Adaptation repeatedly uses complex structural genomic variation

Science, Journal Year: 2025, Volume and Issue: 388(6744)

Published: April 17, 2025

Structural elements are widespread across genomes, but their complexity and role in repeatedly driving local adaptation remain unclear. In this work, we use phased genome assemblies to show that adaptive divergence cryptic color pattern a stick insect is underlain by structural variation, not simple chromosomal inversion. We found populations of insects on two mountains associated with translocations have also been inverted. These differ size origin each mountain, they overlap partially involve some the same gene regions. Moreover, variation subject divergent selection arose without introgression between species. Our results how provides mechanism for repeated bouts adaptation.

Language: Английский

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Complex evolutionary processes maintain an ancient chromosomal inversion

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(25)

Published: June 13, 2023

Genome re-arrangements such as chromosomal inversions are often involved in adaptation. As such, they experience natural selection, which can erode genetic variation. Thus, whether and how remain polymorphic for extended periods of time remains debated. Here we combine genomics, experiments, evolutionary modeling to elucidate the processes maintaining an inversion polymorphism associated with use a challenging host plant (Redwood trees) Timema stick insects. We show that is maintained by combination processes, finding roles life-history trade-offs, heterozygote advantage, local adaptation different hosts, gene flow. models multi-layered regimes balancing selection flow provide resilience help buffer populations against loss variation, potential future evolution. further has persisted millions years not result recent introgression. thus find rather than being nuisance, complex interplay provides mechanism long-term maintenance

Language: Английский

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Ploidy as a leaky reproductive barrier: mechanisms, rates and evolutionary significance of interploidy gene flow

Annals of Botany, Journal Year: 2024, Volume and Issue: unknown

Published: June 13, 2024

Abstract Background Whole-genome duplication (polyploidization) is a dominant force in sympatric speciation, particularly plants. Genome doubling instantly poses barrier to gene flow owing the strong crossing incompatibilities between individuals differing ploidy. The strength of barrier, however, varies from species and recent genetic investigations revealed cases rampant interploidy introgression multiple ploidy-variable species. Scope Here, we review novel insights into frequency natural systems summarize underlying mechanisms promoting flow. Field surveys, occasionally complemented by experiments, suggest frequent opportunities for flow, direction diploid tetraploid, (higher) polyploids. However, scarcity accompanying population evidence virtual lack integration these approaches leave levels realized nature largely unknown. Finally, discuss potential consequences genome permeability on polyploid speciation adaptation highlight avenues that have just recently been opened very first genomic studies Standing stark contrast with rapidly accumulating evolutionary importance homoploid introgression, similar are yet be documented. Conclusions genomics era provides opportunity re-evaluate role adaptation. To achieve this goal, interdisciplinary bordering ecology genetics needed.

Language: Английский

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triangulaR:an R package for identifying AIMs and building triangle plots using SNP data from hybrid zones

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

Published: April 1, 2024

Abstract Hybridization provides a window into the speciation process and reshuffles parental alleles to produce novel recombinant genotypes. The presence or absence of specific hybrid classes across zone can provide support for various modes reproductive isolation. Early generation be distinguished by their combination index interclass heterozygosity, which estimated with molecular data. Hybrid heterozygosity are routinely calculated studies zones, but available resources next-generation sequencing datasets computationally demanding tools visualizing those metrics as triangle plot lacking. Here, we resource identifying ancestry- informative markers (AIMs) from SNP datasets, calculating relationship plot. Our methods implemented in R package triangulaR . We validate our simulating genetic data between groups at low, medium, high levels divergence. find that accurate precise estimates obtained sample sizes low five individuals per group. explore allele frequency difference thresholds AIM identification, how this threshold influences accuracy precision estimates. contextualize interpretation plots describing theoretical expectations covariance under Hardy-Weinberg Equilibrium recommendations best practices AIMs building plots.

Language: Английский

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Integrating hybridization and introgression into host–parasite epidemiology, ecology, and evolution

Trends in Parasitology, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Language: Английский

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Extensive Admixture Among Karst‐Obligate Salamanders Reveals Evidence of Recent Divergence and Gene Exchange Through Aquifers

Ecology and Evolution, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 1, 2025

Karst ecosystems often contain extraordinary biodiversity, but the complex underground aquifers of karst regions present challenges for assessing and conserving stygobiont diversity investigating their evolutionary history. We examined karst-obligate salamanders

Language: Английский

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Geography and Environment Shape Spatial Genetic Variation and Predict Climate Maladaptation Across Isolated and Disjunct Populations of Pinus muricata

