Ludovic DUvaux, Carole Smadja, Julia Ferrari, Within and between species, multigene families (MF) are known to be highly diverse in terms of both Copy Number Variation (CNV) and allelic diversity. Accordingly, within and between population diversities of MF have a strong potential to result from, or to fuel, local adaptation – and possibly speciation. However, these diversities have seldom been contrasted and their relative evolutionary dynamics remain poorly understood. The host-plant races of the pea aphid provide an excellent system to understand these dynamics in the context of speciation with gene flow. Notably, Chemosensory MF (CMF) – e.g. Olfactory Receptors (OR), Gustatory Receptors (GR), Odorant Binding Proteins (OBP) – are critically important for specific host plant recognition, i.e. putatively a main cause of reproductive isolation.
We sequenced 120 individuals from 8 races using a target enrichment protocol and Solexa sequencing – guaranteeing a median coverage of 150X. In doing so, we assessed CNV and nucleotidic diversity at about 3000 exons (from CMF, other MF and control genes) and 650 promoters of CMF genes.
Preliminary results show CNV is widespread, as it occurs in 65% of all exons (even surprisingly up to 57% for control exons). As with SNPs in single copy genes, most CNV in non CMF genes is shared among races. In contrast, for targets linked to chemosensory genes – notably GR exons and promoters – CNV tends to structure by race. Also, the rate of duplication appears higher for CMF: OR, OBP and promoters show significantly more CNV than other MF. Together, these results suggest that many CMF genes may evolve under positive selection and contribute to adaptation to host plants. In order to better understand the genetic basis of adaptation, work is ongoing to link patterns of CNV (i) to the history of gene flow between races; and (ii) to observed differences in gene expression within and between races across native and non-native host plants.
The two subspecies of the house mouse Mus musculus musculus and M. m. domesticus have evolved in allopatry for half a million years before meeting secondarily in Europe 5000 years ago, forming a narrow hybrid zone with unfit hybrids. Previous studies have shown that these incipient species recognise each other through signals present in urine and mate assortatively in the contact zone. This suggests a reinforcement process in this zone where prezygotic isolation would evolve as a response to selection against hybridisation.
Our study addresses the genetic basis of sexual isolation between these two subspecies by analyzing divergence of two large multigene families involved in chemosensory recognition. On the signaling side, we focused on the Major Urinary Proteins (MUP), a cluster of more than 21 duplicated genes known to act as pheromones in the house mouse. On the reception side, we focused on their potential receptors, the vomeronasal receptors (VR), a very large multigene family composed of more than 200 genes, expressed in the vomeronasal organ of the mouse and known to be involved in pheromone recognition.
Since assortative mating is displayed in the hybrid zone, we predicted strong sign of divergence between the two subspecies at our candidate families provided that they are involved in sexual isolation. Moreover, if reinforcing selection is acting on the mate recognition system in the hybrid zone, we expected a stronger signature of selection in the genomic regions baring VR and MUP genes in individuals of the hybrid zone as compared to individuals residing in allopatric zones of the distribution range.
By combining several high-throughput genomic methods such as RNA-seq and exome sequencing, we tested these predictions and explored divergence affecting the VR and MUP gene families at the sequence, expression and structural levels.
Genomic regions of low recombination are expected to contribute to the accumulation of incompatibilities allowing speciation with gene flow to occur. While chromosomal inversions are well documented in such processes, the role of Robertsonian (Rb) fusions (that join two acrocentric chromosomes by their centromere to form a metacentric one) is less clear. The house mouse is an emblematic model of Rb variation since one subspecies, M. m. domesticus, displays >80 Rb races. Previous cytogenetic studies demonstrated a decrease in recombination rates along the proximal 50% of Rb chromosomes in both homozygotes and heterozygotes. This study explores the role of Rb fusions in reducing gene flow by investigating their effect on genome admixture between two subspecies of the house mouse. In Denmark where the two taxa form a tension zone, M. m. domesticus carries 3 Rb fusions while M. m. musculus has an all-acrocentric karyotype. Genome admixture was assessed using 127 SNPs diagnostic of the two subspecies and covering the proximal 25% of 3 chromosomal arms involved in Rb fusions and 2 acrocentrics. We compared patterns of genomic admixture in the proximal regions to those at 86 diagnostic loci randomly distributed in the genome by fitting a genomic cline model with 3 parameters (centre and slope in each subspecific context). In the domesticus genomic context, Rb clines were much steeper than that of the average reference loci. Their centre was displaced in favour of musculus, however, due to introgression of large chromosomal blocks, and both of these patterns were stronger for the most proximal loci. This is compatible with the predicted effects of reduced recombination in Rb fusions coupled with incompatibilities in these genomic regions. In addition, clines for acrocentrics were smoother than average in the musculus genomic context, suggesting that other undescribed effects are acting, such as a possible advantage of domesticus acrocentric centromeres.