Early dispersal of domestic horses into the Great Plains and northern Rockies

Abstract

The horse is central to many Indigenous cultures across the American Southwest and the Great Plains. However, when and how horses were first integrated into Indigenous lifeways remain contentious, with extant models derived largely from colonial records. We conducted an interdisciplinary study of an assemblage of historic archaeological horse remains, integrating genomic, isotopic, radiocarbon, and paleopathological evidence. Archaeological and modern North American horses show strong Iberian genetic affinities, with later influx from British sources, but no Viking proximity. Horses rapidly spread from the south into the northern Rockies and central plains by the first half of the 17th century CE, likely through Indigenous exchange networks. They were deeply integrated into Indigenous societies before the arrival of 18th-century European observers, as reflected in herd management, ceremonial practices, and culture.

Performance of qpAdm-based screens for genetic admixture on admixture-graph-shaped histories and stepping-stone landscapes

“…First, we outline two published rotating qpAdm protocols (Narasimhan et al 2019, Lazaridis et al 2022) that are typical for this class of protocols (see further examples in Skoglund et al 2017, Harney et al 2019, Olalde et al 2019, Calhoff et al 2021, Fernandes et al 2021, Librado et al 2021, Allentoft et al 2022, Bergström et al 2022, Oliveira et al 2022, Taylor et al 2023). Lazaridis et al .…”

“…Models with targets pre-dating proxy sources are encountered in high-throughput qpAdm screens, but do not constitute a majority of models (Narasimhan et al 2019, Librado et al 2021, Allentoft et al 2022, Bergström et al 2022, Lazaridis et al 2022, Taylor et al 2023). We also explore FDR of the proximal non-rotating (Harney et al 2018, van de Loosdrecht et al 2018, Narasimhan et al 2019, Prendergast et al 2019, Wang et al 2020, Calhoff et al 2021, Wang et al 2021, Zhang et al 2021, Changmai et al 2022a, Changmai et al 2022b, Maróti et al 2022, Brielle et al 2023, Lee et al 2023), distal rotating (Narasimhan et al 2019, Librado et al 2021, Allentoft et al 2022, Bergström et al 2022, Lazaridis et al 2022, Taylor et al 2023), and distal non-rotating protocols (Haak et al 2015, Mathieson et al 2015, Lazaridis et al 2016, Antonio et al 2019, Mathieson et al 2018, Marcus et al 2020, Yang et al 2020, Papac et al 2021, Yaka et al 2021, Patterson et al 2022) ( Tables 1 and 2 ). In the distal protocols, only qpAdm models where target group’s sampling date is strictly contemporaneous with or post-dates sampling of both proxy sources were considered.…”

“…Eight years later we find qpAdm -based protocols routinely employed in large-scale screens of ancient human or animal populations for admixture (often between closely related sources) and used as formal tests for admixture (see Lazaridis et al 2016, Skoglund et al 2017, Harney et al 2018, Mathieson et al 2018, Antonio et al 2019, Narasimhan et al 2019, Fernandes et al 2020, Marcus et al 2020, Ning et al 2020, Wang et al 2020, Yang et al 2020, Calhoff et al 2021, Papac et al 2021, Librado et al 2021, Sirak et al 2021, Wang et al 2021, Yaka et al 2021, Zhang et al 2021, Allentoft et al 2022, Bergström et al 2022, Changmai et al 2022a, Changmai et al 2022b, Gnecchi-Ruscone et al 2022, Lazaridis et al 2022, Maróti et al 2022, Oliveira et al 2022, Patterson et al 2022, Brielle et al 2023, Lee et al 2023, Taylor et al 2023 for examples). qpAdm fits admixture models to a matrix of f 4 -statistics of the form f 4 (“left” group i , “left” group j ; “right” group i , “right” group j ), which in the absence of missing data at the group level can be reduced to a smaller matrix f 4 (target group, “left” group j ; “right” group 1 , “right” group j ), considering algebraic relationships between different f 4 -statistics (Peter 2016).…”

“…This new type of qpAdm protocols, termed “rotating” protocol, has been adopted in archaeogenetics widely (see, e.g., Skoglund et al 2017, Harney et al 2019, Narasimhan et al 2019, Olalde et al 2019, Calhoff et al 2021, Fernandes et al 2021, Librado et al 2021, Allentoft et al 2022, Bergström et al 2022, Lazaridis et al 2022, Oliveira et al 2022, Taylor et al 2023). The most extreme version of the “rotating” protocol simply divides a set of reference populations into all possible combinations of “right” and “proxy source” subsets of certain sizes and rotates these combinations through successive qpAdm analyses.…”

“…When evaluating the totality of multiple qpAdm tests, the simplest feasible models (e.g., one-way, i.e., unadmixed) are favoured, and increasingly complex models are explored upon the rejection of simpler models. Model rejection for the simplest models is made according to a chosen p -value threshold such that qpAdm models are considered feasible or “fitting” the data when the p -value is above such a threshold (Skoglund et al 2017, Harney et al 2018, Narasimhan et al 2019, Olalde et al 2019, Yang et al 2020, Calhoff et al 2021, Fernandes et al 2021, Librado et al 2021, Zhang et al 2021, Allentoft et al 2022, Bergström et al 2022, Lazaridis et al 2022, Oliveira et al 2022, Taylor et al 2023). As an additional criterion of a fitting model, all inferred admixture proportions (Harney et al 2018, Olalde et al 2019, Yang et al 2020, Zhang et al 2021, Allentoft et al 2022, Lazaridis et al 2022, Oliveira et al 2022), or proportions ± 2 standard errors (Narasimhan et al 2019), may be required to lie between 0 and 1.…”