Disseminated Mucor indicus infection in a marmoset (Callithrix sp.).

Mucormycosis is rarely described in Platyrrhines. Herein, we describe the pathologic and molecular features of a gastric and hepatic infection by Mucor indicus in a marmoset (Callithrix sp.).

Cortical Morphology and White Matter Tractography of Three Phylogenetically Distant Primates: Evidence for a Simian Elaboration.

Comparative neuroimaging has been used to identify changes in white matter architecture across primate species phylogenetically close to humans, but few have compared the phylogenetically distant species. Here, we acquired postmortem diffusion imaging data from ring-tailed lemurs (Lemur catta), black-capped squirrel monkeys (Saimiri boliviensis), and rhesus macaques (Macaca mulatta). We were able to establish templates and surfaces allowing us to investigate sulcal, cortical, and white matter anatomy. The results demonstrate an expansion of the frontal projections of the superior longitudinal fasciculus complex in squirrel monkeys and rhesus macaques compared to ring-tailed lemurs, which correlates with sulcal anatomy and the lemur's smaller prefrontal granular cortex. The connectivity of the ventral pathway in the parietal region is also comparatively reduced in ring-tailed lemurs, with the posterior projections of the inferior longitudinal fasciculus not extending toward parietal cortical areas as in the other species. In the squirrel monkeys we note a very specific occipito-parietal anatomy that is apparent in their surface anatomy and the expansion of the posterior projections of the optical radiation. Our study supports the hypothesis that the connectivity of the prefrontal-parietal regions became relatively elaborated in the simian lineage after divergence from the prosimian lineage.

Anatomy and dietary specialization influence sensory behaviour among sympatric primates.

Senses form the interface between animals and environments, and provide a window into the ecology of past and present species. However, research on sensory behaviours by wild frugivores is sparse. Here, we examine fruit assessment by three sympatric primates (Alouatta palliata, Ateles geoffroyi and Cebus imitator) to test the hypothesis that dietary and sensory specialization shape foraging behaviours. Ateles and Cebus groups are comprised of dichromats and trichromats, while all Alouatta are trichomats. We use anatomical proxies to examine smell, taste and manual touch, and opsin genotyping to assess colour vision. We find that the frugivorous spider monkeys (Ateles geoffroyi) sniff fruits most often, omnivorous capuchins (Cebus imitator), the species with the highest manual dexterity, use manual touch most often, and that main olfactory bulb volume is a better predictor of sniffing behaviour than nasal turbinate surface area. We also identify an interaction between colour vision phenotype and use of other senses. Controlling for species, dichromats sniff and bite fruits more often than trichromats, and trichromats use manual touch to evaluate cryptic fruits more often than dichromats. Our findings reveal new relationships among dietary specialization, anatomical variation and foraging behaviour, and promote understanding of sensory system evolution.

Grit your teeth and chew your food: Implications of food material properties and abrasives for rates of dental microwear formation in laboratory Sapajus apella (Primates).

