scholarly journals The genetic scenario of Mercheros: an under-represented group within the Iberian Peninsula

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
André Flores-Bello ◽  
Neus Font-Porterias ◽  
Julen Aizpurua-Iraola ◽  
Sara Duarri-Redondo ◽  
David Comas
Keyword(s):  
Iberian Peninsula ◽  
Demographic History ◽  
Ethnically Diverse ◽  
Human Populations ◽  
Minority Ethnic Group ◽  
Fine Scale ◽  
Genome Wide ◽  
Wide Range ◽  
Y Chromosome Str ◽  
Western Eurasia

Abstract Background The general picture of human genetic variation has been vastly depicted in the last years, yet many populations remain broadly understudied. In this work, we analyze for the first time the Merchero population, a Spanish minority ethnic group that has been scarcely studied and historically persecuted. Mercheros have been roughly characterised by an itinerant history, common traditional occupations, and the usage of their own language. Results Here, we examine the demographic history and genetic scenario of Mercheros, by using genome-wide array data, whole mitochondrial sequences, and Y chromosome STR markers from 25 individuals. These samples have been complemented with a wide-range of present-day populations from Western Eurasia and North Africa. Our results show that the genetic diversity of Mercheros is explained within the context of the Iberian Peninsula, evidencing a modest signal of Roma admixture. In addition, Mercheros present low genetic isolation and intrapopulation heterogeneity. Conclusions This study represents the first genetic characterisation of the Merchero population, depicting their fine-scale ancestry components and genetic scenario within the Iberian Peninsula. Since ethnicity is not only influenced by genetic ancestry but also cultural factors, other studies from multiple disciplines are needed to further explore the Merchero population. As with Mercheros, there is a considerable gap of underrepresented populations and ethnic groups in publicly available genetic data. Thus, we encourage the consideration of more ethnically diverse population panels in human genetic studies, as an attempt to improve the representation of human populations and better reconstruct their fine-scale history.

scholarly journals Patterns of genetic differentiation and the footprints of historical migrations in the Iberian Peninsula

2018 ◽  
Author(s):  
Clare Bycroft ◽  
Ceres Fernandez-Rozadilla ◽  
Clara Ruiz-Ponte ◽  
Inés Quintela-García ◽  
Ángel Carracedo ◽  
...  
Keyword(s):  
Population Structure ◽  
Genetic Differentiation ◽  
Iberian Peninsula ◽  
Association Studies ◽  
Demographic History ◽  
African Ancestry ◽  
Population History ◽  
Human Populations ◽  
Fine Scale ◽  
The North

Genetic differences within or between human populations (population structure) has been studied using a variety of approaches over many years. Recently there has been an increasing focus on studying genetic differentiation at fine geographic scales, such as within countries. Identifying such structure allows the study of recent population history, and identifies the potential for confounding in association studies, particularly when testing rare, often recently arisen variants. The Iberian Peninsula is linguistically diverse, has a complex demographic history, and is unique among European regions in having a centuries-long period of Muslim rule. Previous genetic studies of Spain have examined either a small fraction of the genome or only a few Spanish regions. Thus, the overall pattern of fine-scale population structure within Spain remains uncharacterised. Here we analyse genome-wide genotyping array data for 1,413 Spanish individuals sampled from all regions of Spain. We identify extensive fine-scale structure, down to unprecedented scales, smaller than 10 Km in some places. We observe a major axis of genetic differentiation that runs from east to west of the peninsula. In contrast, we observe remarkable genetic similarity in the north-south direction, and evidence of historical north-south population movement. Finally, without making particular prior assumptions about source populations, we show that modern Spanish people have regionally varying fractions of ancestry from a group most similar to modern north Moroccans. The north African ancestry results from an admixture event, which we date to 860 - 1120 CE, corresponding to the early half of Muslim rule. Our results indicate that it is possible to discern clear genetic impacts of the Muslim conquest and population movements associated with the subsequent Reconquista.

