Columbian mammoth mitogenomes from Mexico uncover the species' complex evolutionary history

The Columbian mammoth (Mammuthus columbi) was the only mainland mammoth species endemic to the Americas. Paleogenomic studies suggest that M. columbi originated from ancient hybridization between woolly mammoths (Mammuthus primigenius) and steppe mammoths (Mammuthus trogontherii). While its habitat once extended from North to Central America, genetic data are currently only available across Canada and the USA, leaving gaps in our understanding of the demographic history of mammoths in the continent. To expand the spatial sampling of M. columbi genetic data to tropical latitudes and study the species from a wider range distribution, we generated 61 capture-enriched M. columbi mitogenomes from the Basin of Mexico. Bayesian phylogenetic analyses suggest a divergent evolutionary relationship of the Basin of Mexico Columbian mammoths to other North American mammoths, challenging previous hypotheses based only on the sampling of only USA and Canada specimens. Our data provides a comprehensive reconstruction of their evolutionary history and its demographic trajectory in the Americas, showing the feasibility for studying megafauna outside northern latitudes. The data here available comprises screening data for 77 sequencing libraries described in Arrieta-Donato et al., 2025, as well as mitochondrial sequencing data for 67 individuals for which capture enrichment mitochondrial data was generated.