Genomic basis of parallel adaptation varies with divergence in Arabidopsis and its relatives

Proceedings of the National Academy of Sciences, Год журнала: 2021, Номер 118(21)

Опубликована: Май 17, 2021

Parallel adaptation provides valuable insight into the predictability of evolutionary change through replicated natural experiments. A steadily increasing number studies have demonstrated genomic parallelism, yet magnitude this parallelism varies depending on whether populations, species, or genera are compared. This led us to hypothesize that scales with genetic divergence between lineages, but is case and underlying processes remain unknown. Here, we resequenced seven parallel lineages two

Язык: Английский

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The role of alternative splicing in adaptation and evolution

Trends in Ecology & Evolution, Год журнала: 2021, Номер 37(4), С. 299 - 308

Опубликована: Дек. 14, 2021

Язык: Английский

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Replicated Evolution in Plants

Annual Review of Plant Biology, Год журнала: 2023, Номер 74(1), С. 697 - 725

Опубликована: Янв. 6, 2023

Similar traits and functions commonly evolve in nature. Here, we explore patterns of replicated evolution across the plant kingdom discuss processes responsible for such patterns. We begin this review by defining theoretical, genetic, ecological concepts that help explain it. then focus our attention on empirical cases at phenotypic genotypic levels. find replication ecotype level is common, but evidence repeated speciation surprisingly sparse. On other hand, strategies physiological mechanisms similar biomes appears to be pervasive. conclude highlighting where future efforts can us bridge understanding different levels biological organization. Earth's landscape diverse also repeats itself. Organisms seem have followed suit.

Язык: Английский

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Understanding natural selection and similarity: Convergent, parallel and repeated evolution

Molecular Ecology, Год журнала: 2023, Номер 32(20), С. 5451 - 5462

Опубликована: Сен. 19, 2023

Parallel and convergent evolution offer some of the most compelling evidence for significance natural selection in evolution, as emergence similar adaptive solutions is unlikely to occur by random chance alone. However, these terms are often employed inconsistently, leading misinterpretation confusion, recently proposed definitions have unintentionally diminished emphasis on solutions. Here, I examine various conceptual frameworks related parallel propose a consolidated framework that enhances our comprehension evolutionary patterns. The primary aim this harmonize concepts together with idea similarity. Both involve result environmental challenges. distinction lies ancestral phenotypes. takes place when phenotypes (before selection) lineages similar. Convergent happens distinct selection). Because an ancestral-based will inevitably lead cases where uncertainty may arise, includes general term, repeated which can be used term applying genotypes well responses pressures. Based argument genetic similarity frequently arise without selection, posits sequences not great interest unless linked actions or origins (mutation, standing variation, gene flow) locations sequences.Os casos de evolução paralela e convergente apresentam-se como provas convincentes da relevância selecção no processo evolutivo, já que é improvável soluções adaptativas semelhantes evoluam apenas por acaso. No entanto, estes dois termos são utilizados frequentemente forma inconsistente definições recentemente propostas diminuíram involuntariamente ênfase na semelhantes. Nesta contribuição, examino os quadros conceptuais relacionadas com proponho um quadro consolidado aumenta compreensão destes padrões evolutivos. O objectivo desta contribuição harmonizar conceitos juntamente similaridade. Ambos implicam resultado pressões evolutivas. A distinção reside nos fenótipos ancestrais: ocorre quando ancestrais (antes selecção) das linhagens eram acontece tinham distintos selecção). Dado uma baseada ancestralidade caracteres levará, inevitavelmente, em incerteza pode surgir, sugiro inclusão termo geral: repetida, ser aplicado à genótipos semelhantes, assim respostas ambientais. Com base argumentação similaridade genética surgir sem selecção, eu postulo similitude sequências genéticas não grande interesse, menos esteja relacionada às ações ou origens (mutação, variação existente, fluxo génico) localizações semelhantes.La evolución y ofrecen algunas las pruebas más contundentes la importancia selección en evolución, ya es improbable emergencia soluciones similares se produzca únicamente casualidad. Sin embargo, estos términos emplean menudo inconsistente, lo lugar interpretaciones erróneas confusión. Además, definiciones recientemente propuestas han restado importancia, involuntariamente, similares. En este artículo, diversos marcos conceptuales con convergente, propongo un marco mejora nuestra comprensión patrones El objetivo principal armonizar los conceptos similitud. implican presiones La distinción radica fenotipos ancestrales: ocurre cuando ancestrales selección) linajes eran produce lijanes tenían selección). una basada ancestralidad conducirá inevitablemente puede incertidumbre distinción, el incluye término general: utilizarse laxo aplicable genotipos similares, así respuestas ambientales. Basándose argumento similitud frecuentemente sin selección, postula secuencias gran interés esté vinculada acciones o orígenes (mutación, variación flujo genético) ubicaciones

