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343 results for “genomic divergence”
Data from: AFLP genome scans suggest divergent selection on colour patterning in allopatric colour morphs of a cichlid fish
Genome scan-based tests for selection are directly applicable to natural populations to study the genetic and evolutionary mechanisms behind phenotypic differentiation. We conducted AFLP genome scans in three distinct geographic colour morphs of the cichlid fish Tropheus moorii to assess whether the extant, allopatric colour pattern differentiation can be explained by drift and to identify markers mapping to genomic regions possibly involved in colour patterning. The tested morphs occupy adjacent shore sections in southern Lake Tanganyika and are separated from each other by major habitat barriers. The genome scans revealed significant genetic structure between morphs, but a very low proportion of loci fixed for alternative AFLP alleles in different morphs. This high level of polymorphism within morphs suggested that colour pattern differentiation did not result exclusively from neutral processes. Outlier detection methods identified six loci with excess differentiation in the comparison between a bluish and a yellow-blotch morph and five different outlier loci in comparisons of each of these morphs with a red morph. As population expansions and the genetic structure of Tropheus make the outlier approach prone to false-positive signals of selection, we examined the correlation between outlier locus alleles and colour phenotypes in a genetic and phenotypic cline between two morphs. Distributions of allele frequencies at one outlier locus were indeed consistent with linkage to a colour locus. Despite the challenges posed by population structure and demography, our results encourage the cautious application of genome scans to studies of divergent selection in subdivided and recently expanded populations.
Data from: The impact of selection, gene flow and demographic history on heterogeneous genomic divergence: threespine sticklebacks in divergent environments
Heterogeneous genomic divergence between populations may reflect selection, but should also be seen in conjunction with gene flow and drift, particularly population bottlenecks. Marine and freshwater threespine stickleback (Gasterosteus aculeatus) populations often exhibit different lateral armor plate morphs. Moreover, strikingly parallel genomic footprints across different marine-freshwater population pairs are interpreted as parallel evolution and gene reuse. Nevertheless, in some geographic regions like the North Sea and Baltic Sea different patterns are observed. Freshwater populations in coastal regions are often dominated by marine morphs, suggesting that gene flow overwhelms selection, and genomic parallelism may also be less pronounced. We used RAD sequencing for analyzing 28,888 SNPs in two marine and seven freshwater populations in Denmark, Europe. Freshwater populations represented a variety of environments: river populations accessible to gene flow from marine sticklebacks and large and small isolated lakes with and without fish predators. Sticklebacks in an accessible river environment showed minimal morphological and genome-wide divergence from marine populations, supporting the hypothesis of gene flow overriding selection. Allele frequency spectra suggested bottlenecks in all freshwater populations, and particularly two small lake populations. However, genomic footprints ascribed to selection could nevertheless be identified. No genomic regions were consistent freshwater-marine outliers, and parallelism was much lower than in other comparable studies. Two genomic regions previously described to be under divergent selection in freshwater and marine populations were outliers between different freshwater populations. We ascribe these patterns to stronger environmental heterogeneity among freshwater populations in our study as compared to most other studies, although the demographic history involving bottlenecks should also be considered in the interpretation of results.
Data from: Clines on the seashore: the genomic architecture underlying rapid divergence in the face of gene flow
Adaptive divergence and speciation may happen despite opposition by gene flow. Identifying the genomic basis underlying divergence with gene flow is a major task in evolutionary genomics. Most approaches (e.g. outlier scans) focus on genomic regions of high differentiation. However, not all genomic architectures potentially underlying divergence are expected to show extreme differentiation. Here, we develop an approach that combines hybrid zone analysis (i.e. focuses on spatial patterns of allele frequency change) with system-specific simulations to identify loci inconsistent with neutral evolution. We apply this to a genome-wide SNP set from an ideally-suited study organism, the intertidal snail Littorina saxatilis, which shows primary divergence between ecotypes associated with different shore habitats. We detect many SNPs with clinal patterns, most of which are consistent with neutrality. Among non-neutral SNPs, most are located within three large putative inversions differentiating ecotypes. Many non-neutral SNPs show relatively low levels of differentiation. We discuss potential reasons for this pattern, including loose linkage to selected variants, polygenic adaptation and a component of balancing selection within populations (which may be expected for inversions). Our work is in line with theory predicting a role for inversions in divergence, and emphasises that genomic regions contributing to divergence may not always be accessible with methods purely based on allele frequency differences. These conclusions call for approaches that take spatial patterns of allele frequency change into account in other systems.
