Parallel reduction in flowering time from de novo mutations enable evolutionary rescue in colonizing lineages

Fulgione, Andrea; Neto, Célia; Elfarargi, Ahmed F; Tergemina, Emmanuel; Ansari, Shifa; Göktay, Mehmet; Dinis, Herculano; Döring, Nina; Flood, Pádraic J.; Rodriguez-Pacheco, Sofia; Walden, Nora; Koch, Marcus A.; Roux, Fabrice; Hermisson, Joachim; Hancock, Angela M.

doi:10.1038/s41467-022-28800-z

Cited by 36 publications

(83 citation statements)

References 125 publications

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“…The genomic location of NRAMP1 may contribute to the high TD rate in the region as this gene is located in the subtelomeric region (~50 kb from the telomere), where recombination rate and thus the probability of TD events may be increased ( 29 ). However, we found no TDs in or around NRAMP1 in Santo Antão accessions ( 15 ) and very little evidence in previously sequenced worldwide A. thaliana genomes ( 25 – 28 ). Only two accessions harbored any evidence for TDs in the region, and only one of these (in Oua-0) shows what appears to be an intact TD containing the entire NRAMP1 coding sequence (fig.…”

Section: Resultscontrasting

confidence: 86%

“…Overall, we found unexpectedly little evidence for hard selective sweeps across the genome ( Fig. 6A ), especially given the large proportion of variants inferred to be fixed by selection during the initial phase after colonization ( 15 ). This discrepancy may be due to the relatively short time a hard sweep signal is expected to persist in a population after fixation ( 15 , 36 ).…”

Section: Resultsmentioning

confidence: 82%

“…To reconstruct the emergence and evolutionary dynamics of IRT1 130X and the NRAMP1 TDs in Fogo, it is first necessary to understand the genome-wide demographic history of Arabidopsis in Fogo. Previously, we showed that Fogo was colonized from Santo Antão through a strong bottleneck that removed nearly all genetic variation, and that the Fogo population remained constrained in size and panmictic for ~900 years ( 15 ). Here, we examined relationships between subpopulations within Fogo.…”

Section: Resultsmentioning

confidence: 99%

“…Arabidopsis colonized Fogo ~3 to 5 ka from Santo Antão, an island ~250 km to the north ( Fig. 1A ) ( 15 ). Fogo and Santo Antão are both volcanic islands in the Cape Verde archipelago, but the two islands have different pedogenic histories.…”

Section: Introductionmentioning

confidence: 99%

“…While Fogo is an active stratovolcano, which experienced several eruptions over the past few thousand years, including the most recent in 2015, the last eruption on Santo Antão was much more ancient (~90 ka) ( 16 ). Today, the two island populations are genetically distinct from one another and from the continental populations due to severe colonization bottlenecks, which eliminated 99.4% of all shared variation, resulting in a phylogenetic speciation event ( 15 ).…”

Section: Introductionmentioning

confidence: 99%

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A two-step adaptive walk rewires nutrient transport in a challenging edaphic environment

et al. 2022

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Most well-characterized cases of adaptation involve single genetic loci. Theory suggests that multilocus adaptive walks should be common, but these are challenging to identify in natural populations. Here, we combine trait mapping with population genetic modeling to show that a two-step process rewired nutrient homeostasis in a population of Arabidopsis as it colonized the base of an active stratovolcano characterized by extremely low soil manganese (Mn). First, a variant that disrupted the primary iron (Fe) uptake transporter gene ( IRT1 ) swept quickly to fixation in a hard selective sweep, increasing Mn but limiting Fe in the leaves. Second, multiple independent tandem duplications occurred at NRAMP1 and together rose to near fixation in the island population, compensating the loss of IRT1 by improving Fe homeostasis. This study provides a clear case of a multilocus adaptive walk and reveals how genetic variants reshaped a phenotype and spread over space and time.

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Section: Resultscontrasting

confidence: 86%

Section: Resultsmentioning

confidence: 82%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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A two-step adaptive walk rewires nutrient transport in a challenging edaphic environment

et al. 2022

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Multivariate selection and the making and breaking of mutational pleiotropy

Svensson

2022

Evol Ecol

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The role of mutations have been subject to many controversies since the formation of the Modern Synthesis of evolution in the early 1940ties. Geneticists in the early half of the twentieth century tended to view mutations as a limiting factor in evolutionary change. In contrast, natural selection was largely viewed as a “sieve” whose main role was to sort out the unfit but which could not create anything novel alone. This view gradually changed with the development of mathematical population genetics theory, increased appreciation of standing genetic variation and the discovery of more complex forms of selection, including balancing selection. Short-term evolutionary responses to selection are mainly influenced by standing genetic variation, and are predictable to some degree using information about the genetic variance–covariance matrix (G) and the strength and form of selection (e. g. the vector of selection gradients, β). However, predicting long-term evolution is more challenging, and requires information about the nature and supply of novel mutations, summarized by the mutational variance–covariance matrix (M). Recently, there has been increased attention to the role of mutations in general and M in particular. Some evolutionary biologists argue that evolution is largely mutation-driven and claim that mutation bias frequently results in mutation-biased adaptation. Strong similarities between G and M have also raised questions about the non-randomness of mutations. Moreover, novel mutations are typically not isotropic in their phenotypic effects and mutational pleiotropy is common. Here I discuss the evolutionary origin and consequences of mutational pleiotropy and how multivariate selection directly shapes G and indirectly M through changed epistatic relationships. I illustrate these ideas by reviewing recent literature and models about correlational selection, evolution of G and M, sexual selection and the fitness consequences of sexual antagonism.

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