Язык: Английский

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Transcriptional activity of transposable elements along an elevational gradient in Arabidopsis arenosa

Mobile DNA, Год журнала: 2021, Номер 12(1)

Опубликована: Фев. 27, 2021

Abstract Background Plant genomes can respond rapidly to environmental changes and transposable elements (TEs) arise as important drivers contributing genome dynamics. Although some were reported be induced by various abiotic or biotic factors, there is a lack of general understanding on how environment influences the activity diversity TEs. Here, we combined common garden experiment with short-read sequencing investigate genomic abundance expression 2245 consensus TE sequences (containing retrotransposons DNA transposons) in an alpine Arabidopsis arenosa . To disentangle trends from local differentiation, leveraged four foothill-alpine population pairs different mountain regions. Seeds each eight populations raised under treatments that differed temperature irradiance, two factors varying elevation. RNA-seq analysis was performed leaves young plants test for effect elevation subsequently irradiance sequences. Results Genomic varied greatly between regions line neutral divergence among regions, representing distinct genetic lineages A. Accounting intraspecific variation abundance, found consistent transcriptomic response across suggesting parallelism expression. In particular retrotransposon LTR Copia (e.g. Ivana Ale clades) Gypsy Athila CRM but also non-LTR LINE transposon TIR MuDR consistently origin. responding specifically belonged same classes well additional clades containing potentially stress-responsive Sire Tar, Reina). Conclusions Our study demonstrated harbours considerable whose varies its native range. Some may contain transcriptionally active natural gradient. This further contribute ultimately provide new regulatory mechanisms face challenges.

Язык: Английский

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Genetic assimilation of ancestral plasticity during parallel adaptation to zinc contamination in Silene uniflora

Nature Ecology & Evolution, Год журнала: 2023, Номер 7(3), С. 414 - 423

Опубликована: Янв. 26, 2023

Abstract Phenotypic plasticity in ancestral populations is hypothesized to facilitate adaptation, but evidence piecemeal and often contradictory. Further, whether increases the probability of parallel adaptive changes has not been explored. The most general finding that responses a new environment are reversed following adaptation (known as reversion). We investigated contribution evolution gene expression two independently evolved lineages zinc-tolerant Silene uniflora . found pattern reversion driven by absence widespread stress response zinc-adapted plants compared with zinc-sensitive plants. show moves closer optimum value influences among genes likely be involved chance recruited repeatedly during adaptation. However, despite convergence levels between adapted lineages, does influence how similar values become. Surprisingly, we also observed fitness becomes genetically determined fixed, is, assimilated. These results emphasize important role

Язык: Английский

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Repeated colonisation of alpine habitats by Arabidopsis arenosa involved parallel adjustments of leaf cuticle traits

New Phytologist, Год журнала: 2025, Номер unknown

Опубликована: Март 17, 2025

Summary Cuticle function can be pivotal to plant success in different environments. Yet, the occurrence of intraspecific adjustments cuticle traits resulting from acclimation or adaptation habitats remains poorly understood. Here, we used genetically well‐characterised populations Arabidopsis arenosa investigate whether were adjusted as part parallel evolution a foothill an alpine ecotype. Six and six populations, representing at least three independent evolutionary origins ecotype, reciprocal transplantation experiments, eco‐physiological, biochemical structural levels. The genetic basis behind these was assessed by combining selection scans differential gene expression analysis. Overall, showed reduced cuticular transpiration conjunction with consistently altered wax composition, higher accumulation two fatty alcohols iso‐alkanes. Genomic analysis unravelled nine genes associated metabolism showing allelic differentiation compared lowland populations. In silico revealed differences between ecotypes for several related metabolism. Repeated ecotypic together architecture ecotype points adaptive value colonisation habitats.

