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37 results for “Ancient hybridization”
Recent hybrids recapitulate ancient hybrid outcomes
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Data from: Geographic range dynamics drove ancient hybridization in a lineage of angiosperms
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Species divergence and repeated ancient hybridization in a Sulawesian lake system
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Data from: Ancient hybrid origin of the eastern wolf not yet off the table: a comment on Rutledge et al.
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Data from: Cryptic hybridization between the ancient lineages of Natterer's bat (Myotis nattereri)
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Ancient hybridization leads to the repeated evolution of red flowers across a monkeyflower radiation
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Phylogeny and evolution of Cupressaceae: updates on intergeneric relationships and new insights on ancient intergeneric hybridization
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The origin of the parrotfish species Scarus compressus in the Tropical Eastern Pacific: region-wide hybridization between ancient species pairs
<p class="Normal1"><span><span><span><span><span><span><span><span><span><span><span><b>Background: </b></span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>An increasing number of hybrid zones with varying evolutionary outcomes have been documented from different reef fish families. In the Tropical Eastern Pacific (TEP), four species of parrotfishes occur in sympatry on rocky reefs from Baja California to Ecuador: <i>Scarus. compressus</i>,<i>S. ghobban</i>, <i>S. perrico</i>, and <i>S. rubroviolaceus</i>; and have complex phylogeographic histories. The most divergent,<i>S. perrico</i>, belongs to a Tropical American clade that diverged from a Central Indo-Pacific ancestor in the late Miocene (6.6 Ma). We tested the hypothesis that <i>S. compressus</i>was the result of ongoing hybridization among the other three species by sequencing four nuclear markers and a mitochondrial locus in samples spanning 2/3 of the latitudinal extent of the TEP. </span></span></span></span></span></span></span></span></span></span></span></p> <p class="Normal1"><span><span><span><span><span><span><span><span><span><span><span><b>Results: </b></span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>A structure model of all samples indicated that K=3 was the best fit to the nuclear data and that individuals identified as <i>S. compressus</i>had admixed assignment values (Q). Power analyses indicated our data could correctly detect and assign pure adults and F1 hybrids with > 0.90 probability, and correct assignment of F2 was also high in some cases. NewHybrids models revealed that 89.8% (n= 59) of the <i>Scarus compressus </i>samples were F1 hybrids of crosses between divergent species pairs: <i>S. perrico </i>× <i>S. ghobban</i>and <i>S. perrico </i>× <i>S. rubroviolaceus</i>. Similarly, <i>S.</i><i>ghobban </i>and <i>S. rubroviolaceus</i>were also hybridizing, with ½ of the admixed individuals assigned to F1 hybrids and the remainder likely deep generation hybrids. We observed strong mito-nuclear discordance in all three hybrid pairs, but found little evidence for accelerated mt vs. nuclear evolution in the paternal species. Bayesian analysis of Migrate models favours gene flow between <i>S. perrico</i>and <i>S. ghobban</i>, but not other species pairs. </span></span></span></span></span></span></span></span></span></span></span></p> <p class="Normal1"><span><span><span><span><span><span><span><span><span><span><span><b>Conclusions: </b></span></span></span></span></span></span></span></span></span></span></span><span><span><span><span><span><span><span><span><span><span><span>Mating between species whose ancestors diverged in the late Miocene is giving rise to region wide, hybrid complex, characterized by a high frequency of parental and F1 genotypes but a low frequency of deep generation hybrids. Trimodal structure, combined with reproductive evidence for fertility of both male and female F1 hybrids, suggest that fitness declines sharply in later generation hybrids. In contrast, the hybrid population of the two younger species had similar frequencies of F1 and > F1 hybrids. These differences are consistent with a model of accelerating post-mating incompatibility with time. Mitochondrial genotypes in hybrids, suggests indiscriminate mating by male <i>S. perrico</i>is driving pre-zygotic breakdown, which may reflect the isolation of this endemic species in the TEP for millions of years and weak selection for conspecific mate recognition. Despite overlapping habitat use, high rates of hybridization, and evidence for historical gene flow, species boundaries are maintained by post-mating processes in this complex. </span></span></span></span></span></span></span></span></span></span></span></p>
Data from: Ancient hybridizations among the ancestral genomes of bread wheat
The allohexaploid bread wheat genome consists of three closely related subgenomes (A, B, and D), but a clear understanding of their phylogenetic history has been lacking. We used genome assemblies of bread wheat and five diploid relatives to analyze genome-wide samples of gene trees, as well as to estimate evolutionary relatedness and divergence times. We show that the A and B genomes diverged from a common ancestor ~7 million years ago and that these genomes gave rise to the D genome through homoploid hybrid speciation 1 to 2 million years later. Our findings imply that the present-day bread wheat genome is a product of multiple rounds of hybrid speciation (homoploid and polyploid) and lay the foundation for a new framework for understanding the wheat genome as a multilevel phylogenetic mosaic.
