The impact of selection, gene flow and demographic history on heterogeneous genomic divergence: three-spine sticklebacks in divergent environments

2015 ◽  
Vol 25 (1) ◽  
pp. 238-259 ◽  
Author(s):  
Anne-Laure Ferchaud ◽  
Michael M. Hansen
Keyword(s):  
Gene Flow ◽  
Demographic History ◽  
Genomic Divergence ◽  
Selection Gene ◽  
The Impact

scholarly journals The genomic impact of European colonization of the Americas

2019 ◽  
Author(s):  
Linda Ongaro ◽  
Marilia O. Scliar ◽  
Rodrigo Flores ◽  
Alessandro Raveane ◽  
Davide Marnetto ◽  
...  
Keyword(s):  
Gene Flow ◽  
Demographic History ◽  
Colonial Era ◽  
Genome Wide ◽  
A Genome ◽  
European Colonization ◽  
High Degree ◽  
The Impact ◽  
North And South America ◽  
North And South

AbstractThe human genetic diversity of the Americas has been shaped by several events of gene flow that have continued since the Colonial Era and the Atlantic slave trade. Moreover, multiple waves of migration followed by local admixture occurred in the last two centuries, the impact of which has been largely unexplored.Here we compiled a genome-wide dataset of ∼12,000 individuals from twelve American countries and ∼6,000 individuals from worldwide populations and applied haplotype-based methods to investigate how historical movements from outside the New World affected i) the genetic structure, ii) the admixture profile, iii) the demographic history and iv) sex-biased gene-flow dynamics, of the Americas.We revealed a high degree of complexity underlying the genetic contribution of European and African populations in North and South America, from both geographic and temporal perspectives, identifying previously unreported sources related to Italy, the Middle East and to specific regions of Africa.

scholarly journals The demographic history and mutational load of African hunter-gatherers and farmers

2017 ◽  
Author(s):  
Marie Lopez ◽  
Athanasios Kousathanas ◽  
Hélène Quach ◽  
Christine Harmant ◽  
Patrick Mouguiama-Daouda ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Demographic History ◽  
Purifying Selection ◽  
Human Populations ◽  
Mutational Load ◽  
Sequencing Data ◽  
Hunter Gatherers ◽  
African Populations ◽  
The Impact

AbstractThe distribution of deleterious genetic variation across human populations is a key issue in evolutionary biology and medical genetics. However, the impact of different modes of subsistence on recent changes in population size, patterns of gene flow, and deleterious mutational load remains unclear. Here, we report high-coverage exome sequencing data from various populations of rainforest hunter-gatherers and farmers from central Africa. We find that the recent demographic histories of hunter-gatherers and farmers differed considerably, with population collapses for hunter-gatherers and expansions for farmers, accompanied by increased gene flow. We show that purifying selection against deleterious alleles is of similar efficiency across African populations, in contrast with Europeans where we detect weaker purifying selection. Furthermore, the per-individual mutation load of rainforest hunter-gatherers is similar to that of farmers, under both additive and recessive models. Our results indicate that differences in the cultural practices and demographic regimes of African populations have not resulted in large differences in mutational burden, and highlight the beneficial role of gene flow in reshaping the distribution of deleterious genetic variation across human populations.

scholarly journals Analysis of whole-genome re-sequencing data of ducks reveals a diverse demographic history and extensive gene flow between Southeast/South Asian and Chinese populations

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Fan Jiang ◽  
Ruiyi Lin ◽  
Changyi Xiao ◽  
Tanghui Xie ◽  
Yaoxin Jiang ◽  
...  
Keyword(s):  
Gene Flow ◽  
South Asia ◽  
South Asian ◽  
Demographic History ◽  
Nervous System Development ◽  
Chromosome 1 ◽  
Whole Genome ◽  
Chinese Populations ◽  
Asian Populations ◽  
History Of