Data from: Genomic and geographic footprints of differential introgression between two divergent fish species (Solea spp.)
Investigating variation in gene flow across the genome between closely related species is important to understand how reproductive barriers shape genome divergence before speciation is complete. An efficient way to characterize differential gene flow is to study how the genetic interactions that take place in hybrid zones selectively filter gene exchange between species, leading to heterogeneous genome divergence. In the present study, genome-wide divergence and introgression patterns were investigated between two sole species, Solea senegalensis and Solea aegyptiaca, using restriction-associated DNA sequencing (RAD-Seq) to analyse samples taken from a transect spanning the hybrid zone. An integrative approach combining geographic and genomic clines methods with an analysis of individual locus introgression accounting for the demographic history of divergence was conducted. Our results showed that the two sole species have come into secondary contact postglacially, after experiencing a prolonged period (ca. 1.1 to 1.8 Myrs) of allopatric separation. Secondary contact resulted in the formation of a tension zone characterized by strong reproductive isolation, allowing introgression in only a minor fraction of the genome. We found multiple evidence for a preferential direction of introgression in the S. aegyptiaca genetic background, indicating a possible recent or ongoing movement of the hybrid zone. Deviant introgression signals found in the opposite direction suggested that S. senegalensis could have possibly undergone adaptive introgression that has not yet spread throughout the entire species range. Our study thus illustrates the varied outcomes of genetic interactions between divergent gene pools that recently met after a long history of divergence.
Data from: ddRAD‐seq data reveal significant genome‐wide population structure and divergent genomic regions that distinguish the mallard and close relatives in North America
Recently evolved species typically share genetic variation across their genomes due to incomplete lineage sorting and/or ongoing gene flow. Given only subtle allele frequency differences at most loci and the expectation that divergent selection may affect only a tiny fraction of the genome, distinguishing closely related species based on multi‐locus data requires substantial genomic coverage. In this study, we used ddRAD‐seq to sample the genomes of five recently diverged, New World "mallards" (Anas spp.), a group of dabbling duck species characterized by diagnosable phenotypic differences but minimal genetic differentiation. With increased genomic sampling, we aimed to characterize population structure within this group and identify genomic regions that may have experienced divergent selection during speciation. We analyzed 3,017 autosomal ddRAD‐seq loci and 177 loci from the Z‐chromosome. In contrast to previous studies, the ddRAD‐seq data were sufficient to assign individuals to their respective species or subspecies and to generate estimates of gene flow in a phylogenetic framework. We find limited evidence of contemporary gene flow between the dichromatic mallard and several monochromatic taxa, but find evidence for historical gene flow between some monochromatic species pairs. We conclude that the overall genetic similarity of these taxa likely reflects retained ancestral polymorphism rather than recent and extensive gene flow. Thus, despite recurring cases of hybridization in this group, our results challenge the current dogma predicting the genetic extinction of the New World monochromatic dabbling ducks via introgressive hybridization with mallards. Moreover, ddRAD‐seq data were sufficient to identify previously unknown outlier regions across the Z‐chromosome and several autosomal chromosomes, regions that may have been involved in the diversification of species in this recent radiation.
Data from: Genome-wide assessment of diversity and divergence among extant Galápagos giant tortoise species
Genome-wide assessments allow for fuller characterization of genetic diversity, finer-scale population delineation, and better detection of demographically significant units to guide conservation compared to those based on "traditional" markers. Galapagos giant tortoises (Chelonoidis spp.) have long provided a case study for how evolutionary genetics may be applied to advance species conservation. Ongoing efforts to bolster tortoise populations, which have declined by 90%, have been informed by analyses of mitochondrial DNA sequence and microsatellite genotypic data, but could benefit from genome-wide markers. Taking this next step, we used double-digest restriction-site associated DNA sequencing to collect genotypic data at >26,000 single nucleotide polymorphisms (SNPs) for 117 individuals representing all recognized extant Galapagos giant tortoise species. We then quantified genetic diversity, population structure, and compared results to estimates from mitochondrial DNA and microsatellite loci. Our analyses detected 12 genetic lineages concordant with the 11 named species as well as previously described structure within one species, C. becki. Furthermore, the SNPs provided increased resolution, detecting admixture in four individuals. SNP-based estimates of diversity and differentiation were significantly correlated with those derived from nuclear microsatellite loci and mitochondrial DNA sequences. The SNP toolkit presented here will serve as a resource for advancing efforts to understand tortoise evolution, species radiations, and aid conservation of the Galapagos tortoise species complex.
