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.

Biogeography of squirrel monkeys (genus Saimiri): South-central Amazon origin and rapid pan-Amazonian diversification of a lowland primate.

The squirrel monkey, Saimiri, is a pan-Amazonian Pleistocene radiation. We use statistical phylogeographic methods to create a mitochondrial DNA-based timetree for 118 squirrel monkey samples across 68 localities spanning all Amazonian centers of endemism, with the aim of better understanding (1) the effects of rivers as barriers to dispersal and distribution; (2) the area of origin for modern Saimiri; (3) whether ancestral Saimiri was a lowland lake-affiliated or an upland forest taxa; and (4) the effects of Pleistocene climate fluctuation on speciation. We also use our topology to help resolve current controversies in Saimiri taxonomy and species relationships. The Rondônia and Inambari centers in the southern Amazon were recovered as the most likely areas of origin for Saimiri. The Amazon River proved a strong barrier to dispersal, and squirrel monkey expansion and diversification was rapid, with all speciation events estimated to occur between 1.4 and 0.6Ma, predating the last three glacial maxima and eliminating climate extremes as the main driver of squirrel monkey speciation. Saimiri expansion was concentrated first in central and western Amazonia, which according to the "Young Amazon" hypothesis was just becoming available as floodplain habitat with the draining of the Amazon Lake. Squirrel monkeys also expanded and diversified east, both north and south of the Amazon, coincident with the formation of new rivers. This evolutionary history is most consistent with a Young Amazon Flooded Forest Taxa model, suggesting Saimiri has always maintained a lowland wetlands niche and was able to greatly expand its range with the transition from a lacustrine to a riverine system in Amazonia. Saimiri vanzolinii was recovered as the sister group to one clade of Saimiri ustus, discordant with the traditional Gothic vs. Roman morphological division of squirrel monkeys. We also found paraphyly within each of the currently recognized species: S. sciureus, S. ustus, and S. macrodon. We discuss evidence for taxonomic revision within the genus Saimiri, and the need for future work using nuclear markers.

The effects of ecology and evolutionary history on robust capuchin morphological diversity.

Recent molecular work has confirmed the long-standing morphological hypothesis that capuchins are comprised of two distinct clades, the gracile (untufted) capuchins (genus Cebus, Erxleben, 1777) and the robust (tufted) capuchins (genus Sapajus Kerr, 1792). In the past, the robust group was treated as a single, undifferentiated and cosmopolitan species, with data from all populations lumped together in morphological and ecological studies, obscuring morphological differences that might exist across this radiation. Genetic evidence suggests that the modern radiation of robust capuchins began diversifying ∼2.5 Ma, with significant subsequent geographic expansion into new habitat types. In this study we use a morphological sample of gracile and robust capuchin craniofacial and postcranial characters to examine how ecology and evolutionary history have contributed to morphological diversity within the robust capuchins. We predicted that if ecology is driving robust capuchin variation, three distinct robust morphotypes would be identified: (1) the Atlantic Forest species (Sapajus xanthosternos, S. robustus, and S. nigritus), (2) the Amazonian rainforest species (S. apella, S. cay and S. macrocephalus), and (3) the Cerrado-Caatinga species (S. libidinosus). Alternatively, if diversification time between species pairs predicts degree of morphological difference, we predicted that the recently diverged S. apella, S. macrocephalus, S. libidinosus, and S. cay would be morphologically comparable, with greater variation among the more ancient lineages of S. nigritus, S. xanthosternos, and S. robustus. Our analyses suggest that S. libidinosus has the most derived craniofacial and postcranial features, indicative of inhabiting a more terrestrial niche that includes a dependence on tool use for the extraction of imbedded foods. We also suggest that the cranial robusticity of S. macrocephalus and S. apella are indicative of recent competition with sympatric gracile capuchin species, resulting in character displacement.

Morphology and mitochondrial phylogenetics reveal that the Amazon River separates two eastern squirrel monkey species: Saimiri sciureus and S. collinsi.

Saimiri has a complicated taxonomic history, and there is continuing disagreement about the number of valid taxa. Despite these controversies, one point of consensus among morphologists has been that the eastern Amazonian populations of squirrel monkeys form a single terminal taxon, Saimiri sciureus sciureus (Linnaeus, 1758). This group is distributed to both the north and south of the middle to lower Amazon River and in the Marajó Archipelago. However, a recent molecular study by Lavergne and colleagues suggested that the Saimiri sciureus complex (comprised of S. s. sciureus sensu lato, S. s. albigena, S. s. macrodon, and S. s. cassiquiarensis) was paraphyletic. The discordance between morphological and molecular studies prompted us to conduct a new multidisciplinary analysis, employing a combination of morphological, morphometric, and molecular markers. Our results suggest the currently recognized taxon S. s. sciureus contains two distinct species, recognized by the Phylogenetic Species Concept: Saimiri sciureus (Linnaeus, 1758) and Saimiri collinsi Osgood, 1916. East Amazonian squirrel monkeys north of the Amazon have a gray crown (S. sciureus), and south of the Amazon, the crown is yellow (S. collinsi). Morphometric measurements also clearly distinguish between the two species, with the most important contributing factors including width across upper canines for both sexes. For males, the mean zygomatic breadth was significantly wider in S. sciureus compared to S. collinsi, and for females, the width across the upper molars was wider in S. sciureus compared to S. collinsi. Mitochondrial phylogenetic analyses support this separation of the eastern Amazonian squirrel monkeys into two distinct taxa, recovering one clade (S. sciureus) distributed to the north of the Amazon River, from the Negro River and Branco River to the Guiana coast and the Brazilian state of Amapá, and another clade (S. collinsi) south of the Amazon River, from the region of the Tapajós River to the state of Maranhão, as well as within the Marajó Archipelago. The revalidation of the species S. collinsi was corroborated by all of the methods in the study, as the clades recovered in our molecular study are congruent with the pattern of morphological variation. We confirm both the paraphyly of the Saimiri sciureus complex and the paraphyly of the subspecies S. s. sciureus as defined in the current literature.

