Global adaptation confounds the search for local adaptation

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.

Download Full-text

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

10.1101/009084 ◽

2014 ◽

Cited By ~ 2

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.

Download Full-text

Population Genetics and Evolution Analysis Reveal Diversity and Origin of Ammopiptanthus in China.

10.21203/rs.3.rs-779119/v1 ◽

2021 ◽

Author(s):

Guai-qiang Chai ◽

Yizhong Duan ◽

Peipei Jiao ◽

Zhongyu Du ◽

Furen Kang

Keyword(s):

Genetic Diversity ◽

Genetic Structure ◽

Genetic Differentiation ◽

Association Studies ◽

Natural Populations ◽

Principal Component ◽

Nucleotide Polymorphisms ◽

Future Design ◽

Ammopiptanthus Nanus ◽

Genome Wide

Abstract Background：Elucidating and revealing the population genetic structure, genetic diversity and recombination is essential for understanding the evolution and adaptation of species. Ammopiptanthus, which is an endangered survivor from the Tethys in the Tertiary Period, is the only evergreen broadleaf shrub grown in Northwest of China. However, little is known about its genetic diversity and underlying adaptation mechanisms. Results：Here, 111 Ammopiptanthus individuals collected from fifteen natural populations in estern China were analyzed by means of the specific locus amplified fragment sequencing (SLAF-seq). Based on the single nucleotide polymorphisms (SNPs) and insertions and deletions (InDels) detected by SLAF-seq, genetic diversity and markers associated with climate and geographical distribution variables were identified. The results of genetic diversity and genetic differentiation revealed that all fifteen populations showed medium genetic diversity, with PIC values ranging from 0.1648 to 0.3081. AMOVA and Fst indicated that a low genetic differentiation existed among populations. Phylogenetic analysis showed that NX-BG and NMG-DQH of fifteen populations have the highest homology，while the genetic structure analysis revealed that these Ammopiptanthus germplasm accessions were structured primarily along the basis of their geographic collection, and that an extensive admixture occurred in each group. In addition, the genome-wide linkage disequilibrium (LD) and principal component analysis showed that Ammopiptanthus nanus had a more diverse genomic background, and all genetic populations were clearly distinguished, although different degrees of introgression were detected in these groups. Conclusion：Our study could provide guidance to the future design of association studies and the systematic utilization and protection of the genetic variation characterizing the Ammopiptanthus.

Download Full-text

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

10.1101/2022.01.12.476036 ◽

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.

Download Full-text

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

10.1101/385377 ◽

2018 ◽

Cited By ~ 1

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.

Download Full-text

Low but significant genetic differentiation underlies biologically meaningful phenotypic divergence in a large Atlantic salmon population

10.1101/022178 ◽

2015 ◽

Author(s):

Tutku Aykanat ◽

Susan E Johnston ◽

Panu Orell ◽

Eero Niemelä ◽

Jaakko Erkinaro ◽

...

Keyword(s):

Life History ◽

Genetic Differentiation ◽

Atlantic Salmon ◽

Genetic Divergence ◽

Natural Populations ◽

Structured Populations ◽

Life History Strategies ◽

Adaptive Divergence ◽

Juvenile Growth ◽

Significant Genetic Differentiation

Despite decades of research assessing the genetic structure of natural populations, the biological meaning of low yet significant genetic divergence often remains unclear due to a lack of associated phenotypic and ecological information. At the same time, structured populations with low genetic divergence and overlapping boundaries can potentially provide excellent models to study adaptation and reproductive isolation in cases where high resolution genetic markers and relevant phenotypic and life history information are available. Here, we combined SNP-based population inference with extensive phenotypic and life history data to identify potential biological mechanisms driving fine scale sub-population differentiation in Atlantic salmon (Salmo salar) from the Teno River, a major salmon river in Europe. Two sympatrically occurring sub-populations had low but significant genetic differentiation (FST = 0.018) and displayed marked differences in the distribution of life history strategies, including variation in juvenile growth rate, age at maturity and size within age classes. Large, late-maturing individuals were virtually absent from one of the two sub-populations and there were significant differences in juvenile growth rates and size-at-age after oceanic migration between individuals in the respective sub-populations. Our findings suggest that different evolutionary processes affect each sub-population and that hybridization and subsequent selection may maintain low genetic differentiation without hindering adaptive divergence.

