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

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.

scholarly journals Genomic footprints of local adaptation along elevation gradients associate with present phenotypic variation in teosintes

2019 ◽  
Author(s):  
M-A. Fustier ◽  
N.E. Martínez-Ainsworth ◽  
A. Venon ◽  
H. Corti ◽  
A. Rousselet ◽  
...  
Keyword(s):  
Climate Change ◽  
Gene Flow ◽  
Local Adaptation ◽  
Phenotypic Variation ◽  
Allele Frequencies ◽  
Maize Breeding ◽  
Elevation Gradients ◽  
Common Gardens ◽  
Molecular Determinants ◽  
Set Up

AbstractLocal adaptation across species range is widespread. Yet, much has to be discovered on its environmental drivers, the underlying functional traits and their molecular determinants. Because elevation gradients display continuous environmental changes at a short geographical scale, they provide an exceptional opportunity to investigate these questions. Here, we used two common gardens to phenotype 1664 plants from 11 populations of annual teosintes. These populations were sampled across two elevation gradients in Mexico. Our results point to a syndrome of adaptation to altitude with the production of offspring that flowered earlier, produced less tillers, and larger, longer and heavier grains with increasing elevation. We genotyped these plants for 178 outlier single nucleotide polymorphisms (SNPs), which had been chosen because they displayed excess of allele differentiation and/or correlation with environmental variables in six populations with contrasted altitudes. A high proportion of outlier SNPs associated with the phenotypic variation of at least one trait. We tested phenotypic pairwise correlations between traits, and found that the higher the correlation, the greater the number of common associated SNPs. In addition, allele frequencies at 87 of the outlier SNPs correlated with an environmental component best summarized by altitudinal variation on a broad sample of 28 populations. Chromosomal inversions were enriched for both phenotypically-associated and environmentally-correlated SNPs. Altogether, our results are consistent with the set-up of an altitudinal syndrome promoted by local adaptation of teosinte populations in the face of gene flow. We showed that pleiotropy is pervasive and potentially has constrained the evolution of traits. Finally, we recovered variants underlying phenotypic variation at adaptive traits. Because elevation mimics climate change through space, these variants may be relevant for future maize breeding.Author summaryAcross their native range, species encounter a diversity of habitats promoting local adaptation of geographically distributed populations. While local adaptation is widespread, much has yet to be discovered about the conditions of its emergence, the targeted traits, their molecular determinants and the underlying ecological drivers. Here we employed a reverse ecology approach, combining phenotypes and genotypes, to mine the determinants of local adaptation of teosinte populations distributed along two steep altitudinal gradients in Mexico. Evaluation of 11 populations in two common gardens located at mid-elevation pointed to the set-up of an altitudinal syndrome, in spite of gene flow. We scanned genomes to identify loci with allele frequencies shifts along elevation. Interestingly, variation at these loci was commonly associated to variation of phenotypes. Because elevation mimics climate change through space, these variants may be relevant for future maize breeding.

scholarly journals Mechanisms of ecological divergence with gene flow in a reef-building coral on an isolated atoll in Western Australia

2021 ◽  
Author(s):  
Luke Thomas ◽  
Jim Underwood ◽  
Noah H Rose ◽  
Zach L Fuller ◽  
Laurence Dugal ◽  
...  
Keyword(s):  
Climate Change ◽  
Heat Stress ◽  
Gene Flow ◽  
Western Australia ◽  
Cell Signalling ◽  
Extreme Environments ◽  
Common Garden ◽  
Allele Frequencies ◽  
Its2 Region ◽  
Strong Linkage Disequilibrium

