioxus mitochondrial DNA, chordate phylogeny, and the
limits of inference based on comparisons of sequences. Syst. Biol. 47: 61-76.
Noro, M., Masuda, R., Dubrovo, I. A., Yoshida, M. C., and Kato, M. (1998). Molecular phylogenetic
inference of the woolly mammoth Mammuthus primigenius, based on complete sequences of mitochon-
drial cytochrome b and 12S ribosomal RNA genes. J. Mol. Evol. 46: 314-326.
Noubhani, A. (1988). Etude de la Variabilite de Numidotherium koholense Jaeger 1986 (Proboscidea). Unpub-
lished Thesis, Universite Pierre et Marie Curie (Paris VI), Paris.
Novacek, M. J. (1986). The skull of leptictid insectivorans and the higher-level classification of eutherian
mammals. Bull. Am. Mus. Nat. Hist. 183: 1-112.
Novacek, M. J. (1992a). Mammalian phylogeny: Shaking the tree. Nature 356: 121-125.
Novacek, M. J. (1992b).Fossils, topologies, missing data, and the higher level phylogeny of eutherian mam-
mals. Syst. Biol. 41: 58-73.
Novacek, M. J. (1993). Reflections on higher mammalian phylogenetics. J. Mammal. Evol. 1: 3-30.
Ohdachi, S., Masuda, R., Abe, H., Adachi, J., Dokuchaev, N. E., Haukisalmi, V., and Yoshida, M. C.
(1997). Phylogeny of Eurasian soricine shrews (Insectivora, Mammalia) inferred from the mitochondrial
cytochrome b gene sequences. Zool. Sci. 14: 527-532.
Okada, N. (1991). SINEs. Curr. Opin. Genet. Dev. 1: 498-504.
O’Leary, M. A. (1998). Phylogenetic and morphometric reassessment of the dental evidence for a mesony-
chian and cetacean clade. In: The Emergence of Whales: Evolutionary Patterns in the Origin of Cetacea,
J. G. M. Thewissen, ed., Plenum Press, New York (in press).
O’Leary, M. A., and Rose, K. D. (1995). Postcranial skeleton of the early Eocene mesonychid Pachyaena
(Mammalia: Mesonychia). J. Vert. Paleontol. 15: 401-430.
Owen, R. (1848). Description of teeth and portions of jaws of two extinct anthracotheroid quadrupeds (Hyo-
potamus vectianus and Hyop. bovinus) discovered by the Marchioness of Hastings in the Eocene deposits
on the N.W. coast of the Isle of Wight: With an attempt to develope Cuvier’s idea of the classification
of pachyderms by the number of their toes. Q. J. Geol. Sci. 4: 103-141.
Ozawa, T., Hayashi, S., and Mikhelson, V. M. (1997). Phylogenetic position of mammoth and Stellar’s sea
cow within Tethytheria demonstrated by mitochondrial DNA sequences. J. Mol. Evol. 44: 406-413.
Patton, J. L., and da Silva, M. N. F. (1995). A review of the spiny mouse genus Scolomys (Rodentia:
Muridae: Sigmodontinae) with the description of a new species from the western Amazon of Brazil.
Proc. Biol. Soc. Wash. 108: 319-337.
Patton, J. L., dos Reis, S. F., and da Silva, M. N. F. (1996). Relationships among didelphid marsupials
based on sequence variation in the mitochondrial cytochrome b gene. J. Mammal. Evol. 3: 3-29.
Pearson, H. S. (1923). Some skulls of Perchoerus (Thinohyus) from the White River and John Day Forma-
tions. Bull. Am. Mus. Nat. Hist. 48: 61-96.
Pearson, H. S. (1927). On the skulls of Early Tertiary Suidae, together with an account of the otic region in
some other primitive Artiodactyla. Phil. Trans. Roy. Soc. Lond. B 215: 389-460.