Data from: Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)
Interspecies hybridization has been recently recognized as potentially common in wild animals, but the extent to which it shapes modern genomes is still poorly understood. Distinguishing historical hybridization events from other processes leading to phylogenetic discordance among different markers requires a well-resolved species tree that considers all modes of inheritance, and overcomes systematic problems due to rapid lineage diversification by sampling large genomic character sets. Here we assessed genome-wide phylogenetic variation across a diverse mammalian family, Felidae (cats). We combined genotypes from a genome-wide SNP array with additional autosomal, X- and Y-linked variants to sample ~150 kilobases of nuclear sequence, in addition to complete mitochondrial genomes generated using light-coverage Illumina sequencing. We present the first robust felid timetree that accounts for unique maternal, paternal, and biparental evolutionary histories. Signatures of phylogenetic discordance were abundant in the genomes of modern cats, in many cases indicating hybridization as the most likely cause. Comparison of big cat whole-genome sequences revealed a substantial reduction of X-linked divergence times across several large recombination coldspots, which were highly enriched for signatures of selection-driven post-divergence hybridization between the ancestors of the snow leopard and lion lineages. These results highlight the mosaic origin of modern felid genomes and the influence of sex chromosomes and sex-biased dispersal in post-speciation gene flow. A complete resolution of the Tree of Life will require comprehensive genomic sampling of biparental and sex-limited genetic variation to identify and control for phylogenetic conflict caused by ancient admixture and sex-biased differences in genomic transmission.
Data from: Genetic admixture supports an ancient hybrid origin of the endangered Hawaiian duck
Speciation is regarded primarily as a bifurcation from an ancestral species into two distinct taxonomic units, but gene flow can create different signals of phylogenetic relationships among different loci. We evaluated several hypotheses that could account for phylogenetic discord between mitochondrial DNA (mtDNA) and nuclear DNA (nuDNA) within Hawaiian ducks (Anas wyvilliana), including stochastic lineage sorting, mtDNA capture, and widespread genomic introgression. Our results best support the hypothesis that the contemporary Hawaiian duck is descended from an ancient hybridization event between the mallard (A. platyrhynchos) and Laysan duck (A. laysanensis). Whereas mtDNA clearly shows a sister-relationship between Hawaiian ducks and mallards, nuDNA is consistent with a genetic mosaic with nearly equal contributions from Laysan ducks and mallards. In addition, coalescent analyses suggest that gene flow from either mallard or Laysan duck, depending on the pre-defined tree topology, is necessary to explain contemporary genetic diversity in Hawaiian ducks, and these estimates are more consistent with ancient, rather than contemporary, hybridization. Time since divergence estimates suggest that the genetic admixture event occurred around the Pleistocene-Holocene boundary, which is further supported by circumstantial evidence from the Hawaiian sub-fossil record. Although the extent of reproductive isolation from either putative parental taxon is not currently known, these species are phenotypically, genetically, and ecologically different, and they meet primary criteria used in avian taxonomy for species designation. Thus, the available data are consistent with an admixed origin, and support the hypothesis that the Hawaiian duck may represent a young hybrid species.
Data from: Ancient hybridization and genomic stabilization in a swordtail fish
A rapidly increasing body of work is revealing that the genomes of distinct species often exhibit hybrid ancestry, presumably due to postspeciation hybridization between closely related species. Despite the growing number of documented cases, we still know relatively little about how genomes evolve and stabilize following hybridization, and to what extent hybridization is functionally relevant. Here, we examine the case of Xiphophorus nezahualcoyotl, a teleost fish whose genome exhibits significant hybrid ancestry. We show that hybridization was relatively ancient and is unlikely to be ongoing. Strikingly, the genome of X. nezahualcoyotl has largely stabilized following hybridization, distinguishing it from examples such as human–Neanderthal hybridization. Hybridization-derived regions are remarkably distinct from other regions of the genome, tending to be enriched in genomic regions with reduced constraint. These results suggest that selection has played a role in removing hybrid ancestry from certain functionally important regions. Combined with findings in other systems, our results raise many questions about the process of genomic stabilization and the role of selection in shaping patterns of hybrid ancestry in the genome.
Data from: Phylogenomic evidence for ancient hybridization in the genomes of living cats (Felidae)
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Data from: Ancient hybridizations among the ancestral genomes of bread wheat
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Data from: Genetic admixture supports an ancient hybrid origin of the endangered Hawaiian duck
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The origin of the parrotfish species Scarus compressus in the Tropical Eastern Pacific: region-wide hybridization between ancient species pairs
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Data from: Ancient hybridization and genomic stabilization in a swordtail fish
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