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

Published: Feb. 6, 2025

ABSTRACT Assessing the evolutionary potential of rare species with limited migration amidst ongoing climate change requires an understanding patterns genetic variation and local adaptation. In contrast to large distributions population sizes most pines, Pinus muricata (bishop pine) occurs in a few isolated populations along coastal western North America is listed as threatened by IUCN. To quantify how current influenced distribution environment, we generated reduced representation DNA sequencing data for extant P. (12 locations, 7828 loci). We assessed geographic differentiation diversity used genetic‐environment association (GEA) analyses characterise contribution environmental variables adaptation structure. Based on these inferences, quantified genomic offset relative estimate maladaptation under mild (SSP1‐2.6) severe (SSP5‐8.5) scenarios across 2041–2060 2081–2100. Despite occurring small, populations, was not low . Population was, however, defined hierarchy spatial scales, stands generally forming genetically identifiable groups latitude environments. GEA implicated temperature‐ soil‐related strongly contributing Estimates future varied non‐linearly latitude, increased severity projections over time, were predicted increases annual temperature. Our results suggest that isolation have shaped among disjunct factors may shape risk projected change.

Language: Английский

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The Winner Takes It All: a single genotype of Kalanchoe ×houghtonii is a global invader

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 7, 2025

Abstract Background and Aims Invasive alien plant species pose a global challenge, their impact is amplified by globalisation the accelerating pace of climate change. In mild-climate regions, drought-tolerant invasive plants showing broad environmental tolerance have competitive advantage. One example Kalanchoe × houghtonii (Crassulaceae), popularly known as “mother millions”. It hybrid resulting from interploid cross between K. daigremontiana delagoensis , both native to Madagascar. propagated an ornamental plant, has emerged invader in less than century. Four morphotypes this been identified, with different ploidy levels varying capacities. Here we aim investigate genomic variability behind invasion success . Methods We sampled 57 accessions houghtonii, daigremontiana, closely related taxa, including old herbarium materials, all over world. analysed genome size, chromosome numbers, sequenced whole genome, complete plastome sequence each accession, studied diversity ribosomal RNA genes. also performed detailed phylogenomic study using nuclear BUSCO Key Results Our reveals genetic cytogenetic morphotypes, shows that single tetraploid genotype (morphotype A) dominates populations, emerging first reported clonal capable worldwide colonisation. Morphotype A striking uniformity, high phenotypic plasticity, extremely rates vegetative reproduction, representing “general-purpose genotype”. Conclusions The astonishing reproductive capacity, adaptability speed at which colonising new regions spread highlight importance understanding hybridisation polyploidy ecosystems. findings call for need risk assessments before developing hybrids breeding may exhibit characteristics.

Language: Английский

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Interploidy gene flow does not prevent adaptive genetic differentiation in sympatric populations of Epidendrum fulgens and E. puniceoluteum (Orchidaceae)

Botanical Journal of the Linnean Society, Journal Year: 2025, Volume and Issue: unknown

Published: March 6, 2025

Abstract Polyploids often exhibit ecological divergence from diploid parents, but the relative importance of selection in speciation by polyploidy remains to be tested most systems. Here we use transcriptome-derived single nucleotide polymorphisms (SNPs) test whether increased gene flow between Epidendrum fulgens and tetraploid E. puniceoluteum (Orchidaceae) sympatry could prevent adaptation contrasting habitats (sand dunes swamps, respectively), infer genes probably under differential selection. Additionally, used species distribution data for climatic niche a subset synonymous SNPs past demographic signatures. We found no evidence introgression transcribed portion their genomes. For differentiated loci species, annotated biological processes related replication machineries also responses habitat features. that niches slightly diverge due tolerance lower temperatures wider amplitude precipitation fulgens, which explains species’ distinct signatures changes. By combining transcriptomics with comparisons, shed light on potential role adaptive originating maintaining plant biodiversity Neotropical coastal environments.

Language: Английский

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triangulaR: an R package for identifying AIMs and building triangle plots using SNP data from hybrid zones

Heredity, Journal Year: 2025, Volume and Issue: unknown

Published: April 12, 2025

Abstract Hybridization provides a window into the speciation process and reshuffles parental alleles to produce novel recombinant genotypes. Presence or absence of specific hybrid classes across zone can provide support for various modes reproductive isolation. Early generation be distinguished by their combination index interclass heterozygosity, which estimated with molecular data. Hybrid heterozygosity are routinely calculated studies zones, but available resources next-generation sequencing datasets computationally demanding tools visualizing triangle plots lacking. Here, we resource identifying ancestry-informative markers (AIMs) from single nucleotide polymorphism (SNP) datasets, calculating relationship as plot. Our methods implemented in R package triangulaR . We validate our on an empirical dataset simulations genetic data between two groups at low, medium, high levels divergence. accurate precise estimates sample sizes low five individuals per group, similar error another program estimation, bgchm explore allele frequency difference thresholds AIM identification, how this threshold influences accuracy precision estimates. contextualize interpretation describing theoretical expectations under Hardy-Weinberg Equilibrium recommendations best practices AIMs building plots.

Language: Английский

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