143-Pos-Doc-Relatorio-Fabio-Roxo

Prévia do material em texto

Câmpus de Botucatu 
 
Instituto de Biociências – Seção Técnica Acadêmica 
Distrito de Rubião Júnior, 250 - CEP 18618-970 – Botucatu – SP - Brasil. 
Tel.: (14) 3880 0788/0789/0790 – fax: (14) 3815 3744 - sta@ibb.unesp.br 
RELATÓRIO DE PÓS-DOUTORADO 
PARECER DA ASSESSORIA CIENTÍFICA: 
 
Relator...........: Prof(a) Dr(a) 
Pedido nº.......: 431 – SisPROPe 
Interessado(a): Fábio Fernandes Roxo 
Período..........: 01/04/2014 à 31/03/2016 
Supervisor(a).: Claudio de Oliveira 
 
Parecer: 
( X ) Aprovado 
( ) Em análise (necessário retornar ao relator após modificações) 
( ) Denegado 
 
Avaliação: ( ) Excelente 
 ( X ) Muito Bom 
 ( ) Muito Bom com deficiências facilmente sanáveis 
 ( ) Bom 
 ( ) Bom com deficiência 
 ( ) Regular 
 ( ) Com sérias deficiências 
 
Analisar o projeto segundo os seguintes parâmetros: 
1-Justificativa; 
2-Fundamentação Científica; 
3-Relevância para o avanço da área; 
4-Metodologia 
5-Relevância dos recursos financeiros para o desenvolvimento do projeto. 
 
Análise: 
O trabalho realizado teve alta relevância científica e tecnológica gerando o número muito 
grande de publicações científicas colaborativas entre o grupo do Brasil e grupos do 
exterior. Pelas publicações resultantes do projeto é possível ver a alta produtividade e a 
qualidade da pesquisa realizada. Em termos de relatório científico, senti falta de uma 
melhor organização, com pelo menos um resumo/abstract das atividades realizadas e de 
perspectivas futuras. 
 
 
 
 
Data: 12/04/2019 
 
 
Assinatura: 
22/01/2019 :: UNESP : Reitoria - SisPROPe ::
http://prope.unesp.br/sisprope/sis/posdoc_unesp/criar_pedido.php?id_perfil=8&pedido=431 1/3
STA CPP funcionário
 
 
(Exibir instruções)
 
Pedido=431 (resolução 49/2013) (concluído - concluído)
Resoluções Pós-Doutorado
Para visualizar os anexos, click sobre o respectivo ícone 
 
I - Dados do Candidato
CPF: * 328 . 707 . 598 - 51 Pesquisar
 
Nome: Fábio Fernandes Roxo
E-mail: roxoff@hotmail.com.br
 Documentos necessários:
 Cópia do Currículo Lattes atualizado (informe o link do Lattes na página de dados
pessoais);
 Cópia do RG;
 Para estrangeiros, RNE ou protocolo. Enviar também cópia de página dopassaporte com visto de permanência no Brasil, em vigência, ou protocolo;
Cópia do CPF;
Cópia do diploma de doutorado ou Ata da defesa da tese;
Cópia da apólice do seguro com período de vigência (início e término) (exigido
somente após homologação do pedido);
 
II - Dados do Supervisor Responsável
Nome completo: Claudio de Oliveira
Campus: Campus de Botucatu
Unidade: Instituto de Biociências de Botucatu
Departamento: DEPARTAMENTO DE MORFOLOGIA
E-mail: claudio@ibb.unesp.br
Telefone: 38800464
 Documentos necessários:
 Currículo Lattes atualizado (atualizar o link do Lattes em Meus dados);
 
III - Dados do Programa
Título do Projeto: *
Usando Métodos Comparativos Filogenômicos para 
Entender a Diversificação dos Peixes da Superfamília Loricarioidea
Área de Pesquisa: * CIÊNCIAS BIOLÓGICAS
Local de realização: *
Campus de Botucatu
Instituto de Biociências de Botucatu
Palavras-chave: *
 
Filogenia Biogeografia Evoluçao
Peixes Neotropical Siluriformes 
(indicar no mínimo três (3) e no máximo seis (6) palavras-chave que
identifiquem a área ou sub-área de atuação do projeto.)
Período de realização: * início: 01/04/2014 término: 31/03/2016 (dd/mm/aaaa)
 Documentos necessários:
Cópia do projeto de pesquisa.
 
 
 Dados dos supervisores de Extensão e/ou de Atividades de Formação Docente:
Nome dos Supervisor de Atividades de
Formação Docente:
Claudio de Oliveira
Departamento:
Disciplina(s):
Semeste/Ano:
Carga Horária:
 
Nome do Supervisor de Atividades de
Extensão:
Claudio de Oliveira
Departamento:
Atividades:
Início
Pós-doutorado
SisPROPe - Pós-Doc na UnespSisPROPe - Pós-Doc na Unesp
UNIVERSIDADE ESTADUAL PAULISTA
"JÚLIO DE MESQUITA FILHO"
Reitoria - PROPe
 Meus dados | Sair
 
Usuário: sta-IBB
http://prope.unesp.br/sisprope/sis/home.php?id_perfil=4
http://prope.unesp.br/sisprope/sis/home.php?id_perfil=8
javascript:funcMostrarEsconder_Instrucoes(1)
http://www.unesp.br/portal#!/prope/pos-doutorado/resolucao-unesp-pos-doutorado/
http://buscatextual.cnpq.br/buscatextual/visualizacv.do?id=K4511454E4
http://prope.unesp.br/pessoa/index.php?cpf1=328&cpf2=707&cpf3=598&cpf4=51
http://prope.unesp.br/pessoa/ver_arquivo.php?arquivo=2783_rg_0.pdf
http://prope.unesp.br/pessoa/ver_arquivo.php?arquivo=2783_cpf_0.pdf
http://prope.unesp.br/pessoa/ver_arquivo.php?arquivo=2783_DiplDout_0.pdf
http://prope.unesp.br/sisprope/sis/posdoc_unesp/ver_arquivo.php?arquivo=431_ApoliceSeguro_0.pdf
http://lattes.cnpq.br/0297419882161114
http://prope.unesp.br/sisprope/sis/usuario/meus_dados.php?id_perfil=2
http://prope.unesp.br/sisprope/sis/posdoc_unesp/ver_arquivo.php?arquivo=431_ProjPesq_0.pdf
http://prope.unesp.br/sisprope/sis/home.php?id_perfil=8
http://www.unesp.br/
http://www.unesp.br/prope
http://prope.unesp.br/sisprope/sis/usuario/meus_dados.php?id_perfil=8
http://prope.unesp.br/sisprope/logoff.php
http://prope.unesp.br/sisprope/sis/usuario/meus_dados.php?id_perfil=8
22/01/2019 :: UNESP : Reitoria - SisPROPe ::
http://prope.unesp.br/sisprope/sis/posdoc_unesp/criar_pedido.php?id_perfil=8&pedido=431 2/3
Limite máximo de caracteres: 3000
Semeste/Ano:
Carga Horária:
Declaração de Realização de Atividade de Formação Docente e Extensionista.
 
 
IV - Declaração de Cessão de Direitos de Propriedade intelectual dos resultados gerados durante o Programa de
Pós-Doutorado.
(Exibir Anexo II)
Aceita a cessão de direito? sim não
 
 
Indique, a seguir, caso seja pertinente, as informações sobre a sua bolsa e/ou o seu afastamento, 
 em tempo integral, remunerado.
 
V - Financiamento
 Há bolsa para realização do pós-doutorado? sim não
 
TERMO DE COMPROMISSO DE PÓS-DOUTORADO
 
MODALIDADE SEM BOLSA
 
Eu, Fábio Fernandes Roxo, aprovado(a) para participar do Programa de Pós-Doutorado do(a) Instituto de Biociências
de Botucatu, declaro estar ciente das regras do Programa e demais normas universitárias, e comprometo-me a cumpri-las.
Declaro, ainda, estar ciente de que o Pós-Doutorado não gera vínculo empregatício com a Universidade Estadual Paulista
"Júlio de Mesquita Filho" - UNESP, e que possuo meios para me manter durante o período de realização do Pós-Doutorado.
 
Candidato de acordo: sim não 
 
VI - Vínculo empregatício em instituição de ensino/pesquisa ou empresa.
 Afastamento em tempo integral ou parcial remunerado? sim não
 
VII - Etapas após o envio do projeto:
 - Análise documental:
Verificação, pela PROPe, dos anexos e dos campos preenchidos. 
 
Documentação correta? sim não 
 
 - Encaminhamento pela PROPe:
encaminhar para: Parecerista CPP
 
 - Parecer da Assessoria Científica:
Parecer * aprovado denegado
Avaliação: * Bom
Análise: *
 Obs.: Analisar o projeto segundo os seguintes parâmetros: 1-Justificativa; 2-Fundamentação Científica; 3-Relevância
para o avanço da área; 4-Metodologia e 5-Relevância dos recursos financeiros para o desenvolvimento do projeto.
 
 - Homologação pela unidade - Comissão Permanente de Pesquisa (CPP):
Homologa? * sim não
Justificativa: *
Obs.: Ao homologar a inscrição, a CPP deve informar o diretor da unidade.
 
 - Apólice de Seguro, com vigência de início e fim:
 Após o pedido homologado, cabe à CPP disponibilizar, no sistema, a cópia da Apólice de Seguro do estagiário.
 
Nenhum arquivo selecionadoEscolher arquivo
substituir 
(arquivo pdf único; máximo 1,5Mb)
Cópia da Apólice de Seguro, com vigência de início e fim.
 
 - Finalizar (concluir) o pós-doutorado:
 Esta opção é para o pós-doutorado que foi concluído totalmente. É necessário anexar o Relatório Final para que o
"certificado" seja emitido pela CPP. O campo para anexar o Relatório Final será disponibilizado após efetivar a "conclusão". 
 Para desistirdesta opção, click em "não".
O projeto apresentado na verdade se trata de uma grande proposta 
de trabalho, coordenado pelo supervisor, em colaboração com 
pesquisadores internacionais, envolvendo o uso de novas técnicas 
moleculares. Nessa proposta é apresentada algumas das atividades 
javascript:funcMostrarEsconderAnexoII(1)
http://prope.unesp.br/sisprope/sis/posdoc_unesp/ver_arquivo.php?arquivo=431_ApoliceSeguro_0.pdf
22/01/2019 :: UNESP : Reitoria - SisPROPe ::
http://prope.unesp.br/sisprope/sis/posdoc_unesp/criar_pedido.php?id_perfil=8&pedido=431 3/3
Deseja concluir o pós-doutorado? *
 sim não
Comentários:
O Pos-doc foi concluído satisfatoriamente.
Término efetivo: *
 (data para certificado)
31/03/2016 (dd/mm/aaaa)
 
 - Relatório Final:
 Após o término do pós-doutorado ou cancelamento do pedido, o supervisor deverá anexar o Relatório Final.
Relatório Final.
 - Relatório Final - Avaliação:
 
 Relatório Final ainda não foi avaliado.
Aprovado? sim não 
 
justificativa: *
 
 
Não há pendências neste pedido.
 
