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 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 Crypsis Decreases with Elevation in a Lizard

Diversity ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 236 ◽  
Author(s):  
Gregorio Moreno-Rueda ◽  
Laureano G. González-Granda ◽  
Senda Reguera ◽  
Francisco J. Zamora-Camacho ◽  
Elena Melero
Keyword(s):  
Local Adaptation ◽  
Sierra Nevada ◽  
Elevational Gradient ◽  
Bare Soil ◽  
High Elevation ◽  
Dorsal Skin ◽  
Se Spain ◽  
Psammodromus Algirus ◽  
Selection For ◽  
High Elevations

Predation usually selects for visual crypsis, the colour matching between an animal and its background. Geographic co-variation between animal and background colourations is well known, but how crypsis varies along elevational gradients remains unknown. We predict that dorsal colouration in the lizard Psammodromus algirus should covary with the colour of bare soil—where this lizard is mainly found—along a 2200 m elevational gradient in Sierra Nevada (SE Spain). Moreover, we predict that crypsis should decrease with elevation for two reasons: (1) Predation pressure typically decreases with elevation, and (2) at high elevation, dorsal colouration is under conflicting selection for both crypsis and thermoregulation. By means of standardised photographies of the substratum and colourimetric measurements of lizard dorsal skin, we tested the colour matching between lizard dorsum and background. We found that, along the gradient, lizard dorsal colouration covaried with the colouration of bare soil, but not with other background elements where the lizard is rarely detected. Moreover, supporting our prediction, the degree of crypsis against bare soil decreased with elevation. Hence, our findings suggest local adaptation for crypsis in this lizard along an elevational gradient, but this local adaptation would be hindered at high elevations.

scholarly journals The impact of global selection on local adaptation and reproductive isolation

2019 ◽  
Author(s):  
Gertjan Bisschop ◽  
Derek Setter ◽  
Marina Rafajlović ◽  
Stuart J.E. Baird ◽  
Konrad Lohse
Keyword(s):  
Gene Flow ◽  
Reproductive Isolation ◽  
Local Adaptation ◽  
Genetic Load ◽  
Divergent Selection ◽  
Mutation Process ◽  
Genome Wide ◽  
The Impact ◽  
Two Populations ◽  
Global Selection

AbstractDespite the homogenising effect of strong gene flow between two populations, adaptation under symmetric divergent selection pressures results in partial reproductive isolation: adaptive substitutions act as local barriers to gene flow, and if divergent selection continues unimpeded, this will result in complete reproductive isolation of the two populations, i.e. speciation. However, a key issue in framing the process of speciation as a tension between local adaptation and the homogenising force of gene flow is that the mutation process is blind to changes in the environment and therefore tends to limit adaptation. Here we investigate how globally beneficial mutations (GBMs) affect divergent local adaptation and reproductive isolation. When phenotypic divergence is finite, we show that the presence of GBMs limits local adaptation, generating a persistent genetic load at the loci which contribute to the trait under divergent selection and reducing genome-wide divergence. Furthermore, we show that while GBMs cannot prohibit the process of continuous differentiation, they induce a substantial delay in the genome-wide shutdown of gene flow.

scholarly journals The impact of global selection on local adaptation and reproductive isolation

2020 ◽  
Vol 375 (1806) ◽  
pp. 20190531 ◽  
Author(s):  
Gertjan Bisschop ◽  
Derek Setter ◽  
Marina Rafajlović ◽  
Stuart J. E. Baird ◽  
Konrad Lohse
Keyword(s):  
Gene Flow ◽  
Reproductive Isolation ◽  
Local Adaptation ◽  
Genetic Load ◽  
Divergent Selection ◽  
Mutation Process ◽  
Genome Wide ◽  
The Impact ◽  
Two Populations ◽  
Global Selection

Despite the homogenizing effect of strong gene flow between two populations, adaptation under symmetric divergent selection pressures results in partial reproductive isolation: adaptive substitutions act as local barriers to gene flow, and if divergent selection continues unimpeded, this will result in complete reproductive isolation of the two populations, i.e. speciation. However, a key issue in framing the process of speciation as a tension between local adaptation and the homogenizing force of gene flow is that the mutation process is blind to changes in the environment and therefore tends to limit adaptation. Here we investigate how globally beneficial mutations (GBMs) affect divergent local adaptation and reproductive isolation. When phenotypic divergence is finite, we show that the presence of GBMs limits local adaptation, generating a persistent genetic load at the loci that contribute to the trait under divergent selection and reducing genome-wide divergence. Furthermore, we show that while GBMs cannot prohibit the process of continuous differentiation, they induce a substantial delay in the genome-wide shutdown of gene flow. This article is part of the theme issue ‘Towards the completion of speciation: the evolution of reproductive isolation beyond the first barriers’.

scholarly journals The Advantages of Segregation and the Evolution of Sex

Genetics ◽  
2003 ◽  
Vol 164 (3) ◽  
pp. 1099-1118 ◽  
Author(s):  
Sarah P Otto
Keyword(s):  
Sexual Reproduction ◽  
Asexual Reproduction ◽  
Deleterious Mutations ◽  
Evolution Of Sex ◽  
Beneficial Mutations ◽  
Selection Regime ◽  
Strong Selection ◽  
Genome Wide ◽  
Low Levels

