Mitochondrial relationships and divergence dates of the African colobines: evidence of Miocene origins for the living colobus monkeys

Novel Gammapapillomavirus type in the nasal cavity of a wild red colobus (Piliocolobus tephrosceles)

Papillomaviruses (PVs) are double-stranded, circular, epitheliotropic DNA viruses causing benign warts (papillomas) or inducing dysplasia that can progress to cancer. Although they have been identified in all vertebrate taxa, most classified types are human PVs (HPVs); relatively little is known about PVs in other species. Here we characterize a novel Gammapapillomavirus type, PtepPV1, from a nasal swab of a wild red colobus (Piliocolobus tephrosceles) in Kibale National Park, Uganda. The virus has a genome of 6576 bases, encoding the seven canonical early (E) ORFs (E6, E7, E1, E2, E4, E1^E4 and E8^E2) and two late (L) ORFs (L1 and L2) of the gammapapillomaviruses, and is 81.0% similar to HPV-mSK_118, detected in a cutaneous wart from an immunocompromised human patient, in the L1 gene at the amino acid level. Alphapapillomaviruses (genus Alphapapillomavirus) cause anogenital carcinomas such as cervical cancer and have been described previously in several nonhuman primates. However, the first gammapapillomavirus (genus Gammapapillomavirus), which cause transient cutaneous infections, was not described until 2019 in a healthy rhesus macaque (Macaca mulatta) genital swab. The new virus from red colobus, PtepPV1, has many genomic features encoded by high-risk oncogenic PVs, such as the E7 gene LXSXE and CXXC motifs, suggesting potential for pRb and zinc-finger binding, respectively. To our knowledge, PtepPV1 is also the first reported nonhuman primate PV found in the nasal cavity. PtepPV1 expands the known host range, geographical distribution, tissue tropism and biological characteristics of nonhuman primate PVs.

Social network dynamics, infant loss, and gut microbiota composition in female Colobus vellerosus during time periods with alpha male challenges

The gut microbiota of group-living animals is strongly influenced by their social interactions, but it is unclear how it responds to social instability. We investigated whether social instability associated with the arrival of new males and challenges to the alpha male position could explain differences in the gut microbiota in adult female Colobus vellerosus at Boabeng-Fiema, Ghana. First, we used a data set collected during May-August 2007 and May 2008-2009 that consisted of (i) 50 fecal samples from adult females in eight social groups for V4 16S rRNA sequencing to determine gut microbiota composition, and (ii) demographic and behavioral data ad libitum to determine male immigration, challenges to the alpha male position, and infant births and deaths. Sørensen and Bray-Curtis beta diversity indices (i.e., between-sample microbiota variation) were predicted by year, alpha male stability, group identity, and age. Next, we used a more detailed behavioral data set collected during focal observations of adult females in one group with a prolonged alpha male takeover and three cases of infant loss, to create 12-month versus 3-month 1-m proximity networks that preceded and overlapped the gut microbiome sampling period in that group. The long versus short-term networks were not correlated, suggesting temporal variation in proximity networks. In this group, beta diversity among the five adult females was predicted by similarity in infant loss status and short-term (rather than yearly) 1-m proximity ties. Although the mechanism driving this association needs to be further investigated in future studies, our findings indicate that alpha male takeovers are associated with gut microbiota variation and highlight the importance of taking demographic and social network dynamics into account.

Aspects of molar form and dietary proclivities of African colobines

This study investigates aspects of molar form in three African colobine species: Colobus polykomos, Colobus angolensis, and Piliocolobus badius. Our samples of C. polykomos and P. badius are from the Taï Forest, Ivory Coast; our sample of C. angolensis is from Diani, Kenya. To the extent that protective layers surrounding seeds are hard, we predicted that molar features related to hard-object feeding would be more pronounced in Colobus than they are Piliocolobus, as seed-eating generally occurs at higher frequencies in species of the former. We further predicted that among the colobines we studied, these features would be most pronounced in Taï Forest C. polykomos, which feeds on Pentaclethra macrophylla seeds encased within hard and tough seed pods. We compared overall enamel thickness, enamel thickness distribution, absolute crown strength, cusp tip geometry, and flare among molar samples. Sample sizes per species and molar type varied per comparison. We predicted differences in all variables except overall enamel thickness, which we expected would be invariant among colobines as a result of selection for thin enamel in these folivorous species. Of the variables we examined, only molar flare differed significantly between Colobus and Piliocolobus. Our findings suggest that molar flare, an ancient feature of cercopithecoid molars, was retained in Colobus but not in Piliocolobus, perhaps as a result of differences in the seed-eating proclivities of the two genera. Contrary to predictions, none of the aspects of molar form we investigated tracked current dietary differences in seed-eating between the two Colobus species. Finally, we explored the possibility that molar flare and absolute crown strength, when analyzed together, might afford greater differentiation among these colobine species. A multivariate t test of molar flare and absolute crown strength differentiated C. polykomos and P. badius, possibly reflecting known niche divergence between these two sympatric Taï Forest species.

Keeping 21st Century Paleontology Grounded: Quantitative Genetic Analyses and Ancestral State Reconstruction Re-Emphasize the Essentiality of Fossils

Advances in genetics and developmental biology are revealing the relationship between genotype and dental phenotype (G:P), providing new approaches for how paleontologists assess dental variation in the fossil record. Our aim was to understand how the method of trait definition influences the ability to reconstruct phylogenetic relationships and evolutionary history in the Cercopithecidae, the Linnaean Family of monkeys currently living in Africa and Asia. We compared the two-dimensional assessment of molar size (calculated as the mesiodistal length of the crown multiplied by the buccolingual breadth) to a trait that reflects developmental influences on molar development (the inhibitory cascade, IC) and two traits that reflect the genetic architecture of postcanine tooth size variation (defined through quantitative genetic analyses: MMC and PMM). All traits were significantly influenced by the additive effects of genes and had similarly high heritability estimates. The proportion of covariate effects was greater for two-dimensional size compared to the G:P-defined traits. IC and MMC both showed evidence of selection, suggesting that they result from the same genetic architecture. When compared to the fossil record, Ancestral State Reconstruction using extant taxa consistently underestimated MMC and PMM values, highlighting the necessity of fossil data for understanding evolutionary patterns in these traits. Given that G:P-defined dental traits may provide insight to biological mechanisms that reach far beyond the dentition, this new approach to fossil morphology has the potential to open an entirely new window onto extinct paleobiologies. Without the fossil record, we would not be able to grasp the full range of variation in those biological mechanisms that have existed throughout evolution.

