Cladistic analysis of extant and fossil African papionins using craniodental data

Description and taxonomic assessment of fossil Cercopithecidae from the Pliocene Galili Formation (Ethiopia)

The Mount Galili Formation in the Afar region, Ethiopia, samples a critical time in hominin evolution, 4.4 to 3.8 Ma, documenting the last appearance of Ardipithecus and the origin of Australopithecus. This period is also important in the evolution of cercopithecids, especially the origin of Theropithecus in general and Theropithecus oswaldi lineage in particular. Galili has provided a total of 655 cercopithecid specimens that include crania, mandibles, isolated teeth and postcrania. All the fossils were recovered from the Lasdanan (5.3-4.43 Ma), Dhidinley (4.43-3.9 Ma) and Shabeley Laag (∼3.92-3.8 Ma) Members. Here, we described and analyzed 362 fossils employing both qualitative and quantitative methods. Descriptions of the material were supplemented with dental metrics and cranial shape analysis using three-dimensional geometric morphometrics. Results indicate the presence of at least six cercopithecid taxa: Theropithecus oswaldi serengetensis (n = 28), Theropithecus sp. (n = 2), three non-Theropithecus papionin groups (n = 134) and one colobine-size group (n = 58). The T. o. serengetensis represents the earliest form of the lineage, documented from ∼3.9 Ma Galili sediments. The three Galili papionins include a smaller taxon, a medium-sized taxon comparable to Pliopapio alemui and a large papionin overlapping in size with Soromandrillus, Gorgopithecus and Dinopithecus. The majority of Galili colobines have closest affinities to Kuseracolobus aramisi and some overlap with other taxa. Papionins dominate the Galili cercopithecid collection, although colobines are still fairly common (approximately 25% of the sample). Thus, Galili sample is like Kanapoi (4.2-4.1 Ma) and Gona (5.2-3.9 Ma) localities but distinct from Aramis, suggesting paleoecological similarity to the former sites. On the other hand, Theropithecus is less abundant at Galili than geologically younger Hadar (3.4-3.2 Ma) and Woranso-Mille (3.8-3.6 Ma) sites. Whether this difference is due to sampling, time or landscape variation requires further investigation.

Implications of outgroup selection in the phylogenetic inference of hominoids and fossil hominins

Understanding the phylogenetic relationships among hominins and other hominoid species is critical to the study of human origins. However, phylogenetic inferences are dependent on both the character data and taxon sampling used. Previous studies of hominin phylogenetics have used Papio and Colobus as outgroups in their analyses; however, these extant monkeys possess many derived traits that may confound the polarities of morphological changes among living apes and hominins. Here, we consider Victoriapithecus and Ekembo as more suitable outgroups. Both Victoriapithecus and Ekembo are anatomically well known and are widely accepted as morphologically primitive stem cercopithecoid and hominoid taxa, respectively, making them more appropriate for inferring polarity for later-occurring hominoid- and hominin-focused analyses. Craniodental characters for both taxa were scored and then added to a previously published matrix of fossil hominin and extant hominoid taxa, replacing outgroups Papio and Colobus over a series of iterative analyses using both parsimony and Bayesian inference methods. Neither the addition nor replacement of outgroup taxa changed tree topology in any analysis. Importantly, however, bootstrap support values and posterior probabilities for nodes supporting their relationships generally increased compared to previous analyses. These increases were the highest at extant hominoid and basal hominin nodes, recovering the molecular ape phylogeny with considerably higher support and strengthening the inferred relationships among basal hominins. Interestingly, however, the inclusion of both extant and fossil outgroups reduced support for the crown hominid node. Our findings suggest that, in addition to improving character polarity estimation, including fossil outgroups generally strengthens confidence in relationships among extant hominoid and basal hominins.

A new approach to exploratory data analysis in hominin phylogenetic reconstruction

The phylogenetic relationships between fossil hominin taxa have been a contentious topic for decades. Recent discoveries of new taxa, rather than resolving the issue, have only further confused it. Compounding this problem are the limitations of some of the tools frequently used by paleoanthropologists to analyze these relationships. Most commonly, phylogenetic questions are investigated using analytical methods such as maximum parsimony and Bayesian analysis. While these are useful analytical tools, these tree-building methods can have limitations when investigating taxa that may have complex evolutionary histories. Exploratory data analysis can provide information about patterns in a dataset that are obscured by tree-based methods. These patterns include phylogenetic signal conflict, which is not depicted in tree-based methods. Signal conflict can have a number of sources, including methodological issues with character choice, taxonomic issues, homoplasy, and gene flow between taxa. In this study, an exploratory data analysis of fossil hominin morphological data is conducted using the tree-based analytical method neighbor-joining and the network-based analytical method neighbor-net with the goal of visualizing phylogenetic signal conflict within a hominin morphological data set. The data set is divided into cranial regions, and each cranial region is analyzed individually to investigate which regions of the skull contain the highest levels of signal conflict. Results of this analysis show that conflicting phylogenetic signals are present in the hominin fossil record during the relatively speciose period between 3 and 1 Ma, and they also indicate that levels of signal conflict vary by cranial region. Possible sources of these conflicting signals are then explored. Exploratory data analyses such as this can be a useful tool in generating phylogenetic hypotheses and in refining character choice. This study also highlights the value network-based approaches can bring to the hominin phylogenetic analysis toolkit.

A review of Theropithecus oswaldi with the proposal of a new subspecies

Theropithecus oswaldi darti, as currently understood, is the oldest Theropithecus taxon in the fossil record and the earliest subspecies in the Theropithecusoswaldi lineage. Theropithecus oswaldi darti is typified at the site of Makapansgat in South Africa, and a similar form (T. o. cf. darti) is usually recognized at Hadar, Dikika, some Middle Awash localities, and Woranso-Mille in Ethiopia. This taxon is also tentatively believed to occur in Kenya at Kanam and Koobi Fora and in Member C of the Shungura Formation in Ethiopia. While there is a general consensus that the East African 'darti' specimens are sufficiently similar to each other, there has always been a question of whether they are too distinct from the South African type material of T. o. darti to belong to the same subspecies. Here we conduct a morphological comparison of the different samples previously assigned to T. o. darti and T. o. cf. darti. The results of our analyses overwhelmingly support the hypothesis that the East African samples are distinct from the South African ones, and they are likely distinct in geological age as well. Therefore, we propose a new subspecies designation for the material previously termed T. o. cf. darti from East Africa: Theropithecus (Theropithecus) oswaldi ecki subsp. nov. We also formally recognize Theropithecus (Theropithecus) oswaldi serengetensis (Dietrich, 1942) for specimens from Laetoli, Woranso-Mille, and perhaps Galili.

The earliest most complete skeleton of Theropithecus

The middle Pliocene site of Woranso-Mille in the Afar Region of Ethiopia has yielded numerous significant early hominin fossils representing multiple, coexisting taxa. Here we report on another significant discovery, the oldest partial skeleton of the papionin, Theropithecus. The specimen was recovered from the Aralee Issie collection area over multiple field seasons from 2004 through 2019. The specimen was unearthed in situ from the fluvial facies of the Mesgid Dora Tuff dated to 3.66-3.57 Ma. The partial skeleton, ARI-VP-1/26, is that of a subadult male lacking a skull. In the absence of unambiguously associated craniodental remains, the male status of the specimen was established from the dimensions of the long bones in comparison to those of other Theropithecus from Woranso-Mille. ARI-VP-1/26 is noteworthy because it preserves partial hand and foot skeletons, including a complete set of metacarpals from the left side. The theropith status of ARI-VP-1/26 was established based on the detailed anatomy of the postcranial skeleton, especially the proximal and distal humerus, proximal radius, and proximal femur. The morphology of the postcranium of ARI-VP-1/26 is consistent with that of recognized Theropithecus from Woranso-Mille and, specifically, with specimens recognized as Theropithecus oswaldi cf. darti from other sites. The ratio of the lengths of the first metacarpal to metacarpals 2-5 in ARI-VP-1/26 is intermediate between that seen in extant Papio and Theropithecus. In Theropithecus gelada and Theropithecus brumpti, the pairing of pollical and indical metacarpals of near equal length contributes to the species' high opposability index and is associated with a 'manual grazing' feeding habit. Cercopithecids constitute 43% of the identified vertebrates at Aralee Issie, and T. oswaldi cf. darti is the most common mammalian species. The monkeys of Aralee Issie lived in an open shrubland habitat, but the specific reasons for their high prevalence at the site are unclear.

The anatomy of the hindlimb of Theropithecus brumpti (Cercopithecidae, Papionini): Morphofunctional implications

Theropithecus brumpti is a primate known from numerous craniodental specimens in the Plio-Pleistocene Shungura Formation (Lower Omo Valley, Ethiopia), but the anatomy of its hindlimb is documented only by a few associated and mostly incomplete postcranial specimens. The adaptations of T. brumpti are still debated, with its substrate preferences and its use of squatting postures recently discussed based on anatomical differences when compared with its extant representative, Theropithecus gelada. Here, we describe an associated femur and tibia (L 869-1 and L 869-2) of a presumed T. brumpti male and a partial foot (L 865-1r and L 865-1t) of a male T. brumpti, dated to ca. 2.6 Ma and ca. 2.32 Ma respectively. Based on univariate and bivariate morphometric analyses, we provide new data on the morphological correlates of substrate preferences and postural behaviors of this fossil species. Our results are in agreement with previous analyses and present T. brumpti as a predominantly terrestrial primate. We demonstrate the presence of osteological correlates associated with the use of squatting behaviors in T. brumpti but also point to significant anatomical differences between this paleontological species and T. gelada. These differences blur the functional value of characters previously identified as diagnostic of T. gelada and its postural behavior. We further document the postcranial distinctiveness of the Theropithecus clade in relation to the Papio clade. This study thus provides new insights into the postcranial anatomy and paleoecology of an abundant fossil primate from the Plio-Pleistocene of eastern Africa.

A Pleistocene assemblage of near-modern Papio hamadryas from the Middle Awash study area, Afar Rift, Ethiopia

OBJECTIVES

The aim of this study is to assess a new assemblage of papionin fossils (n = 143) recovered from later Pleistocene sediments in the Middle Awash study area in the Afar Rift of Ethiopia.

MATERIALS AND METHODS

We collected metric and qualitative data to compare the craniodental and postcranial anatomy of the papionin fossils with subspecies of modern Papio hamadryas and with Plio-Pleistocene African papionins. We also estimated sex and ontogenetic age.

RESULTS

The new fossils fit well within the range of morphological variation observed for extant P. hamadryas, overlapping most closely in dental size and proportions with the P. h. cynocephalus individuals in our extant samples, and well within the ranges of P. h. anubis and P. h. hamadryas. The considerable overlap in craniodental anatomy with multiple subspecies precludes subspecific diagnosis. We therefore referred 143 individuals to P. hamadryas ssp. The majority of the individuals assessed for ontogenetic age fell into middle- and old-adult age categories based on the degree of dental wear. Males (26%) were better represented than females (12%) among individuals preserving the canine-premolar honing complex.

DISCUSSION

These new near-modern P. hamadryas fossils provide a window into population-level variation in the later Pleistocene. Our findings echo previous suggestions from genomic studies that the papionin family tree may have included a ghost population and provide a basis for future testing of hypotheses regarding hybridization in the recent evolutionary history of this taxon.

Dental topography and dietary specialization in Papionini primates

Our understanding of primate adaptive evolution depends on appreciating the way in which dental functional morphology affects food processing. The Papionini tribe of Cercopithecoidea primates shows great dietary versatility and ecological adaptations to resource seasonality across the African and Asian ecosystems, however, there are few studies focusing on the occlusal topography of the bilophodont teeth and the effect of tooth wear in the crown shape. Here, we explore the relationship between wear-related dental functional morphology and dietary ecological constraints within the Papionini. Three-dimensional (3D) polygonal meshes of the upper permanent molar row (M1-3) were obtained in a large papionine sample (838 specimens) of known dietary preferences including species from six genera (Cercocebus, Lophocebus, Macaca, Mandrillus, Papio, and Theropithecus). All the sample was classified in four diet categories and four topographic metrics (orientation patch count rotated, OPCR; Dirichlet normal energy, DNE; occlusal relief, OR; and ambient occlusion, portion de ciel visible, PCV) were measured for each tooth-type according to wear stage (lightly and moderately worn) to determine diet-related interspecific morphological changes with long-term functionality. The results indicate that hard-object feeders (Cercocebus and Lophocebus) and grass eaters (Theropithecus gelada) exhibit a pattern of occlusal complexity (OPCR), surface curvature (DNE), relief (OR), and morphological wear resistance (PCV) that is significantly different from the omnivores and folivore-frugivore species (Mandrillus and Macaca) despite the overall homogeneity of the bilophodont dentition. A multifactorial ANOVA showed that the topographic metrics were sensitive to tooth wear as expected. The results also indicate that the interspecific variability of dental topography of the upper molars reflects dietary specializations rather than phylogenetic proximity. These findings support the hypothesis that evolutionary convergence processes could have affected the Papionini, clustering the hard-object feeders (Lophocebus and Cercocebus) together in the morphospace, and clearly discriminating this group from the graminivorous and frugivores-folivores.

Biochronology of South African hominin-bearing sites: A reassessment using cercopithecid primates

Despite recent advances in chronometric techniques (e.g., Uranium-Lead [U-Pb], cosmogenic nuclides, electron spin resonance spectroscopy [ESR]), considerable uncertainty remains regarding the age of many Plio-Pleistocene hominin sites, including several in South Africa. Consequently, biochronology remains important in assessments of Plio-Pleistocene geochronology and provides direct age estimates of the fossils themselves. Historically, cercopithecid monkeys have been among the most useful taxa for biochronology of early hominins because they are widely present and abundant in the African Plio-Pleistocene record. The last major studies using cercopithecids were published over 30 y ago. Since then, new hominin sites have been discovered, radiometric age estimates have been refined, and many changes have occurred in cercopithecid taxonomy and systematics. Thus, a biochronological reassessment using cercopithecids is long overdue. Here, we provide just such a revision based on our recent study of every major cercopithecid collection from African Plio-Pleistocene sites. In addition to correlations based on shared faunal elements, we present an analysis based on the dentition of the abundant cercopithecid Theropithecus oswaldi , which increases in size in a manner that is strongly correlated with geological age ( r 2 ∼0.83), thereby providing a highly accurate age-estimation tool not previously utilized. In combination with paleomagnetic and U-Pb data, our results provide revised age estimates and suggest that there are no hominin sites in South Africa significantly older than ∼2.8 Ma. Where conflicting age estimates exist, we suggest that additional data are needed and recall that faunal estimates have ultimately proved reliable in the past (e.g., the age of the KBS Tuff).

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

Simple Summary

Over the last two decades of biological research, our understanding of how genes determine dental development and variation has expanded greatly. Here, we explore how this new knowledge can be applied to the fossil record of cercopithecid monkeys. We compare a traditional paleontological method for assessing dental size variation with measurement approaches derived from quantitative genetics and developmental biology. We find that these new methods for assessing dental variation provide novel insight to the evolution of the cercopithecid monkey dentition, different from the insight provided by traditional size measurements. When we explore the variation of these traits in the cercopithecid fossil record, we find that the variation is outside the range predicted based on extant variation alone. Our 21st century biological approach to paleontology reveals that we have even more to learn from fossils than previously recognized.

