A Y-chromosomal survey of Ecuador's multi-ethnic population reveals new insights into the tri-partite population structure and supports an early Holocene age of the rare Native American founder lineage C3-MPB373

Patricia Villaescusa; Maria Seidel; Michael Nothnagel; Thomaz Pinotti; Fabricio González-Andrade; Oscar Alvarez-Gila; Marian M de Pancorbo; Lutz Roewer

doi:10.1016/j.fsigen.2020.102427

A Y-chromosomal survey of Ecuador's multi-ethnic population reveals new insights into the tri-partite population structure and supports an early Holocene age of the rare Native American founder lineage C3-MPB373

Forensic Sci Int Genet. 2021 Mar:51:102427. doi: 10.1016/j.fsigen.2020.102427. Epub 2020 Nov 16.

Authors

Patricia Villaescusa¹, Maria Seidel², Michael Nothnagel³, Thomaz Pinotti⁴, Fabricio González-Andrade⁵, Oscar Alvarez-Gila⁶, Marian M de Pancorbo⁷, Lutz Roewer²

Affiliations

¹ BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain. Electronic address: patricia.villaescusa89@gmail.com.
² Department of Forensic Genetics, Institute of Legal Medicine and Forensic Sciences, Charité-Universitätsmedizin Berlin, Berlin, Germany.
³ Department of Statistical Genetics and Bioinformatics, Cologne Center for Genomics, University of Cologne, Cologne, Germany; University Hospital Cologne, Cologne, Germany.
⁴ Laboratório de Biodiversidade e Evolução Molecular (LBEM), Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil; Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
⁵ Central University of Ecuador, Faculty of Medical Sciences, Quito, Ecuador.
⁶ Department of Medieval, Early Modern and American History, Faculty of Letters, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain.
⁷ BIOMICs Research Group, Lascaray Research Center, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain.

PMID: 33254102
DOI: 10.1016/j.fsigen.2020.102427

Abstract

Ecuador is a multiethnic and pluricultural country with a complex history defined by migration and admixture processes. The present study aims to increase our knowledge on the Ecuadorian Native Amerindian groups and the unique South American Y-chromosome haplogroup C3-MPB373 through the analysis of up to 23 Y-chromosome STRs (Y-STRs) and several Y-SNPs in a sample of 527 Ecuadorians from 7 distinct populations and geographic areas, including Kichwa and non-Kichwa Native Amerindians, Mestizos and Afro-Ecuadorians. Our results reveal the presence of C3-MPB373 both in the Amazonian lowland Kichwa with frequencies up to 28 % and, for the first time, in notable proportions in Kichwa populations from the Ecuadorian highlands. The substantially higher frequencies of C3-MPB373 in the Amazonian lowlands found in Kichwa and Waorani individuals suggest a founder effect in that area. Notably, estimates for the time to the most recent common ancestor (TMRCA) in the range of 7.2-9.0 kya point to an ancient origin of the haplogroup and suggest an early Holocene expansion of C3-MPB373 into South America. Finally, the pairwise genetic distances (R_ST) separate the Kichwa Salasaka from all the other Native Amerindian and Ecuadorian groups, indicating a so far hidden diversity among the Kichwa-speaking populations and suggesting a more southern origin of this population. In sum, our study provides a more in-depth knowledge of the male genetic structure of the multiethnic Ecuadorian population, as well as a valuable reference dataset for forensic use.

Keywords: C3-MPB373; Ecuador; Kichwas; Y-SNPs; Y-STRs.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Chromosomes, Human, Y*
DNA Fingerprinting
Ecuador
Ethnicity / genetics*
Genetics, Population*
Haplotypes
Humans
Indians, South American / genetics*
Male
Microsatellite Repeats
Polymorphism, Single Nucleotide