The effects of climate and demographic history in shaping genomic variation across populations of the Desert Horned Lizard ( Phrynosoma platyrhinos )

2021 ◽  
Author(s):  
Keaka Farleigh ◽  
Sarah A. Vladimirova ◽  
Christopher Blair ◽  
Jason T. Bracken ◽  
Nazila Koochekian ◽  
...  
Keyword(s):  
Demographic History ◽  
Genomic Variation ◽  
Phrynosoma Platyrhinos

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 Evolution of genomic variation in the burrowing owl in response to recent colonization of urban areas

2018 ◽  
Vol 285 (1878) ◽  
pp. 20180206 ◽  
Author(s):  
Jakob C. Mueller ◽  
Heiner Kuhl ◽  
Stefan Boerno ◽  
Jose L. Tella ◽  
Martina Carrete ◽  
...  
Keyword(s):  
Urban Areas ◽  
Demographic History ◽  
Genomic Variation ◽  
Rural Populations ◽  
Urban Habitat ◽  
Restricted Gene Flow ◽  
Athene Cunicularia ◽  
Urban Populations ◽  
Burrowing Owl ◽  
Standing Variation

When a species successfully colonizes an urban habitat it can be expected that its population rapidly adapts to the new environment but also experiences demographic perturbations. It is, therefore, essential to gain an understanding of the population structure and the demographic history of the urban and neighbouring rural populations before studying adaptation at the genome level. Here, we investigate populations of the burrowing owl ( Athene cunicularia ), a species that colonized South American cities just a few decades ago. We assembled a high-quality genome of the burrowing owl and re-sequenced 137 owls from three urban–rural population pairs at 17-fold median sequencing coverage per individual. Our data indicate that each city was independently colonized by a limited number of founders and that restricted gene flow occurred between neighbouring urban and rural populations, but not between urban populations of different cities. Using long-range linkage disequilibrium statistics in an approximate Bayesian computation approach, we estimated consistently lower population sizes in the recent past for the urban populations in comparison to the rural ones. The current urban populations all show reduced standing variation in rare single nucleotide polymorphisms (SNPs), but with different subsets of rare SNPs in different cities. This lowers the potential for local adaptation based on rare variants and makes it harder to detect consistent signals of selection in the genome.

scholarly journals Chromosome-level assembly of the Atlantic silverside genome reveals extreme levels of sequence diversity and structural genetic variation

2020 ◽  
Author(s):  
Anna Tigano ◽  
Arne Jacobs ◽  
Aryn P. Wilder ◽  
Ankita Nand ◽  
Ye Zhan ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Structural Variation ◽  
Demographic History ◽  
Genome Structure ◽  
Genomic Variation ◽  
Adaptive Divergence ◽  
Effective Population ◽  
Atlantic Silverside ◽  
A Genome ◽  
Chromosome Level

AbstractThe levels and distribution of standing genetic variation in a genome can provide a wealth of insights about the adaptive potential, demographic history, and genome structure of a population or species. As structural variants are increasingly associated with traits important for adaptation and speciation, investigating both sequence and structural variation is essential for wholly tapping this potential. Using a combination of shotgun sequencing, 10X Genomics linked reads and proximity-ligation data (Chicago and Hi-C), we produced and annotated a chromosome-level genome assembly for the Atlantic silverside (Menidia menidia) - an established ecological model for studying the phenotypic effects of natural and artificial selection - and examined patterns of genomic variation across two individuals sampled from different populations with divergent local adaptations. Levels of diversity varied substantially across each chromosome, consistently being highly elevated near the ends (presumably near telomeric regions) and dipping to near zero around putative centromeres. Overall, our estimate of the genome-wide average heterozygosity in the Atlantic silverside is the highest reported for a fish, or any vertebrate, to date (1.32-1.76% depending on inference method and sample). Furthermore, we also found extreme levels of structural variation, affecting ~23% of the total genome sequence, including multiple large inversions (> 1 Mb and up to 12.6 Mb) associated with previously identified haploblocks showing strong differentiation between locally adapted populations. These extreme levels of standing genetic variation are likely associated with large effective population sizes and may help explain the remarkable adaptive divergence among populations of the Atlantic silverside.

scholarly journals Ocean-wide genomic variation in Gray's beaked whales, Mesoplodon grayi

2021 ◽  
Vol 8 (3) ◽  
Author(s):  
M. V. Westbury ◽  
K. F. Thompson ◽  
M. Louis ◽  
A. A. Cabrera ◽  
M. Skovrind ◽  
...  
Keyword(s):  
Population Structure ◽  
Demographic History ◽  
South Australia ◽  
Population Connectivity ◽  
Genomic Variation ◽  
Suitable Habitat ◽  
Effective Population ◽  
Beaked Whales ◽  
Marine Megafauna ◽  
Demographic Patterns

