scholarly journals Genome-wide patterns of divergence during speciation: the lake whitefish case study

2012 ◽  
Vol 367 (1587) ◽  
pp. 354-363 ◽  
Author(s):  
S. Renaut ◽  
N. Maillet ◽  
E. Normandeau ◽  
C. Sauvage ◽  
N. Derome ◽  
...  
Keyword(s):  
Reproductive Isolation ◽  
Genomic Islands ◽  
Next Generation Sequencing Data ◽  
Adaptive Divergence ◽  
Phenotypic Traits ◽  
Lake Whitefish ◽  
Sequencing Data ◽  
Species Pairs ◽  
Selective Forces ◽  
Genomic Regions

The nature, size and distribution of the genomic regions underlying divergence and promoting reproductive isolation remain largely unknown. Here, we summarize ongoing efforts using young (12 000 yr BP) species pairs of lake whitefish ( Coregonus clupeaformis ) to expand our understanding of the initial genomic patterns of divergence observed during speciation. Our results confirmed the predictions that: (i) on average, phenotypic quantitative trait loci (pQTL) show higher F ST values and are more likely to be outliers (and therefore candidates for being targets of divergent selection) than non-pQTL markers; (ii) large islands of divergence rather than small independent regions under selection characterize the early stages of adaptive divergence of lake whitefish; and (iii) there is a general trend towards an increase in terms of numbers and size of genomic regions of divergence from the least (East L.) to the most differentiated species pair (Cliff L.). This is consistent with previous estimates of reproductive isolation between these species pairs being driven by the same selective forces responsible for environment specialization. Altogether, dwarf and normal whitefish species pairs represent a continuum of both morphological and genomic differentiation contributing to ecological speciation. Admittedly, much progress is still required to more finely map and circumscribe genomic islands of speciation. This will be achieved through the use of next generation sequencing data but also through a better quantification of phenotypic traits moulded by selection as organisms adapt to new environmental conditions.

scholarly journals GAMtools: an automated pipeline for analysis of Genome Architecture Mapping data

2017 ◽  
Author(s):  
Robert A. Beagrie ◽  
Markus Schueler
Keyword(s):  
Next Generation Sequencing Data ◽  
Genome Architecture ◽  
Sequencing Data ◽  
Cell Nuclei ◽  
Automated Mapping ◽  
Chromatin Interactions ◽  
Genome Wide ◽  
Quality Control Metrics ◽  
Genomic Regions ◽  
Analytical Tools

AbstractGenome Architecture Mapping (GAM) is a recently developed method for mapping chromatin interactions genome-wide. GAM is based on sequencing genomic DNA extracted from thin cryosections of cell nuclei. As a new approach, GAM datasets require specialized analytical tools and approaches. Here we present GAMtools, a pipeline for analysing GAM datasets. GAMtools covers the automated mapping of raw next-generation sequencing data generated by GAM, detection of genomic regions present in each nuclear slice, calculation of quality control metrics, generation of inferred proximity matrices, plotting of heatmaps and detection of genomic features for which chromatin interactions are enriched/depleted.

THE GENETIC ARCHITECTURE OF REPRODUCTIVE ISOLATION DURING SPECIATION-WITH-GENE-FLOW IN LAKE WHITEFISH SPECIES PAIRS ASSESSED BY RAD SEQUENCING

Evolution ◽  
2013 ◽  
Vol 67 (9) ◽  
pp. 2483-2497 ◽  
Author(s):  
Pierre-Alexandre Gagnaire ◽  
Scott A. Pavey ◽  
Eric Normandeau ◽  
Louis Bernatchez
Keyword(s):  
Gene Flow ◽  
Reproductive Isolation ◽  
Genetic Architecture ◽  
Rad Sequencing ◽  
Lake Whitefish ◽  
Species Pairs

scholarly journals Convergent adaptation and ecological speciation result from unique genomic mechanisms in sympatric extremophile fishes

2021 ◽  
Author(s):  
Ryan S Greenway ◽  
Anthony P Brown ◽  
Henry Camarillo ◽  
Cassandra Delich ◽  
Kerry L McGowan ◽  
...  
Keyword(s):  
Reproductive Isolation ◽  
Convergent Evolution ◽  
Spatial Scales ◽  
Rapid Evolution ◽  
Nuclear Genome ◽  
Genomic Islands ◽  
Adaptive Divergence ◽  
Biological Organization ◽  
Genomic Level ◽  
Multiple Levels

Divergent selection along ecological gradients can lead to speciation, and replicated speciation events occur when populations of multiple lineages undergo divergence following colonization of similar environments. In such instances, it remains unclear to what extent reproductive isolation evolves via convergent mechanisms at the genomic level due to biases in the types of systems typically used to study convergent evolution. We used a unique system in which three species of poeciliid fishes occur in sympatry in an extremely toxic, hydrogen sulfide (H2S)-rich spring and an adjacent nonsulfidic stream to examine shared patterns of adaptive divergence across multiple levels of biological organization. Despite extremely small spatial scales, we found strong genetic differentiation between populations in sulfidic and nonsulfidic habitats mediated by strong selection against migrants between habitat types. High levels of reproductive isolation were accompanied by convergent patterns of adaptation in morphological and physiological traits, as well as genome-wide patterns of gene expression across all three species. Furthermore, the mitochondrial genomes of each species exhibit shared signatures of selection on key genes involved in H2S toxicity. However, contrary to predictions of speciation theory, analyses of divergence across the nuclear genome neither revealed evidence for clear genomic islands of speciation nor substantial congruence of outlier regions across population pairs. Instead, heterogenous regions of divergence spread across the genome suggest that selection for polygenic physiological adaptations likely facilitated the rapid evolution of high levels of reproductive isolation. Overall, we demonstrate that substantial convergence across multiple levels of biological organization can be mediated by non-convergent modifications at the genomic level. By disentangling environmental variation in natural selection from lineage-specific evolution in this system of highly divergent, yet sympatric lineages, our results emphasize the outsized role of the genomic substrate upon which selection acts in driving convergent evolution at the phenotypic level.