Abstract

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.

Early Pleistocene large mammals from Maka'amitalu, Hadar, lower Awash Valley, Ethiopia

The Early Pleistocene was a critical time period in the evolution of eastern African mammal faunas, but fossil assemblages sampling this interval are poorly known from Ethiopia's Afar Depression. Field work by the Hadar Research Project in the Busidima Formation exposures (~2.7-0.8 Ma) of Hadar in the lower Awash Valley, resulted in the recovery of an early Homo maxilla (A.L. 666-1) with associated stone tools and fauna from the Maka'amitalu basin in the 1990s. These assemblages are dated to ~2.35 Ma by the Bouroukie Tuff 3 (BKT-3). Continued work by the Hadar Research Project over the last two decades has greatly expanded the faunal collection. Here, we provide a comprehensive account of the Maka'amitalu large mammals (Artiodactyla, Carnivora, Perissodactyla, Primates, and Proboscidea) and discuss their paleoecological and biochronological significance. The size of the Maka'amitalu assemblage is small compared to those from the Hadar Formation (3.45-2.95 Ma) and Ledi-Geraru (2.8-2.6 Ma) but includes at least 20 taxa. Bovids, suids, and Theropithecus are common in terms of both species richness and abundance, whereas carnivorans, equids, and megaherbivores are rare. While the taxonomic composition of the Maka'amitalu fauna indicates significant species turnover from the Hadar Formation and Ledi-Geraru deposits, turnover seems to have occurred at a constant rate through time as taxonomic dissimilarity between adjacent fossil assemblages is strongly predicted by their age difference. A similar pattern characterizes functional ecological turnover, with only subtle changes in dietary proportions, body size proportions, and bovid abundances across the composite lower Awash sequence. Biochronological comparisons with other sites in eastern Africa suggest that the taxa recovered from the Maka'amitalu are broadly consistent with the reported age of the BKT-3 tuff. Considering the age of BKT-3 and biochronology, a range of 2.4-1.9 Ma is most likely for the faunal assemblage.

Biomechanical correlates of zygomaxillary-surface shape in papionin primates and the effects of hard-object feeding on mangabey facial form

Extant African papioninans are distinguished from macaques by the presence of excavated facial fossae; however, facial excavation differs among taxa. Mangabeys (Cercocebus, Rungwecebus, and Lophocebus) exhibit fossae that invade the zygomatic forming pronounced suborbital fossae (SOFs). Larger-bodied Papio, Mandrillus, and Theropithecus have lateral rostral fossae with minimal/absent suborbital fossae. Because prior studies have shown that mangabeys exhibit adaptations to anterior dental loading (e.g., palatal retraction), it is plausible that mangabey SOFs represent structural accommodation to masticatory-system shape rather than facial allometry, as commonly hypothesized. We analyzed covariation between zygomaxillary-surface shape, masticatory-system shape, and facial size in 141 adult crania of Macaca fascicularis, Papio kindae, Cercocebus, and Lophocebus. These taxa represent the range of papionin SOF expression while minimizing size variation (narrow allometry). Masticatory-system landmarks (39) registered palate shape, bite points, masticatory muscle attachments, and the temporomandibular joint. Semilandmarks (450) captured zygomaxillary-surface shape. Following Procrustes superimposition with semilandmark sliding and principal components analyses, multivariate regression was used to explore allometry, and two-block partial least-squares analyses (within-configuration and separate-blocks) were used to examine covariation patterns. Scores on principal components 1-2 and the first partial least-square (PLS1) separate mangabeys from Macaca and Papio. Both zygomaxillary-surface shape and masticatory-system shape are correlated with size within taxa and facial morphotypes; however, regression distributions indicate morphotype shape differences are non-allometric. PLS1 accounts for ∼95% of shape covariance (p < 0.0001) and shows strong linear correlations (r-PLS = ∼0.95, p < 0.0001) between blocks. Negative PLS1 scores in mangabeys reflect deep excavation of the suborbital malar surface, palatal retraction, and anterior displacement of jaw adductor muscles and the temporomandibular joint. Neither PC1 nor PLS1 scores ordinate specimens by facial size. Taken together, these results fail to support the allometric hypothesis but suggest that mangabey zygomaxillary morphology is closely linked with adaptations to hard-object feeding.

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.

Ontogenetic allometry and scaling in catarrhine crania

In studies of ontogenetic allometry, ontogenetic scaling has often been invoked to explain cranial morphological differences between smaller and larger forms of closely related taxa. These scaled variants in shape have been hypothesized to be the result of the extension or truncation of common growth allometries. In this scenario, change in size is the determining factor, perhaps under direct selection, and changes in cranial shapes are byproducts, not under direct selection themselves. However, many of these conclusions are based on studies that used bivariate generalizations of shape. Even among multivariate analyses of growth allometries, there are discrepancies as to the prevalence of ontogenetic scaling among primates, how shared the trajectories need to be, and which taxa evince properties of scaled variants. In this investigation, we use a large, comparative ontogenetic sample, geometric morphometric methods, and multivariate statistical tests to examine ontogenetic allometry and evaluate if differences in cranial shape among closely related catarrhines of varying sizes are primarily driven by size divergence, that is, ontogenetic scaling. We then evaluate the hypothesis of size as a line of least evolutionary resistance in catarrhine cranial evolution. We found that patterns of ontogenetic allometry vary among taxa, indicating that ontogenetic scaling sensu stricto does not often account for most morphological differences and that large and small taxa within clades are generally not scaled variants. The presence of a variety of ontogenetic pathways for the evolution of cranial shapes provides indirect evidence for selection acting directly on the cranial shape, rather than on size alone.

