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160 results for “introgressive hybridization”
Pollinator and host sharing lead to hybridization and introgression in Panamanian free-standing figs, but not in their pollinator wasps
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Introgression between Sphyrapicus nuchalis and S. varius sapsuckers in a hybrid zone in west-central Alberta
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Data from: Hare pseudo-reference genome from: the genomic impact of historical hybridization with massive mitochondrial DNA introgression
<p><b>Background:</b> The extent to which selection determines interspecific patterns of genetic exchanges enlightens the role of adaptation in evolution and speciation. Often reported extensive interspecific introgression could be selection-driven, but also result from demographic processes, especially in cases of invasive species replacements, which can promote introgression at their front. Because invasion and selective sweeps similarly mold variation, population genetics evidence for selection can only be gathered in an explicit demographic framework. The Iberian hare, <i>Lepus granatensis</i>, displays in its northern range extensive mitochondrial DNA introgression from <i>L. timidus</i>, an arctic/boreal species that it replaced locally after the last glacial maximum. We use whole-genome sequencing to infer geographic and genomic patterns of nuclear introgression and fit a neutral model of species replacement with hybridization, allowing us to evaluate how selection influenced introgression genome-wide, including for mtDNA.</p> <p><b>Results:</b> Although the average nuclear and mtDNA introgression patterns are strongly contrasted, they fit a single neutral model of post-glacial invasive replacement of <i>timidus</i> by <i>granatensis</i>. Outliers of elevated introgression include several genes related to immunity, spermatogenesis, and mitochondrial metabolism. Introgression is reduced on the X-chromosome and in low recombining regions.</p> <p><b>Conclusion:</b> General nuclear and mtDNA patterns of introgression can be explained by purely demographic processes. Hybrid incompatibilities and interplay between selection and recombination locally modulate levels of nuclear introgression. Selection promoted introgression of some genes involved in conflicts, either interspecific (parasites) or possibly cytonuclear. In the latter case, nuclear introgression could mitigate the potential negative effects of alien mtDNA on mitochondrial metabolism and male-specific traits.</p>
Data from: Mapping reduced introgression loci to the X chromosome of the hybridizing field crickets, Gryllus firmus and G. pennsylvanicus
The genomic architecture of barriers to gene exchange during the speciation process is poorly understood. The genomic islands model suggests that loci associated with barriers to gene exchange prevent introgression of nearby genomic regions via linkage disequilibrium. But few analyses of the actual genomic location of non-introgressing loci in closely related species exist. In a previous study Maroja et al. showed that in the hybridizing field crickets, Gryllus firmus and G. pennsylvanicus, 50 non-introgressing loci are localized on two autosomal regions and the X chromosome, but they were not able to map the loci along the X chromosome because they used a male informative cross. Here, we localize the introgressing and non-introgressing loci on the X chromosome and reveal that all X-linked non-introgressing loci are restricted to a 50-cM region with 10 of these loci mapped to a single location. We discuss the implications of this finding to speciation.
