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675 results for “Introgression”
Fig. 1. A in Altai Mountains - cradle of hybrids and introgressants: A case study in Veronica subg. Pseudolysimachium (Plantaginaceae)
Fig. 1. A, Genetic composition based on K = 5 of first-level STRUCTURE results and number of individuals included from that particular locality. Genetic composition of the localities with more than one individual has been averaged. Key to the colors is given in a separate inset. B–D, Probability of ancestry of each individual (horizontal axis; total 233 individuals) to each of K = 4, 5, 6 populations (vertical axis). The five populations correspond mostly to the morphotypes hypothesized for species and putative hybrids. V. ×alt, V. ×altaica; V. ×gri, V. ×grisea; V. ×kol, V. ×kolyvanensis; V. ×sap, V. ×sapozhnikovii; V. ×sch, V. ×schmakovii; V. ×ses, V. ×sessiliflora; V. ×smi, V. ×smirnovii; V. are, V. arenosa; V. inca, V. incana; V. lon, V. longifolia; V. pinn, V. pinnata; V. porp, V. porphyriana; V. reve, V. reverdattoi; V. saj, V. sajanensis; V. spic, V. spicata; V. spur, V. spuria; V. ×taig, V. ×taigischensis; uniden, unidentified.
Fig. 5 in Altai Mountains - cradle of hybrids and introgressants: A case study in Veronica subg. Pseudolysimachium (Plantaginaceae)
Fig. 5. Results of the G-PhoCS analysis for effective population sizes, and gene flow using only pure individuals (no admixture). The inferred current effective population size (Ne) of each species are given for all the five species. The direction of the arrows represents the probability of migration among the species both in forward and reverse directions. The width of the bars represents the effective population size of each species. For population size estimation, we used the equations Ne (effective population size) = θ / 4μg; and T (divergence time) = τ · g / μ; where substitution rate/site/year (μ) = 2.44E-9, generation time for population (g) = 10 years. Migration rates are based on per generation parameter (Msx = msx · θx / 4), which is the proportion of individuals in population x arrived by migration from another population per generation. Gene flow has been calculated using the total migration rate, cases where the total rate is low, it approximates the probability of gene flow between the two species. However, for higher rates, we adjusted probabilities into rates with the equation P = 1 − e−m (where P = the probability of gene flow, e = exponent, and m = total migration rate; following vonHoldt & al., 2016). The phylogenetic tree on which the G-PhoCS analysis has been based is given in suppl. Fig. S2. For complete details, see in Materials and Methods as well as suppl. Tables S4 and S5 for migration rates (msx), τ and θ values, and divergence times.
Fig. 3 in Altai Mountains - cradle of hybrids and introgressants: A case study in Veronica subg. Pseudolysimachium (Plantaginaceae)
Fig. 3. Chromosome localization of rDNA and genomic in situ hybridization (GISH) in Veronica. Mitotic chromosome complements of: A, V. porphyriana; B, V. ×schmakovii; C, V. spicata; D, V. pinnata; E, V. longifolia; and F, V. incana hybridized with 35S (red fluorescence) and 5S (purple) rDNA probes. G, Mitotic chromosomes of V. ×schmakovii hybridized with gDNA of V. longifolia (red) and V. porphyriana (green). — Chromosomes were counterstained with DAPI. Scale bars, 10 μm.
