Disrupted dispersal and its genetic consequences: Comparing protected and threatened baboon populations (Papio papio) in West Africa

Notes on the conservation threats to the western lesser spot-nosed monkey (Cercopithecus petaurista buettikoferi) in the Bijagós Archipelago (Guinea-Bissau, West Africa)

The lesser spot-nosed monkey (Cercopithecus petaurista) is a widely distributed West African guenon, which is generally considered less vulnerable to local extinctions than many sympatric primate species. Guinea-Bissau harbours the westernmost populations of the species, which is thought to be very rare or even extinct on the mainland, but to have putative populations on some islands of the Bijagós Archipelago. However, due to a lack of regional studies, baseline information on these insular populations is missing. We collected baseline data on the anthropogenic activities that possibly threaten the long-term conservation of this primate by using non-systematic ethnographic methodologies. The species was reported to be decreasing in number or rare by locals on two of the islands, and we identified two main conservation threats to it: generalised habitat loss/degradation, and hunting. While subsistence hunting has been recorded before in these areas, we report, to the best of our knowledge for the first time for these islands, the presence of a semi-organised commercial wild meat trade. The carcasses of western lesser spot-nosed monkeys were observed being stored and shipped from seaports to be sold at urban hubs (Bissau and Bubaque Island). The effect of commercial trade on the species could be severe, considering the small, naturally occurring, carrying capacities typical of insular ecosystems. The results of this study highlight the importance of understanding the leading social drivers of wild meat hunting of lesser spot-nosed monkeys on the Bijagós Archipelago, and the need to conduct baseline research on these insular populations, for which qualitative and quantitative methods could be combined.

Assessing the recovery of Y chromosome microsatellites with population genomic data using Papio and Theropithecus genomes

Y chromosome markers can shed light on male-specific population dynamics but for many species no such markers have been discovered and are available yet, despite the potential for recovering Y-linked loci from available genome sequences. Here, we investigated how effective available bioinformatic tools are in recovering informative Y chromosome microsatellites from whole genome sequence data. In order to do so, we initially explored a large dataset of whole genome sequences comprising individuals at various coverages belonging to different species of baboons (genus: Papio) using Y chromosome references belonging to the same genus and more distantly related species (Macaca mulatta). We then further tested this approach by recovering Y-STRs from available Theropithecus gelada genomes using Papio and Macaca Y chromosome as reference sequences. Identified loci were validated in silico by a) comparing within-species relationships of Y chromosome lineages and b) genotyping male individuals in available pedigrees. Each STR was selected not to extend in its variable region beyond 100 base pairs, so that loci can be developed for PCR-based genotyping of non-invasive DNA samples. In addition to assembling a first set of Papio and Theropithecus Y-specific microsatellite markers, we released TYpeSTeR, an easy-to-use script to identify and genotype Y chromosome STRs using population genomic data which can be modulated according to available male reference genomes and genomic data, making it widely applicable across taxa.

The importance of well protected forests for the conservation genetics of West African colobine monkeys

In tropical forests, anthropogenic activities are major drivers of the destruction and degradation of natural habitats, causing severe biodiversity loss. African colobine monkeys (Colobinae) are mainly folivore and strictly arboreal primates that require large forests to subsist, being among the most vulnerable of all nonhuman primates. The Western red colobus Piliocolobus badius and the King colobus Colobus polykomos inhabit highly fragmented West African forests, including the Cantanhez Forests National Park (CFNP) in Guinea-Bissau. Both species are also found in the largest and best-preserved West African forest-the Taï National Park (TNP) in Ivory Coast. Colobine monkeys are hunted for bushmeat in both protected areas, but these exhibit contrasting levels of forest fragmentation, thus offering an excellent opportunity to investigate the importance of well-preserved forests for the maintenance of evolutionary potential in these arboreal primates. We estimated genetic diversity, population structure, and demographic history by using microsatellite loci and mitochondrial DNA. We then compared the genetic patterns of the colobines from TNP with the ones previously obtained for CFNP and found contrasting genetic patterns. Contrary to the colobines from CFNP that showed very low genetic diversity and a strong population decline, the populations in TNP still maintain high levels of genetic diversity and we found no clear signal of population decrease in Western red colobus and a limited decrease in King colobus. These results suggest larger and historically more stable populations in TNP compared to CFNP. We cannot exclude the possibility that the demographic effects resulting from the recent increase of bushmeat hunting are not yet detectable in TNP using genetic data. Nevertheless, the fact that the TNP colobus populations are highly genetically diverse and maintain large effective population sizes suggests that well-preserved forests are crucial for the maintenance of populations, species, and probably for the evolutionary potential in colobines.