Skull variation in Afro-Eurasian monkeys results from both adaptive and non-adaptive evolutionary processes

Afro-Eurasian monkeys originated in the Miocene and are the most species-rich modern primate family. Molecular and fossil data have provided considerable insight into their evolutionary divergence, but we know considerably less about the evolutionary processes that underlie these differences. Here, we apply tests developed from quantitative genetics theory to a large (n > 3000) cranio-mandibular morphometric dataset, investigating the relative importance of adaptation (natural selection) and neutral processes (genetic drift) in shaping diversity at different taxonomic levels, an approach applied previously to monkeys of the Americas, apes, hominins, and other vertebrate taxa. Results indicate that natural selection, particularly for differences in size, plays a significant role in diversifying Afro-Eurasian monkeys as a whole. However, drift appears to better explain skull divergence within the subfamily Colobinae, and in particular the African colobine clade, likely due to habitat fragmentation. Small and declining population sizes make it likely that drift will continue in this taxon, with potentially dire implications for genetic diversity and future resilience in the face of environmental change. For the other taxa, many of whom also have decreasing populations and are threatened, understanding adaptive pressures similarly helps identify relative vulnerability and may assist with prioritising scarce conservation resources.

Mitochondrial genetic diversity and divergence dating of Angolan colobus monkeys (Colobus angolensis) in the eastern forests of Kenya and Tanzania: Implications for subspeciation and reconstructing historical biogeography

Whether the Colobus angolensis that reside in the fragmented forests in eastern Kenya and Tanzania represent one subspecies or two has been debated for 50 years. Morphological and more recent genetic and ecological studies suggest that these populations represent two subspecies, C. a. palliatus and C. a. sharpei. However, their distribution of mitochondrial variation remains unresolved since the genetic study only characterized four populations at the range ends. Therefore, we characterized five populations in the area of the hypothesized subspecies divide. We identified eight new haplotypes which, combined with those previously identified, provided 26 haplotypes from nine populations for analysis. Haplotypes found south of the Rufiji River cluster together but separately from northern haplotypes. The largest sequence differences within cytochrome b occur between population pairs representing opposite sides of the river; their mean difference (1.5%) is more than that of other primate subspecies. Analysis of molecular variance attributes most of the variation to that north versus south of the river. These results support the previous subspecies distinction between C. a. palliatus (northern) and C. a. sharpei (southern), divided by the Rufiji River. The estimated time of the most recent common ancestor of all haplotypes indicates that the subspecies have been isolated from each other for approximately 550,000 years. The common ancestor of northern and southern haplogroups was 370,000 and 290,000 years ago, respectively. Nevertheless, the correlation between genetic and geographic distances suggests that isolation-by-distance contributed to population structuring. Significant variation among populations, with only three haplotypes shared between populations, also indicates that an extended period of isolation drove population distinctiveness. Considering these results, we evaluate hypotheses about the founding and differentiation of these subspecies during Pleistocene climatic fluctuations and propose a novel, more direct migration route from Central Africa to their current range navigating Lake Tanganyika, the central Tanzanian corridor, and the Rufiji River.

Masticatory and ingestive effort in Procolobus verus, a small-bodied African colobine

The olive colobus (Procolobus verus) is the smallest extant colobine. Based on the axiom that folivory is associated with larger body mass, the olive colobus is expected to be less folivorous than its sister taxon Piliocolobus badius, but previous studies show that the opposite is true. Here we test the hypothesis that masticatory and ingestive effort in the olive colobus is greater due to allometric factors related to bite force scaling and throughput of ingested foods. We analyzed oral processing data collected on olive colobus in the Taï Forest, Ivory Coast, between May 2016 and May 2018. We compare these with previously published data on P. badius and Colobus polykomos from Taï. In terms of overall feeding effort, olive colobus invest more effort (i.e., chewing cycles) than the larger colobines. When contrasts are restricted to commonly consumed foods, this greater energetic investment is not consistently observed. Ingestion of young leaves is associated with a reduced number of masticatory cycles in all three colobine species. A slightly elevated average effort in the olive colobus during young leaf feeding suggests this food source is more challenging in smaller monkeys, but mature leaf processing effort is generally the same among Taï colobines. Thus, for olive colobus, leaf ductility may be more problematic than leaf toughness in terms of masticatory effort. While there may be an allometric cost to being a small colobine, food selectivity is an important mitigating factor.

Can morphotaxa be assessed with photographs? Estimating the accuracy of two-dimensional cranial geometric morphometrics for the study of threatened populations of African monkeys

The classification of most mammalian orders and families is under debate and the number of species is likely greater than currently recognized. Improving taxonomic knowledge is crucial, as biodiversity is in rapid decline. Morphology is a source of taxonomic knowledge, and geometric morphometrics applied to two dimensional (2D) photographs of anatomical structures is commonly employed for quantifying differences within and among lineages. Photographs are informative, easy to obtain, and low cost. 2D analyses, however, introduce a large source of measurement error when applied to crania and other highly three dimensional (3D) structures. To explore the potential of 2D analyses for assessing taxonomic diversity, we use patas monkeys (Erythrocebus), a genus of large, semi-terrestrial, African guenons, as a case study. By applying a range of tests to compare ventral views of adult crania measured both in 2D and 3D, we show that, despite inaccuracies accounting for up to one-fourth of individual shape differences, results in 2D almost perfectly mirror those in 3D. This apparent paradox might be explained by the small strength of covariation in the component of shape variance related to measurement error. A rigorous standardization of photographic settings and the choice of almost coplanar landmarks are likely to further improve the correspondence of 2D to 3D shapes. 2D geometric morphometrics is, thus, appropriate for taxonomic comparisons of patas ventral crania. Although it is too early to generalize, our results corroborate similar findings from previous research in mammals, and suggest that 2D shape analyses are an effective heuristic tool for morphological investigation of small differences.