Abstract Background The most prolific duck genetic resource in the world is located in Southeast/South Asia but little is known about the domestication and complex histories of these duck populations. Results Based on whole-genome resequencing data of 78 ducks (Anas platyrhynchos) and 31 published whole-genome duck sequences, we detected three geographic distinct genetic groups, including local Chinese, wild, and local Southeast/South Asian populations. We inferred the demographic history of these duck populations with different geographical distributions and found that the Chinese and Southeast/South Asian ducks shared similar demographic features. The Chinese domestic ducks experienced the strongest population bottleneck caused by domestication and the last glacial maximum (LGM) period, whereas the Chinese wild ducks experienced a relatively weak bottleneck caused by domestication only. Furthermore, the bottleneck was more severe in the local Southeast/South Asian populations than in the local Chinese populations, which resulted in a smaller effective population size for the former (7100–11,900). We show that extensive gene flow has occurred between the Southeast/South Asian and Chinese populations, and between the Southeast Asian and South Asian populations. Prolonged gene flow was detected between the Guangxi population from China and its neighboring Southeast/South Asian populations. In addition, based on multiple statistical approaches, we identified a genomic region that included three genes (PNPLA8, THAP5, and DNAJB9) on duck chromosome 1 with a high probability of gene flow between the Guangxi and Southeast/South Asian populations. Finally, we detected strong signatures of selection in genes that are involved in signaling pathways of the nervous system development (e.g., ADCYAP1R1 and PDC) and in genes that are associated with morphological traits such as cell growth (e.g., IGF1R). Conclusions Our findings provide valuable information for a better understanding of the domestication and demographic history of the duck, and of the gene flow between local duck populations from Southeast/South Asia and China.

scholarly journals The first steps toward a global pandemic: Reconstructing the demographic history of parasite host switches in its native range

2021 ◽  
Author(s):  
Maeva Techer ◽  
John Roberts ◽  
Reed Cartwright ◽  
Alexander Mikheyev
Keyword(s):  
Gene Flow ◽  
Honey Bee ◽  
Varroa Destructor ◽  
Temporal Dynamics ◽  
Demographic History ◽  
Apis Cerana ◽  
Host Switching ◽  
New Host ◽  
Global Pandemic ◽  
Novel Host

Abstract Host switching allows parasites to expand their niches. However, successful switching may require suites of adaptations and may decrease performance on the old host. As a result, reductions in gene flow accompany many host switches, driving speciation. Because host switches tend to be rapid, it is difficult to study them in real time and their demographic parameters remain poorly understood. As a result, fundamental factors that control subsequent parasite evolution, such as the size of the switching population or the extent of immigration from the original host, remain largely unknown. To shed light on the host switching process, we explored how host switches occur in independent host shifts by two ectoparasitic honey bee mites (Varroa destructor and V. jacobsoni). Both switched to the western honey bee (Apis mellifera) after it was brought into contact with their ancestral host (Apis cerana), ~70 and ~12 years ago, respectively. Varroa destructor subsequently caused worldwide collapses of honey bee populations. Using whole-genome sequencing on 63 mites collected in their native ranges from both the ancestral and novel hosts, we were able to reconstruct the known temporal dynamics of the switch. We further found multiple previously undiscovered mitochondrial lineages on the novel host, along with genetic equivalent of tens of individuals that were involved in the initial host switch. Despite being greatly reduced, some gene flow remains between mites adapted to different hosts. Our findings suggest that while reproductive isolation may facilitate fixation of traits beneficial for exploitation of the new host, ongoing genetic exchange may allow genetic amelioration of inbreeding effects.

scholarly journals Population structure and demographic history of the chukar partridge Alectoris chukar in China

2013 ◽  
Vol 59 (4) ◽  
pp. 458-474 ◽  
Author(s):  
Sen Song ◽  
Shijie Bao ◽  
Ying Wang ◽  
Xinkang Bao ◽  
Bei An ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Gene Flow ◽  
North America ◽  
Demographic History ◽  
Population Expansion ◽  
Northwest China ◽  
Population History ◽  
Extant Species ◽  
History Of ◽  
Chukar Partridge