 
Comentários PROPe (visualização permitida apenas aos analistas da PROPe):
 
Pedido=431 (resolução 49/2013) (concluído - concluído)
 
Críticas, dúvidas e sugestões de sistema: sistemas.prope@reitoria.unesp.br
 
Política de Privacidade Política de Serviço
UNESP - Universidade Estadual Paulista "Júlio de Mesquita Filho" 
 
Desenvolvido por Aptor Software - Dúvidas e sugestões: http://prope.unesp.br/falecomaprope/
http://prope.unesp.br/sisprope/sis/posdoc_unesp/ver_arquivo.php?arquivo=431_RelatorioFinal_0.pdf
http://www.unesp.br/politicas/privacy.htm
http://www.unesp.br/politicas/servico.htm
http://www.aptor.com.br/
http://prope.unesp.br/falecomaprope/
1	
	
RELATÓRIO PROJETO SISPROPE 
 
Universidade Estadual Paulista – UNESP 
Instituto de Biociências de Botucatu, Departamento de Morfologia 
Laboratório de Biologia e Genética de Peixes 
 
 
 
 
Usando Métodos Comparativos Filogenômicos para Entender a 
Diversificação dos Peixes da Superfamília Loricarioidea 
 
 
 
 
 Dr. Claudio de Oliveira Dr. Fábio Fernandes Roxo 
 Orientador Aluno 
 
 
 
Botucatu / SP 
Outubro – 2018 
2	
	
1. Trabalhos publicados durante o desenvolvimento do projeto (26 trabalhos – 
2015/2016/2017/2018). Valores do Fator de Impacto tem como fonte o JCR. 
• Azevedo-Santos, VM, Roxo, FF (2015) A new species of the genus Pareiorhina (Teleostei: 
Siluriformes: Loricariidae) from the upper rio Paraná basin, southeastern Brazil. Zootaxa, 
3937 (2): 377–385. Fator de impacto: 1.16. 
• Costa-Silva, GJ, Rodriguez, MS, Roxo, FF, Foresti, F, Oliveira, C (2015) Using Different 
Methods to Access the Difficult Task of Delimiting Species in a Complex Neotropical 
Hyperdiverse Group. PLoS ONE. 10(9): e0135075. doi:10.1371/journal.pone.0135075. 
Fator de impacto: 3.5. 
• Tagliacollo, VA, Roxo, FF, Duke-Sylvester, SM, Oliveira, C, Albert, JS (2015) 
Biogeographical signature of river capture events in Amazonian lowlands. Journal of 
Biogeography, 42(12): 2349–2362. Fator de impacto: 4.1. 
• Silva, GSC, Roxo, FF, Oliveira, C (2015) Two new species of Pseudancistrus 
(Siluriformes, Loricariidae) from the Amazon basin, northern Brazil. ZooKeys, 482: 21–
34. Fator de impacto: 1.28. 
• Ochoa, LE, Pereira, LHG, Costa-Silva, GJ, Roxo, FF, Batista, JS, Formiga, K, Foresti, F, 
Oliveira, C (2015) Genetic structure and historical diversification of catfish 
Brachyplatystoma platynemum (Siluriformes: Pimelodidae) in the Amazon basin with 
implications for its conservation. Ecology and Evolution, 5(10): 2005–2020. Fator de 
impacto: 3.1. 
• Roxo, FF, Silva, GSC, Oliveira, C (2015) A new species of Hisonotus (Siluriformes, 
Loricariidae) from rio São Francisco basin, Brazil. ZooKeys, 498: 127–143. Fator de 
impacto: 1.28. 
• Roxo, FF, Silva, GSC, Ochoa, LE, Oliveira, C (2015) Description of a new genus and three 
new species of Otothyrinae (Siluriformes, Loricariidae). ZooKeys (Online), 534: 103–134. 
Fator de impacto: 1.28. 
• Roxo, FF, Ochoa, LE, Silva, GSC, Oliveira, C (2015) Rhinolekos capetinga: a new 
cascudinho species (Loricariidae, Otothyrinae) from the rio Tocantins basin and comments 
on its ancestral dispersal route. ZooKeys, 481: 109–130. Fator de impacto: 1.28. 
3	
	
• Roxo, FF, Ochoa, LE, Costa-Silva, GJ, Oliveira, C (2015) Species delimitation in 
Neoplecostomus (Siluriformes: Loricariidae) using morphologic and genetic approaches 
DNA Barcodes. DNA Barcodes, 3: 110–117. Fator de impacto: 1.1. 
• Mariguela, TC, Roxo, FF, Foresti, F, Oliveira, C (2016) Phylogeny and biogeography of 
Triportheidae (Teleostei: Characiformes) based on molecular data. Molecular 
Phylogenetics and Evolution, 96: 130–139. Fator de impacto: 4.2. 
• Roxo, FF, Silva, GSC, Waltz, BT, Melo, JEG (2016) A new species of Hisonotus 
(Siluriformes: Otothyrinae) from the upper rio Paraná and rio São Francisco basins, Brazil. 
Zootaxa, 4109(2): 227–238. Fator de impacto: 1.16. 
• Silva, GS, Roxo, FF, Melo, BF, Oliveira, C (2016). New species of Curculionichthys 
(Siluriformes: Loricariidae) from the eastern Guiana Shield. Zootaxa, 4175(3): 281–291. 
Fator de impacto: 1.16. 
• Silva, GS, Roxo, FF, Ochoa, LE, Oliveira, C (2016). Description of a new catfish genus 
(Siluriformes, Loricariidae) from the Tocantins River basin in central Brazil, with 
comments on the historical zoogeography of the new taxon. ZooKeys, (598): 129. Fator 
de impacto: 1.28. 
• Silva, GS, Roxo, FF, Lujan, NK, Tagliacollo, VA, Zawadzki, CH, Oliveira, C (2016). 
Transcontinental dispersal, ecological opportunity and origins of an adaptive radiation in 
the Neotropical catfish genus Hypostomus (Siluriformes: Loricariidae). Molecular Ecology, 
25: 1511–1529. Fator de impacto: 6.1. 
• Silva, GS, Roxo, FF, Oyakawa, OT (2016). Description of a new species of Pareiorhina 
(Siluriformes: Loricariidae) from the rio São Francisco basin, Brazil. Zootaxa, 4107(3): 
381–391. Fator de impacto: 1.16. 
• Zawadzki, CH, Roxo, FF, da Graça, WJ (2016). Hisonotus pachysarkos, a new species of 
cascudinho from the rio Ivaí basin, upper rio Paraná system, Brazil (Loricariidae: 
Otothyrinae). Ichthyological Exploration of Freshwaters, 26(4): 373–383. Fator de 
impacto: 1.01. 
• Roxo, FF, Melo, BF, Silva, GSC, Oliveira, C (2017) New species of Parotocinclus 
(Siluriformes: Loricariidae) from coastal drainages of Rio de Janeiro, southeastern Brazil. 
Zootaxa, 4232: 260–270. Fator de impacto: 1.16. 
4	
	
• Silva, GSC, Covain, R., Oliveira, C, Roxo, FF (2017) Description of two new species of 
Lithoxus (Hypostominae: Loricariidae) from rio Jari and rio Amapá basins, Brazilian 
Guiana Shield. Zootaxa, 4347: 151–168. Fator de impacto: 1.16. 
• Roxo, FF, Dias, AC, Silva, GSC, Oliveira, C (2017) Two new species of Curculionichthys 
(Siluriformes: Loricariidae) from the rio Amazonas basin, Brazil. Zootaxa, 4341: 258–270. 
Fator de impacto: 1.16. 
• Roxo, FF, Silva, GSC, Zawadzki, CH, Oliveira, C (2017) Neoplecostomus canastra, a new 
catfish (Teleostei: Siluriformes) species from upper Rio Paraná basin. Zootaxa, 4294: 226–
240. Fator de impacto: 1.16. 
• Ochoa, LE, Roxo, FF, Donascimiento, C, Sabaj, MH, Datovo, A, Alfaro, M, Oliveira, C 
(2017) Multilocus analysis of the catfish family Trichomycteridae (Teleostei: Ostariophysi: 
Siluriformes) supporting a monophyletic Trichomycterinae. Molecular Phylogenetics and 
Evolution, 115: 71–81, Fator de impacto: 4.2. 
• Roxo, FF, Lujan, NK, Tagliacolo, VA, Waltz, BT, Silva, GSC, Oliveira, C, Albert, JS 
(2017) Shift from slow- to fast-water habitats accelerates lineage and phenotype evolution 
in a clade of Neotropical suckermouth catfishes (Loricariidae: Hypoptopomatinae). PLoS 
One, e0178240. Fator de impacto: 3.5. 
• Roxo, FF, Mello, BF, Silva, GSC, Oliveira, C (2017) Description ofa new species of 
Gymnotocinclus from the rio Tocantins basin with phylogenetic analysis of the subfamily 
Hypoptopomatinae (Siluriformes: Loricariidae). Zootaxa, 4268: 337. Fator de impacto: 
1.16. 
• Roxo, FF, Silva, GSC, Melo, BF (2018) Hisonotus devidei, a new species from the São 
Francisco basin, Brazil (Siluriformes: Loricariidae). Journal of Fish Biology, 92: 1–15, 
2018. Fator de impacto: 1.7. 
• Souza, CS, Costa-Silva, GJ, Roxo, FF, Foresti, F, Oliveira, C (2018) Genetic and 
Morphological Analyses Demonstrate That Schizolecis guntheri (Siluriformes: 
Loricariidae) Is Likely to Be a Species Complex. Frontiers in Genetics, 9: 1–9. Fator de 
impacto: 4.1. 
• Silva, GSC, Roxo, FF, Souza, CS, Oliveira, C (2018) Two new species of Corumbataia 
(Hypoptopomatinae: Loricariidae) from Rio Corrente, upper Rio Paraná basin, Brazil. 
Zootaxa, 4483 (2): 317–330. Fator de impacto: 1.16.	 	
5	
	
 
 
Para uma melhor apresentação do conteúdo desenvolvido no 
período de vigência do projeto o restante do relatório será 
apresentado em Inglês. 
 
