Introgression, also known as introgressive hybridization, refers to the process that genetic components from the gene pool of one population transfer to the other via constant backcrossing. ...Introgression is widespread in nature, which plays important roles in increasing genetic diversity and improving adaptability to the environment, and in turn, influences the evolutionary progress of animals, plants and humans. Being as an important evolutionary event, researchers pay great attention to the detection of introgression, the introgression direction, the introgression timing, the pattern of introgression and so on. With the rapid development of high-throughput sequencing technologies, methods to detect and characterize introgression based on genome-wide data are continuously developed. In this review, we summarize a series of methods for introgression detection, and introduce the design principles and applications of these methods. We also discuss the maintenance and selection of gene segments after introgression. This review provides a relatively comprehensive reference for the studies on introgression.
Abstract
Recent analyses suggest that cross-species gene flow or introgression is common in nature, especially during species divergences. Genomic sequence data can be used to infer introgression ...events and to estimate the timing and intensity of introgression, providing an important means to advance our understanding of the role of gene flow in speciation. Here, we implement the multispecies-coalescent-with-introgression model, an extension of the multispecies-coalescent model to incorporate introgression, in our Bayesian Markov chain Monte Carlo program Bpp. The multispecies-coalescent-with-introgression model accommodates deep coalescence (or incomplete lineage sorting) and introgression and provides a natural framework for inference using genomic sequence data. Computer simulation confirms the good statistical properties of the method, although hundreds or thousands of loci are typically needed to estimate introgression probabilities reliably. Reanalysis of data sets from the purple cone spruce confirms the hypothesis of homoploid hybrid speciation. We estimated the introgression probability using the genomic sequence data from six mosquito species in the Anopheles gambiae species complex, which varies considerably across the genome, likely driven by differential selection against introgressed alleles.
The genetic diversity of our crop plants has been substantially reduced during the process of domestication and breeding. This reduction in diversity necessarily constrains our ability to expand a ...crop’s range of cultivation into environments that are more extreme than those in which it was domesticated, including into “sustainable” agricultural systems with reduced inputs of pesticides, water, and fertilizers. Conversely, the wild progenitors of crop plants typically possess high levels of genetic diversity, which underlie an expanded (relative to domesticates) range of adaptive traits that may be of agricultural relevance, including resistance to pests and pathogens, tolerance to abiotic extremes, and reduced dependence on inputs. Despite their clear potential for crop improvement, wild relatives have rarely been used systematically for crop improvement, and in no cases, have full sets of wild diversity been introgressed into a crop. Instead, most breeding efforts have focused on specific traits and dealt with wild species in a limited and typically ad hoc manner. Although expedient, this approach misses the opportunity to test a large suite of traits and deploy the full potential of crop wild relatives in breeding for the looming challenges of the 21st century. Here we review examples of hybridization in several species, both intentionally produced and naturally occurring, to illustrate the gains that are possible. We start with naturally occurring hybrids, and then examine a range of examples of hybridization in agricultural settings.
Global trade has considerably accelerated biological invasions. The annual tropical teosintes, the closest wild relatives of maize, were recently reported as new agricultural weeds in two European ...countries, Spain and France. Their prompt settlement under climatic conditions differing drastically from that of their native range indicates rapid genetic evolution. We performed a phenotypic comparison of French and Mexican teosintes under European conditions and showed that only the former could complete their life cycle during maize cropping season. To test the hypothesis that crop-to-wild introgression triggered such rapid adaptation, we used single nucleotide polymorphisms to characterize patterns of genetic variation in French, Spanish, and Mexican teosintes as well as in maize germplasm. We showed that both Spanish and French teosintes originated from Zea mays ssp. mexicana race “Chalco,” a weedy teosinte from the Mexican highlands. However, introduced teosintes differed markedly from their Mexican source by elevated levels of genetic introgression from the high latitude Dent maize grown in Europe. We identified a clear signature of divergent selection in a region of chromosome 8 introgressed from maize and encompassing ZCN8, a major flowering time gene associated with adaptation to high latitudes. Moreover, herbicide assays and sequencing revealed that French teosintes have acquired herbicide resistance via the introgression of a mutant herbicide-target gene (ACC1) present in herbicide-resistant maize cultivars. Altogether, our results demonstrate that adaptive crop-to-wild introgression has triggered both rapid adaptation to a new climatic niche and acquisition of herbicide resistance, thereby fostering the establishment of an emerging noxious weed.