The deep oceans of the Southern Hemisphere are home to several elusive and poorly studied marine megafauna. In the absence of robust observational data for these species, genetic data can aid inferences on population connectivity, demography and ecology. A previous investigation of genetic diversity and population structure in Gray's beaked whale ( Mesoplodon grayi ) from Western Australia and New Zealand found high levels of mtDNA diversity, no geographic structure and stable demographic history. To further investigate phylogeographic and demographic patterns across their range, we generated complete mitochondrial and partial nuclear genomes of 16 of the individuals previously analysed and included additional samples from South Africa ( n = 2) and South Australia ( n = 4), greatly expanding the spatial range of genomic data for the species. Gray's beaked whales are highly elusive and rarely observed, and our data represents a unique and geographically broad dataset. We find relatively high levels of diversity in the mitochondrial genome, despite an absence of population structure at the mitochondrial and nuclear level. Demographic analyses suggest these whales existed at stable levels over at least the past 1.1 million years, with an approximately twofold increase in female effective population size approximately 250 thousand years ago, coinciding with a period of increased Southern Ocean productivity, sea surface temperature and a potential expansion of suitable habitat. Our results suggest that Gray's beaked whales are likely to be resilient to near-future ecosystem changes, facilitating their conservation. Our study demonstrates the utility of low-effort shotgun sequencing in providing ecological information on highly elusive species.

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 Demography and Selection Shape Transcriptomic Divergence in Field Crickets

2017 ◽  
Author(s):  
Thomas Blankers ◽  
Sibelle T. Vilaça ◽  
Isabelle Waurick ◽  
David A. Gray ◽  
R. Matthias Hennig ◽  
...  
Keyword(s):  
Gene Flow ◽  
Mating Behavior ◽  
Genetic Divergence ◽  
Demographic History ◽  
Strong Support ◽  
Genomic Variation ◽  
Field Cricket ◽  
History Of ◽  
Gryllus Rubens ◽  
Genetic Signatures

ABSTRACTGene flow, demography, and selection can result in similar patterns of genomic variation and disentangling their effects is key to understanding speciation. Here, we assess transcriptomic variation to unravel the evolutionary history of Gryllus rubens and Gryllus texensis, cryptic field cricket species with highly divergent mating behavior. We infer their demographic history and screen their transcriptomes for footprints of selection in the context of the inferred demography. We find strong support for a long history of bidirectional gene flow, which ceased during the late Pleistocene, and a bottleneck in G. rubens consistent with a peripatric origin of this species. Importantly, the demographic history has likely strongly shaped patterns of neutral genetic differentiation (empirical FST distribution). Concordantly, FST based selection detection uncovers a large number of outliers, likely comprising many false positives, echoing recent theoretical insights. Alternative genetic signatures of positive selection, informed by the demographic history of the sibling species, highlighted a smaller set of loci; many of these are candidates for controlling variation in mating behavior. Our results underscore the importance of demography in shaping overall patterns of genetic divergence and highlight that examining both demography and selection facilitates a more complete understanding of genetic divergence during speciation.

scholarly journals Analysis of 427 genomes reveals moso bamboo population structure and genetic basis of property traits

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Hansheng Zhao ◽  
Shuai Sun ◽  
Yulong Ding ◽  
Yue Wang ◽  
Xianghua Yue ◽  
...  
Keyword(s):  
Balancing Selection ◽  
Demographic History ◽  
Small Population ◽  
Moso Bamboo ◽  
Genomic Variation ◽  
Nucleotide Polymorphisms ◽  
Phylogenetic Groups ◽  
Low Genetic Diversity ◽  
Genetic Mechanisms ◽  
Whole Genome Resequencing

AbstractMoso bamboo (Phyllostachys edulis) is an economically and ecologically important nontimber forestry species. Further development of this species as a sustainable bamboo resource has been hindered by a lack of population genome information. Here, we report a moso bamboo genomic variation atlas of 5.45 million single-nucleotide polymorphisms (SNPs) from whole-genome resequencing of 427 individuals covering 15 representative geographic areas. We uncover low genetic diversity, high genotype heterozygosity, and genes under balancing selection underlying moso bamboo population adaptation. We infer its demographic history with one bottleneck and its recently small population without a rebound. We define five phylogenetic groups and infer that one group probably originated by a single-origin event from East China. Finally, we conduct genome-wide association analysis of nine important property-related traits to identify candidate genes, many of which are involved in cell wall, carbohydrate metabolism, and environmental adaptation. These results provide a foundation and resources for understanding moso bamboo evolution and the genetic mechanisms of agriculturally important traits.

scholarly journals Genetic variation in Pan species is shaped by demographic history and underlies lineage-specific functions

2018 ◽  
Author(s):  
Sojung Han ◽  
Aida M. Andrés ◽  
Tomas Marques-Bonet ◽  
Martin Kuhlwilm
Keyword(s):  
Genetic Variation ◽  
Pan Paniscus ◽  
Demographic History ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Age At Menarche ◽  
Rapid Decline ◽  
Female Reproduction ◽  
Effective Population ◽  
Physiological Differences

