Hybridization is a natural process happening with or without human intervention. It is an important evolutionary phenomenon that helps understanding complex mechanisms such as speciation. Hybrid zones between related species are thus regarded as “natural laboratories”. So mating between genetically divergent species or populations is quite common in nature.
Key insights into the process of speciation can be provided by comparing the genes flow rates throughout the whole genome and therefore underlie reproductive isolation. Some recent studies (2008) led by Geraldes et al., reported the geographical distribution of Y chromosome lineages in wild populations of rabbits from Iberia and southern France. This revealed that Y chromosomes showed a high level of differentiation between rabbit subspecies on either side of the existing hybrid zone. This was in clear contradiction with the evident gene flow detected at other loci from other chromosomes. This suggests that the Y chromosome might play a key role in reproductive isolation. This a new case species with mosaic patterns of differentiation across their genomes.
Comparisons of introgression levels between the Y chromosome, the X chromosome, the autosomes, and mitochondrial DNA are essential to the knowledge of speciation genetics. Particularly, the important role of the sex chromosomes in reproductive isolation predicts that genetic markers found on these chromosomes will often show restricted gene flow compared to other loci.
An alternative explanation can also be suggested. Relative levels of differentiation might simply echo the rate of ancestral lineage sorting (due to differences in effective population size) which is expected to be fastest for the Y and the mitochondrial DNA, followed by the X chromosome, and finally the non-sexual chromosomes. Crossing test can be useful to assess the validity of either hypothesis.
Multilocus surveys of population differentiation will be increasingly used in the speciation research nascent field. Soon we will be witnessing entire genomes scanned for introgression in hybridizing species. However this method will still be challenged by the fact that we still ignore what does an outlier locus look like? In fact, this is a common problem with other genomic researches….
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