An assessment of the postcranial skeleton of the Paracolobus mutiwa (Primates: Colobinae) specimen KNM-WT 16827 from Lomekwi, West Turkana, Kenya

The postcranium of a large-bodied colobine monkey attributed to Paracolobus mutiwa from the site of Lomekwi, West Turkana, Kenya, is described. The partial skeleton (KNM-WT 16827) was recovered from locality LO 1, dated to 2.58-2.53 Ma, and preserves postcranial elements including fragments of scapula, humerus, proximal ulna, proximal radius, os coxae, proximal femur, astragalus, and calcaneus. KNM-WT 16827 was identified as P. mutiwa based on cranial similarities to the holotype female maxilla (KNM-ER 3843) and the holotype of Paracolobus chemeroni (KNM-BC 3), but is currently the only specimen of this taxon with associated cranial and postcranial elements. The skeleton is morphologically distinct from other large cercopithecid specimens from the Turkana Basin, including several assigned to Cercopithecoides williamsi, Cercopithecoides kimeui, Rhinocolobus turkanaensis, and Theropithecus oswaldi and differs from KNM-BC 3 in the larger cranium and shorter and more robust long bones. KNM-WT 16827 has forelimb and hindlimb features exhibiting a mixture of traits more associated with terrestrial locomotor behavior, including robust humeral deltoid tuberosity, retroflexed humeral medial epicondyle, deep ulnar trochlear notch, relatively short lower iliac height, prominent femoral greater trochanter, asymmetrical astragalar trochlea, and weak digit flexor grooves on the calcaneus. KNM-WT 16827 is also proportionally distinct from KNM-BC 3 and other Turkana Basin specimens attributed to large-bodied taxa such as C. williamsi, C. kimeui, R. turkanaensis, and T. oswaldi in having relatively shorter limbs and smaller tarsals. The traits shared with P. chemeroni and other extinct taxa are either typical for colobines, or likely due to P. mutiwa and P. chemeroni sharing adaptations for terrestrial locomotion relative to extant colobinans. Although a full cranial assessment is needed, based on its postcranial morphology KNM-WT 16827 is distinct from KNM-BC 3, C. williamsi, R. turkanaensis, Theropithecus, and extant colobines, warranting further analyses to better assess the taxonomic assignment of the specimen.

Tectonics, climate and the diversification of the tropical African terrestrial flora and fauna

Tropical Africa is home to an astonishing biodiversity occurring in a variety of ecosystems. Past climatic change and geological events have impacted the evolution and diversification of this biodiversity. During the last two decades, around 90 dated molecular phylogenies of different clades across animals and plants have been published leading to an increased understanding of the diversification and speciation processes generating tropical African biodiversity. In parallel, extended geological and palaeoclimatic records together with detailed numerical simulations have refined our understanding of past geological and climatic changes in Africa. To date, these important advances have not been reviewed within a common framework. Here, we critically review and synthesize African climate, tectonics and terrestrial biodiversity evolution throughout the Cenozoic to the mid-Pleistocene, drawing on recent advances in Earth and life sciences. We first review six major geo-climatic periods defining tropical African biodiversity diversification by synthesizing 89 dated molecular phylogeny studies. Two major geo-climatic factors impacting the diversification of the sub-Saharan biota are highlighted. First, Africa underwent numerous climatic fluctuations at ancient and more recent timescales, with tectonic, greenhouse gas, and orbital forcing stimulating diversification. Second, increased aridification since the Late Eocene led to important extinction events, but also provided unique diversification opportunities shaping the current tropical African biodiversity landscape. We then review diversification studies of tropical terrestrial animal and plant clades and discuss three major models of speciation: (i) geographic speciation via vicariance (allopatry); (ii) ecological speciation impacted by climate and geological changes, and (iii) genomic speciation via genome duplication. Geographic speciation has been the most widely documented to date and is a common speciation model across tropical Africa. We conclude with four important challenges faced by tropical African biodiversity research: (i) to increase knowledge by gathering basic and fundamental biodiversity information; (ii) to improve modelling of African geophysical evolution throughout the Cenozoic via better constraints and downscaling approaches; (iii) to increase the precision of phylogenetic reconstruction and molecular dating of tropical African clades by using next generation sequencing approaches together with better fossil calibrations; (iv) finally, as done here, to integrate data better from Earth and life sciences by focusing on the interdisciplinary study of the evolution of tropical African biodiversity in a wider geodiversity context.

New dentognathic fossils of Noropithecus bulukensis (Primates, Victoriapithecidae) from the late Early Miocene of Buluk, Kenya

The late Early Miocene site of Buluk, Kenya, has yielded fossil remains of several catarrhine primates, including 16 dentognathic specimens of the stem cercopithecoid Noropithecus bulukensis. With the exception of the large sample of Victoriapithecus macinnesi from the middle Miocene of Maboko Island, Kenya, the majority of stem cercopithecoid taxa are represented by small sample sizes. We describe and analyze 91 new cercopithecoid fossils collected from Buluk between 2004 and 2018, including several previously undescribed tooth positions for N. bulukensis, and provide the first evaluation of dental metric and morphological variation in this sample. The results show that the expanded Buluk sample exhibits high levels of dental variation in the postcanine tooth row, similar to V. macinnesi at Maboko, but this variation is consistent with a single-species hypothesis. Subtle differences in the shape of the I¹, breadth of the C¹ and P³, relative breadth of M¹, upper and lower molar distal shelf lengths, the degree of M₂ basal flare, and a less-developed lower molar distal lophid differentiate the dentition of N. bulukensis from V. macinnesi. Although differences exist between the N. bulukensis and V. macinnesi dental samples, the high degree of variation within each sample complicates the identification of many individual specimens. New partial maxillae and mandibles allow reassessment of previously described diagnostic differences between N. bulukensis and V. macinnesi, negating upper molar arcade shape as a diagnostic feature and confirming the existence of differences in mandibular symphyseal morphology. Overall, new fossils from Buluk provide new evidence of the dentognathic anatomy of a medium-sized cercopithecoid that coexisted with a diverse group of noncercopithecoid catarrhines at the end of the early Miocene.