AbstractIn diploids, sexual reproduction promotes both the segregation of alleles at the same locus and the recombination of alleles at different loci. This article is the first to investigate the possibility that sex might have evolved and been maintained to promote segregation, using a model that incorporates both a general selection regime and modifier alleles that alter an individual’s allocation to sexual vs. asexual reproduction. The fate of different modifier alleles was found to depend strongly on the strength of selection at fitness loci and on the presence of inbreeding among individuals undergoing sexual reproduction. When selection is weak and mating occurs randomly among sexually produced gametes, reductions in the occurrence of sex are favored, but the genome-wide strength of selection is extremely small. In contrast, when selection is weak and some inbreeding occurs among gametes, increased allocation to sexual reproduction is expected as long as deleterious mutations are partially recessive and/or beneficial mutations are partially dominant. Under strong selection, the conditions under which increased allocation to sex evolves are reversed. Because deleterious mutations are typically considered to be partially recessive and weakly selected and because most populations exhibit some degree of inbreeding, this model predicts that higher frequencies of sex would evolve and be maintained as a consequence of the effects of segregation. Even with low levels of inbreeding, selection is stronger on a modifier that promotes segregation than on a modifier that promotes recombination, suggesting that the benefits of segregation are more likely than the benefits of recombination to have driven the evolution of sexual reproduction in diploids.

Genome‐wide epigenetic isolation by environment in a widespread Anolis lizard

2019 ◽  
Vol 29 (1) ◽  
pp. 40-55 ◽  
Author(s):  
Guinevere O. U. Wogan ◽  
Michael L. Yuan ◽  
D. Luke Mahler ◽  
Ian J. Wang
Keyword(s):  
Anolis Lizard ◽  
Genome Wide ◽  
Isolation By Environment

scholarly journals SNP-level FST outperforms window statistics for detecting soft sweeps in local adaptation

2022 ◽  
Author(s):  
Tiago da Silva Ribeiro ◽  
José A Galván ◽  
John E Pool
Keyword(s):  
Genetic Differentiation ◽  
Local Adaptation ◽  
Genetic Variant ◽  
Real Data ◽  
Selective Sweeps ◽  
Functional Categories ◽  
Genome Scans ◽  
Genome Wide ◽  
A Genome ◽  
Local Selection

Local adaptation can lead to elevated genetic differentiation at the targeted genetic variant and nearby sites. Selective sweeps come in different forms, and depending on the initial and final frequencies of a favored variant, very different patterns of genetic variation may be produced. If local selection favors an existing variant that had already recombined onto multiple genetic backgrounds, then the width of elevated genetic differentiation (high FST) may be too narrow to detect using a typical windowed genome scan, even if the targeted variant becomes highly differentiated. We therefore used a simulation approach to investigate the power of SNP-level FST (specifically, the maximum SNP FST value within a window) to detect diverse scenarios of local adaptation, and compared it against whole-window FST and the Comparative Haplotype Identity statistic. We found that SNP FST had superior power to detect complete or mostly complete soft sweeps, but lesser power than window-wide statistics to detect partial hard sweeps. To investigate the relative enrichment and nature of SNP FST outliers from real data, we applied the two FST statistics to a panel of Drosophila melanogaster populations. We found that SNP FST had a genome-wide enrichment of outliers compared to demographic expectations, and though it yielded a lesser enrichment than window FST, it detected mostly unique outlier genes and functional categories. Our results suggest that SNP FST is highly complementary to typical window-based approaches for detecting local adaptation, and merits inclusion in future genome scans and methodologies.

scholarly journals Evolutionary inference from QST-FST comparisons: disentangling local adaptation from altitudinal gradient selection in snapdragon plants

2018 ◽  
Author(s):  
Sara Marin ◽  
Juliette Archambeau ◽  
Vincent Bonhomme ◽  
Mylène Lascoste ◽  
Benoit Pujol
Keyword(s):  
Local Adaptation ◽  
Natural Populations ◽  
Common Garden ◽  
Global Scale ◽  
Structured Populations ◽  
Adaptive Divergence ◽  
Adaptation To Climate Change ◽  
Phenotypic Differentiation ◽  
Multiple Populations ◽  
Environmental Demand

ABSTRACTPhenotypic differentiation among natural populations can be explained by natural selection or by neutral processes such as drift. There are many examples in the literature where comparing the effects of these processes on multiple populations has allowed the detection of local adaptation. However, these studies rarely identify the agents of selection. Whether population adaptive divergence is caused by local features of the environment, or by the environmental demand emerging at a more global scale, for example along altitudinal gradients, is a question that remains poorly investigated. Here, we measured neutral genetic (FST) and quantitative genetic (QST) differentiation among 13 populations of snapdragon plants (Antirrhinum majus) in a common garden experiment. We found low but significant genetic differentiation at putatively neutral markers, which supports the hypothesis of either ongoing pervasive homogenisation via gene flow between diverged populations or reproductive isolation between disconnected populations. Our results also support the hypothesis of local adaptation involving phenological, morphological, reproductive and functional traits. They also showed that phenotypic differentiation increased with altitude for traits reflecting the reproduction and the phenology of plants, thereby confirming the role of such traits in their adaptation to environmental differences associated with altitude. Our approach allowed us to identify candidate traits for the adaptation to climate change in snapdragon plants. Our findings imply that environmental conditions changing with altitude, such as the climatic envelope, influenced the adaptation of multiple populations of snapdragon plants on the top of their adaptation to local environmental features. They also have implications for the study of adaptive evolution in structured populations because they highlight the need to disentangle the adaptation of plant populations to climate envelopes and altitude from the confounding effects of selective pressures acting specifically at the local scale of a population.

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