Abstract Pleistocene climate fluctuations have shaped the patterns of genetic diversity observed in extant species. Although the effects of recent glacial cycles on genetic diversity have been well studied on species in Europe and North America, genetic legacy of species in the Pleistocene in north and northwest of China where glaciations was not synchronous with the ice sheet development in the Northern Hemisphere or or had little or no ice cover during the glaciations’ period, remains poorly understood. Here we used phylogeographic methods to investigate the genetic structure and population history of the chukar partridge Alec-toris chukar in north and northwest China. A 1,152 – 1,154 bp portion of the mtDNA CR were sequenced for all 279 specimens and a total number of 91 haplotypes were defined by 113 variable sites. High levels of gene flow were found and gene flow estimates were greater than 1 for most population pairs in our study. The AMOVA analysis showed that 81% and 16% of the total genetic variability was found within populations and among populations within groups, respectively. The demographic history of chukar was examined using neutrality tests and mismatch distribution analyses and results indicated Late Pleistocene population expansion. Results revealed that most populations of chukar experienced population expansion during 0.027 ? 0.06 Ma. These results are at odds with the results found in Europe and North America, where population expansions occurred after Last Glacial Maximum (LGM, 0.023 to 0.018 Ma). Our results are not consistent with the results from avian species of Tibetan Plateau, either, where species experienced population expansion following the retreat of the extensive glaciation period (0.5 to 0.175 Ma).

Abstract P221: The Impact of Prevalent and New-onset Cardiometabolic Risk on the Incidence of Hepatic Steatosis

Circulation ◽  
2020 ◽  
Vol 141 (Suppl_1) ◽  
Author(s):  
Ehimen C Aneni ◽  
Marcio S Bittencourt ◽  
Miguel Caínzos Achirica ◽  
Michael J Blaha ◽  
Ahmed M Soliman ◽  
...  
Keyword(s):  
Risk Factors ◽  
Waist Circumference ◽  
Hepatic Steatosis ◽  
Cardiometabolic Risk ◽  
Demographic History ◽  
Cardiometabolic Risk Factors ◽  
Forest Plot ◽  
Anthropometric Measures ◽  
The Impact ◽  
New Onset

Background: Little is known about hepatic steatosis (HS) incidence and its relationship to underlying or new-onset cardiometabolic risk. This study aims to assess the incidence of hepatic steatosis in an asymptomatic population and to determine its relationship to both prevalent and new-onset cardiometabolic risk factors. Methods: We analyzed retrospective data from a voluntary employer-sponsored routine health promotion evaluation at the Preventive Medicine Center of the Hospital Israelita Albert Einstein (São Paulo, Brazil) collected from October 2004 to December 2016.Medical and demographic history, anthropometric measures including blood pressure, body mass index (BMI) and waist circumference, and fasting blood samples were obtained. Participants also had ultrasonography to assess for HS. We included data from 8,448 individuals who had complete cardiometabolic and ultrasound data at baseline and repeated all tests at least 6 months later. Results: The mean age (standard deviation, SD) of participants was 40 (9) years. Over a mean (SD) follow-up of 3.4 (2.3) years, the incidence of HS was 14.7%. As shown in the table, diabetes, poor physical activity, elevated waist circumference and cigarette smoking at baseline were independently associated with hepatic steatosis. There was an additive effect of the increasing cardiometabolic risk factors (see graph) on the risk of developing HS. Participants with new-onset cardiometabolic risk factors also had a higher risk of incident HS after accounting for baseline demographics and cardiometabolic risk factors (see forest plot). This was most pronounced for incident obesity (BMI ≥ 30 Kg/m 2 ). Conclusion: In this relatively young population, the incidence of HS was high and was both independently and collectively associated with baseline cardiometabolic risk. New-onset cardiometabolic risk tracks with incident HS. This study emphasizes the need for assessing and mitigating cardiometabolic risk in the prevention of HS.

scholarly journals Long-Term Reciprocal Gene Flow in Wild and Domestic Geese Reveals Complex Domestication History

2020 ◽  
Vol 10 (9) ◽  
pp. 3061-3070 ◽  
Author(s):  
Marja E Heikkinen ◽  
Minna Ruokonen ◽  
Thomas A White ◽  
Michelle M Alexander ◽  
İslam Gündüz ◽  
...  
Keyword(s):  
Gene Flow ◽  
Wild Form ◽  
Nucleotide Polymorphisms ◽  
Anser Anser ◽  
Domestic Species ◽  
Genome Wide ◽  
Domestication Process ◽  
Historical Writings ◽  
The Impact

