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675 results for “Introgression”
Data from: Asymmetric introgression between the M and S molecular forms of the malaria vector, Anopheles gambiae, maintains divergence despite extensive hybridisation.
The suggestion that genetic divergence can arise and/or be maintained in the face of gene flow, has been contentious since first proposed. Partially reproductively isolated taxa have been highlighted as offering unique opportunities for identifying the mechanisms underlying the maintenance of divergence with gene flow. The African malaria vector, Anopheles gambiae s.s., is widely regarded as consisting of two sympatric forms, thought by many to represent incipient species, the M and S molecular forms. However, there has been much debate about the extent of reproductive isolation between M and S, with one view positing that divergence may have arisen and is being maintained in the presence of gene flow, and the other proposing a more advanced speciation process with little realized gene flow due to low fitness of hybrids. These hypotheses have been difficult to address because hybrids are typically very rare (<1%). Here, we assess samples from an area of high hybridisation and demonstrate that hybrids are fit and responsible for extensive introgression. Nonetheless, we show that strong divergent selection at a subset of loci combined with highly asymmetric introgression has enabled M and S to remain genetically differentiated despite extensive gene flow. We propose that the extent of reproductive isolation between M and S varies across West Africa resulting in a "geographic mosaic of reproductive isolation"; a finding which adds further complexity to our understanding of divergence in this taxon and which has considerable implications for transgenic control strategies.
Data from: Scale and direction of adaptive introgression between black cottonwood (Populus trichocarpa) and balsam poplar (P. balsamifera)
Introgression can introduce novel genetic variation at a faster rate than mutation alone, and result in adaptive introgression when adaptive alleles are maintained in the recipient genome over time by natural selection. A previous study from our group demonstrated adaptive introgression from Populus balsamifera into P. trichocarpa in a target genomic region. Here we expanded our local ancestry analysis to the whole genome of both parents to provide a comprehensive, unbiased view of introgression patterns and to identify additional candidate regions for adaptive introgression genome-wide. Populus trichocarpa is a large, fast-growing tree of mild coastal regions of the Pacific northwest, whereas P. balsamifera is a smaller stature tree of continental and boreal regions with intense winter-cold. The species are parapatric with extensive hybridization. Here, using local ancestry analysis, we detected asymmetric patterns of introgression across the whole genome of these two species of poplar trees adapted to contrasting environments, with stronger introgression from P. balsamifera to P. trichocarpa than vice versa. Admixed P. trichocarpa individuals showed more genomic regions with unusually high levels of introgression (19 regions) compared with admixed P. balsamifera (9 regions) but also the largest introgressed peak (1.02 Mb). Our analysis also revealed numerous candidate regions for adaptive introgression with strong signals of selection, notably related to disease resistance, and enriched for genes that may play crucial roles for survival and adaptation. Furthermore, we revealed overrepresentation of subtelomeric regions in P. balsamifera introgression into P. trichocarpa and possible protection of the sex-determining regions from interspecific gene flow.
Data from: Introgression of chromosome segments from multiple alien species in wheat breeding lines with wheat streak mosaic virus resistance
Pyramiding of alien-derived Wheat streak mosaic virus (WSMV) resistance and resistance enhancing genes in wheat is a cost-effective and environmentally safe strategy for disease control. PCR-based markers and cytogenetic analysis with genomic in situ hybridisation were applied to identify alien chromatin in four genetically diverse populations of wheat (Triticum aestivum) lines incorporating chromosome segments from Thinopyrum intermedium and Secale cereale (rye). Out of 20 experimental lines, 10 carried Th. intermedium chromatin as T4DL*4Ai#2S translocations, while, unexpectedly, 7 lines were positive for alien chromatin (Th. intermedium or rye) on chromosome 1B. The newly described rye 1RS chromatin, transmitted from early in the pedigree, was associated with enhanced WSMV resistance. Under field conditions, the 1RS chromatin alone showed some resistance, while together with the Th. intermedium 4Ai#2S offered superior resistance to that demonstrated by the known resistant cultivar Mace. Most alien wheat lines carry whole chromosome arms, and it is notable that these lines showed intra-arm recombination within the 1BS arm. The translocation breakpoints between 1BS and alien chromatin fell in three categories: (i) at or near to the centromere, (ii) intercalary between markers UL-Thin5 and Xgwm1130 and (iii) towards the telomere between Xgwm0911 and Xbarc194. Labelled genomic Th. intermedium DNA hybridised to the rye 1RS chromatin under high stringency conditions, indicating the presence of shared tandem repeats among the cereals. The novel small alien fragments may explain the difficulty in developing well-adapted lines carrying Wsm1 despite improved tolerance to the virus. The results will facilitate directed chromosome engineering producing agronomically desirable WSMV-resistant germplasm.