Oldest colobine calcaneus from East Asia (Zhaotong, Yunnan, China)

Apart from a juvenile hominoid, the locality of Shuitangba (southwestern China, 6.5-6.0 Ma) has yielded a mandible and proximal femur attributed to the colobine genus Mesopithecus. A complete colobine calcaneus also accompanies this material, but its association with the other Mesopithecus material remains to be confirmed. These fossil elements are very important as they represent the oldest known colobines from East Asia, extend the dispersal of Mesopithecus to southwestern China, and underscore its close affinities and potential ancestry to the odd-nosed colobines. The present article focuses on the functional morphology of this complete calcaneus to reconstruct the positional habits, infer the paleocology, and understand the dispersal patterns of this fossil colobine. The studied characters corroborate the attribution of this element to colobines and support potential affinities with the Mesopithecus remains of the same locality. Functionally, characters such as the long and narrow tuber calcanei, the short proximal calcaneal region, and the relatively extended and long and narrow proximal calcaneoastragalar facet appear to enable habitual pedal flexion with conjunct inversion that accommodate the foot on diversely oriented and differently sized arboreal substrates. On the other hand, the relatively short distal calcaneal region is functionally related to (mainly terrestrial) quadrupedal activities, wherein thrust and rapid flexion are required. This combination of characters suggests that the Shuitangba colobine could move at ease on arboreal substrates and was also able to occasionally use terrestrial substrates. The potential affinities of this calcaneus to Mesopithecus and its positional profile most likely imply an eastward migration via forested corridors. In Shuitangba, this fossil colobine could trophically and positionally exploit a wide range of habitats successfully coexisting with resident hominoids.

Skeletal morphology of the lesula (Cercopithecus lomamiensis) and the evolution of guenon locomotor behavior

OBJECTIVES

The guenons (tribe Cercopithecini) are a diverse and primarily arboreal radiation of Old World monkeys from Africa. However, preliminary behavioral observations of the lesula (Cercopithecus lomamiensis), a little-known guenon species described in 2012, report it spending substantial amounts of time on the ground. New specimens allow us to present the first description of lesula postcranial morphology and apply a comparative functional morphology approach to supplement our knowledge of its locomotor behavior.

MATERIALS AND METHODS

To infer the substrate use preferences of the lesula, 22 postcranial variables correlated with locomotion were assessed in a sample of 151 adult guenon specimens, including two C. lomamiensis. Using multivariate statistical analyses, we predict the amount of time the lesula spends on the ground relative to the comparative sample.

RESULTS

Results suggest that the lesula spends nearly half its time on the ground, and the two available individuals were classified as semiterrestrial and terrestrial with strong support. Comparisons with two outgroup cercopithecid taxa (Colobus guereza and Macaca mulatta) demonstrate that, as a group, guenons retain signals of a generalized, semiterrestrially adapted postcranium compared to specialized arboreal cercopithecids.

DISCUSSION

These results corroborate preliminary behavioral observations of the lesula as a semiterrestrial to terrestrial primate and imply multiple evolutionary transitions in substrate use among the guenon radiation. A broader view of cercopithecoid evolution suggests that a semiterrestrial ancestor for extant guenons is more parsimonious than an arboreal one, indicating that the arboreal members of the group are probably recently derived from a more semiterrestrial ancestor.

A window into the early evolutionary history of Cercopithecidae: Late Miocene evidence from Chad, Central Africa

Central Africa is known as a major center of diversification for extant Old World Monkeys (OWM) and yet has a poorly documented fossil record of monkeys. Here we report a new colobine monkey (Cercopithecoides bruneti sp. nov.) from the Central African hominin-bearing fossiliferous area of Toros-Menalla, Chad at ca. 7 Ma. In addition to filling a gap in the spatial and temporal record of early OWM evolutionary history, we assess the ecomorphological diversity of early OWM by providing evidence on the onset of a folivorous diet and a partial reacquisition of terrestrial locomotor habits among Miocene colobines. We also support the phylogenetic affinities of the genus Cercopithecoides among the stem group of the extant African colobine monkeys.

Is Colobus guereza gallarum a valid endemic Ethiopian taxon?

Black-and-white colobus (Colobus guereza Rüppell, 1835) are arboreal Old World monkeys inhabiting large parts of the deciduous and evergreen forests of sub-Saharan Africa. Two of the eight subspecies of Colobus guereza are endemic to Ethiopia: C. g. gallarum and C. g. guereza. However, the validity of the Ethiopian taxa is debated and observed morphological differences were attributed to clinal variation within C. g. guereza. To date, no molecular phylogeny of the Ethiopian guerezas is available to facilitate their taxonomic classification. We used mitochondrial DNA markers from 94 samples collected across Ethiopia to reconstruct a phylogeny of respective mitochondrial lineages. In our phylogenetic reconstruction, augmented by orthologous sequence information of non-Ethiopian black-and-white colobus from GenBank, we found two major Ethiopian mitochondrial clades, with one being largely congruent with the distribution of C. g. guereza. The second clade was found only at two locations in the eastern part of the putative range of C. g. gallarum. This second lineage clustered with the lowland form, C. g. occidentalis, from central Africa, whereas the C. g. guereza lineages clustered with C. g. caudatus and C. g. kikuyuensis from Kenya and northern Tanzania. These two guereza lineages diverged around 0.7 million years ago. In addition, mitochondrial sequence information does not support unequivocally a distinction of C. g. caudatus and C. g. kikuyuensis. Our findings indicate a previous biogeographic connection between the ranges of C. g. occidentalis and C. g. gallarum and a possible secondary invasion of Ethiopia by members of the C. g. guereza–C. g. caudatus–C. g. kikuyuensis clade. Given these phylogenetic relationships, our study supports the two-taxa hypothesis, making C. g. gallarum an Ethiopian endemic, and, in combination with the taxon's very restricted range, makes it one of the most endangered subspecies of black-and-white colobus.

