Phylogenetic relationships, population demography, and species delimitation of the Alouatta belzebul species complex (Atelidae: Alouattinae).

Howler monkeys (genus Alouatta) exhibit the most extensive distribution among platyrrhines, comprising Mesoamerican and South American species groups, with the South American group including the Brazilian endemic A. belzebul species complex encompassing A. belzebul, A. discolor, and A. ululata. We herein analyzed their phylogenetic relationship, nucleotide and haplotype diversity, and population demography based on the mitochondrial gene cytochrome b. The phylogenetic and median-joining network analyses distinguished A. discolor, distributed in the west bank of the Xingu River, from A. belzebul on the east bank. This river is a zoogeographic barrier for these species. We did not find evidence of phylogenetic structure between the A. belzebul populations of opposite banks of the Tocantins River, likely related to the changes in the position of this river to the northeast in the late Pleistocene. The A. belzebul along this river showed great morphologic and haplotype diversity, and A. belzebul from the Amazon have kept a larger population size than A. discolor. We herein describe the karyotype of A. discolor, which was similar to those described for A. ululata and A. belzebul. Our results showed two well-defined and supported clades for A. discolor and A. belzebul. However, a new assessment of A. ululata across a large distribution of sampling is required due to the lack of a clear phylogenetic structure.

Cranial and endocranial diversity in extant and fossil atelids (Platyrrhini: Atelidae): A geometric morphometric study.

OBJECTIVES: Platyrrhines constitute a diverse clade, with the modern Atelidae exhibiting the most variation in cranial and endocast morphology. The processes responsible for this diversification are not well understood. Here, we present a geometric morphometric study describing variation in cranial and endocranial shape of 14 species of Alouatta, Ateles, Brachyteles, and Lagothrix and two extinct taxa, Cartelles and Caipora. METHODS: We examined cranial and endocranial shape variation among species using images reconstructed from CT scans and geometric morphometric techniques based on three-dimensional landmarks and semilandmarks. Principal components analyses were used to explore variation, including the Procrustes shape coordinates, summing the logarithm of the Centroid Size, the common allometric component, and residual shape components. RESULTS: Differences in endocranial shape are related to a relative increase or decrease in the volume of the neocortex region with respect to brainstem and cerebellum regions. The relative position of the brainstem varies from a posterior position in Alouatta to a more ventral position in Ateles. The shape of both the cranium and endocast of Caipora is within the observed variation of Brachyteles. Cartelles occupies the most differentiated position relative to the extant taxa, especially in regards to its endocranial shape. CONCLUSIONS: The pattern of variation in the extant species in endocranial shape is similar to the variation observed in previous cranial studies, with Alouatta as an outlier. The similarities between Caipora and Brachyteles were unexpected and intriguing given the frugivorous adaptations inferred from the fossil's dentition. Our study shows the importance of considering both extant and fossil species when studying diversification of complex traits.

Functional characterization of enhancer evolution in the primate lineage.

BACKGROUND: Enhancers play an important role in morphological evolution and speciation by controlling the spatiotemporal expression of genes. Previous efforts to understand the evolution of enhancers in primates have typically studied many enhancers at low resolution, or single enhancers at high resolution. Although comparative genomic studies reveal large-scale turnover of enhancers, a specific understanding of the molecular steps by which mammalian or primate enhancers evolve remains elusive. RESULTS: We identified candidate hominoid-specific liver enhancers from H3K27ac ChIP-seq data. After locating orthologs in 11 primates spanning around 40 million years, we synthesized all orthologs as well as computational reconstructions of 9 ancestral sequences for 348 active tiles of 233 putative enhancers. We concurrently tested all sequences for regulatory activity with STARR-seq in HepG2 cells. We observe groups of enhancer tiles with coherent trajectories, most of which can be potentially explained by a single gain or loss-of-activity event per tile. We quantify the correlation between the number of mutations along a branch and the magnitude of change in functional activity. Finally, we identify 84 mutations that correlate with functional changes; these are enriched for cytosine deamination events within CpGs. CONCLUSIONS: We characterized the evolutionary-functional trajectories of hundreds of liver enhancers throughout the primate phylogeny. We observe subsets of regulatory sequences that appear to have gained or lost activity. We use these data to quantify the relationship between sequence and functional divergence, and to identify CpG deamination as a potentially important force in driving changes in enhancer activity during primate evolution.

