Inferring Population History and Demography Using Microsatellites, Mitochondrial Dna, and Major Histocompatibility Complex (Mhc) Genes

Abstract

Microsatellites and mitochondrial DNA (mtDNA) have traditionally been used in population genetics because of their variability and presumed neutrality, whereas genes of the major histocompatibility complex (MHC) are increasingly of interest because strong selective pressures shape their standing variation. Despite the potential for MHC genes, microsatellites, and mtDNA sequences to complement one another in deciphering population history and demography, the three are rarely used in tandem. Here we report on MHC, microsatellite, and mtDNA variability in a single large population of the eastern tiger salamander (Ambystoma tigrinum tigrinum). We use the mtDNA mismatch distribution and, on microsatellite data, the imbalance index and bottleneck tests to infer aspects of population history and demography. Haplotype and allelic variation was high at all loci surveyed, and heterozygosity was high at the nuclear loci. We find concordance among neutral molecular markers that suggests our study population originated from post-Pleistocene expansions of multiple, fragmented sources that shared few migrants. Differences in N e estimates derived from haploid and diploid genetic markers are potentially attributable to secondary contact among source populations that experienced rapid mtDNA divergence and comparatively low levels of nuclear DNA divergence. We find strong evidence of natural selection acting on MHC genes and estimate long-term effective population sizes (N e ) that are very large, making small selection intensities significant evolutionary forces in this population.

Maned wolves retain moderate levels of genetic diversity and gene flow despite drastic habitat fragmentation

“…Analysis of genetic variation can provide essential information about population history and demography, which is relevant for endangered species management (Bos et al 2008). The first genetic studies on maned wolves were conducted mostly on Brazilian populations, reporting levels of heterozygosity around 0.7 and no genetic signatures of geographic structure (Rodrigues et al 2006, Salim et al 2007, Fontoura- Rodrigues et al 2008, Prates 2008, Do Passo Ramalho 2011, Lion et al 2011, Do Passo Ramalho et al 2014.…”

Detecting population structure in a high gene-flow species, Atlantic herring (Clupea harengus): direct, simultaneous evaluation of neutral vs putatively selected loci

“…MHC genes encode proteins in the vertebrate immune response, and molecular variation among alleles has been linked directly to fitness and survival (Bos et al, 2008). For example, disease challenge trials on Atlantic salmon confirm that polymorphism at the MHC genes are associated with increased disease resistance (Grimholt et al, 2003).…”

Nucleotide diversity based on csd gene of the black giant honey bee, Apis laboriosa (Hymenoptera: Apidae)

“…To date, trans-specific polymorphism of alleles has been reported in several other organisms, including the major histocompatibility complex (MHC) of jawed vertebrates (Klein, 1987;Hughes & Nei, 1988;Takahata & Nei, 1990; Taka- hata et al, 1992), the self-incompatibility S locus of plants (Ioerger et al, 1990;Richman et al, 1996;Charlesworth & Awadalla, 1998), and the het-c heterokaryon incompatibility locus of fungi (Wu et al, 1998;May et al, 1999). The MHC and S alleles have been used to analyze population genetic structure and infer relative coalescence times and population history in many organisms Yuhki & O'Brien, 1990;Richman et al, 1996;Miller & Withler, 1997;Richman & Kohn, 1999;Bos et al, 2008). If trans-specific polymorphism of the csd gene really exists between the A. dorsata s.s. and A. laboriosa, the csd gene can be used in the future to determine the historical population size and study the speciation process under eusocial organization.…”