TY - JOUR
T1 - Ancient mitochondrial genome diversity in South America
T2 - Contributions from Quebrada del Toro, Northwestern Argentina
AU - Russo, María Gabriela
AU - Arencibia, Valeria
AU - Emery, Matthew
AU - Bettera Marcat, Gianina
AU - Seldes, Verónica
AU - Mercolli, Pablo
AU - Soria, Silvia
AU - Maldonado, Lucas
AU - Kamenetzky, Laura
AU - Avena, Sergio
AU - Dejean, Cristina
AU - Stone, Anne C.
N1 - Funding Information:
This work was supported by Regents' Professor funding (to ACS), Agencia Nacional de Promoción Científica y Tecnológica (Grant Number: PICT 2017‐4044), Fundación Científica Felipe Fiorellino (Subsidio intramuros 2019), and Fundación de Historia Natural Félix de Azara (Subsidio intramuros 2019).
Funding Information:
This study was possible thanks to a Postdoctoral fellowship granted by CONICET and Universidad Maimónides to MGR. MGR's research stay at ASU was also funded by CONICET and Universidad Maimónides. The authors acknowledge resources and support from the Biodesign Institute core facilities at ASU. We thank Angelina García and Pía Tavella for providing details of the samples from Central Argentina included in this study and for sharing their insights on the results. We also thank Alexandra Gottlieb, Martín Ramírez, and Marcela Rodriguero for kindly sharing their knowledge on phylogenetic reconstruction. We also thank the Editors and three anonymous reviewers for their helpful suggestions that improved this study. This work was supported by Regents' Professor funding (to ACS), Agencia Nacional de Promoción Científica y Tecnológica (Grant Number: PICT 2017-4044), Fundación Científica Felipe Fiorellino (Subsidio intramuros 2019), and Fundación de Historia Natural Félix de Azara (Subsidio intramuros 2019).
Funding Information:
This study was possible thanks to a Postdoctoral fellowship granted by CONICET and Universidad Maimónides to MGR. MGR's research stay at ASU was also funded by CONICET and Universidad Maimónides. The authors acknowledge resources and support from the Biodesign Institute core facilities at ASU.
Publisher Copyright:
© 2023 Wiley Periodicals LLC.
PY - 2023/8
Y1 - 2023/8
N2 - Objectives: The objective of this study was to enhance our understanding of the population history in South America, specifically Northwestern Argentina, by analyzing complete ancient mitogenomes of individuals from the Ojo de Agua archeological site (970 BP) in Quebrada del Toro (Salta, Argentina). Materials and Methods: We analyzed teeth from four individuals from the site Ojo de Agua (970 ± 60 BP), located in Quebrada del Toro (Andean region of Northwestern Argentina). DNA extracts were converted to double-stranded DNA libraries and indexed using unique dual-indexing primer combinations. DNA libraries were then enriched for the complete mitochondrial genome, pooled at equimolar concentrations, and sequenced on an Illumina® MiSeq™ platform. Reads from high quality libraries were trimmed, merged, and then mapped to the revised Cambridge Reference Sequence. The aDNA damage patterns were assessed and contamination estimated. Finally, variants were called, filtered, and the consensus mitogenome was constructed and used for haplogroup assignment. We also compiled available mitogenome sequences from ancient and present-day populations from the Southcentral Andes and other surrounding regions in Argentina. Maximum Likelihood and Bayesian phylogenetic reconstructions were obtained using the generated dataset. Results: We successfully obtained the complete mitogenome sequence from one individual with an average depth coverage of 102X. We discovered a novel haplotype that was assigned to haplogroup D1. Phylogenetic reconstructions suggests that this haplotype falls within the sister branches of the D1j lineage, forming a well-supported clade. The estimate TMRCA of this clade that includes D1j and its sister branches ranged between 12,535 and 18,669 ya. Discussion: The sequence analyzed in this study represents the first ancient mitogenome from within the valley region in Northwestern Argentina. We found that a representative of a lineage highly associated with D1j was already present approximately 1000 BP in the region. Our results agree with the proposed origin of D1j in other regions north of Patagonia and independent of the Pacific coast fast migratory route, contrary to what was originally hypothesized. This study highlights the lack of information regarding pre-Hispanic genetic diversity and contributes to the knowledge about the peopling process in South America.
AB - Objectives: The objective of this study was to enhance our understanding of the population history in South America, specifically Northwestern Argentina, by analyzing complete ancient mitogenomes of individuals from the Ojo de Agua archeological site (970 BP) in Quebrada del Toro (Salta, Argentina). Materials and Methods: We analyzed teeth from four individuals from the site Ojo de Agua (970 ± 60 BP), located in Quebrada del Toro (Andean region of Northwestern Argentina). DNA extracts were converted to double-stranded DNA libraries and indexed using unique dual-indexing primer combinations. DNA libraries were then enriched for the complete mitochondrial genome, pooled at equimolar concentrations, and sequenced on an Illumina® MiSeq™ platform. Reads from high quality libraries were trimmed, merged, and then mapped to the revised Cambridge Reference Sequence. The aDNA damage patterns were assessed and contamination estimated. Finally, variants were called, filtered, and the consensus mitogenome was constructed and used for haplogroup assignment. We also compiled available mitogenome sequences from ancient and present-day populations from the Southcentral Andes and other surrounding regions in Argentina. Maximum Likelihood and Bayesian phylogenetic reconstructions were obtained using the generated dataset. Results: We successfully obtained the complete mitogenome sequence from one individual with an average depth coverage of 102X. We discovered a novel haplotype that was assigned to haplogroup D1. Phylogenetic reconstructions suggests that this haplotype falls within the sister branches of the D1j lineage, forming a well-supported clade. The estimate TMRCA of this clade that includes D1j and its sister branches ranged between 12,535 and 18,669 ya. Discussion: The sequence analyzed in this study represents the first ancient mitogenome from within the valley region in Northwestern Argentina. We found that a representative of a lineage highly associated with D1j was already present approximately 1000 BP in the region. Our results agree with the proposed origin of D1j in other regions north of Patagonia and independent of the Pacific coast fast migratory route, contrary to what was originally hypothesized. This study highlights the lack of information regarding pre-Hispanic genetic diversity and contributes to the knowledge about the peopling process in South America.
KW - ancient DNA
KW - mitogenome
KW - Northwestern Argentina
KW - Southcentral Andes
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U2 - 10.1002/ajpa.24795
DO - 10.1002/ajpa.24795
M3 - Article
C2 - 37323114
AN - SCOPUS:85162037723
SN - 0002-9483
VL - 181
SP - 597
EP - 610
JO - American Journal of Biological Anthropology
JF - American Journal of Biological Anthropology
IS - 4
ER -