Download Full-text

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 ◽

10.1186/1471-2164-15-403 ◽

2014 ◽

Vol 15 (1) ◽

pp. 403 ◽

Cited By ~ 35

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

Download Full-text

Genetic differentiation of mainland-island sheep of Greece: Implications for identifying candidate genes for long-term local adaptation

PLoS ONE ◽

10.1371/journal.pone.0257461 ◽

2021 ◽

Vol 16 (9) ◽

pp. e0257461

Author(s):

Antonios Kominakis ◽

Eirini Tarsani ◽

Ariadne L. Hager-Theodorides ◽

Ioannis Mastranestasis ◽

Dimitra Gkelia ◽

...

Keyword(s):

Genetic Differentiation ◽

Candidate Genes ◽

Local Adaptation ◽

Ecological Niches ◽

P Value ◽

Positional Candidate ◽

Island Populations ◽

Significant Marker ◽

Genome Wide ◽

Wide Range

In Greece, a number of local sheep breeds are raised in a wide range of ecological niches across the country. These breeds can be used for the identification of genetic variants that contribute to local adaptation. To this end, 50k genotypes of 90 local sheep from mainland Greece (Epirus, n = 35 and Peloponnesus, n = 55) were used, as well as 147 genotypes of sheep from insular Greece (Skyros, n = 21), Lemnos, n = 36 and Lesvos, n = 90). Principal components and phylogenetic analysis along with admixture and spatial point patterns analyses suggested genetic differentiation of ‘mainland-island’ populations. Genome scans for signatures of selection and genome-wide association analysis (GWAS) pointed to one highly differentiating marker on OAR4 (FST = 0.39, FLK = 21.93, FDR p-value = 0.10) that also displayed genome wide significance (FDR p-value = 0.002) during GWAS. A total number of 6 positional candidate genes (LOC106990429, ZNF804B, TEX47, STEAP4, SRI and ADAM22) were identified within 500 kb flanking regions around the significant marker. In addition, two QTLs related to fat tail deposition are reported in genomic regions 800 kb downstream the significant marker. Based on gene ontology analysis and literature evidence, the identified candidate genes possess biological functions relevant to local adaptation that worth further investigation.

Download Full-text

MICROGEOGRAPHIC DIFFERENTIATION OF CHROMOSOMAL AND ENZYME POLYMORPHISMS IN DROSOPHILA PERSIMILIS

Genetics ◽

10.1093/genetics/85.4.681 ◽

1977 ◽

Vol 85 (4) ◽

pp. 681-695 ◽

Cited By ~ 1

Author(s):

Charles E Taylor ◽

Jeffrey R Powell

Keyword(s):

Habitat Preferences ◽

Natural Populations ◽

Genetic Load ◽

Heterogeneous Environments ◽

Behavioral Differences ◽

Chromosome Inversion ◽

Enzyme Polymorphisms ◽

Drosophila Persimilis ◽

Spatially Varying ◽

Spatially Varying Selection

ABSTRACT We studied microgeographic and temporal genetic differentiation in natural populations of Drosophila persimilis with respect to chromosome inversion and enzyme polymorphisms. Both inversion frequencies and allozyme frequencies varied significantly over short distances. Neither differed significantly between morning and evening collections. Because several studies of the dispersal behavior of this species have been performed, we attempt to fit the observed data to mathematical models which relate dispersion to random genetic drift and to spatially varying selection coefficients. We conclude that the observations are due at least partly to behavioral differences among genotypes. i.e., habitat preferences. These results have implications for genetic load theory and models of selection in heterogeneous environments.

Download Full-text