I took an evolutionary biology course last semester wherein we discussed how to use mtdna vs ndna as a method to determine introgression.
Quote:
Members of Mike Arnold’s lab have tested evolutionary hypotheses in a wide array of organisms – including fungi, plants and animals. In spite of the taxonomic diversity reflected in this work, there is a unifying theme. This theme is well described by the title of a 1954 Evolution paper authored by the plant evolutionary biologists, Edgar Anderson and Ledyard Stebbins – “Hybridization as an Evolutionary Stimulus”. Thus, our group has examined a range of phenomena associated with the process of gene exchange between organisms in nature. The data collected have derived from analyses of population genetics, phylogenetics, reproductive biology, pollinator behavior, eco-physiology, molecular evolution and, most recently, linkage/QTL mapping of fitness traits.
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http://www.genetics.uga.edu/people_bio_arnold_m.html
I got the impression that people should already really understand this. Also Arnold pushed hard the idea that you need repeated studies over time to really understand if introgression is occurring.