Publications

Below is a list of articles published, submitted or in press that have been possible thanks to the funding of the 2015-2016 Biodiversa COFUND call. They all integrate the following sentence in the acknowledgement section:

This research was funded through the 2015-2016 BiodivERsA COFUND call for research proposals, with the national funders ANR (ANR-16-EBI3-0014), FCT (Biodiversa/0003/2015) and PT-DLR (01LC1617A)“.

Chikhi L , Rodriguez WV, Grusea S, Santos P, Boitard S, Mazet O (in press). The IICR (inverse instantaneous coalescence rate) as a summary of genomic diversity: insights into demographic inference and model choice. Heredity.

Abstract:

Several inferential methods using genomic data have been proposed to quantify and date population size changes in the history of species. At the same time an increasing number of studies have shown that population structure can generate spurious signals of population size change. Recently, Mazet et al. (2016) introduced, for a sample size of two, a time dependent parameter which they called the IICR (inverse instantaneous coalescence rate). The IICR is equivalent to a population size in panmictic models, but not necessarily in structured models. It is characterized by a temporal trajectory that suggests population size changes, as a function of the sampling scheme, even when the total population size was constant. Here, we extend the work of Mazet et al. (2016) by (i) showing how the IICR can be computed for any demographic model of interest, under the coalescent, (ii) applying this approach to models of population structure (1D and 2D stepping-stone, split models, two- and three-island asymmetric gene flow, continent-island models), (iii) stressing the importance of the sampling strategy in generating different histories, (iv)  arguing that IICR plots can be seen as summaries of genomic information that can thus be used for model choice or model exclusion (v) applying this approach to the question of admixture between humans and Neanderthals. Altogether these results are potentially important given that the widely used PSMC (pairwise sequentially Markovian coalescent) method of Li and Durbin (2011) estimates the IICR of the sample, not necessarily the history of the populations.

You can find the version that was submitted in March 2017 here and the supplementary material here.