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343 results for “genomic divergence”
Fig. 1 in Mitochondrial genome divergence supports an ancient origin of circatidal behaviour in the Anurida maritima (Collembola: Neanuridae) species group
Fig. 1 Aggregation behaviour in Anurida bisetosa. A. bisetosa is a collembolan from the intertidal zone. It has 5 + 5 ocelli (top left inset). Bottom graph: Aggregation behaviour over time. Mean distance between animals was calculated at 30-min intervals. Five replicates were run for ~ 27 h each (each indicated using a different colour.
Supporting data for: A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence
<p>This upload contains genome assemblies and annotation files for four planarian species. </p> <h2>Genome assemblies</h2> <p>The genome assemblies are deposited as FASTA files with the ending '.fa.gz'.</p> <h2>Genome annotations</h2> <p>The genome annotations are deposited as gff3 files and contain the 'ENCODE' keyword.</p> <p>Integration into Wormbase are currently ongoing to provide userfriendly access.</p> <h2>Transposable element annotation</h2> <p>Transposable element annotation performed with the EDTA pipeline are deposited as GFF3 files with the file ending '.EDTA.TEanno.gff3.gz'.</p> <h2>Satellite DNA</h2> <p>Repetitive satellite regions annotated using RepeatExplorer and SRF are deposited as GFF3 files with the ending 'satDNA.gff3'.</p>
Genome-wide comparisons reveal extensive divergence within the lichen photobiont genus Trebouxia
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Data from: Functional and population genomic divergence within and between two species of killifish adapted to different osmotic niches
Adaptation to salinity affects species distributions, promotes speciation, and guides many evolutionary patterns in fishes. To uncover the basis of a complex trait like osmoregulation, genome-level analyses are sensible. We combine population genomic scans with genome expression profiling to discover candidate genes and pathways associated with divergence between osmotic environments. We compared transcriptome sequence divergence between multiple freshwater and saltwater populations of the rainwater killifish, Lucania parva. We also compared sequence divergence between L. parva and its sister species, Lucania goodei, a freshwater specialist. We found highly differentiated single nucleotide polymorphisms (SNPs) between freshwater and saltwater L. parva populations in cell junction and ion transport genes, including V-type H+ ATPase. Between species, we found divergence in reproduction and osmotic stress genes. Genes that were differentially expressed between species during osmotic acclimation included genes involved in ion transport and cell volume regulation. Gene sets that were divergent in coding sequence and divergent in expression did not overlap, although they did converge in function. Like many studies using genomic scans, our approach may miss some loci that contribute to adaptation but have complicated patterns of allelic variation. Our study suggests that gene expression and coding sequence may evolve independently as populations adapt to a complex physiological challenge.
Data from: A flicker of hope: genomic data distinguish Northern Flicker taxa despite low levels of divergence
Next-generation sequencing technologies are increasingly being employed to explore patterns of genomic variation in avian taxa previously characterized using morphology and/or traditional genetic markers. The hybridization dynamics of the Northern Flicker complex have received considerable attention, primarily due to the conspicuous plumage differences among these birds and the geographically extensive hybrid zone between the Red-shafted (Colaptes auratus cafer) and Yellow-shafted (Colaptes auratus auratus) flickers in the Great Plains region of North America. However, no traditional molecular techniques have been able to differentiate these 2 morphologically well-defined taxa from one another, or conclusively from the closely related Gilded Flicker (Colaptes chrysoides). Here, we use a next-generation sequencing approach to assess the genetic diversity and evolutionary history of these 3 taxa. We confirm the overall low levels of differentiation found using traditional molecular markers, but are able to distinguish between the 3 taxa for the first time, using a dataset of thousands of SNP loci distributed across the genome. Through demographic modeling and phylogenetic reconstructions, we find that Red-shafted and Yellow-shafted flickers are likely sister taxa, and that their divergence from the Gilded Flicker was comparatively older. The low level of divergence and lack of fixed differences in our dataset between Red-shafted and Yellow-shafted flickers, in particular, suggests whole-genome re-sequencing may be necessary to assess the dynamics of their hybridization and identify the genetic basis of their striking differences in plumage.