Data from: Parallel plumage color evolution and introgressive hybridization in wheatears
Genetic and phenotypic mosaics, in which various phenotypes and different genomic regions show discordant patterns of species or population divergence, offer unique opportunities to study the role of ancestral and introgressed genetic variation in phenotypic evolution. Here, we investigated the evolution of discordant phenotypic and genetic divergence in a monophyletic clade of four songbird taxa – pied wheatear (O. pleschanka), Cyprus wheatear (O. cypriaca), and western and eastern subspecies of black-eared wheatear (O. h. hispanica and O. h. melanoleuca). Phenotypically, black back and neck-sides distinguish pied and Cyprus wheatears from the white-backed/necked black-eared wheatears. Meanwhile, mitochondrial variation only distinguishes western black-eared wheatear. In the absence of nuclear genetic data, and given frequent hybridization among eastern black-eared and pied wheatear, it remains unclear whether introgression is responsible for discordance between mitochondrial divergence patterns and phenotypic similarities, or whether plumage coloration evolved in parallel. Multispecies coalescent analyses of about 20'000 SNPs obtained from RAD data mapped to a draft genome assembly resolve the species tree, provide evidence for the parallel evolution of color phenotypes, and establish western and eastern black-eared wheatears as independent taxa that should be recognized as full species. The presence of the entire admixture spectrum in the Iranian hybrid zone and the detection of footprints of introgression from pied into eastern black-eared wheatear beyond the hybrid zone despite strong geographic structure of ancestry proportions furthermore suggest a potential role for introgression in parallel plumage color evolution. Our results support the importance of standing heterospecific and/or ancestral variation in phenotypic evolution.
Data from: Reticulate evolution, introgression, and intertribal gene capture in an allohexaploid grass
Recent molecular phylogenetic studies of polyploid plants have successfully clarified complex patterns of reticulate evolution. In this study of Elymus repens, an allohexaploid member of the wheat tribe Triticeae, chloroplast and nuclear DNA data reveal an extreme reticulate pattern, revealing at least five distinct gene lineages coexisting within the species, acquired through a possible combination of allohexaploidy and introgression from both within and beyond the Triticeae. Earlier cytogenetic studies of E. repens suggested that Hordeum (genome H) and Pseudoroegneria (St) were genome donors to E. repens. Chloroplast DNA data presented here (from the rpoA gene and from the region between trnT and trnF) identify three potential maternal genome donors (Pseudoroegneria, Thinopyrum, and Dasypyrum), and information from previous molecular work suggests that, of these, Pseudoroegneria is the most likely maternal donor. Nuclear starch synthase gene data indicate that both Hordeum and Pseudoroegneria have contributed to the nuclear genome of E. repens, in agreement with cytogenetic data. However, these data also show unexpected contributions from Taeniatherum, and from two additional donors of unknown identity. One of the sequences of unknown origin falls within the Triticeae, but is not closely associated with any of the sampled diploid genera. The second falls outside of the clade containing Triticeae and its outgroup Bromus, suggesting the acquisition of genetic material from a surprisingly divergent source. Bias toward the amplification of certain starch synthase variants has complicated attempts to thoroughly sample from within individuals, but the data clearly indicate a complex pattern of reticulate evolution, consistent not only with allohexaploidy, but also with introgression from unexpectedly divergent sources.
