scholarly journals The maintenance of standing genetic variation: gene flow versus selective neutrality in Atlantic stickleback fish

2021 ◽  
Author(s):  
Quiterie Haenel ◽  
Laurent Guerard ◽  
Andrew D. C. MacColl ◽  
Daniel Berner
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Selective Neutrality

scholarly journals The maintenance of standing genetic variation: gene flow versus selective neutrality in Atlantic stickleback fish

2021 ◽  
Author(s):  
Quiterie Haenel ◽  
Laurent Guerard ◽  
Andrew MacColl ◽  
Daniel Berner
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Variants ◽  
Sequence Data ◽  
Purifying Selection ◽  
Whole Genome Sequence ◽  
Adaptive Genetic Variation ◽  
Fitness Consequences ◽  
Selective Neutrality ◽  
Polygenic Adaptation

Adaptation to derived habitats often occurs from standing genetic variation (SGV). The maintenance within ancestral populations of genetic variants favorable in derived habitats is commonly ascribed to long-term antagonism between purifying selection and gene flow resulting from hybridization across habitats. A largely unexplored alternative idea based on quantitative genetic models of polygenic adaptation is that variants favored in derived habitats are neutral in ancestral populations when their frequency is relatively low. To explore the latter, we first identify genetic variants important to the adaptation of threespine stickleback fish to a rare derived habitat – nutrient-depleted acidic lakes – based on whole-genome sequence data. Sequencing marine stickleback from six locations across the Atlantic ocean then allows us to infer that the frequency of these derived variants in the ancestral habitat is unrelated to the likely opportunity for gene flow of these variants from acidic-adapted populations. This result is consistent with the selective neutrality of derived variants within the ancestor. Our study thus supports an underappreciated explanation for the maintenance of SGV, and calls for a better understanding of the fitness consequences of adaptive genetic variation across habitats and genomic backgrounds.

Habitat differentiation between estuarine and inland Hibiscus tiliaceus L. (Malvaceae) as revealed by retrotransposon-based SSAP marker

2011 ◽  
Vol 59 (6) ◽  
pp. 515 ◽  
Author(s):  
Tian Tang ◽  
Lian He ◽  
Feng Peng ◽  
Suhua Shi
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Distance ◽  
Genetic Variance ◽  
Genetic Relationships ◽  
Principal Coordinate Analysis ◽  
Geographical Isolation ◽  
Tidal Zone ◽  
Ecological Scale ◽  
Habitat Differentiation

Hibiscus tiliaceus L. (Malvaceae) is a pantropical coastal tree that extends to the tidal zone. In this study, the retrotransposon sequence-specific amplified polymorphism (SSAP) technique was used in order to understand the genetic variation between four population pairs of H. tiliaceus from repeated estuarine and inland habitat contrasts in China. The estuarine populations were consistently more genetic variable compared with the inland ones, which may be attributed to extensive gene flow via water-drifted seeds and/or retrotransposon activation in stressful estuarine environments. An AMOVA revealed that 8.9% of the genetic variance could be explained by the habitat divergence within site, as compared with only 4.9% to geographical isolation between sites, which indicates significant habitat differentiation between the estuarine and inland populations. The estuarine populations were less differentiated (ΦST = 0.115) than the inland (ΦST = 0.152) implying frequent gene interchange in the former. Accordingly, the principal coordinate analysis of genetic distance between individuals revealed that genetic relationships are not fully consistent with the geographic association. These results suggest that despite substantial gene flow via sea-drifted seeds, habitat-related divergent selection could be one of the primary mechanisms that drive habitat differentiation in H. tiliaceus at a local ecological scale.

scholarly journals Landscape permeability and individual variation in a dispersal-linked gene jointly determine genetic structure in the Glanville fritillary butterfly

2018 ◽  
Author(s):  
Michelle F. DiLeo ◽  
Arild Husby ◽  
Marjo Saastamoinen
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Structure ◽  
Individual Variation ◽  
Landscape Fragmentation ◽  
Landscape Matrix ◽  
Fragmented Landscapes ◽  
Dispersal Traits ◽  
Glanville Fritillary Butterfly ◽  
Large Decline