Special issue: Comparative biogeography of Neotropical primates.

New research presented in this special issue of Molecular Phylogenetics and Evolution on the "Phylogeny and Biogeography of Neotropical Primates" greatly improves our understanding of the evolutionary history of the New World monkeys and provides insights into the multiple platyrrhine radiations, diversifications, extinctions, and recolonizations that have taken place over time and over space in the Neotropics. Here, we synthesize genetic and biogeographic research from the past several years to construct an overarching hypothesis for platyrrhine evolution. We also highlight continuing controversies in Neotropical primate biogeography, such as whether the location of origin of platyrrhines was Africa or Asia; whether Patagonian fossil primates are stem or crown platyrrhines; and whether cis- and trans-Andean Neotropical primates were subject to vicariance through Andes mountain building, or instead diversified through isolation in mountain valleys after skirting around the Andes on the northwestern coast of South America. We also consider the role of the Amazon River and its major tributaries in shaping platyrrhine biodiversity, and how and when primates from the Amazon reached the Atlantic Forest. A key focus is on primate colonizations and extirpations in Central America, the Andes, and the seasonally dry tropical forests and savannas (such as the Llanos, Caatinga, and Cerrado habitats), all ecosystems that have been understudied up until now for primates. We suggest that most primates currently inhabiting drier open habitats are relatively recent arrivals, having expanded from rainforest habitats in the Pleistocene. We point to the Pitheciidae as the taxonomic group most in need of further phylogenetic and biogeographic research. Additionally, genomic studies on the Platyrrhini are deeply needed and are expected to bring new surprises and insights to the field of Neotropical primate biogeography.

Spatial and temporal patterns of diversification on the Amazon: A test of the riverine hypothesis for all diurnal primates of Rio Negro and Rio Branco in Brazil.

The role of Amazonian rivers as drivers of speciation through vicariance remains controversial. Here we explore the riverine hypothesis by comparing spatial and temporal concordances in pattern of diversification for all diurnal primates of Rio Negro and its largest tributary, Rio Branco. We built a comprehensive comparative phylogenetic timetree to identify sister lineages of primates based on mitochondrial cytochrome b DNA sequences from 94 samples, including 19 of the 20 species of diurnal primates from our study region and 17 related taxa from elsewhere. Of the ten primate genera found in this region, three had populations on opposite banks of Rio Negro that formed reciprocally monophyletic clades, with roughly similar divergence times (Cebus: 1.85 Ma, HPD 95% 1.19-2.62; Callicebus: 0.83 Ma HPD 95% 0.36-1.32, Cacajao: 1.09 Ma, 95% HPD 0.58-1.77). This also coincided with time of divergence of several allopatric species of Amazonian birds separated by this river as reported by other authors. Our data offer support for the riverine hypothesis and for a Plio-Pleistocene time of origin for Amazonian drainage system. We showed that Rio Branco was an important geographical barrier, limiting the distribution of six primate genera: Cacajao, Callicebus, Cebus to the west and Pithecia, Saguinus, Sapajus to the east. The role of this river as a vicariant agent however, was less clear. For example, Chiropotes sagulata on the left bank of the Rio Branco formed a clade with C. chiropotes from the Amazonas Department of Venezuela, north of Rio Branco headwaters, with C. israelita on the right bank of the Rio Branco as the sister taxon to C. chiropotes+C. sagulata. Although we showed that the formation of the Rio Negro was important in driving diversification in some of our studied taxa, future studies including more extensive sampling of markers across the genome would help determine what processes contributed to the evolutionary history of the remaining primate genera.

Biogeography of the marmosets and tamarins (Callitrichidae).

