Extensive standing genetic variation from a small number of founders enables rapid adaptation in Daphnia

Chaturvedi, Anurag; Zhou, Jian; Raeymaekers, Joost; Czypionka, Thomas; Orsini, Luisa; Jackson, Craig E.; Spanier, Katina I.; Shaw, Joseph R.; Colbourne, John K.; Meester, Luc De

doi:10.1038/s41467-021-24581-z

Cited by 40 publications

(44 citation statements)

References 56 publications

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“…Irregular urchins have elongated arms during the pre-feeding stage and some are known to alter the length of their post-oral arms in response to food after feeding starts e.g. 23 , 34 D. excentricus has demonstrable phenotypic plasticity after feeding starts 23 , 25 and has been previously reported to have the canonical pre-feeding response 24 . The differences between our observations and those of Miner 24 could be due to the different populations tested (Goleta, CA vs Orcas Island, WA) or our ability to detect the small magnitude of change (~ 5% reduction 24 ).…”

Section: Discussionmentioning

confidence: 99%

The evolution of neurosensation provides opportunities and constraints for phenotypic plasticity

Chen

Adams

2022

Sci Rep

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Phenotypic plasticity is widely regarded as important for enabling species resilience to environmental change and for species evolution. However, insight into the complex mechanisms by which phenotypic plasticity evolves in nature is limited by our ability to reconstruct evolutionary histories of plasticity. By using part of the molecular mechanism, we were able to trace the evolution of pre-feeding phenotypic plasticity across the class Echinoidea and identify the origin of plasticity at the base of the regular urchins. The neurosensory foundation for plasticity was ancestral within the echinoids. However, coincident development of the plastic trait and the neurosensory system was not achieved until the regular urchins, likely due to pleiotropic effects and linkages between the two colocalized systems. Plasticity continues to evolve within the urchins with numerous instances of losses associated with loss of sensory abilities and neurons, consistent with a cost of maintaining these capabilities. Thus, evidence was found for the neurosensory system providing opportunities and constraints to the evolution of phenotypic plasticity.

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Section: Discussionmentioning

confidence: 99%

The evolution of neurosensation provides opportunities and constraints for phenotypic plasticity

Chen

Adams

2022

Sci Rep

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“…These characteristics of pollination system increase genetic diversity ( Fattorini and Glover 2020 ) and provide standing variants for soft sweeps. The population size at bottleneck in the Eurasian population was larger than those in East Asian and Xishuangbanna ( Qi et al 2013 ), implying that standing variation enabled the Eurasian population to rapidly adapt the environment ( Chaturvedi et al 2021 ); however, duration of bottleneck in Eurasian was longer than those in East Asian and Xishuangbanna ( Qi et al 2013 ). These hinted that standing variation might contribute little to adaption of the environment and the Eurasian population recovery ( Orr and Unckless 2014 ; Schrider and Kern 2017 ).…”

Section: Discussionmentioning

confidence: 99%

Population-specific, recent positive selection signatures in cultivatedCucumis sativusL. (cucumber)

Lin

Zhang

Song

et al. 2022

G3 Genes|Genomes|Genetics

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Population-specific, positive selection promotes the diversity of populations, and drives local adaptations in the population. However, little is known about population-specific, recent positive selection in the populations of cultivated cucumber (Cucumis sativus L.). Based on a genomic variation map of individuals worldwide, we implemented a Fisher’s combination method by combining four haplotype-based approaches: integrated haplotype score (iHS), number of segregating sites by length (nSL), cross-population extended haplotype homozygosity (XP-EHH), and Rsb. Overall, we detected 331, 2,147, and 3,772 population-specific, recent positive selective sites in the East Asian, Eurasian, and Xishuangbanna populations, respectively. Moreover, we found these sites were related to processes for reproduction, response to abiotic and biotic stress, and regulation of developmental processes, indicating adaptations to their microenvironments. Meanwhile, the selective genes associated with traits of fruits were also observed, such as the gene related to the shorter fruit length in Eurasian and the gene controlling flesh thickness in the Xishuangbanna. In addition, we noticed that soft sweeps were common in the East Asian and Xishuangbanna populations. Genes involved in hard or soft sweeps were related to developmental regulation and abiotic and biotic stress resistance. Our study offers a comprehensive candidate dataset of population-specific, selective signatures in cultivated cucumber populations. Our methods provide guidance for the analysis of population-specific, positive selection. These findings will help explore the biological mechanisms of adaptation and domestication of cucumber.

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“…Mounting empirical evidence suggests that standing genetic variation is the main source of genetic variation for the early phases of adaptation in nature (e.g., Renaut et al 2011; Jones et al 2012; Lescak et al 2015; Haenel et al 2019; Lai et al 2019; Chaturvedi et al 2021; Louis et al 2021; Owens et al 2021; Whiting et al 2021; see also Barrett & Schluter 2008; Messer & Petrov 2012; De Lafontaine et al 2018). Whether and how rapidly a population can adapt to a new ecological challenge therefore depends on how efficiently selection can reshape pre-existing alleles into new optimal combinations.…”

Section: The Adaptive Limitation Hypothesis Of Inversionsmentioning

confidence: 99%

Chromosomal inversions can limit adaptation to new environments

Roesti

Gilbert

Samuk

2022

Preprint

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Chromosomal inversions are often thought to facilitate local adaptation and population divergence because they can link multiple adaptive alleles into non-recombining genomic blocks. Selection should thus be more efficient in driving inversion-linked adaptive alleles to high frequency in a population, particularly in the face of maladaptive gene flow. But, what if ecological conditions and hence selection on inversion-linked alleles change? Reduced recombination within inversions could then constrain the formation of optimal combinations of pre-existing alleles under these new ecological conditions. Here, we outline this idea of inversions limiting adaptation and divergence when ecological conditions change across time or space. We reason that the benefit of inversions for local adaptation and divergence under one set of ecological conditions can come with a concomitant constraint for adaptation to novel sets of ecological conditions. This limitation of inversions to adaptation may also provide one possible explanation for why inversions are often maintained as polymorphisms within species.

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Extensive standing genetic variation from a small number of founders enables rapid adaptation in Daphnia

Cited by 40 publications

References 56 publications

The evolution of neurosensation provides opportunities and constraints for phenotypic plasticity

The evolution of neurosensation provides opportunities and constraints for phenotypic plasticity

Population-specific, recent positive selection signatures in cultivatedCucumis sativusL. (cucumber)

Chromosomal inversions can limit adaptation to new environments

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