 
 
 
6	
	
2. Background on loricarioids and project justification 
Loricarioidea is the largest monophyletic group of catfishes endemic to the neotropics (de 
Pinna 1998; Britto 2002; Sullivan et al. 2006), with about 1,420 valid species (Eschmeyer & Fong 
2013) assigned to six family-level taxa; Astroblepidae (61 species), Callichthyidae (200 species), 
Loricariidae (870 species), Nematogenyidae (1 species), Scoloplacidae (6 species) and 
Trichomycteridae (273 species). Loricarioid fishes are widely distributed throughout freshwater 
habitats in tropical South America and southern Central America (Reis et al. 2003; Nelson 2006). 
In addition to their exceptional species richness, loricarioids exhibit a wide range of morphological, 
physiological and ecological specializations, occupying many habitats and trophic levels, including 
obligate herbivores, parasites (e.g. Vandellia) and the only known wood-eating fish species 
(Panaque) (Reis 1998; Nelson et al. 1999; de Pinna 1998; Britto 2002). The sucker-shaped mouth 
and spoon-shaped teeth morphologies of loricariids allow many species to forage on algae and 
cling to substrate surfaces (Schaefer & Lauder 1986), and astroblepids even has the ability to climb 
waterfalls (Reis et al. 2003). 
 The monophyly of the Loricarioidea is supported by several salient morphological 
characters, most notably the presence of integumentary teeth (odontodes) on the external surface 
of the head and body, a reduced gas bladder, and encapsulated expansions of the parapophysis of 
the first vertebrae (Reis et al. 2003). Among loricarioids, the families Scoloplacidae, 
Callichthyidae, and Loricariidae possess bony dermal plates, and Astroblepidae and Loricariidae 
share the presence of a suctorial mouth. The phylogenetic position of the Astroblepidae as sister to 
Loricariidae suggests the loss of armor plating in Astroblepidae (de Pinna 1998; Britto 2002). 
Within Loricarioidea the family-level phylogeny is well established from both morphological and 
molecular datasets (de Pinna 1998; Britto 2002; Sullivan et al. 2006; Lundberg et al. 2007), 
however the species-level relationships within each family main in subfamilies level remain poorly 
documented (e.g. Reis et al. 2003; Roxo et al. 2012a, b). 
The great diversity of loricarioid fishes provides abundant materials for the study of 
fundamental questions both in evolution and ecology: What intrinsic organismal features and 
external environmental factors promoted or restricted diversification within loricarioid clades? 
Why do some clades have such high species richness (as Loricariidae with 870 species) whereas 
other clades have such low diversity (as Scoloplacidae with six species and Nematogenyidae with 
only one species)? How can a dozen or more species from a single subfamily, all with seemingly 
7	
	
equivalent ecological requirements in terms of habitat and food resources, coexist sympatrically 
within a single river system? 
Here we propose to address these questions through a combination of phylogenomic, 
macroecological and community phylogenetic approaches. The first step will be to assemble a 
species-dense molecular phylogeny for the hyperdiverse superfamily Loricarioidea using a 
genome-wide sampling of orthologous loci of the Ultraconserved Elements (UCEs) through Next-
generation sequencing (McCormack et al. 2012; Faircloth et al. 2012, 2013). We will then use the 
resulting phylogenies to investigate the tempo and modes of loricarioid diversification, including 
analyses of body size evolution (Haldane 1949; Schmidt-Nielsen 1984, 1997; Blanckenhorn 2000; 
Albert & Johnson 2011), macroevolution (Stanley 1973, 1979, 1998; McKinney 1990; Jablonski 
1997, 2007, 2008), and geographic range evolution (Ree et al. 2005; Ree & Smith 2008). In doing 
so, we will further expand the newly emerging tools of macroevolutionary biology (sensu Harmon 
et al. 2003; Paradis 2003, 2012; Slater et al. 2012) into one of the world’s most diverse and 
ecologically important clades of freshwater fishes. 
A thorough osteological phylogeny has been proposed for Loricarioidea (de Pinna 1998; 
Britto 2002), however no single group of researchers has assembled a comprehensive set of tissue 
samples to reconstruct a wide sampled molecular phylogeny and combine to a robust 
morphological dataset to the group. Thus, we propose to combine the intellectual and genetic 
resources of researchers in the US and in Brazil to reconstruct the phylogeny of Loricarioidea, 
assessing the most species-dense taxon sampling of these groups to date to study the diversification 
dynamics and understand the distributions of species and ecosystems in light of Earth history 
processes that shape landscape evolution. 
 
3. What are UCEs and why they are useful? 
 As their name implies, ultraconserved elements (UCEs) are highly conserved regions of 
organismal genomes shared among evolutionary distant taxa - for instance, birds share many UCEs 
with humans. UCEs were first described in humans by Bejerano et al. (2004) and subsequently 
identified in several classes of organisms (Siepel et al. 2005). After that, Miller et al. (2007) 
identified additional regions of high conservation elements in vertebrate genomes. 
Because UCEs are conserved across disparate taxa (e.g. Hardison et al. 1997; Loots et al. 
2000; Boffelli et al. 2003; Kellis et al. 2003; Margulies et al. 2003; Woolfe et al. 2005), UCEs are 
8	
	
also universal genetic markers in the sense that the locations (or loci) that we can target in humans 
are identical, in many cases, to the loci that we can target in different animal lineages (Dermitzakis 
et al. 2005; Siepel et al. 2005; Stephen et al. 2008; Janes et al. 2011). 
The UCEs can be used as molecular marker to access variable DNA regions adjacent to 
UCE locations (flanking DNA), and these data are useful for reconstructing the evolutionary 
history and population-level relationships of many organisms (Faircloth et al. 2012). Additionally, 
it is now possible to conduct large-scale searches for conserved sequences and to use the results of 
such searches to help stimulate new hypotheses and drive experimentation (Nobrega et al. 2003, 
2004; Frazer et al. 2004; Woolfe et al. 2005). 
 Because they are distributed throughout the genome, UCEs can be treated as independent 
loci in phylogenetic analysis and are particularly valuable in species tree methods (Knowles, 2009), 
which increase dramatically in power as the number of loci increases. Though they still represent 
only a fraction of the total genome, UCE enrichment and sequencing methods capture many more 
loci than a traditional Sanger sequencing approach (hundreds or thousands versus ten or less) and 
cost far less than whole-genome methods (US$120 per sample versus US$2,000 or more). 
 
4. References 
Albert, J.S.,Johnson, D.M. (2011) Diversity and evolution of body size in fishes. Evolutionary 
Biology, 39(3): 324-340. 
Bejerano, G., Pheasant, M., Makunin, I., Stephen, S., Kent, W.J., Mattick, J.S., Haussler, D. (2004) 
Ultraconserved Elements in the Human Genome. Science, 304(5675): 1321-1325. 
Blanckenhorn, W.U. (2000) The Evolution of Body Size: What Keeps Organisms Small? The 
Quarterly Review of Biology, 75(4): 385-407. 
Boffelli, D., McAuliffe, J., Ovcharenko, D., Lewis, K.D., Ovcharenko, I., Pachter, L., and Rubin, 
E.M. (2003) Phylogenetic shadowing of primate sequences to find functional regions of the 
human genome. Science, 299: 1391-1394. 
Britto, M.R. (2002) Análise filogenética da ordem Siluriformes com ênfase nas relações da 
superfamília Loricarioidea (Teleostei: Ostariophysi). Tese de Doutorado, Instituto de 
Biociências, Universidade Estadual de São Paulo, São Paulo, pp. 512. 
Dermitzakis, E.T., Reymond, A., Antonarakis, S.E. (2005) Conserved non-genic sequences - an 
unexpected feature of mammalian genomes. Nature Reviews Genetics, 6:151-157. 
9	
	
Eschmeyer, W. (2013) Catalog of fishes. Electronic publication in “World Wide Web” 
<http://www.calacademy.org/research/ichthyology/catalog> (06.02.13). 
Faircloth, B.C., McCormack, J.E., Crawford, N.G., Harvey, M.G., Brumfield, R.T., Glenn, T.C. 
(2012) Ultraconserved elements anchor thousands of genetic markers for target enrichment 
spanning multiple evolutionary timescales. Systematic Biology, 61: 717-726. 
Faircloth, B.C., Sorenson, L., Santini, F., Alfaro, M.E. (2013) A Phylogenomic Perspective on the 
Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved 
Elements (UCEs). PLOS ONE, 8(6): e65923. 
Frazer, K.A., Tao, H., Osoegawa, K., de Jong, P.J., Chen, X., Doherty, M.F., Cox, D.R. (2004) 
Noncoding sequences conserved in a limited number of mammals in the SIM2 interval are 
frequently functional. Genome Research, 14: 367-372. 
Haldane, J.B.S. (1949) Suggestions as to quantitative measurement of rates of evolution. Evolution, 
3(1): 51-56. 
Hardison, R.C., Oeltjen, J., Miller, W. (1997) Long human-mouse sequence alignments reveal 
novel regulatory elements: Reasons to sequence the mouse genome. Genome Research, 7: 
959-966. 
Harmon, L.J., Schulte, J.A., Larson, A., Losos, J.B. (2003) Tempo and mode of evolutionary 
radiation in iguanian lizards. Science, 301(5635): 961-964. 
Janes, D.E., Chapus, C., Gondo, Y., Clayton, D.F., Sinha, S., Blatti, C.A., Organ, C.L., Fujita, 
M.K., Balakrishnan, C.N., Edwards, S.V. (2011) Reptiles and mammals have differentially 
retained long conserved noncoding sequences from the Amniote ancestor. Genome Biology 
and Evolution, 3: 102-113. 
Jablonski, D. (1997) Body-size evolution in cretaceous molluscs and the status of Cope's rule. 
Nature, 385: 250-252. 
Jablonski, D. (2007) Biotic Interactions and Macroevolution: Extensions and Mismatches Across 
Scales and Levels. Evolution, 62(4): 715-739. 
Jablonski, D. (2008) Extinction and the spatial dynamics of biodiversity. PNAS, 105: 11528-
11535. 
Kellis, M., Patterson, N., Endrizzi, M., Birren, B., Lander, E.S. (2003) Sequencing and comparison 
of yeast species to identify genes and regulatory elements. Nature, 423: 241-254. 
10	
	
