scholarly journals Demographic history and genomics of local adaptation in blue tit populations

2020 ◽  
Vol 13 (6) ◽  
pp. 1145-1165 ◽  
Author(s):  
Charles Perrier ◽  
Quentin Rougemont ◽  
Anne Charmantier
Keyword(s):  
Local Adaptation ◽  
Demographic History ◽  
Blue Tit

scholarly journals Demographic history and genomics of local adaptation in blue tit populations

2019 ◽  
Author(s):  
Perrier Charles ◽  
Rougemont Quentin ◽  
Charmantier Anne
Keyword(s):  
Local Adaptation ◽  
Evolutionary Biology ◽  
Demographic History ◽  
Habitat Type ◽  
Divergent Selection ◽  
Effective Population ◽  
Blue Tit ◽  
Demographic Modeling ◽  
Local Selection ◽  
Spatio Temporal

AbstractUnderstanding the genomic processes underlying local adaptation is a central aim of modern evolutionary biology. This task requires identifying footprints of local selection but also estimating spatio-temporal variation in population demography and variation in recombination rate and diversity along the genome. Here, we investigated these parameters in blue tit populations inhabiting deciduous versus evergreen forests and insular versus mainland areas, in the context of a previously described strong phenotypic differentiation. Neighboring population pairs of deciduous and evergreen habitats were weakly genetically differentiated (FST = 0.004 on average), nevertheless with a statistically significant effect of habitat type on the overall genetic structure. This low differentiation was consistent with the strong and long-lasting gene flow between populations, inferred by demographic modeling. In turn, insular and mainland populations were moderately differentiated (FST = 0.08 on average), in line with the inference of moderate ancestral migrations, followed by isolation since the end of the last glaciation. Effective population sizes were overall large, yet smaller on the island than on the mainland. Weak and non-parallel footprints of divergent selection between deciduous and evergreen populations were consistent with their high connectivity and the probable polygenic nature of local adaptation in these habitats. In turn, stronger footprints of divergent selection were identified between long isolated insular versus mainland birds, and were more often found in regions of low recombination as expected from theory. Lastly, we identified a genomic inversion on the mainland, spanning 2.8Mb. These results provide insights into the demographic history and genetic architecture of local adaptation in blue tit populations at multiple geographic scales.

scholarly journals Genomic Patterns of Local Adaptation under Gene Flow in Arabidopsis lyrata

2019 ◽  
Vol 36 (11) ◽  
pp. 2557-2571 ◽  
Author(s):  
Tuomas Hämälä ◽  
Outi Savolainen
Keyword(s):  
Gene Flow ◽  
Local Adaptation ◽  
Demographic History ◽  
Rate Variation ◽  
Arabidopsis Lyrata ◽  
Trade Offs ◽  
Northern Latitudes ◽  
Local Selection ◽  
Empirical Level ◽  
Selected Traits

AbstractShort-scale local adaptation is a complex process involving selection, migration, and drift. The expected effects on the genome are well grounded in theory but examining these on an empirical level has proven difficult, as it requires information about local selection, demographic history, and recombination rate variation. Here, we use locally adapted and phenotypically differentiated Arabidopsis lyrata populations from two altitudinal gradients in Norway to test these expectations at the whole-genome level. Demography modeling indicates that populations within the gradients diverged <2 kya and that the sites are connected by gene flow. The gene flow estimates are, however, highly asymmetric with migration from high to low altitudes being several times more frequent than vice versa. To detect signatures of selection for local adaptation, we estimate patterns of lineage-specific differentiation among these populations. Theory predicts that gene flow leads to concentration of adaptive loci in areas of low recombination; a pattern we observe in both lowland-alpine comparisons. Although most selected loci display patterns of conditional neutrality, we found indications of genetic trade-offs, with one locus particularly showing high differentiation and signs of selection in both populations. Our results further suggest that resistance to solar radiation is an important adaptation to alpine environments, while vegetative growth and bacterial defense are indicated as selected traits in the lowland habitats. These results provide insights into genetic architectures and evolutionary processes driving local adaptation under gene flow. We also contribute to understanding of traits and biological processes underlying alpine adaptation in northern latitudes.

scholarly journals Population structure, demographic history and local adaptation of the grass carp

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Yubang Shen ◽  
Le Wang ◽  
Jianjun Fu ◽  
Xiaoyan Xu ◽  
Gen Hua Yue ◽  
...  
Keyword(s):  
Population Structure ◽  
Local Adaptation ◽  
Grass Carp ◽  
Demographic History

scholarly journals Thermal adaptation rather than demographic history drives genetic structure inferred by copy number variants in a marine fish