Data from: Hybridization and adaptive introgression in a marine invasive species in native habitats
<p><span>Hybridization</span> <span>of distinct populations or species is an important evolutionary driving force. For invasive species, hybridization can enhance their competitive advantage in the non-native range as a source of adaptive novelty by introgression of selectively favoured alleles. </span><span>W</span><span>e use </span><span>single-nucleotide polymorphism arrays (SNP-chips) to assess genetic diversity and population structure in the invasive ctenophore <em>Mnemiopsis</em> <em>leidyi</em> </span><span>in native habitats along the USA east coast. H</span><span>ybrids are present at the distribution border of the two lineages. However, our data suggests selection against hybrids in stable habitats, while hybrids are selected for in fluctuating environments. H</span><span>ybrid populations thriving in extreme and unstable environments of the native range, such as the Chesapeake Bay, could accelerate the invasion success if translocated. For <em>M. leidyi</em>, this is especially relevant as low salinity currently limits its invasion range in western Eurasia. </span><span>Hybridization status is thus important but currently disregarded to determine high-risk areas for ballast water exchange.</span></p>
Data from: Postzygotic barriers persist despite ongoing introgression in hybridizing Mimulus species
<p>The evolution of postzygotic isolation is thought to be a key step in maintaining species boundaries upon secondary contact, yet the dynamics and persistence of hybrid incompatibilities in naturally hybridizing species are not well understood. Here, we explore these issues using genetic mapping in three independent populations of recombinant inbred lines between naturally hybridizing monkeyflowers <em>Mimulus guttatus</em> and <em>M. nasutus</em> from the sympatric Catherine Creek population. We discover that the three <em>M. guttatus</em> founders differ dramatically in admixture history, with nearly a quarter of one founder's genome introgressed from <em>M. nasutus</em>. Comparative genetic mapping in the three RIL populations reveals three new putative inversions, each one segregating among the <em>M. guttatus</em> founders, two due to admixture. We find strong, genome-wide transmission ratio distortion in all RILs, but patterns are highly variable among the three populations. At least some of this distortion appears to be explained by epistatic selection favoring parental genotypes, but tests of inter-chromosomal linkage disequilibrium also reveal multiple candidate Dobzhansky-Muller incompatibilities. We also map several genetic loci for hybrid pollen viability, including two interacting pairs that coincide with peaks of distortion. Remarkably, even with this limited sample of three <em>M. guttatus</em> lines, we discover abundant segregating variation for hybrid incompatibilities with <em>M. nasutus,</em> suggesting this population harbors diverse contributors to postzygotic isolation. Moreover, even with substantial admixture, hybrid incompatibilities between <em>Mimulus</em> species persist, suggesting postzygotic isolation might be a potent force in maintaining species barriers in this system. </p>
Table 2 in Altai Mountains - cradle of hybrids and introgressants: A case study in Veronica subg. Pseudolysimachium (Plantaginaceae)
<p><b>Table 2.</b> Details of AMOVA in each group with different combination without including the putative hybrid.</p><table><tbody><tr><th></th><th>Source of variation</th><th>Variance components</th><th>Percentage of variation</th><th>Fixation index</th></tr></tbody><tbody><tr><th>Global AMOVA based on <i>K</i> = 5 results of STRUCTURE including all the putative pure 174 individuals</th><td>Among Species</td><td>14</td><td>16</td><td></td></tr><tr><td>Within Species</td><td>74</td><td>84</td><td></td></tr><tr><td>TOTAL</td><td>88</td><td>100</td><td><i>F</i> ST: 0.16*</td></tr><tr><th>Hierarchical AMOVA based on <i>K</i> = 5 results of STRUCTURE including all the putative pure 174 individuals</th><td>Among Groups</td><td>7.2</td><td>8.13</td><td><i>F</i> CT: 0.08*</td></tr><tr><td>Among Species</td><td>7.1</td><td>8.01</td><td><i>F</i> SC: 0.09*</td></tr><tr><td>Within Species</td><td>74.3</td><td>83.86</td><td><i>F</i> ST: 0.16*</td></tr><tr><td>TOTAL</td><td>88.6</td><td>100</td><td></td></tr></tbody></table><p><i>F</i> <sub>ST</sub>, correlation within populations relative to total; <i>F</i> <sub>CT</sub>, correlation within groups relative to total; <i>F</i> <sub>SC</sub>, correlation within populations relative to groups.* <i>P</i> <0.001, 10,000 permutations.</p>