Data from: Genomic regions repeatedly involved in divergence among plant-specialized pea aphid biotypes
Understanding the genetic bases of biological diversification is a long-standing goal in evolutionary biology. Here we investigate whether replicated cases of adaptive divergence involve the same genomic regions in the pea aphid, Acyrthosiphon pisum, a large complex of genetically differentiated biotypes, each specialized on different species of legumes. A previous study identified genomic regions putatively involved in host-plant adaptation and/or reproductive isolation by performing a hierarchical genome scan in three biotypes. This led to the identification of 11 FST outliers among 390 polymorphic microsatellite markers. In this study, the outlier status of these 11 loci was assessed in eight biotypes specialized on other host plants. Four of the 11 previously identified outliers showed greater genetic differentiation among these additional biotypes than expected under the null hypothesis of neutral evolution (α<0.01). Whether these hotspots of genomic divergence result from adaptive events, intrinsic barriers or reduced recombination is discussed.
Data from: Inter-chromosomal coupling between vision and pigmentation genes during genomic divergence
Recombination between loci underlying mate choice and ecological traits is a major evolutionary force acting against speciation with gene flow. The evolution of linkage disequilibrium between such loci is therefore a fundamental step in the origin of species. Here, we show that this process can take place in the absence of physical linkage in hamlets—a group of closely related reef fishes from the wider Caribbean that differ essentially in colour pattern and are reproductively isolated through strong visually-based assortative mating. Using full-genome analysis, we identify four narrow genomic intervals that are consistently differentiated among sympatric species in a backdrop of extremely low genomic divergence. These four intervals include genes involved in pigmentation (sox10), axial patterning (hoxc13a), photoreceptor development (casz1) and visual sensitivity (SWS and LWS opsins) that develop islands of long-distance and inter-chromosomal linkage disequilibrium as species diverge. The relatively simple genomic architecture of species differences facilitates the evolution of linkage disequilibrium in the presence of gene flow.
Data from: Genomic patterns of diversity and divergence of two introduced salmonid species in Patagonia, South America
Invasive species have become widespread in aquatic environments throughout the world, yet there are few studies that have examined genomic variation of multiple introduced species in newly colonized environments. In this study, we contrast genomic variation in two salmonid species (anadromous Chinook Salmon, Oncorhynchus tshawytscha, 11,579 SNPs and resident Brook Charr Salvelinus fontinalis, 13,522 SNPs) with differing invasion success after introduction to new environments in South America relative to populations from their native range in North America. Estimates of genetic diversity were not significantly different between introduced and source populations for either species, indicative of propagule pressure that has been shown to maintain diversity in founding populations relative to their native range. Introduced populations also demonstrated higher connectivity and gene flow than those in their native range. Evidence for candidate loci under divergent selection was observed, but was limited to specific introduced populations and was not widely evident. Patterns of genomic variation were consistent with general dispersal potential of each species and therefore also the notion that life history variation may contribute to both invasion success and subsequent genetic structure of these two salmonids in Patagonia.
