TY - BOOK
T1 - Deciphering Equine Evolution and Spatial Ancestry with Ancient Data
AU - Jónsson, Hákon
PY - 2015
Y1 - 2015
N2 - High-throughput sequencing has opened ancient DNA research to genomics, revolutionizing the amount of genetic information retrievable from archaeological and paleontological remains. Paleogenomics is still in infancy and requires substantial improvements in computational methods tailored to the specific nature of such data. In this thesis, we developed such methods. We first present an explicit statistical model of post-mortem biochemical DNA damage, which allows for quantifying and accounting for DNA damage related mis-incorporations in downstream analyses. We next embed this approach in the analysis of environmental bacterial sequences, which generally dominate ancient DNA extracts, and in the first pipeline completely devoted to the computational analysis of raw ancient DNA sequences. We then develop a spatially explicit method for determining which extant populations show the greatest genetic anity to ancient individuals, which often represents the key question in human paleogenomic projects. We applied the computational infrastructure developed to complete the genomic characterization of extant members of the genus Equus, which is composed of horses, asses and zebras. We sequenced the extinct quagga zebra to 8x coverage and recover the demographic history for the genus over the last 2 million years. We found di erent demographic dynamics across species, except for a subset which showed synchronous responses to major climate changes. We discovered substantial evidence of gene-flow between lineages despite considerable heterogeneity in chromosomal organization. Finally, we explored the genetic footprint of horse domestication and reconstructed the population context in which domestication took place, by sequencing complete genomes of ancient horses significantly predating domestication. We found support for the “cost-of-domestication” hypothesis in horses, as pre-domestic genomes showed fewer deleterious alleles than domestic horse genomes, and we identify signatures of selective sweeps across domestic breeds, likely representing key genetic drivers of the horse domestication process. These were mostly involved in locomotion, cardiac physiology, limb development and behavior.
AB - High-throughput sequencing has opened ancient DNA research to genomics, revolutionizing the amount of genetic information retrievable from archaeological and paleontological remains. Paleogenomics is still in infancy and requires substantial improvements in computational methods tailored to the specific nature of such data. In this thesis, we developed such methods. We first present an explicit statistical model of post-mortem biochemical DNA damage, which allows for quantifying and accounting for DNA damage related mis-incorporations in downstream analyses. We next embed this approach in the analysis of environmental bacterial sequences, which generally dominate ancient DNA extracts, and in the first pipeline completely devoted to the computational analysis of raw ancient DNA sequences. We then develop a spatially explicit method for determining which extant populations show the greatest genetic anity to ancient individuals, which often represents the key question in human paleogenomic projects. We applied the computational infrastructure developed to complete the genomic characterization of extant members of the genus Equus, which is composed of horses, asses and zebras. We sequenced the extinct quagga zebra to 8x coverage and recover the demographic history for the genus over the last 2 million years. We found di erent demographic dynamics across species, except for a subset which showed synchronous responses to major climate changes. We discovered substantial evidence of gene-flow between lineages despite considerable heterogeneity in chromosomal organization. Finally, we explored the genetic footprint of horse domestication and reconstructed the population context in which domestication took place, by sequencing complete genomes of ancient horses significantly predating domestication. We found support for the “cost-of-domestication” hypothesis in horses, as pre-domestic genomes showed fewer deleterious alleles than domestic horse genomes, and we identify signatures of selective sweeps across domestic breeds, likely representing key genetic drivers of the horse domestication process. These were mostly involved in locomotion, cardiac physiology, limb development and behavior.
UR - https://soeg.kb.dk/permalink/45KBDK_KGL/fbp0ps/alma99122549271005763
M3 - Ph.D. thesis
BT - Deciphering Equine Evolution and Spatial Ancestry with Ancient Data
PB - Natural History Museum of Denmark, Faculty of Science, University of Copenhagen
ER -