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

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Pervasive gene flow despite strong and varied reproductive barriers in swordtails

Nature Ecology & Evolution, Journal Year: 2025, Volume and Issue: unknown

Published: March 26, 2025

Abstract The evolution of reproductive barriers leads to the formation new species. However, recent research has demonstrated that hybridization been pervasive across tree life even in presence strong barriers. Using swordtail fishes (genus Xiphophorus ), an emerging model system, we document overlapping mechanisms act as gene flow between birchmanni and cortezi by combining genomic sequencing from natural hybrid populations, experimental laboratory crosses, behavioural assays, sperm measures developmental studies. We show assortative mating plays a role maintaining subpopulations with distinct ancestry within populations. F 2 hybrids identify several regions strongly impact viability. Strikingly, two these underlie genetic incompatibilities X. its sister species malinche . Our results demonstrate ancient played origin this shared incompatibility. Moreover, mismatch at incompatible remarkably similar consequences for phenotypes survival × hybrids. findings varied shape exchange naturally hybridizing highlight complex evolutionary outcomes hybridization.

Language: Английский

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Localizing Post-Admixture Adaptive Variants with Object Detection on Ancestry-Painted Chromosomes

Molecular Biology and Evolution, Journal Year: 2023, Volume and Issue: 40(4)

Published: March 22, 2023

Abstract Gene flow between previously differentiated populations during the founding of an admixed or hybrid population has potential to introduce adaptive alleles into new population. If allele is common in one source population, but not other, then as rises frequency genetic ancestry from containing will increase nearby well. Patterns have therefore been used identify post-admixture positive selection humans and other animals, including examples immunity, metabolism, animal coloration. A method identifies regions genome that local “outliers” compared with distribution across rest genome, considering each locus independently. However, we lack theoretical models for expected distributions under various demographic scenarios, resulting false positives negatives. Further, patterns distant sites are often independent. As a result, current methods tend infer wide genomic many genes selection, limiting biological interpretation. Instead, develop deep learning object detection applied images generated ancestry-painted genomes. This approach preserves information surrounding context avoids pitfalls user-defined summary statistics. We find robust variety misspecifications using simulated data. Applied human genotype data Cabo Verde, localize known single narrow region multiple long windows obtained two ancestry-based methods.

Language: Английский

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The fitness of an introgressing haplotype changes over the course of divergence and depends on its size and genomic location

PLoS Biology, Journal Year: 2023, Volume and Issue: 21(7), P. e3002185 - e3002185

Published: July 17, 2023

The genomic era has made clear that introgression, or the movement of genetic material between species, is a common feature evolution. Examples both adaptive and deleterious introgression exist in variety systems. What unclear how fitness an introgressing haplotype changes as species diverge size changes. In simple model, we show may more easily occur into parts genome which have not diverged heavily from ancestor. key insight alleles shared background are likely to positive epistatic interactions, increasing larger block. regions where few existing substitutions disrupted, this epistasis can be than incompatibilities with recipient genome. Further, early process divergence, large haplotypes favored individual alleles. This model consistent observations relationship recombination rate frequency across genome; however, it generates several novel predictions. First, suggests exist, negative, recently pairs. Furthermore, replaces derived variation will at sites carrying ancestral variants. These predictions tested example Drosophila melanogaster , some support for both. Finally, provides potential alternative explanation asymmetry direction expectations higher rapidly populations slowly evolving ones.

Language: Английский

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Microgeographic population structuring in a genus of California trapdoor spiders and discovery of an enigmatic new species (Euctenizidae: Promyrmekiaphila korematsui sp. nov.)

Ecology and Evolution, Journal Year: 2024, Volume and Issue: 14(3)

Published: March 1, 2024

Abstract The recognition and delineation of cryptic species remains a perplexing problem in systematics, evolution, delimitation. Once recognized as such, complexes provide fertile ground for studying genetic divergence within the context phenotypic ecological (or lack thereof). Herein we document discovery new trapdoor spider, Promyrmekiaphila korematsui sp. nov. Using subgenomic data obtained via target enrichment, phylogeography California endemic genus its constituent species, which also includes P. clathrata winnemem . Based on these show pattern strong geographic structuring among populations but cannot entirely discount recent gene flow that are parapatric, particularly deeply diverged lineages data, addition to revealing undescribed allude potential differentiation where likely come into close contact. Alternatively, cohesion genetically divergent suggests some level is ongoing or occurred past. Despite considerable field collection efforts over many years, additional sampling zones contact both needed completely resolve dynamics at population–species interface.

