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 language | English |
|---|---|
| Pages (from-to) | 137-150 |
| Number of pages | 14 |
| Journal | Molecular Phylogenetics and Evolution |
| Volume | 124 |
| DOIs | |
| Publication status | Published - 1 Jul 2018 |
| Externally published | Yes |
Keywords
- Neotropical primates
- Phylogeny
- Single nucleotide polymorphisms (SNPs)
- Species tree
- Ultraconserved elements (UCEs)
Cite this
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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 journal › Article › Research › peer-review
TY - JOUR
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.
PY - 2018/7/1
Y1 - 2018/7/1
N2 - 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.
AB - 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.
KW - Neotropical primates
KW - Phylogeny
KW - Single nucleotide polymorphisms (SNPs)
KW - Species tree
KW - Ultraconserved elements (UCEs)
UR - http://www.scopus.com/inward/record.url?scp=85044169918&partnerID=8YFLogxK
U2 - 10.1016/j.ympev.2018.02.023
DO - 10.1016/j.ympev.2018.02.023
M3 - Article
C2 - 29545109
AN - SCOPUS:85044169918
VL - 124
SP - 137
EP - 150
JO - Molecular Phylogenetics and Evolution
JF - Molecular Phylogenetics and Evolution
SN - 1055-7903
ER -