scholarly journals The great tit HapMap project: a continental-scale analysis of genomic variation in a songbird

2019 ◽  
Author(s):  
Lewis G. Spurgin ◽  
Mirte Bosse ◽  
Frank Adriaensen ◽  
Tamer Albayrak ◽  
Christos Barboutis ◽  
...  
Keyword(s):  
Positive Selection ◽  
Recombination Rate ◽  
Demographic History ◽  
Great Tit ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Hapmap Project ◽  
Widespread Species ◽  
Continental Scale ◽  
Genome Wide

AbstractA major aim of evolutionary biology is to understand why patterns of genomic diversity vary among populations and species. Large-scale genomic studies of widespread species are useful for studying how the environment and demographic history shape patterns of genomic divergence, and with the continually decreasing cost of sequencing and genotyping, such studies are now becoming feasible. Here, we carry out one of the most geographically comprehensive surveys of genomic variation in a wild vertebrate to date; the great tit (Parus major) HapMap project. We screened ca 500,000 SNP markers across 647 individuals from 29 populations, spanning almost the entire geographic range of the European great tit subspecies. We found that genome-wide variation was consistent with a recent colonisation across Europe from a single refugium in South-East Europe, with bottlenecks and reduced genetic diversity in island populations. Differentiation across the genome was highly heterogeneous, with clear “islands of differentiation” even among populations with very low levels of genome-wide differentiation. Low local recombination rate in the genome was a strong predictor of high local genomic differentiation (FST), especially in island and peripheral mainland populations, suggesting that the interplay between genetic drift and recombination is a key driver of highly heterogeneous differentiation landscapes. We also detected genomic outlier regions that were confined to one or more peripheral great tit populations, most likely as a result of recent directional selection at the range edges of this species. Haplotype-based measures of selection were also related to recombination rate, albeit less strongly, and highlighted population-specific sweeps that likely resulted from positive selection. These regions under positive selection contained candidate genes associated with morphology, thermal adaptation and colouration, providing promising avenues for future investigation. Our study highlights how comprehensive screens of genomic variation in wild organisms can provide unique insights into evolution.

scholarly journals Genome-wide diversity and global migration patterns in dromedaries follow ancient caravan routes

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Sara Lado ◽  
Jean Pierre Elbers ◽  
Angela Doskocil ◽  
Davide Scaglione ◽  
Emiliano Trucchi ◽  
...  
Keyword(s):  
Demographic History ◽  
Genomic Diversity ◽  
Phylogeographic Structure ◽  
Arid Environments ◽  
Migration Patterns ◽  
Migration Rates ◽  
Global Migration ◽  
Genome Wide ◽  
A Genome ◽  
Scale Population

AbstractDromedaries have been essential for the prosperity of civilizations in arid environments and the dispersal of humans, goods and cultures along ancient, cross-continental trading routes. With increasing desertification their importance as livestock species is rising rapidly, but little is known about their genome-wide diversity and demographic history. As previous studies using few nuclear markers found weak phylogeographic structure, here we detected fine-scale population differentiation in dromedaries across Asia and Africa by adopting a genome-wide approach. Global patterns of effective migration rates revealed pathways of dispersal after domestication, following historic caravan routes like the Silk and Incense Roads. Our results show that a Pleistocene bottleneck and Medieval expansions during the rise of the Ottoman empire have shaped genome-wide diversity in modern dromedaries. By understanding subtle population structure we recognize the value of small, locally adapted populations and appeal for securing genomic diversity for a sustainable utilization of this key desert species.

scholarly journals Landscape drivers of genomic diversity and divergence in woodland Eucalyptus

2019 ◽  
Author(s):  
Kevin Murray ◽  
Jasmine Janes ◽  
Helen Bothwell ◽  
Ashley Jones ◽  
Rose Andrew ◽  
...  
Keyword(s):  
Geographic Distance ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
High Genetic Diversity ◽  
Genome Wide ◽  
Isolation By Environment ◽  
Genetic Patterns ◽  
Discrete Population ◽  
Eucalyptus Albens ◽  
Eucalyptus Sideroxylon