Data from: Speciation and introgression between Mimulus nasutus and Mimulus guttatus
Mimulus guttatus and M. nasutus are an evolutionary and ecological model sister species pair differentiated by ecology, mating system, and partial reproductive isolation. Despite extensive research on this system, the history of divergence and differentiation in this sister pair is unclear. We present and analyze a population genomic data set which shows that M. nasutus budded from a central Californian M. guttatus population within the last 200 to 500 thousand years. In this time, the M. nasutus genome has accrued genomic signatures of the transition to predominant selfing, including an elevated proportion of nonsynonymous variants, an accumulation of premature stop codons, and extended levels of linkage disequilibrium. Despite clear biological differentiation, we document genomic signatures of ongoing, bidirectional introgression. We observe a negative relationship between the recombination rate and divergence between M. nasutus and sympatric M. guttatus samples, suggesting that selection acts against M. nasutus ancestry in M. guttatus.
Data from: Introgression maintains the genetic integrity of the sex-determining chromosome of the fungus Neurospora tetrasperma
Genome evolution is driven by a complex interplay of factors, including selection, recombination, and introgression. The regions determining sexual identity are particularly dynamic parts of eukaryotic genomes that are prone to molecular degeneration associated with suppressed recombination. In the fungus Neurospora tetrasperma, it has been proposed that this molecular degeneration is counteracted by the introgression of non-degenerated DNA from closely related species. In this study, we used comparative and population genomic analyses of variation among 92 genomes from eight phylogenetically and reproductively isolated lineages of N. tetrasperma, and its three closest relatives, to investigate the factors shaping the evolutionary history of the genomes. We found that suppressed recombination extends across at least 6 Mbp (~63%) of the mating-type (mat) chromosome in N. tetrasperma, and is associated with decreased genetic diversity, which is likely the result primarily of selection at linked sites. Furthermore, analyses of molecular evolution revealed an increased mutational load in this region, relative to recombining regions. However, comparative genomic and phylogenetic analyses indicate that the mat chromosomes are temporarily regenerated via introgression from sister species; six out of eight lineages show introgression into one of their mat chromosomes, with at least three other Neurospora species acting as donors. The introgressed tracts have been driven to fixation in lineages, suggesting that they confer an adaptive advantage in natural populations, and our analyses support the presence of selective sweeps in at least one of the lineages. Thus, these data strongly support the previously hypothesized role of introgression as a mechanism for the maintenance of mating-type determining chromosomal regions.
Restricted X chromosome introgression and support for Haldane's rule in hybridizing damselflies
<p>Contemporary hybrid zones act as natural laboratories for the investigation of species boundaries and allow to shed light on the little understood roles of sex chromosomes in species divergence. Sex chromosomes are considered to function as a hotspot of genetic divergence between species; indicated by less genomic introgression compared to autosomes during hybridisation. Moreover, they are thought to contribute to Haldane's rule which states that hybrids of the heterogametic sex are more likely to be inviable or sterile. To test these hypotheses, we used contemporary hybrid zones of <i>Ischnura elegans</i>, a damselfly species that has been expanding its range into the northern and western regions of Spain, leading to chronic hybridization with its sister species <i>Ischnura graellsii</i>. We analysed genome-wide SNPs in the Spanish <i>I. elegans</i> and <i>I. graellsii</i> hybrid zone and found (i) that the X chromosome shows less genomic introgression compared to autosomes and (ii) that males are underrepresented among admixed individuals as predicted by Haldane's rule. This is the first study in Odonata that suggests a role of the X chromosome in reproductive isolation. Moreover, our data adds to the few studies on species with X0 sex determination system and contradicts the hypothesis that the absence of a Y chromosome causes exceptions to Haldane's rule.</p>
Genome assembly of a commercial tomato hybrid (Funtelle) for haplotyping an introgression that confers TMV resistance
