Adaptive and maladaptive introgression in grapevine domestication

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(24)

Published: June 5, 2023

Domesticated grapevines spread to Europe around 3,000 years ago. Previous studies have revealed genomic signals of introgression from wild cultivated grapes in Europe, but the time, mode, pattern, and biological effects these events not been investigated. Here, we studied resequencing data 345 samples spanning distributional range (Vitis vinifera ssp. sylvestris) (V. vinifera) grapes. Based on machine learning-based population genetic analyses, detected evidence for a single domestication grapevine, followed by continuous gene flow between European (EU) over past ~2,000 y, especially EU wine We also inferred that soft-selective sweeps were dominant artificial selection. Gene pathways associated with synthesis aromatic compounds enriched regions both selected introgressed, suggesting an important resource improving flavor Despite potential benefits grape improvement, introgressed fragments introduced higher deleterious burden, most SNPs structural variants hidden heterozygous state. Cultivated benefited adaptive grapes, has increased load. In general, our study beneficial harmful is critical breeding grapevine take advantage resources.

Language: Английский

---

Resilience of genetic diversity in forest trees over the Quaternary

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Oct. 14, 2024

The effect of past environmental changes on the demography and genetic diversity natural populations remains a contentious issue has rarely been investigated across multiple, phylogenetically distant species. Here, we perform comparative population genomic analyses demographic inferences for seven widely distributed ecologically contrasting European forest tree species based concerted sampling 164 their ranges. For all species, effective size, N

Language: Английский

---

Population genomics highlights structural variations in local adaptation to saline coastal environments in woolly grape

Journal of Integrative Plant Biology, Journal Year: 2024, Volume and Issue: 66(7), P. 1408 - 1426

Published: April 5, 2024

ABSTRACT Structural variations (SVs) are a feature of plant genomes that has been largely unexplored despite their significant impact on phenotypic traits and local adaptation to abiotic biotic stress. In this study, we employed woolly grape ( Vitis retordii ), species native the tropical subtropical regions East Asia with both coastal inland habitats, as valuable model for examining SVs adaptation. We assembled haplotype‐resolved chromosomal reference genome grape, conducted population genetic analyses based whole‐genome sequencing (WGS) data from populations. The demographic revealed recent bottlenecks in all populations asymmetric gene flow population. total, 1,035 genes associated adaptive regulation salt stress, radiation, environmental were detected underlying selection by SNPs population, which 37.29% 65.26% SNPs, respectively. Candidate such FSD2 , RGA1 AAP8 tolerance found be highly differentiated selected during process habitats SV regions. Our study highlights importance adaptation; candidate related stress climatic environments important genomic resources future breeding programs grapevine its rootstocks.

Language: Английский

---

Recombination Variation Shapes Phylogeny and Introgression in Wild Diploid Strawberries

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(3)

Published: March 1, 2023

Abstract Introgressive hybridization is widespread in wild plants and has important consequences. However, frequent between species makes the estimation of species’ phylogeny challenging, little known about genomic landscape introgression as it results from complex interactions multiple evolutionary processes. Here, we reconstructed ten diploid strawberries with whole genome resequencing data then investigated influence recombination rate variation on introgression. We found that regions low showed reduced levels incomplete lineage sorting introgression, concentrated phylogenetic signals, thus contributing to most likely tree strawberries. revealed across genus Fragaria, an average proportion approximately 4.1% extant genome. Introgression tends be retained high rates gene density. Furthermore, identified four SLF genes under selective sweeps may play potential roles possible regain self-incompatibility by ancient Altogether, our study yielded novel insights into history characteristics provides evidence for role plant mating system transitions.

Language: Английский

---

Ghost admixture in eastern gorillas

Nature Ecology & Evolution, Journal Year: 2023, Volume and Issue: 7(9), P. 1503 - 1514

Published: July 27, 2023

Abstract Archaic admixture has had a substantial impact on human evolution with multiple events across different clades, including from extinct hominins such as Neanderthals and Denisovans into modern humans. In great apes, archaic been identified in chimpanzees bonobos but the possibility of not explored other species. Here, we address this question using high-coverage whole-genome sequences all four extant gorilla subspecies, six newly sequenced eastern gorillas previously unsampled geographic regions. Using approximate Bayesian computation neural networks to model demographic history gorillas, find signature an ‘ghost’ lineage common ancestor western gorillas. We infer that up 3% genome these individuals is introgressed diverged more than 3 million years ago This introgression event took place before split mountain lowland probably 40 thousand may have influenced perception bitter taste When comparing landscapes humans bonobos, consistent depletion fragments X chromosome However, protein-coding content detectable possibly consequence stronger genetic drift

Language: Английский

---

Introgression and incomplete lineage sorting blurred phylogenetic relationships across the genomes of sclerophyllous oaks from southwest China

Cladistics, Journal Year: 2024, Volume and Issue: 40(4), P. 357 - 373

Published: Jan. 10, 2024

Resolving evolutionary relationships among closely related species with interspecific gene flow is challenging. Genome-scale data provide opportunities to clarify complex in and observe variations across the genomes of such species. The Himalayan-Hengduan subalpine oaks have a nearly completely sympatric distribution southwest China probably constitute syngameon. In this study, we mapped resequencing from different group Quercus aquifolioides reference genome obtain high-quality filtered single nucleotide polymorphism (SNP) dataset. We also assembled their plastomes. reconstructed phylogenetic relationships, explored level pattern introgression these investigated tree variation using sliding windows. same or plastomes were found be shared extensively within specific geographical area. Phylogenomic analyses genome-wide SNP that most clade showed genetic coherence, but several connected by introgression. trees obtained windows are highly heterogeneous therefore obscured. Our study all form obscured observed empirically best explained conjunction incomplete lineage sorting.