AbstractSpatial genetic patterns are influenced by numerous factors, and they can vary even among coexisting, closely related species due to differences in dispersal and selection. Eucalyptus (L’Héritier 1789; the “eucalypts”) are foundation tree species that provide essential habitat and modulate ecosystem services throughout Australia. Here we present a study of landscape genomic variation in two woodland eucalypt species, using whole genome sequencing of 388 individuals of Eucalyptus albens and Eucalyptus sideroxylon. We found exceptionally high genetic diversity (π ≈ 0.05) and low genome-wide, inter-specific differentiation (FST = 0.15). We found no support for strong, discrete population structure, but found substantial support for isolation by geographic distance (IBD) in both species. Using generalised dissimilarity modelling, we identified additional isolation by environment (IBE). Eucalyptus albens showed moderate IBD, and environmental variables have a small but significant amount of additional predictive power (i.e., IBE). Eucalyptus sideroxylon showed much stronger IBD, and moderate IBE. These results highlight the vast adaptive potential of these species, and set the stage for testing evolutionary hypotheses of interspecific adaptive differentiation across environments.

scholarly journals Genomic relatedness and diversity of Swedish native cattle breeds

2019 ◽  
Vol 51 (1) ◽  
Author(s):  
Maulik Upadhyay ◽  
Susanne Eriksson ◽  
Sofia Mikko ◽  
Erling Strandberg ◽  
Hans Stålhammar ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Phylogenetic Trees ◽  
Genetic Relatedness ◽  
Demographic History ◽  
Genomic Diversity ◽  
Founder Population ◽  
Southern Sweden ◽  
Cattle Breeds ◽  
Genome Wide ◽  
Native Cattle

Abstract Background Native cattle breeds are important genetic resources given their adaptation to the local environment in which they are bred. However, the widespread use of commercial cattle breeds has resulted in a marked reduction in population size of several native cattle breeds worldwide. Therefore, conservation management of native cattle breeds requires urgent attention to avoid their extinction. To this end, we genotyped nine Swedish native cattle breeds with genome-wide 150 K single nucleotide polymorphisms (SNPs) to investigate the level of genetic diversity and relatedness between these breeds. Results We used various SNP-based approaches on this dataset to connect the demographic history with the genetic diversity and population structure of these Swedish cattle breeds. Our results suggest that the Väne and Ringamåla breeds originating from southern Sweden have experienced population isolation and have a low genetic diversity, whereas the Fjäll breed has a large founder population and a relatively high genetic diversity. Based on the shared ancestry and the constructed phylogenetic trees, we identified two major clusters in Swedish native cattle. In the first cluster, which includes Swedish mountain cattle breeds, there was little differentiation among the Fjäll, Fjällnära, Swedish Polled, and Bohus Polled breeds. The second cluster consists of breeds from southern Sweden: Väne, Ringamåla and Swedish Red. Interestingly, we also identified sub-structuring in the Fjällnära breed, which indicates different breeding practices on the farms that maintain this breed. Conclusions This study represents the first comprehensive genome-wide analysis of the genetic relatedness and diversity in Swedish native cattle breeds. Our results show that different demographic patterns such as genetic isolation and cross-breeding have shaped the genomic diversity of Swedish native cattle breeds and that the Swedish mountain breeds have retained their authentic distinct gene pool without significant contribution from any of the other European cattle breeds that were included in this study.

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 Selection and gene flow define polygenic barriers between incipient butterfly species

2020 ◽  
Author(s):  
Steven M. Van Belleghem ◽  
Jared M. Cole ◽  
Gabriela Montejo-Kovacevich ◽  
Caroline N. Bacquet ◽  
W. Owen McMillan ◽  
...  
Keyword(s):  
Gene Flow ◽  
Recombination Rate ◽  
Genomic Variation ◽  
Species Boundaries ◽  
Secondary Contact ◽  
Butterfly Species ◽  
Demographic Modeling ◽  
Incipient Species ◽  
Genome Wide ◽  
Genomic Divergence

AbstractCharacterizing the genetic architecture of species boundaries remains a difficult task. Hybridizing species provide a powerful system to identify the factors that shape genomic variation and, ultimately, identify the regions of the genome that maintain species boundaries. Unfortunately, complex histories of isolation, admixture and selection can generate heterogenous genomic landscapes of divergence which make inferences about the regions that are responsible for species boundaries problematic. However, as the signal of admixture and selection on genomic loci varies with recombination rate, their relationship can be used to infer their relative importance during speciation. Here, we explore patterns of genomic divergence, admixture and recombination rate among hybridizing lineages across the Heliconius erato radiation. We focus on the incipient species, H. erato and H. himera, and distinguish the processes that drive genomic divergence across three contact zones where they frequently hybridize. Using demographic modeling and simulations, we infer that periods of isolation and selection have been major causes of genome-wide correlation patterns between recombination rate and divergence between these incipient species. Upon secondary contact, we found surprisingly highly asymmetrical introgression between the species pair, with a paucity of H. erato alleles introgressing into the H. himera genomes. We suggest that this signal may result from a current polygenic species boundary between the hybridizing lineages. These results contribute to a growing appreciation for the importance of polygenic architectures of species boundaries and pervasive genome-wide selection during the early stages of speciation with gene flow.

