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675 results for “Introgression”
Expression data from testes and abdomen in fertile and sterile introgression males
GEO Series GSE21734. Drosophila melanogaster; Drosophila simulans. 12 samples. Type: Expression profiling by array.
Regulatory dissection of the severe COVID-19 risk locus introgressed by Neanderthals.
GEO Series GSE176233. Homo sapiens; synthetic construct. 8 samples. Type: Other.
The spatial signature of introgression after a biological invasion with hybridization
<p><strong>Simulated Data and Custom Scripts</strong></p> <p>This repository contains data for performing simulations with SPLATCHE3 and the custom R scripts used in the following manuscript: Quilodrán CS, Tsoupas A and M Currat. 2020. The spatial signature of introgression after a biological invasion with hybridization. Frontiers in Ecology and Evolution.</p> <p>There are three main folders (.zip files): </p> <ul> <li>Settings: the setting files of SPLATCHE3 used in all explored scenarios. The example folder for each scenario (01_newset) contains the setting file and setting folder needed to run SPLATCHE3. This example folder contains a single simulation of the interbreeding rate (MigrRate_P1_to_P2 and MigrRate_P2_to_P1) that generates an output of 10,000 simulated loci. The folder also contains a public version of SPLATCHE3 for Linux. The software version for other platforms (Mac OS X and Windows) can be obtained from “http://www.splatche.com/splatche3".</li> <li>Results: all results obtained in the different scenarios. The three simulations in a square world are presented for the invasive (NC files) and local organisms (NCbis). The neanderthal scenario presents the simulated proportion of introgression in modern humans sampled in France and China. </li> <li>Rcustom: custom R functions and files used for plotting the results. </li> </ul> <p>There are also four R scripts for plotting all main figures in the manuscript. </p> <p><strong>Acknowledgments </strong><br> This study was financed by grants from the Swiss National Science Foundation n° 31003A_182577 to MC and P400PB_183930 to CSQ. All computations were performed using the High-Performance Computing (HPC) cluster at baobab.unige.ch</p>
Data from: Age estimates for an adaptive lake fish radiation, its mitochondrial introgression, and an unexpected sister group: Sailfin silversides of the Malili Lakes system in Sulawesi
Background: The Malili Lakes system in central Sulawesi (Indonesia) is a hotspot of freshwater biodiversity in the Wallacea, characterized by endemic species flocks like the sailfin silversides (Teleostei: Atherinomorpha: Telmatherinidae) radiation. Phylogenetic reconstructions of these freshwater fishes have previously revealed two Lake Matano Telmatherina lineages (sharpfins and roundfins) forming an ancient monophyletic group, which is however masked by introgressive hybridization of sharpfins with riverine populations. The present study uses mitochondrial data, newly included taxa, and different external calibration points, to estimate the age of speciation and hybridization processes, and to test for phylogeographic relationships between Kalyptatherina from ancient islands off New Guinea, Marosatherina from SW Sulawesi, and the Malili Lakes flock. Results: Contrary to previous expectations, Kalyptatherina is the closest relative to the Malili Lakes Telmatherinidae, and Marosatherina is the sister to this clade. Palaeogeographic reconstructions of Sulawesi suggest that the closer relationship of the Malili Lakes radiation to Kalypatherina might be explained by a 'terrane-rafting' scenario, while proto-Marosatherina might have colonized Sulawesi by marine dispersal. The most plausible analysis conducted here implies an age of c. 1.9 My for the onset of divergence between the two major clades endemic to Lake Matano. Diversification within both lineages is apparently considerably more recent (c. 1.0 My); stream haplotypes present in the sharpfins are of even more recent origin (c. 0.4 My). Conclusions: Sulawesi's Telmatherinidae have most likely originated in the Sahul Shelf area, have possibly reached the island by both, marine dispersal and island/terrane-rafting, and have colonized the Malili Lakes system from rivers. Estimates for the split between the epibenthic sharpfins and the predominantly pelagic to benthopelagic roundfins in Lake Matano widely coincide with geological age estimates of this rift lake. Diversification within both clades clearly predates hybridization events with stream populations. For Lake Matano, these results support a scenario of initial benthic-pelagic divergence after colonization of the lake by riverine populations, followed by rapid radiation within both clades within the last 1 My. Secondary hybridization of stream populations with the sharpfins occurred more recently, and has thus most likely not contributed to the initial divergence of this benthic species flock.
Data from: Dobzhansky-Muller incompatibilities, dominance drive, and sex-chromosome introgression at secondary contact zones: a simulation study
Dobzhansky-Muller (DM) incompatibilities involving sex chromosomes have been proposed to account for Haldane's rule (lowered fitness among hybrid offspring of the heterogametic sex) as well as Darwin's corollary (asymmetric fitness costs with respect to the direction of the cross). We performed simulation studies of a hybrid zone to investigate the effects of different types of DM incompatibilities on cline widths and positions of sex-linked markers. From our simulations, X-Y incompatibilities generate steep clines for both X-linked and Y-linked markers; random effects may produce strong noise in cline center positions when migration is high relative to fitness costs, but X- and Y-centers always coincide strictly. X-autosome and Y-autosome incompatibilities also generate steep clines, but systematic shifts in cline centers occur when migration is high relative to selection, as a result of a dominance drive linked to Darwin's corollary. Interestingly, sex-linked genes always show farther introgression than the associated autosomal genes. We discuss ways of disentangling the potentially confounding effects of sex biases in migration, we compare our results to those of a few documented contact zones, and we stress the need to study independent replicates of the same contact zone.
