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98 results for “hybrid speciation”
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>
Data from: Transgressive segregation in mating traits drives hybrid speciation
<p><span>Hybridization can instantaneously generate novel genetic variation, which can promote ecological speciation by creating novel adaptive phenotypes. However, it remains unclear how hybridization, creating novel mating phenotypes (e.g., mating season, genitalia shapes, sexual displays, mate preferences), affects speciation especially when the phenotypes do not confer adaptive advantages. Here, based on individual-based evolutionary simulations, we propose that transgressive segregation of mating traits can drive incipient hybrid speciation. Simulations demonstrated that incipient hybrid speciation occurred most frequently when the hybrid population received moderate continued immigration from parental lineages</span><span> causing </span><span>recurrent episodes of hybridization. Recurrent hybridization constantly generated genetic variation, which </span><span>promoted</span> <span>the rapid stochastic evolution of mating phenotypes</span><span> in a hybrid population.</span><span> The stochastic evolution continued until a novel mating phenotype came to dominate the hybrid population, which reproductively isolates the hybrid population from parental lineages. However, too </span><span>frequent hybridization rather hindered the evolution of reproductive isolation by inflating the variation of mating phenotypes to produce phenotypes allowing mating with parental lineages. Simulations also revealed conditions for long-term persistence of hybrid species after their incipient emergence. </span><span>Our results suggest that recurrent transgressive segregation of mating phenotypes can offer a plausible explanation for hybrid speciation and radiations that involved little adaptive ecological divergence.</span></p>
Data from: The role of deep hybridization in fern speciation: Examples from the Thelypteridaceae
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Data from: Transgressive segregation in mating traits drives hybrid speciation
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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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Loss of ecologically important genetic variation in late generation hybrids reveals links between adaptation and speciation
Adaptation to contrasting environments occurs when advantageous alleles accumulate in each population, but it remains largely unknown whether these same advantageous alleles create genetic incompatibilities that can cause intrinsic reproductive isolation leading to speciation. Identifying alleles that underlie both adaptation and reproductive isolation is further complicated by factors such as dominance and genetic interactions among loci, which can affect both processes differently and obscure potential links between adaptation and speciation. Here, we use a combination of field and glasshouse experiments to explore the connection between adaptation and speciation while accounting for dominance and genetic interactions. We created a hybrid population with equal contributions from four contrasting ecotypes of Senecio lautus (Asteraceae), which produced hybrid genomes both before (F1 hybrid generation) and after (F4 hybrid generation) recombination among the parental ecotypes. In the glasshouse, plants in the second generation (F2 hybrid generation) showed reduced fitness as a loss of fertility, but fertility was recovered in subsequent generations suggesting that genetic variation underlying fertility reduction was lost in subsequent generations. To quantify the effects of losing genetic variation at the F2 generation on the fitness of later generation hybrids, we used a reciprocal transplant to test for fitness differences between parental ecotypes, and F1 and F4 hybrids in all four parental habitats. Compared to the parental ecotypes and F1 hybrids, variance in F4 hybrid fitness was lower, and lowest in habitats that showed stronger native-ecotype advantage, suggesting that stronger natural selection for the native ecotype reduced fitness variation in the F4 hybrids. Fitness trade-offs that were present in the parental ecotypes and F1 hybrids were absent in the F4 hybrid. Together, these results suggest that the genetic variation lost after the F2 generation was likely associated with both adaptation and intrinsic reproductive isolation among populations adapted to contrasting environments.
Assortative mating in hybrid zones is remarkably ineffective in promoting speciation
<p>Partial prezygotic isolation is often viewed as more important than partial postzygotic isolation (low fitness of hybrids) early in the process of speciation. I simulate secondary contact between two populations ('species') to examine effects of assortative mating and low hybrid fitness in preventing blending. A small reduction in hybrid fitness (e.g., by 10%) produces a narrower hybrid zone than a strong but imperfect mating preference (e.g., 10x stronger preference for conspecific over heterospecific mates). In the latter case, rare F1 hybrids find each other attractive (due to assortative mating), leading to the buildup of a continuum of intermediates. The weakness of assortative mating compared to reduced fitness of hybrids in preventing blending is robust to varying genetic bases of these traits. Assortative mating is most powerful in limiting blending when it is encoded by a single locus, is essentially complete, or when there is a large mate search cost. In these cases assortative mating is likely to cause hybrids to have low fitness, due to frequency-dependent mating disadvantage of individuals of rare mating types. These results prompt a questioning of the concept of partial prezygotic isolation, since it is not very isolating unless there is also postzygotic isolation.</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>
Fig. 3 in Genetic Differentiation Of Ukrainian Populations Of Eusomus Ovulum (Coleoptera, Curculionidae): Evidence Of Multiple Hybrid Speciation
Fig. 3. Polyclonal structure of studied Eusomus ovlulum samples inUkraine.
Fig. 2 in Genetic Differentiation Of Ukrainian Populations Of Eusomus Ovulum (Coleoptera, Curculionidae): Evidence Of Multiple Hybrid Speciation
Fig. 2. The electrophoretic spectra of the esterases in the Eusomus ovulum specimens.
Fig. 1 in Genetic Differentiation Of Ukrainian Populations Of Eusomus Ovulum (Coleoptera, Curculionidae): Evidence Of Multiple Hybrid Speciation
Fig. 1. Geographic localization of Eusomus ovulum samples.
Integrating top-down and bottom-up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone
<p><span>Understanding the phenotypic and genetic architecture of reproductive isolation is a longstanding goal of speciation research. In several systems, large-effect loci contributing to barrier phenotypes have been characterized, but such causal connections are rarely known for more complex genetic architectures. In this study, we combine 'top-down' and 'bottom-up' approaches with demographic modeling toward an integrated understanding of speciation across a monkeyflower hybrid zone. Previous work suggests that pollinator visitation acts as a primary barrier to gene flow between two divergent red- and yellow-flowered ecotypes of <em>Mimulus</em> <em>aurantiacus</em>. Several candidate isolating traits and anonymous SNP loci under divergent selection have been identified, but their genomic positions remain unknown. Here, we report findings from demographic analyses that indicate this hybrid zone formed by secondary contact, but that subsequent gene flow was restricted by widespread barrier loci across the genome. Using a novel, geographic cline-based genome scan, we demonstrate that candidate barrier loci are broadly distributed across the genome, rather than mapping to one or a few 'islands of speciation.' Quantitative trait locus (QTL) mapping reveals that most floral traits are polygenic, with little evidence that QTL co-localize, indicating that most traits are genetically independent. Finally, we find little evidence that QTL and candidate barrier loci overlap, suggesting that some loci contribute to other forms of reproductive isolation. Our findings highlight the challenges of understanding the genetic architecture of reproductive isolation and reveal that barriers to gene flow aside from pollinator isolation may play an important role in this system.</span></p>
Integrating top-down and bottom-up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone
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Assortative mating in hybrid zones is remarkably ineffective in promoting speciation
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Data from: Homoploid hybrid speciation in a marine pelagic fish
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Recent speciation and hybridization in Icelandic deep-sea isopods: An integrative approach using genomics and proteomics.
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Supporting data: Phylogenomic analyses re-examine the evolution of reinforcement and hypothesized hybrid speciation in Phlox wildflowers
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Loss of ecologically important genetic variation in late generation hybrids reveals links between adaptation and speciation
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Data from: Repeatable genomic outcomes along the speciation continuum: Insights from pine hybrid zones (genus Pinus)
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Historical climate change dynamics facilitated speciation and hybridization between highland and lowland species of Baripus ground beetles from Patagonia
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