Gene flow increases fitness at the warm edge of a species' range

The field of landscape genetics relates habitat features and genetic information to infer dispersal and genetic connectivity between populations or individuals distributed across a landscape. Such studies usually focus on a small portion of a species range, and the degree to which these geographically restricted results can be extrapolated to different areas of a species range remains poorly understood. Studies that have focused on spatial replication in landscape genetics processes either evaluate a small number of sites, are informed by a small set of genetic markers, analyze only a small subset of environmental variables, or implement models that do not fully explore parameter space. Here, we used a broadly distributed ectothermic lizard (Sceloporus occidentalis, Western Fence lizard) as a model species to evaluate the full role of topography, climate, vegetation, and roads on dispersal and genetic differentiation. We conducted landscape genetics analyses in five areas within the Sierra Nevada mountain range, using thousands of ddRAD genetic markers distributed across the genome, implemented in the landscape genetics program ResistanceGA. Across study areas, we found a great deal of consistency in the variables impacting genetic connectivity, but also noted site-specific differences in the factors in each study area. High-elevation colder areas were consistently found to be barriers to gene flow, as were areas of high ruggedness and slope. High temperature seasonality and high precipitation during the winter wet season also presented a substantial barrier to gene flow in a majority of study areas. The effect of other landscape variables on genetic differentiation was more idiosyncratic and depended on specific attributes at each site. Vegetation type was found to substantially affect gene flow only in the southernmost Sequoia site, likely due to a higher proportion of desert habitat here, thereby fragmenting habitats that have lower costs to dispersal. The effect of roads also varied between sites and may be related to differences in road usage and amount of traffic in each area. Across study areas, canyons were always substantially implicated as facilitators to dispersal and key features linking populations and maintaining genetic connectivity across landscapes. We emphasize that spatial data layers are complex and multidimensional, and a careful consideration of associations between variables is vital to form sound conclusions about the critical factors affecting dispersal and genetic connectivity across space.

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Genomic assessment of local adaptation in dwarf birch to inform assisted gene flow

10.1101/727156 ◽

2019 ◽

Author(s):

James S. Borrell ◽

Jasmin Zohren ◽

Richard A. Nichols ◽

Richard J. A. Buggs

Keyword(s):

Climate Change ◽

Gene Flow ◽

Local Adaptation ◽

Environmental Variables ◽

Allele Frequencies ◽

Species Range ◽

Conservation Action ◽

Mean Temperature ◽

Diurnal Range ◽

Dwarf Birch

AbstractWhen populations of a rare species are small, isolated and declining under climate change, some populations may become locally maladapted. Detecting this maladaptation may allow effective rapid conservation interventions, even if based on incomplete knowledge. Population maladaptation may be estimated by finding genome-environment associations (GEA) between allele frequencies and environmental variables across a local species range, and identifying populations whose allele frequencies do not fit with these trends. We can then design assisted gene flow strategies for maladapted populations, to adjust their allele frequencies, entailing lower levels of intervention than with undirected conservation action. Here, we investigate this strategy in Scottish populations of the montane plant dwarf birch (Betula nana). In genome-wide single nucleotide polymorphism (SNP) data we found 267 significant associations between SNP loci and environmental variables. We ranked populations by maladaptation estimated using allele frequency deviation from the general trends at these loci; this gave a different prioritization for conservation action than the Shapely Index, which seeks to preserve rare neutral variation. Populations estimated to be maladapted in their allele frequencies at loci associated with annual mean temperature were found to have reduced catkin production. Using an environmental niche modelling (ENM) approach, we found annual mean temperature (35%), and mean diurnal range (15%), to be important predictors of the dwarf birch distribution. Intriguingly, there was a significant correlation between the number of loci associated with each environmental variable in the GEA, and the importance of that variable in the ENM. Together, these results suggest that the same environmental variables determine both adaptive genetic variation and species range in Scottish dwarf birch. We suggest an assisted gene flow strategy that aims to maximize the local adaptation of dwarf birch populations under climate change by matching allele frequencies to current and future environments.

