A antropologia biológica elucida-nos

UID/ANT/04038/2013Non-human primates are our closest relatives and we share with them several traits and evolutionary trends. For example, we all have an opposable thumb, large and well-developed eyes, large brains and very slow development, with the progeny highly dependent on the mother for long periods of time. Because of this evolutionary proximity, the field of Primatology is one of the disciplines included in Biological Anthropology that aims to understand human evolution and adaptation. The well-recognized primate intelligence had a crucial role shaping the human evolutionary path, thus being one of the main research areas in Biological Anthropology. Ecological and social challenges posed by the environment may have act as the evolutionary engine to the development of the complex cognitive capacities of this well succeeded taxonomic group. Therefore, understanding the socio-ecological diversity of primate societies and its determinants is crucial to better understand human evolution. Porque razão quando olhamos para um primata não-humano lhe reconhecemos características ou comportamentos que imediatamente classificamos como sendo humanas? Isto acontece porque os primatas não-humanos são os nossos parentes mais próximos e com eles partilhamos inúmeras características e tendências evolutivas. É o caso por exemplo do polegar opositor, visão desenvolvida e em profundidade, alargamento do cérebro ou um desenvolvimento muito longo com crias muito dependentes da progenitora. Esta proximidade evolutiva faz com que a primatologia seja uma das disciplinas da Antropologia Biológica, que visa compreender a evolução e adaptação humana. A reconhecida inteligência dos primatas teve um papel determinante para o percurso evolutivo dos humanos e por isso tem constituído um dos principais focos de interesse da Antropologia Biológica. Sabe-se que os desafios ecológicos e sociais propostos pelo ambiente terão atuado como motor evolutivo para o desenvolvimento das capacidades cognitivas deste grupo tão bem sucedido. Por esta razão, o estudo da diversidade dos sistemas sócio-ecologicos dos primatas não-humanos e as suas determinantes são essenciais para compreender o percurso evolutivo dos humanos.publishersversionpublishe

Kinship and intragroup social dynamics in two sympatric African Colobus species

SFRH/BPD/87396/2012 UID/ANT/04038/2013Kinship has been described as a major factor shaping primates’ social dynamics, with individuals biasing their affiliative interactions to their related counterparts. However, it has also been demonstrated that, under certain circumstances, social bonding can be established in the absence of kin. The fact that Colobus polykomos (western black-and-white colobus) and Procolobus badius temminckii (Temminck’s red colobus) often live in sympatry (subject to the same ecological/anthropogenic pressures) but exhibit contrasting social systems makes them good models to test which factors shape their social systems. We investigated the influence of kinship on intragroup social dynamics of one focal group of each species present in Cantanhez National Park, Guinea-Bissau. Between October 2008 and June 2009 we used focal sampling to collect information on the individuals’ nearest neighbors and ad libitum sampling to collect data on intragroup social interactions. We estimated pairwise relatedness using fecal DNA from 9 individuals of Colobus polykomos and 15 individuals of Procolobus badius temminckii genotyped at 15 microsatellite loci. We found that, in the focal group of Colobus polykomos, individuals showed no preference to interact or be spatially closer to related partners. Moreover, mainly unrelated females and related males composed the focal group of Procolobus badius temminckii but grooming was most frequent among female dyads and only rarely involved male dyads. We conclude that kinship is not an important factor determining the social bonding in either study species, suggesting that other factors, e.g., anthropogenic, ecological, may be at play shaping these groups’ social bonding.authorsversionpublishe

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

notes on the present distribution and conservation of the sooty mangabey (Cercocebus atys) in Guinea-Bissau, West Africa