Table 1 in Altai Mountains - cradle of hybrids and introgressants: A case study in Veronica subg. Pseudolysimachium (Plantaginaceae)
<p><b>Table 1.</b> Details of sampled morphotypes and their geographical distribution.</p><table><tbody><tr><th>Serial no.</th><th>Species</th><th>Distribution</th><th>Latitude</th><th>Longitude</th><th>Number of individuals</th></tr></tbody><tbody><tr><th>1</th><td><i>V. ×altaica</i></td><td>Russia</td><td>50.9158</td><td>82.3274</td><td>12</td></tr><tr><th>2</th><td><i>V. ×grisea</i></td><td>Russia</td><td>50.6399</td><td>86.3131</td><td>9</td></tr><tr><th>3</th><td><i>V. ×kolyvanensis</i></td><td>Russia</td><td>51.7684</td><td>82.1381</td><td>6</td></tr><tr><th>4</th><td><i>V. ×sapozhnikovii</i></td><td>Mongolia</td><td></td><td></td><td>1</td></tr><tr><th>5</th><td><i>V. ×schmakovii</i></td><td>Russia</td><td>50.1567</td><td>88.2953</td><td>11</td></tr><tr><th>6</th><td><i>V. ×sessiliflora</i></td><td>Russia</td><td>50.3437</td><td>87.4315</td><td>13</td></tr><tr><th>7</th><td><i>V. ×smirnovii</i></td><td>Mongolia</td><td>46.3533</td><td>91.2095</td><td>6</td></tr><tr><th>8</th><td><i>V. arenosa</i></td><td>Mongolia</td><td></td><td></td><td>3</td></tr><tr><th>9a</th><td><i>V. incana</i></td><td>Russia</td><td>50.6461</td><td>86.3144</td><td>10</td></tr><tr><th>9b</th><td><i>V. incana</i></td><td>Russia</td><td>51.3924</td><td>82.2084</td><td>24</td></tr><tr><th>10</th><td><i>V. longifolia</i></td><td>Russia</td><td>53.3346</td><td>84.2004</td><td>27</td></tr><tr><th>11</th><td><i>V. pinnata</i></td><td>Russia</td><td>50.3501</td><td>87.4125</td><td>22</td></tr><tr><th>12</th><td><i>V. porphyriana</i></td><td>Russia</td><td>51.0431</td><td>85.6399</td><td>36</td></tr><tr><th>13</th><td><i>V. reverdattoi</i></td><td>Russia</td><td>50.4940</td><td>91.3311</td><td>1</td></tr><tr><th>14</th><td><i>V. sajanensis</i></td><td>Russia</td><td>56.1262</td><td>92.9057</td><td>2</td></tr><tr><th>15</th><td><i>V. spicata</i></td><td>Russia</td><td>50.3605</td><td>82.2448</td><td>37</td></tr><tr><th>16</th><td><i>V. spuria</i></td><td>Russia</td><td>51.7684</td><td>82.1381</td><td>7</td></tr><tr><th>17</th><td><i>V. taigischensis</i></td><td>Russia</td><td>53.0584</td><td>93.3399</td><td>3</td></tr><tr><th>TOTAL</th><td>17 morphotypes (10 taxonomically described pure forms; 7 taxonomically described putative hybrids forms; 3 individuals were not identified, they are listed in suppl. Table S1)</td></tr></tbody></table>
Hybridization dynamics and extensive introgression in the Daphnia longispina species complex: new insights from a high-quality Daphnia galeata reference genome
<p>Supplementary data for the Genome Biology and Evolution paper <a href="http://dx.doi.org/10.1093/gbe/evab267">10.1093/gbe/evab267</a></p>
Extensive introgression at late stages of species formation: Insights from grasshopper hybrid zones
<p><span class="TextRun SCXW104780834 BCX0"><span class="NormalTextRun SCXW104780834 BCX0">The</span><span class="NormalTextRun SCXW104780834 BCX0"> process of species formation is </span><span class="NormalTextRun SCXW104780834 BCX0">characterised by the accumulation</span><span class="NormalTextRun SCXW104780834 BCX0"> of </span><span class="NormalTextRun SCXW104780834 BCX0">multiple reproductive barriers. The evolution</span><span class="NormalTextRun SCXW104780834 BCX0"> of </span><span class="NormalTextRun SCXW104780834 BCX0">hybrid male sterility, or Haldane's rule, typically characterises later stages of species formation, when total </span><span class="NormalTextRun SCXW104780834 BCX0">reproductive isolation is </span><span class="NormalTextRun SCXW104780834 BCX0">strongest.</span><span class="NormalTextRun SCXW104780834 BCX0"> Yet, understanding how </span><span class="NormalTextRun SCXW104780834 BCX0">quickly reproductive barriers evolve and their consequences for maintaining genetic boundaries between emerging species </span><span class="NormalTextRun SCXW104780834 BCX0">remains a challenging task because </span><span class="NormalTextRun SCXW104780834 BCX0">it requires studying</span><span class="NormalTextRun SCXW104780834 BCX0"> taxa that hybridise in nature. Here, we address these questions using the meadow grasshopper </span></span><span class="TextRun SCXW104780834 BCX0"><span class="NormalTextRun SCXW104780834 BCX0">Pseudochorthippus parallelus</span></span><span class="TextRun SCXW104780834 BCX0"><span class="NormalTextRun SCXW104780834 BCX0">,</span><span class="NormalTextRun SCXW104780834 BCX0"> where populations that </span><span class="NormalTextRun SCXW104780834 BCX0">show multiple reproductive barriers, including hybrid male sterility,</span><span class="NormalTextRun SCXW104780834 BCX0"> hybridise in two natural hybrid zones</span><span class="NormalTextRun SCXW104780834 BCX0">.