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 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 Transcriptional repression by Drosophila and mammalian Polycomb group proteins in transfected mammalian cells.

1994 ◽  
Vol 14 (3) ◽  
pp. 1721-1732 ◽  
Author(s):  
C A Bunker ◽  
R E Kingston
Keyword(s):  
Binding Sites ◽  
Transcriptional Repression ◽  
Fusion Proteins ◽  
Mammalian Cells ◽  
Polycomb Group ◽  
Polycomb Group Proteins ◽  
Related Gene ◽  
Activation Domains ◽  
Sex Combs ◽  
Significant Homology

The Polycomb group (Pc-G) genes are essential for maintaining the proper spatially restricted expression pattern of the homeotic loci during Drosophila development. The Pc-G proteins appear to function at target loci to maintain a state of transcriptional repression. The murine oncogene bmi-1 has significant homology to the Pc-G gene Posterior sex combs (Psc) and a highly related gene, Suppressor two of zeste [Su(z)2]. We show here that the proteins encoded by bmi-1 and the Pc-G genes Polycomb (Pc) and Psc as well as Su(z)2 mediate repression in mammalian cells when targeted to a promoter by LexA in a cotransfection system. These fusion proteins repress activator function by as much as 30-fold, and the effect on different activation domains is distinct for each Pc-G protein. Repression is observed when the LexA fusion proteins are bound directly adjacent to activator binding sites and also when bound 1,700 bases from the promoter. These data demonstrate that the products of the Pc-G genes can significantly repress activator function on transiently introduced DNA. We suggest that this function contributes to the stable repression of targeted loci during development.

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.

A Microsatellite-Based Multilocus Screen for the Identification of Local Selective Sweeps

Genetics ◽  
2002 ◽  
Vol 160 (2) ◽  
pp. 753-763 ◽  
Author(s):  
Christian Schlötterer
Keyword(s):  
Microsatellite Loci ◽  
Selective Sweep ◽  
Demographic History ◽  
Human Populations ◽  
Selective Sweeps ◽  
Test Statistic ◽  
Data Set ◽  
History Of ◽  
Microsatellite Mutation ◽  
Genomic Regions

AbstractWith the availability of completely sequenced genomes, multilocus scans of natural variability have become a feasible approach for the identification of genomic regions subjected to natural and artificial selection. Here, I introduce a new multilocus test statistic, ln RV, which is based on the ratio of observed variances in repeat number at a set of microsatellite loci in two groups of populations. The distribution of ln RV values captures demographic history of the populations as well as variation in microsatellite mutation among loci. Given that microsatellite loci associated with a recent selective sweep differ from the remainder of the genome, they are expected to fall outside of the distribution of neutral ln RV values. The ln RV test statistic is applied to a data set of 94 loci typed in eight non-African and two African human populations.

scholarly journals Transcriptional repression by Drosophila and mammalian Polycomb group proteins in transfected mammalian cells

1994 ◽  
Vol 14 (3) ◽  
pp. 1721-1732
Author(s):  
C A Bunker ◽  
R E Kingston
Keyword(s):  
Binding Sites ◽  
Transcriptional Repression ◽  
Fusion Proteins ◽  
Mammalian Cells ◽  
Polycomb Group ◽  
Polycomb Group Proteins ◽  
Related Gene ◽  
Activation Domains ◽  
Sex Combs ◽  
Significant Homology

The Polycomb group (Pc-G) genes are essential for maintaining the proper spatially restricted expression pattern of the homeotic loci during Drosophila development. The Pc-G proteins appear to function at target loci to maintain a state of transcriptional repression. The murine oncogene bmi-1 has significant homology to the Pc-G gene Posterior sex combs (Psc) and a highly related gene, Suppressor two of zeste [Su(z)2]. We show here that the proteins encoded by bmi-1 and the Pc-G genes Polycomb (Pc) and Psc as well as Su(z)2 mediate repression in mammalian cells when targeted to a promoter by LexA in a cotransfection system. These fusion proteins repress activator function by as much as 30-fold, and the effect on different activation domains is distinct for each Pc-G protein. Repression is observed when the LexA fusion proteins are bound directly adjacent to activator binding sites and also when bound 1,700 bases from the promoter. These data demonstrate that the products of the Pc-G genes can significantly repress activator function on transiently introduced DNA. We suggest that this function contributes to the stable repression of targeted loci during development.

scholarly journals The timing of human adaptation from Neanderthal introgression

2020 ◽  
Author(s):  
Sivan Yair ◽  
Kristin M. Lee ◽  
Graham Coop
Keyword(s):  
Demographic History ◽  
Low Frequency ◽  
Modern Human ◽  
Allele Frequencies ◽  
Population Divergence ◽  
Human Populations ◽  
Human Adaptation ◽  
Adaptive Introgression ◽  
History Of ◽  
Spatio Temporal

