scholarly journals Genomic data support management of anadromous Arctic Char fisheries in Nunavik by highlighting neutral and putatively adaptive genetic variation

2021 ◽  
Author(s):  
Xavier Dallaire ◽  
Normandeau Éric ◽  
Julien Mainguy ◽  
Jean‐Éric Tremblay ◽  
Louis Bernatchez ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Genomic Data ◽  
Arctic Char ◽  
Adaptive Genetic Variation ◽  
Data Support

scholarly journals The genomics of adaptation

2012 ◽  
Vol 279 (1749) ◽  
pp. 5024-5028 ◽  
Author(s):  
Jacek Radwan ◽  
Wiesław Babik
Keyword(s):  
Genetic Variation ◽  
Natural Selection ◽  
Royal Society ◽  
Genetic Basis ◽  
Genomic Data ◽  
Evolutionary Change ◽  
Introductory Article ◽  
Technological Advances ◽  
A Genome ◽  
Genome Level

The amount and nature of genetic variation available to natural selection affect the rate, course and outcome of evolution. Consequently, the study of the genetic basis of adaptive evolutionary change has occupied biologists for decades, but progress has been hampered by the lack of resolution and the absence of a genome-level perspective. Technological advances in recent years should now allow us to answer many long-standing questions about the nature of adaptation. The data gathered so far are beginning to challenge some widespread views of the way in which natural selection operates at the genomic level. Papers in this Special Feature of Proceedings of the Royal Society B illustrate various aspects of the broad field of adaptation genomics. This introductory article sets up a context and, on the basis of a few selected examples, discusses how genomic data can advance our understanding of the process of adaptation.

Putatively adaptive genetic variation in the giant California sea cucumber ( Parastichopus californicus ) as revealed by environmental association analysis of restriction‐site associated DNA sequencing data

2018 ◽  
Vol 27 (24) ◽  
pp. 5035-5048 ◽  
Author(s):  
Amanda Xuereb ◽  
Christopher M. Kimber ◽  
Janelle M. R. Curtis ◽  
Louis Bernatchez ◽  
Marie‐Josée Fortin
Keyword(s):  
Genetic Variation ◽  
Dna Sequencing ◽  
Association Analysis ◽  
Sea Cucumber ◽  
Restriction Site ◽  
Sequencing Data ◽  
Adaptive Genetic Variation ◽  
Environmental Association

scholarly journals Adaptive genetic variation at three loci in South African vervet monkeys (Chlorocebus pygerythrus) and the role of selection within Primates

2018 ◽  
Author(s):  
Willem G Coetzer ◽  
Trudy R Turner ◽  
Christopher A Schmitt ◽  
J Paul Grobler
Keyword(s):  
Genetic Variation ◽  
South African ◽  
Vervet Monkey ◽  
Climatic Conditions ◽  
Primate Species ◽  
Annual Rainfall ◽  
Future Research ◽  
Vervet Monkeys ◽  
Adaptive Genetic Variation ◽  
Chlorocebus Pygerythrus

Vervet monkeys (Chlorocebus pygerythrus) are one of the most widely distributed non-human primate species found in South Africa. They occur across all the South African provinces, inhabiting a large variety of habitats. These habitats vary sufficiently that it can be assumed that various factors such as pathogen diversity could influence populations in different ways. In turn, these factors could lead to varied levels of selection at specific fitness linked loci. The Toll-like Receptor (TLR) gene family, which play an integral role in vertebrate innate immunity, is a group of fitness linked loci which has been the focus of much research. In this study, we assessed the level of genetic variation at partial sequences of two TLR loci (TLR4 and 7) and a reproductively linked gene, acrosin (ACR), across the different habitat types within the vervet monkey distribution range. Gene variation and selection estimates were also made among 11 – 21 primate species. Low levels of genetic variation for all three gene regions were observed within vervet monkeys , with only two polymorphic sites identified for TLR4, three sites for TLR7 and one site for ACR . TLR7 variation was positively correlated with high mean annual rainfall, which was linked to increased pathogen abundance. The observed genetic variation at TLR4 might have been influenced by numerous factors including pathogens and climatic conditions. The ACR exonic regions showed no variation in vervet monkeys, which could point to the occurrence of a selective sweep. The TLR4 and TLR7 results for the among primate analyses was mostly in line with previous studies, indicating a higher rate of evolution for TLR4. Within primates, ACR also showed signs of positive selection, which was congruent with previous reports on mammals. Important additional information to the already existing vervet monkey knowledge base was gained from this study, which can guide future research projects on this highly researched taxon as well as help conservation agencies with future management planning involving possible translocations of this species.

scholarly journals Potential for rapid genetic adaptation to warming in a Great Barrier Reef coral

2017 ◽  
Author(s):  
Mikhail V. Matz ◽  
Eric A. Treml ◽  
Galina V. Aglyamova ◽  
Madeleine J. H. van Oppen ◽  
Line K. Bay
Keyword(s):  
Genetic Variation ◽  
Great Barrier Reef ◽  
Coral Cover ◽  
Reef Coral ◽  
Biophysical Model ◽  
Detectable Effect ◽  
Genetic Adaptation ◽  
Barrier Reef ◽  
Biophysical Modeling ◽  
Adaptive Genetic Variation

AbstractCan genetic adaptation in reef-building corals keep pace with the current rate of sea surface warming? Here we combine population genomic, biophysical modeling, and evolutionary simulations to predict future adaptation of the common coralAcropora milleporaon the Great Barrier Reef. Loss of coral cover in recent decades did not yet have detectable effect on genetic diversity in our species. Genomic analysis of migration patterns closely matched the biophysical model of larval dispersal in favoring the spread of existing heat-tolerant alleles from lower to higher latitudes. Given these conditions we find that standing genetic variation could be sufficient to fuel rapid adaptation ofA. milleporato warming for the next 100-200 years, although random thermal anomalies would drive increasingly severe mortality episodes. However, this adaptation will inevitably cease unless the warming is slowed down, since no realistic mutation rate could replenish adaptive genetic variation fast enough.

scholarly journals Inferring Adaptive Introgression Using Hidden Markov Models

2020 ◽  
Author(s):  
Jesper Svedberg ◽  
Vladimir Shchur ◽  
Solomon Reinman ◽  
Rasmus Nielsen ◽  
Russell Corbett-Detig
Keyword(s):  
Markov Models ◽  
Hidden Markov ◽  
Genomic Data ◽  
Diverse Populations ◽  
Powerful Method ◽  
Adaptive Genetic Variation ◽  
Adaptive Introgression ◽  
Population Genomic ◽  
Significant Interest ◽  
Selection Parameters

AbstractAdaptive introgression - the flow of adaptive genetic variation between species or populations - has attracted significant interest in recent years and it has been implicated in a number of cases of adaptation, from pesticide resistance and immunity, to local adaptation. Despite this, methods for identification of adaptive introgression from population genomic data are lacking. Here, we present Ancestry_HMM-S, a Hidden Markov Model based method for identifying genes undergoing adaptive introgression and quantifying the strength of selection acting on them. Through extensive validation, we show that this method performs well on moderately sized datasets for realistic population and selection parameters. We apply Ancestry_HMM-S to a dataset of an admixed Drosophila melanogaster population from South Africa and we identify 17 loci which show signatures of adaptive introgression, four of which have previously been shown to confer resistance to insecticides. Ancestry_HMM-S provides a powerful method for inferring adaptive introgression in datasets that are typically collected when studying admixed populations. This method will enable powerful insights into the genetic consequences of admixture across diverse populations. Ancestry_HMM-S can be downloaded from https://github.com/jesvedberg/Ancestry_HMM-S/.

scholarly journals A spectral theory for Wright’s inbreeding coefficients and related quantities

PLoS Genetics ◽  
2021 ◽  
Vol 17 (7) ◽  
pp. e1009665
Author(s):  
Olivier François ◽  
Clément Gain
Keyword(s):  
Population Structure ◽  
Genetic Variation ◽  
Population Genetic ◽  
Principal Component ◽  
Large Data ◽  
Population Subdivision ◽  
Adaptive Genetic Variation ◽  
Genomic Locus ◽  
Inbreeding Coefficients ◽  
Definition Of

Wright’s inbreeding coefficient, FST, is a fundamental measure in population genetics. Assuming a predefined population subdivision, this statistic is classically used to evaluate population structure at a given genomic locus. With large numbers of loci, unsupervised approaches such as principal component analysis (PCA) have, however, become prominent in recent analyses of population structure. In this study, we describe the relationships between Wright’s inbreeding coefficients and PCA for a model of K discrete populations. Our theory provides an equivalent definition of FST based on the decomposition of the genotype matrix into between and within-population matrices. The average value of Wright’s FST over all loci included in the genotype matrix can be obtained from the PCA of the between-population matrix. Assuming that a separation condition is fulfilled and for reasonably large data sets, this value of FST approximates the proportion of genetic variation explained by the first (K − 1) principal components accurately. The new definition of FST is useful for computing inbreeding coefficients from surrogate genotypes, for example, obtained after correction of experimental artifacts or after removing adaptive genetic variation associated with environmental variables. The relationships between inbreeding coefficients and the spectrum of the genotype matrix not only allow interpretations of PCA results in terms of population genetic concepts but extend those concepts to population genetic analyses accounting for temporal, geographical and environmental contexts.

