Ancient and modern genomics of the Ohlone Indigenous population of California

Abstract

Significance California supports a high cultural and linguistic diversity of Indigenous peoples. In a partnership of researchers with the Muwekma Ohlone tribe, we studied genomes of eight present-day tribal members and 12 ancient individuals from two archaeological sites in the San Francisco Bay Area, spanning ∼2,000 y. We find that compared to genomes of Indigenous individuals from throughout the Americas, the 12 ancient individuals are most genetically similar to ancient individuals from Southern California, and that despite spanning a large time period, they share distinctive ancestry. This ancestry is also shared with present-day tribal members, providing evidence of genetic continuity between past and present Indigenous individuals in the region, in contrast to some popular reconstructions based on archaeological and linguistic information.

Retracted: Extracting the practices of paleogenomics: A study of ancient DNA labs and research in relation to Native Americans and Indigenous peoples

“…While some studies have unfolded with the consent and partnership of descendant communities (Cui et al, 2013;Lindo et al, 2017;Malhi & Bader, 2019;Matisoo-Smith, 2019;Severson et al, 2022), many others, arguably the far majority of studies, have not (Cortez et al, 2021;Tsosie et al, 2020). The rapid growth of sequenced ancient genomes-from several dozen to thousands in the last decade (Sedig, 2019)-has led to accusations of a "bone rush" as laboratories have sprinted to find sources of data ahead of their scientific competitors (Fox, 2019), and some with the explicit goal to "industrialize" the processing of remains (Lewis-Kraus, 2019).…”

ancIBD - Screening for identity by descent segments in human ancient DNA

“…Sikora et al, 2017, Ferrando-Bernal et al, 2020]. First efforts to identify IBD based on imputed data have been fruitful [Kivisild et al, 2021, Allentoft et al, 2022, Ariano et al, 2022, Severson et al, 2022a], but those earlier works require higher coverage not routinely available for aDNA. Importantly, they do not include a systematic evaluation of the IBD calling pipelines but performance when screening for IBD is expected to decay for short segments and low-coverage data.…”

Spatiotemporal impacts of the Anthropocene on small mammal communities, and the role of small biological preserves in maintaining biodiversity

“…While differences in small mammal communities between the Holocene and today are reflective of broadscale environmental change over time, they also reflect land stewardship by indigenous communities. Native Californians have lived in this region for thousands of years and continue to cultivate their traditional practices here today (Severson et al, 2022). The ancestors of the native peoples of this region, the Muwekma Ohlone, actively managed plants and animals across all three archeological sites during the Holocene (Bocek and Reese, 1992).…”