Pickford, M. (1983). On the origins of Hippopotamidae together with descriptions of two new species, a new
genus and a new subfamily from the Miocene of Kenya. Geobios 16: 193-217.
Pickford, M. (1989). Update on hippo origins. C.R. Acad. Sci. Paris Ser. II 309: 163-168.
Pickford, M. (1990). Decouverte de Kenyapotamus en Tunisie. Ann. Paleontol. 76: 277-283.
Prothero, D. R. (1993). Ungulate phylogeny: Molecular vs. morphological evidence. In: Mammal Phylogeny:
Placentals, F. S. Szalay, M. J. Novacek, and M. C. McKenna, eds., pp. 173-181, Springer-Verlag,
New York.
Prothero, D. R., Manning, E. M., and Fischer, M. (1988). The phylogeny of the ungulates. In: The Phylogeny
and Classification of the Tetrapods, Vol. 2. Mammals, M. J. Benton, ed., pp. 201-234, Clarendon Press,
Oxford.
Randi, E., Lucchini, V., and Hoong Diong, C. (1996). Evolutionary genetics of the Suiformes as recon-
structed using mtDNA sequencing. J. Mammal. Evol. 3: 163-194.
Randi, E., Mucci, N., Pierpaoli, M., and Douzery, E. (1998). New phylogenetic perspectives on the Cervidae
(Artiodactyla) are provided by the mitochondrial cytochrome b gene. Proc. Roy. Soc. Lond. B 265: 1-9.
Roosevelt, T. (1910). African Game Trails, Charles Scribner’s Sons, New York.
Rose, K. D. (1985). Comparative osetology of North American dichobunid artiodactyls. J. Paleontol. 59:
1203-1226.
Evolution of Artiodactyla and Cetacea 181
Rose, K. D. (1990). Postcranial skeletal remains and adaptations in early Eocene mammals from the Willwood
Formation, Bighorn Basin, Wyoming. In: Dawn of the Age of Mammals in the Northern Part of the
Rocky Mountain Interior, North America, T. M. Bown and K. D. Rose, eds., pp. 107-133, Geological
Society of America, Special Paper, Boulder, CO.
Rose, K. D. (1996). On the origin of the order Artiodactyla. Proc. Natl. Acad. Sci. USA 93: 1705-1709.
Ruedi, M., and Fumagalli, L. (1996). Genetic structure of gymnures (genus Hylomys; Erinaceidae) on con-
tinental islands of Southeast Asia: Historical effects of fragmentation. J. Zool. Syst. Evol. Res. 34:
153-162.
Schaeffer, B. (1947). Notes on the origin and function of the artiodactyl tarsus. Am. Mus. Novit. 1356:
1-24.
Schaeffer, B. (1948). The origin of a mammalian ordinal character. Evolution 2: 164-175.
Schwartz, D. M. (1996). Snatching scientific secrets from the hippo's gaping jaws. Smithsonian 26: 90-101.
Scott, W. B. (1940). The mammalian fauna of the White River Oligocene. Part IV. Artiodactyla. Trans. Am.
Phil. Soc. 28: 363-746.
Shimamura, M., Yasue, H., Ohshima, K., Abe, H., Kato, H., Kishiro, T., Goto, M., Munechika, I., and
Okada, N. (1997). Molecular evidence from retroposons that whales form a clade within even-toed ungu-
lates. Nature 388: 666-670.
Shoshani, J., Groves, C. P., Simons, E. L., and Gunnell, G. F. (1996). Primate phylogeny: Morphological
vs molecular results. Mol. Phylogenet. Evol. 5: 102-154.
Simons, E. L. (1991). Early Tertiary elephant-shrews from Egypt and the origin of the Macroscelidea. Proc.
Natl. Acad. Sci. USA 88: 9734-9737.
Simpson, C. D. (1984). Artiodactyls. In: Orders and Families of Recent Mammals of the World, S. Anderson
and J. K. Jones, eds., pp. 563-587, John Wiley & Sons, New York.