Contrasting Rates of LINE-1 Amplification among New World Primates of the Atelidae Family.

LINE-1 (L1) retrotransposons constitute the dominant category of transposons in mammalian genomes. L1 elements are active in the vast majority of mammals, and only a few cases of L1 extinction have been documented. The only possible case of extinction in primates was suggested for South American spider monkeys. However, these previous studies were based on a single species. We revisited this question with a larger phylogenetic sample, covering all 4 genera of Atelidae and 3 species of spider monkeys. We used an enrichment method to clone recently inserted L1 elements and performed an evolutionary analysis of the sequences. We were able to identify young L1 elements in all taxa, suggesting that L1 is probably still active in all Atelidae examined. However, we also detected considerable variations in the proportion of recent elements indicating that the rate of L1 amplification varies among Atelidae by a 3-fold factor. The extent of L1 amplification in Atelidae remains overall lower than in other New World monkeys. Multiple factors can affect the amplification of L1, such as the demography of the host and the control of transposition. These factors are discussed in the context of host life history.

The rise and fall of a genus: Complete mtDNA genomes shed light on the phylogenetic position of yellow-tailed woolly monkeys, Lagothrix flavicauda, and on the evolutionary history of the family Atelidae (Primates: Platyrrhini).

Using complete mitochondrial genome sequences, we provide the first molecular analysis of the phylogenetic position of the yellow-tailed woolly monkey, Lagothrix flavicauda (a.k.a. Oreonax flavicauda), a critically endangered neotropical primate endemic to northern Perú. The taxonomic status and phylogenetic position of yellow-tailed woolly monkeys have been debated for many years, but in this study both Bayesian and maximum likelihood phylogenetic reconstructions unequivocally support a monophyletic woolly monkey clade that includes L. flavicauda as the basal taxon within the radiation. Bayesian dating analyses using several alternative calibrations suggest that the divergence of yellow-tailed woolly monkeys from other Lagothrix occurred in the Pleistocene, ∼2.1Ma, roughly 6.5 my after the divergence of woolly monkeys from their sister genus, Brachyteles. Additionally, comparative analysis of the cytochrome oxidase subunit 2 (COX2) gene shows that genetic distances between yellow-tailed woolly monkeys and other Lagothrix from across the genus' geographic distribution fall well within the range of between-species divergences seen in a large number of other platyrrhine primate genera at the same locus and outside the range of between-genus divergences. Our results thus confirm a position within Lagothrix for the yellow-tailed woolly monkey and strongly suggest that the name Oreonax be formally considered a synonym for this genus. This revision in taxonomic status does not change the dire conservation threats facing the yellow-tailed woolly monkey in Perú, where the remaining wild population is estimated at only ∼10,000 individuals living in a highly fragmented landscape.

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.

Trypanoxyuris (Paraoxyuronema) lagothricis (Nematoda: Oxyuridae) in Lagothrix cana (Primates: Atelidae) from Brazil.

During necropsy of a specimen of Lagothrix cana (É. Geoffroy, 1812) (Primates: Atelidae) from the Brazilian Amazon, pinworms were found in the large intestine. The intensity of infection was 64 parasites (17 males and 47 females) and there were no gross pathological changes related to parasitism. After morphological analysis the parasites were identified as Trypanoxyuris (Paraoxyuronema) lagothricis (Buckley, 1931) (Nematoda: Oxyuridae). This is the first record of this oxyurid species in primates in Brazil.

Chromosome evolution in new world monkeys (Platyrrhini).

During the last decades, New World monkey (NWM, Platyrrhini, Anthropoideae) comparative cytogenetics has shed light on many fundamental aspects of genome organisation and evolution in this fascinating, but also highly endangered group of neotropical primates. In this review, we first provide an overview about the evolutionary origin of the inferred ancestral NWM karyotype of 2n = 54 chromosomes and about the lineage-specific chromosome rearrangements resulting in the highly divergent karyotypes of extant NWM species, ranging from 2n = 16 in a titi monkey to 2n = 62 in a woolly monkey. Next, we discuss the available data on the chromosome phylogeny of NWM in the context of recent molecular phylogenetic analyses. In the last part, we highlight some recent research on the molecular mechanisms responsible for the large-scale evolutionary genomic changes in platyrrhine monkeys.