Dental microwear analysis has been employed in studies of a wide range of modern and fossil animals, yielding insights into the biology/ecology of those taxa. Some researchers have suggested that dental microwear patterns ultimately relate back to the material properties of the foods being consumed, whereas others have suggested that, because exogenous grit is harder than organic materials in food, grit should have an overwhelming impact on dental microwear patterns. To shed light on this issue, laboratory-based feeding experiments were conducted on tufted capuchin monkeys [Sapajus apella] with dental impressions taken before and after consumption of different artificial foods. The foods were (1) brittle custom-made biscuits laced with either of two differently-sized aluminum silicate abrasives, and (2) ductile custom-made "gummies" laced with either of the two same abrasives. In both cases, animals were allowed to feed on the foods for 36 hours before follow-up dental impressions were taken. Resultant casts were analyzed using a scanning electron microscope. We asked five questions: (1) would the animals consume different amounts of each food item, (2) what types of dental microwear would be formed, (3) would rates of dental microwear differ between the consumption of biscuits (i.e., brittle) versus gummies (i.e., ductile), (4) would rates of dental microwear differ between foods including larger- versus smaller-grained abrasives, and (5) would rates of dental microwear differ between molar shearing and crushing facets in the animals in these experiments? Results indicated that (1) fewer biscuits were consumed when laced with larger-grained abrasives (as opposed to smaller-grained abrasives), but no such difference was observed in the consumption of gummies, (2) in all cases, a variety of dental microwear features was formed, (3) rates of dental microwear were higher when biscuits versus gummies were consumed, (4) biscuits laced with larger-grained abrasives caused a higher percentage of new features per item consumed, and (5) the only difference between facets occurred with the processing of biscuits, where crushing facets showed a faster rate of wear than shearing facets. These findings suggest that the impact of exogenous grit on dental microwear is the result of a dynamic, complex interaction between (at the very least) grit size, food material properties, and time spent feeding - which is further evidence of the multifactorial nature of dental microwear formation.

Macronutrient composition of olive baboon (Papio anubis) milk: A comparison to rhesus macaque (Macaca mulatta) milk.

This study was designed to (1) characterize the macronutrient composition of olive baboon (Papio anubis) milk, (2) compare baboon milk composition to that of rhesus macaques (Macaca mulatta), and (3) evaluate the association between the proportion of milk energy derived from protein and relative growth rate within anthropoid primates. A single milk sample was collected from each of eight lactating olive baboons ranging between 47- and 129-days postparturition and six rhesus macaques from 15- to 92-days living at the same institution under identical management conditions. Macronutrient composition (water, fat, protein sugar, and ash) was determined using standard techniques developed at the Nutrition Laboratory at the Smithsonian National Zoological Park. Baboon milk on average contained 86.0% ± 0.6% water, 4.7% ± 0.5% fat, 1.6% ± 0.04% protein, 7.3% ± 0.07% sugar, and 0.165% ± 0.007% ash. Baboon milk gross energy (GE) averaged 0.81 ± 0.04 kcal/g with 51.9% ± 2.6% from fat, 11.8% ± 0.7% from protein, and 36.2% ± 2.0% from sugar. Baboon milk demonstrated strong similarity to milk composition of the closely phylogenetically related rhesus macaque (86.1% ± 0.3% water, 4.1% ± 0.4% fat, 1.69% ± 0.05% protein, 7.71% ± 0.08% sugar, 0.19% ± 0.01% ash, and 0.78 kcal/g). There was no statistical difference between baboon and macaque milk in the proportions of energy from fat, sugar, and protein. Baboon milk can be described as a high sugar, moderate fat, and low protein milk with moderate energy density, which is consistent with their lactation strategy characterized by frequent, on-demand nursing and relatively slow life history compared to nonprimate mammal taxa. The milk energy from protein of both baboon and macaque (12.8% ± 0.3%) milk was intermediate between the protein milk energy of platyrrhine (19.3%-23.2%) and hominoid (8.9%-12.6%) primates, consistent with their relative growth rates also being intermediate. Compared to these cercopithecid monkeys, platyrrhine primates have both higher relative growth rates and higher milk energy from protein, while apes tend to be lower in both.

Historical antecedents and recent innovations in pitheciid (titi, saki, and uakari) feeding ecology.

The modern pitheciids (titis, sakis, and uakaris) of northern South America represent one of the earliest radiations of platyrrhines and demonstrate morphological adaptations and ecological strategies for seed eating. While seeds can provide reliable resources for relatively long periods of time, they are often well protected by thick husks and hard seed coverings. Seeds also tend to be rich in lipids, but they may also be high in indigestible fiber. Even though seed eaters are found in each major primate radiation, only the pitheciids demonstrate primary adaptations for eating seeds. In this partly historical, partly contemporary review, I examine the ecological and anatomical correlates of seed eating. It is dedicated to two well-known field primatologists: ecologist and conservationist J. Márcio Ayres; and anatomist and ecologist Warren G. Kinzey. Using observations in Kinzey (1992, Am J Phys Anthropol, 88, pp. 499-514) as a framework, I provide context and analysis for the intervening three decades of pitheciid research to identify what we know about this understudied group of primates and propose directions for future work.

