A phylogenomic perspective on the robust capuchin monkey (Sapajus) radiation: First evidence for extensive population admixture across South America

Marcela G.M. Lima, José de Sousa e. Silva-Júnior, David Černý, Janet C. Buckner, Alexandre Aleixo, Jonathan Chang, Jimmy Zheng, Michael E. Alfaro, Amely Martins, Anthony Di Fiore, Jean P. Boubli, Jessica W. Lynch Alfaro

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2 Citations (Scopus)

Abstract

Phylogenetic relationships amongst the robust capuchin monkeys (genus Sapajus) are poorly understood. Morphology-based taxonomies have recognized anywhere from one to twelve different species. The current IUCN (2017) classification lists eight robust capuchins: S. xanthosternos, S. nigritus, S. robustus, S. flavius, S. libidinosus, S. cay, S. apella and S. macrocephalus. Here, we assembled the first phylogenomic data set for Sapajus using ultra-conserved elements (UCEs) to reconstruct a capuchin phylogeny. All phylogenomic analyses strongly supported a deep divergence of Sapajus and Cebus clades within the capuchin monkeys, and provided support for Sapajus nigritus, S. robustus and S. xanthosternos as distinct species. However, the UCE phylogeny lumped the putative species S. cay, S. libidinosus, S. apella, S. macrocephalus, and S. flavius together as a single widespread lineage. A SNP phylogeny constructed from the UCE data was better resolved and recovered S. flavius and S. libidinosus as sister species; however, S. apella, S. macrocephalus, and S. cay individuals were recovered in two geographic clades, from northeastern and southwestern Amazon, rather than clustering by currently defined morphospecies. STRUCTURE analysis of population clustering revealed widespread admixture among Sapajus populations within the Amazon and even into the Cerrado and Atlantic Forest. Difficulty in assigning species by morphology may be a result of widespread population admixture facilitated through frequent movement across major rivers and even ecosystems by robust capuchin monkeys.

Original languageEnglish
Pages (from-to)137-150
Number of pages14
JournalMolecular Phylogenetics and Evolution
Volume124
DOIs
Publication statusPublished - 1 Jul 2018
Externally publishedYes

Keywords

  • Neotropical primates
  • Phylogeny
  • Single nucleotide polymorphisms (SNPs)
  • Species tree
  • Ultraconserved elements (UCEs)

Cite this

Lima, Marcela G.M. ; Silva-Júnior, José de Sousa e. ; Černý, David ; Buckner, Janet C. ; Aleixo, Alexandre ; Chang, Jonathan ; Zheng, Jimmy ; Alfaro, Michael E. ; Martins, Amely ; Di Fiore, Anthony ; Boubli, Jean P. ; Lynch Alfaro, Jessica W. / A phylogenomic perspective on the robust capuchin monkey (Sapajus) radiation : First evidence for extensive population admixture across South America. In: Molecular Phylogenetics and Evolution. 2018 ; Vol. 124. pp. 137-150.
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abstract = "Phylogenetic relationships amongst the robust capuchin monkeys (genus Sapajus) are poorly understood. Morphology-based taxonomies have recognized anywhere from one to twelve different species. The current IUCN (2017) classification lists eight robust capuchins: S. xanthosternos, S. nigritus, S. robustus, S. flavius, S. libidinosus, S. cay, S. apella and S. macrocephalus. Here, we assembled the first phylogenomic data set for Sapajus using ultra-conserved elements (UCEs) to reconstruct a capuchin phylogeny. All phylogenomic analyses strongly supported a deep divergence of Sapajus and Cebus clades within the capuchin monkeys, and provided support for Sapajus nigritus, S. robustus and S. xanthosternos as distinct species. However, the UCE phylogeny lumped the putative species S. cay, S. libidinosus, S. apella, S. macrocephalus, and S. flavius together as a single widespread lineage. A SNP phylogeny constructed from the UCE data was better resolved and recovered S. flavius and S. libidinosus as sister species; however, S. apella, S. macrocephalus, and S. cay individuals were recovered in two geographic clades, from northeastern and southwestern Amazon, rather than clustering by currently defined morphospecies. STRUCTURE analysis of population clustering revealed widespread admixture among Sapajus populations within the Amazon and even into the Cerrado and Atlantic Forest. Difficulty in assigning species by morphology may be a result of widespread population admixture facilitated through frequent movement across major rivers and even ecosystems by robust capuchin monkeys.",
keywords = "Neotropical primates, Phylogeny, Single nucleotide polymorphisms (SNPs), Species tree, Ultraconserved elements (UCEs)",
author = "Lima, {Marcela G.M.} and Silva-J{\'u}nior, {Jos{\'e} de Sousa e.} and David Čern{\'y} and Buckner, {Janet C.} and Alexandre Aleixo and Jonathan Chang and Jimmy Zheng and Alfaro, {Michael E.} and Amely Martins and {Di Fiore}, Anthony and Boubli, {Jean P.} and {Lynch Alfaro}, {Jessica W.}",
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Lima, MGM, Silva-Júnior, JDSE, Černý, D, Buckner, JC, Aleixo, A, Chang, J, Zheng, J, Alfaro, ME, Martins, A, Di Fiore, A, Boubli, JP & Lynch Alfaro, JW 2018, 'A phylogenomic perspective on the robust capuchin monkey (Sapajus) radiation: First evidence for extensive population admixture across South America', Molecular Phylogenetics and Evolution, vol. 124, pp. 137-150. https://doi.org/10.1016/j.ympev.2018.02.023

A phylogenomic perspective on the robust capuchin monkey (Sapajus) radiation : First evidence for extensive population admixture across South America. / Lima, Marcela G.M.; Silva-Júnior, José de Sousa e.; Černý, David; Buckner, Janet C.; Aleixo, Alexandre; Chang, Jonathan; Zheng, Jimmy; Alfaro, Michael E.; Martins, Amely; Di Fiore, Anthony; Boubli, Jean P.; Lynch Alfaro, Jessica W.

In: Molecular Phylogenetics and Evolution, Vol. 124, 01.07.2018, p. 137-150.

Research output: Contribution to journalArticleResearchpeer-review

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T1 - A phylogenomic perspective on the robust capuchin monkey (Sapajus) radiation

T2 - First evidence for extensive population admixture across South America

AU - Lima, Marcela G.M.

AU - Silva-Júnior, José de Sousa e.

AU - Černý, David

AU - Buckner, Janet C.

AU - Aleixo, Alexandre

AU - Chang, Jonathan

AU - Zheng, Jimmy

AU - Alfaro, Michael E.

AU - Martins, Amely

AU - Di Fiore, Anthony

AU - Boubli, Jean P.

AU - Lynch Alfaro, Jessica W.

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KW - Neotropical primates

KW - Phylogeny

KW - Single nucleotide polymorphisms (SNPs)

KW - Species tree

KW - Ultraconserved elements (UCEs)

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