Data from: Adaptive genomic divergence under high gene flow between freshwater and brackish-water ecotypes of prickly sculpin (Cottus asper) revealed by Pool-Seq
Understanding the genomic basis of adaptive divergence in the presence of gene flow remains a major challenge in evolutionary biology. In prickly sculpin (Cottus asper), an abundant euryhaline fish in northwestern North America, high genetic connectivity among brackish-water (estuarine) and freshwater (tributary) habitats of coastal rivers does not preclude the build-up of neutral genetic differentiation and emergence of different life history strategies. Because these two habitats present different osmotic niches, we predicted high genetic differentiation at known teleost candidate genes underlying salinity tolerance and osmoregulation. We applied whole-genome sequencing of pooled DNA samples (Pool-Seq) to explore adaptive divergence between two estuarine and two tributary habitats. Paired-end sequence reads were mapped against genomic contigs of European Cottus, and the gene content of candidate regions was explored based on comparisons with the threespine stickleback genome. Genes showing signals of repeated differentiation among brackish-water and freshwater habitats included functions such as ion transport and structural permeability in freshwater gills, which suggests that local adaptation to different osmotic niches might contribute to genomic divergence among habitats. Overall, the presence of both repeated and unique signatures of differentiation across many loci scattered throughout the genome is consistent with polygenic adaptation from standing genetic variation and locally variable selection pressures in the early stages of life history divergence.
Data from: Chironomus riparius (Diptera) genome sequencing reveals the impact of minisatellite transposable elements on population divergence
Active transposable elements (TEs) may result in divergent genomic insertion and abundance patterns among conspecific populations. Upon secondary contact, such divergent genetic backgrounds can theoretically give rise to classical Dobzhansky-Muller incompatibilities (DMI), thus contributing to the evolution of endogenous genetic barriers and eventually cause population divergence. We investigated differential TE abundance among conspecific populations of the non-biting midge Chironomus riparius and evaluated their potential role in causing endogenous genetic incompatibilities between these populations. We focussed on a Chironomus-specific TE, the minisatellite-like Cla-element, whose activity is associated with speciation in the genus. Using a newly generated and annotated draft genome for a genomic study with five natural C. riparius populations, we found highly population-specific TE insertion patterns with many private insertions. A significant correlation of the pairwise FST estimated from genome-wide single nucleotide polymorphisms (SNPs) and the FST estimated from TEs, is consistent with drift as the major force driving TE population differentiation. However, the significantly higher Cla-element FST level due to a high proportion of differentially fixed Cla-element insertions also indicates selection against segregating (i.e. heterozygous) insertions. With reciprocal crossing experiments and fluorescent in-situ hybridisation of Cla-elements to polytene chromosomes, we documented phenotypic effects on female fertility and chromosomal mispairings. We propose that the inferred negative selection on heterozygous Cla-element insertions may cause endogenous genetic barriers and therefore acts as DMI among C. riparius populations. The intrinsic genomic turnover exerted by TEs may thus have a direct impact on population divergence that is operationally different from drift and local adaptation.
Data from: Genome-wide markers reveal a complex evolutionary history involving divergence and introgression in the Abert's squirrel (Sciurus aberti) species group
Background: Genetic introgression between divergent lineages is now considered more common than previously appreciated, with potentially important consequences for adaptation and speciation. Introgression is often asymmetric between populations and patterns can vary for different types of loci (nuclear vs. organellar), complicating phylogeographic reconstruction. The taxonomy of the ecologically specialized Abert's squirrel species group has been controversial, and previous studies based on mitochondrial data have not fully resolved the evolutionary relationships among populations. Moreover, while these studies identified potential areas of secondary contact between divergent lineages, the possibility for introgression has not been tested. Results: We used RAD-seq to unravel the complex evolutionary history of the Abert's squirrel species group. Although some of our findings reinforce inferences based on mitochondrial data, we also find significant areas of discordance. Discordant signals generally arise from previously undetected introgression between divergent populations that differentially affected variation at mitochondrial and nuclear loci. Most notably, our results support earlier claims (disputed by mitochondrial data) that S. aberti kaibabensis, found only on the north rim of the Grand Canyon, is highly divergent from other populations. However, we also detected introgression of S. aberti kaibabensis DNA into other S. aberti populations, which likely accounts for the previously inferred close genetic relationship between this population and those south of the Grand Canyon. Conclusions: Overall, the evolutionary history of Abert's squirrels appears to be shaped largely by divergence during periods of habitat isolation. However, we also found evidence for interbreeding during periods of secondary contact resulting in introgression, with variable effects on mitochondrial and nuclear markers. Our results support the emerging view that populations often diversify under scenarios involving both divergence in isolation and gene flow during secondary contact, and highlight the value of genome-wide datasets for resolving such complex evolutionary histories.