scholarly journals Genome-wide Characterization of Shared and Distinct Genetic Components that Influence Blood Lipid Levels in Ethnically Diverse Human Populations

2013 ◽  
Vol 92 (6) ◽  
pp. 904-916 ◽  
Author(s):  
Marc A. Coram ◽  
Qing Duan ◽  
Thomas J. Hoffmann ◽  
Timothy Thornton ◽  
Joshua W. Knowles ◽  
...  
Keyword(s):  
Ethnically Diverse ◽  
Blood Lipid ◽  
Human Populations ◽  
Lipid Levels ◽  
Genetic Components ◽  
Genome Wide ◽  
Blood Lipid Levels

scholarly journals Inference and analysis of population-specific fine-scale recombination maps across 26 diverse human populations

2019 ◽  
Vol 5 (10) ◽  
pp. eaaw9206 ◽  
Author(s):  
Jeffrey P. Spence ◽  
Yun S. Song
Keyword(s):  
Binding Sites ◽  
Demographic History ◽  
Dna Binding Protein ◽  
Polycomb Group ◽  
Human Populations ◽  
Polycomb Group Proteins ◽  
Fine Scale ◽  
Population Differences ◽  
Recombination Rates ◽  
History Of

Fine-scale rates of meiotic recombination vary by orders of magnitude across the genome and differ between species and even populations. Studying cross-population differences has been stymied by the confounding effects of demographic history. To address this problem, we developed a demography-aware method to infer fine-scale recombination rates and applied it to 26 diverse human populations, inferring population-specific recombination maps. These maps recapitulate many aspects of the history of these populations including signatures of the trans-Atlantic slave trade and the Iberian colonization of the Americas. We also investigated modulators of the local recombination rate, finding further evidence that Polycomb group proteins and the trimethylation of H3K27 elevate recombination rates. Further differences in the recombination landscape across the genome and between populations are driven by variation in the gene that encodes the DNA binding protein PRDM9, and we quantify the weak effect of meiotic drive acting to remove its binding sites.

scholarly journals The counteracting effects of demography on functional genomic variation: the Roma paradigm

2021 ◽  
Author(s):  
Neus Font-Porterias ◽  
Rocio Caro-Consuegra ◽  
Marcel Lucas-Sánchez ◽  
Marie Lopez ◽  
Aaron Giménez ◽  
...  
Keyword(s):  
Gene Flow ◽  
Rare Variants ◽  
Demographic History ◽  
Genomic Variation ◽  
Human Populations ◽  
History Plays ◽  
High Coverage ◽  
Roma Population ◽  
Genome Wide ◽  
Whole Exome

Abstract Demographic history plays a major role in shaping the distribution of genomic variation. Yet the interaction between different demographic forces and their effects in the genomes is not fully resolved in human populations. Here we focus on the Roma population, the largest transnational ethnic minority in Europe. They have a South Asian origin and their demographic history is characterized by recent dispersals, multiple founder events and extensive gene flow from non-Roma groups. Through the analyses of new high-coverage whole exome sequences and genome-wide array data for 89 Iberian Roma individuals together with forward simulations, we show that founder effects have reduced their genetic diversity and proportion of rare variants, gene flow has counteracted the increase in mutational load, runs of homozygosity show ancestry-specific patterns of accumulation of deleterious homozygotes, and selection signals primarily derive from pre-admixture adaptation in the Roma population sources. The present study shows how two demographic forces, bottlenecks and admixture, act in opposite directions and have long-term balancing effects on the Roma genomes. Understanding how demography and gene flow shape the genome of an admixed population provides an opportunity to elucidate how genomic variation is modelled in human populations.

scholarly journals Inference and analysis of population-specific fine-scale recombination maps across 26 diverse human populations

