The sampling scheme matters: Pan troglodytes troglodytes and P. t. schweinfurthii are characterized by clinal genetic variation rather than a strong subspecies break.

Populations of an organism living in marked geographical or evolutionary isolation from other populations of the same species are often termed subspecies and expected to show some degree of genetic distinctiveness. The common chimpanzee (Pan troglodytes) is currently described as four geographically delimited subspecies: the western (P. t. verus), the nigerian-cameroonian (P. t. ellioti), the central (P. t. troglodytes) and the eastern (P. t. schweinfurthii) chimpanzees. Although these taxa would be expected to be reciprocally monophyletic, studies have not always consistently resolved the central and eastern chimpanzee taxa. Most studies, however, used data from individuals of unknown or approximate geographic provenance. Thus, genetic data from samples of known origin may shed light on the evolutionary relationship of these subspecies. We generated microsatellite genotypes from noninvasively collected fecal samples of 185 central chimpanzees that were sampled across large parts of their range and analyzed them together with 283 published eastern chimpanzee genotypes from known localities. We observed a clear signal of isolation by distance across both subspecies. Further, we found that a large proportion of comparisons between groups taken from the same subspecies showed higher genetic differentiation than the least differentiated between-subspecies comparison. This proportion decreased substantially when we simulated a more clumped sampling scheme by including fewer groups. Our results support the general concept that the distribution of the sampled individuals can dramatically affect the inference of genetic population structure. With regard to chimpanzees, our results emphasize the close relationship of equatorial chimpanzees from central and eastern equatorial Africa and the difficult nature of subspecies definitions.

The geographic distribution of genetic diversity within gorillas.

Gorillas, like all non-human great apes, are endangered. Understanding the distribution of genetic diversity across their range is important because low diversity may arise in small populations through increased inbreeding, and, by reducing reproductive fitness, may lead to decreased chances of persistence of a given population. Previous studies found higher genetic diversity in the western (Gorilla gorilla) than in the eastern gorillas (Gorilla beringei), but rarely employed individuals of known geographic origin to investigate the distribution of diversity across multiple populations. The present study fills that gap by analyzing 1,161 individuals from nine sites across all four currently recognized Gorilla subspecies. Genetic diversity at each site was estimated using published data from seven highly-variable microsatellite loci. We found that the small and fragmented populations of Cross River gorillas, eastern lowland gorillas and mountain gorillas were less diverse than any of the five analyzed western lowland gorilla populations. The higher levels of genetic variation within the western lowland gorillas might be best explained by the facts that they (i) exhibit larger present and past effective population sizes than the other subspecies and (ii) maintain higher rates of gene flow through the existence of largely continuous habitat within their range. With regard to conservation, the high genetic diversity within western lowland gorillas is encouraging and retention of dispersal corridors between already protected areas is essential. Am. J. Primatol. 77:974-985, 2015. © 2015 Wiley Periodicals, Inc.

Characterization of MHC class II B polymorphism in multiple populations of wild gorillas using non-invasive samples and next-generation sequencing.

Genes encoded by the major histocompatibility complex (MHC) are crucial for the recognition and presentation of antigens to the immune system. In contrast to their closest relatives, chimpanzees and humans, much less is known about variation in gorillas at these loci. This study explored the exon 2 variation of -DPB1, -DQB1, and -DRB genes in 46 gorillas from four populations while simultaneously evaluating the feasibility of using fecal samples for high-throughput MHC genotyping. By applying strict similarity- and frequency-based analysis, we found, despite our modest sample size, a total of 18 alleles that have not been described previously, thereby illustrating the potential for efficient and highly accurate MHC genotyping from non-invasive DNA samples. We emphasize the importance of controlling for multiple potential sources of error when applying this massively parallel short-read sequencing technology to PCR products generated from low concentration DNA extracts. We observed pronounced differences in MHC variation between species, subspecies and populations that are consistent with both the ancient and recent demographic histories experienced by gorillas.

The genetic population structure of wild western lowland gorillas (Gorilla gorilla gorilla) living in continuous rain forest.

To understand the evolutionary histories and conservation potential of wild animal species it is useful to assess whether taxa are genetically structured into different populations and identify the underlying factors responsible for any clustering. Landscape features such as rivers may influence genetic population structure, and analysis of structure by sex can further reveal effects of sex-specific dispersal. Using microsatellite genotypes obtained from noninvasively collected fecal samples we investigated the population structure of 261 western lowland gorillas (WLGs) (Gorilla gorilla gorilla) from seven locations spanning an approximately 37,000 km(2) region of mainly continuous rain forest within Central African Republic (CAR), Republic of Congo and Cameroon. We found our sample to consist of two or three significantly differentiated clusters. The boundaries of the clusters coincided with courses of major rivers. Moreover, geographic distance detoured around rivers better-explained variation in genetic distance than straight line distance. Together these results suggest that major rivers in our study area play an important role in directing WLG gene flow. The number of clusters did not change when males and females were analyzed separately, indicating a lack of greater philopatry in WLG females than males at this scale.

Mapping the depressed brain: a meta-analysis of structural and functional alterations in major depressive disorder.

BACKGROUND: Depression has a lifetime prevalence of up to 20%. Neuroimaging methods have revealed various structural and functional changes that occur in a human brain during a depressive episode. However, we still lack information concerning the extent to which structural and functional changes co-occur in a depressed brain. Furthermore, it is difficult to evaluate from a merely qualitative literature review what regional brain changes in volume and activation are robust across depressed patient samples and consistent across imaging centers. METHODOLOGY AND PRINCIPLE FINDINGS: This study is a meta-analysis from 10 selected studies published previously. We applied the statistical anatomical/activation likelihood estimate method (ALE) in a total of 176 depressed patients and 175 controls for the MRI modality and in a total of 102 depressed patients and 94 controls for the PET modality to quantitatively identify those brain regions that show concordant alteration in the midst of a depressive episode across imaging modalities and study sites. We find a convergent change in the limbic-cortical brain circuit in depression compared to controls of both Positron Emission Tomography (PET) and Magnetic Resonance Imaging (MRI) data. The specific changes include lower gray matter volumes in the amygdala, the dorsal frontomedian cortex, and the right paracingulate cortex, as well as increases in glucose metabolism in the right subgenual and pregenual anterior cingulate cortices. CONCLUSIONS/SIGNIFICANCE: Our current findings represent an important first step towards a more focused approach to neuroimaging unipolar depression. The regions identified could serve as a specific region-of-interest-for-disease template for both individual in vivo imaging studies and postmortem histopathologic exploration.