Language: Английский

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Pervasive gene flow despite strong and varied reproductive barriers in swordtails

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: April 20, 2024

One of the mechanisms that can lead to formation new species occurs through evolution reproductive barriers. However, recent research has demonstrated hybridization been pervasive across tree life even in presence strong Swordtail fishes (genus

Language: Английский

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Genetic Regulatory Perturbation of Gene Expression Impacted by Genomic Introgression in Fiber Development of Allotetraploid Cotton

Advanced Science, Journal Year: 2024, Volume and Issue: 11(40)

Published: Aug. 28, 2024

Abstract Interspecific genomic introgression is an important evolutionary process with respect to the generation of novel phenotypic diversity and adaptation. A key question how gene flow perturbs expression networks regulatory interactions. Here, population two species allopolyploid cotton ( Gossypium ) delineate perturbations regarding fiber development accompanying quality change utilized. De novo assembly recipient parent G. hirsutum Emian22) genome allowed identification variation segments (ISs) in 323 lines (ILs) from donor barbadense 3–79). It documented dynamics by sequencing 1,284 transcriptomes developing fibers characterized genetic mediated using a multi‐locus model. Introgression individual homoeologous genes exhibiting extreme low or high bias can lead parallel their non‐introgressed duplicates, implying shared yet divergent fate duplicated following allopolyploidy. Additionally, IL N182 improved characterized, candidate GhFLAP1 related length validated. This study outlines framework for understanding introgression‐mediated polyploids, provides insights targeted breeding superior upland fiber.

Language: Английский

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A review of catfish (Siluriformes) hybridization

Reviews in Fish Biology and Fisheries, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 5, 2025

Language: Английский

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Museum Skins Enable Identification of Introgression Associated with Cytonuclear Discordance

Systematic Biology, Journal Year: 2024, Volume and Issue: 73(3), P. 579 - 593

Published: April 5, 2024

Abstract Increased sampling of genomes and populations across closely related species has revealed that levels genetic exchange during after speciation are higher than previously thought. One obvious manifestation such is strong cytonuclear discordance, where the divergence in mitochondrial DNA (mtDNA) differs from for nuclear genes more (or less) expected differences between mtDNA (nDNA) population size mutation rate. Given genome-scale data sets coalescent modeling, we can now confidently identify cases discordance test specifically historical or recent introgression as cause. Using sampling, combining exon capture museum specimens recently collected tissues showcase how genomic tools resolve complex evolutionary histories brachyotis group rock-wallabies (Petrogale). In particular, applying phylogenomic approaches assess role demographic processes driving patterns a ancient hybridization. We find described well supported monophyletic taxa nDNA genes, but not mtDNA, with involving at least 4 operational taxonomic units which diverged 183–278 kya. ABC modeling gene trees supports some taxon pairs discordance. substantial body involved, this evidence flow surprising. Heterogenous were identified do appear to be associated chromosome species. These previous results suggest dynamic past climates monsoonal tropics could have promoted reticulation among

Language: Английский

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The Distribution and Dispersal of Large Haploblocks in a Superspecies

Molecular Ecology, Journal Year: 2025, Volume and Issue: unknown

Published: March 17, 2025

ABSTRACT Haploblocks are regions of the genome that coalesce to an ancestor as a single unit. Differentiated haplotypes in these can result from accumulation mutational differences low‐recombination chromosomal regions, especially when selective sweeps occur within geographically structured populations. We introduce method identify large well‐differentiated haploblock (LHBRs), based on variance standardised heterozygosity (ViSHet) nucleotide polymorphism (SNP) genotypes among individuals, calculated across genomic region (500 SNPs our case). apply this greenish warbler ( Phylloscopus trochiloides ) ring species, using newly assembled reference and at more than 1 million 257 individuals. Most chromosomes carry distinctive LHBR, containing 4–6 distinct associated with geography, enabling detection hybridisation events transition zones between differentiated LHBRs have exceptionally low within‐haplotype variation moderately between‐haplotype distance, suggesting their establishment through recurrent varying geographic scales. Meiotic drive is potentially powerful mechanism producing such sweeps, likely often represent centromeric where recombination restricted. Links populations enable introgression favoured we one showing highly discordant distribution compared most genome, being present two distantly separated similar latitudes both east central Asia. Our results set stage for detailed studies haploblocks, including location, gene content contribution reproductive isolation.

Language: Английский

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