Pollinator and host sharing lead to hybridization and introgression in Panamanian free-standing figs, but not in their pollinator wasps
<p>Obligate pollination mutualisms, in which plant and pollinator lineages depend on each other for reproduction, often exhibit high levels of species-specificity. However, cases in which two or more pollinator species share a single host species (host sharing), or two or more host species share a single pollinator species (pollinator sharing), are known to occur in the current ecological time. Further, evidence for host switching in evolutionary time is increasingly being recognized in these systems. The degree to which departures from strict specificity differentially affect the potential for hybridization and introgression in the associated host or pollinator is unclear. We addressed this question using genome-wide sequence data from five sympatric Panamanian free-standing fig species (<em>Ficus</em> subgenus <em>Pharmacosycea</em>, section <em>Pharmacosycea</em>) and their six associated fig pollinator wasp species (<em>Tetrapus</em>). Two of the five fig species, <em>F. glabrata</em> and <em>F. maxima</em>, were found to regularly share pollinators. In these species, ongoing hybridization was demonstrated by the detection of several first-generation (F1) hybrid individuals, and historical introgression was indicated by phylogenetic network analysis. In contrast, although two of the pollinator species regularly share hosts, all six species were genetically distinct and deeply divergent, with no evidence for either hybridization or introgression. This pattern is consistent with results from other obligate pollination mutualisms, suggesting that, in contrast to their host plants, pollinators appear to be reproductively isolated, even when different species of pollinators mate in shared hosts.</p>
The contribution of Neanderthal introgression and natural selection to neurodegenerative diseases
<p>Files used to create binary annotations for LDSC in the following repository: https://github.com/RHReynolds/als-neanderthal-analysis.</p> <p>See the following link for details: https://github.com/RHReynolds/als-neanderthal-analysis/tree/main/raw_data/01_annotations</p>
High heterogeneity in genomic differentiation between phenotypically divergent songbirds: A test of mitonuclear co-introgression
<p>Comparisons of genomic variation among closely related species often show more differentiation in mitochondrial DNA (mtDNA) and sex chromosomes than in autosomes, a pattern expected due to the differing effective population sizes and evolutionary dynamics of these genomic components. Yet, introgression can cause species pairs to deviate dramatically from general differentiation trends. The yellowhammer (<em>Emberiza</em> <em>citrinella</em>) and pine bunting (<em>E</em>. <em>leucocephalos</em>) are hybridizing avian sister species that differ greatly in appearance and moderately in nuclear DNA, but that show no mtDNA differentiation. This discordance is best explained by adaptive mtDNA introgression—a process that can select for co-introgression at nuclear genes with mitochondrial functions (mitonuclear genes). To better understand these discordant differentiation patterns and characterize nuclear differentiation in this system, we investigated genome-wide differentiation between allopatric yellowhammers and pine buntings and compared it to what was seen previously in mtDNA. We found significant nuclear differentiation that was highly heterogeneous across the genome, with a particularly wide differentiation peak on the sex chromosome Z. We further investigated mitonuclear gene co-introgression between yellowhammers and pine buntings and found support for this process in the direction of pine buntings into yellowhammers. Genomic signals indicative of co-introgression were common in mitonuclear genes coding for subunits of the mitoribosome and electron transport chain complexes. Such introgression of mitochondrial DNA and mitonuclear genes provides a possible explanation for the patterns of high genomic heterogeneity in genomic differentiation seen among some species groups.</p>
Experimental introgression in Drosophila: Asymmetric postzygotic isolation associated with chromosomal inversions and an incompatibility locus on the X chromosome
<p>Interspecific gene flow (introgression) is an important source of new genetic variation, but selection against it can reinforce reproductive barriers between interbreeding species. We used an experimental approach to trace the role of chromosomal inversions and incompatibility genes in preventing introgression between two partly sympatric <em>Drosophila virilis</em> group species, <em>D. flavomontana </em>and<em> D. montana</em>. We backcrossed F<sub>1</sub> hybrid females from a cross between <em>D. flavomontana female </em>and<em> D. montana </em>male with the males of the parental species for two generations and sequenced pools of parental strains and their reciprocal 2<sup>nd</sup> generation backcross (BC<sub>2</sub>mon and BC<sub>2</sub>fla) females. Contrasting the observed amount of introgression (mean hybrid index, HI) in BC<sub>2</sub> female pools along the genome to simulations under different scenarios allowed us to identify chromosomal regions of restricted and increased introgression. We found no deviation from the HI expected under a neutral null model for any chromosome for the BC<sub>2</sub>mon pool, suggesting no evidence for genetic incompatibilities in backcrosses towards <em>D. montana</em>. In contrast, the BC<sub>2</sub>fla pool showed high variation in the observed HI between different chromosomes, and massive reduction of introgression on the X chromosome (large X-effect). We find that this observation is compatible with reduced recombination combined with at least one dominant incompatibility locus residing within the X inversion(s). Overall, our study suggests that genetic incompatibilities arising within chromosomal inversions can play an important role in speciation.</p>
