Dataset Information

Disentangling Signatures of Selection Before and After European Colonization in Latin Americans.

ABSTRACT: Throughout human evolutionary history, large-scale migrations have led to intermixing (i.e., admixture) between previously separated human groups. Although classical and recent work have shown that studying admixture can yield novel historical insights, the extent to which this process contributed to adaptation remains underexplored. Here, we introduce a novel statistical model, specific to admixed populations, that identifies loci under selection while determining whether the selection likely occurred post-admixture or prior to admixture in one of the ancestral source populations. Through extensive simulations, we show that this method is able to detect selection, even in recently formed admixed populations, and to accurately differentiate between selection occurring in the ancestral or admixed population. We apply this method to genome-wide SNP data of ∼4,000 individuals in five admixed Latin American cohorts from Brazil, Chile, Colombia, Mexico, and Peru. Our approach replicates previous reports of selection in the human leukocyte antigen region that are consistent with selection post-admixture. We also report novel signals of selection in genomic regions spanning 47 genes, reinforcing many of these signals with an alternative, commonly used local-ancestry-inference approach. These signals include several genes involved in immunity, which may reflect responses to endemic pathogens of the Americas and to the challenge of infectious disease brought by European contact. In addition, some of the strongest signals inferred to be under selection in the Native American ancestral groups of modern Latin Americans overlap with genes implicated in energy metabolism phenotypes, plausibly reflecting adaptations to novel dietary sources available in the Americas.

SUBMITTER: Mendoza-Revilla J

PROVIDER: S-EPMC9034689 | biostudies-literature | 2022 Apr

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Disentangling Signatures of Selection Before and After European Colonization in Latin Americans.

Mendoza-Revilla Javier J Chacón-Duque J Camilo JC Fuentes-Guajardo Macarena M Ormond Louise L Wang Ke K Hurtado Malena M Villegas Valeria V Granja Vanessa V Acuña-Alonzo Victor V Jaramillo Claudia C Arias William W Barquera Rodrigo R Gómez-Valdés Jorge J Villamil-Ramírez Hugo H Silva de Cerqueira Caio C CC Badillo Rivera Keyla M KM Nieves-Colón Maria A MA Gignoux Christopher R CR Wojcik Genevieve L GL Moreno-Estrada Andrés A Hünemeier Tábita T Ramallo Virginia V Schuler-Faccini Lavinia L Gonzalez-José Rolando R Bortolini Maria-Cátira MC Canizales-Quinteros Samuel S Gallo Carla C Poletti Giovanni G Bedoya Gabriel G Rothhammer Francisco F Balding David D Fumagalli Matteo M Adhikari Kaustubh K Ruiz-Linares Andrés A Hellenthal Garrett G

Molecular biology and evolution 20220401 4

Throughout human evolutionary history, large-scale migrations have led to intermixing (i.e., admixture) between previously separated human groups. Although classical and recent work have shown that studying admixture can yield novel historical insights, the extent to which this process contributed to adaptation remains underexplored. Here, we introduce a novel statistical model, specific to admixed populations, that identifies loci under selection while determining whether the selection likely o ...[more]

PMID: 35460423

Similar Datasets

Project description:BACKGROUND:Species showing complex life cycles provide excellent opportunities to study the genetic associations between life cycle stages, as selective pressures may differ before and after metamorphosis. The European eel presents a complex life cycle with two metamorphoses, a first metamorphosis from larvae into glass eels (juvenile stage) and a second metamorphosis into silver eels (adult stage). We tested the hypothesis that different genes and gene pathways will be under selection at different life stages when comparing the genetic associations between glass eels and silver eels. RESULTS:We used two sets of markers to test for selection: first, we genotyped individuals using a panel of 80 coding-gene single nucleotide polymorphisms (SNPs) developed in American eel; second, we investigated selection at the genome level using a total of 153,423 RAD-sequencing generated SNPs widely distributed across the genome. Using the RAD approach, outlier tests identified a total of 2413 (1.57%) potentially selected SNPs. Functional annotation analysis identified signal transduction pathways as the most over-represented group of genes, including MAPK/Erk signalling, calcium signalling and GnRH (gonadotropin-releasing hormone) signalling. Many of the over-represented pathways were related to growth, while others could result from the different conditions that eels inhabit during their life cycle. CONCLUSIONS:The observation of different genes and gene pathways under selection when comparing glass eels vs. silver eels supports the adaptive decoupling hypothesis for the benefits of metamorphosis. Partitioning the life cycle into discrete morphological phases may be overall beneficial since it allows the different life stages to respond independently to their unique selection pressures. This might translate into a more effective use of food and niche resources and/or performance of phase-specific tasks (e.g. feeding in the case of glass eels, migrating and reproducing in the case of silver eels).

