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134 results for “genomics of speciation”
Data from: Can the genomics of ecological speciation be predicted across the divergence continuum from host races to species? A case study in Rhagoletis
<p>Studies assessing the predictability of evolution typically focus on short-term adaptation within populations or the repeatability of change among lineages. A missing consideration in speciation research is to determine whether natural selection predictably transforms standing genetic variation within populations into differences between species. Here, we test whether host-related selection on diapause timing anticipates genome-wide differentiation during ecological speciation by comparing ancestral hawthorn and newly formed apple-infesting host races of <i>Rhagoletis pomonella </i>to their sibling species <i>R. mendax</i> that attacks blueberries. The responses of 57,857 single nucleotide polymorphisms in a diapause study on the hawthorn race strongly predicted the direction and magnitude of genomic divergence among the three flies at a field site in Fennville, Michigan, USA. As anticipated, the apple race and <i>R. mendax</i> show parallel changes in the frequencies of putative inversions on three chromosomes associated with the earlier fruiting times of apples and blueberries compared to hawthorns. A diapause experiment on <i>R. mendax</i> revealed compensatory mutations throughout the genome accounting for the earlier eclosion of blueberry, but not apple flies. Thus, a degree of predictability, although not complete, exists in the genomics of diapause across the ecological speciation continuum in <i>Rhagoletis</i>. The generality of this result is placed in the context of other similar systems.</p>
Genomic signatures of isolation, hybridization, and selection during speciation of island finches
<p><strong>Data associated</strong> to the study <em>Genomic signatures of isolation, hybridization, and selection during speciation of island finches</em></p> <p><strong>Contents</strong></p> <ul> <li>Table_S9_samples_accession_nos.xlsx: Editable Excel matrix with sample names and accession numbers.</li> <li>RAD_SNPs_stacks_42424_loci.vcf.tar.gz: VCF file (gzip-compressed tarball) containing SNPs in 42,424 loci, based on analyses of restriction site-associated DNA (RAD) sequencing using Stacks.</li> <li>RAD_SNPs_standard_variant_calling.vcf.tar.gz: VCF file (gzip-compressed tarball) containing 131,661 SNPs from standard variant calling pipelines.</li> <li>mitochondrial_markers_full_data.nex: Nexus file containing mitochondrial (mt) sequences used for mt-phylogeny. Partitioned for COX2, tRNA-Lys, ATP8, and ATP6. </li> <li>sequences_nuclear_genotype_with_zebra_finch_TG.tar.gz: Directory (gzip-compressed tarball) containing genotype sequence (heterozygous sites with IUPAC codes) alignments of nuclear markers in nexus files. In addition to the study species, the sequence for zebra finch <em>Taeniopygia guttata</em> is included with sample code TG.</li> <li>sequences_nuclear_phased_and_mitochondrial_haplotypes_matching.tar.gz: Directory (gzip-compressed tarball) containing phased sequence (haplotype) alignments of nuclear markers in nexus files. These include only those individuals that match individuals sequenced for mitochondrial markers (also included here). In case of recombining loci, both the full locus and the largest non-recombining block are represented.</li> <li>sequences_nuclear_phased_haplotypes_all.tar.gz: Directory (gzip-compressed tarball) containing phased sequence (haplotype) alignments of nuclear markers in nexus files. These include all individuals. In case of recombining loci, both the full locus and the largest non-recombining block are represented.</li> <li>microsatellite_dataset.xlsx: Microsatellite datasets for the study species and additional outgroups. <ul> </ul> <p>Sequences and short read datasets available from NCBI; accession numbers in Table S9 (Table_S9_samples_accession_nos.xlsx).</p> </li> </ul> <p> </p> <p><strong>Study summary</strong></p> <p>Sister species occurring sympatrically on islands are rare and offer unique opportunities to understand how speciation can proceed in the face of gene flow. The São Tomé grosbeak is a massive-billed, ‘giant’ finch endemic to the island of São Tomé in the Gulf of Guinea, where it has diverged from its co-occurring sister species the Príncipe seedeater, an average-sized finch that also inhabits two neighbouring islands. Here, we show that the grosbeak carries a large number of unique alleles different from all three Príncipe seedeater populations, but also shares many alleles with the sympatric São Tomé population of the seedeater, a genomic signature signifying divergence in isolation as well as subsequent introgressive hybridization. Furthermore, genomic segments that remain unique to the grosbeak are situated close to genes, including genes that determine bill morphology, suggesting the preservation of adaptive variation through natural selection during divergence with gene flow. This study reveals a complex speciation process whereby genetic drift, introgression, and selection during periods of isolation and secondary contact all have shaped the diverging genomes of these sympatric island endemic finches.</p>
Genomic evidence of speciation by fusion in a recent radiation of grasshoppers
<p><span>Post-divergence gene flow can trigger a number of creative evolutionary outcomes, ranging from the transfer of beneficial alleles across species boundaries (<em>i.e.</em>, adaptive introgression) to the formation of new species (<em>i.e.</em>, hybrid speciation). While neutral and adaptive introgression has been broadly documented in nature, hybrid speciation is assumed to be rare and the evolutionary and ecological context facilitating this phenomenon still remains controversial. Through combining genomic and phenotypic data, we evaluate the hypothesis that the dual feeding regime (based on both </span><span>scrub legumes and gramineous herbs)</span><span> of the taxonomically controversial grasshopper <em>Chorthippus saulcyi</em> <em>algoaldensis</em> resulted from hybridization between the sister taxa </span><em><span>C. binotatus </span></em><span>(that exclusively feeds on scrub legumes) and </span><em><span>C. saulcyi</span></em><span><em> </em>(that only feeds on </span><span>gramineous herbs)</span><span>. Genetic clustering analyses and inferences from coalescent-based demographic simulations confirm that <em>C. s. algoaldensis</em> represents an independently evolving lineage and support the ancient hybrid origin of this taxon (<em>ca. </em>1.4 Ma), which sheds light on its uncertain phylogenetic position and might explain its broader trophic niche. We propose a Pleistocene hybrid speciation model where range shifts resulting from climatic oscillations can promote the formation of hybrid swarms and facilitate its long-term persistence through geographic isolation from parental forms in topographically complex landscapes.</span></p>
Whole-genome analysis of multiple wood ant population pairs supports similar speciation histories, but different degrees of gene flow, across their European ranges
<p>The application of demographic history modelling and inference to the study of divergence between species has become a cornerstone of speciation genomics. Speciation histories are usually reconstructed by analysing single populations from each species, assuming that the inferred population history represents the actual speciation history. However, this assumption may not be met when species diverge with gene flow, e.g., when secondary contact may be confined to specific geographic regions. Here, we tested whether divergence histories inferred from heterospecific populations may vary depending on their geographic locations, using the two wood ant species <em>Formica polyctena</em> and <em>F. aquilonia</em>. We performed whole-genome resequencing of 20 individuals sampled in multiple locations across the European ranges of both species. Then, we reconstructed the histories of distinct heterospecific population pairs using a coalescent-based approach. Our analyses always supported a scenario of divergence with gene flow, suggesting that divergence started in the Pleistocene (ca. 500 kya) and occurred with continuous asymmetrical gene flow from <em>F. aquilonia</em> to <em>F. polyctena</em> until a recent time, when migration became negligible (2-19 kya). However, we found support for contemporary gene flow in a sympatric pair from Finland, where the species hybridise, but no signature of recent bidirectional gene flow elsewhere. Overall, our results suggest that divergence histories reconstructed from a few individuals may be applicable at the species level. Nonetheless, the geographical context of populations chosen to represent their species should be taken into account, as it may affect estimates of migration rates between species when gene flow is spatially heterogeneous.</p>
The role of neutral and adaptive genomic variation in population diversification and speciation in two ground squirrel species of conservation concern
<p>Understanding the neutral (demographic) and adaptive processes leading to the differentiation of species and populations is a critical component of evolutionary and conservation biology. In this context, recently diverged taxa represent a unique opportunity to study the process of genetic differentiation. Northern and southern Idaho ground squirrels (Urocitellus brunneus – NIDGS, and U. endemicus - SIDGS, respectively) are a recently diverged pair of sister species that have undergone dramatic declines in the last 50 years and are currently found in metapopulations across restricted spatial areas with distinct environmental pressures. Here we genotyped single-nucleotide polymorphisms (SNPs) from buccal swabs with restriction site-associated DNA sequencing (RADseq). With these data we evaluated neutral genetic structure at both the inter- and intraspecific level, and identified putatively adaptive SNPs using population structure outlier detection and genotype-environment association (GEA) analyses. At the interspecific level, we detected a clear separation between NIDGS and SIDGS, and evidence for adaptive differentiation putatively linked to torpor patterns. At the intraspecific level, we found evidence of both neutral and adaptive differentiation. For NIDGS, elevation appears to be the main driver of adaptive differentiation, while neutral variation patterns match and expand information on the low connectivity between some populations identified in previous studies using microsatellite markers. For SIDGS, neutral substructure generally reflected natural geographic barriers, while adaptive variation reflected differences in land cover and temperature, as well as elevation. These results clearly highlight the roles of neutral and adaptive processes for understanding the complexity of the processes leading to species and population differentiation, which can have important conservation implications in susceptible and threatened species.</p>
Genomic evidence of speciation by fusion in a recent radiation of grasshoppers
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Whole-genome analysis of multiple wood ant population pairs supports similar speciation histories, but different degrees of gene flow, across their European ranges
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Data From: Estimation of genome-wide coupling in rattlesnake hybrids provides insight into the process of speciation and its progress
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Data from: Can the genomics of ecological speciation be predicted across the divergence continuum from host races to species? A case study in Rhagoletis
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Data from: Population genomics, local adaptation, and cryptic speciation in a temperate reef fish, the black surfperch, <em>Embiotoca jacksoni</em>, using genome-wide resequencing
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The role of neutral and adaptive genomic variation in population diversification and speciation in two ground squirrel species of conservation concern
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Data from: Island size shapes genomic diversity in a great speciator (Aves: Zosterops)
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Data from: Contrasting signatures of genomic divergence during sympatric speciation
<p>The transition from "well-marked varieties" into "well-defined species" has puzzled evolutionary biologists ever since Darwin — especially when extensive gene flow between incipient species is possible due to the lack of physical barriers (sympatric speciation). Gene flow counteracts the build-up of genome-wide differentiation, which is both a hallmark of speciation and forms the underlying basis of irreversible reproductive barriers (incompatibilities) that ultimately complete the speciation process. Theory predicts that the genetic architecture of divergently selected traits can influence whether sympatric speciation occurs. However, empirical data to test this prediction remain rare and are often difficult to synthesize across animal taxa due to idiosyncrasies in their biology and evolutionary histories. Here, within a young species complex of Neotropical cichlid fish (<i>Amphilophus spp.</i>), we analyzed genomic divergence among populations and species, and the genetic architecture of traits that have been suggested to be important for this divergence, by generating a new genome assembly and re-sequencing 453 genomes. We found that species differing in mono/oligogenic traits affecting ecological performance and/or mate choice show remarkably localized genomic differentiation. In contrast, differentiation between species that diverged in polygenic traits is widespread and much higher overall, consistent with the evolution of effective and stable genome-wide barriers to gene flow. Thus, we conclude that simple trait architectures are not always as conducive to speciation-with-gene-flow as previously suggested, whereas, unexpectedly, polygenic architectures can promote rapid and stable speciation in sympatry.</p>
Data from: Genomic signatures of sympatric speciation with historical and contemporary gene flow in a tropical anthozoan (Hexacorallia: Actiniaria)
Sympatric diversification is increasingly thought to have played an important role in the evolution of biodiversity around the globe. However, an in situ sympatric origin for co-distributed taxa is difficult to demonstrate empirically because different evolutionary processes can lead to similar biogeographic outcomes- especially in ecosystems that can readily facilitate secondary contact due to a lack of hard barriers to dispersal. Here we use a genomic (ddRADseq), model-based approach to delimit a species complex of tropical sea anemones that are co-distributed on coral reefs throughout the Tropical Western Atlantic. We use coalescent simulations in fastsimcoal2 to test competing diversification scenarios that span the allopatric-sympatric continuum. We recover support that the corkscrew sea anemone Bartholomea annulata (Le Sueur, 1817) is a cryptic species complex, co-distributed throughout its range. Simulation and model selection analyses suggest these lineages arose in the face of historical and contemporary gene flow, supporting a sympatric origin, but an alternative secondary contact model also receives appreciable model support. Leveraging the genome of Exaiptasia diaphana we identify five loci under divergent selection between cryptic B. annulata lineages that fall within mRNA transcripts or CDS regions. Our study provides a rare empirical, genomic example of sympatric speciation in a tropical anthozoan. Finally, these data represent the first range-wide molecular study of any tropical sea anemone, underscoring that anemone diversity is under described in the tropics, and highlighting the need for additional systematic studies into these ecologically and economically important species.
Data from: Genomic data reject the hypothesis of sympatric ecological speciation in a clade of Desmognathus salamanders
Closely related taxa with dissimilar morphologies are often considered to have diverged via natural selection favoring different phenotypes. However, some studies have found these scenarios to be paired with limited or no genetic differentiation. Desmognathus quadramaculatus and D. marmoratus are sympatric salamander species thought to represent a case of ecological speciation based on distinct morphologies, but the results of previous studies have not resolved corresponding patterns of lineage divergence. Here, we use genome-wide data to test this hypothesis of ecological speciation. Population structure analyses partitioned individuals geographically, but not morphologically, into two adjacent regions of western North Carolina: Pisgah and Nantahala. Phylogenetic analyses confirmed the nominal species are non-monophyletic and resolved deep divergence between the two geographic clusters. Model-testing overwhelmingly supported the hypothesis that lineage divergence followed geography. Finally, ecological niche modeling showed that Pisgah and Nantahala individuals occupy different climatic niches, and geographic boundaries for the two lineages correspond to a difference in precipitation regimes across southern Appalachia. Overall, we reject the previous hypothesis of ecological speciation based on microhabitat partitioning. Instead, our results suggest that there are two cryptic lineages, each containing the same pair of morphotypes.
Data from: Genomic, phenotypic, and environmental correlates of speciation in the midwife toads (Alytes)
<p>This package includes the following : </p> <ul> <li>A matrix of 5,111 SNPs genotyped in the subgenus <em>Alytes </em>(Ao_complex_5111loci.str)</li> <li>A matrix of 3,535 SNPs genotyped in<em> A. o. lusitanicus</em>,<em> A. o. pertinax</em> and<em> A. cisternasii </em>(OC_3535loci.str)</li> <li>A matrix of 15,211 SNPs genotyped in <em>A. o. pertinax</em> and <em>A. dickhilleni</em> (OD_15211loci.str)</li> <li>SNP matrices (.str), Q estimates and environemental suitability estimates (Q_transect_xxx.txt), distances along transects (dist_transect_xxx.txt), hzar inputs (Input_HZ_xxx.csv), lists of diagnostic loci (HZ_xxx_diag_loci.csv) and R commands (HZ_xxx.r), as used to analyze the hybrid zones coded as CAN, HUE, POR, MAD, GAL, PYR</li> <li>Locus-by-locus cline parameters for the eight hybrid zones considered (Clines_HZ_xxx.csv) and R commands used for vizualization (Clines.Display.r)</li> <li>Occurrence records of <em>Alytes</em> (Occurence_dataset.csv)</li> <li>Bioacoustic dataset (Bioacoustic_dataset.csv), and the R commands used for analyses (Bioacoustics.r)</li> <li>Morphometric dataset, including raw measurements (Morphometric_dataset.csv), the input file for GroupStruct (Morphometric_dataset_naked.csv), the size-corrected measurements (Morphometric_dataset_corrected.csv), and the R commands used for analyses (Morphometrics.r)</li> <li>Environemental dataset (Environemental_dataset.csv), and the R commands used for analyses (Environmental.r)</li> </ul>
Data sets and analyses for genomics of cryptic speciation in Catharus thrushes
<p>Cryptic speciation may occur when reproductive isolation is recent or the accumulation of morphological differences between sister lineages is slowed by stabilizing selection preventing phenotypic differentiation. In North America, Bicknell's Thrush (<i>Catharus bicknelli</i>) and its sister species, the Gray-cheeked Thrush (<i>Catharus minimus</i>), are parapatrically breeding migratory songbirds, distinguishable in nature only by subtle differences in song and coloration, and were recognized as distinct species only in the 1990s. Previous molecular studies have estimated that the species diverged ~120 - 420 thousand YBP and found very low levels of introgression despite their similarity and sympatry in the spring (prebreeding) migration. To further clarify the history, genetic divergence, genomic structure and adaptive processes in <i>C. bicknelli</i> and <i>C</i>. <i>minimus</i>, we sequenced and assembled high-coverage reference genomes of both species and re-sequenced genomes from population samples of <i>C. bicknelli</i>, <i>C. minimus</i>, and two individuals of the Swainson's Thrush (<i>C. ustulatus</i>). The genome of <i>C. bicknelli</i> exhibits markedly higher abundances of transposable elements compared to other <i>Catharus</i> and chicken. Demographic and admixture analyses confirm moderate genome-wide differentiation (<i>F</i><sub>st</sub> <i>≈</i> 0.10) and limited gene flow between <i>C. bicknelli</i> and C. <i>minimus,</i> but suggest a more recent divergence than estimates based on mtDNA. We find evidence of rapid evolution of the Z-chromosome and elevated divergence consistent with natural selection on genomic regions near genes involved with neuronal processes in <i>C. bicknelli.</i> These genomes are a useful resource for future investigations of speciation, migration, and adaptation in <i>Catharus </i>thrushes.</p>
Recent speciation and hybridization in Icelandic deep-sea isopods: An integrative approach using genomics and proteomics.
<p>The crustacean marine isopod species <i>Haploniscus bicuspis</i> (G.O. Sars, 1877) shows circum-Icelandic distribution in a wide range of environmental conditions and along well-known geographic barriers, such as the Greenland-Iceland-Faroe (GIF) Ridge. We wanted to explore population genetics, phylogeography and cryptic speciation as well as to investigate whether previously described, but unaccepted subspecies have any merit. Using the same set of specimens, we combined mitochondrial COI sequences, thousands of nuclear loci (ddRAD), and proteomic profiles, plus selected morphological characters using Confocal Laser Scanning Microscopy (CLSM). Five divergent genetic lineages were identified by COI and ddRAD, two south and three north of the GIF Ridge. Assignment of populations to the three northern lineages varied and detailed analyses revealed hybridization and gene flow between them, suggesting a single northern species with a complex phylogeographic history. No apparent hybridization was observed among lineages south of the Ridge, inferring the existence of two more species. Differences in proteomic profiles between the three putative species were minimal, implying an ongoing or recent speciation process. Population differentiation was high, even among closely associated populations, and higher in mitochondrial COI than nuclear ddRAD loci. Gene flow is apparently male-biased, leading to hybrid zones and instances of complete exchange of the local nuclear genome through immigrating males. This study did not confirm the existence of subspecies defined by male characters, which probably characterize different male developmental stages.</p>
Genomic insights into rapid speciation within the world's largest tree genus Syzygium
<p><span>Species r</span><span>adiations, despite immense phenotypic variation, can be difficult to resolve phylogenetically when genetic </span><span>change</span><span> poorly matches the rapidity of diversification. Genomic potential furnished by </span><span>palaeopolyploidy,</span><span> and relative roles for </span><span>adaptation, random drift and hybridisation in the </span><span>apportionment of genetic</span><span> variation, remain poorly understood factors.</span><span> Here, we study these aspects in a model radiation, </span><em><span>Syzygium</span></em><span>, the most species-rich tree genus worldwide. </span><span>G</span><span>enomes of 182 distinct species and 58 unidentified taxa are compared against a chromosome-level reference genome of the sea apple, <em>Syzygium</em> <em>grande</em>. We show that while <em>Syzygium</em> shares an ancient genome doubling event with other Myrtales, little evidence exists for recent polyploidy events. </span><span>Phylogenomics confirms that</span><span> <em>Syzygium</em> originated in Australia-New Guinea and diversified in </span><span>multiple migrations</span><span>, eastward to the Pacific and westward to India and Africa</span><span>,</span><span> in </span><span>bursts of speciation </span><span>visible as poorly resolved </span><span>branches</span> <span>on phylogenies. </span><span>Furthermore, </span><span>some sublineages demonstrate genomic clines that recapitulate cladogenetic events, suggesting</span><span> that stepwise geographic speciation, a neutral process, has been important in </span><em><span>Syzygium</span></em><span> diversification</span><span>.</span></p>
Data from: Genomic differentiation during speciation-with-gene-flow: comparing geographic and host-related variation in divergent life history adaptation in Rhagoletis pomonella
A major goal of evolutionary biology is to understand how variation within populations gets partitioned into differences between reproductively isolated species. Here, we examine the degree to which diapause life history timing, a critical adaptation promoting population divergence, explains geographic and host-related genetic variation in ancestral hawthorn and recently derived apple-infesting races of Rhagoletis pomonella. Our strategy involved combining experiments on two different aspects of diapause (initial diapause intensity and adult eclosion time) with a geographic survey of genomic variation across four sites where apple and hawthorn flies co-occur from north to south in the Midwestern USA. The results demonstrated that the majority of the genome showing significant geographic and host-related variation can be accounted for by initial diapause intensity and eclosion time. Local genomic differences between sympatric apple and hawthorn flies were subsumed within broader geographic clines; allele frequency differences within the races across the Midwest were 2 to 3-fold greater than those between the races in sympatry. As a result, sympatric apple and hawthorn populations displayed more limited genomic clustering compared to geographic populations within the races. The findings suggest that with reduced gene flow and increased selection on diapause equivalent to that seen between geographic sites, the host races may be recognized as different genotypic entities in sympatry, and perhaps species, a hypothesis requiring future genomic analysis of related sibling species to R. pomonella to test. Our findings concerning the way selection and geography interplay could be of broad significance for many cases of earlier stages of divergence-with-gene flow, including (1) where only modest increases in geographic isolation and the strength of selection may greatly impact genetic coupling and (2) the dynamics of how spatial and temporal standing variation is extracted by selection to generate differences between new and discrete units of biodiversity.
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