2020 ◽  
Author(s):  
Hugo Cayuela ◽  
Yann Dorant ◽  
Claire Mérot ◽  
Martin Laporte ◽  
Eric Normandeau ◽  
...  
Keyword(s):  
Genetic Structure ◽  
Reproductive Isolation ◽  
Local Adaptation ◽  
Population Genetic Structure ◽  
Copy Number ◽  
Population Genetic ◽  
Demographic History ◽  
Copy Number Variants ◽  
Protein Coding ◽  
Protein Coding Genes

AbstractIncreasing evidence shows that structural variants represent an overlooked aspect of genetic variation with consequential evolutionary roles. Among those, copy number variants (CNVs), including duplicated genomic region and transposable elements (TEs) may contribute to local adaptation and/or reproductive isolation among divergent populations. Those mechanisms suppose that CNVs could be important drivers of population genetic structure, whose study is generally restricted to the use of SNPs. Taking advantage of recent developments allowing CNV analysis from RAD-seq data, we investigated how variation in fitness-related traits, local thermal conditions and demographic history are associated with CNVs, and how subsequent copy number variation drives population genetic structure in a marine fish, the capelin (Mallotus villosus). We collected 1536 DNA samples from 35 sampling sites in the north Atlantic Ocean and identified 6620 CNVs. We found associations between CNVs and the gonadosomatic index, suggesting that duplicated regions could affect female fitness by modulating oocyte production. We also detected 105 CNV candidates associated with water temperature, among which 20% corresponded to genomic regions located within the sequence of protein-coding genes, suggesting local adaptation to cold water by means of gene amplification. We also identified 175 CNVs associated with the divergence of three parapatric glacial lineages, of which 24% were located within protein-coding genes, which might contribute to genetic incompatibilities and ultimately, reproductive isolation. Lastly, our analyses unveiled a hierarchical, complex CNV population structure determined by temperature and local geography, that was very different from that inferred based on SNPs in a previous study. Our findings underscore the complementarity of those two types of markers in population genomics studies.

scholarly journals Local adaptation under gene flow: Recombination, conditional neutrality and genetic trade-offs shape genomic patterns in Arabidopsis lyrata

2018 ◽  
Author(s):  
Tuomas Hämälä ◽  
Outi Savolainen
Keyword(s):  
Gene Flow ◽  
Local Adaptation ◽  
Demographic History ◽  
Rate Variation ◽  
Arabidopsis Lyrata ◽  
Trade Offs ◽  
Northern Latitudes ◽  
Local Selection ◽  
Empirical Level ◽  
Selected Traits

AbstractShort-scale local adaptation is a complex process involving selection, migration and drift. The expected effects on the genome are well grounded in theory, but examining these on an empirical level has proven difficult, as it requires information about local selection, demographic history and recombination rate variation. Here, we use locally adapted and phenotypically differentiated Arabidopsis lyrata populations from two altitudinal gradients in Norway to test these expectations at the whole-genome level. Demography modelling indicates that populations within the gradients diverged less than 2000 years ago and that the sites are connected by gene flow. The gene flow estimates are, however, highly asymmetric with migration from high to low altitudes being several times more frequent than vice versa. To detect signatures of selection for local adaptation, we estimate patterns of lineage specific differentiation among these populations. Theory predicts that gene flow leads to concentration of adaptive loci in areas of low recombination; a pattern we observe in both lowland-alpine comparisons. Although most selected loci display patterns of conditional neutrality, we found indications of genetic trade-offs, with one locus particularly showing high divergence and signs of selection in both populations. Our results further suggest that resistance to solar radiation is an important adaptation to alpine environments, while vegetative growth and bacterial defense are indicated as selected traits in the lowland habitats. These results provide insights into genetic architectures and evolutionary processes driving local adaptation under gene flow. We also contribute to understanding of traits and biological processes underlying alpine adaptation in northern latitudes.

scholarly journals Worldwide population structure, long term demography, and local adaptation of Helicobacter pylori

2015 ◽  
Author(s):  
Valeria Montano ◽  
Xavier Didelot ◽  
Matthieu Foll ◽  
Bodo Linz ◽  
Richard Reinhardt ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Population Structure ◽  
Local Adaptation ◽  
Demographic History ◽  
Gastric Diseases ◽  
Whole Genome Analysis ◽  
Necrosis Factor Alpha ◽  
Worldwide Population ◽  
H Pylori ◽  
Global And Local