scholarly journals Limits and patterns of cytomegalovirus genomic diversity in humans

2015 ◽  
Vol 112 (30) ◽  
pp. E4120-E4128 ◽  
Author(s):  
Nicholas Renzette ◽  
Cornelia Pokalyuk ◽  
Laura Gibson ◽  
Bornali Bhattacharjee ◽  
Mark R. Schleiss ◽  
...  
Keyword(s):  
Human Cytomegalovirus ◽  
Recombination Rate ◽  
Natural Infection ◽  
Genomic Diversity ◽  
Regulatory Proteins ◽  
Upper Limit ◽  
Genome Wide ◽  
Low Diversity ◽  
Dna Processing

Human cytomegalovirus (HCMV) exhibits surprisingly high genomic diversity during natural infection although little is known about the limits or patterns of HCMV diversity among humans. To address this deficiency, we analyzed genomic diversity among congenitally infected infants. We show that there is an upper limit to HCMV genomic diversity in these patient samples, with ∼25% of the genome being devoid of polymorphisms. These low diversity regions were distributed across 26 loci that were preferentially located in DNA-processing genes. Furthermore, by developing, to our knowledge, the first genome-wide mutation and recombination rate maps for HCMV, we show that genomic diversity is positively correlated with these two rates. In contrast, median levels of viral genomic diversity did not vary between putatively single or mixed strain infections. We also provide evidence that HCMV populations isolated from vascular compartments of hosts from different continents are genetically similar and that polymorphisms in glycoproteins and regulatory proteins are enriched in these viral populations. This analysis provides the most highly detailed map of HCMV genomic diversity in human hosts to date and informs our understanding of the distribution of HCMV genomic diversity within human hosts.

scholarly journals A fully integrated machine learning scan of selection in the chimpanzee genome

2020 ◽  
Vol 2 (3) ◽  
Author(s):  
Jessica Nye ◽  
Mayukh Mondal ◽  
Jaume Bertranpetit ◽  
Hafid Laayouni
Keyword(s):  
Machine Learning ◽  
Positive Selection ◽  
Demographic History ◽  
Effective Population ◽  
Fully Integrated ◽  
Genome Wide ◽  
A Genome ◽  
Machine Learning Approach ◽  
History Of ◽  
The Impact

Abstract After diverging, each chimpanzee subspecies has been the target of unique selective pressures. Here, we employ a machine learning approach to classify regions as under positive selection or neutrality genome-wide. The regions determined to be under selection reflect the unique demographic and adaptive history of each subspecies. The results indicate that effective population size is important for determining the proportion of the genome under positive selection. The chimpanzee subspecies share signals of selection in genes associated with immunity and gene regulation. With these results, we have created a selection map for each population that can be displayed in a genome browser (www.hsb.upf.edu/chimp_browser). This study is the first to use a detailed demographic history and machine learning to map selection genome-wide in chimpanzee. The chimpanzee selection map will improve our understanding of the impact of selection on closely related subspecies and will empower future studies of chimpanzee.

scholarly journals Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris

2014 ◽  
Author(s):  
Gavin Douglas ◽  
Gesseca Gos ◽  
Kim Steige ◽  
Adriana Salcedo ◽  
Karl Holm ◽  
...  
Keyword(s):  
Positive Selection ◽  
Whole Genome Duplication ◽  
Gene Loss ◽  
Genome Duplication ◽  
Strong Support ◽  
Plant Evolution ◽  
Flowering Plant ◽  
Whole Genome ◽  
Widespread Species ◽  
Genome Wide

