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

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.

The complete mitochondrial genome of Sapajus flavius（Blonde Capuchin）

“…Bos taurus was used as an outgroup. As it turns out that Sapajus flavius is closest to Sapajus xanthosternos, basically consistent with the existing research (Finstermeier et al 2013;Lima et al 2018) (Figure. 1).…”

Sperm Morphology in Neotropical Primates

“…For species with available values of HL and HW, we composed a scale diagram of the head and the anterior midpiece region of the spermatozoon. The sperm morphometric data in the database mentioned above were superimposed on a phylogeny obtained from Dumas and Mazzoleni [33] with modifications to include all the species represented in the literature [34,35,36,37,38,39].…”

“…Evolution of sperm morphology and morphometry. Mean sperm measurements were superimposed on a phylogeny of neotropical primates (phylogeny from Dumas and Mazzoleni [33] with modifications [34,35,36,37,38,39]). When available, a scale diagram and/or microphotograph of the sperm head and proximal portion of the midpiece were provided for each species.…”

Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression

“…Although introgression once was thought to be relatively rare (especially among animals [23]), genomic studies have uncovered widespread patterns of recent introgression across the tree of life [24]. Evidence for recent or ongoing gene flow is especially common among the primates (e.g., [9,[25][26][27]), sometimes with clear evidence for adaptive introgression (e.g., [28][29][30]). Whether widespread gene flow among primates is emblematic of their initial radiation (which began 60 to 75 mya [13,[31][32][33]) or is a consequence of current conditions-which include higher environmental occupancy and more secondary contactremains an open question [34].…”