AbstractThere is now clear evidence that species across a broad range of taxa harbour extensive heritable variation in dispersal. While studies suggest that this variation can facilitate demographic outcomes such as range expansion and invasions, few have considered the consequences of intraspecific variation in dispersal for the maintenance and distribution of genetic variation across fragmented landscapes. Here we examine how landscape characteristics and individual variation in dispersal combine to predict genetic structure using genomic and spatial data from the Glanville fritillary butterfly. We used linear and latent factor mixed models to identify the landscape features that best predict spatial sorting of alleles in the dispersal-related gene phosphoglucose isomerase (Pgi). We next used structural equation modeling to test if variation in Pgi mediated gene flow as measured by Fst at putatively neutral loci. In a year when the population was expanding following a large decline, individuals with a genotype associated with greater dispersal ability were found at significantly higher frequencies in populations isolated by water and forest, and these populations showed lower levels of genetic differentiation at neutral loci. These relationships disappeared in the next year when metapopulation density was high, suggesting that the effects of individual variation are context dependent. Together our results highlight that 1) more complex aspects of landscape structure beyond just the configuration of habitat can be important for maintaining spatial variation in dispersal traits, and 2) that individual variation in dispersal plays a key role in maintaining genetic variation across fragmented landscapes.Impact summaryUnderstanding how fragmentation affects dispersal and gene flow across human-modified landscapes has long been a goal in evolutionary biology. It is typically assumed that individuals of the same species respond to the landscape in the same way, however growing evidence suggests that individuals can vary considerably in their dispersal traits. While the effects of this individual dispersal variation on range expansions and invasions have been well-characterized, knowledge of how it might mediate genetic responses to landscape fragmentation are almost entirely lacking. Here we demonstrate that individual variation in dispersal is key to the maintenance of genetic variation during a population expansion following a large decline in a butterfly metapopulation. We further show that spatial variation in dispersal is not maintained by the configuration of habitat patches alone, but by a more complex genotype-environment interaction involving the landscape matrix (i.e. landscape features found between habitat patches). This challenges the simplified landscape representations typically used in studies of dispersal evolution that ignore heterogeneity in the landscape matrix. More broadly, our results highlight the interplay of adaptive and neutral processes across fragmented landscapes, suggesting that an understanding of species vulnerability to landscape fragmentation requires consideration of both.

scholarly journals Targeted Sequencing Suggests Wild-Crop Gene Flow Is Central to Different Genetic Consequences of Two Independent Pumpkin Domestications

2021 ◽  
Vol 9 ◽  
Author(s):  
Heather R. Kates ◽  
Fernando López Anido ◽  
Guillermo Sánchez-de la Vega ◽  
Luis E. Eguiarte ◽  
Pamela S. Soltis ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Structure ◽  
Morphological Diversity ◽  
Cucurbita Maxima ◽  
Wild Progenitor ◽  
Breeding Potential ◽  
Trait Improvement ◽  
Wild Progenitors

Studies of domestication genetics enrich our understanding of how domestication shapes genetic and morphological diversity. We characterized patterns of genetic variation in two independently domesticated pumpkins and their wild progenitors to assess and compare genetic consequences of domestication. To compare genetic diversity pre- and post-domestication and to identify genes targeted by selection during domestication, we analyzed ∼15,000 SNPs of 48 unrelated accessions, including wild, landrace, and improved lines for each of two pumpkin species, Cucurbita argyrosperma and Cucurbita maxima. Genetic diversity relative to its wild progenitor was reduced in only one domesticated subspecies, C. argyrosperma ssp. argyrosperma. The two species have different patterns of genetic structure across domestication status. Only 1.5% of the domestication features identified for both species were shared between species. These findings suggest that ancestral genetic diversity, wild-crop gene flow, and domestication practices shaped the genetic diversity of two similar Cucurbita crops in different ways, adding to our understanding of how genetic diversity changes during the processes of domestication and how trait improvement impacts the breeding potential of modern crops.

scholarly journals Geographic patterns of human allele frequency variation: a variant-centric perspective

2020 ◽  
Author(s):  
Arjun Biddanda ◽  
Daniel P. Rice ◽  
John Novembre
Keyword(s):  
Genetic Variation ◽  
Gene Flow ◽  
Genetic Structure ◽  
Allele Frequency ◽  
Human Genetics ◽  
Geographic Region ◽  
Frequency Variation ◽  
Human Genetic Variation ◽  
Alternative Representation ◽  
Geographic Patterns

AbstractA key challenge in human genetics is to describe and understand the distribution of human genetic variation. Often genetic variation is described by showing relationships among populations or individuals, in each case drawing inferences over a large number of variants. Here, we present an alternative representation of human genetic variation that reveals the relative abundance of different allele frequency patterns across populations. This approach allows viewers to easily see several features of human genetic structure: (1) most variants are rare and geographically localized, (2) variants that are common in a single geographic region are more likely to be shared across the globe than to be private to that region, and (3) where two individuals differ, it is most often due to variants that are common globally, regardless of whether the individuals are from the same region or different regions. To guide interpretation of the results, we also apply the visualization to contrasting theoretical scenarios with varying levels of divergence and gene flow. Our variant-centric visualization clarifies the major geographic patterns of human variation and can be used to help correct potential misconceptions about the extent and nature of genetic differentiation among populations.

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.

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