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20 results for “genomic incompatibilities”
Data from: Comparing phylogeographies to reveal incompatible geographical histories within genomes
<p>Modern phylogeography aims at reconstructing the geographic movement of organisms based on their genomic sequences and spatial information. Phylogeographic approaches are often applied to pathogen sequences and therefore tend to neglect the possibility of recombination, which decouples the evolutionary and geographic histories of different parts of the genome. Genomic regions of recombining or reassorting pathogens often originate and evolve at different times and locations, which characterise their unique spatial histories. Measuring the extent of these differences requires new methods to compare geographic information on phylogenetic trees reconstructed from different parts of the genome. Here we develop for the first time a set of measures of phylogeographic incompatibility, aimed at detecting differences between geographical histories in terms of distances between phylogeographies. We study the effect of varying demography and recombination on phylogeographic incompatibilities using coalescent simulations. We further apply these measures to the evolutionary history of human and livestock pathogens, either reassorting or recombining, such as the Victoria and Yamagata lineages of influenza B and the O/ME-SA/Ind-2001 foot-and-mouth disease virus strain. Our results reveal diverse geographical paths of migration that characterise the origins and evolutionary histories of different viral genes and genomic segments. These incompatibility measures can be applied to any phylogeography, and more generally to any phylogeny where each tip has been assigned either a continuous or discrete "trait" independent of the sequence. We illustrate this flexibility with an analysis of the interplay between the phylogeography and phylolinguistics of Uralic-speaking human populations, hinting at patrilinear language transmission.</p>
Data from: Comparing phylogeographies to reveal incompatible geographical histories within genomes
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Data from: The structure and allelic diversity of the self-incompatibility locus (S-locus) in diploid potatoes inferred from genome sequences and transcriptome data from styles and pollen
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Integrative genomic phylogeography reveals signs of mitonuclear incompatibility in a natural hybrid goby population
<p>Hybridization between divergent lineages generates new allelic combinations. One mechanism that can hinder the formation of hybrid populations is mitonuclear incompatibility, i.e. dysfunctional interactions between proteins encoded on the nuclear and mitochondrial genomes (mitogenomes) of diverged lineages. Theoretically, selective pressure due to mitonuclear incompatibility can affect genotypes in a hybrid population in which nuclear genomes and mitogenomes from divergent lineages admix. To directly and thoroughly observe this key process, we <i>de novo</i> sequenced the 747 Mb genome of the coastal goby, <i>Chaenogobius annularis</i>, and investigated its integrative genomic phylogeographics using RNA‐sequencing, RAD‐sequencing, genome re‐sequencing, whole mitogenome sequencing, amplicon‐sequencing, and small RNA‐sequencing. <i>Chaenogobius annularis</i> populations have been geographically separated into Pacific Ocean (PO) and Sea of Japan (SJ) lineages by past isolation events around the Japanese archipelago. Despite the divergence history and potential mitonuclear incompatibility between these lineages, the mitogenomes of the PO and SJ lineages have coexisted for generations in a hybrid population on the Sanriku Coast. Our analyses revealed accumulation of nonsynonymous substitutions in the PO‐lineage mitogenomes, including two convergent substitutions, as well as signals of mitochondrial lineage‐specific selection on mitochondria‐related nuclear genes. Finally, our data implied that a microRNA gene was involved in resolving mitonuclear incompatibility. Our integrative genomic phylogeographic approach revealed that mitonuclear incompatibility can affect genome evolution in a natural hybrid population.</p>
Evidence that genomic incompatibilities and other multilocus processes impact hybrid fitness in a rattlesnake hybrid zone
<p>Hybrid zones provide valuable opportunities to understand the genomic mechanisms that promote speciation by providing insight into factors involved in intermediate stages of speciation. Here we investigate introgression in a hybrid zone between two rattlesnake species (<em>Crotalus viridis</em> and <em>C. oreganus concolor</em>) that have undergone historical allopatric divergence and recent range expansion and secondary contact. We use Bayesian genomic cline models to characterize genomic patterns of introgression between these lineages and identify loci potentially subject to selection in hybrids. We find evidence for a large number of genomic regions with biased ancestry that deviate from the genomic background in hybrids (i.e., excess ancestry loci), which tend to be associated with genomic regions with higher recombination rates. We also identify suites of excess ancestry loci that show highly correlated allele frequencies (including conspecific and heterospecific combinations) across physically unlinked genomic regions in hybrids. Our findings provide evidence for multiple multilocus evolutionary processes impacting hybrid fitness in this system.</p>
Intercontinental dispersal and whole‐genome duplication contribute to loss of self‐incompatibility in a polyploid complex
Premise of the Study <div class="article-section__content en main"> <p>Angiosperm species often shift from self-incompatibility to self-compatibility following population bottlenecks. Across the range of a species, population bottlenecks may result from multiple factors, each of which may affect the geographic distribution and magnitude of mating-system shifts. We describe how intercontinental dispersal and genome duplication facilitate loss of self-incompatibility.</p> Methods <p>Self and outcross pollinations were performed on plants from 24 populations of the <i>Campanula rotundifolia</i> polyploid complex. Populations spanned the geographic distribution and three dominant cytotypes of the species (diploid, tetraploid, hexaploid).</p> Key Results <p>Loss of self-incompatibility was associated with both intercontinental dispersal and genome duplication. European plants were largely self-incompatible, whereas North American plants were intermediately to fully self-compatible. Within both European and North American populations, loss of self-incompatibility increased as ploidy increased. Ploidy change and intercontinental dispersal both contributed to loss of self-incompatibility in North America, but range expansion did not affect self-incompatibility within Europe or North America.</p> Conclusions <p>When species are subject to population bottlenecks arising through multiple factors, each factor can contribute to self-incompatibility loss. In a widespread polyploid complex, the loss of self-incompatibility can be predicted by the cumulative effects of whole-genome duplication and intercontinental dispersal.</p> </div>