2019 ◽  
Author(s):  
Jeffrey P. Spence ◽  
Yun S. Song
Keyword(s):  
Binding Sites ◽  
Demographic History ◽  
Dna Binding Protein ◽  
Polycomb Group ◽  
Human Populations ◽  
Polycomb Group Proteins ◽  
Fine Scale ◽  
Recombination Rates ◽  
Confounding Effect ◽  
History Of

AbstractFine-scale rates of meiotic recombination vary by several orders of magnitude across the genome, and are known to differ between species and even between populations. Studying the differences in recombination maps across populations has been stymied by the confounding effect of differences in demographic history. To address this problem, we developed a method that infers fine-scale recombination rates while taking demography into account and applied our method to infer population-specific recombination maps for each of 26 diverse human populations. These maps recapitulate many aspects of the history of these populations including signatures of the trans-Atlantic slave trade and the Iberian colonization of the Americas. We also investigated modulators of the local recombination rate, finding an unexpected role for Polycomb-group proteins and the tri-methylation of H3K27 in elevating recombination rates. Further differences in the recombination landscape across the genome and between populations are driven by variation in the gene that encodes the DNA-binding protein PRDM9, and we quantify the weak effect of meiotic drive acting to remove its binding sites.

scholarly journals Genome-culture coevolution promotes rapid divergence in the killer whale

2016 ◽  
Author(s):  
Andrew Foote ◽  
Nagarjun Vijay ◽  
Maria Avila-Arcos ◽  
Robin Baird ◽  
John Durban ◽  
...  
Keyword(s):  
Killer Whale ◽  
Demographic History ◽  
Functional Enrichment ◽  
Genetic Structuring ◽  
Dietary Preferences ◽  
Genome Wide ◽  
Wide Range ◽  
Postzygotic Reproductive Isolation ◽  
Rapid Divergence ◽  
Functional Alleles

The interaction between ecology, culture and genome evolution remains poorly understood. Analysing population genomic data from killer whale ecotypes, which we estimate have globally radiated within less than 250,000 years, we show that genetic structuring including the segregation of potentially functional alleles is associated with socially inherited ecological niche. Reconstruction of ancestral demographic history revealed bottlenecks during founder events, likely promoting ecological divergence and genetic drift resulting in a wide range of genome-wide differentiation between pairs of allopatric and sympatric ecotypes. Functional enrichment analyses provided evidence for regional genomic divergence associated with habitat, dietary preferences and postzygotic reproductive isolation. Our findings are consistent with expansion of small founder groups into novel niches by an initial plastic behavioural response, perpetuated by social learning imposing an altered natural selection regime. The study constitutes an important step toward an understanding of the complex interaction between demographic history, culture, ecological adaptation and evolution at the genomic level.

scholarly journals Models of archaic admixture and recent history from two-locus statistics

2018 ◽  
Author(s):  
Aaron P. Ragsdale ◽  
Simon Gravel
Keyword(s):  
Genetic Diversity ◽  
Linkage Disequilibrium ◽  
Evolutionary Biology ◽  
Demographic History ◽  
Population History ◽  
Human Populations ◽  
Evolutionary Models ◽  
Human History ◽  
Wide Range ◽  
Archaic Admixture