Fossil Cercopithecidae from the Early Pliocene Sagantole Formation at Gona, Ethiopia

The Early Pliocene Sagantole Fm. in the Gona Project area, Afar State, Ethiopia, is noted for discoveries of the early hominin Ardipithecus ramidus. A large series of fossil cercopithecid primates dated to between 4.8 and 4.3 Ma has also been collected from these sediments. In this paper, we use qualitative analysis and standard dental and postcranial measures to systematically describe the craniodental remains and tentatively allocate postcrania to taxa where we are able to. We then use these data to compare these specimens to fossil assemblages from contemporary sites, interpret their paleobiology, and discuss implications for the paleoecology of the Gona Sagantole Fm. We recognize three cercopithecid species in the Gona Sagantole Fm. Pliopapio alemui makes up approximately two-thirds of the identifiable specimens; nearly all of the rest are allocated to Kuseracolobus aramisi, and a single molar indicates the presence of a second, somewhat larger but morphologically distinct papionin. Among the Early Pliocene cercopithecids from Gona are also a number of postcranial elements. None of the postcranial remains are directly associated with any of the cranial material. Nonetheless, some of the distal humeri and proximal femora can be tentatively allocated to either Pl. alemui or K. aramisi based on a combination of size, as the latter is approximately 50% larger than the former, and morphology. If these assignments are correct, they suggest K. aramisi was primarily arboreal and similar to most extant colobines, whereas Pl. alemui was more mixed in its substrate use, being more terrestrially adapted than K. aramisi, but less so than extant Papio or Theropithecus. Thus, we interpret the predominance of Pl. alemui over K. aramisi is consistent with a somewhat more open environment at Gona than at Aramis.

Patterns and magnitudes of craniofacial covariation in extant cercopithecids

The cranium contains almost all of the vertebrate sensory organs and plays an essential role in vertebrate evolution. Research on the primate cranium has revealed that it is both highly integrated and modular, but studies have historically focused on covariance between the neurocranium and facial skeleton rather than on bones specific to special senses such as vision. The goal of this work is to investigate patterns and magnitudes of craniofacial covariation in extant cercopithecids with particular attention to the orbits. This study takes a quantitative approach using data collected from 38 homologous cranial landmarks across 11 genera of cercopithecid monkeys (Cercopithecidae, N = 291). These data demonstrate that both patterns and magnitudes of craniofacial covariation differ across Cercopithecidae at subfamily, tribe, and genus levels, with the strongest integration in the papionins (and specifically Papio) and significantly weaker covariation in the colobines, particularly Presbytis. Orbital height does not covary with other measurements of the cranium to the same degree as other cranial traits in Cercopithecidae and is highly constrained across the family. This study has important implications for our understanding of the evolution and development of morphological diversity in the cercopithecid cranium and evolution of the primate eye. This study also highlights the potential error of broad assumptions about generalizing patterns and magnitudes of modularity and integration across primates. Additionally, these findings reiterate the importance of trait selection for interpreting fossil taxonomy, as craniofacial covariation may impact phenotypes commonly used to differentiate fossil primate species.

Cercopithecid fossils from Kanapoi, West Turkana, Kenya (2007-2015)

Recent fieldwork at Kanapoi has expanded the sample of fossil cercopithecids, facilitating a re-appraisal of their taxonomy. The assemblage now includes at least one species of cercopithecin, two papionins, and two colobines. The guenon Nanopithecus browni is similar in dental size to extant Miopithecus. We tentatively re-affirm the identification of Parapapio cf. ado and confirm the presence of Theropithecus. The colobines include a small form tentatively attributed to Kuseracolobus and a second larger species. The Kanapoi fossils represent the oldest occurrences of guenons in Africa and of the important genus Theropithecus, the most abundant and widespread primate in the Neogene of Africa. In the assemblage, Parapapio cf. ado is the most abundant form, comprising the majority of specimens. All of the other taxa are comparatively rare. Colobines make up a small part of the Kanapoi fossil assemblage compared to most other contemporary sites, including Allia Bay, Kenya, where, like Kanapoi, Australopithecus anamensis has been found. The presence of Theropithecus is consistent with the presence of some relatively open habitat at Kanapoi. While the ecological preferences of the small cercopithecin are unknown, most guenons are associated with relatively wooded habitats, as are most colobines, suggesting the availability of at least some wooded areas.

