The evolutionary origin and population history of the grauer gorilla

Trabecular bone variation in the gorilla calcaneus

OBJECTIVES

Calcaneal external shape differs among nonhuman primates relative to locomotion. Such relationships between whole-bone calcaneal trabecular structure and locomotion, however, have yet to be studied. Here we analyze calcaneal trabecular architecture in Gorilla gorilla gorilla, Gorilla beringei beringei, and G. b. graueri to investigate general trends and fine-grained differences among gorilla taxa relative to locomotion.

MATERIALS AND METHODS

Calcanei were micro-CT scanned. A three-dimensional geometric morphometric sliding semilandmark analysis was carried out and the final landmark configurations used to position 156 volumes of interest. Trabecular thickness (Tb.Th), trabecular spacing (Tb.Sp), and bone volume fraction (BV/TV) were calculated using the BoneJ plugin for ImageJ and MATLAB. Non-parametric MANOVAs were run to test for significant differences among taxa in parameter raw values and z-scores. Parameter distributions were visualized using color maps and summarized using principal components analysis.

RESULTS

There are no significant differences in raw BV/TV or Tb.Th among gorillas, however G. b. beringei significantly differs in z-scores for both parameters (p = <0.0271). All three taxa exhibit relatively lower BV/TV and Tb.Th in the posterior half of the calcaneus. This gradation is exacerbated in G. b. beringei. G. b. graueri significantly differs from other taxa in Tb.Sp z-scores (p < 0.001) indicating a different spacing distribution.

DISCUSSION

Relatively higher Tb.Th and BV/TV in the anterior calcaneus among gorillas likely reflects higher forces associated with body mass (transmitted through the subtalar joint) relative to forces transferred through the posterior calcaneus. The different Tb.Sp pattern in G. b. graueri may reflect proposed differences in foot positioning during locomotion.

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.

Comparative genomic analyses provide new insights into evolutionary history and conservation genomics of gorillas

Genome sequencing is a powerful tool to understand species evolutionary history, uncover genes under selection, which could be informative of local adaptation, and infer measures of genetic diversity, inbreeding and mutational load that could be used to inform conservation efforts. Gorillas, critically endangered primates, have received considerable attention and with the recently sequenced Bwindi mountain gorilla population, genomic data is now available from all gorilla subspecies and both mountain gorilla populations. Here, we reanalysed this rich dataset with a focus on evolutionary history, local adaptation and genomic parameters relevant for conservation. We estimate a recent split between western and eastern gorillas of 150,000-180,000 years ago, with gene flow around 20,000 years ago, primarily between the Cross River and Grauer's gorilla subspecies. This gene flow event likely obscures evolutionary relationships within eastern gorillas: after excluding putatively introgressed genomic regions, we uncover a sister relationship between Virunga mountain gorillas and Grauer's gorillas to the exclusion of Bwindi mountain gorillas. This makes mountain gorillas paraphyletic. Eastern gorillas are less genetically diverse and more inbred than western gorillas, yet we detected lower genetic load in the eastern species. Analyses of indels fit remarkably well with differences in genetic diversity across gorilla taxa as recovered with nucleotide diversity measures. We also identified genes under selection and unique gene variants specific for each gorilla subspecies, encoding, among others, traits involved in immunity, diet, muscular development, hair morphology and behavior. The presence of this functional variation suggests that the subspecies may be locally adapted. In conclusion, using extensive genomic resources we provide a comprehensive overview of gorilla genomic diversity, including a so-far understudied Bwindi mountain gorilla population, identify putative genes involved in local adaptation, and detect population-specific gene flow across gorilla species.

Specimens as individuals: Four interventions and recommendations for great ape skeletal collections research and curation

Extensive discourse surrounds the ethics of human skeletal research and curation, but there has yet to be a similar discussion of the treatment of great ape skeletal remains, despite the clear interest in their ethical treatment when alive. Here we trace the history of apes who were killed and collected for natural history museums during the early 20th century and showcase how the guiding research questions of the colonial era continue to influence scholarship. We discuss best practices for improving industry and academic standards of research on, and the curation of, ape remains. The suggested interventions involve restoring individual identity and narrative to great apes while engaging with contextual reflexivity and decolonial theory. The resulting recommendations include contextualizing the individual, piecing individuals back together, challenging/questioning the captive-wild dichotomy, and collaborative international conversations. Our objective is to encourage a conversation regarding ethical and theoretical considerations in great ape skeletal remains research.

