Dental and phylogeographic patterns of variation in gorillas

Ghosts of extinct apes: genomic insights into African hominid evolution

We are accustomed to regular announcements of new hominin fossils. There are now some 6000 hominin fossils, and up to 31 species. However, where are the announcements of African ape fossils? The answer is that there are almost none. Our knowledge of African ape evolution is based entirely on genomic analyses, which show that extant diversity is very young. This contrasts with the extensive and deep diversity of hominins known from fossils. Does this difference point to low and late diversification of ape lineages, or high rates of extinction? The comparative evolutionary dynamics of African hominids are central to interpreting living ape adaptations, as well as understanding the patterns of hominin evolution and the nature of the last common ancestor.

How we study cryptic species and their biological implications: A case study from marine shelled gastropods

Methodological and biological considerations are intertwined when studying cryptic species. A potentially large component of modern biodiversity, the frequency of cryptic species among taxonomic groups is not well documented. The term "cryptic species" is imprecisely used in scientific literature, causing ambiguity when interpreting their evolutionary and ecological significance. This study reviews how cryptic species have been defined, discussing implications for taxonomy and biology, and explores these implications with a case study based on recently published literature on extant shelled marine gastropods. Reviewed gastropods were recorded by species. Records of cryptic gastropods were presented by authors with variable levels of confidence but were difficult to disentangle from inherent biases in the study effort. These complexities notwithstanding, most gastropod species discussed were not cryptic. To the degree that this review's sample represents extinct taxa, the results suggest that a high proportion of shelled marine gastropod species are identifiable for study in the fossil record. Much additional work is needed to provide a more adequate understanding of the relative frequency of cryptic species in shelled marine gastropods, which should start with more explicit definitions and targeted case studies.

Morphological variation of the maxilla in modern humans and African apes

Differences in morphology among modern humans and African apes are frequently used when assessing whether hominin fossils should be attributed to a single species or represent evidence for taxic diversity. A good understanding of the degree and structure of the intergeneric, interspecific, and intraspecific variation, including aspects such as sexual dimorphism and age, are key in this context. Here we explore the variation and differences shown by the maxilla of extant hominines, as maxillary morphology is central in the diagnosis of several hominin taxa. Our sample includes adults of all currently recognized hominine species and subspecies, with a balanced species sex ratio. In addition, we compared the adults with a small sample of late juveniles. The morphology of the maxillae was captured using three-dimensional landmarks, and the size and shape were analyzed using geometric morphometric methods. Key observations are that 1) the maxillae of all extant hominine species and subspecies show statistically significant differences, but complete separation in shape is only seen at the genus level; 2) the degree of variation is not consistent between genera, with subspecies of Gorilla being more different from each other than are species of Pan; 3) the pattern of sexual shape dimorphism is different in Pan, Gorilla, and Homo, often showing opposite trends; and 4) differentiation between maxillary shapes is increased after adjustment for static intraspecific allometry. These results provide a taxonomically up-to-date comparative morphological framework to help interpret the hominin fossil record, and we discuss the practical implications in that context.

New Middle Miocene Ape (Primates: Hylobatidae) from Ramnagar, India fills major gaps in the hominoid fossil record

The fossil record of 'lesser apes' (i.e. hylobatids = gibbons and siamangs) is virtually non-existent before the latest Miocene of East Asia. However, molecular data strongly and consistently suggest that hylobatids should be present by approximately 20 Ma; thus, there are large temporal, geographical, and morphological gaps between early fossil apes in Africa and the earliest fossil hylobatids in China. Here, we describe a new approximately 12.5-13.8 Ma fossil ape from the Lower Siwaliks of Ramnagar, India, that fills in these long-standing gaps with implications for hylobatid origins. This ape represents the first new hominoid species discovered at Ramnagar in nearly a century, the first new Siwalik ape taxon in more than 30 years, and likely extends the hylobatid fossil record by approximately 5 Myr, providing a minimum age for hylobatid dispersal coeval to that of great apes. The presence of crown hylobatid molar features in the new species indicates an adaptive shift to a more frugivorous diet during the Middle Miocene, consistent with other proposed adaptations to frugivory (e.g. uricase gene silencing) during this time period as well.