Shape variation in the facial part of the cranium in macaques and African papionins using geometric morphometrics

Macaques are one of the most successful nonhuman primates, and morphological distinctions from their close relatives, African papionins, are easily detected by the naked eye. Nevertheless, evolutionary allometry often accounts for a large amount of the total variation and potentially hides and precludes the detection of morphological distinctions that exist between macaques and African papionins, thus distorting their phyletic comparison. Geometric morpgometric analyses were performed using landmark coordinates in cranial samples from macaques (N =  135) and African papionins (N =  152) to examine the variation in their facial shape. A common allometric trend was confirmed to represent a moderately long face in macaques as being small-to-moderate-bodied papionins. Macaques possessed many features that were distinct from those of African papionins, while they simultaneously showed a large intrageneric variation in every feature, which precluded the separation of some groups of macaques from African papionins. This study confirmed that a moderately smooth sagittal profile is present in non-Sulawesi macaques. It also confirmed that a well-developed anteorbital drop is distinct in Mandrillus and Theropithecus, but it showed that Papio resembles macaques regarding this feature. This finding showed that apparently equivalent features which can be detected by the naked eye were probably formed by different combinations of the principal patterns. It should be noted that the differences detected here between macaques and African papionins are revealed after appropriate adjustments are made to eliminate the allometric effects over the shape features. While landmark data sets still need to be customized for specific studies, the information provided by this article is expected to help such customization and to improve future phyletic evaluation of the fossil papionins.

Sexual selection in the Kinda baboon

Due to wide variation in the presence and degree of expression of a diverse suite of sexually-selected traits, the tribe Papionini represents an outstanding model for understanding how variation in sexual selection pressures and mechanisms leads to trait evolution. Here, we discuss the particular value of Papio as a model genus for studies of sexual selection, emphasizing the presence of multiple mating systems, and differences in the expression of sexually-selected traits among closely-related species. We draw particular attention to the Kinda baboon (Papio kindae), a comparatively less-studied baboon species, by providing a primer to Kinda baboon morphology, genetics, physiology, and behavior. Based on observations of large group sizes, combined with low degrees of sexual dimorphism and large relative testis size relative to other baboon species, we test the hypothesis that Kinda baboons have evolved under reduced direct, and increased indirect, male-male competition. We present the first long-term data on wild Kinda baboons in Zambia. Kinda baboon females show seasonal peaks in births and reproductive receptivity, and males exhibit a queing-rather than contest-based dominance acquisition with long alpha-male tenure lengths. We finish by making a number of explicit testable predictions about Kinda baboon sexual signals and behaviors, and suggest that Kinda baboons have potential to offer new insights into the selective environments that may have been experienced during homininization.

A new method to quantify mandibular corpus shape in extant great apes and its potential application to the hominoid fossil record

OBJECTIVES

Mandibular corpus robusticity (corpus breadth/corpus height) is the most commonly utilized descriptor of the mandibular corpus in the great ape and hominin fossil records. As a consequence of its contoured shape, linear metrics used to characterize mandibular robusticity are inadequate to quantify the shape of the mandibular corpus. Here, we present an alternative to the traditional assessment of mandibular shape by analyzing the outline of the mandibular corpus in cross-section using landmarks and semilandmarks.

MATERIALS AND METHODS

Outlines of the mandibular corpus in cross-section between M₁ and M₂ were quantified in a sample of hominoids and analyzed using generalized Procrustes analysis, Procrustes ANOVA, CVA, and cluster analysis. Corpus breadth and width were also collected from the same sample and analyzed using regression, ANOVA, and cluster analysis.

RESULTS

Analysis of corpus outline shape revealed significant differences in mandibular corpus shape that are independent of size and sex at the genus level across hominoids. Cluster analysis based on the analysis of corpus outline shape results in almost all specimens grouping based on taxonomic affinity (99.28% correct classification). Comparison of these results to results using traditional measures of mandibular robusticity shows that analysis of the outline of the corpus in cross-section discriminate extant great apes more reliably.

CONCLUSION

The strong taxonomic signal revealed by this analysis indicates that quantification of the outline of the mandibular corpus more fully captures mandibular corpus shape and offers the potential for greater power in discriminating among taxa in the hominoid fossil record.

Selection of Character Coding Method Is Not Phylogenetically Neutral: A Test Case Using Hominoids

The early stages of phylogenetic inference from morphological data involve a sequence of choices about which analytical methods to employ. At each stage, the selection of one method over another can dramatically impact tree inference. Phylogenetic hypotheses are sensitive to decisions relating to which taxa and characters to select for analysis, whether and how to delimit character states, which taxa to use as outgroups, and how to account for character dependence. Using extant hominoids as a test case, I quantify the degree to which phylogenetic inferences are sensitive to the choice of method used to transform continuously scaled variables into categorical traits. I demonstrate that the character coding strategy significantly impacts hypotheses of character state identity and phylogenetic branching patterns. To avoid biasing evolutionary hypotheses, I recommend that continuously scaled characters be analyzed without prior discretization.