Secondary seed dispersal by dung beetles in an Amazonian forest fragment of Colombia: influence of dung type and edge effect.

Seeds of many plant species are secondarily dispersed by dung beetles, but the outcome of this interaction is highly context-specific. Little is known about how certain anthropogenic disturbances affect this plant-animal interaction. The aims of this study were to assess the effect of dung type on secondary dispersal by dung beetles in a forest fragment, and to determine whether this interaction is affected by edge effects. Using pitfall traps, we captured dung beetles attracted to dung of 2 frugivorous mammals: woolly monkeys and howler monkeys. We found differences between both dung beetle assemblages, but these differences were not consistent in time. Using seeds surrounded by both dung types, we carried out a field experiment using seeds of 2 plant species. We found that the probability of secondary dispersal by dung beetles was higher for seeds placed in woolly monkey dung. Finally, we carried out a field experiment using plastic beads as seed mimics to assess edge effects. We found that secondary seed dispersal by dung beetles was negatively affected by edges. The disruption of plant-animal interactions along anthropogenic forest edges could have long-term negative effects on forest dynamics by affecting processes of regeneration.

[Occurrence of Trypanoxyuris (Trypanoxyuris) minutus (Schneider, 1866) (Nematoda, Oxyuridae) in Alouatta guariba clamitans Cabrera, 1940 (Primates, Atelidae) in Minas Gerais, Brazil]. / Ocorrência de Trypanoxyuris (Trypanoxyuris) minutus (Schneider, 1866) (Nematoda, Oxyuridae) em Alouatta guariba clamitans Cabrera, 1940 (Primates, Atelidae) em Minas Gerais, Brasil.

This study aims to register the occurrence of Trypanoxyuris (Trypanoxyuris) minutus in Alouatta guariba clamitans, in Minas Gerais state, Brazil. Two specimens of A. guariba clamitans, died accidentally, have been necropsied for parasitological studies. Only the large intestine and caecum were infected by T. minutus. The parasitism intensity was 6650 parasites and the density was 2.6 parasites/cm3 of large intestine. In the caecum, the mean intensity was 6753 +/- 490.73 parasites, with mean density of 6.23 +/- 5.13 parasites/cm3. The present study supplies information on adult nematodes biometry and this is the first record of T. (T.) minutus in A. guariba clamitans from Minas Gerais State, Brazil.

Sex differences in vocal patterns in the northern muriqui (Brachyteles hypoxanthus).

We investigated whether sex differences in spatial dynamics correlate with rates of staccato and neigh vocalizations in northern muriquis (Brachyteles hypoxanthus) at the Reserva Particular do Patrimônio Natural-Feliciano Miguel Abdala, Minas Gerais, Brazil. A total of 2,727 10 min focal subject samples were collected on 32 adult females and 31 adult males between April 2007 and March 2008. Compared with males, females spent a significantly lower proportion of their time in proximity to other group members and gave staccatos at significantly higher rates while feeding, resting, and traveling. Conversely, males emitted neigh vocalizations at significantly higher rates than females when feeding and resting only. Both sexes gave significantly more staccatos when feeding than when they were engaged in other activities, but their respective rates of neighs did not vary across activities. Both females and males emitted staccato vocalizations at significantly higher rates during times of the year when preferred foods were scarce, but no seasonal differences in the rates of neigh vocalizations were observed in either sex. Females and males showed a reduction in the number of neighbors following staccato vocalizations and an increase in the number of neighbors following neigh vocalizations. Our findings of sex differences in the rates of staccato and neigh vocalizations and the effects of these vocalizations on interindividual spacing are consistent with sex differences in spatial dynamics, and confirm the role of vocal communication in mediating spatial associations in this species.

The Y chromosome of the Atelidae family (Platyrrhini): study by chromosome microdissection.

