Selection-driven trait loss in independently evolved cavefish populations

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: Nov. 28, 2022

Abstract Predicting the outcome of evolution is a central goal modern biology, yet, determining relative contributions deterministic events (i.e., selection) and stochastic drift mutation) to evolutionary process remains major challenge. Systems where same traits have evolved repeatedly provide natural replication that can be leveraged study predictability molecular genetic basis adaptation. Although mutational screens in laboratory demonstrated diversity mutations produce phenocopies one another, systems, similar changes frequently underly phenotypes across independent lineages. This suggests substantial role for constraint determinism supports notion there may characteristics which make certain more likely contribute phenotypic evolution. Here we use large-scale whole genome resequencing Mexican tetra, Astyanax mexicanus , demonstrate selection has played primary repeated both trait loss enhancement cave We identify candidate genes underlying adaptation caves infer mode evolution, revealing on standing variation de novo substantially Finally, show with evidence significantly longer coding regions compared rest genome, this effect most pronounced evolving convergently via mutations. Importantly, our findings first empirical support hypothesis larger targets are substrate indicate features novel environment impact rate at occur.

Language: Английский

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Selection on standing genetic variation mediates convergent evolution in extremophile fish

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(18), P. 5042 - 5054

Published: Aug. 7, 2023

Abstract Hydrogen sulfide is a toxic gas that disrupts numerous biological processes, including energy production in the mitochondria, yet fish Poecilia mexicana species complex have independently evolved tolerance several times. Despite clear evidence for convergence at phenotypic level these fishes, it unclear if repeated evolution of hydrogen result similar genomic changes. To address this gap, we used targeted capture approach to sequence genes associated with processes and toxicity from five sulfidic nonsulfidic populations complex. By comparing variation candidate reference set, identified population structure differentiation, suggesting patterns most are due demographic history not selection. But presence tree discordance subset suggests loci evolving divergently between ecotypes. We two differentiation outlier detoxification mitochondria signatures selection all populations. Further investigation into regions long, shared haplotypes among Together, results reveal on standing genetic putatively adaptive may be driving

Language: Английский

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Genetic basis of speciation and adaptation: from loci to causative mutations

Philosophical Transactions of the Royal Society B Biological Sciences, Journal Year: 2022, Volume and Issue: 377(1855)

Published: May 30, 2022

Does evolution proceed in small steps or large leaps? How repeatable is evolution? constrained the evolutionary process? Answering these long-standing questions biology indispensable for both understanding how extant biodiversity has evolved and predicting organisms ecosystems will respond to changing environments future. Understanding genetic basis of phenotypic diversification speciation natural populations key properly answering questions. The leap forward genome sequencing technologies made it increasingly easier not only investigate architecture but also identify variant sites underlying adaptation populations. Furthermore, recent advances editing are making possible functions each candidate gene from In this article, we discuss technological enable analysis causative genes mutations such can help answer This article part theme issue ‘Genetic speciation: loci mutations’.

Language: Английский

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Ancient dolphin genomes reveal rapid repeated adaptation to coastal waters

Nature Communications, Journal Year: 2023, Volume and Issue: 14(1)

Published: July 18, 2023

Abstract Parallel evolution provides strong evidence of adaptation by natural selection due to local environmental variation. Yet, the chronology, and mode process parallel remains debated. Here, we harness temporal resolution paleogenomics address these long-standing questions, comparing genomes originating from mid-Holocene (8610-5626 years before present, BP) contemporary pairs coastal-pelagic ecotypes bottlenose dolphin. We find that affinity ancient samples coastal populations increases as age decreases. assess youngest genome (5626 at sites previously inferred be under habitats it contained coastal-associated genotypes. Thus, variants rose detectable frequencies close emergence habitat. Admixture graph analyses reveal a reticulate evolutionary history between pelagic populations, sharing standing genetic variation facilitated rapid newly emerged habitats.

Language: Английский

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Multiple genomic solutions for local adaptation in two closely related species (sheep and goats) facing the same climatic constraints

Molecular Ecology, Journal Year: 2023, Volume and Issue: 33(20)

Published: Dec. 27, 2023

Abstract The question of how local adaptation takes place remains a fundamental in evolutionary biology. variation allele frequencies genes under selection over environmental gradients mainly theoretical and its empirical assessment would help understanding happens clines. To bring new insights to this issue we set up broad framework which aimed compare the adaptive trajectories clines two domesticated mammal species co‐distributed diversified landscapes. We sequenced genomes 160 sheep 161 goats extensively managed along gradients, including temperature, rainfall, seasonality altitude, identify biological processes shaping adaptation. Allele at putatively loci were rarely found vary gradually but rather displayed discontinuous shift extremities Of 430 candidate identified, only 6 orthologous between those responded differently pressures, suggesting different putative mechanisms involved these closely related species. Interestingly, 2 impacted by environment, signatures most slope rainfall for sheep, summer temperature spring goats. diversity pathways may result from high number functions adaptations multiple eco‐climatic differential role climatic drivers on species, despite their co‐distribution same gradients. This study describes examples clinal alleles with patterns frequency distributions continuous thus showing genetic responses landscapes opening horizons genomics mammalian beyond.