New sivaladapid primate from Lower Siwalik deposits surrounding Ramnagar (Jammu and Kashmir State), India

Over the past century, numerous vertebrate fossils collected near the town of Ramnagar, India, have proven to be important for understanding the evolution and biogeography of many mammalian groups. Primates from Ramnagar, though rare, include a number of hominoid specimens attributable to Sivapithecus, as well as a single published mandibular fragment preserving the P₄-M₁ of the Miocene adapoid Sivaladapis palaeindicus. Since 2010, we have renewed fossil prospecting in the Lower Siwalik deposits near Ramnagar in an attempt to better understand the evolution, biogeographic timing, and paleoclimatic context of mammalian radiations in Asia, with a particular focus on primates. Our explorations have resulted in the identification of new fossil localities, including the site of Sunetar. The age of Sunetar and the Ramnagar region, in general, is tentatively dated between 14 and 11 Ma. In 2014, a partial right mandible of a sivaladapid primate was recovered at Sunetar, preserving the corpus with P₄ roots and worn M₁-M₃ dentition. Although sivaladapids are known by numerous specimens of two genera (Sivaladapis and Indraloris) at Lower Siwalik sites on the Potwar Plateau (Pakistan) and at the Middle Siwalik locality of Haritalyangar (India), this new specimen is just the second sivaladapid recovered from the Ramnagar region. Our analyses suggest that the new specimen is distinct from all other sivaladapids, and we therefore describe it as a new genus and species close to the base of the Sivaladapinae.

Morphoarchitectural variation in South African fossil cercopithecoid endocasts

Despite the abundance of well-preserved crania and natural endocasts in the South African Plio-Pleistocene cercopithecoid record, which provide direct information relevant to the evolution of their endocranial characteristics, few studies have attempted to characterize patterns of external brain morphology in this highly successful primate Superfamily. The availability of non-destructive penetrating radiation imaging systems, together with recently developed computer-based analytical tools, allow for high resolution virtual imaging and modeling of the endocranial casts and thus disclose new perspectives in comparative paleoneurology. Here, we use X-ray microtomographic-based 3D virtual imaging and quantitative analyses to investigate the endocranial organization of 14 cercopithecoid specimens from the South African sites of Makapansgat, Sterkfontein, Swartkrans, and Taung. We present the first detailed comparative description of the external neuroanatomies that characterize these Plio-Pleistocene primates. Along with reconstruction of endocranial volumes, we combine a semi-automatic technique for extracting the neocortical sulcal pattern together with a landmark-free surface deformation method to investigate topographic differences in morphostructural organization. Besides providing and comparing for the first time endocranial volume estimates of extinct Plio-Pleistocene South African cercopithecoid taxa, we report additional information regarding the variation in the sulcal pattern of Theropithecus oswaldi subspecies, and notably of the central sulcus, and the neuroanatomical condition of the colobine taxon Cercopithecoides williamsi, suggested to be similar for some aspects to the papionin pattern, and discuss potential phylogenetic and taxonomic implications. Further research in virtual paleoneurology, applied to specimens from a wider geographic area, is needed to clarify the polarity, intensity, and timing of cortical surface evolution in cercopithecoid lineages.

Reassessment of Olduvai Bed I cercopithecoids: A new biochronological and biogeographical link to the South African fossil record

Fossil monkeys have long been used as important faunal elements in studies of African Plio-Pleistocene biochronology, particularly in the case of the South African karst cave sites. Cercopithecoid fossils have been known from Tanzania's Olduvai Gorge for nearly a century, with multiple taxa documented including Theropithecus oswaldi and Cercopithecoides kimeui, along with papionins and colobines less clearly attributable to species. A small number of large papionin fossils, including a partial male cranium and partial female skull, have been previously identified as an early form of Papio, but noted as distinct from extant baboons as well as other fossil Papio species. In 2013 we reviewed the Olduvai cercopithecoid material at the National Museum of Tanzania, with a particular focus on the specimens from Beds I-IV. Quantitative and qualitative comparisons of the Olduvai papionins largely confirmed previous observations, with one notable exception. The large papionin taxon from Bed I previously recognized as Papio sp. is more properly recognized as Gorgopithecus major, a taxon previously known only from South Africa. Features shared between the Olduvai specimens and G. major include relatively short and concavo-convex tubular nasals, antero-posteriorly curved upper incisor roots, downwardly curved brow ridges in the midline, and robust zygomatic arches. The recognition of G. major at Olduvai Bed I, a well-known horizon with precise radiometric dates, provides an important biochronological and biogeographical link with South African localities Kromdraai A, Swartkrans Member 1 and possibly Swartkrans Members 2-3 and Cooper's A and D.

Papio Cranium from the Hominin-Bearing Site of Malapa: Implications for the Evolution of Modern Baboon Cranial Morphology and South African Plio-Pleistocene Biochronology

A new partial cranium (UW 88-886) of the Plio-Pleistocene baboon Papio angusticeps from Malapa is identified, described and discussed. UW 88-886 represents the only non-hominin primate yet recovered from Malapa and is important both in the context of baboon evolution as well as South African hominin site biochronology. The new specimen may represent the first appearance of modern baboon anatomy and coincides almost perfectly with molecular divergence date estimates for the origin of the modern P. hamadryas radiation. The fact that the Malapa specimen is dated between ~2.026–2.36 million years ago (Ma) also has implications for the biochronology of other South African Plio-Pleistocene sites where P. angusticeps is found.

Reticulate evolution and the human past: an anthropological perspective

CONTEXT

The evidence is mounting that reticulate (web-like) evolution has shaped the biological histories of many macroscopic plants and animals, including non-human primates closely related to Homo sapiens, but the implications of this non-hierarchical evolution for anthropological enquiry are not yet fully understood. When they are understood, the result may be a paradigm shift in evolutionary anthropology.