<p>Plant crop genome assemblies facilitate the characterization of genetically diverse cultivated and wild germplasm. </p> <p>The cultivated tomato (Solanum lycopersicum) has been improved through the introgression of genetic material from related wild species, including genetic resistance to pandemic strains of Tobacco Mosaic virus (TMV) and tomato mosaic virus (ToMV) originating from Solanum peruvianum. The exact size and the structure of the introgression from Solanum peruvianum containing the TMV/ToMV resistance gene (Tm-2^2 gene) has remained unknown, although it was known to include at least half of the physical length of chromosome 9.<br> <br> We selected a commercial cultivated tomato cultivar called Funtelle, which contains the Tm-2^2 resistance introgression in a hemizygous state, and generated Oxford Nanopore sequencing reads. Using Flye, a genome assembly tool, we assembled the reads. The assembled DNA sequences (contigs) from the Flye assembly are made available here. Subsequently, as described in detail in the associated manuscript, we made use of the assembled contigs for comprehensive haplotyping of the chromosome 9 introgression region in this commercial hybrid.<br> <br> The raw Oxford Nanopore sequencing reads of the Funtelle variety are available via the European Nucleotide Archive under project number PRJEB44956.</p>
A relatively higher mutation rate in African humans is the dominant mechanism causing Neanderthals to appear closer to non-Africans, not introgression
<p>It is widely thought that humans carry genetic legacies due to inter-breeding with Neanderthals, but all methods used to infer legacies ignore recurrent mutations and assume a constant mutation rate. These assumptions cause automatic rejection of a second hypothesis, where a higher mutation rate in Africans caused increased divergence from Neanderthals. Any fair test should strive to treat both hypotheses equally. Here I use mutation spectra, the relative frequencies of different mutating three-base combinations, to compare contrasting expectations from the two hypotheses. I find that putative introgressed bases are strongly enriched for recurrent mutations and lie in regions with unusually high mutation rates, distorted mutation spectra and unusually large African minus non-African heterozygosity differences. Moreover, putative introgressed bases should be absent from Africa and rare outside, yet almost the entire signal of introgression is carried by sites where putative Neanderthal alleles are fixed in non-Africans and at high frequency in Africans. Together, these observations support a model where signals of introgression are driven mostly or even entirely by mutation rate differences between human populations. This new model helps to explain why introgression is inferred ubiquitously, including in scenarios involving great apes where inter-breeding is biologically implausible. </p>
Supplementary material 1 from: Homberger L, Xu J, Brandis D, Chan T-Y, Keirsebelik H, Normant-Saremba M, Schoelynck J, Chu KH, Ewers-Saucedo C (2022) Genetic and morphological evidence indicates the persistence of Japanese mitten crab mitochondrial DNA in Europe for over 20 years and its introgression into Chinese mitten crabs. NeoBiota 73: 137-152. https://doi.org/10.3897/neobiota.73.72566
Table S1. Master spreadsheet with morphological and genetic information for each specimen
Data from: Genetic susceptibility to infectious disease in East African Shorthorn Zebu: a genome-wide analysis of the effect of heterozygosity and exotic introgression
[No abstract entered]
Data from: Genotyping-in-Thousands by Sequencing panel development and application for high-resolution monitoring of introgressive hybridization within sockeye salmon
<p>Stocking programs have been widely implemented to re-establish extirpated fish species to their historical ranges; when employed in species with complex life histories, such management activities should include careful consideration of resulting hybridization dynamics with resident stocks and corresponding outcomes on recovery initiatives. Genetic monitoring can be instrumental for quantifying the extent of introgression over time, however, conventional markers typically have limited power for the identification of advanced hybrid classes, especially at the intra-specific level. Here, we demonstrate a workflow for developing, evaluating, and deploying a Genotyping-in-Thousands by Sequencing (GT-seq) SNP panel with the power to detect advanced hybrid classes to assess the extent and trajectory of intra-specific hybridization, using the sockeye salmon (<em>Oncorhynchus nerka)</em> stocking program in Skaha Lake, British Columbia, as a case