Data from: Adaptive divergence despite strong genetic drift: genomic analysis of the evolutionary mechanisms causing genetic differentiation in the island fox (Urocyon littoralis)
The evolutionary mechanisms generating the tremendous biodiversity of islands have long fascinated evolutionary biologists. Genetic drift and divergent selection are predicted to be strong on islands and both could drive population divergence and speciation. Alternatively, strong genetic drift may preclude adaptation. We conducted a genomic analysis to test the roles of genetic drift and divergent selection in causing genetic differentiation among populations of the island fox (Urocyon littoralis). This species consists of six subspecies, each of which occupies a different California Channel Island. Analysis of 5293 SNP loci generated using Restriction-site Associated DNA (RAD) sequencing found support for genetic drift as the dominant evolutionary mechanism driving population divergence among island fox populations. In particular, populations had exceptionally low genetic variation, small Ne (range = 2.1–89.7; median = 19.4), and significant genetic signatures of bottlenecks. Moreover, islands with the lowest genetic variation (and, by inference, the strongest historical genetic drift) were most genetically differentiated from mainland grey foxes, and vice versa, indicating genetic drift drives genome-wide divergence. Nonetheless, outlier tests identified 3.6–6.6% of loci as high FST outliers, suggesting that despite strong genetic drift, divergent selection contributes to population divergence. Patterns of similarity among populations based on high FST outliers mirrored patterns based on morphology, providing additional evidence that outliers reflect adaptive divergence. Extremely low genetic variation and small Ne in some island fox populations, particularly on San Nicolas Island, suggest that they may be vulnerable to fixation of deleterious alleles, decreased fitness and reduced adaptive potential.
Data from: Population genomics of divergence among extreme and intermediate color forms in a polymorphic insect
Geographic variation in insect coloration is among the most intriguing examples of rapid phenotypic evolution and provides opportunities to study mechanisms of phenotypic change and diversification in closely related lineages. The bumble bee Bombus bifarius comprises two geographically disparate color groups characterized by red-banded and black-banded abdominal pigmentation, but with a range of spatially and phenotypically intermediate populations across western North America. Microsatellite analyses have revealed that B. bifarius in the USA are structured into two major groups concordant with geography and color pattern, but also suggest ongoing gene flow among regional populations. In this study, we better resolve the relationships among major color groups to better understand evolutionary mechanisms promoting and maintaining such polymorphism. We analyze >90,000 and >25,000 single-nucleotide polymorphisms derived from transcriptome (RNAseq) and double digest restriction site associated DNA sequencing (ddRAD), respectively, in representative samples from spatial and color pattern extremes in B. bifarius as well as phenotypic and geographic intermediates. Both ddRAD and RNAseq data illustrate substantial genome-wide differentiation of the red-banded (eastern) color form from both black-banded (western) and intermediate (central) phenotypes and negligible differentiation among the latter populations, with no obvious admixture among bees from the two major lineages. Results thus indicate much stronger background differentiation among B. bifarius lineages than expected, highlighting potential challenges for revealing loci underlying color polymorphism from population genetic data alone. These findings will have significance for resolving taxonomic confusion in this species and in future efforts to investigate color-pattern evolution in B. bifarius and other polymorphic bumble bee species.
Data from: Distinguishing noise from signal in patterns of genomic divergence in a highly polymorphic avian radiation
Recently diverged taxa provide the opportunity to search for the genetic basis of the phenotypes that distinguish them. Genomic scans aim to identify loci that are diverged with respect to an otherwise weakly differentiated genetic background. These loci are candidates for being past targets of selection because they behave differently from the rest of the genome that has either not yet differentiated or that may cross species barriers through introgressive hybridization. Here we use a reduced-representation genomic approach to explore divergence among six species of southern capuchino seedeaters, a group of recently radiated sympatric passerine birds in the genus Sporophila. For the first time in these taxa, we discovered a small proportion of markers that appeared differentiated among species. However, when assessing the significance of these signatures of divergence, we found that similar patterns can also be recovered from random grouping of individuals representing different species. A detailed demographic inference indicates that genetic differences among Sporophila species could be the consequence of neutral processes, which include a very large ancestral effective population size that accentuates the effects of incomplete lineage sorting. As these neutral phenomena can generate genomic scan patterns that mimic those of markers involved in speciation and phenotypic differentiation, they highlight the need for caution when ascertaining and interpreting differentiated markers between species, especially when large numbers of markers are surveyed. Our study provides new insights into the demography of the southern capuchino radiation and proposes controls to distinguish signal from noise in similar genomic scans.
