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

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.

Download Full-text

Gene flow favours local adaptation under habitat choice in ciliate microcosms

Nature Ecology & Evolution ◽

10.1038/s41559-017-0269-5 ◽

2017 ◽

Vol 1 (9) ◽

pp. 1407-1410 ◽

Cited By ~ 39

Author(s):

Staffan Jacob ◽

Delphine Legrand ◽

Alexis S. Chaine ◽

Dries Bonte ◽

Nicolas Schtickzelle ◽

...

Keyword(s):

Gene Flow ◽

Local Adaptation ◽

Habitat Choice

Download Full-text

Gene Flow, Spatial Structure, Local Adaptation, and Assisted Migration in Trees

Genomics of Tree Crops ◽

10.1007/978-1-4614-0920-5_4 ◽

2012 ◽

pp. 71-116 ◽

Cited By ~ 8

Author(s):

Konstantin V. Krutovsky ◽

Jaroslaw Burczyk ◽

Igor Chybicki ◽

Reiner Finkeldey ◽

Tanja Pyhäjärvi ◽

...

Keyword(s):

Gene Flow ◽

Spatial Structure ◽

Local Adaptation ◽

Assisted Migration

Download Full-text

Local adaptation along a sharp rainfall gradient occurs in a native Patagonian grass, Festuca pallescens, regardless of extensive gene flow

Environmental and Experimental Botany ◽

10.1016/j.envexpbot.2019.103933 ◽

2020 ◽

Vol 171 ◽

pp. 103933

Author(s):

Aldana S. López ◽

Dardo R. López ◽

Gonzalo Caballé ◽

Guillermo L. Siffredi ◽

Paula Marchelli

Keyword(s):

Gene Flow ◽

Local Adaptation ◽

Rainfall Gradient ◽

Festuca Pallescens

Download Full-text

The limits to parapatric speciation 3: evolution of strong reproductive isolation in presence of gene flow despite limited ecological differentiation

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2019.0532 ◽

2020 ◽

Vol 375 (1806) ◽

pp. 20190532 ◽

Cited By ~ 1

Author(s):

Alexandre Blanckaert ◽

Claudia Bank ◽

Joachim Hermisson

Keyword(s):

Gene Flow ◽

Reproductive Isolation ◽

Local Adaptation ◽

Theme Issue ◽

Genetic Barrier ◽

Incipient Species ◽

Postzygotic Reproductive Isolation ◽

Minimal Configuration ◽

Parapatric Speciation ◽

Two Populations

Gene flow tends to impede the accumulation of genetic divergence. Here, we determine the limits for the evolution of postzygotic reproductive isolation in a model of two populations that are connected by gene flow. We consider two selective mechanisms for the creation and maintenance of a genetic barrier: local adaptation leads to divergence among incipient species due to selection against migrants, and Dobzhansky–Muller incompatibilities (DMIs) reinforce the genetic barrier through selection against hybrids. In particular, we are interested in the maximum strength of the barrier under a limited amount of local adaptation, a challenge that many incipient species may initially face. We first confirm that with classical two-locus DMIs, the maximum amount of local adaptation is indeed a limit to the strength of a genetic barrier. However, with three or more loci and cryptic epistasis, this limit holds no longer. In particular, we identify a minimal configuration of three epistatically interacting mutations that is sufficient to confer strong reproductive isolation. This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.

Download Full-text

Genomic Patterns of Local Adaptation under Gene Flow in Arabidopsis lyrata

Molecular Biology and Evolution ◽

10.1093/molbev/msz149 ◽

2019 ◽

Vol 36 (11) ◽

pp. 2557-2571 ◽

Cited By ~ 17

Author(s):

Tuomas Hämälä ◽

Outi Savolainen

Keyword(s):

Gene Flow ◽

Local Adaptation ◽

Demographic History ◽

Rate Variation ◽

Arabidopsis Lyrata ◽

Trade Offs ◽

Northern Latitudes ◽

Local Selection ◽

Empirical Level ◽

Selected Traits

AbstractShort-scale local adaptation is a complex process involving selection, migration, and drift. The expected effects on the genome are well grounded in theory but examining these on an empirical level has proven difficult, as it requires information about local selection, demographic history, and recombination rate variation. Here, we use locally adapted and phenotypically differentiated Arabidopsis lyrata populations from two altitudinal gradients in Norway to test these expectations at the whole-genome level. Demography modeling indicates that populations within the gradients diverged <2 kya and that the sites are connected by gene flow. The gene flow estimates are, however, highly asymmetric with migration from high to low altitudes being several times more frequent than vice versa. To detect signatures of selection for local adaptation, we estimate patterns of lineage-specific differentiation among these populations. Theory predicts that gene flow leads to concentration of adaptive loci in areas of low recombination; a pattern we observe in both lowland-alpine comparisons. Although most selected loci display patterns of conditional neutrality, we found indications of genetic trade-offs, with one locus particularly showing high differentiation and signs of selection in both populations. Our results further suggest that resistance to solar radiation is an important adaptation to alpine environments, while vegetative growth and bacterial defense are indicated as selected traits in the lowland habitats. These results provide insights into genetic architectures and evolutionary processes driving local adaptation under gene flow. We also contribute to understanding of traits and biological processes underlying alpine adaptation in northern latitudes.