Helicobacter pylori is an important human pathogen associated with serious gastric diseases. Owing to its medical importance and close relationship with its human host, understanding genomic patterns of global and local adaptation in H. pylori may be of particular significance for both clinical and evolutionary studies. Here we present the first such whole-genome analysis of 60 globally distributed strains, from which we inferred worldwide population structure and demographic history and shed light on interesting global and local events of positive selection, with particular emphasis on the evolution of San-associated lineages. Our results indicate a more ancient origin for the association of humans and H. pylori than previously thought. We identify several important perspectives for future clinical research on candidate selected regions that include both previously characterized genes (e.g. transcription elongation factor NusA and tumor Necrosis Factor Alpha-Inducing Protein Tipα) and hitherto unknown functional genes.

scholarly journals Disentangling adaptation from drift in bottlenecked and reintroduced populations of Alpine ibex

2021 ◽  
Author(s):  
D.M. Leigh ◽  
H.E.L. Lischer ◽  
F. Guillaume ◽  
C. Grossen ◽  
T. Günther
Keyword(s):  
Local Adaptation ◽  
Genetic Drift ◽  
Demographic History ◽  
True Positive Rate ◽  
Detection Methods ◽  
True Positive ◽  
Alpine Ibex ◽  
Snp Data ◽  
Outlier Loci ◽  
Frequency Changes

AbstractIdentifying local adaptation in bottlenecked species is essential for effective conservation management. Selection detection methods are often applied to bottlenecked species and have an important role in species management plans, assessments of the species’ adaptive capacity, and looking for responses to major threats like climate change. Yet, the allele frequency changes driven by selection and exploited in selection detection methods, are similar to those caused by the strong neutral genetic drift expected during a bottleneck. Consequently, it is often unclear what accuracy selection detection methods may offer within bottlenecked populations. In this study, we used simulations to explore if signals of selection could be confidently distinguished from genetic drift across 23 bottlenecked and reintroduced populations of Alpine ibex (Capra ibex). We used the meticulously recorded demographic history of the Alpine ibex to generate a comprehensive simulated SNP data. The simulated SNPs were then used to benchmark the confidence we could place in putative outliers identified through selection scans on empirical Alpine ibex SNP data. Within the simulated dataset, the false positive rates were high for all selection detection methods but fell substantially when two or more selection detection methods were combined. However, the true positive rates were consistently low and became essentially negligible after this increased stringency. Despite the detection of many putative outlier loci in the empirical Alpine ibex RADseq data, none met the threshold needed to distinguish them from genetic drift-driven false positives. Unfortunately, the low true positive rate also creates a paradox, by preventing the exclusion of recent local adaptation within the Alpine ibex.

scholarly journals Long distance migration is a major factor driving local adaptation at continental scale in Coho Salmon

2021 ◽  
Author(s):  
Quentin Rougemont ◽  
Amanda Xuereb ◽  
Xavier Dallaire ◽  
Jean-Sebastien Moore ◽  
Eric Normandeau ◽  
...  
Keyword(s):  
Local Adaptation ◽  
Evolutionary Biology ◽  
Coho Salmon ◽  
Demographic History ◽  
Long Distance ◽  
Homing Behavior ◽  
Association Analyses ◽  
Continental Scale ◽  
History Of ◽  
Genomic Basis

Inferring the genomic basis of local adaptation is a long-standing goal of evolutionary biology. Beyond its fundamental evolutionary implications, such knowledge can guide conservation decisions for populations of conservation and management concern. Here, we investigated the genomic basis of local adaptation in the Coho salmon (Oncorhynchus kisutch) across its entire North American range. We hypothesized that extensive spatial variation in environmental conditions and the species homing behavior may promote the establishment of local adaptation. We genotyped 7,829 individuals representing 217 sampling locations at more than 100,000 high-quality RADseq loci to investigate how recombination might affect the detection of loci putatively under selection and took advantage of the precise description of the demographic history of the species from our previous work to draw accurate population genomic inferences about local adaptation. Results indicated that genetic differentiation scans and genetic-environment association analyses were both significantly affected by variation in recombination rate as low recombination regions displayed an increased number of outliers. By taking these confounding factors into consideration, we revealed that migration distance was the primary selective factor driving local adaptation and partial parallel divergence among distant populations. Moreover, we identified several candidates SNP associated with long distance migration and altitude including a gene known to be involved in adaptation to altitude in other species. The evolutionary implications of our findings are discussed along with conservation applications.

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