Code and Data for manuscript "Floral phenotypic divergence and genomic insights in an Ophrys orchid: Unraveling early speciation processes"
<p>Floral phenotypic divergence and genomic insights in an Ophrys orchid: Unraveling early speciation</p> <p>--------</p> <p>This repository contains all the R code used in the manuscript:</p> <p>* Title: "Floral phenotypic divergence and genomic insights in an Ophrys orchid: Unraveling early speciation"</p> <p>* Authors: Anais Gibert, Schatz Bertrand, Buscail Roselyn, Dominique Nguyen, Baguette Michel, Bartes Nicolas and Joris Bertrand</p> <p>* Year of publication: 2024</p> <p>* doi: https://doi.org/10.1101/2024.03.21.586062</p> <p> </p> <p>Synopsis of the study</p> <p>--------</p> <ul> <li> <p>Adaptive radiation in <em>Ophrys</em> orchids leads to complex floral phenotypes that vary in scent, color and shape.</p> </li> <li> <p>Using a novel pipeline to quantify these phenotypes, we investigated trait divergence at early stages of speciation in six populations of <em>Ophrys aveyronensis</em> experiencing recent allopatry. By integrating different genetic/genomic techniques, we investigated: (i) variation and integration of floral components (scent, color and shape), (ii) phenotypes and genomic regions under divergent selection, and (iii) the genomic bases of trait variation.</p> </li> <li> <p>We identified a large genomic island of divergence, associated with phenotypic variation in particular in floral odor. We detected potential divergent selection on macular color, while convergent selection was suspected on floral morphology and for several volatile olfactive compounds. We also identify candidate genes involved in anthocyanin and in steroid biosynthesis pathways associated with standing genetic variation in color and odor.</p> </li> <li> <p>This study sheds light on early differentiation in <em>Ophrys</em>, revealing patterns that often become invisible over time, i.e., the geographic mosaic of traits under selection and the early appearance of strong genomic divergence. It also supports a crucial genomic region for future investigation and highlights the value of a multifaceted approach in unraveling speciation within taxa with large genomes.</p> </li> </ul> <p> </p> <p>Running the code</p> <p>--------</p> <p>Here we present the data and code for carrying out the analyses, as well as the figures and tables from the article and the supplementary material. Once you have installed the necessary packages, run the commands in 'analysis_share.R'. This script uses several functions available in the '/R' directory.</p> <p>Figures and tables are produced in a 'manuscript/figures' and 'manuscript/tables' directory. <br>The `/data' directory contains the data used in the analyses (data/input or data/output), but also the resulting datasets produced by the code (data/RData/).</p> <p> </p>
Figure 1 in Evidence from mitochondrial genomics supports the lower Mesozoic of South Asia as the time and place of basal divergence of cypriniform fishes (Actinopterygii: Ostariophysi)
Figure 1. Geographical regions of cypriniform fish distribution at the continental scale. The seven region scheme presented here [Africa (Af), South Asia (Sa), East Asia (Ea), Europe (Eu), Siberia (Sb), and western and eastern North America (Wn & En)] is a modification of the conventional Wallace's six region system (Berra, 2001). East Asia, Europe, and Siberia are subdivisions of the Palaearctic region, overlapping with each other. Western and eastern North America are subdivisions of the Nearctic region.
Figure 5. A in Evidence from mitochondrial genomics supports the lower Mesozoic of South Asia as the time and place of basal divergence of cypriniform fishes (Actinopterygii: Ostariophysi)
Figure 5. A reconciled dispersal-vicariance analysis (DIVA; upper) and a simple parsimonious reconstruction (lower) inference of past ranges at the subfamilial level superimposed over divergence time estimates. Open rectangular bars stand for 95% confidence ranges of the divergence time estimates. The scale bar at the bottom represents the geological time scale according to Gradstein, Ogg & Smith (2004). Maps drawn from Smith, Smith & Funnel (1994) indicate onset (220 Mya) and completion (160 Mya) of the Pangaean breakup, and separation of the Indian land mass from Africa (130 Mya), which allowed marine permeation. Arrowheads indicate rifting margins; hatched pattern indicates area of black shale deposits (Olsen, 1997).
Figure 2. The maximum likelihood tree inferred from 14 594 in Evidence from mitochondrial genomics supports the lower Mesozoic of South Asia as the time and place of basal divergence of cypriniform fishes (Actinopterygii: Ostariophysi)
Figure 2. The maximum likelihood tree inferred from 14 594 nucleotide sites of 60 Cypriniformes and six outgroups (lnL = -203 966.535). Numbers at each branch indicate the resampling the estimated log likelihood (RELL) local bootstrap probabilities. Asterisks indicate 100% local bootstrap support. Two major clades of Cyprinidae (A and B) correspond with those presented in Cavender & Coburn (1992).