Language: Английский

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Genomic evidence for contrasting patterns of host‐associated genetic differentiation across shared host‐plant species in leaf‐ and bud‐galling sawflies

Molecular Ecology, Journal Year: 2023, Volume and Issue: 32(7), P. 1791 - 1809

Published: Jan. 10, 2023

Resource specialization and ecological speciation arising through host-associated genetic differentiation (HAD) are frequently invoked as an explanation for the high diversity of plant-feeding insects other organisms with a parasitic lifestyle. While studies have demonstrated numerous examples HAD in insect herbivores, rarity comparative means that we still lack understanding how deterministic is, whether patterns host shifts can be predicted over evolutionary timescales. We applied genome-wide single nucleotide polymorphism mitochondrial DNA sequence data obtained genome resequencing to define species limits compare host-plant use population samples leaf- bud-galling sawflies (Hymenoptera: Tenthredinidae: Nematinae) collected from seven shared willow (Salicaceae: Salix) species. To infer repeatability long-term cophylogenetic patterns, also contrasted phylogenies two galler groups each well phylogeny their Salix hosts estimated based on RADseq data. found clear evidence both focal groups, but leaf gallers more specialized compared most bud gallers. In contrast gallers, exhibited statistically significant signal hosts. The observed discordant resource related radiated parallel across base indicate system, suggest short- diversification dominated by stochasticity and/or lineage-specific effects.

Language: Английский

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Potential Contribution of Ancient Introgression to the Evolution of a Derived Reproductive Strategy in Ricefishes

Genome Biology and Evolution, Journal Year: 2023, Volume and Issue: 15(8)

Published: July 26, 2023

Transitions from no parental care to extensive are costly and involve major changes in life history, behavior, morphology. Nevertheless, Sulawesi ricefishes, pelvic brooding evolved transfer two distantly related lineages within the genera Adrianichthys Oryzias, respectively. Females of species carry their eggs attached belly until fry hatches. Despite phylogenetic distance, both share a set external morphological traits. A recent study found direct gene flow between lineages, suggesting independent evolution derived reproductive strategy. Convergent can, however, also rely on repeated sorting preexisting variation an admixed ancestral population, especially when subjected similar selection pressures. We thus used multispecies coalescent model D-statistics identify gene-tree-species-tree incongruencies, evaluate with respect interspecific not only but other ricefish lineages. general network-like as previously reported, we detected Instead, hybridization ancestor Oryzias common Lake Poso area. further signs introgression confidence interval quantitative trait locus associated O. eversi. Our results hint toward contribution ancient standing genetic Oryzias.

Language: Английский

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Core genes driving climate adaptation in plants

Research Square (Research Square), Journal Year: 2023, Volume and Issue: unknown

Published: Nov. 10, 2023

Closely-related species often use the same genes to adapt similar environments^1,2. However, we know little about why such possess increased adaptive potential, and whether this is conserved across deeper evolutionary time. Classic theory suggests a “cost of complexity”: adaptation should occur via affecting fewer traits reduce deleterious side-effects (i.e. lower pleiotropy)³. Adaptation climate presents natural laboratory test theory, as even distantly-related must contend with stresses⁴. Here, re-analyse genomic data from thousands individuals 25 plant identify suite 108 enriched for signatures repeated local climate. This set includes many well-known functions in abiotic stress response, identifying key that repeatedly drive lodgepole pine Arabidopsis (~ 300 My). Using gene co-expression networks quantify each gene’s pleiotropy, find enrichment greater network centrality/interaction strength broader expression tissues higher pleiotropy), contrary ”cost complexity” theory. These may be particularly important helping both wild crop cope future change, representing candidates study.

Language: Английский

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Digest: Repeated body size evolution in island bats

Evolution, Journal Year: 2024, Volume and Issue: 78(7), P. 1349 - 1350

Published: May 8, 2024

Island ecosystems represent outstanding natural laboratories for studying the interplay between ecology and evolution. Lavery et al., (2024) use genomic approaches to identify a remarkable example of repeated evolution in Hipposideros bats across Solomon Islands archipelago. They show that larger-bodied have independently evolved on different islands, highlighting an exciting new system exploring ecological evolutionary drivers mammals.

Language: Английский

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Human-driven evolution of color in a stonefly mimic

Science, Journal Year: 2024, Volume and Issue: 386(6720), P. 453 - 458

Published: Oct. 24, 2024

Rapid adaptation is thought to be critical for the survival of species under global change, but our understanding human-induced evolution in wild remains limited. We show that widespread deforestation has underpinned repeated color shifts insect populations. Specifically, loss forest led changes across lineages mimic warning coloration a toxic stonefly. Predation experiments suggest relative fitness phenotypes varies between forested and deforested habitats. Genomic analyses 1200 specimens selection at

Language: Английский

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