Data from: Genomic scans reveal multiple mito‐nuclear incompatibilities in population crosses of the copepod Tigriopus californicus
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Integrative genomic phylogeography reveals signs of mitonuclear incompatibility in a natural hybrid goby population
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Data from: Interspecific crossing and genetic mapping reveal intrinsic genomic incompatibility between two Senecio species that form a hybrid zone on Mount Etna, Sicily
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Intercontinental dispersal and whole‐genome duplication contribute to loss of self‐incompatibility in a polyploid complex
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Evidence that genomic incompatibilities and other multilocus processes impact hybrid fitness in a rattlesnake hybrid zone
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Data from: Inbreeding depression in self-incompatible North American Arabidopsis lyrata: disentangling genomic and S-locus specific genetic load
Newly formed selfing lineages may express recessive genetic load and suffer inbreeding depression. This can have a genome-wide genetic basis, or be due to loci linked to genes under balancing selection. Understanding the genetic architecture of inbreeding depression is important in the context of the maintenance of self-incompatibility and understanding the evolutionary dynamics of S-alleles. We addressed this using North-American subspecies of Arabidopsis lyrata. This species is normally self-incompatible and outcrossing, but some populations have undergone a transition to selfing. The goals of this study were to: (1) quantify the strength of inbreeding depression in North-American populations of A. lyrata; and (2) disentangle the relative contribution of S-linked genetic load compared with overall inbreeding depression. We enforced selfing in self-incompatible plants with known S-locus genotype by treatment with CO2, and compared the performance of selfed vs outcrossed progeny. We found significant inbreeding depression for germination rate (δ=0.33), survival rate to 4 weeks (δ=0.45) and early growth (δ=0.07), but not for flowering rate. For two out of four S-alleles in our design, we detected significant S-linked load reflected by an under-representation of S-locus homozygotes in selfed progeny. The presence or absence of S-linked load could not be explained by the dominance level of S-alleles. Instead, the random nature of the mutation process may explain differences in the recessive deleterious load among lineages.
Data from: The genomics of incompatibility factors and sex determination in hybridizing species of Cottus (Pisces)
Cottus rhenanus and Cottus perifretum have formed hybrid lineages and narrow hybrid zones that can be best explained through the action of natural selection. However, the underlying selective forces as well as their genomic targets are not well understood. This study identifies genomic regions in the parental species that cause hybrid incompatibilities and tests whether these manifest in a sex-specific manner to learn about processes that affect natural hybridization in Cottus. Interspecific F2 crosses were analyzed for 255 markers for genetic mapping and to detect transmission distortion as a sign for genetic incompatibilities. The Cottus map consists of 24 linkage groups with a total length of 1575.4 cM. A male heterogametic (XY) sex determination region was found on different linkage groups in the two parental species. Genetic incompatibilities were incomplete, varied among individuals and populations and were not associated with the heterogametic sex. The variance between populations and individuals makes it unlikely that there are species-specific incompatibility loci that could affect the gene pool of natural hybrids in a simple and predictable way. Conserved synteny with sequenced fish genomes permits to genetically study the Cottus genome through the transfer of genomic information from the model fish species. Homology relationships of candidate genomic regions in Cottus indicate that sex determination is not based on the same genomic regions found in other fish species. This suggests a fast evolutionary turnover of the genetic basis of sex determination that, together with the small size of the heterogametic regions, may contribute to the absence of fitness effects related to the Haldane's rule.
Data from: Mechanical incompatibility caused by modifications of multiple male genital structures using genomic introgression in Drosophila
Mechanical incompatibility of male and female genitalia is common in animals with internal fertilization. However, our knowledge regarding the precise mechanisms is limited. One key question regards the susceptibility of the match between male and female genitalia to morphological modification. To address this issue, we generated six different second-chromosome introgression lines possessing partially Drosophila mauritiana-like genital morphology in multiple structures in D. simulans background. Three of the six introgression males showed elevated mobility at some stages during copulation with D. simulans females; this was assumed to be an indication of genital mismatch. Notably, one of the introgression males with D. mauritiana-like enlarged anal plates showed occasional leakage of adhesive ejaculate on the body surface when mated with pure D. simulans females, suggesting apparent structural incompatibility in genital coupling. These observations suggested that both sexual and natural selection shape the anal plate morphology, highlighting the role of this structure as an important component of mechanical isolation. Partial replacement (introgression) by a sibling species genome can induce perturbations in genital coupling mechanics, suggesting that genital compatibility can be susceptible to subtle genomic changes at the early stages of divergence in these species.
Data from: The genomics of incompatibility factors and sex determination in hybridizing species of Cottus (Pisces)
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Data from: The genomic and ecological context of hybridization affects the probability that symmetrical incompatibilities drive hybrid speciation
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Data from: Mechanical incompatibility caused by modifications of multiple male genital structures using genomic introgression in Drosophila
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Data from: Inbreeding depression in self-incompatible North American Arabidopsis lyrata: disentangling genomic and S-locus specific genetic load
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Data from: Hybrid incompatibilities, local adaptation, and the genomic distribution of natural introgression between species
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Recurring urothelial carcinomas show genomic rearrangements incompatible with a direct relationship, implications for tumor development.
GEO Series GSE146870. Homo sapiens. 47 samples. Type: Expression profiling by array.
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