Phylogeography and landscape genetics of tigers (Panthera tigris) and elephants (Elephas maximus) in Thailand

University of Minnesota Ph.D. dissertation. November 2016. Major: Conservation Biology. Advisor: James Smith. 1 computer file (PDF); xiii, 171 pages.Habitat fragmentation and poaching have resulted in population declines in large mammals including tigers (Panthera tigris) and Asian elephants (Elephas maximus) throughout the Indochina biogeographic region in Southeast Asia. Tracking changes in demographic and genetic parameters of elusive, wide-ranging species remain a serious challenge. This dissertation applies noninvasive genetic sampling and phylogeographic and landscape genetic analyses to assess spatial genetic patterns and demography in the Indochinese tiger (P. t. corbetti) and elephants in Thailand’s Tenasserim Range. In Chapter 1, I describe changes in distribution and numbers of tiger and elephant populations in Thailand from 1987-2015. I found that tigers lost a greater percentage of their former habitat than elephants as a result of higher poaching intensity and their naturally low density. At both evolutionary and contemporary timescales, I combined mtDNA and microsatellite data to assess spatial genetic connectivity and demographic history of the Indochinese tiger (P. t. corbetti) in Chapter 2 and elephants in Chapter 3. Phylogeographic analyses based on mtDNA indicated that Amur tigers (P. t. altaica) are recently derived from Indochinese tigers, which is re-classified as a paraphyletic group by the placement of the newly discovered haplotype. Results support the hypothesis of northbound dispersal from Indochina to northeast Asia after the Last Glacial Maximum (LGM) 20 thousand years ago. Compared to the recent radiation in tigers, elephants have two deeply divergent mtDNA clades, which are highly admixed within the Tenasserim landscape. Results support the hypothesis that this landscape was the secondary contact zone during the postglacial period. High mtDNA and microsatellite diversity of tigers and elephants in Indochina, compared to other regions. is due to maintenance of their large and stable long-term effective population sizes. However, as a consequence of fragmentation and genetic drift in a recent timeframe, I estimated low gene flow and detected genetic differentiation into three clusters in tigers within Indochina and at least two clusters in elephants within the Tenasserim Range. My results highlight advantages of integrating genetic with ecological data to quantify impacts of modified landscapes on population dynamics and to devise appropriate management strategies for the species recovery