In order to study the intergeneric variability of the Y chromosome, we describe the hybridization of the Y chromosome of Brachytelesarachnoides, obtained by microdissection, to metaphases of Atelesbelzebuthmarginatus, Lagothrixlagothricha, and Alouatta male specimens. Brachytelesarachnoides (Atelinae) has 62 chromosomes and a very small Y chromosome. Our results showed that the Brachytelesarachnoides Y chromosome probe hybridized to Lagothrixlagothricha metaphases yielding one hybridization signal on only the tiny Y chromosome, and when hybridized with Atelesbelzebuthmarginatus metaphases it yielded one hybridization signal on two thirds of the small acrocentric Y chromosome. However, no hybridization signal was observed in Alouatta metaphases (subfamily Alouattinae), a closely related genus in the Atelidae family. Furthermore, our data support a close phylogenetic relationship among Brachyteles, Ateles, and Lagothrix and their placement in the Atelinae subfamily, but exclude Alouatta from this group indicating its placement as basal to this group.

Hepatitis B virus infection in non-human primates.

Hepatitis B viruses (HBVs) represent a serious public health problem affecting 350 to 400 million HBV carriers worldwide. The virus does not exclusively infect humans, but can also be found in non-human primates as in the families Hominidae (chimpanzee, gorilla, orangutan) and Hylobatidae (gibbon), which are distributed over Africa (chimpanzee and gorilla) and Southeast Asia (orangutan and gibbon), the endemic areas of human HBV. The prevalence of asymptomatic HBV carriers reaches in gibbons 23-33% and in orangutans 15%. The genome organization of non-human primate HBVs is nearly identical to that of human HBVs. Because of this close similarity, the question of cross-transmission of HBV between species has arisen. There are many data on cross-transmission of human HBVs to the non-human primates. However, a cross-transmission of HBVs from non-human primates to humans has not been reported yet. Using more advanced diagnostic methods, the non-human primates have increasingly been identified as a reservoir of several viruses such as lymphocryptoviruses, Cercopithecine herpesvirus 1 (CeHV-1), Simian immunodeficiency virus (SIV), Simian foamy virus (SFV), and HBVs. Thus veterinarians, zookeepers, or people in close contact with non-human primates may potentially become infected with those viruses causing severe diseases. Enhanced awareness of prevalence, genetic relatedness and evolution of non-human primate HBVs will help prevent further spread and cross-transmission of these viruses between humans and non-human primates.

Retropositional events consolidate the branching order among New World monkey genera.

Due to contradicting relationships obtained from various morphological and genetic studies, phylogenetic relationships among New World monkey genera are highly disputed. In the present study, we analyzed the presence/absence pattern of 128 SINE integrations in all New World monkey genera. Among them, 70 were specific for only a single genus, whereas another 18 were present in all New World monkey genera. The 40 remaining insertions were informative to elucidate phylogenetic relationships among genera. Several of them confirmed the monophyly of the three families Cebidae, Atelidae and Pitheciidae as well as of the subfamily Callithrichinae. Further markers provided evidence for a sister grouping of Cebidae and Atelidae to the exclusion of Pitheciidae as well as for relationships among genera belonging to Callithrichinae and Atelidae. Although a close affiliation of Saimiri, Aotus and Cebus to Callithrichinae was shown, the relationships among the three genera remained unresolved due to three contradicting insertions.

Importance of achromatic contrast in short-range fruit foraging of primates.

Trichromatic primates have a 'red-green' chromatic channel in addition to luminance and 'blue-yellow' channels. It has been argued that the red-green channel evolved in primates as an adaptation for detecting reddish or yellowish objects, such as ripe fruits, against a background of foliage. However, foraging advantages to trichromatic primates remain unverified by behavioral observation of primates in their natural habitats. New World monkeys (platyrrhines) are an excellent model for this evaluation because of the highly polymorphic nature of their color vision due to allelic variation of the L-M opsin gene on the X chromosome. In this study we carried out field observations of a group of wild, frugivorous black-handed spider monkeys (Ateles geoffroyi frontatus, Gray 1842, Platyrrhini), consisting of both dichromats (n = 12) and trichromats (n = 9) in Santa Rosa National Park, Costa Rica. We determined the color vision types of individuals in this group by genotyping their L-M opsin and measured foraging efficiency of each individual for fruits located at a grasping distance. Contrary to the predicted advantage for trichromats, there was no significant difference between dichromats and trichromats in foraging efficiency and we found that the luminance contrast was the main determinant of the variation of foraging efficiency among red-green, blue-yellow and luminance contrasts. Our results suggest that luminance contrast can serve as an important cue in short-range foraging attempts despite other sensory cues that could be available. Additionally, the advantage of red-green color vision in primates may not be as salient as previously thought and needs to be evaluated in further field observations.