Knowles, L.L. (2009) Estimating species trees: methods of phylogenetic analysis when there Is 
incongruence across genes. Systematic Biology, 58(5): 463-467. 
Loots, G.G., Locksley, R.M., Blankespoor, C.M., Wang, Z.E., Miller, W., Rubin, E.M., Frazer, 
K.A. (2000) Identification of a coordinate regulator of interleukins 4, 13, and 5 by cross-
species sequence comparisons. Science, 288: 136-140. 
Lundberg, J.G., Sullivan, J.P., Rodiles-Hernandez, R., Hendrickson, D.A. (2007) Discovery of 
African roots for the Mesoamerican Chiapas catfish, Lacantunia enigmatica, requires an 
ancient intercontinental passage. Proceedings of the Academy of Natural Sciences of 
Philadelphia, 156: 39-53. 
Margulies, E.H., Blanchette, M., Haussler, D., Green, E.D. (2003) Identification and 
characterization of multi-species conserved sequences. Genome Research, 13(12): 2507-
2518. 
McCormack, J.E., Faircloth, B.C., Crawford, N.G., Gowaty, P.A., Brumfield, R.T., Glenn, T.C. 
(2012) Ultraconserved elements are novel phylogenomic markers that resolve placental 
mammal phylogeny when combined with species-tree analysis. Genome Research, 22: 746-
754. 
McKinney, M.L. (1990) Trends in body-size evolution. Evolutionary Trends (ed. K.J. McNamara), 
University of Arizona Press, Tucson, AZ, pp. 75-118. 
Miller, W, Rosenbloom, K., Hardison, R.C., Hou, M., Taylor, J., Raney, B., Burhans, R., et al. 
(2007) 28-Way vertebrate alignment and conservation track in the UCSC Genome Browser. 
Genome Research, 17: 1797-1808. 
Nelson, J.S. (2006) Fishes of the World. Wiley, Hoboken, New Jersey, pp. 601. 
Nelson, J.A., Wubah, D.A., Whitmer, M.E., Johnson, E.A., Stewart, D.J. (1999) Wood-eating 
catfishes of the genus Panaque: gut microflora and cellulolytic enzyme activities. Journal of 
Fish Biology, 54(5): 1069-1082. 
Nobrega, M.A., Ovcharenko, I., Afzal, V., Rubin, E.M. (2003) Scanning human gene deserts for 
long-range enhancers. Science, 302: 413. 
Nobrega, M.A., Zhu, Y., Plajzer-Frick, I., Afzal, V., and Rubin, E.M. (2004) Megabase deletions 
of gene deserts result in viable mice. Nature, 431: 988-993. 
Paradis, E. (2003) Analysis of diversification: combining phylogenetic and taxonomic data. 
Proceedings of the Royal Society of London B, 270: 2499-2505. 
11	
	
Paradis, E. (2012) Analysis of Phylogenetics and Evolution using R. New York, Springer, pp. 211. 
de Pinna, M.C.C. (1998) Phylogenetic relationships of Neotropical Siluriformes (Teleostei: 
Ostariophysi): historical overview and synthesis of hypotheses. in: Phylogeny and 
Classification of Neotropical Fishes. Malabarba, L.R., Reis, R.E., Vari, R.P., Lucena, Z.M.S., 
Lucena, C.A.S. (Eds.). EDIPUCRS, Porto Alegre, Brasil, pp. 279-330. 
Ree, R.H., Smith, S.A. (2008) Maximum likelihood inference of geographic range evolution by 
dispersal, local extinction, and cladogenesis. Systematic Biology, 57: 4-14. 
Ree, R.H., Moore, B.R., Webb, C.O., Donoghue, M.J. (2005) A likelihood framework for inferring 
the evolution of geographic range on phylogenetic trees. Evolution, 59: 2299-2311. 
Reis, E.R. (1998) Callichthyidae. Armored Catfishes. Tree of Life Web Project. Retrieved, (07-04-
2007). 
Reis, R.E., Kullander, S.O., Ferraris, C.J. (2003) CLOFFSCA-Check list of the freshwater fishes 
of South and Central America. Edipucrs. 
Roxo, F.F., Zawadzki, C.H. Alexandrou, M.A., Costa Silva, G.J., Chiachio, M.C., Foresti, F., 
Oliveira, C. (2012a) Evolutionary and biogeographic history of the subfamily 
Neoplecostominae (Siluriformes: Loricariidae). Ecology and Evolution, 2: 2438-2449. 
Roxo, F.F., Zawadzki, C.H., Costa Silva, G.J., Chiachio, M.C., Foresti, F., Oliveira, C. (2012b) 
Molecular systematics of the armored neotropical catfish subfamily Neoplecostominae 
(Siluriformes, Loricariidae). Zootaxa, 3390: 33-42. 
Schaefer, S.A., Lauder, G.V. (1986) Historical Transformation of Functional Design: Evolutionary 
Morphology of Feeding Mechanisms in Loricarioid Catfishes. Systematic Zoology (Society 
of Systematic Biologists), 35(4): 489-508. 
Schmidt-Nielsen, K. (1984) Scaling: Why Is Animal Size So Important? Cambridge & New York: 
Cambridge University Press, pp. 241. 
Schmidt-Nielsen, K. (1997) Animal Physiology: Adaptation and Environment (5th ed.). 
Cambridge University Press. 
Siepel, A., Bejerano, G, Pedersen, J.S., Hinrichs, A.S., Hou, M., Rosenbloom, K., Clawson, H., et 
al. (2005) Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. 
Genome Research, 15: 1034-1050. 
12	
	
Slater, G.J., Harmon, L.J., Wegmann, D., Joyce, P., Revell, L.J., Alfaro, M.E. (2012) Fitting 
models of continuous trait evolution to incompletely sampled comparative data usingapproximate Bayesian computation. Evolution, 66(3): 752-762. 
Stanley, S.M. (1973) An explanation for Cope's rule. Evolution, 27: 1-26. 
Stanley, S.M. (1979) Macroevolution. Pattern and Process. W. H. Freeman and Co., San Francisco, 
pp. 332. 
Stanley, S.M. (1998) Macroevolution. Pattern and Process. The Johns Hopkins University Press., 
London, pp. 332. 
Stephen, S., Pheasant, M., Makunin, I.V., Mattick, J.S. (2008) Large-scale appearance of 
ultraconserved elements in tetrapod genomes and slowdown of the molecular clock. 
Molecular Biology and Evolution, 25: 402-408. 
Sullivan, J.P., Lundberg, J.G., Hardman, M. (2006) A phylogenetic analysis of the major groups 
of catfishes (Teleostei: Siluriformes) using rag1 and rag2 nuclear gene sequences. Molecular 
Phylogenetics and Evolution, 41: 636-662. 
Woolfe, A., Goodson, M., Goode, D., Snell, P., McEwen, G., Vavouri, T., Smith, S., North, P., 
Callaway, H., Kelly, K., et al. (2005) Highly conserved non-coding sequences are associated 
with vertebrate development. PLoS Biology, 3: e7. 
13	
	
 
 
 
 
 
 
Final Results and Manuscripts to be Published 
 
 
 
 
	 14	
 
 
 
 
 
 
Appendix – Loricariidae Phylogeny 
 
 
 
 
 
 
	 15	
Phylogenomic reappraisal of the suckermouth armored 
catfish family Loricariidae (Teleostei: Siluriformes) using 
ultraconserved elements 
 
Fábio F. Roxo1, Luz E. Ochoa1, Mark H. Sabaj2, Nathan K. Lujan3, Raphaël Covain4, 
Gabriel S. C. Silva1, Bruno F. Melo1,5, James S. Albert6, Jonathan Chang7, Fausto 
Foresti1, Michael E. Alfaro7, Claudio Oliveira1 
 
1Universidade Estadual Paulista, Departamento de Morfologia, Laboratório de Biologia e Genética 
de Peixes, Botucatu, São Paulo, Brazil; 
2
Department of Ichthyology, The Academy of Natural 
Sciences of Drexel University, 1900 Benjamin Franklin Parkway, Philadelphia, Pennsylvania 
19103, USA; 
3
Department of Biology, University of Toronto Scarborough, Toronto, Ontario, 
M1C1A4, Canada; 
4
Department of Herpetology and Ichthyology, Museum of Natural History, 1 
route de Malagnou, C.P. 6434, CH-1211, Geneva, Switzerland;
 5
Department of Vertebrate Zoology, 
National Museum of Natural History, Smithsonian Institution, Washington DC, USA; 
6
Department 
of Biology, University of Louisiana at Lafayette, Lafayette, Louisiana, USA; 
7
Department of Ecology 
and Evolutionary Biology, University of California, Los Angeles, California 90095, USA. 
 
 
Running title: Phylogenomics of Loricariidae 
 
Corresponding author: Fábio F. Roxo (roxoff@hotmail.com.br) 
 
 
	 16	
Abstract 
Neotropical freshwaters host more than 4,000 fish species, of which almost one quarter 
are suckermouth armored catfishes of the family Loricariidae – the largest catfish 
family and fifth most species-rich vertebrate family on Earth. Given their diversity and 
ubiquitous distribution across many habitat types, loricariids are an excellent system in 
which to investigate factors that create and maintain Neotropical fish diversity, yet 
robust phylogenies needed to support such ecological and evolutionary studies are 
lacking. We seek to buttress the systematic understanding of loricariid catfishes by 
generating a genome-scale data set (1,041 loci, 328,330 bp) for 140 species spanning 75 
genera and five of six previously proposed subfamilies. Both maximum likelihood and 
Bayesian analyses strongly supported monophyly of Loricariidae, with early 
diversification dated to Late Cretaceous at ~65 millions of years ago. Our results also 
corroborate monophyly and previously hypothesized relationships among all examined 
subfamilies: Delturinae was sister to all other analyzed loricariids, with subfamily 
Rhinelepinae diverging next, followed by Loricariinae sister to Hypostominae + 
Hypoptopomatinae. These results reinforce the established backbone of loricariid 
interrelationships and lay a strong foundation for future research to focus on 
intergeneric relationships within subfamilies. 
 
Keywords: cascudos; Neotropics; phylogenomics; plecos; South America; timetree. 
	 17	
1. Introduction 
1.1. General Overview 
Earth’s freshwater ecosystems are extremely biodiverse, containing more than 
13,000 fish species in about 2,500 genera, or about 40–45% of all fishes (Lévêque et al., 
2008). Of the six freshwater realms commonly recognized, the Neotropical realm (South 
America to central Mexico and the Caribbean Islands) is by far the most diverse with over 
4,035 fish species in about 705 genera (Lévêque et al., 2008). The Neotropical realm also 
has highest number of fully freshwater families (43) and the most species-rich vertebrate 
fauna on earth (Lundberg et al., 2000; Berra, 2001; Reis et al., 2003; Lévêque et al., 2005, 
2008; Petry, 2008). Understanding the historical origins and evolutionary processes 
driving Neotropical species diversification has been a great challenge for evolutionary 
biologists. Recent geological/paleontological discoveries (Malabarba et al., 2010; 
Wesselingh and Hoorn, 2011) and the development of advanced phylogenomic 
techniques (Lemmon et al., 2012; Faircloth et al., 2012) provide valuable new tools for 
discerning factors driving cladogenesis in Neotropical freshwater fishes (Faircloth et al., 
2013; Harrington et al., 2016). 
The Neotropical ichthyofauna is predominantly composed of otophysan fishes, 
except Cypriniformes (i.e., Characiformes, Siluriformes and Gymnotiformes) that 
constitute roughly 77% of the total species richness (Albert et al., 2011). Among 
Neotropical otophysan families, Loricariidae is the second most species rich with ~938 
species (after Characidae with ~1123 species; Eschmeyer and Fong, 2017). Loricariids 
range in size from the miniature Nannoplecostomus eleonorae Ribeira, Lima & Pereira 
2012 maturing at 16.2 mm standard length (Ribeiro et al., 2012) to species reaching at 
least 600 mm (Panaque schaeferi Lujan, Hidalgo & Stewart 2010) and 628 mm 
(Acanthicus hystrix Spix & Agassiz 1829) standard length (Lujan et al., 2010). 
	 18	
Loricariid catfishes are easily distinguished from other fish groups by a combination of 
features including body covered with dermal plates and tooth-like odontodes, and 
ventral mouth with fleshy oral disk used to adhere to solid substrates while foraging 
(Geerinckx et al., 2011; Schaefer and Lauder, 1986). Loricariids occupy lotic to lentic 
habitats in small to major hydrographic systems throughout South and Central America, 
from Andean streams over 3,000 meters above sea level to the vast lowland floodplains 
of the Pantanal and Amazonia, and even estuarine ecosystems along the northern South 
American coast. 
 
