The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis

Abstract

Near the end of the Pleistocene epoch, populations of the woolly mammoth (Mammuthus primigenius) were distributed across parts of three continents, from western Europe and northern Asia through Beringia to the Atlantic seaboard of North America. Nonetheless, questions about the connectivity and temporal continuity of mammoth populations and species remain unanswered. We use a combination of targeted enrichment and high-throughput sequencing to assemble and interpret a data set of 143 mammoth mitochondrial genomes, sampled from fossils recovered from across their Holarctic range. Our dataset includes 54 previously unpublished mitochondrial genomes and significantly increases the coverage of the Eurasian range of the species. The resulting global phylogeny confirms that the Late Pleistocene mammoth population comprised three distinct mitochondrial lineages that began to diverge ~1.0–2.0 million years ago (Ma). We also find that mammoth mitochondrial lineages were strongly geographically partitioned throughout the Pleistocene. In combination, our genetic results and the pattern of morphological variation in time and space suggest that male-mediated gene flow, rather than large-scale dispersals, was important in the Pleistocene evolutionary history of mammoths.

Signals of positive selection in mitochondrial protein‐coding genes of woolly mammoth: Adaptation to extreme environments?

“…Raw reads were filtered using AdapterRemoval (Lindgreen, 2012) with the minimum base quality set to 15 and the minimum read lengths set to 30. Seventy additional mitogenome sequences (Chang et al, 2017;Enk et al, 2016;Fellows Yates et al, 2017;Gilbert et al, 2008Gilbert et al, , 2007Krause et al, 2006;Rogaev et al, 2006) were downloaded from GenBank and included in the analysis (Table S1). The C-to-T and G-to-A changes that occurred at the first 10 and last 10 bases of each read were also removed to further avoid potentially incorrect bases.…”

“…Clade 2/A occurred in Asia, but was geographically restricted to northern Siberia and western Beringia, where it coexisted in sympatry with Clade 1(haplogroups D and E) until its extinction (Barnes et al, 2007;Chang et al, 2017;Debruyne et al, 2008). Clade 2/A occurred in Asia, but was geographically restricted to northern Siberia and western Beringia, where it coexisted in sympatry with Clade 1(haplogroups D and E) until its extinction (Barnes et al, 2007;Chang et al, 2017;Debruyne et al, 2008).…”

Climate‐driven ecological stability as a globally shared cause of Late Quaternary megafaunal extinctions: the Plaids and Stripes Hypothesis

“…A reduced degree of latitudinal zonation during the ice age compared to the Holocene suggests that disequilibrial communities were widespread in Europe (Hofreiter et al, ). Similarly, boom and bust cycles of megafauna in Arctic Alaska imply disequilibria on the mammoth steppe (Mann et al, ), as do the frequent range shifts and population bottlenecks that ancient DNA (aDNA) documents for a number of mammal taxa (Shapiro et al, ; Enk et al, ; Chang et al, ; Froese et al, ).…”

Peer Review #2 of "Accessible molecular phylogenomics at no cost: obtaining 14 new mitogenomes for the ant subfamily Pseudomyrmecinae from public data (v0.1)"

“…Mitochondrial genomes are poorly sampled for many taxa and therefore our current knowledge about evolutionary biology of many clades could be improved with the use of public data. Being primarily maternally inherited and non-recombinant, such sequences are often used to study evolutionary biology (Finstermeier et al, 2013;Krzemińska et al, 2017), population genetics (Pečnerová et al, 2017;Kılınç et al, 2018), phylogeography (Chang et al, 2017;Fields et al, 2018), systematics (Lin et al, 2017;Crainey et al, 2018) and conservation (Moritz, 1994;Rubinoff, 2006;Rosel et al, 2017) of various clades (Avise, 1994), specially from subsampled taxa (Gotzek, Clarke & Shoemaker, 2010;Duan, Peng & Qian, 2016) and non-model organisms (Prosdocimi et al, 2012;Tilak et al, 2014;Plese et al, 2018).…”