A mathematical landmark-based method for measuring worn molars in hominoid systematics

Worn teeth pose a major limitation to researchers in the fields of extinct and extant hominoid systematics because they lack clearly identifiable anatomical landmarks needed to take measurements on the crown enamel surface and are typically discarded from a study. This is particularly detrimental when sample sizes for some groups are already characteristically low, if there is an imbalance between samples representing populations, sexes or dietary strategies, or if the worn teeth in question are type specimens of fossil species or other key specimens. This study proposes a methodology based predominantly on mathematically-derived landmarks for measuring size and shape features of molars, irrespective of wear. With 110 specimens of lower second molars from five species of extant hominoids (Pan troglodytes, P. paniscus, Gorilla gorilla, G. beringei, Homo sapiens), n ≥ 20 per species, n ≥ 10 per subspecies, good species separation in morphospace is achieved in a principal components analysis. Classification accuracy in a discriminant function analysis is 96.4% at the species level and 88.2% at the subspecies level (92.7% and 79.1%, respectively, on cross-validation). The classification accuracy compares favorably to that achieved by anatomically-derived measurements based on published research (94% and 84% at the species and subspecies level respectively; 91% and 76% on cross-validation). The mathematical landmarking methodology is rapid and uncomplicated. The results support the use of mathematical landmarks to enable the inclusion of worn molar teeth in dental studies so as to maximize sample sizes and restore balance between populations and/or sexes in hominoid systematic studies.

The Taxonomic and Phylogenetic Affinities of Bunopithecus sericus, a Fossil Hylobatid from the Pleistocene of China

Fossil hylobatids are rare, but are known from late Miocene and Pleistocene sites throughout East Asia. The best-known fossil hylobatid from the Pleistocene of China is a left mandibular fragment with M2-3 (AMNH 18534), recovered from a pit deposit near the village of Yanjinggou in Wanzhou District, Chongqing Province. Matthew and Granger described this specimen in 1923 as a new genus and species, Bunopithecus sericus. Establishing the age of Bunopithecus has proved difficult because the Yanjinggou collection represents a mixed fauna of different ages, but it likely comes from early or middle Pleistocene deposits. Although the Bunopithecus specimen has featured prominently in discussions of hylobatid evolution and nomenclature, its systematic status has never been satisfactorily resolved. The present study reexamines the taxonomic and phylogenetic relationships of Bunopithecus by carrying out a detailed comparative morphometric study of its lower molars in relation to a large sample of modern hylobatids. Our results show that differences in M2 and M3 discriminate extant hylobatids fairly well, at least at the generic level, and that AMNH 18534 is not attributable to Hylobates, Nomascus or Symphalangus. Support for a close relationship between Bunopithecus and Hoolock is more equivocal. In most multivariate analyses, Bunopithecus presents a unique morphological pattern that falls outside the range of variation of any hylobatid taxon, although its distance from the cluster represented by extant hoolocks is relatively small. Our results support the generic distinction of Bunopithecus, which most likely represents an extinct crown hylobatid, and one that may possibly represent the sister taxon to Hoolock.

A genome-wide survey of genetic variation in gorillas using reduced representation sequencing

All non-human great apes are endangered in the wild, and it is therefore important to gain an understanding of their demography and genetic diversity. Whole genome assembly projects have provided an invaluable foundation for understanding genetics in all four genera, but to date genetic studies of multiple individuals within great ape species have largely been confined to mitochondrial DNA and a small number of other loci. Here, we present a genome-wide survey of genetic variation in gorillas using a reduced representation sequencing approach, focusing on the two lowland subspecies. We identify 3,006,670 polymorphic sites in 14 individuals: 12 western lowland gorillas (Gorilla gorilla gorilla) and 2 eastern lowland gorillas (Gorilla beringei graueri). We find that the two species are genetically distinct, based on levels of heterozygosity and patterns of allele sharing. Focusing on the western lowland population, we observe evidence for population substructure, and a deficit of rare genetic variants suggesting a recent episode of population contraction. In western lowland gorillas, there is an elevation of variation towards telomeres and centromeres on the chromosomal scale. On a finer scale, we find substantial variation in genetic diversity, including a marked reduction close to the major histocompatibility locus, perhaps indicative of recent strong selection there. These findings suggest that despite their maintaining an overall level of genetic diversity equal to or greater than that of humans, population decline, perhaps associated with disease, has been a significant factor in recent and long-term pressures on wild gorilla populations.