Data from: Genomics of introgression in the Chinese horseshoe bat (Rhinolophus sinicus) revealed by transcriptome sequencing
Recent genomic studies show that introgression can occur at a genome-wide scale among recently diverged lineages. However, introgression is difficult to distinguish from incomplete lineage sorting (ILS), and these processes are expected to occur together. Moreover, ncDNA introgression is less easily detected than mtDNA introgression, and as such its prevalence is less well understood. The Chinese horseshoe bat (Rhinolophus sinicus) occurs as three distinct forms on mainland China: the subspecies R. s. septentrionalis and two parapatric clades of R. s. sinicus (Central and East R. s. sinicus). Previous work suggested widespread mtDNA introgression between these subspecies; however, no ncDNA introgression was detected. In this study we sampled the coding genomes of all three forms of R. sinicus in order to perform a more sensitive test for ncDNA introgression against an expected background of ILS. We assembled 3548 nuclear protein-coding genes from these and three congeneric species, and built a high-confidence species tree using maximum likelihood and Bayesian concordance methods. Phylogenetic analysis suggested a mosaic genome for Central R. s. sinicus derived from R. s. septentrionalis and East R. s. sinicus. Nuclear DNA introgression between Central R. s. sinicus and R. s. septentrionalis was supported by three different tests, whereas ILS could not be ruled out completely. Our findings, in line with other recent results, indicate that recently diverged taxa undergo large-scale secondary introgression, and that this process likely operates alongside ILS to give rise to phylogenomic discordances or even mosaic genomes.
Data from: Adaptive introgression from distant Caribbean islands contributed to the diversification of a microendemic adaptive radiation of trophic specialist pupfishes
Rapid diversification often involves complex histories of gene flow that leave variable and conflicting signatures of evolutionary relatedness across the genome. Identifying the extent and source of variation in these evolutionary relationships can provide insight into the evolutionary mechanisms involved in rapid radiations. Here we compare the discordant evolutionary relationships associated with species phenotypes across 42 whole genomes from a sympatric adaptive radiation of Cyprinodon pupfishes endemic to San Salvador Island, Bahamas and several outgroup pupfish species in order to understand the rarity of these trophic specialists within the larger radiation of Cyprinodon. 82% of the genome depicts close evolutionary relationships among the San Salvador Island species reflecting their geographic proximity, but the vast majority of variants fixed between specialist species lie in regions with discordant topologies. Top candidate adaptive introgression regions include signatures of selective sweeps and adaptive introgression of genetic variation from a single population in the northwestern Bahamas into each of the specialist species. Hard selective sweeps of genetic variation on San Salvador Island contributed 5 times more to speciation of trophic specialists than adaptive introgression of Caribbean genetic variation; however, four of the 11 introgressed regions came from a single distant island and were associated with the primary axis of oral jaw divergence within the radiation. For example, standing variation in a proto-oncogene (ski) known to have effects on jaw size introgressed into one San Salvador Island specialist from an island 300 km away approximately 10 kya. The complex emerging picture of the origins of adaptive radiation on San Salvador Island indicates that multiple sources of genetic variation contributed to the adaptive phenotypes of novel trophic specialists on the island. Our findings suggest that a suite of factors, including rare adaptive introgression, may be necessary for adaptive radiation in addition to ecological opportunity.