Ghost admixture in eastern gorillas

Archaic admixture has had a substantial impact on human evolution with multiple events across different clades, including from extinct hominins such as Neanderthals and Denisovans into modern humans. In great apes, archaic admixture has been identified in chimpanzees and bonobos but the possibility of such events has not been explored in other species. Here, we address this question using high-coverage whole-genome sequences from all four extant gorilla subspecies, including six newly sequenced eastern gorillas from previously unsampled geographic regions. Using approximate Bayesian computation with neural networks to model the demographic history of gorillas, we find a signature of admixture from an archaic 'ghost' lineage into the common ancestor of eastern gorillas but not western gorillas. We infer that up to 3% of the genome of these individuals is introgressed from an archaic lineage that diverged more than 3 million years ago from the common ancestor of all extant gorillas. This introgression event took place before the split of mountain and eastern lowland gorillas, probably more than 40 thousand years ago and may have influenced perception of bitter taste in eastern gorillas. When comparing the introgression landscapes of gorillas, humans and bonobos, we find a consistent depletion of introgressed fragments on the X chromosome across these species. However, depletion in protein-coding content is not detectable in eastern gorillas, possibly as a consequence of stronger genetic drift in this species.

Morphological variation of the Pan talus relative to that of Gorilla

OBJECTIVES

Differences in talar articular morphology relative to locomotion have recently been found within Pan and Gorilla. Whole-bone talar morphology within, and shared variation among, Pan and Gorilla (sub)species, however, has yet to be investigated. Here we separately analyze talar external shape within Pan (P. t. troglodytes, P. t. schweinfurthii, P. t. verus, P. paniscus) and Gorilla (G. g. gorilla, G. b. beringei, G. b. graueri) relative to degree of arboreality and body size. Pan and Gorilla are additionally analyzed together to determine if consistent shape differences exist within the genera.

MATERIALS AND METHODS

Talar external shape was quantified using a weighted spherical harmonic analysis. Shape variation both within and among Pan and Gorilla was described using principal component analyses. Root mean square distances were calculated between taxon averages, and resampling statistics conducted to test for pairwise differences.

RESULTS

P. t. verus (most arboreal Pan) talar shape significantly differs from other Pan taxa (p < 0.05 for pairwise comparisons) driven by more asymmetrical trochlear rims and a medially-set talar head. P. t. troglodytes, P. t. schweinfurthii, and P. paniscus do not significantly differ (p > 0.05 for pairwise comparisons). All gorilla taxa exhibit significantly different talar morphologies (p < 0.007 for pairwise comparisons). The more terrestrial subspecies of G. beringei and P. troglodytes exhibit a superoinferiorly taller talar head/neck complex.

DISCUSSION

P. t. verus exhibits talar morphologies that have been previously related to more frequent arboreality. The adaptations in the more terrestrial G. beringei and P. troglodytes subspecies may serve to facilitate load transmission.

Carpal allometry of African apes among mammals

OBJECTIVES

Morphological variation in African ape carpals has been used to support the idea that Pan and Gorilla evolved knuckle-walking independently. Little work, however, has focused on the effect of body mass on carpal morphology. Here, we compare carpal allometry in Pan and Gorilla to that of other quadrupedal mammals with similar body mass differences. If allometric trends in Pan and Gorilla carpals mirror those of other mammals with similar body mass variation, then body mass differences may provide a more parsimonious explanation for African ape carpal variation than the independent evolution of knuckle-walking.

MATERIALS AND METHODS

Three linear measurements were collected on the capitate, hamate, lunate, and scaphoid (or scapholunate) of 39 quadrupedal species from six mammalian families/subfamilies. Relationships between linear measurements and estimated body mass were analyzed using reduced major axis regression. Slopes were compared to 0.33 for isometry.

RESULTS

Within Hominidae, higher body mass taxa (Gorilla) have relatively anteroposteriorly wider, mediolaterally wider, and/or proximodistally shorter capitates, hamates, and scaphoids than low body mass taxa (Pan). These allometric relationships are mirrored in most, but not all, mammalian families/subfamilies included in the analysis.

CONCLUSIONS

Within most mammalian families/subfamilies, carpals of high body mass taxa are proximodistally shorter, anteroposteriorly wider, and mediolaterally wider than those of low body mass taxa. These distinctions may be caused by the need to accommodate relatively higher forelimb loading associated with greater body mass. Because these trends occur within multiple mammalian families/subfamilies, some carpal variation in Pan and Gorilla is consistent with body mass differences.

Ape femoral-humeral rigidities and arboreal locomotion

OBJECTIVES

This study investigates patterns of bone functional adaptations in extant apes through comparing hindlimb to forelimb bone rigidity ratios in groups with varying levels of arboreality.