scholarly journals Adaptive divergence and the evolution of hybrid phenotypes in threespine stickleback

2020 ◽  
Author(s):  
Avneet K. Chhina ◽  
Ken A. Thompson ◽  
Dolph Schluter
Keyword(s):  
Reproductive Isolation ◽  
Phenotypic Variation ◽  
Gasterosteus Aculeatus ◽  
Threespine Stickleback ◽  
Adaptive Divergence ◽  
Phenotypic Traits ◽  
Ancestral State ◽  
Ecological Divergence ◽  
Critical Determinant ◽  
Phenotypic Distance

AbstractThe fitness of hybrids is a critical determinant of gene flow between hybridizing populations. If hybrid phenotypes change predictably as parental populations become increasingly divergent, this could provide insight into general mechanisms linking ecological divergence with reproductive isolation. In this study, we used threespine stickleback fish (Gasterosteus aculeatus L.) to examine how phenotypic divergence between populations drives the evolution of dominance, phenotypic variation, and trait ‘mismatch’ in hybrids. We generated F1 and F2 hybrids between 12 freshwater populations—which ranged from highly planktivorous to highly benthic-feeding—and an anadromous population that is highly planktivorous and resembles the ancestral state of derived freshwater populations. We measured 16 phenotypic traits in hybrids and pure parental individuals raised under common conditions. We found that dominance varied markedly among traits. By contrast, dominance for a given trait was typically consistent among populations except for two traits where dominance was predicted by the phenotype of the freshwater parent. We find that multivariate phenotypic variation is greater in hybrids between more divergent parents. Finally, we demonstrate that the extent to which parental traits are ‘mismatched’ in both F1 and F2 hybrids increases with the phenotypic distance between the parent populations. Critically, this relationship was clearer in F1 hybrids than in F2s—largely due to traits having different dominance coefficients and F1s having relatively little phenotypic variation. Our results demonstrate that some aspects of hybrid phenotypes evolve predictably as parental populations diverge. We also find evidence for a possible general mechanistic link between ecological divergence and reproductive isolation—that more divergent parent populations tend to produce hybrids with novel and potentially deleterious multivariate phenotypes.

scholarly journals annotatr: Genomic regions in context

2016 ◽  
Author(s):  
Raymond G. Cavalcante ◽  
Maureen A. Sartor
Keyword(s):  
Binding Sites ◽  
Supplementary Information ◽  
Next Generation Sequencing Data ◽  
Sequencing Data ◽  
Genomic Context ◽  
Biological Interpretation ◽  
R Packages ◽  
Genomic Regions ◽  
Insight Into ◽  
Generation Sequencing

AbstractMotivation:Analysis of next-generation sequencing data often results in a list of genomic regions. These may include differentially methylated CpGs/regions, transcription factor binding sites, interacting chromatin regions, or GWAS-associated SNPs, among others. A common analysis step is to annotate such genomic regions to genomic annotations (promoters, exons, enhancers, etc.). Existing tools are limited by a lack of annotation sources and flexible options, the time it takes to annotate regions, an artificial one-to-one region-to-annotation mapping, a lack of visualization options to easily summarize data, or some combination thereof.Results:We developed the annotatr Bioconductor package to flexibly and quickly summarize and plot annotations of genomic regions. The annotatr package reports all intersections of regions and annotations, giving a better understanding of the genomic context of the regions. A variety of graphics functions are implemented to easily plot numerical or categorical data associated with the regions across the annotations, and across annotation intersections, providing insight into how characteristics of the regions differ across the annotations. We demonstrate that annotatr is up to 27x faster than comparable R packages. Overall, annotatr enables a richer biological interpretation of experiments.Availability:http://bioconductor.org/packages/annotatr/Contact:[email protected] information:Supplementary data are available at Bioinformatics online.

scholarly journals Multiple chromosomal inversions contribute to adaptive divergence of a dune sunflower ecotype

2019 ◽  
Author(s):  
Kaichi Huang ◽  
Rose L. Andrew ◽  
Gregory L. Owens ◽  
Kate L. Ostevik ◽  
Loren H. Rieseberg
Keyword(s):  
Natural Populations ◽  
High Linkage Disequilibrium ◽  
Adaptive Divergence ◽  
Sequencing Data ◽  
Association Analyses ◽  
Chromosomal Inversions ◽  
Sand Sheet ◽  
Genomic Regions ◽  
Helianthus Petiolaris ◽  
Comparative Genetic Mapping

ABSTRACTBoth models and case studies suggest that chromosomal inversions can facilitate adaptation and speciation in the presence of gene flow by suppressing recombination between locally adapted alleles. Until recently, however, it has been laborious and time-consuming to identify and genotype inversions in natural populations. Here we apply RAD sequencing data and newly developed population genomic approaches to identify putative inversions that differentiate a sand dune ecotype of the prairie sunflower (Helianthus petiolaris) from populations found on the adjacent sand sheet. We detected seven large genomic regions that exhibit a different population structure than the rest of the genome and that vary in frequency between dune and non-dune populations. These regions also show high linkage disequilibrium and high heterozygosity between, but not within haplotypes, consistent with the behavior of large inversions, an inference subsequently validated in part by comparative genetic mapping. Genome-environment association analyses show that key environmental variables, including vegetation cover and soil nitrogen, are significantly associated with inversions. The inversions co-locate with previously described “islands of differentiation,” and appear to play an important role in adaptive divergence and incipient speciation within H. petiolaris.

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