Genomics in Pleistocene Park: On the Internal Causes Driving Extinction
Author: Jacob Kostecke (biological sciences)
Faculty mentor: Weilong Hao
Many large mammals from woolly mammoths to saber-tooth tigers went extinct around 10,000 years ago during the last great Ice Age. Though external factors such as ancient human hunting, climate change, and even asteroid impacts have been speculated, the determining forces driving massive extinction remains elusive. Recent analyses on abundant genomic data suggest that elevated genetic mutations can cause extinction. In this study, we took advantage of the recently available and well-preserved mitochondrial DNAs from extinct mammals to identify genetic mechanisms driving the extinction of megafauna. We compared substitution patterns between 25 extinct animals and their living relatives. This was accomplished through the use of the bioinformatic software Geneious Prime and phylogenetic trees. Overall, extinct mammals show more C -> T and A -> G substitutions on the light strand, but fewer G -> A and T -> C substitutions than their living relatives in the Cytochrome C Oxidase, Cytochrome B, ATP Synthase complexes, and NADH Dehydrogenase. This suggests subtle differences in DNA replication and/or repair between the extinct lineages and living relatives. The overall dN/dS ratio was significantly higher in the extinct animals compared to their living relatives, indicating prolonged small population sizes. Our study sheds light on the understanding of mechanistic factors in massive extinction and will help generate knowledge to prevent future extinctions.
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Jacob Kostecke: Genomics in Pleistocene Park: On the Internal Causes Driving Extinction