Language: Английский

---

Interploidy Introgression Shaped Adaptation during the Origin and Domestication History of Brassica napus

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(9)

Published: Sept. 1, 2023

Polyploidy is recurrent across the tree of life and known as an evolutionary driving force in plant diversification crop domestication. How polyploid plants adapt to various habitats has been a fundamental question that remained largely unanswered. Brassica napus major cultivated worldwide, resulting from allopolyploidy between unknown accessions diploid B. rapa oleracea. Here, we used whole-genome resequencing data representing majority morphotypes ecotypes species rapa, oleracea, investigate role polyploidy during To do so, first reconstructed phylogenetic history napus, which supported hypothesis emergence derived hybridization European turnip wild These analyses also showed swede Siberian kale (used vegetable fodder) were domesticated before rapeseed (oil crop). We next observed frequent interploidy introgressions sympatric diploids prominent throughout domestication napus. Introgressed genomic regions shown increase overall genetic diversity tend be localized high recombination. detected numerous candidate adaptive introgressed found evidence some genes these contributed phenotypic adaptation different morphotypes. Overall, our results shed light on origin demonstrate introgression important mechanism fuels rapid species.

Language: Английский

---

Resilience of genetic diversity in forest trees over the Quaternary

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: Jan. 6, 2023

Abstract The effect of past environmental changes on the demography and genetic diversity natural populations remains a contentious issue has rarely been investigated across multiple, phylogenetically distant species. Here, we performed comparative population genomic analyses demographic inferences for seven widely distributed ecologically contrasted European forest tree species based concerted sampling 164 their ranges. For all species, effective size, N e , increased or remained stable over many glacial cycles up to 15 million years in most extreme cases. Hence, surprisingly, drastic associated with Pleistocene have had little impact level dominant despite major shifts geographic Based trajectories time, can be divided into three groups, highlighting importance life history range size determining synchronous variation diversity, time. Altogether, our results indicate that trees were able retain evolutionary potential very long periods time strong changes. One-Sentence Summary Population reveal retained Quaternary.

Language: Английский

---

The Role of Introgression During the Radiation of Endemic Fishes Adapted to Living at Extreme Altitudes in the Tibetan Plateau

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(6)

Published: May 29, 2023

Abstract Recent genomic analyses of evolutionary radiations suggest that ancient introgression may facilitate rapid diversification and adaptive radiation. The loach genus Triplophysa, a with most species endemic to Tibetan Plateau, shows ecological diversity evolution represents potential example radiation linked the uplift Plateau. Here, we interrogate complex history Triplophysa fishes through analysis whole-genome sequences. By reconstructing phylogeny quantifying across this clade, simulating speciation migration processes, confirm extensive gene flow events occurred disparate species. Our results plays more substantial role than incomplete lineage sorting in underpinning phylogenetic discordance Triplophysa. also indicate regions affected by exhibit characteristics lower recombination rates nucleotide associate selection. Simulation tibetana suggests have been Gonghe Movement third resulting founder effects subsequent reduction Ne.

Language: Английский

---

Ancient hybridization leads to the repeated evolution of red flowers across a monkeyflower radiation

Evolution Letters, Journal Year: 2023, Volume and Issue: 7(5), P. 293 - 304

Published: June 5, 2023

The reuse of old genetic variation can promote rapid diversification in evolutionary radiations, but most cases, the historical events underlying this divergence are not known. For example, ancient hybridization generate new combinations alleles that sort into descendant lineages, potentially providing raw material to initiate divergence. In Mimulus aurantiacus species complex, there is evidence for widespread gene flow among members radiation. addition, allelic MaMyb2 responsible differences flower color between closely related ecotypes subspecies puniceus, contributing reproductive isolation by pollinators. Previous work suggested was introgressed red-flowered ecotype puniceus. However, additional taxa within radiation have independently evolved red flowers from their yellow-flowered ancestors, raising possibility introgression had a more origin. study, we used repeated tests admixture whole-genome sequence data across diverse demonstrate has been both and recurrent group. signal removed due selection, suggesting barriers place taxa. Yet, roughly 30 kb region contains currently shared only Patterns admixture, divergence, extended haplotype homozygosity confirm history hybridization, where functional variants preserved positive selection lost counterparts. results study reveal against reduce genomic signatures provide essential facilitates evolution phenotypic traits lineages.

Language: Английский

---