scholarly journals Population genomics of the Anthropocene: urbanization is negatively associated with genome-wide variation in white-footed mouse populations

2015 ◽  
Author(s):  
Jason Munshi-South ◽  
Christine P Zolnik ◽  
Stephen E Harris
Keyword(s):  
Population Genomics ◽  
Isolation By Distance ◽  
Impervious Surface ◽  
Snp Markers ◽  
Environment Modeling ◽  
Evolutionary Potential ◽  
Animal Populations ◽  
Genome Wide ◽  
Isolation By Environment ◽  
White Footed Mouse

Urbanization results in pervasive habitat fragmentation and reduces standing genetic variation through bottlenecks and drift. Loss of genome-wide variation may ultimately reduce the evolutionary potential of animal populations experiencing rapidly changing conditions. In this study, we examined genome-wide variation among 23 white-footed mouse (Peromyscus leucopus) populations sampled along an urbanization gradient in the New York City metropolitan area. Genome-wide variation was estimated as a proxy for evolutionary potential using more than 10,000 SNP markers generated by ddRAD-Seq. We found that genome-wide variation is inversely related to urbanization as measured by percent impervious surface cover, and to a lesser extent, human population density. We also report that urbanization results in enhanced genome-wide differentiation between populations in cities. There was no pattern of isolation by distance among these populations, but an isolation by resistance model based on impervious surface significantly explained patterns of genetic differentiation. Isolation by environment modeling also indicated that urban populations deviate much more strongly from global allele frequencies than suburban or rural populations. This study is the first to examine loss of genome-wide SNP variation along an urban-to-rural gradient and quantify urbanization as a driver of population genomic patterns.

scholarly journals First genome-wide analysis of an endangered lichen reveals isolation by distance and strong population structure

2017 ◽  
Author(s):  
Jessica L. Allen ◽  
Sean K. McKenzie ◽  
Robin S. Sleith ◽  
S. Elizabeth Alter
Keyword(s):  
Genetic Diversity ◽  
Population Genomics ◽  
Isolation By Distance ◽  
Geographic Distance ◽  
Distribution Models ◽  
Extrinsic Factors ◽  
Biogeographic Patterns ◽  
Ecological Requirements ◽  
Genome Wide ◽  
Isolation By Environment

AbstractLichenized fungi are evolutionarily diverse and ecologically important, but little is known about the processes driving diversification and genetic differentiation in these lineages. Though few studies have examined population genetic patterns in lichens, their geographic distributions are often assumed to be wholly shaped by ecological requirements rather than dispersal limitations. Furthermore, while their reproductive structures are observable, the lack of information about recombination mechanisms and rates can make inferences about reproductive strategies difficult. Here we investigate the population genomics ofCetradonia linearis, an endangered lichen narrowly endemic to the southern Appalachians of eastern North America, to test the relative contributions of environmental factors and geographic distance in shaping genetic structure, and to gain insights into the demography and reproductive biology of range restricted fungi. Analysis of genome-wide SNP data indicated strong evidence for both low rates of recombination and for strong isolation by distance, but did not support isolation by environment. Hindcast species distribution models and the spatial distribution of genetic diversity also suggested thatC. linearishad a larger range during the last glacial maximum, especially in the southern portion of its current extent, consistent with previous findings in other southern Appalachian taxa. These results contribute to our understanding of intrinsic and extrinsic factors shaping genetic diversity and biogeographic patterns inC. linearis, and more broadly, in rare and endangered fungi.

scholarly journals Population Genomic Analysis of Two Endemic Schizothoracins Reveals Their Genetic Differences and Underlying Selection Associated with Altitude and Temperature

Animals ◽  
2020 ◽  
Vol 10 (3) ◽  
pp. 447
Author(s):  
Tianyan Yang ◽  
Wei Meng ◽  
Baocheng Guo
Keyword(s):  
Mixed Model ◽  
Isolation By Distance ◽  
Genomic Analysis ◽  
Principal Component ◽  
Mantel Test ◽  
Tibet Plateau ◽  
Tarim River ◽  
Genome Wide ◽  
Isolation By Environment ◽  
Kaidu River

Schizothoracins are a group of cyprinid fishes distributed throughout the Qinghai–Tibet Plateau, which can be classified in three grades: primitive, specialised and highly specialised according to adaptation ability to plateau environments. As the only specialised schizothoracins in Xinjiang, China, Diptychus maculates and Gymnodiptychus dybowskii are ideal materials for adaptive evolution research. Based on single-nucleotide polymorphism (SNP) loci detected by specific-locus amplified fragment (SLAF) technology, the genome-wide genetic diversities of these two species from nine sites in Xinjiang were evaluated. D.maculates in the Muzat River (BM) and G. dybowskii in the Kaidu River (LKG) presented the lowest genetic diversity levels, whereas D. maculates in the Kumarik River (BK) and G.dybowskii in the Kashi River (LK) were just the opposite. Cluster and principal component analysis demonstrated a distant genetic affinity between D. maculates in the Tashkurgan River (BT) and other populations. Outlier SNP loci were discovered both in D. maculates and G. dybowskii. The coalescent Bayenv and latent factor mixed model (LFMM) methods showed that a total of thirteen and eighteen SNPs in D. maculates were associated with altitude and temperature gradient, respectively. No intersection was revealed in G. dybowskii. The results indicated that D. maculates was subject to much greater divergent selection pressure. A strong signal of isolation-by-distance (IBD) was detected across D. maculates (Mantel test, rs = 0.65; p = 0.05), indicating an evident geographical isolation in the Tarim River. Isolation-by-environment (IBE) analysis implied that temperature and altitude selections were more intensive in D. maculates, with greater environmental variation resulting in weak gene flow.