Download Full-text

Divergence with gene flow is driven by local adaptation to temperature and soil phosphorus concentration in teosinte subspecies ( Zea mays parviglumis and Zea mays mexicana )

Molecular Ecology ◽

10.1111/mec.15098 ◽

2019 ◽

Cited By ~ 6

Author(s):

Jonás A. Aguirre‐Liguori ◽

Brandon S. Gaut ◽

Juan Pablo Jaramillo‐Correa ◽

Maud I. Tenaillon ◽

Salvador Montes‐Hernández ◽

...

Keyword(s):

Zea Mays ◽

Gene Flow ◽

Local Adaptation ◽

Soil Phosphorus ◽

Phosphorus Concentration ◽

Divergence With Gene Flow

Download Full-text

The Mobilome of Reptiles: Evolution, Structure, and Function

Cytogenetic and Genome Research ◽

10.1159/000496416 ◽

2019 ◽

Vol 157 (1-2) ◽

pp. 21-33 ◽

Cited By ~ 3

Author(s):

Stéphane Boissinot ◽

Yann Bourgeois ◽

Joseph D. Manthey ◽

Robert P. Ruggiero

Keyword(s):

Gene Flow ◽

Transposable Elements ◽

Genome Size ◽

Local Adaptation ◽

Size Structure ◽

Structure And Function ◽

Genomic Diversity ◽

Genomic Features ◽

And Function

Transposable elements (TE) constitute one of the most variable genomic features among vertebrates, impacting genome size, structure, and composition. Despite their important role in shaping genomic diversity, they have mostly been studied in mammals, which display one of the least diverse genomes in terms of TE diversity. Recent new resources in reptilian genomics have opened a broader perspective about TE evolution in amniotes. We discuss these recent results by showing that TE diversity is high in reptiles, particularly in squamates, with strong heterogeneity in the number of TE classes retained in each lineage, even at short evolutionary scales. More research is needed to uncover the exact mechanisms that regulate TE proliferation in reptiles and to what extent these selfish elements can play a role in local adaptation or in the emergence of barriers to gene flow.

Download Full-text

Evaluation of genetic isolation within an island flora reveals unusually widespread local adaptation and supports sympatric speciation

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2013.0342 ◽

2014 ◽

Vol 369 (1648) ◽

pp. 20130342 ◽

Cited By ~ 24

Author(s):

Alexander S. T. Papadopulos ◽

Maria Kaye ◽

Céline Devaux ◽

Helen Hipperson ◽

Jackie Lighten ◽

...

Keyword(s):

Gene Flow ◽

Local Adaptation ◽

Plant Species ◽

Environmental Gradients ◽

Isolation By Distance ◽

Model Averaging ◽

Dispersal Limitation ◽

Population Divergence ◽

Environmental Pressures ◽

Isolation By Environment

It is now recognized that speciation can proceed even when divergent natural selection is opposed by gene flow. Understanding the extent to which environmental gradients and geographical distance can limit gene flow within species can shed light on the relative roles of selection and dispersal limitation during the early stages of population divergence and speciation. On the remote Lord Howe Island (Australia), ecological speciation with gene flow is thought to have taken place in several plant genera. The aim of this study was to establish the contributions of isolation by environment (IBE) and isolation by community (IBC) to the genetic structure of 19 plant species, from a number of distantly related families, which have been subjected to similar environmental pressures over comparable time scales. We applied an individual-based, multivariate, model averaging approach to quantify IBE and IBC, while controlling for isolation by distance (IBD). Our analyses demonstrated that all species experienced some degree of ecologically driven isolation, whereas only 12 of 19 species were subjected to IBD. The prevalence of IBE within these plant species indicates that divergent selection in plants frequently produces local adaptation and supports hypotheses that ecological divergence can drive speciation in sympatry.

Download Full-text

The interplay between dispersal and gene flow in anadromous Arctic char (Salvelinus alpinus): implications for potential for local adaptation

Canadian Journal of Fisheries and Aquatic Sciences ◽

10.1139/cjfas-2013-0138 ◽

2013 ◽

Vol 70 (9) ◽

pp. 1327-1338 ◽

Cited By ~ 29

Author(s):

Jean-Sébastien Moore ◽

Les N. Harris ◽

Ross F. Tallman ◽

Eric B. Taylor

Keyword(s):

Gene Flow ◽

Local Adaptation ◽

Genetic Model ◽

Salvelinus Alpinus ◽

Arctic Char ◽

Baffin Island ◽

Assignment Method ◽

Natal Habitat ◽

Breeding Condition ◽

Assignment Approach

Dispersal can influence the process of local adaptation, particularly when the dispersers successfully breed in the non-natal habitat. Anadromous Arctic char (Salvelinus alpinus) display a complex migratory behaviour that makes the distinction between breeding and nonbreeding dispersal especially important. This species does not reproduce every year, but individuals must migrate to fresh water to overwinter such that a large proportion of fish running up-river are not in breeding condition and have no potential for gene flow. We used a genetic assignment approach to identify dispersers among populations of char from Baffin Island, Canada. Estimates of dispersal varied between 15.8% and 25.5% depending on the assignment method, suggesting that Arctic char disperse at a higher rate than other salmonids. Nonbreeding individuals were more likely to use non-natal habitats than breeding individuals, thus resulting in estimates of dispersal that overestimate the potential for gene flow among populations. Finally, we parameterized a population genetic model showing that gene flow is probably sufficiently low to allow for local adaptation among populations, given realistic selection coefficients. Our results underscore the importance of understanding patterns of dispersal to appropriately evaluate their potential consequences for local adaptation and management.

Download Full-text