Introgression is the transfer of genetic material between 2 different species via repeated back crossing of the interspecific hybrid and one of the parent species. These are important events to ...understand in the study of molecular evolutionary relationships between species. Previous studies have found regions of introgression within the horse genome, likely hundreds of thousands to millions of years ago from a non-caballine equid that are present in current horse populations. Our hypothesis is, these regions are retained among horses because they are doing something functionally beneficial and are increasing the horse's fitness. After identifying these regions with maximum likelihood estimation in a sample Thoroughbred population, the next steps were to analyze the different haplotypes found in modern horse genomes to find what polymorphisms were inherited together. Once identified, the genotypes of 230 Thoroughbred horse genomes were phased with BEAGLE. The positions tagged by BEAGLE were then viewed in Tassel 5 and a linkage disequilibrium plot was created. The phased genotypes were then analyzed, and the different haplotypes were extracted from the variant call file (vcf), taking into consideration the linkage disequilibrium plot and allele frequencies. Three main haplotypes occurred in this sample population: the reference, orTwilight, haplotype, the non-caballine haplotype, and another haplotype of unknown origin. This pipeline presents the number of haplotypes in the sampled population and which polymorphisms are inherited together, which gives us a better understanding of the origin on the introgressed haplotype(s). The short-term goal is to identify which non-caballine equid is the most prominent donor of the non-caballine haplotype. Ultimately, we will develop software to automate this analysis and identify putatively impactful introgressed regions using recently published data from the Equine-FAANG project. Currently, we are finding what the introgressed regions code for in the context of the horse genome, either non-coding RNA, a gene, or a non-coding region, to narrow down the search when putting together phylogenetic trees. Overall, the more we understand introgression, the better we will be able to piece together evolutionary relationships, how they are essential for rapid adaptation historically, and how they impact gene function in modern populations.
Cytonuclear discordance is commonly observed in phylogenetic studies, yet few studies have tested whether these patterns reflect incomplete lineage sorting or organellar introgression.
Here, we used ...whole-chloroplast sequence data in combination with over 1000 nuclear single-nucleotide polymorphisms to clarify the extent of cytonuclear discordance in wild annual sunflowers (Helianthus), and to test alternative explanations for such discordance.
Our phylogenetic analyses indicate that cytonuclear discordance is widespread within this group, both in terms of the relationships among species and among individuals within species. Simulations of chloroplast evolution show that incomplete lineage sorting cannot explain these patterns in most cases. Instead, most of the observed discordance is better explained by cytoplasmic introgression. Molecular tests of evolution further indicate that selection may have played a role in driving patterns of plastid variation – although additional experimental work is needed to fully evaluate the importance of selection on organellar variants in different parts of the geographic range.
Overall, this study represents one of the most comprehensive tests of the drivers of cytonuclear discordance and highlights the potential for gene flow to lead to extensive organellar introgression in hybridizing taxa.
Abstract
Polyploidy is recurrent across the tree of life and known as an evolutionary driving force in plant diversification and crop domestication. How polyploid plants adapt to various habitats has ...been a fundamental question that remained largely unanswered. Brassica napus is a major crop cultivated worldwide, resulting from allopolyploidy between unknown accessions of diploid B. rapa and B. oleracea. Here, we used whole-genome resequencing data of accessions representing the majority of morphotypes and ecotypes from the species B. rapa, B. oleracea, and B. napus to investigate the role of polyploidy during domestication. To do so, we first reconstructed the phylogenetic history of B. napus, which supported the hypothesis that the emergence of B. napus derived from the hybridization of European turnip of B. rapa and wild B. oleracea. These analyses also showed that morphotypes of swede and Siberian kale (used as vegetable and fodder) were domesticated before rapeseed (oil crop). We next observed that frequent interploidy introgressions from sympatric diploids were prominent throughout the domestication history of B. napus. Introgressed genomic regions were shown to increase the overall genetic diversity and tend to be localized in regions of high recombination. We detected numerous candidate adaptive introgressed regions and found evidence that some of the genes in these regions contributed to phenotypic diversification and adaptation of different morphotypes. Overall, our results shed light on the origin and domestication of B. napus and demonstrate interploidy introgression as an important mechanism that fuels rapid diversification in polyploid species.