MATERIALS AND METHODS

Using CT scans, bone rigidity (J) was calculated at three regions of interest (ROI) along femoral and humeral diaphyses in Homo, Pongo, Pan, and Gorilla with further comparisons made between species and subspecies divisions within Pan and Gorilla.

RESULTS

Consistent with previous work on extant hominoids, species exhibited differences in midshaft femoral to humeral (F/H) rigidity ratios. Results of the present study confirm that these midshaft differences extend to 35% and 65% diaphyseal ROIs. Modern humans, exhibiting larger ratios, and orangutans, exhibiting smaller ratios, bracketed the intermediate African apes in comparisons. Within some African apes, limb rigidity ratios varied significantly between taxonomic groups. Eastern gorillas exhibited the highest mean ratios and chimpanzees the lowest at all three ROIs. In posthoc comparisons, chimpanzees and bonobos did not differ in relative limb rigidity ratios at any of the three ROIs. However, western gorillas were more similar to bonobos than eastern gorillas at 50% and 35% ROIs, but not at the 65% ROI.

CONCLUSION

Species, and to a lesser extent subspecies, can be distinguished by F/H limb rigidity ratios according to broad positional behavior patterns at multiple regions of interest along the diaphyses. Similarity of bonobos and western gorillas is in line with behavioral data of bonobos being the most terrestrial of Pan species, and western gorillas the most arboreal of the Gorilla groups.

Holocene bidirectional river system along the Kenya Rift and its influence on East African faunal exchange and diversity gradients

Although biodiversity in East Africa is overall extremely high, species richness is not geographically uniform for fishes and mammals. We investigated the biogeographic relevance of past river activity in the Kenya Rift. We show that during a humid period 12,000 to 8,000 years ago, a river system connected currently isolated rift lakes and was partly connected to the Nile. While this river system formed pathways for the dispersal of fishes between lakes, it also acted as a barrier to the range expansion of forest mammals. This fairly recent hydrological connectivity between lakes has been a key driver of modern biodiversity patterns in East Africa. Climate-driven changes in drainage networks on multimillennial timescales are an important hypothesis in biodiversity research.

East Africa is a global biodiversity hotspot and exhibits distinct longitudinal diversity gradients from west to east in freshwater fishes and forest mammals. The assembly of this exceptional biodiversity and the drivers behind diversity gradients remain poorly understood, with diversification often studied at local scales and less attention paid to biotic exchange between Afrotropical regions. Here, we reconstruct a river system that existed for several millennia along the now semiarid Kenya Rift Valley during the humid early Holocene and show how this river system influenced postglacial dispersal of fishes and mammals due to its dual role as a dispersal corridor and barrier. Using geomorphological, geochronological, isotopic, and fossil analyses and a synthesis of radiocarbon dates, we find that the overflow of Kenyan rift lakes between 12 and 8 ka before present formed a bidirectional river system consisting of a “Northern River” connected to the Nile Basin and a “Southern River,” a closed basin. The drainage divide between these rivers represented the only viable terrestrial dispersal corridor across the rift. The degree and duration of past hydrological connectivity between adjacent river basins determined spatial diversity gradients for East African fishes. Our reconstruction explains the isolated distribution of Nilotic fish species in modern Kenyan rift lakes, Guineo-Congolian mammal species in forests east of the Kenya Rift, and recent incipient vertebrate speciation and local endemism in this region. Climate-driven rearrangements of drainage networks unrelated to tectonic activity contributed significantly to the assembly of species diversity and modern faunas in the East African biodiversity hotspot.

Body proportions and environmental adaptation in gorillas

OBJECTIVES

Limb length and trunk proportions are determined in a large, taxonomically and environmentally diverse sample of gorillas and related to variation in locomotion, climate, altitude, and diet.

MATERIALS AND METHODS

The sample includes 299 gorilla skeletons, 115 of which are infants and juveniles, distributed between western lowland (G. gorilla gorilla), low and high elevation grauer (G. beringei graueri), and Virunga mountain gorillas (G. b. beringei). Limb bone and vertebral column lengths scaled to body mass are compared between subgroups by age group.

RESULTS

All G. beringei have relatively short 3rd metapodials and manual proximal phalanges compared to G. gorilla, and this difference is apparent in infancy. All G. beringei also have shortened total limb lengths relative to either body mass or vertebral column length, although patterns of variation in individual skeletal elements are more complex, and infants do not display the same patterns as adults. Mountain gorillas have relatively long clavicles, present in infancy, and a relatively long thoracic (but not lumbosacral) vertebral column.

