Biogeography and Phylogeography of Mammals of Southeast Asia: A Comparative Analysis Utilizing Macro and Microevolution




Hawkins, Melissa T. R.

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The tropical rainforests of Southeast Asia are some of the most threatened ecosystems on the planet, yet few systematic studies have been done to evaluate the mammalian communities with respect to biogeographic and phylogenetic relationships. By comparing both large and small scale evolutionary histories of mammals across this landscape we can better understand patterns of endemism and biodiversity. Here I combine cutting edge high-throughput sequencing technology using museum specimens, with two field expeditions to Kinabalu Park in Sabah, Malaysia to determine phylogeographic patterns in several families of understudied mammals distributed across Southeast Asia. From this we have deduced several biogeographic patterns regarding distribution and movement of species across the Sunda shelf. A micro-evolutionary study of the small mammal communities of Kinabalu Park was completed across two sister mountain peaks, Mount Kinabalu (4,101 m) and Mount Tambuyukon (2,569 m), in Sabah, Malaysia. These were the first systematic elevational transects completed on Mount Tambuyukon, and we document several species on this mountain for the first time. In order to generate large genomic datasets for degraded DNA samples (derived from museum specimens up to ~120 years old) we developed a set of RNA probes to successfully enrich mammalian mitochondrial genomes across almost 50% of extant mammalian diversity. We tested these probes on a diversity of mammalian orders and species to determine the efficiency of multiplexing and diluting probes to reduce the cost per sample of in-solution enrichment. Following our field expeditions to Mount Kinabalu we generated the first complete phylogeny for the squirrel genus Dremomys. Here we found paraphyly in the genus, with a Bornean endemic (Dremomys everetti), representing a morphologically divergent species of Sundasciurus, with significant convergence on the phenotype of the Dremomys squirrels. The Indonesian island of Sulawesi has been intriguing to biogeographers since the days of A.R. Wallace, with the iconic "Wallace's Line" separating two major groups of floral and faunal assemblages on either side of this barrier. The macroevolutionary patterns of the endemic Sulawesi squirrels were deduced for the first time here (from museum specimens we generated large genomic datasets of whole mitogenomes and ultraconserved elements), resulting in possibly the oldest example of in-situ diversification in this geologically complex island system. We also identified an ancient mitochondrial introgression event, dating to the Miocene. This research has identified several biologically interesting patterns, and processes that will be valuable to the conservation of this increasingly threatened landscape.


This work was embargoed by the author and will not be publicly available until August 2020.


Biogeography, Evolution, Genomics, Mammals, Museomics, Phylogeography