Simpson, G. G. (1961). Principles of Animal Taxonomy, Columbia University Press, New York.
Smith, A. B. (1994). Rooting molecular trees: Problems and strategies. Biol. J. Linn. Soc. 51: 279-292.
Smith, M. F. (1998). Phylogenetic relationships and geographic structure in pocket gophers in the genus
Thomomys. Mol. Phylogenet. Evol. 9: 1-14.
Smith, M. F., and Patton, J. L. (1993). The diversification of South American murid rodents: Evidence from
mitochondrial DNA sequence data for the akodontine tribe. Biol. J. Linn. Soc. 50: 149-177.
Smith, M. R., Shivji, M. S., Waddell, V. G., and Stanhope, M. J. (1996). Phylogenetic evidence from the
IRBP gene for the paraphyly of toothed whales, with mixed support for Cetacea as a suborder of Artio-
dactyla. Mol. Biol. Evol. 13: 918-922.
Stanley, H. F., Kadwell, M., and Wheeler, J. C. (1994). Molecular evolution of the family Camelidae: A
mitochondrial DNA study. Proc. R. Soc. Lond. B 256: 1-6.
Stehlin, H. G. (1899). Ueber die Geschichte des Suiden-Gebisses. Abh. Schweiz. Palaont. Ges. 26: 1-336.
Stehlin, H. G. (1910). Die Saugetiere des schweizerischen Eocaens. Sechster Teil. Abh. Schweiz. Palaont.
Ges. 36:839-1164.
Sudre. J. (1978). Les Artiodactyles de l’Eocene moyen et superieur d’Europe occidentale; systematique et
evolution. Mem. Trav. EPHE Inst. Montpellier 7: 1-229.
Sudre, J., and Erfurt, J. (1996). Les Artiodactyles du gisement Ypresien terminal de Premontre (Aisne, France).
Palaeovertebrata 25: 391-414.
Sudre, J., Russell, D. E., Louis, P., and Savage, D. E. (1983). Les Artiodactyles de L’Eocene inferieur
d’Europe, Premiere partie. Bull. Mus. Nat. Hist. Nat. Paris 5: 281-333.
Sullivan, J., and Swofford, D. L. (1997). Are guinea pigs rodents? The importance of adequate models in
molecular phylogenetics. J. Mammal. Evol. 4: 77-86.
Swofford, D. L., Olsen, G. J., Waddell, P. J., and Hillis, D. M. (1996). Phylogenetic inference. In: Molec-
ular Systematics, 2nd ed., D. M. Hillis, C. Moritz, and B. K. Mable, eds., pp. 407-510, Sinauer Asso-
ciates, Sunderland, MA.
Taberlet, P., Fumagalli, L., and J. Hausser. (1994). Chromosomal versus mitochondrial DNA evolution:
Tracking the evolutionary history of the southwestern European populations of the Sorex araneus group
(Mammalia, Insectivora). Evolution 48: 623-636.
Talbot, S. L., and Shields, G. F. (1996). A phylogeny of the bears (Ursidae) inferred from complete sequences
of three mitochondrial genes. Mol. Phylogenet. Evol. 5: 567-575.
Tanaka, K., Solis, C. D., Masangkay,J. S., Maeda, K., Kawamoto, Y., and Namikawa, T. (1996). Phy-
logenetic relationship among all living species of the genus Bubalus based on DNA sequences of the
cytochrome b gene. Biochem. Genet. 34: 443-452.
Thewissen, J. G. M. (1994). Phylogenetic aspects of cetacean origins: A morphological perspective. J. Mam-
mal. Evol. 2: 157-184.
Thewissen, J. G. M., and Hussain, S. T. (1990). Postcranial osteology of the most primitive artiodactyl
Diacodexis pakistanensis (Dichobunidae). Anat. Histol. Embryol. 19: 37-48.