Project description:Translational Relevance Historically, African Americans have been underrepresented in clinical cancer research. Diversity helps to ensure equal access to new cancer therapies and better treatment for everyone. Cancer research is increasingly focused on classifying patients according to molecular profiles for particular groups. We provide a detailed molecular analysis from paired NSCLC tissues that identified differential coding and noncoding RNA expression in NSCLC from African Americans (AA) and European Americans (EA). Similar to other tumor types, we determined that race-enriched gene and microRNA expression signatures suggest a more aggressive disease in African Americans. Based on predicted drug resistance to adjuvant chemotherapies, AA may not equally benefit from the same range of clinical drugs as EA. Our findings provide a rationale for integrating coding and noncoding transcriptome profiles, along with clinical, demographic, and genomic data, when determining treatment options. Abstract Purpose: To determine if racial differences in gene and microRNA expression translates to differences in lung tumor biology with clinical relevance in African Americans (AA) and European Americans (EA). Experimental Design: The NCI-Maryland Case Control Study includes seven Baltimore City hospitals and is overrepresented with AA patients (~40%). Patients that underwent curative NSCLC surgery between 1998 and 2014 were enrolled. Comparative molecular profiling used mRNA (n = 22 AAs and n = 19 EAs) and microRNA (n = 42 AAs and n = 55 EAs) expression arrays to track differences in paired fresh frozen normal tissues and lung tumor specimens from AA and EA. Pathway enrichment, predicted drug response, tumor microenvironment infiltration, cancer immunotherapy antigen profiling, and microRNA target enrichment were assessed. Results: AA-enriched differential gene expression was characterized by stem-cell and invasion pathways. Differential gene expression in lung tumors from EA were primarily characterized by cell proliferation pathways. Population-specific gene expression was partly driven by population-specific miRNA expression profiles. Drug susceptibility predictions revealed a strong inverse correlation between AA resistance and EA sensitivity to the same panel of drugs. Statistically significant differences in M1 and M2 macrophage infiltration was observed in AA (P <0.05), however, PD-L1, PD-L2 expression was similar between both. Conclusions: Comparative transcriptomic profiling revealed clear differences in lung tumor biology between AA and EA. Increased participation by AA in lung cancer clinical trials are needed to integrate, and leverage, transcriptomic differences with other clinical information to maximize therapeutic benefit in both AA and EA.

Project description:Abstract The search for selection signatures in wild boars was meant to assist in identifying genomic regions associated with adaptation to environmental conditions. The aim of our study was to seek selection signatures in European wild boars of Russia. We studied 66 wild boars from 20 different regions in four different climatic zones. DNA samples were genotyped using Porcine SNP60 BeadChips and GeneSeek SNP-chips (Illumina, San Diego, USA). Quality control procedures were carried out resorting to PLINK v1.9; briefly, individuals with genotype call rates of < 0.8 and SNPs with call rates of < 0.3 or minor allele frequencies less than 0.99 were excluded. Also, we resorted to “–LD” to make prune filtering in Plink. In total 37065 markers from full subset of SNPs were used for subsequent analysis. We removed close relatives with enabling option --rel-cutoff 0.75. After filtering 11271 SNPs remained and total genotyping rate of obtained dataset was 98.4%. We subsequently identified SNPs, which had cross within log-likelihood ratio scores (LLRS) values > 2, in addition to integrated Haplotype Score (iHS) values > 2. After comparing 2 methods we detected 6 common elements in “IHS” and “LLRS” - ASGA0101898 – intergenic variant; H3GA0020102 – intergenic variant; ASGA0093835 - intron variant, RBFOX1 (RNA binding fox-1 homolog 1) is a Protein Coding gene, RNA-binding protein that regulates alternative splicing events by binding to 5’-UGCAUGU-3’ elements, regulates alternative splicing of tissue-specific exons and of differentially spliced exons during erythropoiesis; ASGA0098807 - DSG3 (Desmoglein 3) is a Protein Coding gene, component of intercellular desmosome junctions, involved in the interaction of plaque proteins and intermediate filaments mediating cell-cell adhesion; MARC0064247 – non coding transcript exon variant ENSSSCG00000035431, ASGA0020755 – intron variant, ARHGAP30 Rho GTPase activating protein 30). The result of the research will assist in revealing genetic regions associated with adaptation of the Russian wild boars. This research was supported by the Russian Scientific Foundation (RSF) within Project No. 19-16-00109.

Dataset Information

Disentangling Signatures of Selection Before and After European Colonization in Latin Americans.

Publications

Disentangling Signatures of Selection Before and After European Colonization in Latin Americans.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets