Disentangling the effects of geographic peripherality and habitat suitability on neutral and adaptive genetic variation in Swiss stone pine

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.

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

10.1101/114173 ◽

2017 ◽

Cited By ~ 4

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.

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

PLoS Genetics ◽

10.1371/journal.pgen.1009665 ◽

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.

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Patterns of adaptive genetic variation in forest tree species; the reproductive enviroment as an evolutionary force in Picea abies

Forest Genetics and Sustainability - Forestry Sciences ◽

10.1007/978-94-017-1576-8_6 ◽

2000 ◽

pp. 49-58 ◽

Cited By ~ 11

Author(s):

Tore Skrøppa ◽

Øystein Johnsen

Keyword(s):

Genetic Variation ◽

Picea Abies ◽

Tree Species ◽

Forest Tree ◽

Adaptive Genetic Variation ◽

Forest Tree Species ◽

Evolutionary Force

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Consequences of climatic change for distributions

Effects of Climate Change on Birds ◽

10.1093/oso/9780198824268.003.0013 ◽

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.

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

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1820663116 ◽

2019 ◽

Vol 116 (21) ◽

pp. 10418-10423 ◽

Cited By ~ 67

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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Predicting Adaptive Genetic Variation of Loblolly Pine (Pinus taeda L.) Populations Under Projected Future Climates Based on Multivariate Models

Journal of Heredity ◽

10.1093/jhered/esz065 ◽

2019 ◽

Vol 110 (7) ◽

pp. 857-865 ◽

Cited By ~ 3

Author(s):

Mengmeng Lu ◽

Konstantin V Krutovsky ◽

Carol A Loopstra

Keyword(s):

Climate Change ◽

South Carolina ◽

Genetic Variation ◽

Loblolly Pine ◽

Greenhouse Gas Emission ◽

Isolation By Distance ◽

Adaptive Genetic Variation ◽

Climate Conditions ◽

Geographical Regions ◽

Bioclimatic Variables

Abstract Greenhouse gas emission and global warming are likely to cause rapid climate change within the natural range of loblolly pine over the next few decades, thus bringing uncertainty to their adaptation to the environment. Here, we studied adaptive genetic variation of loblolly pine and correlated genetic variation with bioclimatic variables using multivariate modeling methods—Redundancy Analysis, Generalized Dissimilarity Modeling, and Gradient Forests. Studied trees (N = 299) were originally sampled from their native range across eight states on the east side of the Mississippi River. Genetic variation was calculated using a total of 44,317 single-nucleotide polymorphisms acquired by exome target sequencing. The fitted models were used to predict the adaptive genetic variation on a large spatial and temporal scale. We observed east-to-west spatial genetic variation across the range, which presented evidence of isolation by distance. Different key factors drive adaptation of loblolly pine from different geographical regions. Trees residing near the northeastern edge of the range, spanning across Delaware and Maryland and mountainous areas of Virginia, North Carolina, South Carolina, and northern Georgia, were identified to be most likely impacted by climate change based on the large difference in genetic composition under current and future climate conditions. This study provides new perspectives on adaptive genetic variation of loblolly pine in response to different climate scenarios, and the results can be used to target particular populations while developing adaptive forest management guidelines.

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Rapid climate-driven evolution of the invasive species Mytilus galloprovincialis over the past century

Anthropocene Coasts ◽

10.1139/anc-2019-0012 ◽

2020 ◽

Vol 3 (1) ◽

pp. 14-29

Author(s):

Guo-Dong Han ◽

Yun-Wei Dong

Keyword(s):

Invasive Species ◽

Genetic Variation ◽

Mytilus Galloprovincialis ◽

Climatic Factors ◽

Northwestern Pacific ◽

Past Century ◽

Nucleotide Polymorphisms ◽

Adaptive Genetic Variation ◽

The Past ◽

Wide Range

Climate-driven adaptive genetic variation is one of the most important ways for organisms to tolerate environmental change and succeed in altered environments. To understand rapid climate-driven evolution, and how this evolution might shift biogeographic distributions in response to global change, we measured the adaptive genetic variation to the local environment of a marine invasive species Mytilus galloprovincialis. The genetic structure of eight populations from the Mediterranean Sea, northeastern Atlantic, northeastern Pacific, and northwestern Pacific were determined using genome-wide screens for single nucleotide polymorphisms. The relationships of genetic variation to environmental (seawater and air) temperature were analyzed using redundancy analysis and BayeScEnv analysis to evaluate the impacts of temperature on the genetic divergences among these eight populations. We found that the genetic compositions were significantly different among populations and the adaptive genetic variation was associated with temperature variables. Further, we identified some genetic markers exhibiting signatures of divergent selection in association with environmental features that can be used in the future to closely monitor adaptive variation in this species. Our results suggest that divergent climatic factors have driven adaptive genetic variation in M. galloprovincialis over the past century. The rapid evolutionary adaptation has played a pivotal role in enabling this species to invade a wide range of thermal habitats successfully. Species like M. galloprovincialis that possess high levels of genetic variation may not only be especially capable of invading new habitats with different environmental conditions, but also poised to cope rapidly and successfully with rising global temperatures.

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