DISCUSSION

A variety of environmental factors likely contributed to observed patterns of morphological variation among extant gorillas. We interpret the short hand and foot bones of all G. beringei as genetic adaptations to greater terrestriality in the last common ancestor of G. beringei; variation in other limb lengths to climatic adaptation, both genetic and developmental; and the larger thorax of G. b. beringei to adaptation to reduced oxygen pressure at high altitudes, again as a product of both genetic differences and environmental influences during development.

Facial asymmetry tracks genetic diversity among Gorilla subspecies

Mountain gorillas are particularly inbred compared to other gorillas and even the most inbred human populations. As mountain gorilla skeletal material accumulated during the 1970s, researchers noted their pronounced facial asymmetry and hypothesized that it reflects a population-wide chewing side preference. However, asymmetry has also been linked to environmental and genetic stress in experimental models. Here, we examine facial asymmetry in 114 crania from three Gorilla subspecies using 3D geometric morphometrics. We measure fluctuating asymmetry (FA), defined as random deviations from perfect symmetry, and population-specific patterns of directional asymmetry (DA). Mountain gorillas, with a current population size of about 1000 individuals, have the highest degree of facial FA (explaining 17% of total facial shape variation), followed by Grauer gorillas (9%) and western lowland gorillas (6%), despite the latter experiencing the greatest ecological and dietary variability. DA, while significant in all three taxa, explains relatively less shape variation than FA does. Facial asymmetry correlates neither with tooth wear asymmetry nor increases with age in a mountain gorilla subsample, undermining the hypothesis that facial asymmetry is driven by chewing side preference. An examination of temporal trends shows that stress-induced developmental instability has increased over the last 100 years in these endangered apes.

The complex Y-chromosomal history of gorillas

Studies of the evolutionary relationships among gorilla populations using autosomal and mitochondrial sequences suggest that male-mediated gene flow may have been important in the past, but data on the Y-chromosomal relationships among the gorilla subspecies are limited. Here, we genotyped blood and noninvasively collected fecal samples from 12 captives and 257 wild male gorillas of known origin representing all four subspecies (Gorilla gorilla gorilla, G. g. diehli, G. beringei beringei, and G. b. graueri) at 10 Y-linked microsatellite loci resulting in 102 unique Y-haplotypes for 224 individuals. We found that western lowland gorilla (G. g. gorilla) haplotypes were consistently more diverse than any other subspecies for all measures of diversity and comprised several genetically distinct groups. However, these did not correspond to geographical proximity and some closely related haplotypes were found several hundred kilometers apart. Similarly, our broad sampling of eastern gorillas revealed that mountain (G. b. beringei) and Grauer's (G. b. graueri) gorilla Y-chromosomal haplotypes did not form distinct clusters. These observations suggest structure in the ancestral population with subsequent mixing of differentiated haplotypes by male dispersal for western lowland gorillas, and postisolation migration or incomplete lineage sorting due to short divergence times for eastern gorillas.

Gorilla calcaneal morphological variation and ecological divergence

OBJECTIVES

The primate foot has been extensively investigated because of its role in weight-bearing; however, the calcaneus has been relatively understudied. Here we examine entire gorilla calcaneal external shape to understand its relationship with locomotor behavior.

MATERIALS AND METHODS

Calcanei of Gorilla gorilla gorilla (n = 43), Gorilla beringei graueri (n = 20), and Gorilla beringei beringei (n = 15) were surface or micro-CT scanned. External shape was analyzed through a three-dimensional geometric morphometric sliding semilandmark analysis. Semilandmarks were slid relative to an updated Procrustes average in order to minimize the bending energy of the thin plate spline interpolation function. Shape variation was summarized using principal components analysis of shape coordinates. Procrustes distances between taxa averages were calculated and resampling statistics run to test pairwise differences. Linear measures were collected and regressed against estimated body mass.

RESULTS

All three taxa exhibit statistically different morphologies (p < .001 for pairwise comparisons). G. g. gorilla demonstrates an anteroposteriorly elongated calcaneus with a deeper cuboid pivot region and mediolaterally flatter posterior talar facet. G. b. beringei possesses the flattest cuboid and most medially-angled posterior talar facets. G. b. graueri demonstrates intermediate articular facet morphology, a medially-angled tuberosity, and an elongated peroneal trochlea.

DISCUSSION

Articular facet differences separate gorillas along a locomotor gradient. G. g. gorilla is adapted for arboreality with greater joint mobility, while G. b. beringei is adapted for more stereotypical loads associated with terrestriality. G. b. graueri's unique posterolateral morphology may be due to a secondary transition to greater arboreality from a more terrestrial ancestor.