Background. Hordeum bulbosum L. is the only wild species of the genus Hordeum , the gene pool of which is successfully used in introgressive hybridization to increase the genetic diversity of ...H. vulgare L. When creating introgression forms based on hybrids of H. vulgare with H. bulbosum , it is necessary to take into consideration the ploidy of the parent species, and their genetic features that determine the intensity of the process of H. bulbosum chromosomes elimination in embryogenesis. The purpose of our investigation was to study the features associated with the elimination of bulbous barley chromosomes in embryos obtained in various combinations of crosses involving the tetraploid hybrid H. bulbosum with H. vulgare for its effective use in obtaining introgression lines of H. vulgare . Material and methods. The analysis was performed on 9-15 days old embryos obtained in crosses of the tetraploid hybrid F2 ( H. bulbosum A17 (4x) × H. vulgare ‘Borwina’ (4x)) (HbHbHvHv) with ‘Igri’ (2x) and ‘Borwina’ (2x) barley varieties, with H. bulbosum A17 (4x), as well as during its self-pollination. The chromosomal composition of embryos of different ages was analyzed on squashed embryo slides using genomic in situ hybridization (GISH). Results. Among the 11-15 days old embryos obtained from self-pollination of the hybrid, approximately half of the studied ones were mixoploids, while in other embryos the majority of cells contained only the genomic material of H. vulgare . The elimination process was very intensive in crosses of the hybrid with the barley varieties ‘Igri’ (2x) and ‘Borwina’ (2x), and by day 10-11 after pollination cells containing only the genomic material of H. vulgare predominated in all embryos, regardless of the direction of crossing and the variety used. Hybrid embryos with a stable chromosomal composition resulted from a cross of a tetraploid hybrid with H. bulbosum A17 (4x). Embryos with recombinant H. vulgare chromosomes carrying alien genetic material of bulbous barley were identified in all types of crosses. Conclusion. The most efficient way for the mass production of introgression lines of cultivated barley varieties based on the partially fertile hybrid F2 ( H. bulbosum A17 (4x) × H. vulgare ‘Borwina’ (4x)), is the crossing with varieties of H. vulgare (2x). The progeny from such crosses will contain only cultivated barley plants, among which it is possible to identify forms with the introgression of H. bulbosum and use already the first generation from their self-pollination for selecting H. vulgare lines carrying the genetic material of bulbous barley in both homologs.
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•Petunia is the sister group of Calibrachoa + Fabiana.•High levels of gene tree discordance were estimated in the shallower nodes of the phylogeny.•Ancient and ongoing interspecific ...gene flow were detected within all three genera.•Petunia and Calibrachoa, genera with distinct chromosome numbers, potentially hybridized during their radiation.
Despite the overarching history of species divergence, phylogenetic studies often reveal distinct topologies across regions of the genome. The sources of these gene tree discordances are variable, but incomplete lineage sorting (ILS) and hybridization are among those with the most biological importance. Petunia serves as a classic system for studying hybridization in the wild. While field studies suggest that hybridization is frequent, the extent of reticulation within Petunia and its closely related genera has never been examined from a phylogenetic perspective. In this study, we used transcriptomic data from 11 Petunia, 16 Calibrachoa, and 10 Fabiana species to illuminate the relationships between these species and investigate whether hybridization played a significant role in the diversification of the clade. We inferred that gene tree discordance within genera is linked to hybridization events along with high levels of ILS due to their rapid diversification. Moreover, network analyses estimated deeper hybridization events between Petunia and Calibrachoa, genera that have different chromosome numbers. Although these genera cannot hybridize at the present time, ancestral hybridization could have played a role in their parallel radiations, as they share the same habitat and life history.
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