The roles of recombination and selection in shaping genomic divergence in an incipient ecological species complex
<p>Speciation genomic studies have revealed that genomes of diverging lineages are shaped jointly by the actions of gene flow and selection. These evolutionary forces acting in concert with processes such as recombination and genome features such as gene density shape a mosaic landscape of divergence. We investigated the roles of recombination and gene density in shaping the patterns of differentiation and divergence between the cyclically parthenogenetic ecological sister-taxa, <i>Daphnia pulicaria </i>and <i>Daphnia pulex. </i>First, we assembled a phased chromosome-scale genome assembly using trio-binning for <i>D. pulicaria</i> and constructed a genetic map using an F2-intercross panel to understand sex-specific recombination rate heterogeneity.<i> </i>Finally, we used a ddRADseq dataset with broad geographic sampling of <i>D. pulicaria, D. pulex, </i>and their hybrids to understand the patterns of genome-scale divergence and demographic parameters. Our study provides the first sex-specific estimates of recombination rates for a cyclical parthenogen, and unlike other eukaryotic species, we observed male-biased heterochiasmy in <i>D. pulicaria</i>, which may be related to this somewhat unique breeding mode. Additionally, regions of high gene density and recombination are generally more divergent than regions of suppressed recombination. Outlier analysis indicated that divergent genomic regions are likely driven by selection on <i>D. pulicaria</i>, the derived lineage colonizing a novel lake habitat. Together, our study supports a scenario of selection acting on genes related to local adaptation shaping genome-wide patterns of differentiation despite high local recombination rates in this species complex. Finally, we discuss the limitations of our data in light of demographic uncertainty.</p>
Addiitional Files: The diagrams of population structure, highly divergent regions, GC content and Nanopore reads depth, SNP number and Nanopore reads depth, and analyses of co-linearity against Nipponbare reference genome in 251 accessions.
<p>Additional Files for " <strong>A Super Pan-Genomic Landscape of Rice".</strong></p> <p>Addtional File1: Supplementary File1.Population structure of 251 rice accessions inferred by ADMIXTURE from K=6 to K=15.</p> <p>Additional File2: Supplementary File2.The diagram of co-linearity for assembled genome against Nipponbare refercne genome in 251 rice accessions.</p> <p>Additional File3: Supplementary File3. Highly divergent regions based on SV.</p> <p>Additional File4: Supplementary File4. The diagram of SNP number and Nanopore reads depth per 100kb windows in 251 rice accessions.</p> <p>Additonal File5:Supplementary File5. The diagram of GC content and the Nanopore reads depth per 10kb windows in 251 rice accessions.</p> <p> </p>
Clines on the seashore: The genomic architecture underlying rapid divergence in the face of gene flow
<p>Adaptive divergence and speciation may happen despite opposition by gene flow. Identifying the genomic basis underlying divergence with gene flow is a major task in evolutionary genomics. Most approaches (e.g., outlier scans) focus on genomic regions of high differentiation. However, not all genomic architectures potentially underlying divergence are expected to show extreme differentiation. Here, we develop an approach that combines hybrid zone analysis (i.e., focuses on spatial patterns of allele frequency change) with system-specific simulations to identify loci inconsistent with neutral evolution. We apply this to a genome-wide SNP set from an ideally suited study organism, the intertidal snail <em>Littorina saxatilis</em>, which shows primary divergence between ecotypes associated with different shore habitats. We detect many SNPs with clinal patterns, most of which are consistent with neutrality. Among non-neutral SNPs, most are located within three large putative inversions differentiating ecotypes. Many non-neutral SNPs show relatively low levels of differentiation. We discuss potential reasons for this pattern, including loose linkage to selected variants, polygenic adaptation and a component of balancing selection within populations (which may be expected for inversions). Our work is in line with theory predicting a role for inversions in divergence, and emphasizes that genomic regions contributing to divergence may not always be accessible with methods purely based on allele frequency differences. These conclusions call for approaches that take spatial patterns of allele frequency change into account in other systems.</p>
Data from: Latitudinal divergence in a wide-spread amphibian: contrasting patterns of neutral and adaptive genomic variation
Stochastic effects from demographic processes and selection are expected to shape the distribution of genetic variation in spatially heterogeneous environments. As the amount of genetic variation is central for long-term persistence of populations, understanding how these processes affect variation over large-scale geographic gradients is pivotal. We investigated the distribution of neutral and putatively adaptive genetic variation, and reconstructed demographic history in the moor frog (Rana arvalis) using 136 individuals from 15 populations along a 1700 km latitudinal gradient from northern Germany to northern Sweden. Using ddRAD-seq we obtained 27590 SNPs, and identified differentiation outliers and SNPs associated with growing season length. Populations grouped into a southern and a northern cluster, representing two phylogeographical lineages from different post-glacial colonization routes. Hybrid index estimation and demographic model selection showed strong support for a southern and northern lineage and evidence of gene flow between regions located on each side of a contact zone. However, patterns of past gene flow over the contact zone differed between neutral and putatively adaptive SNPs. While neutral nucleotide diversity was higher along the southern than the northern part of the gradient, nucleotide diversity in differentiation outliers showed the opposite pattern suggesting differences in the relative strength of selection and drift along the gradient. Variation associated with growing season length decreased with latitude along the southern part of the gradient, but not along the northern part where variation was lower, suggesting stronger climate-mediated selection in the north. Outlier SNPs included loci involved in immunity and developmental processes.
