Comparative landscape evolutionary genomics of West-African primates: a contribution of the anthropological biology to their conservation plan

Start and End of the Project
June 2016 to May 2019

Principal Investigator
Profª. Doutora Tânia Minhós


Research Team

Researcher Institucional Affiliation
 Tania Minhós Fundação Calouste Gulbenkian (IGC)
 Catarina Casanova CAPP/ISCSP, Universidade de Lisboa
 Joana Sousa ULHT/Guiné-Bissau
 João Torres ICETA/UP
 Lounès Chikhi
 Fundação Calouste Gulbenkian (IGC)
 Maria Joana Ferreira da Silva CAPP/ISCSP, Universidade de Lisboa
 Michael Bruford The University of Cardiff


Institutional Partners

 Fundação Calouste Gulbenkian, Instituto Gulbenkian Ciência Portugal
 Instituto de Ciências, Tecnologias e Agroambiente da Universidade do Porto Portugal



Project Description

West-African non-human primates (WANHP) are among the world’s most threatened taxa and their habitat, the Upper Guinean Forests hotspot, is one of the most critically anthropogenic-fragmented regions on the planet.
Habitat loss and fragmentation (HL&F) often restricts gene flow and erode genetic diversity, which may increase extinction risk. Monitoring genetic consequences on populations is the first step for WANHP conservation management. Biological anthropologists have used PCR-based neutral genetic markers to monitor HL&F consequences on key social-ecological aspects, such as demography, parasite infection, disruption of mating patterns and gene flow.
A considerable number of inconsistencies arose, which may result from species-specific resilience to HL&F or from inability to consider different temporal and geographic scales. While the evolutionary processes responsible for the species genetic variation pattern can be identified using a broad-scale, the impact of recent HL&F on mating system, dispersal strategies or susceptibility to parasite infections is frequently population-specific and context-dependent, and should be evaluated at a fine-scale. The degree of human-wildlife conflicts often depends on local human communities features but most fragmentation genetics studies fail to consider this crucial information. Moreover, the use of few neutral genetic markers does not allow disentangling between recent HL&F and historical processes and cannot draw conclusions on loss of adaptively important variation. Wrongly informed conservation actions may be detrimental to the species’ adaptive potential.

A global conservation strategy for WANHPs should be based on accurate information for several populations on both neutral and adaptive genetic changes following HL&F and on the disruption of socio-ecological patterns by local human-wildlife conflicts. 
This project proposes to study the genetic effects of HL&F on key socio-ecological parameters of threatened WANHP using a comparative landscape genomics framework. We will focus on the forest-dwelling Colobus polykomos and Procolobus badius and the ecologically plastic Papio papio, three WANHP species almost completely sympatric but displaying a remarkably different response to the same HL&F pressures. Our aims are:
  1. to understand how HL&F affects the demographic and socio- ecological parameters,
  2. which environmental context(s) drives local genetic adaptation.
Our ultimate goal is to significantly improve WANHP long-term conservation management.
Our study will be multi-dimensional. Anthropological, parasitological, genomic and ecological data will be collected in five different countries across West Africa at fragments of different sizes.
Sampling design in landscape genetics does not require a large number of individuals but instead, should consider the broadest range of environmental conditions experimented by a species. We will assemble 75 good-quality DNA extracts collected along the West Africa latitudinal environmental gradient, covering the three WANHP distribution range. In each sampling location, we will gather 60 faecal DNA extracts to study the three main modes of parasite transmission to wild primates. We will investigate human-WANHP interactions, using an array of quantitative and qualitative techniques.
A large amount of data is already available:
  1. a species occurrence database of 2,540 entries for all colobus taxa across Africa for species distribution modelling;
  2. a preliminary species distribution model for P. papio;
  3. more than 400 DNA extracts for genomic and parasitological analyses collected in four different countries for the three WANHP;
  4. parasitological data for Guinea-Bissau colobus;
  5. data on interactions between human and Guinea-Bissau WANHP, collected during FCT-funded projects.
Our team is multi-disciplinary and include three of the world’s most prominent scientists on evolutionary and conservation biology and landscape genomics; two experienced and worldwide acknowledged WANHP conservation geneticists, one senior specialist on wild WANHP parasites; two international authorities on human-WANHP conflicts and one auspicious researcher on WANHP ecological modelling. 
For the first time landscape genomics tools will be applied to study the consequences of HL&F on wild WANHP survival.
Among other important outcomes, we will develop hundreds of thousands of species-specific markers, identify the environmental and anthropogenic factors impacting the genetic patrimony and health of WANHP and significantly advance the understanding on patterns of demographic and adaptive genetic variation across West Africa. Our study is designed to have a significant impact on conservation management of WANHP.


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