scholarly journals Population structure, adaptation and divergence of the meadow spittlebug, Philaenus spumarius (Hemiptera, Aphrophoridae), revealed by genomic and morphological data

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11425
Author(s):  
Sofia G. Seabra ◽  
Ana S.B. Rodrigues ◽  
Sara E. Silva ◽  
Ana Carina Neto ◽  
Francisco Pina-Martins ◽  
...  
Keyword(s):  
Gene Flow ◽  
Western Europe ◽  
Population Genomics ◽  
Isolation By Distance ◽  
Plant Diseases ◽  
Morphological Data ◽  
Philaenus Spumarius ◽  
Mitochondrial Coi ◽  
Temperature And Precipitation ◽  
Genome Wide

Understanding patterns of population differentiation and gene flow in insect vectors of plant diseases is crucial for the implementation of management programs of disease. We investigated morphological and genome-wide variation across the distribution range of the spittlebug Philaenus spumarius (Linnaeus, 1758) (Hemiptera, Auchenorrhyncha, Aphrophoridae), presently the most important vector of the plant pathogenic bacterium Xylella fastidiosa Wells et al., 1987 in Europe. We found genome-wide divergence between P. spumarius and a very closely related species, P. tesselatus Melichar, 1899, at RAD sequencing markers. The two species may be identified by the morphology of male genitalia but are not differentiated at mitochondrial COI, making DNA barcoding with this gene ineffective. This highlights the importance of using integrative approaches in taxonomy. We detected admixture between P. tesselatus from Morocco and P. spumarius from the Iberian Peninsula, suggesting gene-flow between them. Within P. spumarius, we found a pattern of isolation-by-distance in European populations, likely acting alongside other factors restricting gene flow. Varying levels of co-occurrence of different lineages, showing heterogeneous levels of admixture, suggest other isolation mechanisms. The transatlantic populations of North America and Azores were genetically closer to the British population analyzed here, suggesting an origin from North-Western Europe, as already detected with mitochondrial DNA. Nevertheless, these may have been produced through different colonization events. We detected SNPs with signatures of positive selection associated with environmental variables, especially related to extremes and range variation in temperature and precipitation. The population genomics approach provided new insights into the patterns of divergence, gene flow and adaptation in these spittlebugs and led to several hypotheses that require further local investigation.

scholarly journals Environmental and geographic data optimize ex situ collections and the preservation of adaptive evolutionary potential

2020 ◽  
Author(s):  
Lionel N. Di Santo ◽  
Jill A. Hamilton
Keyword(s):  
Genetic Variation ◽  
Genetic Differentiation ◽  
Plant Species ◽  
Isolation By Distance ◽  
Allelic Diversity ◽  
Genetic Data ◽  
Ex Situ ◽  
Evolutionary Potential ◽  
Isolation By Environment ◽  
The Impact

AbstractMaintenance of biodiversity, through seed banks and botanical gardens where the wealth of species’ genetic variation may be preserved ex situ, is a major goal of conservation. However, challenges can persist in optimizing ex situ collections where trade-offs exist between expense, effort, and conserving species evolutionary potential, particularly when genetic data is not available. Within this context, we evaluate the genetic consequences of guiding population preservation using geographic (isolation-by-distance, IBD) and environmental (isolation-by-environment, IBE) data for ex situ collections where provenance data is available. We use 19 genetic and genomic datasets from 15 plant species to (i) assess the proportion of population genetic differentiation explained by geographic and environmental factors, and (ii) simulate ex situ collections prioritizing source populations based on pairwise geographic or environmental distances. Specifically, we test the impact prioritizing sampling based on environmental and geographic distances may have on capturing neutral, functional or putatively adaptive genetic diversity and differentiation. We find that collectively IBD and IBE explain a substantial proportion of genetic differences among functional (median 45%) and adaptive (median 71%) loci, but not for neutral loci (median 21.5%). Simulated ex situ collections reveal that inclusion of IBD and IBE increases both allelic diversity and genetic differentiation captured among populations, particularly for loci that may be important for adaptation. Thus, prioritizing population collections using environmental and geographic distance data can impact genetic variation captured ex situ. This provides value for the vast majority of plant species for which we have no genetic data, informing conservation of genetic variation needed to maintain evolutionary potential within collections.