Cis-regulatory evolution in a wild primate: Infection-associated genetic variation drives differential expression of MHC-DQA1 in vitro

Few studies have combined genetic association analyses with functional characterization of infection-associated SNPs in natural populations of nonhuman primates. Here, we investigate the relationship between host genetic variation, parasitism and natural selection in a population of red colobus (Procolobus rufomitratus tephrosceles) in Kibale National Park, Uganda. We collected parasitological, cellular and genomic data to test the following hypotheses: (i) MHC-DQA1 regulatory genetic variation is associated with control of whipworm (Trichuris) infection in a natural population of red colobus; (ii) infection-associated SNPs are functional in driving differential gene expression in vitro; and (iii) balancing selection has shaped patterns of variation in the MHC-DQA1 promoter. We identified two SNPs in the MHC-DQA1 promoter, both in transcription factor binding sites, and both of which are associated with decreased control of Trichuris infection. We characterized the function of both SNPs by testing differences in gene expression between the two alleles of each SNP in two mammalian cell lines. Alleles of one of the SNPs drove differential gene expression in both cell lines, while the other SNP drove differences in expression in one of the cell lines. Additionally, we found evidence of balancing selection acting on the MHC-DQA1 promoter, including extensive trans-species polymorphisms between red colobus and other primates, and an excess of intermediate-frequency alleles relative to genome-wide, coding and noncoding RADseq data. Our data suggest that balancing selection provides adaptive regulatory flexibility that outweighs the consequences of increased parasite infection intensity in heterozygotes.

How did bonobos come to range south of the congo river? Reconsideration of the divergence of Pan paniscus from other Pan populations

While investigating the genetic structure in wild bonobos,(1) we realized that the widely accepted scenario positing that the Pleistocene appearance of the Congo River separated the common ancestor of chimpanzees (Pan troglodytes) and bonobos (P. paniscus) into two species is not supported by recent geographical knowledge about the formation of the Congo River. We explored the origin of bonobos using a broader biogeographical perspective by examining local faunas in the central African region. The submarine Congo River sediments and paleotopography of central Africa show that the Congo River has functioned as a geographical barrier for the last 34 million years. This evidence allows us to hypothesize that when the river was first formed, the ancestor of bonobos did not inhabit the current range of the species on the left bank of the Congo River but that, during rare times when the Congo River discharge decreased during the Pleistocene, one or more founder populations of ancestral Pan paniscus crossed the river to its left bank. The proposed scenario for formation of the Congo River and the corridor hypothesis for an ancestral bonobo population is key to understanding the distribution of great apes and their evolution.

Resurrection of the Island Rule: Human-Driven Extinctions Have Obscured a Basic Evolutionary Pattern

Islands are or have been occupied by unusual species, such as dwarf proboscideans and giant rodents. The discussion of the classical but controversial island rule-which states that mammalian body sizes converge on intermediate sizes on islands-has been stimulated by these unusual species. In this study, we use an unprecedented global data set of the distributions and body sizes of late Quaternary mammal species and a novel analytical method to analyze body size evolution on islands. The analyses produced strong support for the island rule. Islands have suffered massive human-driven losses of species, and we found that the support for the island rule was substantially stronger when the many late Quaternary extinct species were also considered (particularly the tendency for dwarfing in large taxa). The decisive support for the island rule in this study confirms that evolution plays out in a markedly different way on islands and that human impact may obscure even fundamental evolutionary patterns.

The Hand of Cercopithecoides williamsi (Mammalia, Primates): Earliest Evidence for Thumb Reduction among Colobine Monkeys

Thumb reduction is among the most important features distinguishing the African and Asian colobines from each other and from other Old World monkeys. In this study we demonstrate that the partial skeleton KNM-ER 4420 from Koobi Fora, Kenya, dated to 1.9 Ma and assigned to the Plio-Pleistocene colobine species Cercopithecoides williamsi, shows marked reduction of its first metacarpal relative to the medial metacarpals. Thus, KNM-ER 4420 is the first documented occurrence of cercopithecid pollical reduction in the fossil record. In the size of its first metacarpal relative to the medial metacarpals, C. williamsi is similar to extant African colobines, but different from cercopithecines, extant Asian colobines and the Late Miocene colobines Microcolobus and Mesopithecus. This feature clearly links the genus Cercopithecoides with the extant African colobine clade and makes it the first definitive African colobine in the fossil record. The postcranial adaptations to terrestriality in Cercopithecoides are most likely secondary, while ancestral colobinans (and colobines) were arboreal. Finally, the absence of any evidence for pollical reduction in Mesopithecus implies either independent thumb reduction in African and Asian colobines or multiple colobine dispersal events out of Africa. Based on the available evidence, we consider the first scenario more likely.

Revisiting the phylogenetic relationships, biogeography, and taxonomy of spider monkeys (genus Ateles) in light of new molecular data

Spider monkeys (Ateles) are one of the most endangered groups of primates in the Neotropics. The genus is widely distributed from Mexico to the north of Bolivia and includes many morphologically distinct forms in terms of pelage color and patterning. The taxonomy, phylogenetic relationships, and biogeographic history of the genus have been subject to much debate, making scientific communication difficult and creating challenges for conservation actions. We extracted DNA from samples of all currently recognized species of spider monkeys collected from across the geographic range of the genus, sequenced ∼3.5 kilobases of coding sequence from the mitochondrial genome, and used this large dataset to (a) infer the phylogenetic relationships among the different forms of spider monkeys, (b) evaluate whether currently recognized species of spider monkeys form reciprocally monophyletic groups that are concordant with contemporary classifications, and (c) estimate divergence dates among the different lineages of Ateles. We found that all proposed species of spider monkeys for which we have samples from multiple localities indeed appear to form monophyletic groups. However, in contrast to previous studies, several of our analyses robustly inferred Ateles marginatus from northeast Brazil as the sister taxon to all other spider monkeys. A Bayesian dating analysis suggests that the most recent common ancestor of extant Ateles dates to ∼6.7 Ma, in the late Miocene, and most species-level splits within the genus took place in the late Pliocene, suggesting that the modern diversity in spider monkeys cannot be explained principally by isolation and divergence of populations in forest refugia during the Pleistocene. Based on our new phylogenetic inference and dating analysis, we propose a revised biogeographic scenario for the evolution of this genus.

Early guenon from the late Miocene Baynunah Formation, Abu Dhabi, with implications for cercopithecoid biogeography and evolution

A newly discovered fossil monkey (AUH 1321) from the Baynunah Formation, Emirate of Abu Dhabi, United Arab Emirates, is important in a number of distinct ways. At ∼ 6.5-8.0 Ma, it represents the earliest known member of the primate subfamily Cercopithecinae found outside of Africa, and it may also be the earliest cercopithecine in the fossil record. In addition, the fossil appears to represent the earliest member of the cercopithecine tribe Cercopithecini (guenons) to be found anywhere, adding between 2 and 3.5 million y (∼ 50-70%) to the previous first-appearance datum of the crown guenon clade. It is the only guenon--fossil or extant--known outside the continent of Africa, and it is only the second fossil monkey specimen so far found in the whole of Arabia. This discovery suggests that identifiable crown guenons extend back into the Miocene epoch, thereby refuting hypotheses that they are a recent radiation first appearing in the Pliocene or Pleistocene. Finally, the new monkey is a member of a unique fauna that had dispersed from Africa and southern Asia into Arabia by this time, suggesting that the Arabian Peninsula was a potential filter for cross-continental faunal exchange. Thus, the presence of early cercopithecines on the Arabian Peninsula during the late Miocene reinforces the probability of a cercopithecoid dispersal route out of Africa through southwest Asia before Messinian dispersal routes over the Mediterranean Basin or Straits of Gibraltar.

The role of ecological opportunity in shaping disparate diversification trajectories in a bicontinental primate radiation

Exceptional species and phenotypic diversity commonly are attributed to ecological opportunity (EO). The conventional EO model predicts that rates of lineage diversification and phenotypic evolution are elevated early in a radiation only to decline later in response to niche availability. Foregut fermentation is hypothesized to be a key innovation that allowed colobine monkeys (subfamily Colobinae), the only primates with this trait, to successfully colonize folivore adaptive zones unavailable to other herbivorous species. Therefore, diversification rates also are expected to be strongly linked with the evolution of traits related to folivory in these monkeys. Using dated molecular phylogenies and a dataset of feeding morphology, I test predictions of the EO model to evaluate the role of EO conferred by foregut fermentation in shaping the African and Asian colobine radiations. Findings from diversification methods coupled with colobine biogeographic history provide compelling evidence that decreasing availability of new adaptive zones during colonization of Asia together with constraints presented by dietary specialization underlie temporal changes in diversification in the Asian but not African clade. Additionally, departures from the EO model likely reflect iterative diversification events in Asia.

Discovery and full genome characterization of two highly divergent simian immunodeficiency viruses infecting black-and-white colobus monkeys (Colobus guereza) in Kibale National Park, Uganda

Background

African non-human primates (NHPs) are natural hosts for simian immunodeficiency viruses (SIV), the zoonotic transmission of which led to the emergence of HIV-1 and HIV-2. However, our understanding of SIV diversity and evolution is limited by incomplete taxonomic and geographic sampling of NHPs, particularly in East Africa. In this study, we screened blood specimens from nine black-and-white colobus monkeys (Colobus guereza occidentalis) from Kibale National Park, Uganda, for novel SIVs using a combination of serology and “unbiased” deep-sequencing, a method that does not rely on genetic similarity to previously characterized viruses.

Results

We identified two novel and divergent SIVs, tentatively named SIVkcol-1 and SIVkcol-2, and assembled genomes covering the entire coding region for each virus. SIVkcol-1 and SIVkcol-2 were detected in three and four animals, respectively, but with no animals co-infected. Phylogenetic analyses showed that SIVkcol-1 and SIVkcol-2 form a lineage with SIVcol, previously discovered in black-and-white colobus from Cameroon. Although SIVkcol-1 and SIVkcol-2 were isolated from the same host population in Uganda, SIVkcol-1 is more closely related to SIVcol than to SIVkcol-2. Analysis of functional motifs in the extracellular envelope glycoprotein (gp120) revealed that SIVkcol-2 is unique among primate lentiviruses in containing only 16 conserved cysteine residues instead of the usual 18 or more.

Conclusions

Our results demonstrate that the genetic diversity of SIVs infecting black-and-white colobus across equatorial Africa is greater than previously appreciated and that divergent SIVs can co-circulate in the same colobine population. We also show that the use of “unbiased” deep sequencing for the detection of SIV has great advantages over traditional serological approaches, especially for studies of unknown or poorly characterized viruses. Finally, the detection of the first SIV containing only 16 conserved cysteines in the extracellular envelope protein gp120 further expands the range of functional motifs observed among SIVs and highlights the complex evolutionary history of simian retroviruses.

[Review of mtDNA in molecular evolution studies]

Mitochondria are old organelles found in most eukaryotic cells. Due to its rapid mutation ratio, mitochondrial DNA (mtDNA) has been widely used as a DNA marker in molecular studies and has long been suggested to undergo neutral evolution or purifying selection. Mitochondria produces 95% of the adenosine triphosphate (ATP) needed for locomotion, and heat for thermoregulation. Recent studies had found that mitochondria play critical roles in energy metabolism, and proved that functional constraints acting on mitochondria, due to energy metabolism and/or thermoregulation, influence the evolution of mtDNA. This review summarizes mitochondrial genome composition, evolution, and its applications in molecular evolution studies (reconstruction of species phylogenesis, the relationship between biological energy metabolism and mtDNA evolution, and the mtDNA codon reassignment influences the adaptation in different creatures).

Early cercopithecid monkeys from the Tugen Hills, Kenya

The modern Old World Monkeys (Superfamily Cercopithecoidea, Family Cercopithecidae) can be traced back into the late Miocene, but their origin and subsequent diversification is obscured by the scarcity of terrestrial fossil sites in Africa between 15 and 6 Ma. Here, we document the presence of cercopithecids at 12.5 Ma in the Tugen Hills of Kenya. These fossils add 3 My to the known antiquity of crown Cercopithecidae. The two specimens represent one or possibly two species of early colobine, and their morphology suggests that they were less folivorous than their modern relatives.