Язык: Английский

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The importance of considering the evolutionary history of polyploids when assessing climatic niche evolution

Journal of Biogeography, Год журнала: 2022, Номер 50(1), С. 86 - 100

Опубликована: Окт. 10, 2022

Abstract Aim Although whole‐genome duplication (WGD) is an important speciation force, we still lack a consensus on the role of niche differentiation in polyploid evolution. In addition, genome doubling per se vs. later divergence evolution remains obscure. One reason for this might be that intraspecific genetic structure complexes and interploidy gene flow often neglected ecological studies. Here, aim to investigate which extent these evolutionary processes impact our inference autopolyploids. Location Europe. Taxon Arabidopsis arenosa (Brassicaceae). Methods Leveraging total 352 cytotyped populations diploid‐autotetraploid A. , examined differences among climatic niches diploid tetraploid lineages both globally, independently each lineage with respect its closest relative. Then, tested whether there was effect additional introgression from other sympatric but ancestrally divergent tetraploids. Results Ecological shift tetraploids only detected when assignment considered. We found different patterns (i.e. conservatism, contraction or expansion) compared relatives. observed ruderal . Main conclusions The not driven by WGD rather reflects dynamic post‐WGD species, involving migration out their ancestral area lineages. Our study supports following WGD—which usually remain undetected studies neglecting history polyploids—may play key adaptation polyploids challenging environments.

Язык: Английский

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Environmental response in gene expression and DNA methylation reveals factors influencing the adaptive potential of Arabidopsis lyrata

eLife, Год журнала: 2022, Номер 11

Опубликована: Окт. 28, 2022

Understanding what factors influence plastic and genetic variation is valuable for predicting how organisms respond to changes in the selective environment. Here, using gene expression DNA methylation as molecular phenotypes, we study environmentally induced among Arabidopsis lyrata plants grown at lowland alpine field sites. Our results show that highly plastic, many more genes are differentially expressed between sites than populations. These responsive evolve under strong constraint – strength of purifying selection on coding sequence high, while rate adaptive evolution low. We find, however, positive cis-regulatory variants has likely contributed maintenance genetically variable environmental responses, but such segregate only distantly related In contrast expression, genic regions largely insensitive environment, not associated with differential expression. Besides genes, detect effects transposable elements (TEs): TEs high-altitude site have higher levels, suggestive a broad-scale TE activation. Compared population, native environment harbor an excess recent insertions, observe specific families enriched within genes. findings provide insight into forces shaping variation. also highlight responses can rapidly create novel heritable stressful conditions.

Язык: Английский

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Repeated colonization of alpine habitats by Arabidopsis arenosa viewed through freezing resistance and ice management strategies

Plant Biology, Год журнала: 2022, Номер 24(6), С. 939 - 949

Опубликована: Июль 14, 2022

Success or failure of plants to cope with freezing temperatures can critically influence plant distribution and adaptation new habitats. Especially in alpine environments, frost is a likely major selective force driving adaptation. In Arabidopsis arenosa (L.) Lawalrée, populations have evolved independently different mountain ranges, enabling studying mechanisms acclimation environments. We tested for heritable, parallel differentiation resistance, cold potential ice management strategies using eight foothill populations. Plants from three European ranges (Niedere Tauern, Făgăraș Tatra Mountains) were grown seeds tetraploid four common gardens, together diploid the Mountains. Freezing resistance was assessed controlled treatments measuring effective quantum yield photosystem II, by infrared video thermography cryomicroscopy. The ecotype had higher than ecotype, whereby this more pronounced However, no ecotypic found one region (Făgăraș), where ancient lineage evolutionary history. Upon freezing, an lens within lacuna between palisade spongy parenchyma tissues formed separation leaf tissues, mechanism not previously reported herbaceous species. dynamic adjustment temperature conditions may be particularly important environments characterized large fluctuations. Furthermore, formation extracellular useful strategy avoid tissue damage during freezing.

Язык: Английский

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