The Drivers of Mitochondrial DNA Divergences

Mitochondrial phylogeography uses the relationship between matrilineal genealogy and geography to explain speciation, phylogeny and population structure. Several hypotheses on what maintains the parapatric matrilines have been proposed: philopatry, incomplete lineage sorting, vicariance and natural selection on female-linked traits. The small lizard Urosaurus nigricaudus of the peninsula of Baja California, Mexico and southern California, USA has six parapatric matrilines that differ by substantial mtDNA divergence. In this study, I investigate what drives and maintains the deep mtDNA discontinuities in this species. I precisely locate the mtDNA lineage breaks and investigate the presence of physical barriers in those areas. I sequence the entire mtDNA genome and then test the following hypotheses: unrestricted nDNA gene flow occurs across the species; mtDNA divergences correspond to the geological events; and that functional diversifying selection is involved in the maintenance of mtDNA discordances. I use thousands of nDNA SNP loci to test the first and last hypotheses. The time-calibrated genealogy cannot reject the hypothesis that the mtDNA discordances originated due to a series of vicariant events that happened on the peninsula starting in the late Miocene. For millions of years, females have dispersed beyond their place of birth, and yet, they do not cross the mtDNA contact zones. Thus, I reject the hypothesis of female philopatry as an explanation for the mtDNA discontinuities. In the mtDNA contact zones, females from two lineages co-exist in a small area with no barriers forbidding dispersal beyond the mtDNA breaks. The analysis with nDNA SNPs fails to reject the hypothesis of unrestricted nDNA gene flow throughout the peninsula (K=1). Thus, analyses also reject the hypotheses of vicariance and incomplete lineage sorting as explaining the continuing mtDNA discontinuities. Selective pressure analyses point to purifying selection as the evolutionary force acting in the mitogenome of this lizard, thus rejecting the hypothesis that habitat adaptation maintains the mtDNA discontinuities. My results reject most of the proposed hypothesis for the maintenance of mtDNA discontinuities and create exciting opportunities for further investigation on the role of other female-linked traits in the maintenance of mtDNA discontinuities, such as mito-nuclear functional compensation and female behavior.Ph.D.2019-11-16 00:00:0