The marmosets and tamarins, Family Callitrichidae, are Neotropical primates with over 60 species and subspecies that inhabit much of South America. Although callitrichids exhibit a remarkable widespread distribution, attempts to unravel their biogeographic history have been limited by taxonomic confusion and the lack of an appropriate statistical biogeographic framework. Here, we construct a time-calibrated multi-locus phylogeny from GenBank data and the callitrichid literature for 38 taxa. We use this framework to conduct statistical biogeographic analyses of callitrichids using BioGeoBEARS. The DIVAj model is the best supported reconstruction of biogeographic history among our analyses and suggests that the most recent common ancestor to the callitrichids was widespread across forested regions c. 14 Ma. There is also support for multiple colonizations of the Atlantic forest region from the Amazon basin, first by Leontopithecus c. 11 Ma and later by Callithrix c. 5 Ma. Our results show support for a 9 million year old split between a small-bodied group and large-bodied group of tamarins. These phylogenetic data, in concert with the consistent difference in body size between the two groups and geographical patterns (small-bodied tamarins and large-bodied tamarins have an unusually high degree of geographic overlap for congeners) lend support to our suggestion to split Saguinus into two genera, and we propose the use of distinct generic names; Leontocebus and Saguinus, respectively.

Capuchin monkey research priorities and urgent issues.

The "Capuchin research community roundtable: working together towards a comparative biology of Cebus and Sapajus" was held at the International Primatological Society Congress in Cancún, Mexico, August 2012. Goals of the roundtable were to strengthen interactions among the capuchin research community, and to prioritize and coordinate research and training in a more systematic and interactive way in light of increasing conservation urgency. New phylogenetic and biogeographic evidence highlights the distinct evolutionary histories of the two radiations of capuchin monkeys, Cebus (untufted or gracile capuchins) and Sapajus (tufted or robust capuchins), that were formerly lumped under Cebus, and points to a higher number of species, or Evolutionarily Significant Units, in each compared to past capuchin taxonomies. Many of the lesser-known species face increasing fragmentation and destruction of habitat, and most populations of still non-threatened species face encroachment from human settlements. Here, we present capuchin research priorities and urgent issues based on the discussion by capuchin researchers in the roundtable. These include a call for the immediate end to the use of the name Cebus apella and the employment of the term Sapajus spp. instead for captive robust capuchins of unknown origin; for the implementation of rapid assessments for previously unstudied capuchin species or populations in biomes of interest; for the development of standardized methods to allow for comparative analyses across capuchin field sites; and for the creation and maintenance of an open-access website for capuchin monkey data. Finally, we planned the creation of an international Capuchin Action Network, to help disseminate research information; to work as a research community in a more efficient, collaborative manner; to help prioritize research and conservation goals as a community of experts; and to strengthen our political voice.

Activity budget, diet, and habitat use in the critically endangered Ka'apor capuchin monkey (Cebus kaapori) in Pará State, Brazil: a preliminary comparison to other capuchin monkeys.

The Ka'apor capuchin, Cebus kaapori, is perhaps the most endangered primate of the Brazilian Amazon. Endemic to a region with extreme intensification of habitat-degrading activities, it survives in remnant populations in a completely fragmented landscape. Before now, the only data available were isolated observations of feeding, locality records, and information on population densities and group size obtained during census. Here we present the first data on the activity budget, diet, and daily path length of the species, and compare our preliminary results with those for other capuchin monkeys. A group of nine Ka'apor capuchins was monitored over a period of four months during the dry season in the Goianésia do Pará municipality, Pará, Brazil. We used instantaneous scan sampling (n = 4,647 scans) to construct an activity budget for the monkeys, and we identified the plants in their diet to species level (n = 41 plant taxa), allowing us to compare dietary overlap with other gracile capuchin species, as well as with the robust capuchin (Sapajus spp.), a potential competitor present throughout the range of the Ka'apor capuchin. Like other species of gracile capuchins, C. kaapori was highly frugivorous, with the vast majority of the feeding records of arils and fruit pulp (74%), supplemented by arthropods (13%) and seeds (10%), although diet composition was highly variable across months. The group used a total area of 62.4 ha during the study period, and average daily path length was 2,173 m (±400 m), with the entire home range utilized in every month of the study. We found significant overlap in the diet of the Ka'apor capuchin and Sapajus, highlighting the urgency to increase knowledge of the ecological needs of C. kaapori and understand synergistic effects of sympatry with competitive species, increasing forest fragmentation, and widespread human impact on C. kaapori sustainability.

Pleistocene diversification of living squirrel monkeys (Saimiri spp.) inferred from complete mitochondrial genome sequences.

In order to enhance our understanding of the evolutionary history of squirrel monkeys (Saimiri spp.), we newly sequenced and analyzed data from seven complete mitochondrial genomes representing six squirrel monkey taxa. While previous studies have lent insights into the taxonomy and phylogeny of the genus, phylogenetic relationships and divergence date estimates among major squirrel monkey clades remain unclear. Using maximum likelihood and Bayesian procedures, we inferred a highly resolved phylogenetic tree with strong support for a sister relationship between Saimiri boliviensis and all other Saimiri, for monophyly of Saimiri oerstedii and Saimiri sciureus sciureus, and for Saimiri sciureus macrodon as the sister lineage to the S. oerstedii/S. s. sciureus clade. We inferred that crown lineages for extant squirrel monkeys diverged around 1.5 million years ago (MYA) in the Pleistocene Epoch, with other major clades diverging between 0.9 and 1.1 MYA. Our results suggest a relatively recent timeline of squirrel monkey evolution and challenge previous conceptions about the diversification of the genus and its expansion into Central America.