Population genomics of fish

 Stage · Stage M2  · 5 mois    Bac+5 / Master   Museum National d'Histoire Naturelle (UMR7205 - ISYEB) · Paris (France)

 Date de prise de poste : 16 janvier 2023


population genetics simulations coalescent theory




In the Pacific Ocean, coral reefs are characterised by a decrease in species richness moving away from the "Coral Triangle", in accordance with the Theory of Island Biogeography (TIB). The TIB predicts the distribution of species based on colonization / extinction rates: species richness at a given point is a function of its distance from a propagule source (the Coral Triangle in the Pacific). This theory has recently been extended to account for trophic relationships (T-TIB) (Gravel et al. 2011), which adds the constraint that consumer species can only colonize a habitat if their prey(s) are already present. The combination of both theories thus predicts higher extinction rates and lower colonization rates with increasing distance from the source (TIB) and/or with decreasing trophic niche width (T-TIB). Unfortunately, the relationship between trophic niche and genetic diversity in general, and in the Pacific context more specifically, has never been studied. To fill this gap, we recently sequenced ~4500 nuclear loci in 576 individuals from 41 coral reef fish species sampled in Moorea by following a target enriched gene capture protocol (Li et al. 2018). The gut content of a subsample of these fishes have also been investigated through a meta-barcoding approach to uncover the trophic network of this fish fauna. After reconstructing the historical demography of each species and defined an index of demographic stability, preliminary results show an increase of demographic stability for species with larger trophic niche. However, whether specialist species underwent cycles of extinction/recolonization (hereafter, E/C) and generalist remaining stable after a first occupancy, it remains to be tested. Furthermore, estimation of genetic diversity can be biased in species with large fecundity if the variance in reproductive success is not taken into account (Hedgecock et al. 2011).



To go beyond the relationship between genetic diversity and the trophic network, we will simultaneously i) test another prediction of the T-TIB theory(i.e.,  if specialist species harbour signature of extinction/colonization (E/C) models while generalist species are more stable through time); ii) test whether multiple coalescent merger (Sargsyan et al. 2018) models provide better fit to the data than Kingman’s n-coalescent. More specifically, the Master project will be articulated in two steps:

  1. Investigate using simulations the properties of E/C models using both forward (using Slim) and backward coalescent approaches (using Fastsimcoal and msprime, to take multiple coalescence into account). In particular, we will focus on the summary statistics that may provide more power to correctly estimate demographic parameters and can distinguish (eventually) multiple coalescent models vs the n-coalescent.
  2. The knowledge gained in step1 will be fruitful to correctly apply approximate Bayesian computation (Bertorelle et al. 2010) methods (and interpret their results) to the 41 reef fish species from Moorea.


DESCRIPTION OF DATA if applicable (Data must be available before the start of the internship):

The student will work (in step 2) on the genetic data already available from 576 fish individuals belonging to 41 species. The genetic data consists of a panel of ~4500 nuclear loci sequenced under an enriched target gene capture protocol (Li et al. 2018).


  • Forward and backward (multiple mergers and n-coalescent) simulations of genetic data
  • Approximate Bayesian computation coupled with Random Forest algorithm to estimate demographic parameters in real data


Procédure :

Date limite : None

Offre publiée le 26 octobre 2022, affichage jusqu'au 24 décembre 2022