Direct estimation of the spontaneous mutation rate by short-term mutation accumulation lines in<i>Chironomus riparius</i>

Oppold, Ann-Marie; Pfenninger, Markus

doi:10.1002/evl3.8

Cited by 64 publications

(94 citation statements)

References 35 publications

(51 reference statements)

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“…From the remaining twelve candidate mutations, we confirmed ten and identified two false-positives ( Figure S2 and Table S3). This results in falsepositive rate of 16.7%, which is similar to previously reported rates in other insects (Keightley et al 2014(Keightley et al , 2015Oppold and Pfenninger 2017). With correction for the false positive rate, we estimate the mutation rate per site per haploid genome per generation as 43/(2468379192*2*27)*0.833 = 2.7x10 -10 (95% CI 1.9x10 -10 -3.5x10 -10 ).…”

Section: Low Spontaneous Mutation Rate In Pea Aphidssupporting

confidence: 80%

Low spontaneous mutation rate and Pleistocene radiation of pea aphids

Fazalova

Nevado

2019

Preprint

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Accurate estimates of divergence times are essential to understand the evolutionary history of species. It allows linking evolutionary histories of the diverging lineages with past geological, climatic and other changes in environment and shed light on the processes involved in speciation.The pea aphid radiation includes multiple host races adapted to different legume host plants. It is thought that diversification in this system occurred very recently, over the past 8,000 to 16,000 years. This young age estimate was used to link diversification in pea aphids to the onset of human agriculture, and lead to the establishment of the pea aphid radiation as a model system in the study of speciation with gene flow. Here, we re-examine the age of the pea aphid radiation, by combining a mutation accumulation experiment with a genome-wide estimate of divergence between distantly related pea aphid host races. We estimate the spontaneous mutation rate for pea aphids as 2 . 2 7 ൈ 1 0 ି ଵ per haploid genome per parthenogenic generation. Using this estimate of mutation rate and the genome-wide genetic differentiation observed between pea aphid host races, we show that the pea aphid radiation is much more ancient than assumed previously, predating Neolithic agriculture by several hundreds of thousands of years. Our results rule out human agriculture as the driver of diversification of the pea aphid radiation, and call for re-assessment of the role of allopatric isolation during Pleistocene climatic oscillations in divergence of the pea aphid complex.

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Section: Low Spontaneous Mutation Rate In Pea Aphidssupporting

confidence: 80%

Low spontaneous mutation rate and Pleistocene radiation of pea aphids

Fazalova

Nevado

2019

Preprint

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“…Individual resequencing data were mapped with bwa mem (-M -R $individual-read-group) and processed following the GATK best-practice pipeline (McKenna et al, 2010). The detailed pipeline with applied modifications is described in Oppold and Pfenninger (2017).…”

Section: Inference Of Demographic Population History With Individuamentioning

confidence: 99%

“…Oppold & Pfenninger, 2017), we parameterized several species-specific population genetic models to simulate the actual drift expectation in terms of F ST distributions (Supporting information 5). Despite our substantial effort to obtain realistic empirical parameter estimates and therewith model neutral divergence among the populations, all applied models failed to reproduce the empirical F ST distribution.…”

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confidence: 99%

The genomic footprint of climate adaptation in Chironomus riparius

et al. 2018

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The gradual heterogeneity of climatic factors poses varying selection pressures across geographic distances that leave signatures of clinal variation in the genome. Separating signatures of clinal adaptation from signatures of other evolutionary forces, such as demographic processes, genetic drift and adaptation, to nonclinal conditions of the immediate local environment is a major challenge. Here, we examine climate adaptation in five natural populations of the harlequin fly Chironomus riparius sampled along a climatic gradient across Europe. Our study integrates experimental data, individual genome resequencing, Pool-Seq data and population genetic modelling. Common-garden experiments revealed significantly different population growth rates at test temperatures corresponding to the population origin along the climate gradient, suggesting thermal adaptation on the phenotypic level. Based on a population genomic analysis, we derived empirical estimates of historical demography and migration. We used an F outlier approach to infer positive selection across the climate gradient, in combination with an environmental association analysis. In total, we identified 162 candidate genes as genomic basis of climate adaptation. Enriched functions among these candidate genes involved the apoptotic process and molecular response to heat, as well as functions identified in studies of climate adaptation in other insects. Our results show that local climate conditions impose strong selection pressures and lead to genomic adaptation despite strong gene flow. Moreover, these results imply that selection to different climatic conditions seems to converge on a functional level, at least between different insect species.

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“…Wild populations of C. riparius harbors ample genetic variation and have a large effective population size (~10 6 , (Oppold & Pfenninger, 2017)). In addition, the high number of offspring per breeding pair likely render selection processes on quantitative traits very effective (Pfenninger, 2017).…”

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confidence: 99%

Rapid adaptation to high temperatures in Chironomus riparius

Foucault

Wieser

Waldvogel

et al. 2018

Ecology and Evolution

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Effects of seasonal or daily temperature variation on fitness and physiology of ectothermic organisms and their ways to cope with such variations have been widely studied. However, the way multivoltines organisms cope with temperature variations from one generation to the next is still not well understood. The aim of this study was to investigate whether the multivoltine midge Chironomus riparius Meigen (1803) responds mainly via acclimation as predicted by current theories or whether rapid genetic adaptation is involved. To investigate this issue, a common garden approach has been applied. A mix of larvae from five European populations was raised in the laboratory at three different pre‐exposure temperatures (PET): 14, 20, and 26°C. After three and five generations, respectively, larvae were exposed to three treatment temperatures (TT): 14, 20, and 26°C. Mortality was monitored for the first 48 hr and after emergence. After three generations, significant mortality rate differences depended on an interaction of PET and TT. This finding supports the hypothesis that chironomids respond rapidly to climatic variation via adaptive mechanisms and to a lesser extent via phenotypic plasticity. The result of the experiment indicates that three generations were sufficient to adapt to warm temperature, decreasing the mortality rate, highlighting the potential for chironomids to rapidly respond to seasonally changing conditions.

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Direct estimation of the spontaneous mutation rate by short-term mutation accumulation lines inChironomus riparius

Cited by 64 publications

References 35 publications

Low spontaneous mutation rate and Pleistocene radiation of pea aphids

Low spontaneous mutation rate and Pleistocene radiation of pea aphids

The genomic footprint of climate adaptation in Chironomus riparius

Rapid adaptation to high temperatures in Chironomus riparius

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