Thewissen, J. G. M., and Hussain, S. T. (1998). Systematic review of the Pakicetidae, early and middle
182 Luckett and Hong
Eocene Cetacea (Mammalia) from Pakistan and India. In: Dawn of the Age of Mammals in Asia, K. C.
Beard and M. R. Dawson, eds., pp. 220-238, Bull. Carnegie Mus. Nat. Hist. No. 34, Pittsburgh, PA.
Thewissen, J. G. M., Madar, S. I., and Hussain, S. T. (1996). Ambulocetus natans, an Eocene cetacean
(Mammalia) from Pakistan. Cour. Forsch.-Inst. Senckenberg 28: 1-86.
Thomas, W. K., and Martin, S. L. (1993). A recent origin of marmots. Mol. Phylogenet. Evol. 2: 330-336.
Tobien, H. (1985). Zur Osteologie von Masillabune (Mammalia, Artiodactyla, Haplobunodontidae) aus dem
Mitteleozan der Fossilfundstatte Messel bei Darmstadt (S-Hessen, Bundesrepublik Deutschland). Geol.
Jb. Hessen 113: 5-58.
Viret, J. (1961). Artiodactyla. In: Traite de Paleontologie, Vol. VI, J. Piveteau, ed., pp. 887-1084, Masson
et Cie, Paris.
Wagele, J. W. (1995). On the information content of characters in comparative morphology and molecular
systematics. J. Zool. Syst. Evol. Res. 33: 42-47.
Weaver, M. E., Jump, E. B., and McKean, C. F. (1966). The eruption pattern of deciduous teeth in miniature
swine. Anat. Rec. 154: 81-86.
Webb, S. D., and Taylor, B. E. (1980). The phylogeny of hornless ruminants and a description of the cranium
of Archaeomeryx. Bull. Am. Mus. Nat. Hist. 167: 121-157.
Weber, M. (1904). Die Saugetiere, Gustav Fischer, Jena.
Weber, M. (1928). Die Saugetiere, Zweite Auflage, Gustav Fischer, Jena.
West, R. M. (1971). Deciduous dentition of the Early Tertiary Phenacodontidae (Condylarthra, Mammalia).
Am. Mus. Novitates 2461: 1-37.
Wilson, D. E., and Reeder, D. M. (1993). Mammal Species of the World: A Taxonomic and Geographic
Reference, 2nd ed., Smithsonian Institution Press, Washington, DC.
Xia, D., Yu, C.-A., Kim, H., Xia, J.-Z., Kachurin, A. M., Zhang, L., Yu, L., and Deisenhofer, J. (1997).
Crystal structure of the cytochrome bc1 complex from bovine heart mitochondria. Science 277: 60-66.
Xu, X., and Arnason, U. (1996). A complete sequence of the mitochondrial genome of the Western lowland
gorilla. Mol. Biol. Evol. 13: 691-698.
Xu, X., and Arnason, U. (1997). The complete mitochondrial DNA sequence of the white rhinoceros, Ce-
ratotherium simum, and comparison with the mtDNA sequence of the Indian rhinoceros, Rhinoceros
unicornis. Mol. Phylogenet. Evol. 7: 189-194.
Xu, X., Janke, A., and Arnason, U. (1996). The complete mitochondrial DNA sequence of the greater Indian
rhinoceros, Rhinoceros unicornis, and the phylogenetic relationship among Carnivora, Perissodactyla,
and Artiodactyla (+Cetacea). Mol. Biol. Evol. 13: 1167-1173.
Yoder, A. D., Cartmill, M., Ruvolo, M., Smith, K., and Vilgalys, R. (1996). Ancient single origin for
Malagasy primates. Proc. Natl. Acad. Sci. USA 93: 5122-5126.
Zittel, K. A. von (1925). Text-Book of Palaeontology, Vol. HI. Mammalia, Macmillan, London.