Understanding the mechanisms driving phenotypic variation in traits facing intensified selection from climate change is a crucial step in developing effective conservation and restoration initiatives. This is particularly true for reef-building corals, which are among the most vulnerable to climate change and are in dramatic decline globally. At the Rowley Shoals in Western Australia, the prominent reef flat becomes exposed on low tide and the stagnant water in the shallow atoll lagoons heats up, creating a natural laboratory for characterising the mechanisms that control phenotypic responses to different environments. We combined whole genome re-sequencing, common garden heat stress experiments, transcriptome-wide gene expression analyses, and symbiont metabarcoding to explore the mechanisms that facilitate survival in contrasting habitat conditions. Our data show that, despite high gene flow between habitats, spatially varying selection drives subtle shifts in allele frequencies at hundreds of loci. These changes were concentrated into several islands of divergence spanning hundreds of SNPs that showed strong linkage disequilibrium and were associated with a coordinated increase in minor allele frequencies in corals taken from the lagoon habitat, where the range of environmental conditions is greatest. Common garden heat stress assays showed individuals from the lagoon exhibited higher bleaching resistance than colonies from the reef slope, and RNAseq identified pronounced physiological differences between the corals from the two habitats, primarily associated with molecular pathways including cell signalling, ion transport and metabolism. Despite the pronounced physioloigical and environmental differences between habitats, metabarcoding of the Symbiodiniaceae ITS2 region revealed all colonies to be associated exclusively with the genus Cladocopium, with no detectable differences between habitats. This study contributes to the growing number of studies documenting the complex mechanisms that facilitate coral survival in extreme environments, and showcases the utility of combining multiple sequencing techniques to unravel complex climate-related traits.

scholarly journals The effects of phenotypic plasticity and local adaptation on forecasts of species range shifts under climate change

2014 ◽  
Vol 17 (11) ◽  
pp. 1351-1364 ◽  
Author(s):  
Fernando Valladares ◽  
Silvia Matesanz ◽  
François Guilhaumon ◽  
Miguel B. Araújo ◽  
Luis Balaguer ◽  
...  
Keyword(s):  
Climate Change ◽  
Phenotypic Plasticity ◽  
Local Adaptation ◽  
Species Range ◽  
Range Shifts

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

2019 ◽  
Vol 13 (1) ◽  
pp. 161-175 ◽  
Author(s):  
James S. Borrell ◽  
Jasmin Zohren ◽  
Richard A. Nichols ◽  
Richard J. A. Buggs
Keyword(s):  
Gene Flow ◽  
Local Adaptation ◽  
Dwarf Birch

scholarly journals Using connectivity to identify climatic drivers of local adaptation

2017 ◽  
Author(s):  
Stewart L. Macdonald ◽  
John Llewelyn ◽  
Ben L. Phillips
Keyword(s):  
Gene Flow ◽  
Local Adaptation ◽  
Environmental Variables ◽  
Evolutionary Biology ◽  
Landscape Connectivity ◽  
Environmental Drivers ◽  
Lizard Species ◽  
Trait Variation ◽  
Vast Number ◽  
Climatic Drivers

AbstractThis preprint has been reviewed and recommended by Peer Community In Evolutionary Biology (http://dx.doi.org/10.24072/pci.evolbiol.100034). Despite being able to conclusively demonstrate local adaptation, we are still often unable to objectively determine the climatic drivers of local adaptation. Given the rapid rate of global change, understanding the climatic drivers of local adaptation is vital. Not only will this tell us which climate axes matter most to population fitness, but such knowledge is critical to inform management strategies such as translocation and targeted gene flow. While simple assessments of geographic trait variation are useful, geographic variation (and its associations with environment) may represent plastic, rather than evolved, differences. Additionally, the vast number of trait–environment combinations makes it difficult to determine which aspects of the environment populations adapt to. Here we argue that by incorporating a measure of landscape connectivity as a proxy for gene flow, we can differentiate between trait–environment relationships underpinned by genetic differences versus those that reflect phenotypic plasticity. By doing so, we can rapidly shorten the list of trait–environment combinations that may be of adaptive significance. We demonstrate how this reasoning can be applied using data on geographic trait variation in a lizard species from Australia's Wet Tropics rainforest. Our analysis reveals an overwhelming signal of local adaptation for the traits and environmental variables we investigated. Our analysis also allows us to rank environmental variables by the degree to which they appear to be driving local adaptation. Although encouraging, methodological issues remain: we point to these issue in the hope that the community can rapidly hone the methods we sketch here. The promise is a rapid and general approach to identifying the environmental drivers of local adaptation.