AbstractAdmixture has the potential to facilitate adaptation by providing alleles that are immediately adaptive in a new environment or by simply increasing the long term reservoir of genetic diversity for future adaptation. A growing number of cases of adaptive introgression are being identified in species across the tree of life, however the timing of selection, and therefore the importance of the different evolutionary roles of admixture, is typically unknown. Here, we investigate the spatio-temporal history of selection favoring Neanderthal-introgressed alleles in modern human populations. Using both ancient and present-day samples of modern humans, we integrate the known demographic history of populations, namely population divergence and migration, with tests for selection. We model how a sweep placed along different branches of an admixture graph acts to modify the variance and covariance in neutral allele frequencies among populations at linked loci. Using a method based on this model of allele frequencies, we study previously identified cases of Neanderthal adaptive introgression. From these, we identify cases in which Neanderthal introgressed alleles were quickly beneficial and other cases in which they persisted at low frequency for some time. For some of the alleles that persisted at low frequency, we show that selection likely independently favored them later on in geographically separated populations. Our work highlights how admixture with ancient hominins has contributed to modern human adaptation, contextualizes observed levels of Neanderthal ancestry in present-day and ancient samples, and identifies cases of temporally varying selection that are sometimes shared across large geographic distances.

scholarly journals Global demographic history of human populations inferred from whole mitochondrial genomes

2018 ◽  
Vol 5 (8) ◽  
pp. 180543 ◽  
Author(s):  
Eleanor F. Miller ◽  
Andrea Manica ◽  
William Amos
Keyword(s):  
Demographic History ◽  
Population Expansion ◽  
Human Populations ◽  
Population Mixing ◽  
Neolithic Transition ◽  
Current Location ◽  
Geographical Regions ◽  
Population Sizes ◽  
History Of ◽  
Complete Mtdna

The Neolithic transition has led to marked increases in census population sizes across the world, as recorded by a rich archaeological record. However, previous attempts to detect such changes using genetic markers, especially mitochondrial DNA (mtDNA), have mostly been unsuccessful. We use complete mtDNA genomes from over 1700 individuals, from the 1000 Genomes Project Phase 3, to explore changes in populations sizes in five populations for each of four major geographical regions, using a sophisticated coalescent-based Bayesian method (extended Bayesian skyline plots) and mutation rates calibrated with ancient DNA. Despite the power and sophistication of our analysis, we fail to find size changes that correspond to the Neolithic transitions of the study populations. However, we do detect a number of size changes, which tend to be replicated in most populations within each region. These changes are mostly much older than the Neolithic transition and could reflect either population expansion or changes in population structure. Given the amount of migration and population mixing that occurred after these ancient signals were generated, we caution that modern populations will often carry ghost signals of demographic events that occurred far away from their current location.

scholarly journals ARGON: Fast, Whole-Genome Simulation of the Discrete Time Wright-Fisher Process

2016 ◽  
Author(s):  
Pier Francesco Palamara
Keyword(s):  
Discrete Time ◽  
Demographic History ◽  
Memory Performance ◽  
Real Data ◽  
Supplementary Information ◽  
Human Populations ◽  
Data Sets ◽  
Recombination Rates ◽  
Coalescent Model ◽  
Fisher Model

AbstractMotivationSimulation under the coalescent model is ubiquitous in the analysis of genetic data. The rapid growth of real data sets from multiple human populations led to increasing interest in simulating very large sample sizes at whole-chromosome scales. When the sample size is large, the coalescent model becomes an increasingly inaccurate approximation of the discrete time Wright-Fisher model (DTWF). Analytical and computational treatment of the DTWF, however, is generally harder.ResultsWe present a simulator (ARGON) for the DTWF process that scales up to hundreds of thousands of samples and whole-chromosome lengths, with a time/memory performance comparable or superior to currently available methods for coalescent simulation. The simulator supports arbitrary demographic history, migration, Newick tree output, variable mutation/recombination rates and gene conversion, and efficiently outputs pairwise identical-bydescent (IBD) sharing data.AvailabilityARGON (version 0.1) is written in Java, open source, and freely available at https://github.com/pierpal/[email protected] informationSupplementary data are available online.

Widespread Gene Flow Model Explains the Genetic–Morphological Variation in a Giant Water Bug Species Under Fine-Scale Spatial Sampling

2019 ◽  
Vol 113 (3) ◽  
pp. 160-170
Author(s):  
Fabiano Stefanello ◽  
Rodolpho S T Menezes ◽  
José Ricardo I Ribeiro ◽  
Eduardo A B Almeida
Keyword(s):  
Population Dynamics ◽  
Gene Flow ◽  
Morphological Variation ◽  
Flow Model ◽  
Demographic History ◽  
Spatial Sampling ◽  
Fine Scale ◽  
Freshwater Organisms ◽  
History Of ◽  
The Last Glacial

Abstract The population dynamics of freshwater organisms are expected to be related to the connectivity among comparable streams, ponds, or rivers in a patchy habitat. Here, we investigated the population dynamics of the giant water bug, Belostoma angustum Lauck 1964 (Hemiptera: Belostomatidae), in a fine-scale spatial sampling, and evaluated which gene flow model previously described for freshwater organisms could explain the genetic–morphological variation in this species. For these purposes, we evaluated genetic and morphological variations, as well as the demographic history of this freshwater insect. Our genetic analyses showed a lack of geographical structure within B. angustum populations across the evaluated range, concordant with widespread gene flow model. Our findings of the demographic history of B. angustum suggest recent and rapid expansion beginning during the late Pleistocene after the Last Glacial Maximum. Likewise, we did not find geographically structured morphological variation in B. angustum, except for body size. The lack of structure of genetic–morphological variation in B. angustum could be explained by a stepping ponds system resulting in the widespread gene flow detected among populations of this species. The warmer and wetter climatic conditions after the last glacial period may have favored the demographic expansion of B. angustum populations due to the increasing of potential freshwater habitats and food resources. This favorable habitat probably allowed the stepping ponds dispersal mode resulting in the verified geographically unstructured genetic–morphological variation.

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