Abstract Hybridization has frequently been observed between wild and domestic species and can substantially impact genetic diversity of both counterparts. Geese show some of the highest levels of interspecific hybridization across all bird orders, and two of the goose species in the genus Anser have been domesticated providing an excellent opportunity for a joint study of domestication and hybridization. Until now, knowledge of the details of the goose domestication process has come from archaeological findings and historical writings supplemented with a few studies based on mitochondrial DNA. Here, we used genome-wide markers to make the first genome-based inference of the timing of European goose domestication. We also analyzed the impact of hybridization on the genome-wide genetic variation in current populations of the European domestic goose and its wild progenitor: the graylag goose (Anser anser). Our dataset consisted of 58 wild graylags sampled around Eurasia and 75 domestic geese representing 14 breeds genotyped for 33,527 single nucleotide polymorphisms. Demographic reconstruction and clustering analysis suggested that divergence between wild and domestic geese around 5,300 generations ago was followed by long-term genetic exchange, and that graylag populations have 3.2–58.0% admixture proportions with domestic geese, with distinct geographic patterns. Surprisingly, many modern European breeds share considerable (> 10%) ancestry with the Chinese domestic geese that is derived from the swan goose Anser cygnoid. We show that the domestication process can progress despite continued and pervasive gene flow from the wild form.

Staying close: short local dispersal distances on a managed forest of two Patagonian Nothofagus species

2020 ◽  
Vol 93 (5) ◽  
pp. 652-661 ◽  
Author(s):  
Georgina Sola ◽  
Verónica El Mujtar ◽  
Leonardo Gallo ◽  
Giovanni G Vendramin ◽  
Paula Marchelli
Keyword(s):  
Gene Flow ◽  
Genetic Structure ◽  
Spatial Genetic Structure ◽  
Pollen Dispersal ◽  
Dispersal Distance ◽  
Restricted Gene Flow ◽  
Fine Scale ◽  
Gene Dispersal ◽  
Mature Trees ◽  
The Impact

Abstract Understanding the impact of management on the dispersal potential of forest tree species is pivotal in the context of global change, given the implications of gene flow on species evolution. We aimed to determine the effect of logging on gene flow distances in two Nothofagus species from temperate Patagonian forests having high ecological relevance and wood quality. Therefore, a total of 778 individuals (mature trees and saplings) of Nothofagus alpina and N. obliqua, from a single plot managed 20 years ago (2.85 hectares), were mapped and genotyped at polymorphic nuclear microsatellite loci. Historical estimates of gene dispersal distance (based on fine-scale spatial genetic structure) and contemporary estimates of seed and pollen dispersal (based on spatially explicit mating models) were obtained. The results indicated restricted gene flow (gene distance ≤ 45 m, both pollen and seed), no selfing and significant seed and pollen immigration from trees located outside the studied plot but in the close surrounding area. The size of trees (diameter at breast height and height) was significantly associated with female and/or male fertility. The significant fine-scale spatial genetic structure was consistent with the restricted seed and pollen dispersal. Moreover, both estimates of gene dispersal (historical and contemporary) gave congruent results. This suggests that the recent history of logging within the study area has not significantly influenced on patterns of gene flow, which can be explained by the silviculture applied to the stand. The residual tree density maintained species composition, and the homogeneous spatial distribution of trees allowed the maintenance of gene dispersal. The short dispersal distance estimated for these two species has several implications both for understanding the evolution of the species and for defining management, conservation and restoration actions. Future replication of this study in other Nothofagus Patagonian forests would be helpful to validate our conclusions.

scholarly journals Estimating the impact of divergent mating phenology between residents and migrants on the potential for gene flow

2019 ◽  
Vol 9 (7) ◽  
pp. 3770-3783
Author(s):  
Colin Bonner ◽  
Nina A. Sokolov ◽  
Sally Erin Westover ◽  
Michelle Ho ◽  
Arthur E. Weis
Keyword(s):  
Gene Flow ◽  
The Impact
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