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Gene swamping alters evolution during range expansions in the protist Tetrahymena thermophila

Biology Letters ◽

10.1098/rsbl.2020.0244 ◽

2020 ◽

Vol 16 (6) ◽

pp. 20200244

Author(s):

Felix Moerman ◽

Emanuel A. Fronhofer ◽

Andreas Wagner ◽

Florian Altermatt

Keyword(s):

Genetic Variation ◽

Gene Flow ◽

Tetrahymena Thermophila ◽

Species Range ◽

Ph Gradient ◽

Life History Strategies ◽

Range Edge ◽

Asymmetric Dispersal ◽

Accelerated Evolution ◽

Range Core

At species’ range edges, individuals often face novel environmental conditions that may limit range expansion until populations adapt. The potential to adapt depends on genetic variation upon which selection can act. However, populations at species’ range edges are often genetically depauperate. One mechanism increasing genetic variation is reshuffling existing variation through sex. Sex, however, can potentially limit adaptation by breaking up existing beneficial allele combinations (recombination load). The gene swamping hypothesis predicts this is specifically the case when populations expand along an abiotic gradient and asymmetric dispersal leads to numerous maladapted dispersers from the range core swamping the range edge. We used the ciliate Tetrahymena thermophila as a model for testing the gene swamping hypothesis. We performed replicated range expansions in landscapes with or without a pH-gradient, while simultaneously manipulating the occurrence of gene flow and sexual versus asexual reproduction. We show that sex accelerated evolution of local adaptation in the absence of gene flow, but hindered it in the presence of gene flow. However, sex affected adaptation independently of the pH-gradient, indicating that both abiotic gradients and the biotic gradient in population density lead to gene swamping. Overall, our results show that gene swamping alters adaptation in life-history strategies.

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Genomic signatures of spatially divergent selection at clownfish range margins

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2021.0407 ◽

2021 ◽

Vol 288 (1952) ◽

pp. 20210407

Author(s):

René D. Clark ◽

Matthew L. Aardema ◽

Peter Andolfatto ◽

Paul H. Barber ◽

Akihisa Hattori ◽

...

Keyword(s):

Gene Flow ◽

Candidate Genes ◽

Local Adaptation ◽

Genetic Drift ◽

Divergent Selection ◽

Species Range ◽

Evolutionary Forces ◽

The Core ◽

Range Edge ◽

Genomic Signatures

Understanding how evolutionary forces interact to drive patterns of selection and distribute genetic variation across a species' range is of great interest in ecology and evolution, especially in an era of global change. While theory predicts how and when populations at range margins are likely to undergo local adaptation, empirical evidence testing these models remains sparse. Here, we address this knowledge gap by investigating the relationship between selection, gene flow and genetic drift in the yellowtail clownfish, Amphiprion clarkii, from the core to the northern periphery of the species range. Analyses reveal low genetic diversity at the range edge, gene flow from the core to the edge and genomic signatures of local adaptation at 56 single nucleotide polymorphisms in 25 candidate genes, most of which are significantly correlated with minimum annual sea surface temperature. Several of these candidate genes play a role in functions that are upregulated during cold stress, including protein turnover, metabolism and translation. Our results illustrate how spatially divergent selection spanning the range core to the periphery can occur despite the potential for strong genetic drift at the range edge and moderate gene flow from the core populations.

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Population and phylogenetic analysis of the cinnamoyl coA reductase gene in Eucalyptus globulus (Myrtaceae)

Australian Journal of Botany ◽

10.1071/bt04195 ◽

2005 ◽

Vol 53 (8) ◽

pp. 827 ◽

Cited By ~ 17

Author(s):

Gay E. McKinnon ◽

Brad M. Potts ◽

Dorothy A. Steane ◽

René E. Vaillancourt

Keyword(s):

Phylogenetic Analysis ◽

Gene Flow ◽

Eucalyptus Globulus ◽

Incomplete Lineage Sorting ◽

Restriction Analysis ◽

Species Range ◽

Phylogeographic Structure ◽

Cinnamoyl Coa Reductase ◽

Haplotypic Diversity ◽

Coa Reductase

Low-copy number nuclear genes are currently emerging as new markers for phylogenetic and phylogeographic analysis. This study used the single-copy gene for cinnamoyl coA reductase (CCR) to gain insights into the evolutionary history of the forest tree Eucalyptus globulus Labill. (subgenus Symphyomyrtus, section Maidenaria). A population analysis based on CCR restriction fragments from E. globulus was combined with a phylogenetic analysis of 1.5 kb of CCR sequence from the major haplotypes. Two highly divergent CCR lineages were found in E. globulus. One lineage was prominent throughout the species’ range and was identified in 16 other Maidenaria species by restriction analysis. The second lineage, which was prominent in the northern part of the species’ range, was found only in species of the E. globulus complex and surprisingly showed homology to CCR from Eucalyptus saligna Smith (subgenus Symphyomyrtus, section Latoangulatae). This finding may reflect either incomplete lineage sorting in CCR, or reticulate evolution. No statistically significant phylogeographic structure (geographic clustering of closely related haplotypes) was detected. However, patterns of CCR haplotypic diversity were congruent with patterns of chloroplast DNA diversity in several respects, and divided the range of E. globulus into four regions, supporting (1) former gene flow between King Island and western Tasmania, (2) gene flow between northern Tasmania, the Furneaux Group and Victoria, and (3) a genetic disjunction between north-eastern and south-eastern Tasmania, consistent with separate histories for these two regions.

