Reproductive endocrinology of wild female woolly monkeys (Lagothrix lagotricha poeppigii) during puberty, ovarian cyclicity, and pregnancy.

Behavioral observations can provide clues about female reproductive status. However, the study of the endocrine dynamics that underlie processes such as puberty, ovulation, conception, and gestation, may help increase our understanding of female reproductive biology. We used noninvasive methods to study female reproductive endocrinology in wild woolly monkeys (genus Lagothrix). We extracted ovarian steroid hormones from fecal samples collected non-invasively to examine changes in the concentrations of progesterone and estrogen metabolites (pregnanediol-3-glucuronide and estrone-3-glucuronide, respectively) during periods of female puberty, ovarian cyclicity, and pregnancy. The two subadult females in our study showed significant increases in ovarian hormone concentrations before disappearing and presumably dispersing, suggesting that they might reach the onset of puberty before emigrating from their natal groups. Ovarian cycle length in adult females was, on average, ~22 days (N = 21). Of the 10 cycling females, five conceived and four gave birth to offspring, with an average gestation period of ~214 days, but the infant born to the female with the shortest estimated gestation period (182 days) disappeared within a month after parturition. The fact that less than half of all cycling females conceived, and that only three out of five of those females gave birth to offspring that survived past the first month, suggests that reproduction is energetically costly for female woolly monkeys. Ovarian cycle length and gestation period among woolly monkeys are similar to those in their closest relatives, spider monkeys and muriquis suggesting that reproductive physiology may be highly conserved among females within the Tribe Atelini.

A RAD-sequencing approach to genome-wide marker discovery, genotyping, and phylogenetic inference in a diverse radiation of primates.

Until recently, most phylogenetic and population genetics studies of nonhuman primates have relied on mitochondrial DNA and/or a small number of nuclear DNA markers, which can limit our understanding of primate evolutionary and population history. Here, we describe a cost-effective reduced representation method (ddRAD-seq) for identifying and genotyping large numbers of SNP loci for taxa from across the New World monkeys, a diverse radiation of primates that shared a common ancestor ~20-26 mya. We also estimate, for the first time, the phylogenetic relationships among 15 of the 22 currently-recognized genera of New World monkeys using ddRAD-seq SNP data using both maximum likelihood and quartet-based coalescent methods. Our phylogenetic analyses robustly reconstructed three monophyletic clades corresponding to the three families of extant platyrrhines (Atelidae, Pitheciidae and Cebidae), with Pitheciidae as basal within the radiation. At the genus level, our results conformed well with previous phylogenetic studies and provide additional information relevant to the problematic position of the owl monkey (Aotus) within the family Cebidae, suggesting a need for further exploration of incomplete lineage sorting and other explanations for phylogenetic discordance, including introgression. Our study additionally provides one of the first applications of next-generation sequencing methods to the inference of phylogenetic history across an old, diverse radiation of mammals and highlights the broad promise and utility of ddRAD-seq data for molecular primatology.

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

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.