Data from: Genomics of rapid ecological divergence and parallel adaptation in four tidal marsh sparrows
Theory suggests that different taxa having colonized a similar, challenging environment will show parallel or lineage-specific adaptations to shared selection pressures, but empirical examples of parallel evolution in independent taxa are exceedingly rare. We employed comparative genomics to identify parallel and lineage-specific responses to selection within and among four species of North American sparrows that represent four independent, post-Pleistocene colonization events by an ancestral, upland subspecies and a derived salt marsh specialist. We identified multiple cases of parallel adaptation in these independent comparisons following salt marsh colonization, including selection on twelve candidate genes linked to osmoregulation. In addition to detecting shared genetic targets of selection across multiple comparisons, we found many novel, species-specific signatures of selection, including evidence of selection on loci associated with both physiological and behavioral mechanisms of osmoregulation. Demographic reconstructions of all four species highlighted their recent divergence and small effective population sizes, as expected given their rapid radiation into saline environments. Our results highlight the interplay of both shared and lineage-specific selection pressures in the colonization of a biotically and abiotically challenging habitat and confirm theoretical expectations that steep environmental clines can drive repeated and rapid evolutionary diversification in birds.
Data from: Patterns of genomic and allochronic strain divergence in the fall armyworm, Spodoptera frugiperda
<p>Speciation is the process through which reproductive isolation develops between distinct populations. Because this process takes time, speciation studies often necessarily examine populations within a species that are at various stages of divergence. The fall armyworm, <em>Spodoptera frugiperda </em>(J.E.Smith), is comprised of two strains (R=Rice & C=Corn) that serve as a novel system to explore population divergence in sympatry. Here, we use ddRADSeq data to show that fall armyworm strains in the field are largely genetically distinct, but some interstrain hybridization occurs. Although we detected F1 hybrids of both R- and C-strain maternal origin, only hybrids with R-strain mtDNA were found to contribute to subsequent generations, possibly indicating a unidirectional barrier to gene flow. Although these strains have been previously defined as 'host plant-associated,' we recovered an equal proportion of R- and C-strain individuals in fields dominated by C-strain host plants. As an alternative to host associated divergence, we tested the hypothesis that differences in nightly activity patterns could account for reproductive isolation by genotyping temporally-collected moths. Our data indicates that strains exhibit a significant shift in the timing of their nightly activities in the field. This divergence in phenology creates a prezygotic reproductive barrier that likely maintains the genetic isolation between strains. Thus, we conclude that it may be ecologically inaccurate to refer to the C- and R- strain as 'host-associated' and they should more appropriately be considered 'allochronic strains.'</p>
Supporting data for: Whole genome sequencing reveals fine-scale environment associated divergence near the range limits of a temperate reef fish
<p>Environmental variation is increasingly recognized as an important driver of diversity in marine species despite the lack of physical barriers to dispersal and the presence of pelagic stages in many taxa. A robust understanding of the genomic and ecological processes involved in structuring populations is lacking for most marine species, often hindering management and conservation action. Cunner (<em>Tautogolabrus adspersus</em>), is a temperate reef fish with both pelagic early life history stages and strong site-associated homing as adults; the species is also of interest for use as a cleaner fish in salmonid aquaculture in Atlantic Canada. We aimed to characterize genomic and geographic differentiation of cunner in the Northwest Atlantic. To achieve this, a chromosome-level genome assembly for cunner was produced and used to characterize spatial population structure throughout Atlantic Canada using whole genome resequencing. The genome assembly spanned 0.72 Gbp and 24 chromosomes; whole genome resequencing of 803 individuals from 20 locations from Newfoundland to New Jersey identified approximately 11 million genetic variants. Principal component analysis revealed four regional Atlantic Canadian groups. Pairwise F<sub>ST</sub> and selection scans revealed signals of differentiation and selection at discrete genomic regions, including adjacent peaks on chromosome 10 across multiple pairwise comparisons (<em>i.e.</em>, F<sub>ST</sub> 0.5–0.75). Redundancy analysis suggested association of environmental variables related to benthic temperature and oxygen range with genomic structure. Results suggest regional scale diversity in this temperate reef fish and can directly inform the collection and translocation of cunner for aquaculture applications and the conservation of wild populations throughout the Northwest Atlantic.</p>
Data from: Genomics of the divergence continuum in an African plant biodiversity hotspot, I: drivers of population divergence in Restio capensis (Restionaceae)
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Data from: Genome-wide signals of drift and local adaptation during rapid lineage divergence in a songbird
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Data from: Seascape genomics reveals adaptive divergence in a connected and commercially important mollusc, the greenlip abalone (Haliotis laevigata), along a longitudinal environmental gradient
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Data from: On the causes of rapid diversification in the Páramos: Isolation by ecology and genomic divergence in Espeletia
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Data from: Genomic tests of the species-pump hypothesis: recent island connectivity cycles drive population divergence but not speciation in Caribbean crickets across the Virgin Islands
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Data from: Genomic patterns of diversity and divergence of two introduced salmonid species in Patagonia, South America
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