</span><span class="NormalTextRun SCXW104780834 BCX0"> </span><span class="NormalTextRun SCXW104780834 BCX0">Using mitochondrial data, we infer that such populations have diverged some 100,000 years ago, </span></span><span class="TextRun SCXW104780834 BCX0"><span class="NormalTextRun SCXW104780834 BCX0">at the beginning of the last </span><span class="NormalTextRun SCXW104780834 BCX0">glacial </span><span class="NormalTextRun SCXW104780834 BCX0">cycle in Europe</span></span><span class="TextRun SCXW104780834 BCX0"><span class="NormalTextRun SCXW104780834 BCX0">.</span><span class="NormalTextRun SCXW104780834 BCX0"> </span><span class="NormalTextRun SCXW104780834 BCX0">Nuclear data shows that </span><span class="NormalTextRun SCXW104780834 BCX0">contraction</span><span class="NormalTextRun SCXW104780834 BCX0">s</span><span class="NormalTextRun SCXW104780834 BCX0"> at multiple glacial refugia, and post-glacial expansions have facilitated genetic differentiation between lineages that today interact in hybrid zones. We find </span><span class="NormalTextRun SCXW104780834 BCX0">extensive introgression throughout the </span><span class="NormalTextRun SCXW104780834 BCX0">sampled </span><span class="NormalTextRun SCXW104780834 BCX0">species range, </span><span class="NormalTextRun SCXW104780834 BCX0">irrespective of current strength of reproductive isolation. Populations</span><span class="NormalTextRun SCXW104780834 BCX0"> exhibiting hybrid male sterility</span><span class="NormalTextRun SCXW104780834 BCX0"> in two hybrid zones show </span><span class="NormalTextRun SCXW104780834 BCX0">repeatable patterns of genomic differentiation</span><span class="NormalTextRun SCXW104780834 BCX0">,</span><span class="NormalTextRun SCXW104780834 BCX0"> consistent with shared genomic constraints </span><span class="NormalTextRun SCXW104780834 BCX0">affecting ancestral divergence or with the </span><span class="NormalTextRun SCXW104780834 BCX0">role </span><span class="NormalTextRun SCXW104780834 BCX0">of those regions </span><span class="NormalTextRun SCXW104780834 BCX0">in reproductive isolation. Together, our results suggest that </span><span class="NormalTextRun SCXW104780834 BCX0">reproductive barriers that characterise late stages of species formation</span><span class="NormalTextRun SCXW104780834 BCX0"> can evolve relatively quickly within species, particularly when associated </span><span class="NormalTextRun SCXW104780834 BCX0">with</span><span class="NormalTextRun SCXW104780834 BCX0"> strong demographic changes. </span><span class="NormalTextRun SCXW104780834 BCX0">Moreover, we show that such barriers persist in the face of</span><span class="NormalTextRun SCXW104780834 BCX0"> extensive gene flow, allowing future studies to identify </span><span class="NormalTextRun SCXW104780834 BCX0">associated </span><span class="NormalTextRun SCXW104780834 BCX0">genomic regions.</span></span><span class="EOP SCXW104780834 BCX0"> </span></p>
Introgressive hybridization erodes morphological divergence between lentic and lotic habitats in an endangered minnow
<p>Introgressive hybridization may erode phenotypic divergence along environmental gradients, collapsing locally adapted populations into a hybrid swarm. Alternatively, introgression may promote phenotypic divergence by providing variation on which natural selection can act. In freshwater fishes, water flow often selects for divergent morphological traits in lake versus stream habitats. We tested the effects of introgression on lake-stream morphological divergence in the minnow Owens Tui Chub (<em>Siphateles</em> <em>bicolor</em> <em>snyderi</em>), which has been rendered endangered by introgression from the introduced Lahontan Tui Chub (<em>Siphateles</em> <em>bicolor</em> <em>obesa</em>). Using geometric morphometric analysis of 457 individual Tui Chub from thirteen populations, we found that both the native and introgressing parent taxa exhibited divergent body and caudal fin shapes in lake vs. stream habitats, but their trajectories of divergence were distinct. In contrast, introgressed populations exhibited intermediate body and caudal fin shapes that were not differentiated by habitat type, indicating that introgression has eroded phenotypic divergence along the lentic-lotic gradient throughout the historic range of the Owens Tui Chub. Individuals within hybrid populations were less morphologically variable than those within parent populations, suggesting hybrid adaptation to selective agents other than water flow or loss of variance by drift.</p>