UIDB/04038/2020 UIDP/04038/2020The West-African sooty mangabey (Cercocebus atys) is threatened by habitat loss, hunting for meat consumption, and mortality during crop-foraging events. The species’ overall demographic trend is unknown. Presence and distribution in Guinea-Bissau, a country neighbored by Senegal and Republic of Guinea, was confirmed in 1946 but the species was declared extinct in 1989 and not observed in subsequent countrywide expeditions. Narratives of its presence across southern Guinea-Bissau are scattered in reports and occurrence in the eastern part was reported in 2017, but the limits of its distribution are currently unknown. Here, we present recent geo-referenced visual and molecular-based records of the sooty mangabey for three protected areas in southern Guinea-Bissau collected as part of a region-wide survey. Individuals were observed in Cufada Lagoons Natural Park (2015) and Dulombi National Park (NP) (2016) and photographed in Boé NP (2007, 2015 and 2020). Thirty-six samples collected in Boé NP (2017) were identified as sooty mangabey using a 402 base pair fragment of the mitochondrial cytochrome b gene. Our work suggests a wider distribution in Guinea-Bissau than previously described, augments knowledge of the populations’ current habitat use and threats, and has implications for efforts to conserve the species in West Africa. Considering the sooty mangabey as the reservoir of the simian immunodeficiency virus that led to the human variant, HIV-2, confirmation that the Guinea-Bissau population is not extinct may lead to a better understanding of early viral jump to humans and consequent epidemic spread, specifically of the HIV-2 Subgroup A. We highlight the need for extra conservation measures by Guinea-Bissau authorities.publishersversionpublishe

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.info:eu-repo/semantics/publishedVersio

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

Dietary flexibility of western red colobus in two protected areas with contrasting anthropogenic pressure

Food distribution and abundance can affect intra- and inter-dietary variation in non-human primates, influencing feeding ecology and altering behaviour. Natural and/or human-induced actions can influence the dynamics between primates and the environment, with associated impacts on socio-ecology and demography. This relationship in anthropogenic landscapes, however, is poorly understood. Here, we use DNA metabarcoding to obtain high resolution dietary diversity data, and multivariate generalised linear models to investigate variation in the diet of this threatened primate. We characterise the diet of the western red colobus (Piliocolobus badius) in both the better preserved Gola Rainforest National Park (GRNP, Sierra Leone), and in the fragmented forests of Cantanhez National Park (CNP, Guinea-Bissau), and evaluate biological, ecological and temporal differences. Dietary plant species richness was high in both protected areas, and the type of plants consumed varied significantly across seasons, space, and time. Although we identify dependence on a few key plants, red colobus in CNP consumed a higher average number of plant taxa than in GRNP, and 11% of the diet consisted of cultivated foods (e.g. mango). This is the first time a molecular approach has been used to investigate red colobus diet, and reveal dietary flexibility in degraded forests. Predicting the consequences of dietary change on long-term population persistence, however, remains a significant knowledge gap. Nevertheless, our results provide critical information to inform targeted regional conservation planning and implementation

Disrupted dispersal and its genetic consequences: Comparing protected and threatened baboon populations (Papio papio) in West Africa(PLoS ONE (2018) 13:4 (e0194189) DOI: 10.1371/journal.pone.0194189)

UID/ANT/04038/2013The Data Availability statement for this paper is incorrect. The correct statement is: The data underlying this study have been uploaded to the Open Science Framework and are accessible using the following link: https://osf.io/6evq2/. The following information is missing from the Acknowledgments section: The primer sequences contained in S3 Appendix were provided to the authors by Dr. Christian Roos.publishersversionpublishe

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

Dispersal is a demographic process that can potentially counterbalance the negative impacts of anthropogenic habitat fragmentation. However, mechanisms of dispersal may become modified in populations living in human-dominated habitats. Here, we investigated dispersal in Guinea baboons (Papio papio) in areas with contrasting levels of anthropogenic fragmentation, as a case study. Using molecular data, we compared the direction and extent of sex-biased gene flow in two baboon populations: from Guinea-Bissau (GB, fragmented distribution, human-dominated habitat) and Senegal (SEN, continuous distribution, protected area). Individual-based Bayesian clustering, spatial autocorrelation, assignment tests and migrant identification suggested female-mediated gene flow at a large spatial scale for GB with evidence of contact between genetically differentiated males at one locality, which could be interpreted as male-mediated gene flow in southern GB. Gene flow was also found to be female-biased in SEN for a smaller scale. However, in the southwest coastal part of GB, at the same geographic scale as SEN, no sex-biased dispersal was detected and a modest or recent restriction in GB female dispersal seems to have occurred. This population-specific variation in dispersal is attributed to behavioural responses to human activity in GB. Our study highlights the importance of considering the genetic consequences of disrupted dispersal patterns as an additional impact of anthropogenic habitat fragmentation and is potentially relevant to the conservation of many species inhabiting human-dominated environments.publishe

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

Abstract 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