Bonjour,
Une offre de stage en Master 2 est disponible au Centre de Recherche sur la Biodiversité et l’Environnement (CRBE), à l’Université Paul Sabatier de Toulouse.
Cordialement,
Philippe Gaubert.
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Adaptive genomics of pangolins applied to their conservation and global trade tracing
Supervisors:
Philippe Gaubert & Emilie Lecompte (CRBE – IRD / Université Paul Sabatier)
Sean P. Heighton (MPES – CNRS / Université de Caen Normandie)
Background:
Pangolins have become a central part of conservation action due to their notorious label of being the most trafficked wild mammals in the world. Novel comparative and population genomic research on all eight species across their global distributions are starting to shed light on their risk of extinction, evolution and population dynamics. These pieces of evidence through neutral markers are being put together to develop best conservation genetic practices for protecting these Evolutionarily Distinct and Globally Endangered (EDGE) species and their populations, including the identification and management of conservation units (CUs). However, to truly understand pangolin evolution and support conservation genetic practices (i.e. translocations and identification of CUs or admixed species and populations) that are robust, studies on the adaptive genomic signature in pangolins are paramount.
Aim & Objectives:
Here we propose an internship Master project with the aim of understanding the adaptation of pangolin species and their populations using both phylogenomic and population genomics approaches, in order to improve conservation genetic management. Objectives are to:
(i) Identify key genes under selection across species and populations
(ii) Explore their associations with populations and environments
(iii) Define conservation genetic guidelines for improved management based on neutral+adaptive population structuring
(iv) Use this information to trace the global pangolin trade through machine-learning methodologies
Methods:
The candidate will have access to already sequenced full genomes, extracted and aligned ± 3 200 orthologous genes, and mapped gene-capture data (670 loci at ± 35x depth) of around 900 individuals across the eight species, generated as part of the project PANGO-GO (https://anr.fr/Project-ANR-17-CE02-0001). Gene-capture data include around 250 loci directly linked to genes found to be of adaptive importance in other vertebrate species to environmental and biological variation. The candidate will use this already produced genomic data to identify and categorize genes and SNPs under selection at (i) a species level using shifts in substitutions of gene alignments (e.g. dN/dS ratios) and phylogenetic approaches (substitution rate variation) from genomes and orthologous genes, as well as (ii) a population level using outlier detection (e.g., Fst and association to gene characteristics) and genotype-environment associations (GEAs) from gene-capture data. Tracing of the global pangolin trade will be conducted under a neural network spatial assignment approach implemented in the R package Locator.
Skills sought:
• Background or experience in bioinformatics
• Ability to work in Linux bash and/or R environments
• Previous experience in analyses of selection; python scripting is advantageous
Pertinent publications:
Heighton, S.P., Allio, R., Murienne, J., Salmona, J., Meng, H., Scornavacca, C., Bastos, A.D., Njiokou, F., Pietersen, D.W., Tilak, M.K. and Luo, S.J., 2023. Pangolin genomes offer key insights and resources for the world’s most trafficked wild mammals. Molecular Biology and Evolution, 40(10), p.msad190.
Choo, S.W., Rayko, M., Tan, T.K., Hari, R., Komissarov, A., Wee, W.Y., Yurchenko, A.A., Kliver, S., Tamazian, G., Antunes, A. and Wilson, R.K., 2016. Pangolin genomes and the evolution of mammalian scales and immunity. Genome research, 26(10), pp.1312-1322.
Flanagan SP, Forester BR, Latch EK, Aitken SN, Hoban S. Guidelines for planning genomic assessment and monitoring of locally adaptive variation to inform species conservation. Evol Appl. 2017 Dec 2;11(7):1035-1052. doi: 10.1111/eva.12569. PMID: 30026796; PMCID: PMC6050180.
Latrille, T., Rodrigue, N. and Lartillot, N., 2023. Genes and sites under adaptation at the phylogenetic scale also exhibit adaptation at the population-genetic scale. Proceedings of the National Academy of Sciences, 120(11), p.e2214977120.
Forester, B.R., Landguth, E.L., Hand, B.K. and Balkenhol, N., 2021. Landscape genomics for wildlife research. Population genomics: wildlife, pp.145-184.
Contacts:
Philippe Gaubert – philippe.gaubert@ird.fr
Emilie Lecompte – emilie.lecompte@univ-tlse3.fr.
Sean P. Heighton – seanheighton@gmail.com
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