Data from: Sustained plumage divergence despite weak genomic differentiation and broad sympatry in sister species of Australian woodswallows (Artamus spp.)
<p><span>Plumage divergence can function as a strong premating barrier when species come into secondary contact. When it fails to do so, the results are often genome homogenization and phenotypic hybrids at the zone of contact. This is not the case in the largely sympatric masked woodswallow and white-browed woodswallow species (Passeriformes: Artamidae: Artamus spp) complex in Australia where phenotypic integrity is sustained despite no discernible mitochondrial structure in earlier work. This lack of structure may suggest recent divergence, ongoing gene flow or both, and phenotypic hybrids are reported albeit rarely. Here, we further assessed the population structure and differentiation across the species' nuclear genomes using ddRAD-seq. As found in the mitochondrial genome, no structure or divergence within or between the two species was detected in the nuclear genome. This coarse sampling of the genome nonetheless revealed peaks of differentiation around the genes SOX5 and Axin1. Both are involved in the Wnt/β-catenin signaling pathway, which regulates feather development. Reconstruction of demographic history and estimation of parameters supports a scenario of secondary contact. Our study informs how divergent plumage morphs may arise and be sustained despite whole-genome homogenization and reveals new candidate genes potentially involved in plumage divergence.</span></p>
A highly divergent Wolbachia with a tiny genome in an insect-parasitic tylenchid nematode
<p class="MsoNormal"><em>Wolbachia</em> symbionts are the most successful host-associated microbes on the planet, infecting arthropods and nematodes. Their role in nematodes is particularly enigmatic, with filarial nematode species either 100% infected and dependent on symbionts for reproduction and development, or not at all infected. We have discovered a highly divergent strain of <em>Wolbachia</em> in an insect-parasitic tylenchid nematode, <em>Howardula</em> sp., in a nematode clade that has not previously been known to harbour <em>Wolbachia</em>. While this nematode is 100% infected with <em>Wolbachia</em>, we did not detect it in related species. We sequenced the<em> Howardula</em> symbiont (<em>w</em>How) genome and found that it is highly reduced, comprising only 550 kilobase pairs of DNA, ~35% smaller than the smallest <em>Wolbachia</em> nematode symbiont genomes. The <em>w</em>How genome is a subset of all other <em>Wolbachia</em> genomes and has not acquired any new genetic information. While it has lost many genes, including genes involved in cell wall synthesis and cell division, it has retained the entire heme biosynthesis pathway, suggesting that heme supplementation is critical. <em>w</em>How provides key insights into our understanding of what are the lower limits of <em>Wolbachia</em> cells, as well as the role of <em>Wolbachia</em> symbionts in the biology and convergent evolution of diverse parasitic nematodes.</p>
Fig. 2 in Mitochondrial genome divergence supports an ancient origin of circatidal behaviour in the Anurida maritima (Collembola: Neanuridae) species group
Fig. 2 Phylogenetic and molecular dating analyses. Top: Bayesian divergence time estimation using fixed starting tree. The starting tree is shown on the right and is a maximum likelihood (ML) tree obtained using IQ-TREE. Numbers at the nodes of this ML tree are ultrafast bootstrap support values (%); only values <100 are given. Bottom: Divergence time estimation using the same starting tree, but
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