AbstractChimpanzees (Pan troglodytes) and bonobos (Pan paniscus) are the closest living relatives of humans, but they show distinct behavioral and physiological differences, particularly regarding female reproduction. Despite their recent rapid decline, the demographic histories of the two species have been different during the past one to two million years, likely having an impact on their genomic diversity. Here, we analyze the inferred functional consequences of genetic variation across 69 individuals, making use of the most complete dataset of genomic variation in the Pan clade to date. We test to which extent the demographic history influences the efficacy of purifying selection in these species. We find that small historical effective population sizes (Ne) correlate not only with small genetic diversity, but also with more homozygous deleterious alleles, and an increased proportion of deleterious changes at low frequencies. Furthermore, we exploit the catalog of deleterious protein-coding changes on each lineage to investigate the putative genetic basis for phenotypic differences between chimpanzees and bonobos. We show that bonobo-specific non-synonymous changes are enriched in genes related to age at menarche in humans, suggesting that the prominent physiological differences in the female reproductive system between chimpanzees and bonobos might be explained, in part, by putatively adaptive changes on the bonobo lineage.

scholarly journals Characterizing the demographic history and prion protein variation to infer susceptibility to chronic wasting disease in a naïve population of white-tailed deer (Odocoileus virginianus)

2020 ◽  
Author(s):  
Sarah E Haworth ◽  
Larissa Nituch ◽  
Joseph M Northrup ◽  
Aaron BA Shafer
Keyword(s):  
High Throughput Sequencing ◽  
Chronic Wasting Disease ◽  
Demographic History ◽  
Population Expansion ◽  
Prnp Gene ◽  
Economic Benefits ◽  
Genomic Variation ◽  
Allele Frequencies ◽  
Wasting Disease ◽  
Tissue Samples

AbstractAssessments of the adaptive potential in natural populations are essential for understanding and predicting responses to environmental stressors like climate change and infectious disease. Species face a range of stressors in human-dominated landscapes, often with contrasting effects. White-tailed deer (deer) are expanding in the northern part of their range following decreasing winter severity and increasing forage availability. Chronic wasting disease (CWD), a prion disease affecting cervids, is likewise expanding and represents a major threat to deer and other cervids. We obtained tissue samples from free-ranging deer across their native range in Ontario, Canada which has yet to detect CWD in wild populations of cervids. We used high-throughput sequencing to assess neutral genomic variation, and variation in the PRNP gene that is partly responsible for the protein misfolding when deer contract CWD. Neutral variation revealed a high number of rare alleles and no population structure, and demographic models suggested a rapid historical population expansion. Allele frequencies of PRNP variants associated with CWD susceptibility and disease progression were evenly distributed across the landscape and consistent with deer populations not infected with CWD. We then estimated the selection coefficient of CWD, with simulations showing an observable and rapid shift in PRNP allele frequencies that coincides with the start of a novel CWD epidemic. Sustained surveillance of genomic and PRNP variation can be a useful tool for CWD-free regions where deer are managed for ecological and economic benefits.

EVALUATION OF PTYCHOBOTHRIDEAN CESTODES USING RANDOM AMPLIFIED POLYMORPHIC DNA (RAPD) MARKERS FROM FRESH WATER FISHES IN GODAVARI BASIN (M.S.) INDIA

2017 ◽  
Vol 23 (2) ◽  
Author(s):  
SUNITA BORDE ◽  
ASAWARI FARTADE ◽  
AMOL THOSAR ◽  
RAHUL KHAWAL
Keyword(s):  
Fresh Water ◽  
Rapd Markers ◽  
Random Amplified Polymorphic Dna ◽  
Band Pattern ◽  
Genomic Variation ◽  
Polymorphic Band ◽  
Rapd Profile ◽  
Band Size ◽  
Pcr Product ◽  
The Common

Ptychobothridean genera like Senga and Circumoncobothrium are the common parasites of fresh water fishes. The genotypic study of these parasites was taken by RAPD. The RAPD profile of these two parasites were not similar to each other as depicted by the band pattern in picture. These results suggest the presence of inter-specific polymorphism among cestode parasites of two different genera for RAPD analysis. The present study demonstrated that genetic differentiation of cestode parasites could be accomplished on the basis of genomic variation with polymorphic band pattern using RAPD. All the detected bands (PCR product) were polymorphic and band size ranged from 500-5000 bp in length. The RAPD of profiles using GBO-31, GBO-32, GBO-33, GBO-34, GBO-35 and GBO-36. Primers were able to characterize inter-specific polymorphism among the two genus ( Senga and Circumoncobothrium ). Genetic analysis suggests that Senga and Circumoncobothrium show genetic diversity with respect to RAPD patterns using all the six primers used for the present study. The genetic distance between the analyzed genuses ranged from 0.14 to 0.80. The differentiation of the two parasites on the basis of genetic markers could greatly facilitate study on the biology of these parasites.

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