OBJECTIVE/METHODS

This paper reviews the evidence for reticulated evolution in the non-human primates and human lineage. Then it makes the case for extrapolating this sort of patterning to Homo sapiens and other hominins and explores the implications this would have for research design, method and understandings of evolution in anthropology.

RESULTS/CONCLUSION

Reticulation was significant in human evolutionary history and continues to influence societies today. Anthropologists and human scientists-whether working on ancient or modern populations-thus need to consider the implications of non-hierarchic evolution, particularly where molecular clocks, mathematical models and simplifying assumptions about evolutionary processes are used. This is not just a problem for palaeoanthropology. The simple fact of different mating systems among modern human groups, for example, may demand that more attention is paid to the potential for complexity in human genetic and cultural histories.

Recent advances in primate phylogenomics

The world of primate genomics is expanding rapidly in new and exciting ways owing to lowered costs and new technologies in molecular methods and bioinformatics. The primate order is composed of 78 genera and 478 species, including human. Taxonomic inferences are complex and likely a consequence of ongoing hybridization, introgression, and reticulate evolution among closely related taxa. Recently, we applied large-scale sequencing methods and extensive taxon sampling to generate a highly resolved phylogeny that affirms, reforms, and extends previous depictions of primate speciation. The next stage of research uses this phylogeny as a foundation for investigating genome content, structure, and evolution across primates. Ongoing and future applications of a robust primate phylogeny are discussed, highlighting advancements in adaptive evolution of genes and genomes, taxonomy and conservation management of endangered species, next-generation genomic technologies, and biomedicine.

Mitogenomics of the Old World monkey tribe Papionini

Background

The evolutionary history of the Old World monkey tribe Papionini comprising the genera Macaca, Mandrillus, Cercocebus, Lophocebus, Theropithecus, Rungwecebus and Papio is still matter of debate. Although the African Papionini (subtribe Papionina) are generally considered to be the sister lineage to the Asian Papionini (subtribe Macacina), previous studies based on morphological data, nuclear or mitochondrial sequences have shown contradictory phylogenetic relationships among and within both subtribes. To further elucidate the phylogenetic relationships among papionins and to estimate divergence ages we generated mitochondrial genome data and combined them with previously published sequences.

Results

Our mitochondrial gene tree comprises 33 papionins representing all genera of the tribe except Rungwecebus. In contrast to most previous studies, the obtained phylogeny suggests a division of the Papionini into three main mitochondrial clades with similar ages: 1) Papio, Theropithecus, Lophocebus; 2) Mandrillus, Cercocebus; and 3) Macaca; the Mandrillus + Cercocebus clade appears to be more closely related to Macaca than to the other African Papionini. Further, we find paraphyletic relationships within the Mandrillus + Cercocebus clade as well as in Papio. Relationships among Theropithecus, Lophocebus and Papio remain unresolved. Divergence ages reveal initial splits within the three mitochondrial clades around the Miocene/Pliocene boundary and differentiation of Macaca species groups occurred on a similar time scale as those found between genera of the subtribe Papionina.

Conclusion

Due to the largely well-resolved mitochondrial phylogeny, our study provides new insights into the evolutionary history of the Papionini. Results show some contradictory relationships in comparison to previous analyses, notably the paraphyly within the Cercocebus + Mandrillus clade and three instead of only two major mitochondrial clades. Divergence ages among species groups of macaques are similar to those among African Papionini genera, suggesting that diversification of the mitochondrial genome is of a similar magnitude in both subtribes. However, since our mitochondrial tree represents just a single gene tree that most likely does not reflect the true species tree, extensive nuclear sequence data is required to illuminate the true species phylogeny of papionins and to trace possible ancient hybridization events among lineages.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-014-0176-1) contains supplementary material, which is available to authorized users.

Molecular phylogenetic analysis of the Papionina using concatenation and species tree methods

The Papionina is a geographically widespread subtribe of African cercopithecid monkeys whose evolutionary history is of particular interest to anthropologists. The phylogenetic relationships among arboreal mangabeys (Lophocebus), baboons (Papio), and geladas (Theropithecus) remain unresolved. Molecular phylogenetic analyses have revealed marked gene tree incongruence for these taxa, and several recent concatenated phylogenetic analyses of multilocus datasets have supported different phylogenetic hypotheses. To address this issue, we investigated the phylogeny of the Lophocebus + Papio + Theropithecus group using concatenation methods, as well as alternative methods that incorporate gene tree heterogeneity to estimate a 'species tree.' Our compiled DNA sequence dataset was ∼56 kb pairs long and included 57 independent partitions. All analyses of concatenated alignments strongly supported a Lophocebus + Papio clade and a basal position for Theropithecus. The Bayesian concordance analysis supported the same phylogeny. A coalescent-based Bayesian method resulted in a very poorly resolved species tree. The topological agreement between concatenation and the Bayesian concordance analysis offers considerable support for a Lophocebus + Papio clade as the dominant relationship across the genome. However, the results of the Bayesian concordance analysis indicate that almost half the genome has an alternative history. As such, our results offer a well-supported phylogenetic hypothesis for the Papio/Lophocebus/Theropithecus trichotomy, while at the same time providing evidence for a complex evolutionary history that likely includes hybridization among lineages.