Data from: Integrating Bayesian genomic cline analyses and association mapping of morphological and ecological traits to dissect reproductive isolation and introgression in a Louisiana Iris hybrid zone
Hybrid zones provide unique opportunities to examine reproductive isolation and introgression in nature. We utilized 45,384 Single Nucleotide Polymorphism (SNP) loci to perform association mapping of 14 floral, vegetative, and ecological traits that differ between Iris hexagona and Iris fulva, and to investigate, using a Bayesian Genomic Cline (BGC) framework, patterns of genomic introgression in a large and phenotypically diverse hybrid zone in southern Louisiana. Many loci of small effect-size were consistently found to be associated with phenotypic variation across all traits, and several individual loci were revealed to influence phenotypic variation across multiple traits. Patterns of genomic introgression were quite heterogeneous throughout the Louisiana Iris genome, with I. hexagona alleles tending to be favored over those of I. fulva. Loci that were found to have exceptional patterns of introgression were also found to be significantly associated with phenotypic variation in a small number of morphological traits. However, this was the exception rather than the rule, as most loci that were associated with morphological trait variation were not significantly associated with excess ancestry. These findings provide insights into the complexity of the genomic architecture of phenotypic differences and are a first step towards identifying loci that are associated with both trait variation and reproductive isolation in nature.
Asymmetric allelic introgression across a hybrid zone of the coal tit (Periparus ater) in the central Himalayas
<p>In the Himalayas, a number of secondary contact zones have been described for vicariant vertebrate taxa. However, analyses of genetic divergence and admixture are missing for most of these examples. In this study, we provide a population genetic analysis for the coal tit (<i>Periparus ater</i>) hybrid zone in Nepal. Intermediate phenotypes between the distinctive western 'spot-winged tit' (<i>P. a. melanolophus</i>) and e<span class="msoDel">E</span>astern Himalayan coal tits (<i>P. a. aemodius</i>) occur across a narrow range of less than 100 km in western Nepal. As a peculiarity, another distinctive cinnamon-bellied form is known from a single population so far. Genetic admixture of western and eastern mitochondrial lineages was restricted to the narrow zone of phenotypically intermediate populations. The cline width was estimated 46 km only with a center close to the population of the cinnamon-bellied phenotype. In contrast, allelic introgression of microsatellite loci was asymmetrical from eastern <i>P. a. aemodius</i> into far western populations of phenotypic <i>P. a. melanolophus</i> but not vice versa. Accordingly, the microsatellite cline was about 3.7 times wider than the mitochondrial one.</p>
Introgressive hybridization in the west Pacific pen shells (genus Atrina): Restricted interspecies gene flow within the genome
<p>Abstract</p> <p>A compelling interest in marine biology is to elucidate how species boundaries between sympatric free‐spawning marine invertebrates such as bivalve molluscs are maintained in the face of potential hybridization. Hybrid zones provide the natural resources for us to study the underlying genetic mechanisms of reproductive isolation between hybridizing species. Against this backdrop, we examined the occurrence of introgressive hybridization (introgression) between two bivalves distributed in the western Pacific margin, Atrina japonica and Atrina lischkeana, based on single‐nucleotide polymorphisms (SNPs) derived from restriction site‐associated DNA sequencing. Using 1066 ancestry‐informative SNP sites, we also investigated the extent of introgression within the genome to search for SNP sites with reduced interspecies gene flow. A series of our individual‐level