scholarly journals Genome‐wide patterns of differentiation and spatially varying selection between postglacial recolonization lineages of Populus alba (Salicaceae), a widespread forest tree

2015 ◽  
Vol 207 (3) ◽  
pp. 723-734 ◽  
Author(s):  
Kai N. Stölting ◽  
Margot Paris ◽  
Cécile Meier ◽  
Berthold Heinze ◽  
Stefano Castiglione ◽  
...  
Keyword(s):  
Forest Tree ◽  
Populus Alba ◽  
Genome Wide ◽  
Postglacial Recolonization ◽  
Spatially Varying ◽  
Spatially Varying Selection

scholarly journals Global adaptation confounds the search for local adaptation

2019 ◽  
Author(s):  
Tom R. Booker ◽  
Sam Yeaman ◽  
Michael C. Whitlock
Keyword(s):  
Genetic Differentiation ◽  
Local Adaptation ◽  
Natural Populations ◽  
Wide Distribution ◽  
Structured Populations ◽  
Substantial Contribution ◽  
Beneficial Mutations ◽  
Genome Wide ◽  
Spatially Varying ◽  
Spatially Varying Selection

AbstractSpatially varying selection promotes variance in allele frequencies, increasing genetic differentiation between the demes of a metapopulation. For that reason, outliers in the genome wide distribution of summary statistics measuring genetic differentiation, such as FST, are often interpreted as evidence for alleles which contribute to local adaptation. However, in spatially structured populations, the spread of beneficial mutations with spatially uniform effects can also induce transient genetic differentiation and numerous theoretical studies have suggested that species-wide, or global, adaptation makes a substantial contribution to molecular evolution. In this study, we ask whether such global adaptation affects the genome-wide distribution of FST and generates statistical outliers which could be mistaken for local adaptation. Using forward-in-time population genetic simulations assuming parameters for the rate and strength of beneficial mutations similar to those that have been estimated for natural populations, we show the spread of globally beneficial in parapatric populations can readily generate FST outliers, which may be misinterpreted as evidence for local adaptation. The spread of beneficial mutations causes selective sweeps at flanking sites, so the effects of global versus local adaptation may be distinguished by examining patterns of nucleotide diversity along with FST. Our study suggests that global adaptation should be considered in the interpretation of genome-scan results and the design of future studies aimed at understanding the genetic basis of local adaptation.

scholarly journals Secondary contact and local adaptation contribute to genome-wide patterns of clinal variation in Drosophila melanogaster

2014 ◽  
Author(s):  
Alan O. Bergland ◽  
Ray Tobler ◽  
Josefa Gonzalez ◽  
Paul Schmidt ◽  
Dmitri Petrov
Keyword(s):  
Drosophila Melanogaster ◽  
North America ◽  
Local Adaptation ◽  
Latitudinal Gradients ◽  
Secondary Contact ◽  
Clinal Variation ◽  
Evolutionary Forces ◽  
Genome Wide ◽  
Spatially Varying ◽  
Spatially Varying Selection

Populations arrayed along broad latitudinal gradients often show patterns of clinal variation in phenotype and genotype. Such population differentiation can be generated and maintained by historical demographic events and local adaptation. These evolutionary forces are not mutually exclusive and, moreover, can in some cases produce nearly identical patterns of genetic differentiation among populations. Here, we investigate the evolutionary forces that generated and maintain clinal variation genome-wide among populations ofDrosophila melanogastersampled in North America and Australia. We contrast patterns of clinal variation in these continents with patterns of differentiation among ancestral European and African populations. Using established and novel methods we derive here, we show that recently derived North America and Australia populations were likely founded by both European and African lineages and that this admixture event contributed to genome-wide patterns of parallel clinal variation. The pervasive effects of admixture meant that only a handful of loci could be attributed to the operation of spatially varying selection using an FST outlier approach. Our results provide novel insight into the well-studied system of clinal differentiation inD. melanogasterand provide a context for future studies seeking to identify loci contributing to local adaptation in a wide variety of organisms, including other invasive species as well as some temperate endemics.

Genome-wide set of SNPs reveals evidence for two glacial refugia and admixture from postglacial recolonization in an alpine ungulate

2016 ◽  
Vol 25 (15) ◽  
pp. 3696-3705 ◽  
Author(s):  
Zijian Sim ◽  
Jocelyn C. Hall ◽  
Bill Jex ◽  
Troy M. Hegel ◽  
David W. Coltman
Keyword(s):  
Glacial Refugia ◽  
Genome Wide ◽  
Postglacial Recolonization

scholarly journals Spatially varying selection shapes life history clines among populations of Drosophila melanogaster from sub-Saharan Africa

2015 ◽  
Vol 28 (4) ◽  
pp. 826-840 ◽  
Author(s):  
D. K. Fabian ◽  
J. B. Lack ◽  
V. Mathur ◽  
C. Schlötterer ◽  
P. S. Schmidt ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Life History ◽  
Sub Saharan Africa ◽  
Sub Saharan ◽  
Spatially Varying ◽  
Spatially Varying Selection

scholarly journals The Genetic Consequences of Spatially Varying Selection in the Panmictic American Eel (Anguilla rostrata)