Fruit diet of Alouatta guariba and Brachyteles arachnoides in Southeastern Brazil: comparison of fruit type, color, and seed size.

Fruit is an important food resource for neotropical primates. In this study I compare the fruit diet of sympatric brown howlers (Alouatta guariba) and southern muriquis (Brachyteles arachnoides). Feeding behavior was studied over 12 months and fruit species consumed were identified and assigned to the categories fruit type, fruit color, and seed size. Observed-fruit feeding records were compared with expected records determined from local availability of the fruit of the tree species. I also determined dietary overlap. Fruit consumption occupied 8 and 12% of the feeding time of A. guariba and B. arachnoides, respectively. Fruit from eight tree species were consumed by the former and fruit from twenty-two species by the latter. Patterns of fruit selection of A. guariba and B. arachnoides varied widely. Although howlers and muriquis converge behaviorally by selecting fruit with common attributes (fleshy/unprotected, violet and brown/black-colored), unlike A. guariba, B. arachnoides fed on immature seeds of fleshy/protected and dry fruit. Large seeds were ingested, and defecated intact, by B. arachnoides only. There was little overlap of fruit diet even within categories that had been selected by both, suggesting that dietary divergence is occurring at the interspecific level. Different resource exploitation probably mediates the coexistence of A. guariba and B. arachnoides in low diversity, semideciduous forests, where the environment imposes narrow limits on primate food choices.

A case of infant swapping by wild northern muriquis (Brachyteles hypoxanthus).

Allo-parenting has been observed in a variety of female primates, and typically infants are reunited with their biological mothers assuming that their mothers are alive. We observed an exception to this pattern when two wild northern muriquis (Brachyteles hypoxanthus) exchanged infants of different sexes and then reared their adopted infants through weaning. The process of this exchange began when the infants were 4 and 8 days old, respectively. The mother of a 4-day old female carried and nursed her own daughter and the 8-day old son of a second female. The exchange ended when the second mother was first observed carrying the wrong infant 1.5 days later. This observation raises questions about the age and mechanisms of mother-infant recognition in this species, and about assumptions of mother-infant relatedness based on behavioral observations alone.

Polymorphism of visual pigment genes in the muriqui (Primates, Atelidae).

Colour vision varies within the family Atelidae (Primates, Platyrrhini), which consists of four genera with the following cladistic relationship: {Alouatta[Ateles (Lagothrix and Brachyteles)]}. Spider monkeys (Ateles) and woolly monkeys (Lagothrix) are characteristic of platyrrhine monkeys in possessing a colour vision polymorphism. The polymorphism results from allelic variation of the single-locus middle-to-long wavelength (M/L) cone opsin gene on the X-chromosome. The presence in the population of alleles coding for different M/L photopigments results in a variety of colour vision phenotypes. Such a polymorphism is absent in howling monkeys (Alouatta), which, alone among platyrrhines, acquired uniform trichromatic vision similar to that of Old World monkeys, apes, and humans through opsin gene duplication. Dietary and morphological similarities between howling monkeys and muriquis (Brachyteles) raise the possibility that the two genera share a similar form of colour vision, uniform trichromacy. Yet parsimony predicts that the colour vision of Brachyteles will resemble the polymorphism present in Lagothrix and Ateles. Here we test this assumption. We obtained DNA from the blood or faeces of 18 muriquis and sequenced exons 3 and 5 of the M/L opsin gene. Our results affirm the existence of a single M/L cone opsin gene in the genus Brachyteles. We detected three alleles with predicted lambdamax values of 530, 550, and 562 nm. Two females were heterozygous and are thus predicted to have different types of M/L cone pigment. We discuss the implication of this result towards understanding the evolutionary ecology of trichromatic vision.