Between-group variation in female dispersal, kin composition of groups, and proximity patterns in a black-and-white colobus monkey (Colobus vellerosus)

A growing body of evidence shows within-population variation in natal dispersal, but the effects of such variation on social relationships and the kin composition of groups remain poorly understood. We investigate the link between dispersal, the kin composition of groups, and proximity patterns in a population of black-and-white colobus (Colobus vellerosus) that shows variation in female dispersal. From 2006 to 2011, we collected behavioral data, demographic data, and fecal samples of 77 males and 92 females residing in eight groups at Boabeng-Fiema, Ghana. A combination of demographic data and a genetic network analysis showed that although philopatry was female-biased, only about half of the females resided in their natal groups. Only one group contained female-female dyads with higher average relatedness than randomly drawn animals of both sexes from the same group. Despite between-group variation in female dispersal and kin composition, female-female dyads in most of the study groups had higher proximity scores than randomly drawn dyads from the same group. We conclude that groups fall along a continuum from female dispersed, not kin-based, and not bonded to female philopatric, kin-based, and bonded. We found only partial support for the predicted link between dispersal, kin composition, and social relationships. In contrast to most mammals where the kin composition of groups is a good predictor of the quality of female-female relationships, this study provides further support for the notion that kinship is not necessary for the development and maintenance of social bonds in some gregarious species.

Primate DNA suggests long-term stability of an African rainforest

Red colobus monkeys, due to their sensitivity to environmental change, are indicator species of the overall health of their tropical rainforest habitats. As a result of habitat loss and overhunting, they are among the most endangered primates in the world, with very few viable populations remaining. Traditionally, extant indicator species have been used to signify the conditions of their current habitats, but they have also been employed to track past environmental conditions by detecting previous population fluctuations. Kibale National Park (KNP) in Uganda harbors the only remaining unthreatened large population of red colobus. We used microsatellite DNA to evaluate the historical demography of these red colobus and, therefore, the long-term stability of their habitat. We find that the red colobus population throughout KNP has been stable for at least ∼40,000 years. We interpret this result as evidence of long-term forest stability because a change in the available habitat or population movement would have elicited a corresponding change in population size. We conclude that the forest of what is now Kibale National Park may have served as a Late Pleistocene refuge for many East African species.

Lesula: a new species of Cercopithecus monkey endemic to the Democratic Republic of Congo and implications for conservation of Congo's central basin

In June 2007, a previously undescribed monkey known locally as “lesula” was found in the forests of the middle Lomami Basin in central Democratic Republic of Congo (DRC). We describe this new species as Cercopithecus lomamiensis sp. nov., and provide data on its distribution, morphology, genetics, ecology and behavior. C. lomamiensis is restricted to the lowland rain forests of central DRC between the middle Lomami and the upper Tshuapa Rivers. Morphological and molecular data confirm that C. lomamiensis is distinct from its nearest congener, C. hamlyni, from which it is separated geographically by both the Congo (Lualaba) and the Lomami Rivers. C. lomamiensis, like C. hamlyni, is semi-terrestrial with a diet containing terrestrial herbaceous vegetation. The discovery of C. lomamiensis highlights the biogeographic significance and importance for conservation of central Congo’s interfluvial TL2 region, defined from the upper Tshuapa River through the Lomami Basin to the Congo (Lualaba) River. The TL2 region has been found to contain a high diversity of anthropoid primates including three forms, in addition to C. lomamiensis, that are endemic to the area. We recommend the common name, lesula, for this new species, as it is the vernacular name used over most of its known range.

Genetic signatures of a demographic collapse in a large-bodied forest dwelling primate (Mandrillus leucophaeus)

It is difficult to predict how current climate change will affect wildlife species adapted to a tropical rainforest environment. Understanding how population dynamics fluctuated in such species throughout periods of past climatic change can provide insight into this issue. The drill (Mandrillus leucophaeus) is a large-bodied rainforest adapted mammal found in West Central Africa. In the middle of this endangered monkey's geographic range is Lake Barombi Mbo, which has a well-documented palynological record of environmental change that dates to the Late Pleistocene. We used a Bayesian coalescent-based framework to analyze 2,076 base pairs of mitochondrial DNA across wild drill populations to infer past changes in female effective population size since the Late Pleistocene. Our results suggest that the drill underwent a nearly 15-fold demographic collapse in female effective population size that was most prominent during the Mid Holocene (approximately 3-5 Ka). This time period coincides with a period of increased dryness and seasonality across Africa and a dramatic reduction in forest coverage at Lake Barombi Mbo. We believe that these changes in climate and forest coverage were the driving forces behind the drill population decline. Furthermore, the warm temperatures and increased aridity of the Mid Holocene are potentially analogous to current and future conditions faced by many tropical rainforest communities. In order to prevent future declines in population size in rainforest-adapted species such as the drill, large tracts of forest should be protected to both preserve habitat and prevent forest loss through aridification.

Phylogenetic relationships among the colobine monkeys revisited: new insights from analyses of complete mt genomes and 44 nuclear non-coding markers

Background

Phylogenetic relationships among Asian and African colobine genera have been disputed and are not yet well established. In the present study, we revisit the contentious relationships within the Asian and African Colobinae by analyzing 44 nuclear non-coding genes (>23 kb) and mitochondrial (mt) genome sequences from 14 colobine and 4 non-colobine primates.

Principal Findings

The combined nuclear gene and the mt genome as well as the combined nuclear and mt gene analyses yielded different phylogenetic relationships among colobine genera with the exception of a monophyletic ‘odd-nosed’ group consisting of Rhinopithecus, Pygathrix and Nasalis, and a monophyletic African group consisting of Colobus and Piliocolobus. The combined nuclear data analyses supported a sister-grouping between Semnopithecus and Trachypithecus, and between Presbytis and the odd-nosed monkey group, as well as a sister-taxon association of Pygathrix and Rhinopithecus within the odd-nosed monkey group. In contrast, mt genome data analyses revealed that Semnopithecus diverged earliest among the Asian colobines and that the odd-nosed monkey group is sister to a Presbytis and Trachypithecus clade, as well as a close association of Pygathrix with Nasalis. The relationships among these genera inferred from the analyses of combined nuclear and mt genes, however, varied with the tree-building methods used. Another remarkable finding of the present study is that all of our analyses rejected the recently proposed African colobine paraphyly and hybridization hypothesis and supported reciprocal monophyly of the African and Asian groups.

Significance

The phylogenetic utility of large-scale new non-coding genes was assessed using the Colobinae as a model, We found that these markers were useful for distinguishing nodes resulting from rapid radiation episodes such as the Asian colobine radiation. None of these markers here have previously been used for colobine phylogenetic reconstruction, increasing the spectrum of molecular markers available to mammalian systematics.