1.2. Historical Systematics of Loricariidae 
 Higher classification of the Loricariidae has a complex history going back more 
than a century (see Lujan et al., 2015a; Pereira and Reis, 2017) with significant early 
revisions by Eigenmann and Eigenmann (1890) and Regan (1904). Isbrücker (1980) 
assembled a comprehensive taxonomic catalog of Loricariidae in which he arranged taxa 
into six subfamilies: Lithogeneinae, Neoplecostominae, Hypostominae, Ancistrinae, 
Hypoptopomatinae and Loricariinae. Howes (1983) subsequently used a cladistic 
analysis of myological and osteological data to propose relationships between five 
loricariid subfamilies (Lithogeninae not examined): Hypostominae sister to a trichotomy 
composed of Neoplecostominae, Chaetostominae and Loricariinae + Hypoptopomatinae. 
In cladistic analyses of osteology, Schaefer (1986, 1987) retained the loricariid 
subfamilies proposed by Isbrücker (1980) but noted that Ancistrinae made Hypostominae 
paraphyletic. Schaefer (1987) placed the Lithogeneinae at the base of Loricariidae, and 
considered the Neoplecostominae to be sister to all remaining subfamilies. In an early 
molecular study, Montoya-Burgos et al. (1998) provided evidence for the monophyly of 
Loricariidae but found poor resolutionamong the remaining subfamilies (Lithogeneinae 
	 19	
not examined). Armbruster (2004a) used morphological characters and extensive taxon 
sampling to propose Lithogenes + Astroblepidae sister to all loricariids, and Delturus + 
Upsilodus victori (now Hemipsilichthys gobio (Lütken 1874)) as the first lineage to 
diverge within Loricariidae. Armbruster’s (2004a) analysis also nested a monophyletic 
Hypoptopomatinae within Neoplecostominae and expanded Hypostominae to include 
taxa formerly assigned to Ancistrinae which he downgraded to the tribe Ancistrini. Reis 
et al. (2006) subsequently proposed the new subfamily Delturinae for Delturus and 
Hemipsilichthys. A recent multilocus phylogeny by Lujan et al. (2015a) supported many 
of the higher-level relationships proposed by Armbruster (2004a) and added two clades 
at the subfamilial level: Rhinelepinae and the monotypic ‘Pseudancistrus’ represented by 
‘Pseudancistrus’ genisetiger Fowler 1941 (see Fig. 1 for main phylogenetic relationships 
of Hypostominae proposed by Lujan et al., 2015a). 
 The classification of taxa traditionally assigned to Hypoptopomatinae and 
Neoplecostominae has been especially problematic. Based on morphological characters, 
Schaefer (1997, 1998) considered Hypoptopomatinae to be composed of two 
monophyletic tribes, Hypoptopomatini and Otothyrini. Based on molecular data, 
Chiachio et al. (2008) elevated the Otothyrini to a monophyletic subfamily more closely 
related to Neoplecostominae than Hypoptopomatinae. Cramer et al. (2011) subsequently 
used both nuclear and mitochondrial loci to analyze relationships among nearly all genera 
of Hypoptopomatinae, Neoplecostominae and Otothyrinae. Their analysis supported a 
monophyletic clade composed of all three subfamilies (treated as tribes), but none were 
supported as monophyletic. Likewise, the molecular study by Lujan et al. (2015a) 
supported a close relationship between the three subfamilies (again treated as tribes), and 
failed to group representatives of Hypoptopomatinae into a monophyletic clade. 
Subsequent molecular studies (Roxo et al., 2014, 2017; Silva et al., 2016) have provided 
	 20	
support for the monophyly of each of the three subfamilies with Hypoptopomatinae sister 
to Neoplecostominae + Otothyrinae (see Fig. 2 from Roxo et al. 2014). In a broad 
morphology-based analysis of Loricariidae, Pereira and Reis (2017) provided weak 
support for a clade composed of taxa assigned to Hypoptopomatinae, Neoplecostominae 
and Otothyrinae, and corroborated the monophyly of Neoplecostominae (minus 
Microplecostomus and Pseudotocinclus). Relationships between the few 
hypoptopomatins (Otocinclus, Plesioptopoma) and otothyrins (Eurycheilichthys, 
Parotocinclus) included in their study, however, were inconsistent with previous 
classifications derived from molecular evidence. Morphological and molecular analyses 
have generally agreed on the monophyly and composition of the Neoplecostominae, 
although only molecules support the inclusion of Microplecostomus and Pseudotocinclus; 
furthermore, the assignment of two genera (Euryochus and Hirtella) to the subfamily by 
Pereira and Reis (2017) has not been tested with molecular data. 
Relationships between and within other subfamilies of Loricariidae also remain 
unresolved. For example, some studies have recognized three tribes in Loricariinae: 
Harttiini, Farlowellini and Loricariini (Nijssen and Isbrücker, 1987; Lujan et al., 2015a). 
Others recognize two tribes (Harttiini and Loricariini) with the latter expanded to include 
taxa formerly in Farlowellini (Covain et al., 2016, see Fig. 4). Relationships within 
Hypostominae (hereafter sensu Lujan et al., 2015a) are perhaps the most complex due to 
the large number of genera and species proposed for the subfamily (see Lujan et al., 2015a 
for summary). Armbruster (2004a) recognized five tribes in Hypostominae: Ancistrini, 
Corymbophanini, Hypostomini, Pterygoplichthini and Rhinelepini. Lujan et al. (2015a) 
retained Ancistrini and Hypostomini, but divided the remaining hypostomins among 
seven tribe-level clades: the Chaetostoma Clade, Pseudancistrus Clade, Lithoxus Clade, 
	 21	
‘Pseudancistrus’ Clade, Acanthicus Clade, Hemiancistrus Clade and Peckoltia Clade 
(Fig. 1). 
 We generated a new molecular matrix over sixty times larger than any previous 
DNA-based analysis of the Loricariidae in order to test previous hypotheses and better 
understand the evolution of this large Neotropical fish clade. We also use the new 
phylogenetic results as the basis for a revised discussion of large-scale biogeographical 
patterns in the family. 
 
2. Material and Methods 
2.1. Taxon Sampling 
Our ingroup comprised 163 terminal taxa spanning 140 species and 75 genera 
distributed among all proposed subfamilies of Loricariidae except the Lithogeninae. 
Outgroup taxa included one species of Astroblepidae (Astroblepus grixalvii Humboldt 
1805), three Callichthyidae (Corydoras aeneus (Gill 1858), Aspidoras fuscoguttatus 
Nijssen & Isbrücker 1976, Hoplosternum littorale (Hancock 1828)), one Scoloplacidae 
(Scoloplax dicra Bailey & Baskin 1976), and one Trichomycteridae (Trichomycterus 
areolatus Valenciennes 1846 in Cuvier and Valenciennes, 1846). The tree was rooted 
with two Characidae (Poptella paraguayensis (Eigenmann 1907) in Eigenmann et al., 
1907 and Hyphessobrycon compressus (Meek 1904)). Voucher specimens were fixed in 
96% ethanol or 10% formalin, then transferred to 70% ethanol for permanent storage 
(see Table S1 for catalog and locality data). Institutional acronyms follow Sabaj (2016) 
with inclusion of LGC: Laboratório de Genética da Conservação, Pontifícia 
Universidade Católica de Minas Gerais, Belo Horizonte, Brazil. 
 
2.2. DNA Extraction and Sequencing 
	 22	
Whole genomic DNA was extracted from ethanol preserved muscle samples 
with the DNeasy Tissue Kit (Qiagen) and quantified using the Qubit® dsDNA broad 
range (BR) Assay Kit (Invitrogen – Life Technologies) following manufacturer’s 
instructions. We used a probeset developed for ostariophysan fishes to generate 
sequence data for about 2,500 UCE loci (Sidlauskas et al. in prep.). Library preparation, 
sequencing, and data pipelining were performed at MYcroarray® (Ann Arbor, 
Michigan, USA) using the following protocol: DNA libraries were prepared for the 171 
specimens (163 ingroup taxa and 8 outgroup taxa) by modifying the Nextera (Epicentre 
Biotechnologies) library preparation protocol for solution-based target enrichment 
following Faircloth et al. (2012) and increasing the number of PCR cycles following the 
tagmentation reaction to 20 as recommended by Faircloth et al. (2013). We used the 
Nextera library preparation protocol of in vitro transposition followed by PCR to prune 
the DNA and attach sequencing adapters (Adey et al., 2010), then used the Epicentre 
Nextera kit to prepare transposase-mediated libraries with insert sizes averaging 100 bp 
(95% CI: 45 bp) following Adey et al. (2010). 
To prepare the libaries, whole genomic DNA (concentration of 40 ng/ul) was 
first sheared with a QSonica Q800R instrument and selected to modal lengths of 
approximately 500 nt using a dual-step SPRI bead cleanup. We then converted the DNA 
to Illumina sequencing libraries with a slightly modified version of the NEBNext(R) 
Ultra(TM) DNA Library Prep Kit for Illumina(R). After ligation of sequencing primers, 
libraries were amplified using KAPA HiFi HotStart ReadyMix (Kapa Biosystems) for 
six cycles using the manufacturer's recommended thermal profile and dual P5 and P7 
indexed primers (see Kircher et al., 2012, doi: 10.1093/nar/gkr771, for primer 
configuration). After purification with SPRI beads, libraries were quantified with the 
Quant-iT(TM) Picogreen(R) dsDNA Assay kit (ThermoFisher). We then enriched pools 
	 23	
comprising 100 ng each of eight libraries (800 ng total) using the MYbaits(R) TargetEnrichment system (MYcroarray) following manual version 3.0. After capture cleanup, 
the bead-bound library was re-suspended in the recommended solution and amplified 
for ten cycles using a universal P5/P7 primer pair and KAPA HiFi reagents. After 
purification, each captured library pool was quantified with PicoGreen, and combined 
with all other pools in projected equimolar ratios prior to sequencing. Sequencing was 
performed across two Illumina HiSeq paired-end 100 bp lanes using v4 chemistry. 
 