AbstractWe learn about population history and underlying evolutionary biology through patterns of genetic polymorphism. Many approaches to reconstruct evolutionary histories focus on a limited number of informative statistics describing distributions of allele frequencies or patterns of linkage disequilibrium. We show that many commonly used statistics are part of a broad family of two-locus moments whose expectation can be computed jointly and rapidly under a wide range of scenarios, including complex multi-population demographies with continuous migration and admixture events. A full inspection of these statistics reveals that widely used models of human history fail to predict simple patterns of linkage disequilibrium. To jointly capture the information contained in classical and novel statistics, we implemented a tractable likelihood-based inference framework for demographic history. Using this approach, we show that human evolutionary models that include archaic admixture in Africa, Asia, and Europe provide a much better description of patterns of genetic diversity across the human genome. We estimate that an unidentified, deeply diverged population admixed with modern humans within Africa both before and after the split of African and Eurasian populations, contributing 4-8% genetic ancestry to individuals in world-wide populations.Author SummaryThroughout human history, populations have expanded and contracted, split and merged, and ex-changed migrants. Because these events affected genetic diversity, we can learn about human history by comparing predictions from evolutionary models to genetic data. Here, we show how to rapidly compute such predictions for a wide range of diversity measures within and across populations under complex demographic scenarios. While widely used models of human history accurately predict common measures of diversity, we show that they strongly underestimate the co-occurence of low frequency mutations within human populations in Asia, Europe, and Africa. Models allowing for archaic admixture, the relatively recent mixing of human populations with deeply diverged human lineages, resolve this discrepancy. We use such models to infer demographic models that include both recent and ancient features of human history. We recover the well-characterized admixture of Neanderthals in Eurasian populations, as well as admixture from an as-yet unknown diverged human population within Africa, further suggesting that admixture with deeply diverged lineages occurred multiple times in human history. By simultaneously testing model predictions for a broad range of diversity statistics, we can assess the robustness of common evolutionary models, identify missing historical events, and build more informed models of human demography.

scholarly journals Evolutionary and Medical Consequences of Archaic Introgression into Modern Human Genomes

Genes ◽  
2018 ◽  
Vol 9 (7) ◽  
pp. 358 ◽  
Author(s):  
Olga Dolgova ◽  
Oscar Lao
Keyword(s):  
Demographic History ◽  
Modern Human ◽  
Human Populations ◽  
Human Genomes ◽  
Fitness Consequences ◽  
Genome Wide ◽  
Anatomically Modern Humans ◽  
Genome Wide Data ◽  
History Of ◽  
Health And Disease

The demographic history of anatomically modern humans (AMH) involves multiple migration events, population extinctions and genetic adaptations. As genome-wide data from complete genome sequencing becomes increasingly abundant and available even from extinct hominins, new insights of the evolutionary history of our species are discovered. It is currently known that AMH interbred with archaic hominins once they left the African continent. Current non-African human genomes carry fragments of archaic origin. This review focuses on the fitness consequences of archaic interbreeding in current human populations. We discuss new insights and challenges that researchers face when interpreting the potential impact of introgression on fitness and testing hypotheses about the role of selection within the context of health and disease.

scholarly journals Population-specific sequence and expression differentiation in Europeans

2019 ◽  
Author(s):  
Xueyuan Jiang ◽  
Raquel Assis
Keyword(s):  
Target Genes ◽  
Demographic History ◽  
Copy Number Variations ◽  
Human Populations ◽  
Rna Seq ◽  
Nucleotide Polymorphism ◽  
Specific Sequence ◽  
Single Nucleotide ◽  
Genome Wide ◽  
History Of

AbstractMuch of the enormous phenotypic variation observed across human populations is thought to have arisen from events experienced as our ancestors peopled different regions of the world. However, little is known about the genes involved in these population-specific adaptations. Here we explore this problem by simultaneously examining population-specific sequence and expression differentiation in four human populations. In particular, we design a branch-based statistic to estimate population-specific differentiation in four populations, and apply this statistic to single nucleotide polymorphism (SNP) and RNA-seq data from Italian, British, Finish, and Yoruban populations. As expected, genome-wide estimates of sequence and expression differentiation each independently recapitulate the known demographic history of these four human populations, highlighting the utility of our statistic for identifying genic targets of population-specific adaptations. Application of our statistic reveals that genes containing large copy number variations (CNVs) have elevated levels of population-specific sequence and expression differentiation, consistent with the hypothesis that gene turnover is a key reservoir of adaptive variation. Further, European genes displaying population-specific sequence and expression differentiation are enriched for functions related to epigenetic regulation, immunity, and reproduction. Together, our findings illustrate that population-specific sequence and expression differentiation in humans may preferentially target genes with CNVs and play important roles in a diversity of adaptive and disease-related phenotypes.

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