Reassessment of Dolichopithecus (Kanagawapithecus) leptopostorbitalis, a colobine monkey from the Late Pliocene of Japan

In the original description of Dolichopithecus (Kanagawapithecus) leptopostorbitalis, Iwamoto, Hasegawa and Koizumi, 2005, a moderately large-sized colobine monkey from the Late Pliocene of central Japan, affinities to the European Dolichopithecus rather than to the Transbaikalian Parapresbytis were noted based on the similarities in cranial morphology. Computed tomography scans confirm the presence of the maxillary sinus in the holotype, whereas it is probably absent in specimens of the European Dolichopithecus ruscinensis, the type species of this genus. This feature is either present or absent homogeneously in any given genus of living anthropoids. Its presence or absence is unknown in Parapresbytis, but the distinct morphology of the maxillary incisors in this taxon suggests that this form had different feeding habits from the Japanese colobines. These findings suggest that the Japanese colobine should be referred to henceforth as Kanagawapithecus leptopostorbitalis. Kanagawapithecus shares many important facial and dental features with Dolichopithecus rather than with Parapresbytis, but this association depends largely on the limited availability of comparable materials for the latter. Among colobines, the presence of the maxillary sinus is recorded only in Libypithecus and Cercopithecoides. The maxillary sinus is absent in all modern Asian colobines, implying that Kanagawapithecus is an isolated form without any relationship to living forms. Nevertheless, such phylogenetic interpretations are largely dependent on the restricted fossil evidence from the Pliocene and Pleistocene of eastern Eurasia and will be reexamined when new findings are made.

Nuclear versus mitochondrial DNA: evidence for hybridization in colobine monkeys

BACKGROUND

Colobine monkeys constitute a diverse group of primates with major radiations in Africa and Asia. However, phylogenetic relationships among genera are under debate, and recent molecular studies with incomplete taxon-sampling revealed discordant gene trees. To solve the evolutionary history of colobine genera and to determine causes for possible gene tree incongruences, we combined presence/absence analysis of mobile elements with autosomal, X chromosomal, Y chromosomal and mitochondrial sequence data from all recognized colobine genera.

RESULTS

Gene tree topologies and divergence age estimates derived from different markers were similar, but differed in placing Piliocolobus/Procolobus and langur genera among colobines. Although insufficient data, homoplasy and incomplete lineage sorting might all have contributed to the discordance among gene trees, hybridization is favored as the main cause of the observed discordance. We propose that African colobines are paraphyletic, but might later have experienced female introgression from Piliocolobus/Procolobus into Colobus. In the late Miocene, colobines invaded Eurasia and diversified into several lineages. Among Asian colobines, Semnopithecus diverged first, indicating langur paraphyly. However, unidirectional gene flow from Semnopithecus into Trachypithecus via male introgression followed by nuclear swamping might have occurred until the earliest Pleistocene.

CONCLUSIONS

Overall, our study provides the most comprehensive view on colobine evolution to date and emphasizes that analyses of various molecular markers, such as mobile elements and sequence data from multiple loci, are crucial to better understand evolutionary relationships and to trace hybridization events. Our results also suggest that sex-specific dispersal patterns, promoted by a respective social organization of the species involved, can result in different hybridization scenarios.

Mitochondrial phylogeny of leaf monkeys (genus Presbytis, Eschscholtz, 1821) with implications for taxonomy and conservation

The langurs of the genus Presbytis inhabit tropical rainforests of Sundaland, and with more than 50 color variants grouped in up to eleven species, Presbytis is one of the most diverse Old World monkey genera. The number of taxa and their phylogenetic relationships however remain controversial. To address these issues, we analyzed a 1.8 kb long fragment of the mitochondrial genome, including the cytochrome b gene, the hypervariable region I of the D-loop and the intermediate tRNAs, from individuals representing nine species. Based on our data, we obtained various well-supported terminal clades, which refer mainly to described taxa. Relationships among these clades are not fully resolved, suggesting at least two radiations in the evolutionary history of the genus. According to divergence age estimates, radiations occurred in the late Miocene and the early to middle Pleistocene. Our findings support the revision of the current classification of the genus Presbytis and enable us to discuss implications for conservation. However, further studies including nuclear sequence data are necessary to completely understand the evolutionary history of the genus, and to address possible hybridization events among taxa.

Mitogenomic analysis of Chinese snub-nosed monkeys: Evidence of positive selection in NADH dehydrogenase genes in high-altitude adaptation

Chinese snub-nosed monkeys belong to the genus Rhinopithecus and are limited in distribution to six isolated mountainous areas in the temperate regions of Central and Southwest China. Compared to the other members of the subfamily Colobinae (or leaf-eating monkeys), these endangered primates are unique in being adapted to a high altitude environment and display a remarkable ability to tolerate low temperatures and hypoxia. They thus offer an interesting organismal model of adaptation to extreme environmental stress. Mitochondria generate energy by oxidative phosphorylation (OXPHOS) and play important roles in oxygen usage and energy metabolism. We analyzed the mitochondrial genomes of two Chinese snub-nosed monkey species and eight other colobines in the first attempt to understand the genetic basis of high altitude adaptation in non-human primates. We found significant evidence of positive selection in one Chinese snub-nosed monkey, Rhinopithecus roxellana, which is suggestive of adaptive change related to high altitude and cold weather stress. In addition, our study identified two potentially important adaptive amino acid residues (533 and 3307) in the NADH2 and NADH6 genes, respectively. Surprisingly, no evidence for positive selection was found in Rhinopithecus bieti (the other Chinese snub-nosed monkey analyzed). This finding is intriguing, especially considering that R. bieti inhabits a higher altitudinal distribution than R. roxellana. We hypothesize that a different adaptive genetic basis to high altitude survival exists in R. bieti from those seen in other mammals, and that positive selection and functionally associated mutations in this species may be detected in nuclear genes related to energy and oxygen metabolism. More information on the structure, function, and evolution of mitochondrial and nuclear genomes in Chinese snub-nosed monkeys is required to reveal the molecular mechanisms that underlie adaptations to high altitude survival in non-human primates.