Abb. 1 in Eine alpine Population von überwiegend gestreiften Setina roscida ([Denis & Schiffermüller], 1775), ein Fall von Introgression? (Lepidoptera: Arctiinae)
Abb. 1. Setina irrorella. Oben links gepunktete Form (Vals (GR), 1650 m ü. M; 1.8.1992), unten rechts gestreifte Form (S-chanf (GR), 2300 m ü. M; 26.7.2012) sowie Übergangsformen (Tujetsch (GR), 1820 m ü. M; 23.7.2015 und Müstair (GR), 2100 m ü. M; 19.7.2010). (Foto Jürg Schmid)
Abb. 4 in Eine alpine Population von überwiegend gestreiften Setina roscida ([Denis & Schiffermüller], 1775), ein Fall von Introgression? (Lepidoptera: Arctiinae)
Abb. 4. Männliches Genital, Valven (alle Bilder gleicher Massstab). Oben: aus einer gepunkteten Population von Setina roscida (Ofenpass (GR), 2550 m ü. M; 4.8.2009). Mitte: aus einer gestreif- ten Population von Setina aurita (Brigels (GR), 2480 m ü. M; 18.9.1980). Unten: eine gestreifte S. roscida (Avers (GR), 2530 m ü. M; 6.7.2015). (Gen. präp. und Fotos Jürg Schmid)
Abb. 5 in Eine alpine Population von überwiegend gestreiften Setina roscida ([Denis & Schiffermüller], 1775), ein Fall von Introgression? (Lepidoptera: Arctiinae)
Abb. 5. Unterseiten von Setina aurita, gestreifte Form, links (Maienfeld (GR), 1900 m ü. M; 1.8.2009) und Setina roscida, gestreifte Form, rechts (Avers (GR), 2530 m ü. M; 4.7.2015). (Foto Jürg Schmid)
Abb. 3. Setina roscida und sympatrische S in Eine alpine Population von überwiegend gestreiften Setina roscida ([Denis & Schiffermüller], 1775), ein Fall von Introgression? (Lepidoptera: Arctiinae)
Abb. 3. Setina roscida und sympatrische S. aurita von Avers (GR), um 2500 m ü. M.; 16.7.2009. Oben links: S. roscida, gepunktete Form, darunter Übergangsform. Oben und Mitte rechts: S. roscida, gestreifte Form. Unten Mitte: S. aurita. (Foto Jürg Schmid)
Abb. 2 in Eine alpine Population von überwiegend gestreiften Setina roscida ([Denis & Schiffermüller], 1775), ein Fall von Introgression? (Lepidoptera: Arctiinae)
Abb. 2. Setina aurita. Gepunktete Tieflandform (Rothenbrunnen (GR), 660 m ü. M; 10.9.2004) und gestreifte Höhenform (Maienfeld (GR), 1900 m ü. M; 1.8.2009). (Foto Jürg Schmid)
Power of Bayesian and heuristic tests to detect cross-species introgression with reference to gene flow in the Tamias quadrivittatus group of North American chipmunks
<p>In the past two decades genomic data have been widely used to detect historical gene flow between species in a variety of plants and animals. The Tamias quadrivittatus group of North America chipmunks, which originated through a series of rapid speciation events, are known to undergo massive amounts of mitochondrial introgression. Yet in a recent analysis of targeted nuclear loci from the group, no evidence for cross-species introgression was detected, indicating widespread cytonuclear discordance. The study used the heuristic method HyDe to detect gene flow, which may suffer from low power. Here we use the Bayesian method implemented in the program bpp to reanalyze these data. We develop a Bayesian test of introgression, calculating the Bayes factor via the Savage-Dickey density ratio using the Markov chain Monte Carlo (MCMC) sample under the model of introgression. We take a stepwise approach to constructing an introgression model by adding introgression events onto a well-supported binary species tree. The analysis detected robust evidence for multiple ancient introgression events affecting the nuclear genome, with introgression probabilities reaching 63%. We estimate population parameters and highlight the fact that species divergence times may be seriously underestimated if ancient cross-species gene flow is ignored in the analysis. We examine the assumptions and performance of HyDe, and demonstrate that it lacks power if gene flow occurs between sister lineages or if the mode of gene flow does not match the assumed hybrid speciation model with symmetrical population sizes. Our analyses highlight the power of likelihood-based inference of cross-species gene flow using genomic sequence data.</p>
Adaptive alien genes are maintained amidst a vanishing introgression footprint in a sea squirt
<p>This zenodo archive contains the multi-locus genotype tables for the paper "Falling shoulders ahead: adaptive alien genes maintained amidst vanishing introgression footprint in sea squirts". There are three files in this archive:</p> <ul> <li>Ci_KASP_genotypes_2012.csv: genotype table for individuals sampled in 2012</li> <li>Ci_KASP_genotypes_2021.csv: genotype table for individuals sampled in 2021 as well as control individuals from the two <em>Ciona</em> species</li> <li>Ci_KASP_genotypes_hybrids.csv: genotype table for control hybrids</li> </ul>
Data from: Possible involvement of ghost introgressions in the striking diversity of Vomeronasal type 1 receptor genes in East African cichlids
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Population size differences can lead to biases in phylogenetic inference and introgression detection in the presence of purifying selection
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Out with the old, introgression with the new: Signals of ancient and recent admixture in hybridizing Mesoamerican crocodiles (Crocodylus acutus x Crocodylus moreletii)
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Experimental introgression in Drosophila: Asymmetric postzygotic isolation associated with chromosomal inversions and an incompatibility locus on the X chromosome
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Phylogenomics, introgression, and demographic history of South American true toads (Rhinella)
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Genomic landscape of introgression from the ghost lineage in a gobiid fish uncovers the generality of forces shaping hybrid genomes
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