2.3. Bioinformatics 
Details on UCE sequence analyses available online via the phyluce document 
hub at: https://github.com/faircloth-lab/phyluce (see also Faircloth, 2016). All matrixes 
used in the present study are available at figshare DOI 10.6084/m9.figshare.5611306 
(see Table 1 for information about data of each matriz) and species read information is 
presented in Table S2. After sequencing, adapter contamination, low quality bases, and 
sequences containing ambiguous base calls were trimmed using the illumiprocessor 
software pipeline developed by Faircloth (2013; https://github.com/faircloth-
lab/illumiprocessor). After trimming, we assembled Illumina reads into contigs on a 
species-by-species basis using both Velvet (Zerbino and Birney, 2008) on 
VelvetOptimiser (https://github.com/Victorian-Bioinformatics-
Consortium/VelvetOptimiser) and the Abyss pipeline (Simpson et al., 2009; 
https://github.com/bcgsc/abyss) to test how different assembly programs would affect 
length of the final UCE concatenated matrix, relationships among taxa, and statistical 
node support. Abyss tended to generate larger fragments and more accurate assemblies 
compared to velvet, since it runs read-based error correction prior to assembly, which 
tends to result in more accurate contigs (Faircloth, 2015). 
	 24	
After sequence assembly, we used a custom Python program 
(match_contigs_to_probes.py), present in the phyluce software package (Faircloth, 
2015), integrating LASTZ (Harris, 2007) to align species-specific contigs to our probe-
UCE set. This last program creates a relational database of matches to UCE loci by 
taxon. We then used the get_match_counts.py program (also included in PHYLUCE) to 
query the database and generate FASTA files for UCE loci that were identified across 
all taxa. A custom Python program (seqcap_align_2.py) was then used to align contigs 
using the MUSCLE alignment algorithm (Edgar, 2004) and to perform edge and 
internal trimming to see how each would affect tree topology and node support. Effects 
of trimming can be hard to predict (Faircloth, 2016), so we explored both options for 
our data. We also performed phylogenetic analyses with varying amounts of data (60%, 
75% and 85% of UCEs that are presented in the completed alignment matrices) to 
explore the potentially strong effect of missing data on phylogenetic reconstruction 
(Hosner et al., 2016; Streicher et al., 2016). 
 
2.4. Phylogenetic analyses 
We analyzed the Loricariidae dataset using maximum-likelihood (ML; RAxML 
v8; Stamatakis, 2014) and Bayesian (BI; ExaBayes v1.4; Aberer et al., 2014) 
approaches. For ML analyses, we compared the total data-partitioning schemes with 
models chosen by Partition Finder (Lanfear et al., 2012) using kmeans algoritmus 
(Frandsen et al., 2015) and the GTR+G model applied to the total matrix with no 
partitions. The RAxML analysis was performed on 60%, 75% and 85% of total 
complementary matrix using partitions and no partitions (see Table 1 for all analysis). 
We also analyzed different matrices to compare edge and internal alignment trimming 
(see Table 1 for all matrix schemes). The ML analysis of the concatenated alignment 
	 25	
was performed using the autoMRE function for the extended majority-rule consensus 
tree criterion (available in RAxML v8; Stamatakis, 2014) to assess bootstrap support for 
individual nodes. This option allows the bootstrap convergence test to be conducted, 
which determines if BS replicates sufficient for getting stable support values have been 
computed (Pattengale et al., 2010). The best tree search was performed under the 
parameter –N = 5 which specifies the number of alternative runs on distinct parsimony 
starting trees. 
The Bayesian analysis of the concatenated alignment was performed using 
ExaBayes (Aberer et al., 2014). We performed two independent runs (each with two 
chains [one cold and hot chain] of 1,000,000 generations on our concatenated UCE 
matrix using the GTR+G model for different complementary matrices and alignment 
trimming analyses (see Table 1). Tree space was sampled every 100 generations to yield 
a final total of 10,000 trees. Parameter estimates and ESS values were visualized in 
Tracer v 1.6 (Rambaut et al., 2014) and the last 2,500 trees were sampled after checking 
results for convergence. This allowed us to visualize the log of posterior probability 
within and between independent runs and to ensure that the average standard deviation 
of split frequencies was <1%, effective sample sizes (ESS) were >200, and the potential 
scale reduction factor for estimated parameters was approximately 1.0. We generated 
the 50% most credible set of trees from the posterior distribution of possible topologies 
using the consensus algorithm of ExaBayes (burn-in: 25%; thinning: 500). 
 
2.5. Time calibration 
An uncorrelated relaxed molecular clock (lognormal) was estimated using 
BEAST v.1.8.2 (Drummond et al., 2012). BEAST is unable to handle a data matrix 
>20,000 bp in length, so we down-sampled our dataset to generate a 90% complete edge 
	 26	
trimming alignment matrix comprising 19,846 bp and 187 UCEs (Table 1). This matrix 
comprises UCE loci that are present in at least 90% of taxa and has much less missing 
data compared to the 60%, 75% and 85% complementary matrixes. The best ML tree 
generated from the 75% complete edge trimming alignment matrix was used as a fixed 
topology in the Bayesian search that estimated only the age of each node. 
We included two calibration points to constrain divergence dates in our 
Loricariidae tree. The first calibration point was implemented as a normally distributed 
prior, with an age offset of 120 million years and a standard deviation of 14 million 
years. These date-estimate parameters were selected to match our current understanding 
of the timing of siluriform diversification. Fossil evidence and previous fossil-calibrated 
molecular clock analyses of Siluriformes (Lundberg, 1993; Sullivan et al., 2006; 
Lundberg et al., 2007) indicate an origin for the order during the Lower Cretaceous 
(145–100 Ma). This prior was therefore used to constrain the root age of our tree. 
The second calibration point was based on the callichthyid fossil Corydoras 
revelatus Cockerell 1925, which is the oldest known loricarioid fossil assignable to an 
extant taxon. Cockerell (1925) described the fossil from the Maíz Gordo Formation 
(Giudici and Gascon, 1982) deposited in the lower Eocene between about 56–52 
millions of years ago (MYA) (Del Papa and Salfity, 1999). For this calibration, we 
implemented a lognormal prior offset to 55 MYA with a mean and standard deviation of 
0.5 for the origin of the genus Corydoras (node including C. aeneus and Aspidoras 
fuscoguttatus). 
We used a Birth–Death model prior for diversification likelihood values. The 
BEAST analysis was conducted under a HKY model of molecular evolution for the 
entire matrix and was run for 50 million generations with tree space sampled every 
1,000th generation. Stationarity and sufficient mixing of parameters (ESS >200) was 
	 27	
checked using Tracer v1.6 (Rambaut et al., 2014). A consensus tree was built using 
TreeAnnotator v1.8.2. All clade-age estimates are presented as the mean plus 95% 
highest posterior density (HPD) values. 
 
3. Results 
Sequencing and analyses yielded a total edge trimming matrix comprising756,476 base pairs (bp), 2,482 UCE loci for 171 specimens (163 Loricariidae and eight 
outgroup taxa). The total matrix included 79,682,706 characters, of which 61,797,668 
were nucleotides and 17,885,038 (22.4% of total) were missing data. Mean locus length 
after alignment and trimming was 304 nucleotides (range: 100–1,223). Phylogenies 
inferred from the concatenated datasets were resolved with high statistical support for 
each node and exhibited similar topologies regardless of matrix completeness (60%: 
1,454 loci, 494,488 bp; 75%: 1,041 loci, 328,330 bp; 85%: 471 loci, 102,064 bp), the 
method of analysis (ML and BI), and whether or not we performed partitions among the 
UCEs. 
Therefore, we base our discussion on ML and BI analyses (Figs. 5–8) of the 
edge trimmed, 75% complete concatenated matrix with no partitioning of UCEs. These 
phylogenies had strong support for nearly all nodes (BS >95% in ML analysis, PP 
>0.99) except for 13 nodes in which bootstrap values fell between 50–95% (indicated 
by arrows in Fig. 5). 
 
3.1. Basal relationships 
Both maximum likelihood and Bayesian phylogenetic analyses strongly 
supported the monophyly of Loricariidae, Fig. 5 (BS > 95%, BI = 1). Our results also 
strongly supported the monophyly of four subfamilies (BS > 95%, BI = 1): Delturinae, 
	 28	
Loricariinae, Hypostominae (including taxa formerly placed in Ancistrinae and 
Chaetostominae) and Hypoptopomatinae (including taxa formerly placed in 
Neoplecostominae and Otothyrinae). The family-level status of Rhinelepinae was 
supported based on the position of a single representative (Pseudorinelepis sp.). The 
subfamily Delturinae, represented by Delturus angulicauda (Steindachner, 1877) and D. 
carinotus (La Monte, 1933), was found to be sister to all other loricariids analyzed in 
concordance with previous morphological (Armbruster, 2004a) and molecular (Lujan et 
al., 2015a) hypotheses. The second lineage to diverge inside Loricariidae was the 
subfamily Rhinelepinae followed by Loricariinae sister to Hypostominae + 
Hypoptopomatinae (BS > 95%, BI = 1). 
 
3.2. Relationships within subfamily Loricariinae 
Our analyses (Fig. 6) supported a topology for the subfamily Loricariinae that 
was similar to the recent multilocus phylogeny (Covain et al. 2016). The two tribes, 
Harttiini (represented by Harttia loricariformis Steindachner 1877, H. gracilis 
Oyakawa 1993 and Cteniloricaria platystoma (Günther 1868); missing Harttiella) and 
Loricariini, were strongly monophyletic in our analysis (BS > 95%, PP = 1). Within 
Loricariini, the two subtribes (sensu Covain et al. 2016), Farlowellina and Loricariina, 
were monophyletic in our analysis. Farlowellina (BS > 95%, PP = 1) was represented 
by four genera in our study (Farlowella, Lamontichthys, Sturisoma and 
Sturisomatichthys) compared to the six assigned to that group by Covain et al. (2016; 
Aposturisoma and Pterosturisoma added). Loricariina (BS > 95%, PP = 1) was 
represented by 13 out of the 23 genera previously assigned to that group. A notable 
absence from our study is Metaloricaria, a genus previously considered a monotypic 
	 29	
subtribe (Metaloricariina) in Harttiini (Isbrücker, 1980) or the first lineage to split in 
Loricariina (Covain et al., 2016). 
The earliest lineage to diverge in our Loricariina is Dasyloricaria, a genus that 
occupied a similarly basal position in the study by Covain et al. (2016). In our 
phylogeny, the remaining taxa in Loricariina are divided among three clades: 
Rineloricaria sister to Loricariichthys group + the Loricaria–Pseudohemiodon group 
(sensu Covain et al., 2016). The first genus to diverge within the Loricariichthys group 
was Reganella (not examined by Covain et al., 2016), followed by Loricariichthys sister 
to Limatulichthys + Pseudoloricaria. The only genus of the Loricariichthys group 
missing from our analysis was Hemiodontichthys, which Covain et al. (2016) found to 
be sister to Limatulichthys + Pseudoloricaria. Within the Loricaria–Pseudohemiodon 
group, Spatuloricaria was sister to all remaining taxa as in Covain et al. (2016). Our 
results are also consistent with the two subgroups proposed by Covain et al. (2016): the 
Loricaria group (Brochiloricaria, Loricaria, Paraloricaria) and the Pseudohemiodon 
group (Apistoloricaria, Crossoloricaria, Planiloricaria, Pseudohemiodon, 
Rhadinoloricaria). 
 