Prevalence and Adaptive Impact of Introgression

2021 ◽  
Vol 55 (1) ◽  
Author(s):  
Nathaniel B. Edelman ◽  
James Mallet
Keyword(s):  
Genetic Variation ◽  
Adaptive Evolution ◽  
Genetic Variants ◽  
Genomic Data ◽  
Annual Review ◽  
Publication Date ◽  
Adaptive Introgression ◽  
Changing Environments ◽  
Potential Benefits

Alleles that introgressed between species can influence the evolutionary and ecological fate of species exposed to novel environments. Hybrid offspring of different species are often unfit, and yet it has long been argued that introgression can be a potent force in evolution, especially in plants. Over the last two decades, genomic data have increasingly provided evidence that introgression is a critically important source of genetic variation and that this additional variation can be useful in adaptive evolution of both animals and plants. Here, we review factors that influence the probability that foreign genetic variants provide long-term benefits (so-called adaptive introgression) and discuss their potential benefits. We find that introgression plays an important role in adaptive evolution, particularly when a species is far from its fitness optimum, such as when they expand their range or are subject to changing environments. Expected final online publication date for the Annual Review of Genetics, Volume 55 is November 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

Consequences of climatic change for distributions

2019 ◽  
pp. 165-184
Author(s):  
Brian Huntley
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Species Distributions ◽  
Climatic Changes ◽  
Adaptive Genetic Variation ◽  
Spatial Structuring ◽  
Modelling Studies ◽  
Population Sizes ◽  
Fossil Records

Species’ distributions, population sizes, and community composition are affected, directly and indirectly, by climatic changes, leading to changes in location, extent, and/or quality of distributions, range fragmentation or coalescence, and temporal discontinuities in suitable conditions. Quaternary fossil records document these responses, emphasizing individualism of species’ responses and impermanence of communities. Recent observations document similar changes attributable to recent climatic changes, including rapid decreases and increases in ranges and/or populations. Both also document extinctions associated with rapid climatic changes. Modelling studies predict substantial changes in species’ distributions, population sizes, and communities in response to future climatic changes. Implicit assumptions that genetic variation enabling adaptation is ubiquitous throughout species’ ranges, or that gene flow may be sufficiently rapid to allow adaptation, may be invalid. Work is needed to investigate spatial structuring of adaptive genetic variation and rates of gene flow, and to develop new models. Without this, species extinction risks may be severely underestimated.

scholarly journals Considering adaptive genetic variation in climate change vulnerability assessment reduces species range loss projections

2019 ◽  
Vol 116 (21) ◽  
pp. 10418-10423 ◽  
Author(s):  
Orly Razgour ◽  
Brenna Forester ◽  
John B. Taggart ◽  
Michaël Bekaert ◽  
Javier Juste ◽  
...  
Keyword(s):  
Climate Change ◽  
Genetic Variation ◽  
Environmental Changes ◽  
Landscape Connectivity ◽  
Future Climate ◽  
Future Climate Change ◽  
Adaptive Genetic Variation ◽  
Climate Change Vulnerability ◽  
Species Vulnerability ◽  
Evolutionary Rescue

Local adaptations can determine the potential of populations to respond to environmental changes, yet adaptive genetic variation is commonly ignored in models forecasting species vulnerability and biogeographical shifts under future climate change. Here we integrate genomic and ecological modeling approaches to identify genetic adaptations associated with climate in two cryptic forest bats. We then incorporate this information directly into forecasts of range changes under future climate change and assessment of population persistence through the spread of climate-adaptive genetic variation (evolutionary rescue potential). Considering climate-adaptive potential reduced range loss projections, suggesting that failure to account for intraspecific variability can result in overestimation of future losses. On the other hand, range overlap between species was projected to increase, indicating that interspecific competition is likely to play an important role in limiting species’ future ranges. We show that although evolutionary rescue is possible, it depends on a population’s adaptive capacity and connectivity. Hence, we stress the importance of incorporating genomic data and landscape connectivity in climate change vulnerability assessments and conservation management.

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