Selection-driven trait loss in independently evolved cavefish populations

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

Published: May 3, 2023

Abstract Laboratory studies have demonstrated that a single phenotype can be produced by many different genotypes; however, in natural systems, it is frequently found phenotypic convergence due to parallel genetic changes. This suggests substantial role for constraint and determinism evolution indicates certain mutations are more likely contribute evolution. Here we use whole genome resequencing the Mexican tetra, Astyanax mexicanus , investigate how selection has shaped repeated of both trait loss enhancement across independent cavefish lineages. We show on standing variation de novo substantially adaptation. Our findings provide empirical support hypothesis genes with larger mutational targets substrate indicate features cave environment may impact rate at which occur.

Language: Английский

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Integrative analyses of convergent adaptation in sympatric extremophile fishes

Current Biology, Journal Year: 2024, Volume and Issue: 34(21), P. 4968 - 4982.e7

Published: Oct. 11, 2024

Language: Английский

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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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Whole‐Genome Resequencing Reveals Polygenic Signatures of Directional and Balancing Selection on Alternative Migratory Life Histories

Molecular Ecology, Journal Year: 2024, Volume and Issue: 33(23)

Published: Nov. 4, 2024

ABSTRACT Migration in animals and associated adaptations to contrasting environments are underpinned by complex genetic architecture. Here, we explore the genomic basis of facultative anadromy brown trout ( Salmo trutta ), wherein some individuals migrate sea while others remain resident natal rivers, better understand how alternative migratory tactics (AMTs) maintained evolutionarily. To identify variants with AMTs, sequenced whole genomes for 194 individual from five anadromous–resident population pairs, situated above below waterfalls, different Irish rivers. These waterfalls act as natural barriers upstream migration hence predicted that loci underpinning AMTs should be under similar divergent selection across these replicate pairs. A sliding windows based analysis revealed a highly polygenic adaptive divergence between anadromous populations, encompassing 329 differentiated regions. regions were 292 genes involved various processes crucial including energy homeostasis, reproduction, osmoregulation, immunity, circadian rhythm neural function. Furthermore, examining patterns diversity able link specific biological putative AMT trait classes: migratory‐propensity, migratory‐lifestyle residency. Importantly, outlier possessed higher than background genome, particularly group, suggesting balancing may play role maintaining variation. Overall, results this study provide important insights into architecture evolutionary mechanisms shaping within populations.

Language: Английский

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Integrative analyses of convergent adaptation in sympatric extremophile fishes

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2021, Volume and Issue: unknown

Published: June 28, 2021

Summary The evolution of independent lineages along replicated environmental gradients frequently results in convergent adaptation, yet the degree to which convergence is present across multiple levels biological organization often unclear. Additionally, inherent biases associated with shared ancestry and variation selective regimes geographic replicates pose challenges for confidently identifying patterns convergence. We investigated a system three species poeciliid fishes sympatrically occur toxic spring rich hydrogen sulfide (H 2 S) an adjacent nonsulfidic stream examine adaptive organization. found morphological physiological traits genome-wide gene expression among all species. In addition, there were signatures selection on genes encoding H S toxicity targets mitochondrial genomes each However, analyses nuclear revealed neither evidence substantial genomic islands divergence around involved detoxification nor congruence strongly differentiated regions population pairs. These non-convergent, heterogenous may indicate that tolerance highly polygenic, allele frequency shifts at many loci small effects genome. Alternatively, involve genetic redundancy, non-convergent lineage-specific genome underpinning similar changes phenotypes expression. Overall, we demonstrate variability extent organizational highlight linking scales.

Language: Английский

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