3.3. Relationships within subfamily Hypostominae 
Hypostominae was monophyletic in our analysis (BS > 95%, PP = 1; Fig. 7) and 
internal relationships within this subfamily differed only slightly from the most 
comprehensive previous phylogenetic appraisal by Lujan et al. (2015a). Our analysis 
resolved hypostomins into the same nine subclades identified in Lujan et al. (2015a). At 
this level, the only difference is our identification of a tenth clade for a single taxon, 
Panaque cochliodon (Steindachner, 1879). Unlike Lujan et al. (2015a), our analysis did 
	 30	
not group Panaque with the Hemiancistrus Clade (e.g., Baryancistrus, Parancistrus, 
Spectracanthicus); however, support was low for either placement of Panaque. 
Within Hypostominae, only six nodes had moderate support (i.e., BS = 50% - 
95%, PP = 1), those describing the relationships between the Lithoxus Clade and 
remaining clades, between the Panaque Clade and other members of the Hypostominae, 
between Ancistrus ranunculus Muller, Rapp Py-Daniel & Zuanon 1994 and A. 
cryptophthalmus Reis 1987, between Peckoltia braueri (Eigenmann 1912), P. compta 
de Oliveira, Zuanon, Rapp Py-Daniel & Rocha 2010 and other members of the genus 
Peckoltia, and between Hemiancistrus cerrado Souza, Melo, Chamon & Armbruster 
2008, Hypostomus melanephelis Zawadzki, Oliveira, de Oliveira & Rapp Py-Daniel 
2015 and other members of the genus Hypostomus. 
Within Hypostominae, the Chaetostoma Clade, represented in our analysis by 
the genera Chaetostoma and Dolichancistrus, was the first group to diverge, followed 
by a Pseudancistrus Clade, represented by a single species, P. zawadzkii Silva, Roxo, 
Britzke & Oliveira 2014. The Lithoxus Clade was strongly monophyletic (BS > 95%, 
PP = 1) and represented by two species: Exastilithoxus hoedemani Isbrücker & Nijssen 
1985 and a recently described species of Lithoxus from the Jari basin in Brazil. The 
Lithoxus Clade was sister to the ‘Pseudancistrus’ Clade, represented by a single species 
‘Pseudancistrus’ pectegenitor Lujan, Armbruster & Sabaj-Pérez 2007. 
The tribe Ancistrini sensu Lujan et al. (2015a) was represented in our analysis 
by Ancistrus, Guyanancistrus, Hopliancistrus, Lasiancistrus, Pseudolithoxus, and the 
recently described Araichthys (Zawadzki et al., 2016). This clade was found to be 
strongly supported (BS > 95%, PP = 1). The Acanthicus Clade was represented in our 
analysis by the genera Leporacanthicus, Megalancistrus and Pseudacanthicus. This 
clade was also strongly supported (BS > 95%, PP = 1). 
	 31	
Our results return the Peckoltia Clade with Panaqolus, Peckoltia, Hypancistrus, 
Scobinancistrus, Aphanotorulus (senior synonym of Squaliforma) and 
Spectracanthicus. This clade was strongly supported and sister to the tribe 
Hypostomini, which also received high support (BS > 95%, PP = 1) and comprised the 
genera Pterygoplichthys, Hypostomus and two species of ‘Hemiancistrus’ (‘H.’ 
fuliginosus Cardoso & Malabarba 1999 and ‘H.’ punctulatus Cardoso & Malabarba 
1999). 
 
3.4. Relationships within subfamily Hypoptopomatinae 
Our results identify Hypoptopoma + Acestridium as the first clade to diverge 
from all remaining hypoptopomatins (Fig. 8). The next clade to diverge was composed 
by five species of Otocinclus. Remaining hypoptopomins were distributed among nine 
clades. The first to diverge was the Corumbataia Clade, a newly proposed group 
comprising the genera Corumbataia (including Gymnotocinclus as a junior synonym), 
Curculionichthys, Nannoplecostomus andMicroplecostomus. All nodes within the 
Corumbataia Clade have strong statistical support (BS > 95%, PP = 1). The 
Corumbataia Clade contains two subclades, Nannoplecostomus + Microplecostomus 
(two monotypic genera) and Curculionichthys + Corumbataia. Our analysis included 
two species originally described in Gymnotocinclus, G. anosteos Carvalho, Lehmann A. 
& Reis 2008a (type species) and G. canoeiro Roxo, Silva, Ochoa & Zawadzki 2017. 
However, our results supported a sister-group relationship between G. anosteos and C. 
cuestae Britski 1997 (type species of Corumbataia). Therefore, we reassign G. anosteos 
and G. canoeiro to Corumbataia (Table 2). 
Above the Corumbataia Clade, the next lineage to diverge is the monophyletic 
Schizolecis Clade (BS > 95%, PP = 1) represented by Pseudotothyris obtusa (Miranda 
	 32	
Ribeiro 1911) and the monotypic Schizolecis. The sister relationship between the 
Schizolecis Clade and all remaining members of Hypoptopomatinae was only 
moderately supported (BS = 50% - 95%, PP = 1). 
Above the Schizolecis Clade, the last two lineages were the Neoplecostomus 
Clade and a clade comprising Hisonotus, Microlepidogaster, Rhinolekos and three 
potentially new genera. The Neoplecostomus Clade appeared monophyletic in our 
analysis (BS > 95%, PP = 1) comprising Isbrueckerichthys, Kronichthys, 
Neoplecostomus, Pareiorhina, Pareiorhaphis, Plesioptopoma (monotypic) and 
Pseudotocinclus. Our analysis, however, failed to support the monophyly of 
Pareiorhina and Neoplecostomus (represented herein by two and three species, 
respectively). The type species of Pareiorhina (P. rudolphi (Miranda Ribeiro 1911)) 
was sister to Pseudotocinclus tietensis (Ihering 1907) (its junior synonym, P. 
intermedius being the type species of Pseudotocinclus). On the other hand, 
‘Pareiorhina’ carrancas Bockmann & Ribeiro 2003 was sister to the monotypic 
Plesioptopoma. Although our analysis did not include the type species of 
Neoplecostomus (N. microps), it supported a close relationship between N. bandeirante 
Roxo, Oliveira & Zawadzki 2012 and N. franciscoensis Langeani 1990 with that lineage 
sister to a large clade comprising Neoplecostomus ribeirensis Langeani 1990, 
Isbrueckerichthys saxicola Jerep, Shibatta, Pereira & Oyakawa 2006, Kronichthys 
subteres Miranda Ribeiro 1908, and two species of Pareiorhaphis. All clades inside 
Neoplecostomini were resolved with strong statistical support (BS > 95%, PP = 1), 
except for the sister relationship between P. splendens (Bizerril 1995) and P. parmula 
Pereira 2005 (BS = 50 - 95%, PP = 1). Athough our topology for the Neoplecostomus 
Clade is fairly-well resolved and largely consistent with previous molecular studies 
(Chiachio et al., 2008; Cramer et al., 2011; Roxo et al., 2014; Lujan et al., 2015a; Silva 
	 33	
et al., 2016), it significantly differs from the recent morphology-based phylogeny 
(Pereira & Reis, 2017). 
The last clade in Hypoptopomatinae includes three nominal genera (Hisonotus, 
Microlepidogaster, Rhinolekos) traditionally recognized in the subfamily Otothyrinae 
(e.g., Cramer et al., 2011; Roxo et al., 2014), plus three lineages treated herein as “New 
Genus 1, 2 and 3”, each with high statistical support (BS > 95%, PP = 1). The “New 
Genus 1” contains the species ‘Hisonotus’ bocaiuva Roxo, Silva, Oliveira & Zawadzki 
2013, ‘Parotocinclus’ sp. n. 1 and ‘Parotocinclus’ sp. n. 2; the “New Genus 2” contains 
the species ‘Hisonotus’ acuen Silva, Roxo & Oliveira 2014, ‘H.’ chromodontus Britski 
& Garavello 2007, ‘Parotocinclus’ sp. n. 3 and ‘P.’ aripuanensis Garavello 1988; the 
“New Genus 3” is monotypic with a specimen from the lower Rio São Francisco in 
Sergipe, Brazil. 
Our analysis grouped Microlepidogaster longicolla Calegari & Reis 2010 with 
the type species of Rhinolekos (R. britskii Martins & Langeani 2011a) instead of the 
type species of Microlepidogaster (M. perforata Eigenmann & Eigenmann 1889a); 
therefore we consider that species to be valid as Rhinolekos longicolla (Calegari & Reis 
2010), new combination. Our phylogeny also support the reallocation of 
Eurycheilichthys luisae Reis 2017 into the genus Hisonotus (Table 2). Furthermore, the 
type species of Epactionotus (E. bilineatus Reis & Schaefer 1998) and Otothyropsis (O. 
marapoama Ribeiro, Carvalho & Melo 2005) were placed in a strongly supported clade 
with the type species of Hisonotus (H. notatus Eigenmann & Eigenmann 1889b), 
justifying the synonymization of both Epactionotus Reis & Schaefer 1998 and 
Otothyropsis Ribeiro, Carvalho & Melo 2005 with Hisonotus Eigenmann & Eigenmann 
1889b (Table 2). 
 
	 34	
3.5. Timing of loricariid diversification 
Time tree inferred from the concatenated dataset was based in a 90% 
complementary matrix (187 loci). The mean substitution rate of our time tree was 
estimated at 8.6E -4% per MY. The family Loricariidae (excluding subfamily 
Lithogeninae, not examined), was estimated to have originated during the Late 
Cretaceous, approximately 65.4 MYA (46.4–86.6 MYA 95% HPD; Fig. 9). The first 
group to diverge inside Loricariidae was the subfamily Delturinae, and our analysis 
suggested that this group originated during the Paleocene, approximately 58.6 MYA 
(41.2–77.6 MYA 95% HPD). All remaining subfamilies (Figs. 10–12) were found to 
have originated during the Eocene, with Rhinelepinae originating approximately 46.6 
MYA (33.3–61.8 MYA 95% HPD), Loricariinae approximately 42.4 MYA (30.1–56.2 
MYA 95% HPD) and Hypostominae and Hypoptopomatinae originating approximately 
35.8 MYA (24.8–47.9 MYA 95% HPD). 
 