Comparison of kinship estimates in Santa Inês sheep using microsatellite and genome-wide SNP markers

2021 ◽  
pp. 106399
Author(s):  
Alzira Regina Silva de Deus ◽  
Geice Ribeiro Silva ◽  
Luciano Silva Sena ◽  
Fábio Barros Britto ◽  
Débora Araújo de Carvalho ◽  
...  
Keyword(s):  
Snp Markers ◽  
Genome Wide ◽  
Santa Inês

scholarly journals Genome wide association analyses to understand genetic basis of flowering and plant height under three levels of nitrogen application in Brassica juncea (L.) Czern & Coss

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Javed Akhatar ◽  
Anna Goyal ◽  
Navneet Kaur ◽  
Chhaya Atri ◽  
Meenakshi Mittal ◽  
...  
Keyword(s):  
Plant Height ◽  
Indian Subcontinent ◽  
Association Studies ◽  
Snp Markers ◽  
Genome Wide Association ◽  
Strong Interactions ◽  
N Availability ◽  
Oilseed Crop ◽  
Genome Wide Association Studies ◽  
Genome Wide

AbstractTimely transition to flowering, maturity and plant height are important for agronomic adaptation and productivity of Indian mustard (B. juncea), which is a major edible oilseed crop of low input ecologies in Indian subcontinent. Breeding manipulation for these traits is difficult because of the involvement of multiple interacting genetic and environmental factors. Here, we report a genetic analysis of these traits using a population comprising 92 diverse genotypes of mustard. These genotypes were evaluated under deficient (N75), normal (N100) or excess (N125) conditions of nitrogen (N) application. Lower N availability induced early flowering and maturity in most genotypes, while high N conditions delayed both. A genotyping-by-sequencing approach helped to identify 406,888 SNP markers and undertake genome wide association studies (GWAS). 282 significant marker-trait associations (MTA's) were identified. We detected strong interactions between GWAS loci and nitrogen levels. Though some trait associated SNPs were detected repeatedly across fertility gradients, majority were identified under deficient or normal levels of N applications. Annotation of the genomic region (s) within ± 50 kb of the peak SNPs facilitated prediction of 30 candidate genes belonging to light perception, circadian, floral meristem identity, flowering regulation, gibberellic acid pathways and plant development. These included over one copy each of AGL24, AP1, FVE, FRI, GID1A and GNC. FLC and CO were predicted on chromosomes A02 and B08 respectively. CDF1, CO, FLC, AGL24, GNC and FAF2 appeared to influence the variation for plant height. Our findings may help in improving phenotypic plasticity of mustard across fertility gradients through marker-assisted breeding strategies.

scholarly journals Genome-Wide SNP Markers Based on SLAF-Seq Uncover Breeding Traces in Rapeseed (Brassica napus L.)

2017 ◽  
Vol 8 ◽  
Author(s):  
Qinghong Zhou ◽  
Can Zhou ◽  
Wei Zheng ◽  
Annaliese S. Mason ◽  
Shuying Fan ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Snp Markers ◽  
Brassica Napus L ◽  
Genome Wide

scholarly journals A publicly available repository of ROH islands reveals signatures of selection in different livestock and pet species

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Wim Gorssen ◽  
Roel Meyermans ◽  
Steven Janssens ◽  
Nadine Buys
Keyword(s):  
Association Studies ◽  
Genome Wide Association Studies ◽  
Single Nucleotide ◽  
Future Studies ◽  
Snp Data ◽  
Animal Populations ◽  
Genome Wide ◽  
Starting Point ◽  
Different Populations ◽  
Signatures Of Selection

Abstract Background Runs of homozygosity (ROH) have become the state-of-the-art method for analysis of inbreeding in animal populations. Moreover, ROH are suited to detect signatures of selection via ROH islands and are used in other applications, such as genomic prediction and genome-wide association studies (GWAS). Currently, a vast amount of single nucleotide polymorphism (SNP) data is available online, but most of these data have never been used for ROH analysis. Therefore, we performed a ROH analysis on large medium-density SNP datasets in eight animal species (cat, cattle, dog, goat, horse, pig, sheep and water buffalo; 442 different populations) and make these results publicly available. Results The results include an overview of ROH islands per population and a comparison of the incidence of these ROH islands among populations from the same species, which can assist researchers when studying other (livestock) populations or when looking for similar signatures of selection. We were able to confirm many known ROH islands, for example signatures of selection for the myostatin (MSTN) gene in sheep and horses. However, our results also included multiple other ROH islands, which are common to many populations and not identified to date (e.g. on chromosomes D4 and E2 in cats and on chromosome 6 in sheep). Conclusions We are confident that our repository of ROH islands is a valuable reference for future studies. The discovered ROH island regions represent a unique starting point for new studies or can be used as a reference for future studies. Furthermore, we encourage authors to add their population-specific ROH findings to our repository.

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