Origin and evolution of the vertebrate leukocyte receptors: the lesson from tunicates

International audienceTwo selected receptor genes of the immunoglobulin superfamily (IgSF), one CTX/JAM family member, and one poliovirus receptor-like nectin that have features of adhesion molecules can be expressed by Ciona hemocytes, the effectors of immunity. They can also be expressed in the nervous system (CTX/JAM) and in the ovary (nectin). The genes encoding these receptors are located among one set of genes, spread over Ciona chromosomes 4 and 10, and containing other IgSF members homologous to those encoded by genes present in a tetrad of human (1, 3 + X, 11, 21 + 19q) or bird chromosomes (1, 4, 24, 31) that include the leukocyte receptor complex. It is proposed that this tetrad is due to the two rounds of duplication that affected a single prevertebrate ancestral region containing a primordial leukocyte receptor complex involved in immunity and other developmental regulatory functions

The IICR (inverse instantaneous coalescence rate) as a summary of genomic diversity: insights into demographic inference and model choice

International audienceSeveral 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 characterised 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

The IICR and the non-stationary structured coalescent: towards demographic inference with arbitrary changes in population structure

In the last years, a wide range of methods allowing to reconstruct past population size changes from genome-wide data have been developed. At the same time, there has been an increasing recognition that population structure can generate genetic data similar to those produced under models of population size change. Recently, Mazet et al. (Heredity 116:362-371, 2016) showed that, for any model of population structure, it is always possible to find a panmictic model with a particular function of population size changes, having exactly the same distribution of T 2 (the coalescence time for a sample of size two) as that of the structured model. They called this function IICR (Inverse Instantaneous Coalescence Rate) and showed that it does not necessarily correspond to population size changes under non-panmictic models. Besides, most of the methods used to analyse data under models of population structure tend to arbitrarily fix that structure and to minimise or neglect population size changes. Here, we extend the seminal work of Herbots (PhD thesis, University of London, 1994) on the structured coalescent and propose a new framework, the Non-Stationary Structured Coalescent (NSSC) that incorporates demographic events (changes in gene flow and/or deme sizes) to models of nearly any complexity. We show how to compute the IICR under a wide family of stationary and non-stationary models. As an example we address the question of human and Neanderthal evolution and discuss how the NSSC framework allows to interpret genomic data under this new perspective