Secondary contact, introgressive hybridization and genome stabilization in sticklebacks
<p>Variant data in vcf format and SNPEFF annotation related files for the manuscript "Secondary contact, introgressive hybridization and genome stabilization in sticklebacks".</p>
Archaic Adaptive Introgression in Modern Human Reproductive Genes
<p><strong>README:</strong></p> <p>Modern human genetic data with evidence of adaptive introgression from Neanderthals or Denisovans within circadian rhythm genes. The data was generated from the phased gnomAD 1KGP + HGDP callset (Koenig <em>et al</em>., 2024) and introgressed segments were identified by SPrime (Browning <em>et al</em>., 2018). RAiSD (Alachiotis & Pavlidis, 2018) was used to detect signatures of positive selection within our gene set. Genes of interest were downloaded from Greer et al. (2021). This also includes high resolution images and supplemental tables for<strong> </strong>Archaic Adaptive Introgression in Modern Human Reproductive Genes. All proper citations can be found on the preprint references listed (available here: https://www.biorxiv.org/content/10.1101/2024.11.06.622331v1).</p> <p><strong>SPrime ND_Match Files</strong></p> <p>Raw SPrime identified files that we used for our entire analysis. These were modified to include the archaic allele, archaic allele frequency, and average introgressed segment allele frequency. Note that these have been lifted over (Hinrichs <em>et</em> <em>al</em>., 2006) from GRCh38 (hg38) to GRCh37 (hg19) coordinates to match the genome builds of the archaic samples used in our study. As such, any manually generated variant IDs (chromosome:position:ReferenceAllele_AlternativeAllele naming convention) may no longer match the position they are currently sitting on as they were generated with hg38 coordinates. However, all of these were subsequently filtered out of our final results and any proper SNP IDs (dbSNP labels) will be accurate.</p> <p><strong>RAiSD Outputs</strong></p> <p>We used RAiSD (Alachiotis & Pavlidis, 2018) to detect evidence of positive selection within our dataset. Please note these coordinates are mapped to hg38. </p> <p> </p>
Hybridisation in Primates: Cryptic Admixture and Adaptive Introgression Appendix C Materials
<p>This dataset includes supporting tables and figures for my PhD thesis at the University of Toronto, entitled "Hybridisation in Primates: Cryptic Admixture and Adaptive Introgression" in partial fulfillment of the degree requires for the Department of Anthropology (Evolutionary Anthropology). The data contains Tables C1-B13 and high resolution images for Figures 4.1-4.5.</p>
Data from: When virulence originates from nonagricultural hosts: evolutionary and epidemiological consequences of introgressions following secondary contacts in Venturia inaequalis
In pathogens, introgressions through secondary contacts between divergent populations from agricultural and nonagricultural disease reservoirs are expected to have crucial evolutionary and epidemiological implications. Despite the importance of this question for disease management, experimental demonstrations of these implications remain scarce. Recently, we identified a virulent population of the apple scab pathogen Venturia inaequalis that migrated from nonagricultural hosts to European domestic apple orchards. Here, we investigated the occurrence of gene flow between agricultural and nonagricultural populations sampled in two orchards, and thereafter its consequences on the pathogenicity of hybrids. Population genetic structure and demographic inferences based on the genotypes of 104 strains revealed a high amount of gene flow between the two populations in one orchard. In this site, mating between populations was made possible by the presence of a common host. Our results revealed an invasion of the virulent trait in the agricultural population; a main direction of introgression in hybrids from the agricultural to nonagricultural genetic backgrounds; and a population of hybrids with transgressive traits. We demonstrate a secondary contact with gene flow between divergent populations of pathogens. Our findings highlight evolutionary and epidemiological changes in pathogens and have concrete implications for sustainable disease management.
Data from: Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing
Rapid and inexpensive methods for genomewide single nucleotide polymorphism (SNP) discovery and genotyping are urgently needed for population management and conservation. In hybridized populations, genomic techniques that can identify and genotype thousands of species-diagnostic markers would allow precise estimates of population- and individual-level admixture as well as identification of 'super invasive' alleles, which show elevated rates of introgression above the genomewide background (likely due to natural selection). Techniques like restriction-site-associated DNA (RAD) sequencing can discover and genotype large numbers of SNPs, but they have been limited by the length of continuous sequence data they produce with Illumina short-read sequencing. We present a novel approach, overlapping paired-end RAD sequencing, to generate RAD contigs of >300–400 bp. These contigs provide sufficient flanking sequence for design of high-throughput SNP genotyping arrays and strict filtering to identify duplicate paralogous loci. We applied this approach in five populations of native westslope cutthroat trout that previously showed varying (low) levels of admixture from introduced rainbow trout (RBT). We produced 77 141 RAD contigs and used these data to filter and genotype 3180 previously identified species-diagnostic SNP loci. Our population-level and individual-level estimates of admixture were generally consistent with previous microsatellite-based estimates from the same individuals. However, we observed slightly lower admixture estimates from genomewide markers, which might result from natural selection against certain genome regions, different genomic locations for microsatellites vs. RAD-derived SNPs and/or sampling error from the small number of microsatellite loci (n = 7). We also identified candidate adaptive super invasive alleles from RBT that had excessively high admixture proportions in hybridized cutthroat trout populations.
Comparative gene expression analysis in fruits of a tomato introgression line performing reduced ascorbic acid content
GEO Series GSE26962. Solanum lycopersicum. 24 samples. Type: Expression profiling by array.
Data from: A cryptic invasion within an invasion and widespread introgression in the European water frog complex: consequences of uncontrolled commercial trade and weak international legislation
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Data from: Genomic patterns of introgression in rainbow and westslope cutthroat trout illuminated by overlapping paired-end RAD sequencing
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Data from: Adaptive introgression from distant Caribbean islands contributed to the diversification of a microendemic adaptive radiation of trophic specialist pupfishes
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Data from: Dobzhansky-Muller incompatibilities, dominance drive, and sex-chromosome introgression at secondary contact zones: a simulation study
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Data from: Genomics of introgression in the Chinese horseshoe bat (Rhinolophus sinicus) revealed by transcriptome sequencing
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Data from: Age estimates for an adaptive lake fish radiation, its mitochondrial introgression, and an unexpected sister group: Sailfin silversides of the Malili Lakes system in Sulawesi
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Data from: When virulence originates from nonagricultural hosts: evolutionary and epidemiological consequences of introgressions following secondary contacts in Venturia inaequalis
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