Genome‐wide epigenetic isolation by environment in a widespread
            Anolis
            lizard

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.

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Low genome-wide divergence between two lizard populations with high adaptive phenotypic differentiation

10.22541/au.163250123.31170409/v1 ◽

2021 ◽

Author(s):

Alejandro Llanos-Garrido ◽

Javier Pérez-Tris ◽

José Díaz

Keyword(s):

Local Adaptation ◽

Genetic Divergence ◽

Elevational Gradient ◽

Phenotypic Differentiation ◽

Genome Wide ◽

Isolation By Environment ◽

Psammodromus Algirus ◽

Low Levels ◽

Two Populations ◽

Degree Of Isolation

Usually, adaptive phenotypic differentiation is paralleled by genetic divergence between locally adapted populations. However, adaptation can also happen in a scenario of non-significant genetic divergence due to intense gene flow and/or recent differentiation. While this phenomenon is rarely published, findings on incipient ecologically-driven divergence or isolation by adaptation are relatively common, which could confound our understanding about the frequency at which they actually occur in nature. Here, we explore genome-wide traces of divergence between two populations of the lacertid lizard Psammodromus algirus separated by a 600 m elevational gradient. These populations seem to be differentially adapted to their environments despite showing low levels of genetic differentiation (according to previously studies of mtDNA and microsatellite data). We performed a search for outliers (i.e. loci subject to selection) trying to identify specific loci with FST statistics significantly higher than those expected on the basis of overall, genome-wide estimates of genetic divergence. We find that local phenotypic adaptation (in terms of a wide diversity of characters) was not accompanied by genome-wide differentiation, even when we maximized the chances of unveiling such differentiation at particular loci with FST-based outlier detection tests. Instead, our analyses confirmed the lack of differentiation on the basis of more than 70,000 SNPs, which is concordant with a scenario of local adaptation without any degree of isolation by environment. Our results add evidence to previous studies in which local adaptation does not lead to any kind of isolation (or early stages of ecological speciation), but maintains phenotypic divergence despite the lack of a differentiated genomic background.

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

Animals ◽

10.3390/ani10030447 ◽

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.

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Panmixia across elevation in thermally sensitive Andean dung beetles

10.1101/783233 ◽

2019 ◽

Author(s):

Ethan Linck ◽

Jorge E. Celi ◽

Kimberly S. Sheldon

Keyword(s):

Thermal Tolerance ◽

Climatic Variability ◽

Geographic Distance ◽

Dung Beetles ◽

Range Limits ◽

Realized Niche ◽

Physiological Constraints ◽

Snp Data ◽

Genome Wide ◽

Isolation By Environment

AbstractJanzen’s seasonality hypothesis predicts that organisms inhabiting environments with limited climatic variability will evolve a reduced thermal tolerance breadth compared with organisms experiencing greater climatic variability. In turn, narrow tolerance breadth may select against dispersal across strong temperature gradients, such as those found across elevation. This can result in narrow elevational ranges and generate a pattern of isolation-by-environment, or neutral genetic differentiation correlated with environmental variables that is independent of geographic distance. We tested for signatures of isolation-by-environment across elevation using genome-wide SNP data from five species of Andean dung beetles (subfamily Scarabaeinae) with well-characterized, narrow thermal physiologies and narrow elevational distributions. Contrary to our expectations, we found no evidence of population genetic structure associated with elevation and little signal of isolation- by-environment. Further, elevational ranges for four of five species appear to be at equilibrium and show no evidence of demographic constraints at range limits. Taken together, these results suggest physiological constraints on dispersal may primarily operate outside of a stable realized niche.Abstract Figure

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

10.1101/025007 ◽

2015 ◽

Cited By ~ 2

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.

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

10.1101/237164 ◽

2017 ◽

Cited By ~ 2

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.

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