Genetic evidence of differential dispersal pattern in the Asiatic wild dog: Comparing two populations with different pack sizes

Introduction

Dispersal is a multi-causal, crucial life-history event in shaping the genetic and behavioral structure of mammals. We assessed the dispersal pattern of dholes aka Asiatic wild dog (Cuon alpinus), a social monogamous mammal at two tiger reserves of Maharashtra with different degrees of pack size and competition with tigers i.e. Tadoba-Andhari (TATR, smaller pack size, higher tiger density) and Nawegaon-Nagzira (NNTR, larger pack size, lower tiger density).

Methods

We used the microsatellite data of 174 individual genotypes (98 males and 67 females) to assess the dispersal pattern of dholes from two populations with varying pack size, tiger density, and landscape connectivity using gene flow as a proxy. We compared the population structure, pairwise F statistics, assignment index, and relatedness across a spatial scale.

Results and discussion

Overall, the results suggested a difference in sex-bias dispersal pattern for the two sub-populations, exhibiting significant results for female-biased dispersal in the TATR population with a smaller pack size and higher tiger density. Our study highlights the variability in sex-biased dispersal patterns in two different populations which could be the consequence of different variables such as pack size, tiger density, and geographical scale. The study warrants further quantitative investigation including several factors such as individual behavior, pack composition, pack size, tiger density, etc. In the present Anthropocene era, determining the sex bias in dispersal patterns for a short-range, pack-living carnivore will help in devising an effective conservation management plan for their long-term survival.

Population history of chimpanzees introduced to Lake Victoria's Rubondo Island

Between 1966 to 1969, Bernhard Grzimek (Frankfurt Zoological Society, FZS) introduced chimpanzees (Pan troglodytes) previously held in European institutions to Rubondo Island in Lake Victoria in Tanzania. Earlier publications report various numbers of released animals and that all founders originated from West Africa. We revise these assumptions through consultation of archived FZS records and genetic analyses of surviving descendants. Accordingly, 17 chimpanzees were transported to Africa in four waves, with male-female ratios of 3:8, 1:0, 1:0 and 2:2; one female died in transit. Thus, 16 chimpanzees were released in total. FZS and studbook records allocate a West African provenance to only 19% of the founders and a generic "Africa" origin to 56%. Still, studbook records render it unlikely that any of the founders were captive-born. In addition, our genetic analyses based on biological samples from the current descendants trace the geographical origin of their ancestors back to West Africa (P. t. verus) and Central Africa (P. t. troglodytes). Based on counts of individuals and night nests, we estimate that the population, since 1969, grew to around 35 individuals in 2014 (annual increase 3.3%). Thus, chimpanzees released onto a large forested island free from predators or hunting pressure, habitat destruction and conspecific competition can form a self-sustaining island population without human support.

A refined panel of 42 microsatellite loci to universally genotype catarrhine primates

Microsatellite genotyping is an important genetic method for a number of research questions in biology. Given that the traditional fragment length analysis using polyacrylamide gel or capillary electrophoresis has several drawbacks, microsatellite genotyping-by-sequencing (GBS) has arisen as a promising alternative. Although GBS mitigates many of the problems of fragment length analysis, issues with allelic dropout and null alleles often remain due to mismatches in primer binding sites and unnecessarily long PCR products. This is also true for GBS in catarrhine primates where cross-species amplification of loci (often human derived) is common.We therefore redesigned primers for 45 microsatellite loci based on 17 available catarrhine reference genomes. Next, we tested them in singleplex and different multiplex settings in a panel of species representing all major lineages of Catarrhini and further validated them in wild Guinea baboons (Papio papio) using fecal samples.The final panel of 42 microsatellite loci can efficiently be amplified with primers distributed into three amplification pools.With our microsatellite panel, we provide a tool to universally genotype catarrhine primates via GBS from different sample sources in a cost- and time-efficient way, with higher resolution, and comparability among laboratories and species.

Insights into the evolution of social systems and species from baboon studies

Baboons, members of the genus Papio, comprise six closely related species distributed throughout sub-Saharan Africa and southwest Arabia. The species exhibit more ecological flexibility and a wider range of social systems than many other primates. This article summarizes our current knowledge of the natural history of baboons and highlights directions for future research. We suggest that baboons can serve as a valuable model for complex evolutionary processes, such as speciation and hybridization. The evolution of baboons has been heavily shaped by climatic changes and population expansion and fragmentation in the African savanna environment, similar to the processes that acted during human evolution. With accumulating long-term data, and new data from previously understudied species, baboons are ideally suited for investigating the links between sociality, health, longevity and reproductive success. To achieve these aims, we propose a closer integration of studies at the proximate level, including functional genomics, with behavioral and ecological studies.