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Gene swamping alters evolution during range expansions in the protist Tetrahymena thermophila

10.1101/863340 ◽

2019 ◽

Author(s):

Felix Moerman ◽

Emanuel A. Fronhofer ◽

Andreas Wagner ◽

Florian Altermatt

Keyword(s):

Genetic Variation ◽

Gene Flow ◽

Tetrahymena Thermophila ◽

Species Range ◽

Ph Gradient ◽

Life History Strategies ◽

Range Edge ◽

Asymmetric Dispersal ◽

Accelerated Evolution ◽

Range Core

AbstractAt species’ range edges, individuals often face novel environmental conditions that may limit range expansion until populations adapt. The potential to adapt depends on genetic variation upon which selection can act. However, populations at species’ range edges are often genetically depauperated. One mechanism to increase genetic variation is to reshuffle existing variation through sex. During range expansions, sex can, however, act as a double-edged sword. The gene swamping hypothesis predicts that for populations expanding along an abiotic gradient, sex can hinder adaptation if asymmetric dispersal leads to numerous maladapted dispersers from the range core swamping the range edge. In this study, we experimentally tested the gene swamping hypothesis by performing replicated range expansions in landscapes with or without an abiotic pH-gradient, using the ciliate Tetrahymena thermophila, while simultaneously manipulating the occurrence of gene flow and sex. We show that sex accelerated evolution of local adaptation in the absence of gene flow, but hindered it in the presence of gene flow. The effect of sex, however, was independent of the pH-gradient, indicating that not only abiotic gradients but also the biotic gradient in population density leads to gene swamping. Overall, our results show that gene swamping can affect adaptation in life-history strategies.

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Life in the desert: habitat spatial complexity, gene flow, and functional connectivity in Ivesia webberi

10.22541/au.162453142.24417649/v1 ◽

2021 ◽

Author(s):

Israel Borokini ◽

Kelly Klingler ◽

Mary Peacock

Keyword(s):

Genetic Diversity ◽

Gene Flow ◽

Genetic Structure ◽

Functional Connectivity ◽

Genetic Distance ◽

Isolation By Distance ◽

Species Range ◽

Peripheral Populations ◽

Pairwise Genetic Distance ◽

Isolation By Environment

Habitat protection, by itself, is not sufficient to conserve range-restricted species with disjunct populations. Indeed, it becomes critical to characterize gene flow among the populations and factors that influence functional connectivity in order to design effective conservation programs for such species. In this study, we genotyped 314 individuals of Ivesia webberi, a United States federally threatened Great Basin Desert perennial forb using six microsatellite loci, to estimate genetic diversity and population genetic structure, as well as rates and direction of gene flow among 16 extant I. webberi populations. We assessed the effects of Euclidean distance, landscape features, and ecological dissimilarity on the genetic structure of the sampled populations, while also testing for a relationship between I. webberi genetic diversity and diversity in the vegetative communities. The results show low levels of genetic diversity overall (He = 0.200–0.441; Ho = 0.192–0.605) and high genetic differentiation among populations. Genetic diversity was structured along a geographic gradient, congruent with patterns of isolation by distance. Populations near the species’ range core have relatively high genetic diversity, supporting a central-marginal pattern, while peripheral populations have lower genetic diversity, significantly higher genetic distances, higher relatedness, and evidence of genetic bottlenecks. Genotype cluster admixture results support a predominant west to east gene flow pattern for populations near the species’ range center, as well as smaller genotype clusters with a narrow north to south distribution and little admixture, suggesting that dispersal direction and distance vary on the landscape. Pairwise genetic distance strongly correlates with actual evapotranspiration and precipitation, indicating a role for isolation by environment, which the observed phenological mismatches among the populations also support. The significant correlation between pairwise genetic distance and dissimilarity in the soil seed bank suggest that annual regeneration of the floristic communities contributes to the maintenance of genetic diversity in I. webberi.

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