study. Previous analyses detected significant levels of hybridization between the anadromous (sockeye) and freshwater resident (kokanee) forms of <em>O. nerka</em>, but were restricted to assigning individuals to pure-stock or "hybrid". Simulation analyses indicated our GT-seq panel had high accuracy, efficiency and power (> 94.5%) of assignment to pure-stock sockeye salmon/kokanee, F<sub>1</sub>, F<sub>2</sub>, and B<sub>2</sub> backcross-sockeye/kokanee. Re-analysis of 2016/2017 spawners previously analyzed using TaqMan<span> </span>assays and otolith microchemistry revealed shifts in assignment of some hybrids to adjacent pure-stock or B<sub>2</sub>-backcross classes, while new assignment of 2019 spawners revealed hybrids comprised 31% of the population, ~74% of which were B<sub>2</sub>-backcross or F<sub>2</sub>. Overall, the GT-seq panel development workflow presented here could be applied to virtually any system where genetic stock identification and intra-specific hybridization are important management parameters.</p>
Fig. 10 in Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations
Fig. 10 Spectrograms of chatter calls of pure P. p. leucoptera, pure P. p. jankowskii, and hybrids. a leucoptera, pair #4, Choibalsan, eastern Mongolia. b jankowskii, pair #6, Vladivostok, Russian Far East. c, d Bilingual hybrid, the same bird from the pair #24, Kerulen, eastern Mongolia. e Hybrid with mixed call, pair #39, Kerulen. f Presumably hybrid with mixed call, pair #5, Kerulen. X-axis—time in s; Y-axis—frequency in kHz
Fig. 8 in Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations
Fig. 8 Genetic structure of the contact zone and its vicinities by mtDNA and SNPs. Above—distribution of haplotypes of mitochondrial CR along conditional population numbers I–VI depicted in Fig. 3. Green—western haplotype; red—eastern haplotype. Below— graphical representation of individual contributions from nuclear
Fig. 3 in Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations
Fig. 3 Map of sampling localities for nuclear SNP analysis. Distribution of genotypes of nuclear SNPs revealed by ddRAD analysis are shown with blue circles for Pica pica leucoptera and red circles for Pica pica jankowskii. Bi-colored circles mean mixed (hybrid) genotype: portion of blue/red corresponds to probability of it belonging to one of the groups, as revealed in the Structure analysis. Numbers
Fig. 1 in Introgression at the emerging secondary contact zone of magpie Pica pica subspecies (Aves: Corvidae): integrating data on nuclear and mitochondrial markers, vocalizations, and field observations
Fig. 1 Map of Pica pica s.l. subspecies. The study area in the contact zone is indicated by a rectangle. Question marks indicate regions of unclear subspecies distribution. The white star indicates the terra typica for Pica pica anderssoni in eastern China
Figure 5 from: Espinasa L, Robinson J, Soares D, Hoese G, Toulkeridis T, Toomey III R (2018) Troglomorphic features of Astroblepus pholeter, a cavefish from Ecuador, and possible introgressive hybridization. Subterranean Biology 27: 17-29. https://doi.org/10.3897/subtbiol.27.27098
Figure 5 Specimens collected in 1962 (A modified from Collette 1962) and 2011 (B Modified from Soares and Niemiller 2013) had proportionally longer pectoral fins and maxillary barbels than specimens observed in the field in 2015 (C). Images have been scaled to the same body size (blue arrow). Notice that length of appendages in C–D (red arrows) are progressively smaller than in B and A (red plus yellow and green arrows).
Figure 1 from: Espinasa L, Robinson J, Soares D, Hoese G, Toulkeridis T, Toomey III R (2018) Troglomorphic features of Astroblepus pholeter, a cavefish from Ecuador, and possible introgressive hybridization. Subterranean Biology 27: 17-29. https://doi.org/10.3897/subtbiol.27.27098
Figure 1 Specimens collected in 1962 (holotype, and paratypes of A.pholeter from left to right) 2011, 2015 and 2018. Notice that there is a progressive reduction in the expression of troglomorphic features. After 2011 the skin was distinctly more pigmented and the barbels and fins were shorter. Eyes are also embedded under a thinner dermal layer of skin. In 2011 the population was highly variable.
Figure 3 from: Espinasa L, Robinson J, Soares D, Hoese G, Toulkeridis T, Toomey III R (2018) Troglomorphic features of Astroblepus pholeter, a cavefish from Ecuador, and possible introgressive hybridization. Subterranean Biology 27: 17-29. https://doi.org/10.3897/subtbiol.27.27098
Figure 3 AChaetostomamicrops (Surface catfish) BAstroblepuspholeter (Cave catfish). Both species inhabit the same river drainage.
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