Paleomitogenomics and the Holocene population demography of the Northern Plains bison

Historical population dynamics of the Northern Plains bison was studied by next-generation sequencing of 40 mitochondrial genomes (mtDNA) and radiocarbon dating of the Bison antiquus and B. bison remains from 18 archaeological sites. The determined ages varied from 12,226 to 167 calibrated years before present and helped to calibrate phylogenetic trees and reveal temporal changes in population size. The most recent common ancestor of the mtDNA haplotypes lived in the end of the Last Glacial Maximum. Population dynamics was characterized by three primary periods: terminal Pleistocene population growth starting 14,000 years ago, mid Holocene demographic stability between 6,700 and 2,700 years ago, and late Holocene population decline that began 2,700 years ago. This decline correlated with the introduction of bison mass harvesting, based on the application of fire and new hunting technologies in the late Plains Archaic period. Diversification of mtDNA haplotypes occurred in early Holocene when bison colonized new territories opened after the ice sheets retreated and Lake Agassiz was drained. Holocene mtDNA haplotypes were not found in modern bison. The B. antiquus mtDNA sequences were distributed among the B. bison lineages in phylogenetic trees confirming their close relationship.