Genetics ◽  
2011 ◽  
Vol 190 (2) ◽  
pp. 725-736 ◽  
Author(s):  
Pierre-Alexandre Gagnaire ◽  
Eric Normandeau ◽  
Caroline Côté ◽  
Michael Møller Hansen ◽  
Louis Bernatchez
Keyword(s):  
Anguilla Rostrata ◽  
American Eel ◽  
Spatially Varying ◽  
Spatially Varying Selection

scholarly journals Major QTL controls adaptation to serpentine soils in Mimulus guttatus

2018 ◽  
Author(s):  
Jessica P. Selby ◽  
John H. Willis
Keyword(s):  
Genetic Basis ◽  
Common Garden ◽  
Serpentine Soils ◽  
Mimulus Guttatus ◽  
Fitness Effects ◽  
Spatially Varying ◽  
Spatially Varying Selection ◽  
Physical Challenges ◽  
Two Populations ◽  
Major Qtl

ABSTRACTSpatially varying selection is a critical driver of adaptive differentiation. Yet, there are few examples where the fitness effects of naturally segregating variants that contribute to local adaptation have been measured in the field. This project investigates the genetic basis of adaption to serpentine soils in Mimulus guttatus. Reciprocal transplant studies show that serpentine and non-serpentine populations of M. guttatus are genetically differentiated in their ability to survive on serpentine soils. We mapped serpentine tolerance by performing a bulk segregant analysis on F2 survivors from a field transplant study and identify a single QTL where individuals that are homozygous for the non-serpentine allele do not survive on serpentine soils. This same QTL controls serpentine tolerance in a second, geographically distant population. A common garden study where the two serpentine populations were grown on each other′s soil finds that one of the populations has significantly lower survival on this “foreign” serpentine soil compared to its home soil. So, while these two populations share a major QTL they either differ at other loci involved in serpentine adaptation or have different causal alleles at this QTL. This raises the possibility that serpentine populations may not be broadly tolerant to serpentine soils but may instead be locally adapted to their particular patch. Nevertheless, despite the myriad chemical and physical challenges that plants face in serpentine habitats, adaptation to these soils in M. guttatus has a simple genetic basis.

scholarly journals Evidence for widespread selection in shaping the genomic landscape during speciation of Populus

2019 ◽  
Author(s):  
Jing Wang ◽  
Nathaniel R. Street ◽  
Eung-Jun Park ◽  
Jianquan Liu ◽  
Pär K. Ingvarsson
Keyword(s):  
Recurrent Selection ◽  
Balancing Selection ◽  
Forest Tree ◽  
Species Variation ◽  
Recombination Rates ◽  
Genome Wide ◽  
Genomic Landscape ◽  
Speciation Continuum ◽  
Whole Genome Resequencing

AbstractIncreasing our understanding of how various evolutionary processes drive the genomic landscape of variation is fundamental to a better understanding of the genomic consequences of speciation. However, the genome-wide patterns of within- and between-species variation have not been fully investigated in most forest tree species despite their global ecological and economic importance. Here, we use whole-genome resequencing data from four Populus species spanning the speciation continuum to reconstruct their demographic histories, investigate patterns of diversity and divergence, infer their genealogical relationships and estimate the extent of ancient introgression across the genome. Our results show substantial variation in these patterns along the genomes although this variation is not randomly distributed but is strongly predicted by the local recombination rates and the density of functional elements. This implies that the interaction between recurrent selection and intrinsic genomic features has dramatically sculpted the genomic landscape over long periods of time. In addition, our findings provide evidence that, apart from background selection, recent positive selection and long-term balancing selection are also crucial components in shaping patterns of genome-wide variation during the speciation process.

scholarly journals Nucleotide Polymorphism and Natural Selection at the Pantophysin (Pan I) Locus in the Atlantic Cod, Gadus morhua (L.)

Genetics ◽  
2001 ◽  
Vol 157 (1) ◽  
pp. 317-330 ◽  
Author(s):  
Grant H Pogson
Keyword(s):  
Natural Selection ◽  
Amino Acid ◽  
Gadus Morhua ◽  
Atlantic Cod ◽  
Amino Acid Level ◽  
Amino Acid Substitutions ◽  
Significant Heterogeneity ◽  
Nucleotide Sequence Variation ◽  
Spatially Varying ◽  
Spatially Varying Selection

Abstract Molecular studies of nucleotide sequence variation have rarely attempted to test hypotheses related to geographically varying patterns of natural selection. The present study tested the role of spatially varying selection in producing significant linkage disequilibrium and large differences in the frequencies of two common alleles at the pantophysin (Pan I) locus among five populations of the Atlantic cod, Gadus morhua. Nucleotide sequences of 124 Pan I alleles showed strong evidence for an unusual mix of balancing and directional selection but no evidence of stable geographically varying selection. The alleles were highly divergent at both the nucleotide level (differing on average by 19 mutations) and at amino acid level (each having experienced three amino acid substitutions since diverging from a common ancestral allele). All six amino acid substitutions occurred in a 56-residue intravesicular loop (IV1 domain) of the vesicle protein and each involved a radical change. An analysis of molecular variation revealed significant heterogeneity in the frequencies of recently derived mutations segregating within both allelic classes, suggesting that two selective sweeps may be presently occurring among populations. The dynamic nature of the Pan I polymorphism in G. morhua and clear departure from equilibrium conditions invalidate a simple model of spatially varying selection.

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