scholarly journals A map of climate change-driven natural selection in Arabidopsis thaliana

2018 ◽  
Author(s):  
Moises Exposito-Alonso ◽  
Hernán A. Burbano ◽  
Oliver Bossdorf ◽  
Rasmus Nielsen ◽  
Detlef Weigel ◽  
...  
Keyword(s):  
Climate Change ◽  
Arabidopsis Thaliana ◽  
Natural Selection ◽  
Local Adaptation ◽  
Genetic Variants ◽  
Species Range ◽  
Genome Wide ◽  
Genetic Makeup ◽  
Environmental Limits ◽  
Genome Information

Through the lens of evolution, climate change is an agent of natural selection that forces populations to change and adapt, or face extinction. Current assessments of the risk of biodiversity associated with climate change1, however, do not typically take into account the genetic makeup of populations and how natural selection impacts it2. We made use of the extensive genome information in Arabidopsis thaliana and measured how rainfall-manipulation affected the fitness of 517 natural lines grown in Spain and Germany. This allowed us to directly infer selection along the genome3. Natural selection was particularly strong in the hot-dry Spanish location, killing 63% of lines and significantly changing the frequency of ~5% of all genome-wide variants. A significant portion of this climate-driven natural selection over variants was predictable from signatures of local adaptation (R2=29-52%), as genetic variants found in geographic areas with climates more similar to the experimental sites were positively selected. Field-validated predictions across the species range indicated that Mediterranean and Western Siberian populations — at the edges of the species’ environmental limits — currently experience the strongest climate-driven selection. With more frequent droughts and rising temperatures in Europe4, we forecast an increase in directional natural selection moving northwards from the southern end, and putting many native A. thaliana populations at evolutionary risk.

scholarly journals Genomic signatures of spatially divergent selection at clownfish range margins

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.

scholarly journals Predicting The Potential Distribution of Campsis Grandiflora In China Under Climate Change

2021 ◽  
Author(s):  
Xianheng Ouyang ◽  
Jiangling Pan ◽  
Zhitao Wu ◽  
Anliang Chen
Keyword(s):  
Climate Change ◽  
Geographical Distribution ◽  
Potential Distribution ◽  
Eastern China ◽  
Central China ◽  
Future Climate Change ◽  
Suitable Habitat ◽  
Monthly Precipitation ◽  
Mean Temperature ◽  
Diurnal Range

Abstract As the research of geographical distribution of species shows significant influence on people’s understanding of specie protection and utilization, it is important to study the influence of climate change onto the geographical distribution pattern of plants. Based on 166 distribution records as well as 11 climate and terrain variables with low correlation in China, we used MaxEnt (Maximum Entropy) model and ArcGIS software to predict the potential distribution of Campsis grandiflora under climate change and then determine the dominant climate variables which affect the geographical distribution significantly by analysis. The results show that the area under the curve (AUC) of the train is 0.939, which implies our prediction is accurate. Under the current climate condition, the area of potentially suitable habitat is 238.29×104 km2, mainly distributed in northern China, central China, southern China, and eastern China. The dominant variables affected the geographical distribution of Campsis grandiflora are mean diurnal range, range of annual temperature variation, mean temperature, mean temperature of the coldest season, the driest monthly precipitation, precipitation of the warmest quarter, as well as altitude. In the future climate change scenario, the total area of suitable habitat and highly suitable habitat will increase, whilst the area of moderately suitable habitat and poorly suitable habitat will decrease. In the meantime, the centroid of the potentially suitable area of Campsis grandiflora will migrate to higher latitude areas.

scholarly journals Species-environment relationships of fish and map-based variables in small boreal streams: linkages with climate change and bioassessment

