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. 2022 Nov 30;13(12):2251.
doi: 10.3390/genes13122251.

Unraveling Signatures of Local Adaptation among Indigenous Groups from Mexico

Humberto García-Ortiz  1 , Francisco Barajas-Olmos  1 , Cecilia Contreras-Cubas  1 , Austin W Reynolds  2 , Marlen Flores-Huacuja  1 , Meradeth Snow  3 , Jazmín Ramos-Madrigal  4 , Elvia Mendoza-Caamal  1 , Paulina Baca  1 , Tomás A López-Escobar  1 , Deborah A Bolnick  5 , Silvia Esperanza Flores-Martínez  6 , Rocio Ortiz-Lopez  7   8 , Aleksandar David Kostic  9 , José Rafael Villafan-Bernal  1 , Carlos Galaviz-Hernández  10 , Federico Centeno-Cruz  1 , Alejandra Guadalupe García-Zapién  11 , Tulia Monge-Cázares  1 , Blanca Patricia Lazalde-Ramos  12 , Francisco Loeza-Becerra  13 , María Del Carmen Abrahantes-Pérez  1 , Héctor Rangel-Villalobos  14 , Martha Sosa-Macías  10 , Augusto Rojas-Martínez  7   8 , Angélica Martínez-Hernández  1 , Lorena Orozco  1
Affiliations

Unraveling Signatures of Local Adaptation among Indigenous Groups from Mexico

Humberto García-Ortiz et al. Genes (Basel). .

Abstract

Few studies have addressed how selective pressures have shaped the genetic structure of the current Native American populations, and they have mostly limited their inferences to admixed Latin American populations. Here, we searched for local adaptation signals, based on integrated haplotype scores and population branch statistics, in 325 Mexican Indigenous individuals with at least 99% Native American ancestry from five previously defined geographical regions. Although each region exhibited its own local adaptation profile, only PPARG and AJAP1, both negative regulators of the Wnt/β catenin signaling pathway, showed significant adaptation signals in all the tested regions. Several signals were found, mainly in the genes related to the metabolic processes and immune response. A pathway enrichment analysis revealed the overrepresentation of selected genes related to several biological phenotypes/conditions, such as the immune response and metabolic pathways, in agreement with previous studies, suggesting that immunological and metabolic pressures are major drivers of human adaptation. Genes related to the gut microbiome measurements were overrepresented in all the regions, highlighting the importance of studying how humans have coevolved with the microbial communities that colonize them. Our results provide a further explanation of the human evolutionary history in response to environmental pressures in this region.

Keywords: AJAP1; Native American populations; PPARG; gut microbiome; local adaptation.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Geographical distribution of the 53 Mexican Indigenous communities included. Dot shapes denote the ethnic group and colors their assigned geographic region. Purple: North, green: Northwest, blue: Center, red: South, and yellow: Southeast.
Figure 2
Figure 2
Significant adaptation signals in all tested regions. (A) SNVs under the top 1% distribution of iHS and PBS values in each region, only PBS values are plotted. (B) Genes symbols of selection signals shared by two or more regions. (C) Venn diagram showing both the number of or shared genes in all regions.
Figure 3
Figure 3
PPI networks constructed with significant adaptation signals observed in each region; PPARG and AJAP are highlighted with red and yellow arrows, respectively. (A) North. (B) Northwest. (C) Center. (D) South. (E) Southeast.
See this image and copyright information in PMC

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