Extremely high major histocompatibility complex class IIb gene intron 2 variation and population structure in Chinese alligator

Identifying the processes that maintain genetic diversity within and among populations is a central goal of modern evolutionary genetics. So far, the studies on genetic diversity have mainly focussed on neutral DNA markers, such as mtDNA and microsatellites (Xu et al. 2010). While these markers are very informative in molecular clocks, to examine dispersal patterns of individuals (gene flow) and to classify them by relatedness and paternity analyses. The variation at neutral loci cannot provide direct information on selective processes involving the interaction of individuals with their environment or on the capacity for future adaptive changes (Sommer 2005). With the developments in molecular biology, researchers can directly examine selection at genes that underlie functional traits. Therefore, adaptive nonneutral markers have become especially valuable (Koskinen et al. 2002). One important example comes from the genes of the major histocompatibility complex (MHC). These genes are found in all jawed vertebrates and play a critical role in an organism’s immune response (Karaiskou et al. 2010). High levels of variation in MHC alleles are believed to confer the ability to recognize a wide range of antigens and thus increase resistance to a greater number of environmental pathogens. Chinese alligator (Alligator sinensis) is one of the 23 critically endangered crocodile species in the world. The wild population has been close to extinct during the past decades due to habitat loss and illegal hunting. The investigation indicated that the number of wild Chinese alligators has decreased from 500 individuals in the 1980s to currently less than 120 or 150 individuals (Thorbjarnarson et al. 2002).