Trichromacy increases fruit intake rates of wild capuchins (Cebus capucinus imitator).

Intraspecific color vision variation is prevalent among nearly all diurnal monkeys in the neotropics and is seemingly a textbook case of balancing selection acting to maintain genetic polymorphism. Clear foraging advantages to monkeys with trichromatic vision over those with dichromatic "red-green colorblind" vision have been observed in captive studies; however, evidence of trichromatic advantage during close-range foraging has been surprisingly scarce in field studies, perhaps as a result of small sample sizes and strong impacts of environmental or individual variation on foraging performance. To robustly test the effects of color vision type on foraging efficiency in the wild, we conducted an extensive study of dichromatic and trichromatic white-faced capuchin monkeys (Cebus capucinus imitator), controlling for plant-level and monkey-level variables that may affect fruit intake rates. Over the course of 14 months, we collected behavioral data from 72 monkeys in Sector Santa Rosa, Costa Rica. We analyzed 19,043 fruit feeding events within 1,602 foraging bouts across 27 plant species. We find that plant species, color conspicuity category, and monkey age class significantly impact intake rates, while sex does not. When plant species and age are controlled for, we observe that trichromats have higher intake rates than dichromats for plant species with conspicuously colored fruits. This study provides clear evidence of trichromatic advantage in close-range fruit feeding in wild monkeys. Taken together with previous reports of dichromatic advantage for finding cryptic foods, our results illuminate an important aspect of balancing selection maintaining primate opsin polymorphism.

Effects of substrate and phylogeny on quadrupedal gait in free-ranging platyrrhines.

OBJECTIVES: Primate diagonal sequence (DS) gaits are often argued to be an adaptation for moving and foraging in the fine-branch niche; however, existing data have come predominantly from laboratory studies that are limited in taxonomic breadth and fail to account for the structural and ecological variation of natural substrates. We test the extent to which substrate diameter and orientation influence gait sequence type and limb phase in free-ranging primates, as well as how phylogenetic relatedness might condition response patterns. MATERIALS AND METHODS: We filmed quadrupedal locomotion in 11 platyrrhine species at field sites in Ecuador and Costa Rica and measured the diameter and orientation of locomotor substrates using remote sensors. We quantified limb phase values and classified strides by gait sequence type (N = 988 strides). RESULTS: Our results show that most of the species in our sample consistently used DS gaits, regardless of substrate diameter or orientation; however, all taxa also used asymmetrical and/or lateral sequence gaits. By incorporating phylogenetic eigenvectors into our models, we found significant differences in gait sequence patterns and limb phase values among the major platyrrhine clades, suggesting that phylogeny may be a better predictor of gait than substrate diameter or orientation. DISCUSSION: Our field data generally corroborate locomotor patterns from laboratory studies but capture additional aspects of gait variability and flexibility in response to the complexity of natural environments. Overall, our results suggest that DS gaits are not exclusively tailored to narrow or oblique substrates but are used on arboreal substrates in general.

Ethnic rhinoplasty.

Rhinoplasty is one of the main facial plastic procedures performed worldwide. Ethnic patients today are mainly mixed-race patients. Diagnosis is based on anatomical findings and surgery should be planned based on patients' needs and what they define as beautiful. Different surgical techniques are presented where a structural approach to rhinoplasty is explained. Very little tissue is resected and support structures of the nose are strengthened with sutures and grafts. A gradual approach to the nasal tip is also presented progressing from simple predictable techniques to more complex unpredictable ones. The final result should be noses with greater definition and refinement that are harmonious and blend in with patients' faces.

