scholarly journals Genome-wide patterns of local adaptation in Drosophila melanogaster: adding intra European variability to the map

2018 ◽  
Author(s):  
Lidia Mateo ◽  
Gabriel E. Rech ◽  
Josefa González
Keyword(s):  
Drosophila Melanogaster ◽  
Population Structure ◽  
Local Adaptation ◽  
Population Differentiation ◽  
Nucleotide Polymorphisms ◽  
Low Levels ◽  
Spatially Varying ◽  
Spatially Varying Selection ◽  
Two Populations ◽  
European Populations

ABSTRACTSignatures of spatially varying selection have been investigated both at the genomic and transcriptomic level in several organisms. In Drosophila melanogaster, the majority of these studies have analyzed North American and Australian populations, leading to the identification of several loci and traits under selection. However, populations in these two continents showed evidence of admixture that likely contributed to the observed population differentiation patterns. Thus, disentangling demography from selection is challenging when analyzing these populations. European populations could be a suitable system to identify loci under spatially varying selection provided that no recent admixture from African populations would have occurred. In this work, we individually sequence the genome of 42 European strains collected in populations from contrasting environments: Stockholm (Sweden), and Castellana Grotte, (Southern Italy). We found low levels of population structure and no evidence of recent African admixture in these two populations. We thus look for patterns of spatially varying selection affecting individual genes and gene sets. Besides single nucleotide polymorphisms, we also investigate the role of transposable elements in local adaptation. We concluded that European populations are a good dataset to identify loci under spatially varying selection. The analysis of the two populations sequenced in this work in the context of all the available D. melanogaster data allowed us to pinpoint genes and biological processes relevant for local adaptation. Identifying and analyzing populations with low levels of population structure and admixture should help to disentangle selective from non-selective forces underlying patterns of population differentiation in other species as well.

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.

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 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 Low genome-wide divergence between two lizard populations with high adaptive phenotypic differentiation

2021 ◽  
Author(s):  
Alejandro Llanos-Garrido ◽  
Javier Pérez-Tris ◽  
José Díaz
Keyword(s):  
Local Adaptation ◽  
Genetic Divergence ◽  
Elevational Gradient ◽  
Phenotypic Differentiation ◽  
Genome Wide ◽  
Isolation By Environment ◽  
Psammodromus Algirus ◽  
Low Levels ◽  
Two Populations ◽  
Degree Of Isolation

Usually, adaptive phenotypic differentiation is paralleled by genetic divergence between locally adapted populations. However, adaptation can also happen in a scenario of non-significant genetic divergence due to intense gene flow and/or recent differentiation. While this phenomenon is rarely published, findings on incipient ecologically-driven divergence or isolation by adaptation are relatively common, which could confound our understanding about the frequency at which they actually occur in nature. Here, we explore genome-wide traces of divergence between two populations of the lacertid lizard Psammodromus algirus separated by a 600 m elevational gradient. These populations seem to be differentially adapted to their environments despite showing low levels of genetic differentiation (according to previously studies of mtDNA and microsatellite data). We performed a search for outliers (i.e. loci subject to selection) trying to identify specific loci with FST statistics significantly higher than those expected on the basis of overall, genome-wide estimates of genetic divergence. We find that local phenotypic adaptation (in terms of a wide diversity of characters) was not accompanied by genome-wide differentiation, even when we maximized the chances of unveiling such differentiation at particular loci with FST-based outlier detection tests. Instead, our analyses confirmed the lack of differentiation on the basis of more than 70,000 SNPs, which is concordant with a scenario of local adaptation without any degree of isolation by environment. Our results add evidence to previous studies in which local adaptation does not lead to any kind of isolation (or early stages of ecological speciation), but maintains phenotypic divergence despite the lack of a differentiated genomic background.

scholarly journals Evidence of Spatially Varying Selection Acting on Four Chromatin-Remodeling Loci in Drosophila melanogaster

Genetics ◽  
2008 ◽  
Vol 179 (1) ◽  
pp. 475-485 ◽  
Author(s):  
Mia T. Levine ◽  
David J. Begun
Keyword(s):  
Drosophila Melanogaster ◽  
Chromatin Remodeling ◽  
Spatially Varying ◽  
Spatially Varying Selection

scholarly journals In absence of local adaptation, plasticity and spatially varying selection rule: a view from genomic reaction norms in a panmictic species (Anguilla rostrata)

BMC Genomics ◽  
2014 ◽  
Vol 15 (1) ◽  
pp. 403 ◽  
Author(s):  
Caroline L Côté ◽  
Martin Castonguay ◽  
McWilliam Kalujnaia ◽  
Gordon Cramb ◽  
Louis Bernatchez
Keyword(s):  
Local Adaptation ◽  
Selection Rule ◽  
Reaction Norms ◽  
Anguilla Rostrata ◽  
Spatially Varying ◽  
Spatially Varying Selection

scholarly journals Population structure of morphological traits in Clarkia dudleyana. I. Comparison of FST between allozymes and morphological traits.