2021 ◽  
Author(s):  
Tapio Sutela ◽  
Teppo Vehanen ◽  
Pekka Jounela ◽  
Jukka Aroviita
Keyword(s):  
Climate Change ◽  
Fish Species ◽  
Urban Areas ◽  
Environmental Variables ◽  
Salmo Trutta ◽  
Gasterosteus Aculeatus ◽  
Self Organizing Map ◽  
Pungitius Pungitius ◽  
Mean Temperature ◽  
Small Streams

Species-environment relationships were studied between the occurrence of 13 fish and lamprey species and 9 mainly map-based environmental variables of Finnish boreal small streams. A self-organizing map (SOM) analysis showed strong relationships between the fish species and environmental variables in a single model (explained variance 55.9%). Besides basic environmental variables such as altitude, catchment size, and mean temperature, landcover variables were also explored. A logistic regression analysis indicated that the occurrence probability of brown trout, Salmo trutta L., decreased with an increasing percentage of peatland ditch drainage in the upper catchment. Ninespine stickleback, Pungitius pungitius (L.), and three-spined stickleback, Gasterosteus aculeatus L., seemed to benefit from urban areas in the upper catchment. Discovered relationships between fish species occurrence and land-use attributes are encouraging for the development of fish-based bioassessment for small streams. The presented ordination of the fish species in the mean temperature gradient will help in predicting fish community responses to climate change.

Spatial modeling of the ecological niche of Pinus greggii Engelm (Pinaceae): A species conservation proposal in Mexico

2020 ◽  
Author(s):  
ALDO Rafael MARTINEZ ◽  
Jose Villanueva Diaz ◽  
Ulises Manzanilla-Quiñones ◽  
Jorge Luis Becerra-López ◽  
José Antonio Hernández-Herrera ◽  
...  
Keyword(s):  
Climate Change ◽  
Current Distribution ◽  
Spatial Modeling ◽  
Environmental Variables ◽  
Ecological Niche ◽  
Species Conservation ◽  
Suitable Habitat ◽  
Distribution Models ◽  
Mean Temperature ◽  
Pinus Greggii

Abstract Background Studies in Mexico have shown that the genus Pine has always been under evolutionary changes, however currently they have accelerated as a result of human activities. Pinus greggii is a species restricted by particular environmental conditions of the Sierra Madre Occidental, which is of socio-economic importance in terms of wood production and provides environmental services to the ecosystem. Species distribution models are a relevant geospatial tool in decision making, and notable applications exist such as identifying areas of distribution and zones susceptible to climate change. The objectives of this study were: 1) model and quantify the current distribution, and possible future distribution under four scenarios of climate change; 2) identify the most relevant environmental variables that drive changes in distribution; and 3) to propose adequate zones for the species’ conservation in Mexico. Methods 438 records of Pinus greggii from several national and international databases were obtained, and were cleaned up to get rid of duplicates and overestimations in the models. Climatic, edaphic, and topographic variables were used and were generated 100 distribution models for current and future scenarios with Maxent software. Results The model one under replicated of crossvalidation had the best statistic, with an area under the curve of 0.88 and 0.93 for model training and validation, respectively, a partial ROC of 1.94, and a significant Z test (p < 0.01). The current estimated area of Pinus greggii in Mexico was 617,706.04 ha and the most important environmental variables for current distribution were the annual mean temperature, mean temperature of coldest quarter, and slope. For the 2041–2060 models, annual mean temperature, precipitation of coldest quarter, and slope were most important. The future models (2041–2060) predict a decrease in suitable habitat for the species from 48,403.85 (7.8%; HadGEM2-ES RCP 8.5 model) to 134,680.17 ha (21.8%; CNRM-CM5 RCP 4.5). Conclusions The spatial modeling of current and future conditions of the ecological niche of Pinus greggii in this study allows the proposal of two zones for conservation purpose and in situ restoration for the species in northeastern (Nuevo Leon) and central (Hidalgo) Mexico.

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