New endemic platyrrhine humerus from Haiti and the evolution of the Greater Antillean platyrrhines.

Much debate surrounds the phylogenetic affinities of the endemic Greater Antillean platyrrhines. Thus far, most phylogenetic analyses have been constructed and tested using craniodental characters. We add to this dialog by considering how features of the distal humerus support or refute existing hypotheses for the origins of fossil Caribbean primates, utilizing three-dimensional geometric morphometric data in combination with character based cladistic analyses. We also add to the sample of fossil platyrrhine humeri with the description of UF 114718, a new distal humerus from Haiti. We reconstruct UF 114718 to be a generalized, arboreal quadruped attributed to the species Insulacebus toussantiana. Our results from phylogenetic analyses lend some support to the idea that some Greater Antillean fossil taxa including Xenothrix mcgregori, Antillothrix bernensis, and Insulacebus toussaintiana could form a monophyletic clade that is sister to either extant Platyrrhini or basal pitheciids. Based on the distal humeral data, we reconstruct the earliest ancestral platyrrhine to be a generalized, arboreal quadruped that potentially emphasized pronated arm postures during locomotion and may have engaged in some limited climbing, most similar in shape to early anthropoids and some of the earliest Antillean forms. However, aspects of shape and standard qualitative characters relating to the distal humerus seem to be variable and prone to both homoplasy and reversals; thus these results must be interpreted cautiously and (where possible) within the context provided by other parts of the skeleton.

Can colour vision re-evolve? Variation in the X-linked opsin locus of cathemeral Azara's owl monkeys (Aotus azarae azarae).

BACKGROUND: Do evolutionary specializations lead to evolutionary constraint? This appears plausible, particularly when specialization leads to loss of complex adaptations. In the owl monkey lineage, nocturnality clearly arose from a diurnal ancestor. This behavioural shift was accompanied by morphological changes in the eye and orbit and complete loss of colour vision via missense mutations in the gene encoding the short-wave sensitive visual pigment (SWS opsin). Interestingly, at least one subspecies of owl monkey, Azara's owl monkey (Aotus azarae azarae), has regained activity in daylight. Given that all primate species that are active in daylight, including primarily diurnal species and species that are active during both day and night, have at least dichromatic colour vision, it seems reasonable to propose that dichromacy would be adaptive in A. a. azarae. With a disabled SWS opsin, the main avenue available for Azara's owl monkeys to re-evolve colour vision is via a polymorphism in the intact X-linked opsin locus, which commonly occurs in other New World monkeys. To examine this possibility we assayed variation in the X-linked opsin of A. a. azarae, focusing on the three exons (3, 4 and 5) that control spectral sensitivity. RESULTS: We found low opsin genetic variation on a population level, and no differences at the three main sites that lead to variation in spectral sensitivity in the opsins of other New World monkeys. Two rare alleles with single amino acid variants are segregating in the population, but previous functional studies indicate that these are unlikely to affect spectral sensitivity. CONCLUSIONS: Genetic constraint on the re-evolution of colour vision is likely operating in Azara's owl monkey, which may affect the niche that this subspecies is able to occupy.

Bearded saki feeding strategies on an island in Lago Guri, Venezuela.