Historical Genomes Reveal the Genomic Consequences of Recent Population Decline in Eastern Gorillas

Many endangered species have experienced severe population declines within the last centuries [1, 2]. However, despite concerns about negative fitness effects resulting from increased genetic drift and inbreeding, there is a lack of empirical data on genomic changes in conjunction with such declines [3-7]. Here, we use whole genomes recovered from century-old historical museum specimens to quantify the genomic consequences of small population size in the critically endangered Grauer's and endangered mountain gorillas. We find a reduction of genetic diversity and increase in inbreeding and genetic load in the Grauer's gorilla, which experienced severe population declines in recent decades. In contrast, the small but relatively stable mountain gorilla population has experienced little genomic change during the last century. These results suggest that species histories as well as the rate of demographic change may influence how population declines affect genome diversity.

Significant loss of mitochondrial diversity within the last century due to extinction of peripheral populations in eastern gorillas

Species and populations are disappearing at an alarming rate as a direct result of human activities. Loss of genetic diversity associated with population decline directly impacts species' long-term survival. Therefore, preserving genetic diversity is of considerable conservation importance. However, to assist in conservation efforts, it is important to understand how genetic diversity is spatially distributed and how it changes due to anthropogenic pressures. In this study, we use historical museum and modern faecal samples of two critically endangered eastern gorilla taxa, Grauer's (Gorilla beringei graueri) and mountain gorillas (Gorilla beringei beringei), to directly infer temporal changes in genetic diversity within the last century. Using over 100 complete mitochondrial genomes, we observe a significant decline in haplotype and nucleotide diversity in Grauer's gorillas. By including historical samples from now extinct populations we show that this decline can be attributed to the loss of peripheral populations rather than a decrease in genetic diversity within the core range of the species. By directly quantifying genetic changes in the recent past, our study shows that human activities have severely impacted eastern gorilla genetic diversity within only four to five generations. This rapid loss calls for dedicated conservation actions, which should include preservation of the remaining peripheral populations.

Comparison of hand use and forelimb posture during vertical climbing in mountain gorillas (Gorilla beringei beringei) and chimpanzees (Pan troglodytes)

OBJECTIVES

Studies on grasping and limb posture during arboreal locomotion in great apes in their natural environment are scarce and thus, attempts to correlate behavioral and habitat differences with variation in morphology are limited. The aim of this study is to compare hand use and forelimb posture during vertical climbing in wild, habituated mountain gorillas (Gorilla beringei beringei) and semi-free-ranging chimpanzees (Pan troglodytes) to assess differences in the climbing styles that may relate to variation in hand or forelimb morphology and body size.

MATERIALS AND METHODS

We investigated hand use and forelimb posture during both ascent and descent vertical climbing in 15 wild mountain gorillas and eight semi-free-ranging chimpanzees, using video records obtained ad libitum.

RESULTS

In both apes, forelimb posture was correlated with substrate size during both ascent and descent climbing. While climbing, both apes used power grips and diagonal power grips, including three different thumb postures. Mountain gorillas showed greater ulnar deviation of the wrist during vertical descent than chimpanzees, and the thumb played an important supportive role when gorillas vertically descended lianas.

DISCUSSION

We found that both apes generally had the same grip preferences and used similar forelimb postures on supports of a similar size, which is consistent with their overall similarity in hard and soft tissue morphology of the hand and forelimb. However, some species-specific differences in morphology appear to elicit slightly different grasping strategies during vertical climbing between mountain gorillas and chimpanzees.

New fossil remains of Homo naledi from the Lesedi Chamber, South Africa

The Rising Star cave system has produced abundant fossil hominin remains within the Dinaledi Chamber, representing a minimum of 15 individuals attributed to Homo naledi. Further exploration led to the discovery of hominin material, now comprising 131 hominin specimens, within a second chamber, the Lesedi Chamber. The Lesedi Chamber is far separated from the Dinaledi Chamber within the Rising Star cave system, and represents a second depositional context for hominin remains. In each of three collection areas within the Lesedi Chamber, diagnostic skeletal material allows a clear attribution to H. naledi. Both adult and immature material is present. The hominin remains represent at least three individuals based upon duplication of elements, but more individuals are likely present based upon the spatial context. The most significant specimen is the near-complete cranium of a large individual, designated LES1, with an endocranial volume of approximately 610 ml and associated postcranial remains. The Lesedi Chamber skeletal sample extends our knowledge of the morphology and variation of H. naledi, and evidence of H. naledi from both recovery localities shows a consistent pattern of differentiation from other hominin species.