Whole genome duplication events have occurred repeatedly during flowering plant evolution, and there is growing evidence for predictable patterns of gene retention and loss following polyploidization. Despite these important insights, the rate and processes governing the earliest stages of diploidization remain poorly understood, and the relative importance of genetic drift, positive selection and relaxed purifying selection in the process of gene degeneration and loss is unclear. Here, we conduct whole genome resequencing in Capsella bursa-pastoris, a recently formed tetraploid with one of the most widespread species distributions of any angiosperm. Whole genome data provide strong support for recent hybrid origins of the tetraploid species within the last 100-300,000 years from two diploid progenitors in the Capsella genus. Major-effect inactivating mutations are frequent, but many were inherited from the parental species and show no evidence of being fixed by positive selection. Despite a lack of large-scale gene loss, we observe a decrease in the efficacy of natural selection genome-wide, due to the combined effects of demography, selfing and genome redundancy from whole genome duplication. Our results suggest that the earliest stages of diploidization are associated with quantitative genome-wide decreases in the strength and efficacy of selection rather than rapid gene loss, and that non-functionalization can receive a 'head start' through a legacy of deleterious variants and differential expression originating in parental diploid populations.

scholarly journals Genome-Wide Diversity, Population Structure and Demographic History of Dromedaries in the Central Desert of Iran

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 599 ◽  
Author(s):  
Morteza Bitaraf Sani ◽  
Javad Zare Harofte ◽  
Ahmad Bitaraf ◽  
Saeid Esmaeilkhanian ◽  
Mohammad Hossein Banabazi ◽  
...  
Keyword(s):  
Population Structure ◽  
Population Size ◽  
Balancing Selection ◽  
Demographic History ◽  
Genomic Analysis ◽  
Genotyping By Sequencing ◽  
Genomic Diversity ◽  
Nucleotide Polymorphisms ◽  
Effective Population ◽  
Genome Wide

The development of camel husbandry for good production in a desert climate is very important, thus we need to understand the genetic basis of camels and give attention to genomic analysis. We assessed genome-wide diversity, linkage disequilibrium (LD), effective population size (Ne) and relatedness in 96 dromedaries originating from five different regions of the central desert of Iran using genotyping-by-sequencing (GBS). A total of 14,522 Single Nucleotide Polymorphisms (SNPs) with an average minor allele frequency (MAF) of 0.19 passed quality control and filtering steps. The average observed heterozygosity in the population was estimated at 0.25 ± 0.03. The mean of LD at distances shorter than 40 kb was low (r2 = 0.089 ± 0.234). The camels sampled from the central desert of Iran exhibited higher relatedness than Sudanese and lower than Arabian Peninsula dromedaries. Recent Ne of Iran’s camels was estimated to be 89. Predicted Tajima’s D (1.28) suggested a bottleneck or balancing selection in dromedary camels in the central desert of Iran. A general decrease in effective and census population size poses a threat for Iran’s dromedaries. This report is the first SNP calling report on nearly the chromosome level and a first step towards understanding genomic diversity, population structure and demography in Iranian dromedaries.

scholarly journals Hybrid origins and the earliest stages of diploidization in the highly successful recent polyploid Capsella bursa-pastoris

2015 ◽  
Vol 112 (9) ◽  
pp. 2806-2811 ◽  
Author(s):  
Gavin M. Douglas ◽  
Gesseca Gos ◽  
Kim A. Steige ◽  
Adriana Salcedo ◽  
Karl Holm ◽  
...  
Keyword(s):  
Positive Selection ◽  
Large Scale ◽  
Gene Loss ◽  
Strong Support ◽  
Purifying Selection ◽  
Plant Evolution ◽  
Flowering Plant ◽  
Whole Genome ◽  
Widespread Species ◽  
Genome Wide

Whole-genome duplication (WGD) events have occurred repeatedly during flowering plant evolution, and there is growing evidence for predictable patterns of gene retention and loss following polyploidization. Despite these important insights, the rate and processes governing the earliest stages of diploidization remain poorly understood, and the relative importance of genetic drift, positive selection, and relaxed purifying selection in the process of gene degeneration and loss is unclear. Here, we conduct whole-genome resequencing in Capsella bursa-pastoris, a recently formed tetraploid with one of the most widespread species distributions of any angiosperm. Whole-genome data provide strong support for recent hybrid origins of the tetraploid species within the past 100,000–300,000 y from two diploid progenitors in the Capsella genus. Major-effect inactivating mutations are frequent, but many were inherited from the parental species and show no evidence of being fixed by positive selection. Despite a lack of large-scale gene loss, we observe a decrease in the efficacy of natural selection genome-wide due to the combined effects of demography, selfing, and genome redundancy from WGD. Our results suggest that the earliest stages of diploidization are associated with quantitative genome-wide decreases in the strength and efficacy of selection rather than rapid gene loss, and that nonfunctionalization can receive a “head start” through a legacy of deleterious variants and differential expression originating in parental diploid populations.

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