Genetics ◽  
1995 ◽  
Vol 140 (2) ◽  
pp. 733-744
Author(s):  
R H Podolsky ◽  
T P Holtsford
Keyword(s):  
Population Structure ◽  
Population Differentiation ◽  
Morphological Traits ◽  
Allozyme Variation ◽  
True Value ◽  
Quantitative Genetic ◽  
Allozyme Loci ◽  
Two Populations ◽  
Geographic Group ◽  
Continuous Traits

Abstract Studies of genetic variation at allozyme loci, assumed to be selectively neutral, have provided valuable insights into the genetic structure of numerous populations. The degree to which population structure of allozyme variation reflects that of quantitative traits, however, is not well resolved. Here, we compare estimates of population differentiation (FST) of 11 populations for allozymes with those for nine discrete and nine continuous morphological traits. Overall, the allozymes have the lowest FST estimates, indicating relatively little population differentiation. Excepting two traits, petal width and long internode length, the continuous morphological traits have estimates similar to those from allozymes. The discrete morphological traits tend to have the highest estimates. On a single trait basis, estimates of FST for four discrete and two continuous traits are higher than those for allozymes. A more detailed (narrow-sense quantitative) genetic study of two populations suggests that these estimates of FST may underestimate the true value because of dominance. Clustering analyses show that the pattern of differentiation for the discrete morphological traits strongly reflects the geographical distribution of the populations, whereas the patterns for the continuous traits and allozymes do not. These results suggest that selection has been occurring on the discrete morphological traits, selecting toward a common optimum within each geographic group, and optima differing among geographic groups.

scholarly journals Local adaptation and the evolution of inversions on sex chromosomes and autosomes

2018 ◽  
Vol 373 (1757) ◽  
pp. 20170423 ◽  
Author(s):  
Tim Connallon ◽  
Colin Olito ◽  
Ludovic Dutoit ◽  
Homa Papoli ◽  
Filip Ruzicka ◽  
...  
Keyword(s):  
Gene Flow ◽  
Local Adaptation ◽  
Evolutionary Dynamics ◽  
Deleterious Mutation ◽  
Local Selection ◽  
Theoretical Predictions ◽  
Elevated Rate ◽  
Genomic Regions ◽  
Spatially Varying ◽  
Spatially Varying Selection

Spatially varying selection with gene flow can favour the evolution of inversions that bind locally adapted alleles together, facilitate local adaptation and ultimately drive genomic divergence between species. Several studies have shown that the rates of spread and establishment of new inversions capturing locally adaptive alleles depend on a suite of evolutionary factors, including the strength of selection for local adaptation, rates of gene flow and recombination, and the deleterious mutation load carried by inversions. Because the balance of these factors is expected to differ between X (or Z) chromosomes and autosomes, opportunities for inversion evolution are likely to systematically differ between these genomic regions, though such scenarios have not been formally modelled. Here, we consider the evolutionary dynamics of X-linked and autosomal inversions in populations evolving at a balance between migration and local selection. We identify three factors that lead to asymmetric rates of X-linked and autosome inversion establishment: (1) sex-biased migration, (2) dominance of locally adapted alleles and (3) chromosome-specific deleterious mutation loads. This theory predicts an elevated rate of fixation, and depressed opportunities for polymorphism, for X-linked inversions. Our survey of data on the genomic distribution of polymorphic and fixed inversions supports both theoretical predictions. This article is part of the theme issue ‘Linking local adaptation with the evolution of sex differences'.

scholarly journals Functional Analysis of a Putative Target of Spatially Varying Selection in the Menin1 Gene of Drosophila melanogaster

2018 ◽  
Vol 9 (1) ◽  
pp. 73-80 ◽  
Author(s):  
Nicolas Svetec ◽  
Perot Saelao ◽  
Julie M. Cridland ◽  
Ary A. Hoffmann ◽  
David J. Begun
Keyword(s):  
Functional Analysis ◽  
Drosophila Melanogaster ◽  
Putative Target ◽  
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.

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