Free-ranging bearded sakis (Chiropotes spp.) live in relatively large social groups (22-65+), inhabit very large home ranges (200-1,000 ha), and travel long distances (1.8 to >7 km) each day. While these characteristics would seem to reduce their ability to occupy habitat fragments, several studies suggest otherwise. The key to their success may lie in their dietary adaptations. Bearded sakis are strongly frugivorous, but are primarily seed eaters, and are able to ingest both young and mature fruit. We examined feeding activities of a group of bearded sakis over a 19-month period on a 180 ha island in Lago Guri, Venezuela. Given their feeding adaptations, we predicted that they would minimize peaks and troughs in plant species used for food, limit seasonal variation in the mechanical properties of foods ingested, and balance ingestion of energy-rich foods (e.g. lipids, nonstructural carbohydrates (TNC), and/or free simple sugars). We found that bearded sakis on Danto Manchado had a diverse (plant-based) diet, but two resources (Pradosia caracasana, Sapotaceae, and Oryctanthus alveolatus, Loranthaceae) provided a stable dietary base and were present in the diet almost every month. Second, we found little variation in the mechanical-resistance properties of fruits opened seasonally. Third, they alternated months ingesting foods with high TNC content and months of high lipid content. This may be an attempt to balance energy intake from available foods. Finally, their social propensity to split up into subgroups may predispose them to reduce group sizes to accommodate smaller available areas. We suggest that bearded sakis use both ecological and behavioral mechanisms to survive in smaller-than-typical areas. Longer-term studies (beyond a few generations) of bearded sakis in habitat fragments would allow us to estimate minimum survival area and identify critical resources or resource combinations.

The tempo and mode of New World monkey evolution and biogeography in the context of phylogenomic analysis.

The development and evolution of organisms is heavily influenced by their environment. Thus, understanding the historical biogeography of taxa can provide insights into their evolutionary history, adaptations and trade-offs realized throughout time. In the present study we have taken a phylogenomic approach to infer New World monkey phylogeny, upon which we have reconstructed the biogeographic history of extant platyrrhines. In order to generate sufficient phylogenetic signal within the New World monkey clade, we carried out a large-scale phylogenetic analysis of approximately 40 kb of non-genic genomic DNA sequence in a 36 species subset of extant New World monkeys. Maximum parsimony, maximum likelihood and Bayesian inference analysis all converged on a single optimal tree topology. Divergence dating and biogeographic analysis reconstruct the timing and geographic location of divergence events. The ancestral area reconstruction describes the geographic locations of the last common ancestor of extant platyrrhines and provides insight into key biogeographic events occurring during platyrrhine diversification. Through these analyses we conclude that the diversification of the platyrrhines took place concurrently with the establishment and diversification of the Amazon rainforest. This suggests that an expanding rainforest environment rather than geographic isolation drove platyrrhine diversification.

De Novo Genome Assembly for the Coppery Titi Monkey (Plecturocebus cupreus): An Emerging Nonhuman Primate Model for Behavioral Research.

The coppery titi monkey (Plecturocebus cupreus) is an emerging nonhuman primate model system for behavioral and neurobiological research. At the same time, the almost entire absence of genomic resources for the species has hampered insights into the genetic underpinnings of the phenotypic traits of interest. To facilitate future genotype-to-phenotype studies, we here present a high-quality, fully annotated de novo genome assembly for the species with chromosome-length scaffolds spanning the autosomes and chromosome X (scaffold N50 = 130.8 Mb), constructed using data obtained from several orthologous short- and long-read sequencing and scaffolding techniques. With a base-level accuracy of ∼99.99% in chromosome-length scaffolds as well as benchmarking universal single-copy ortholog and k-mer completeness scores of >99.0% and 95.1% at the genome level, this assembly represents one of the most complete Pitheciidae genomes to date, making it an invaluable resource for comparative evolutionary genomics research to improve our understanding of lineage-specific changes underlying adaptive traits as well as deleterious mutations associated with disease.

A closer look at the "Protopithecus" fossil assemblages: new genus and species from Bahia, Brazil.

