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 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 inDrosophila melanogaster

2016 ◽  
Vol 25 (5) ◽  
pp. 1157-1174 ◽  
Author(s):  
Alan O. Bergland ◽  
Ray Tobler ◽  
Josefa González ◽  
Paul Schmidt ◽  
Dmitri Petrov
Keyword(s):  
Local Adaptation ◽  
Secondary Contact ◽  
Clinal Variation ◽  
Genome Wide

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 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 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 Local adaptation fuels cryptic speciation in terrestrial annelids

2019 ◽  
Author(s):  
Daniel Fernández Marchán ◽  
Marta Novo ◽  
Nuria Sánchez ◽  
Jorge Domínguez ◽  
Darío J. Díaz Cosín ◽  
...  
Keyword(s):  
Geometric Morphometrics ◽  
Cryptic Species ◽  
Local Adaptation ◽  
Evolutionary Biology ◽  
Morphological Evolution ◽  
Phylogenetic Signal ◽  
Regulation Of Transcription ◽  
Cryptic Speciation ◽  
Evolutionary Forces ◽  
Genome Wide

AbstractUncovering the genetic and evolutionary basis of cryptic speciation is a major focus of evolutionary biology. Next Generation Sequencing (NGS) allows the identification of genome-wide local adaptation signatures, but has rarely been applied to cryptic complexes - particularly in the soil milieu - as is the case with integrative taxonomy. The earthworm genus Carpetania, comprising six previously suggested putative cryptic lineages, is a promising model to study the evolutionary phenomena shaping cryptic speciation in soil-dwelling lineages. Genotyping-By-Sequencing (GBS) was used to provide genome-wide information about genetic variability between seventeen populations, and geometric morphometrics analyses of genital chaetae were performed to investigate unexplored cryptic morphological evolution. Genomic analyses revealed the existence of three cryptic species, with half of the previously-identified potential cryptic lineages clustering within them. Local adaptation was detected in more than 800 genes putatively involved in a plethora of biological functions (most notably reproduction, metabolism, immunological response and morphogenesis). Several genes with selection signatures showed shared mutations for each of the cryptic species, and genes under selection were enriched in functions related to regulation of transcription, including SNPs located in UTR regions. Finally, geometric morphometrics approaches partially confirmed the phylogenetic signal of relevant morphological characters such as genital chaetae. Our study therefore unveils that local adaptation and regulatory divergence are key evolutionary forces orchestrating genome evolution in soil fauna.

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 Genomic islands of divergence or opportunities for introgression?

2017 ◽  
Vol 284 (1850) ◽  
pp. 20162414 ◽  
Author(s):  
Rachael A. Bay ◽  
Kristen Ruegg
Keyword(s):  
Gene Flow ◽  
Reproductive Isolation ◽  
Genomic Islands ◽  
Secondary Contact ◽  
Catharus Ustulatus ◽  
Adaptive Introgression ◽  
Evolutionary Forces ◽  
Genome Wide ◽  
Isolating Mechanisms ◽  
Migratory Songbird

In animals, introgression between species is often perceived as the breakdown of reproductive isolating mechanisms, but gene flow between incipient species can also represent a source for potentially beneficial alleles. Recently, genome-wide datasets have revealed clusters of differentiated loci (‘genomic islands of divergence’) that are thought to play a role in reproductive isolation and therefore have reduced gene flow. We use simulations to further examine the evolutionary forces that shape and maintain genomic islands of divergence between two subspecies of the migratory songbird, Swainson's thrush ( Catharus ustulatus ), which have come into secondary contact since the last glacial maximum. We find that, contrary to expectation, gene flow is high within islands and is highly asymmetric. In addition, patterns of nucleotide diversity at highly differentiated loci suggest selection was more frequent in a single ecotype. We propose a mechanism whereby beneficial alleles spread via selective sweeps following a post-glacial demographic expansion in one subspecies and move preferentially across the hybrid zone. We find no evidence that genomic islands are the result of divergent selection or reproductive isolation, rather our results suggest that differentiated loci both within and outside islands could provide opportunities for adaptive introgression across porous species boundaries.

scholarly journals Genome-wide patterns of local adaptation in Western European Drosophila melanogaster natural populations

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Lidia Mateo ◽  
Gabriel E. Rech ◽  
Josefa González
Keyword(s):  
Drosophila Melanogaster ◽  
Local Adaptation ◽  
Natural Populations ◽  
Genome Wide ◽  
Western European
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