I want to know if I can use microsatellite markers to distinguish if individuals in several populations undergo hybridization or introgression? How will the allele frequency change and what would I expect in order to be sure that some individuals are hybrids and some are introgressors?
You may want to check whether the alleles of all loci in the populations are under Hardy Weinberg (HW) equilibrium or not. If they are undergo hybridization, it should be in HW equilibrium, while if there are some introgressions then it will not...
Introgression should not affect whether or not alleles are in Hardy-Weinberg expected proportions, because the population may still be random-mating. In order to detect hybridization or introgression you need private (diagnostic) alleles at moderate frequency in each parental form at sites outside the area of contact, or you need linked loci that show private combinations of alleles. Introgression is inferred when diagnostic alleles at one or several loci have a different spatial distribution to those at other loci. Hybridization is inferred when you see heterozygotes for diagnostic alleles in each form (F1s are heterozygous at all loci with diagnostic alleles). Because of the diversity of alleles at microsatellites you will rarely have diagnostic alleles at sufficient frequency to give you statistical power to detect hybrids and introgression.
Thank you for all your excellent answers! While I still confusing "Introgression is inferred when diagnostic allele at one or several loci have a different spatial distribution to those at other loci" What does "spatial distribution" mean? Does this mean the diagnostic allele frequency will not follow 0.5:0.5 as in F1? Then what about F2, how will the allele frequency change?
Jun Wang, I mean that introgression is when an allele typical of one form is found in the genomic background of another form (a diagnostic allele for form A found in a genome that is mainly diagnostic alleles for form B). This can be picked up by a locus that differs from the general background pattern in the genome. Often this is a different geographic distribution of diagnostic alleles - especially where some alleles have introgressed through a hybrid zone. In other cases introgression might be inferred from difference in gene-trees (perhaps a much deeper coalescence and a different inferred ancestry) such as is shown by purported Neanderthal and Denisovan alleles in modern human genomes.
Thanks, it's a good question - it's a tricky problem to distinguish limited post-speciation/population split interbreeding from recent or ongoing hybridization.
Dear Michael,
How does this work for mitochondrial DNA? All loci are linked in mtDNA; I am ignoring rare recombination events. If the same rare haplotypes are shared among spatially distributed populations, can we accept it as a sign of introgression?
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