The recently extinct large-bodied New World monkey Protopithecus brasiliensis Lund 1836 was named based on a distal humerus and proximal femur found in the Lagoa Santa cave system in the southeastern Brazilian state of Minas Gerais. These bones are from an animal about twice the size of the largest extant platyrrhines. One hundred and seventy-five years later, a nearly complete skeleton was discovered in the Toca da Boa Vista caves in the neighboring state of Bahia and was allocated to the same taxon as it was the first platyrrhine fossil of comparable size found since the originals. Our detailed study of the equivalent elements, however, reveals important morphological differences that do not correspond to intraspecific variation as we know it in related platyrrhine taxa. The presence of both an expanded brachioradialis flange on the humerus and gluteal tuberosity on the femur of the Bahian skeleton distinguishes it from the Lagoa Santa fossil as well as from all other platyrrhines. Further cranial and postcranial evidence suggests a closer relationship of the former with the alouattine Alouatta, while the limited Lund material fits more comfortably with the ateline clade. Therefore, we propose to limit P. brasiliensis Lund to the distal humerus and proximal femur from Lagoa Santa and erect a new genus and species for the skeleton from Toca da Boa Vista. Cartelles coimbrafilhoi was a large-bodied frugivore with a relatively small brain and diverse locomotor repertoire including both suspension and climbing that expands the range of platyrrhine biodiversity beyond the dimensions of the living neotropical primates.

Gene Content and Coding Diversity of the Growth Hormone Loci of Apes.

The growth hormone (GH) locus has experienced a dramatic evolution in primates, becoming multigenic and diverse in anthropoids. Despite sequence information from a vast number of primate species, it has remained unclear how the multigene family was favored. We compared the structure and composition of apes' GH loci as a prerequisite to understanding their origin and possible evolutionary role. These thorough analyses of the GH loci of the chimpanzee, gorilla, and orangutan were done by resorting to previously sequenced bacterial artificial chromosomes (BACs) harboring them, as well as to their respective genome projects data available in GenBank. The GH loci of modern man, Neanderthal, gibbon, and wild boar were retrieved from GenBank. Coding regions, regulatory elements, and repetitive sequences were identified and compared among species. The GH loci of all the analyzed species are flanked by the genes CD79B (5') and ICAM-1 (3'). In man, Neanderthal, and chimpanzee, the loci were integrated by five almost indistinguishable genes; however, in the former two, they rendered three different hormones, and in the latter, four different proteins were derived. Gorilla exhibited six genes, gibbon seven, and orangutan four. The sequences of the proximal promoters, enhancers, P-elements, and a locus control region (LCR) were highly conserved. The locus evolution might have implicated duplications of the ancestral pituitary gene (GH-N) and subsequent diversification of the copies, leading to the placental single GH-V gene and the multiple CSH genes.

Extensive Independent Amplification of Platy-1 Retroposons in Tamarins, Genus Saguinus.

Platy-1 retroposons are short interspersed elements (SINEs) unique to platyrrhine primates. Discovered in the common marmoset (Callithrix jacchus) genome in 2016, these 100 bp mobile element insertions (MEIs) appeared to be novel drivers of platyrrhine evolution, with over 2200 full-length members across 62 different subfamilies, and strong evidence of ongoing proliferation in C. jacchus. Subsequent characterization of Platy-1 elements in Aotus, Saimiri and Cebus genera, suggested that the widespread mobilization detected in marmoset (family Callithrichidae) was perhaps an anomaly. Two additional Callithrichidae genomes are now available, a scaffold level genome assembly for Saguinus imperator (tamarin; SagImp_v1) and a chromosome-level assembly for Saguinus midas (Midas tamarin; ASM2_v1). Here, we report that each tamarin genome contains over 11,000 full-length Platy-1 insertions, about 1150 are shared by both Saguinus tamarins, 7511 are unique to S. imperator, and another 8187 are unique to S. midas. Roughly 325 are shared among the three callithrichids. We identified six new Platy-1 subfamilies derived from Platy-1-8, with the youngest new subfamily, Platy-1-8c_Saguinus, being the primary source of the Saguinus amplification burst. This constitutes the largest expansion of Platy-1 MEIs reported to date and the most extensive independent SINE amplification between two closely related species.

Whole Genome Analysis of SNV and Indel Polymorphism in Common Marmosets (Callithrix jacchus).