4. Discussion 
4.1. Loricariidae 
Our phylogenetic study corroborates the monophyletic status of the family 
Loricariidae in accordance with previous molecular (Roxo et al., 2014, 2017; Lujan et 
al., 2015a; Covain et al., 2016; Silva et al., 2016) and morphological studies 
(Armbruster, 2004a, 2008). Additionaly, our study supports the monophyly of five 
loricariid subfamilies: Delturinae, Hypoptopomatinae, Hypostominae, Loricariinae and 
Rhinelepinae. However, relationships within the subfamilies differ from those of 
previous molecular and morphological studies, especially within the subfamily 
Hypoptopomatinae and Neoplecostominae (Martins et al. 2014; Pereira & Reis, 2017). 
Although our taxon sampling is far to be complete, we do present the first molecular 
	 35	
phylogenetic treatment for several loricariid taxa and the first genome-scale 
phylogenetic analysis for the entire family. 
 
4.2. Subfamily Loricariinae 
Our results are similar to the multilocus phylogeny (Covain et al. 2016) who 
analyzed one nuclear (f-rtn4r) and three mitochondrial (12S, 16S and tRNAVal) loci. 
Both studies supported the monophyly of the subfamily Loricariinae, as well as its two 
tribes Harttiini and Loricariini. Both studies also supported two monophyletic subtribes 
within Loricariini: Farlowellina and the species-rich Loricariina. 
 
4.2.1. Harttiini 
According to Covain et al. (2016), the tribe Harttiini comprises the genera 
Harttia, Cteniloricaria and Harttiella and excludes members of Farlowellina as 
hypothesized by Rapp Py-Daniel (1997). Our analysis, which included Harttia and 
Cteniloricaria, corroborates the exclusion of Farlowellina from Harttiini. 
 
4.2.2. Subtribe Farlowellina 
Within Farlowellina the four analyzed genera were monophyletic (i.e., 
Farlowella, Sturisomatichthys, Sturisoma and Lamontichthys). Relationships among 
members of Farlowellina were also similar to those in Covain et al. (2016), where 
Lamontichthys was the first group to diverge within Farlowellina, Farlowella was s,ister 
to Sturisomatichthys, and this last group was sister to Sturisoma. 
Both Sturisoma and Sturisomatichthys were paraphyletic and structured by 
geographic region in Covain et al. (2016). Therefore, these authors restricted species of 
Sturisoma to the cis-Andean region and proposed that Sturisomatichthyscomprise all 
	 36	
trans-Andean species of Sturisoma and Sturisomatichthys. In Armbruster (2004a, 2008) 
the genera Sturisoma, Sturisomatichthys and Lamontichthys were closely related to 
species of the genus Harttia, a hypothesis rejected by the present and previous 
molecular works (Montoya-Burgos et al., 1998; Covain et al., 2008; Rodriguez et al., 
2011; Lujan et al., 2015a; Covain et al., 2016). 
 
4.2.3. Sub-tribe Loricariina 
We analyzed thirteen genera in the species-rich sub-tribe Loricariina. 
Dasyloricaria was the first group to diverge inside Loricariina; however, we did not 
analyze samples of Metaloricaria – the first group to diverge in Covain et al. (2016) 
followed by Fonchiiloricaria plus Dasyloricaria. 
The second lineage to diverge within Loricariina was Rineloricaria, the most 
species rich genus of the Loricariinae (encompassing 63 valid species, Eschmeyer, 
2017, and numerous undescribed species). Corroborating previous studies, Ixinandria 
steinbachi Regan 1906 (currently valid as Rineloricaria steinbachi) was closely related 
to species of the genus Rineloricaria. However, the genera Hemiloricaria, 
Fonchiiichthys, and Leliella were omitted from our analysis. 
Our results for the Loricariichthys group (including Limatulichthys, 
Loricariichthys and Pseudoloricaria) also largely corroborated those of Covain et al. 
(2016). However, Hemiodontichthys and Furcodontichthys (Covain and Fisch-Muller, 
2007; Covain et al., 2016) were omitted from our analysis, and we found that the 
monotypic genus Reganella was sister to the Loricariichthys group. This contrasts with 
the hypothesis of Covain and Fisch-Muller (2007), and Covain et al. (2016) who found 
Reganella to be included within the Pseudohemiodon group. 
	 37	
The genus Spatuloricaria was sister to Loricaria and the Pseudohemiodon 
group, corroborating the work of Covain et al. (2016). However, relationships among 
members of the Pseudohemiodon group differed from those of Covain et al. (2016). In 
the present study, Pseudohemiodon was sister to Rhadinoloricaria and these two genera 
were sister to Crossoloricaria. In our results, Planiloricaria was the first lineage to 
diverge within the Pseudohemiodon group, whereas in Covain et al. (2016) the first 
group to diverge was the trans-Andean Crossoloricaria. Within the Loricaria group, 
our results recovered the genus Loricaria as sister to Proloricaria, which is consistent 
with the results of Covain et al. (2016), with the exception that the genera 
Brochiloricaria and Paraloricaria were also closely related to Proloricaria in Covain et 
al. (2016) but were both omitted from our analysis. 
 
4.3. Subfamily Hypostominae 
Our results for relationships among Hypostominae genera largely corroborate 
those of Lujan et al. (2015a). Like other previous molecular studies (Montoya-Burgos et 
al., 1998; Cramer et al., 2011; Covain and Fisch-Muller, 2012), our results exclude the 
genus Pseudorinelepis from Hypostominae and support the placement of this genus in 
the separate subfamily Rhinelepinae (along with the closely related genus Rhinelepis), 
with this subfamily being sister to the clade comprising Loricariinae + 
(Hypoptopomatinae + Hypostominae). Our results also largely corroborate those of 
Lujan et al. (2015a) by finding ten tribe-level lineages within Hypostominae (Lujan et 
al., 2015a, found nine). The main difference between our results and those of Lujan et 
al. (2015a) is that we found the Panaque Clade to have branched off separately from the 
Hemiancistrus Clade, whereas Lujan et al. (2015a) found these lineages to be sister to 
each other. 
	 38	
 
4.3.1. Chaetostoma Clade 
The first lineage to diverge within Hypostominae was the Chaetostoma Clade. 
This clade was represented in our analyses by the genera Chaetostoma and 
Dolichancistrus. Lujan et al. (2015a, b) also found these genera to be included in the 
Chaetostoma Clade, along with Andeancistrus, Cordylancistrus, Leptoancistrus and 
Transancistrus. These molecular results are largely congruent with the finding by 
Armbruster (2004a, 2008) of strong morphological support for monophyly of the same 
Chaetostoma Clade; however, the latter studies found the Chaetostoma Clade to be 
closely related to Lithoxus and Exastilithoxus. Our results and those of Lujan et al. 
(2015a) reject this hypothesis. 
 
4.3.2. Pseudancistrus Clade 
As in Lujan et al. (2015a) the Pseudancistrus Clade (comprising only the genus 
Pseudancistrus) was the second lineage to diverge within Hypostominae. It was 
represented in our analyses by only the species P. zawadzkii (Silva et al., 2014b), 
although congeners include P. nigrescens Eigenmann 1912, Pseudancistrus L17, P. 
corantijniensis de Chambrier & Montoya-Burgos 2008, P. depressus (Günther 1868), P. 
barbatus (Valenciennes 1840 in Cuvier and Valenciennes, 1840) and Pseudancistrus sp. 
1 (sensu Covain and Fisch-Muller, 2012; Silva et al., 2014b). De Chambrier and 
Montoya-Burgos (2008) published the first phylogeny of ‘true’ Pseudancistrus species 
based on mitochondrial D-loop data, and found that P. corantijniensis, P. nigrescens, P. 
depressus and P. barbatus formed a well-supported clade. All these species share some 
derived morphological features in common, such as presence of hypertrophied 
	 39	
odontodes along the snout and absence of evertible cheek plates (De Chambrier and 
Montoya-Burgos, 2008; Covain and Fisch-Muller, 2012; Silva et al., 2014b). 
 
4.3.3. Lithoxus Clade 
The Lithoxus Clade (sensu Armbruster, 2004a, 2008, and Lujan et al., 2015a) 
comprises the genera Lithoxus and Exastilithoxus. Species of this clade have only been 
studied in a molecular phylogenetic context by Covain and Fisch-Muller (2012), who 
examined three Lithoxus species and found them to be monophyletic, and by Lujan et 
al. (2015a), who analyzed five Lithoxus species and several Exastilithoxus species, 
finding that a monophyletic Exastilithoxus made Lithoxus paraphyletic. Our study 
examined only one new species of Lithoxus from the eastern limit of the genus’ 
distribution in the Jari basin, Brazil and found it to be sister to Exastilithoxus 
hoedemani. 
 
4.3.4. ‘Pseudancistrus’ Clade 
The ‘Pseudancistrus’ Clade (sensu Lujan et al., 2015a), represented in our 
analysis by the single species ‘Pseudancistrus’ pectegenitor, was found to be sister to 
the Lithoxus Clade. This result differs from Lujan et al. (2015a), who found 
‘Pseudancistrus’ pectegenitor to be strongly supported as sister to ‘Pseudancistrus’ 
sidereus Armbruster 2004b, which together formed a clade that was weakly supported 
as sister to the Acanthicus Clade + (Hemiancistrus Clade + (Hypostomini + Peckoltia 
Clade)). Our results are consistent with those of Covain and Fisch-Muller (2012) and 
Lujan et al. (2015a) in indicating that ‘Pseudancistrus’ pectegenitor should be excluded 
from the true Pseudancistrus (i.e., the Pseudancistrus barbatus group) and placed in a 
new genus of its own or with ‘Pseudancistrus’ sidereus. 
	 40	
 
4.3.5. Ancistrini 
Morphology based phylogenetic and systematic analyses have traditionally 
grouped loricariid species having enlarged and highly evertible cheek odontodes 
together in either the subfamily Ancistrinae (Isbrücker, 1980) or tribe Ancistrini 
(Armbruster, 2004a, 2008). However, molecular analyses (Montoya-Burgos et al., 1998, 
1998; Cramer et al., 2011; Lujan et al., 2015a) have consistently rejected monophyly of 
these taxa, finding instead that the entire evertible cheek spine mechanism has been lost 
several times, creating a suite of highly homoplastic characters that strongly influence 
morphology-based analyses. To resolve this, Lujan et al. (2015a) restricted Ancistrini to 
ten genera that are mostly closely related to the genus Ancistrus. Our analyses found the 
Ancistrini Clade to comprise the genera Ancistrus, Lasiancistrus, Pseudolithoxus,