clustering analyses including the principal component analysis, Bayesian model‐based clustering, and triangle plotting based on ancestry–heterozygosity relationships for an admixed population sample from the Seto Inland Sea (Japan) consistently suggested the presence of specimens with varying degrees of genomic admixture, thereby implying that the two species are not completely isolated. The Bayesian genomic cline analysis identified 10 SNP sites with reduced introgression, each of which was located within a genic region or an intergenic region physically close to a functional gene. No, or very few, heterozygotes were observed at these sites in the hybrid zone, suggesting that selection acts against heterozygotes. Accordingly, we raised the possibility that the SNP sites are within genomic regions that are incompatible between the two species. Our finding of restricted interspecies gene flow at certain genomic regions gives new insight into the maintenance of species boundaries in hybridizing broadcast‐spawning molluscs.</p>
Limited hybridization and introgression despite stocking among endemic Interior Highlands black basses (Centrarchidae: Micropterus)
<p><strong>Aim</strong></p> <p>Smallmouth Bass (<em>Micropterus</em> <em>dolomieu</em>; SMB) are globally popular among anglers and have been widely introduced (i.e., stocked) for population management and sportfishing. Importantly, stocking was prevalent before cryptic diversity within the SMB complex was known, which now includes three newly elevated species: Neosho Bass (<em>M</em>. <em>velox</em>; NB), Little River Bass (<em>M</em>. sp. cf. <em>dolomieu</em> Little River; LRB), and Ouachita Bass (<em>M</em>. sp. cf. <em>dolomieu</em> Ouachita River; OB). We sought to quantify population structure and hybridization and introgression in these three recently described species.</p> <p><strong>Location</strong></p> <p>Species-level diversity, particularly in the basin-restricted LRB and OB in the Ouachita Mountains within the Central Interior Highlands (CIH), North America, suggests the presence of distinct genetic variation that could be eroded by introgression. </p> <p><strong>Methods</strong></p> <p>We estimated interspecific introgression and intraspecific population differentiation in the Smallmouth Bass species complex (SMB-C) using 472 specimens comprising SMB, NB, LRB, and OB, including the naturally sympatric Spotted Bass (<em>M</em>. <em>punctulatus</em>; SPB). Genomic samples were genotyped on a SNP panel of 192 loci designed to detect allele-sharing on multiple hierarchical levels. </p> <p><strong>Results</strong></p> <p>We found low range-wide hybridization between species in the SMB-C and SPB (mostly SMB-C backcrosses), and interspecific heterozygosity varied, indicating differential introgression. Range-wide hybridization between species in the CIH and SMB was similar overall (but mostly F<sub>2</sub> and CIH backcrosses) and was observed in streams with known SMB stocking in connected reservoirs. Interspecific heterozygosity in SMB hybrids was also generally lower, indicating later-generation backcrosses. We found strong population structure in the Ouachita Mountains (LRB and OB). </p> <p><strong>Main Conclusions</strong></p> <p>Despite isolated incidences of natural (SPB) and human-mediated (SMB) introgression, genomic identity appears intact in endemic LRB and OB, suggesting potential ecological or behavioral isolating mechanisms preventing cross-species reproduction. Our findings reveal that genetic variation remains in cryptic, basin-restricted species in the Ouachita Mountains ecoregion that may be managed for long-term conservation.</p>
Asymmetric allelic introgression across a hybrid zone of the coal tit (Periparus ater) in the central Himalayas
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Hybrid zone analysis using coalescent-based estimates of introgression and migration in plateau fence lizards (Sceloporus tristichus)
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Introgressive hybridization in the west Pacific pen shells (genus Atrina): Restricted interspecies gene flow within the genome
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Introgressive hybridization erodes morphological divergence between lentic and lotic habitats in an endangered minnow
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Data from: Hybridization and adaptive introgression in a marine invasive species in native habitats
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