The common marmoset (Callithrix jacchus) is one of the most widely used nonhuman primate models of human disease. Owing to limitations in sequencing technology, early genome assemblies of this species using short-read sequencing suffered from gaps. In addition, the genetic diversity of the species has not yet been adequately explored. Using long-read genome sequencing and expert annotation, we generated a high-quality genome resource creating a 2.898 Gb marmoset genome in which most of the euchromatin portion is assembled contiguously (contig N50 = 25.23 Mbp, scaffold N50 = 98.2 Mbp). We then performed whole genome sequencing on 84 marmosets sampling the genetic diversity from several marmoset research centers. We identified a total of 19.1 million single nucleotide variants (SNVs), of which 11.9 million can be reliably mapped to orthologous locations in the human genome. We also observed 2.8 million small insertion/deletion variants. This dataset includes an average of 5.4 million SNVs per marmoset individual and a total of 74,088 missense variants in protein-coding genes. Of the 4956 variants orthologous to human ClinVar SNVs (present in the same annotated gene and with the same functional consequence in marmoset and human), 27 have a clinical significance of pathogenic and/or likely pathogenic. This important marmoset genomic resource will help guide genetic analyses of natural variation, the discovery of spontaneous functional variation relevant to human disease models, and the development of genetically engineered marmoset disease models.

Cebidae Alu Element Alignments and a Complex Non-Human Primate Radiation.

Phylogenetic relationships among Cebidae species of platyrrhine primates are presently under debate. Studies prior to whole genome sequence (WGS) availability utilizing unidirectional Alu repeats linked Callithrix and Saguinus as sister taxa, based on a limited number of genetic markers and specimens, while the relative positions of Cebus, Saimiri and Aotus remained controversial. Multiple WGS allowed computational detection of Alu-genome junctions, however random mutation and evolutionary decay of these short-read segments prevented phylogenetic resolution. In this study, WGS for four Cebidae genomes of marmoset, squirrel monkey, owl monkey and capuchin were analyzed for full-length Alu elements and each locus was compared to the other three genomes in all possible combinations using orthologous region sequence alignments. Over 2000 candidates were aligned and subjected to visual inspection. Approximately 34% passed inspection and were considered shared in their respective category, 48% failed due to the target being present in all four genomes, having N's in the sequence or other sequence quality anomalies, and 18% were determined to represent near parallel insertions (NP). Wet bench locus specific PCR confirmed the presence of shared Alu insertions in all phylogenetically informative categories, providing evidence of extensive incomplete lineage sorting (ILS) and an abundance of Alu proliferation during the complex radiation of Cebidae taxa.

Recently Integrated Alu Elements in Capuchin Monkeys: A Resource for Cebus/Sapajus Genomics.

Capuchins are platyrrhines (monkeys found in the Americas) within the Cebidae family. For most of their taxonomic history, the two main morphological types of capuchins, gracile (untufted) and robust (tufted), were assigned to a single genus, Cebus. Further, all tufted capuchins were assigned to a single species, Cebus apella, despite broad geographic ranges spanning Central and northern South America. In 2012, tufted capuchins were assigned to their genus, Sapajus, with eight currently recognized species and five Cebus species, although these numbers are still under debate. Alu retrotransposons are a class of mobile element insertion (MEI) widely used to study primate phylogenetics. However, Alu elements have rarely been used to study capuchins. Recent genome-level assemblies for capuchins (Cebus imitator; [Cebus_imitator_1.0] and Sapajus apella [GSC_monkey_1.0]) facilitated large scale ascertainment of young lineage-specific Alu insertions. Reported here are 1607 capuchin specific and 678 Sapajus specific Alu insertions along with candidate oligonucleotides for locus-specific PCR assays for many elements. PCR analyses identified 104 genus level and 51 species level Alu insertion polymorphisms. The Alu datasets reported in this study provide a valuable resource that will assist in the classification of archival samples lacking phenotypic data and for the study of capuchin phylogenetic relationships.