Genomic release-recapture experiment in the wild reveals within-generation polygenic selection in stickleback fish

Laurentino, Telma G.; Moser, Dario; Roesti, Marius; Ammann, Matthias; Frey, Anja; Ronco, Fabrizia; Kueng, Benjamin; Berner, Daniel

doi:10.1038/s41467-020-15657-3

Cited by 26 publications

(26 citation statements)

References 58 publications

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“…g . Crossley et al 2017, Fritz et al 2018, Nosil et al 2018, Weetman et al 2018, Bi et al 2019, Dayan et al 2019, Laurentino et al 2020). Yet their use for studying pest adaptation to agricultural systems has been limited to a few cases (reviewed in Pélissié et al 2018).…”

Section: Discussionmentioning

confidence: 99%

Genome evolution in an agricultural pest following adoption of transgenic crops

Fritz

Hamby

Taylor

et al. 2020

Preprint

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Replacement of synthetic insecticides with transgenic crops for pest management has been both economically and environmentally beneficial. These benefits have often eroded as pests evolved resistance to the transgenic crops, but a broad understanding of the timing and complexity of the adaptive changes which lead to field-evolved resistance in pest species is lacking. Wild populations of Helicoverpa zea, a major lepidopteran crop pest and the target of transgenic Cry toxin-expressing cotton and corn, have recently evolved widespread, damaging levels of resistance. Here, we quantified patterns of genomic change in wild H. zea collected between 2002 and 2017 when adoption rates of Cry-expressing crops expanded in North America. Using a combination of genomic and genotypic approaches, we identified significant temporal changes in allele frequency throughout the genomes of field-collected H. zea. Many of these changes occurred concurrently with increasingly damaging levels of resistance to Cry toxins between 2012 and 2016, in a pattern consistent with polygenic selection. Surprisingly, none of the eleven previously described Cry resistance genes showed signatures of selection in wild H. zea. Furthermore, we observed evidence of a very strong selective sweep in one region of the H. zea genome, yet this strongest change was not additively associated with Cry resistance. This first, whole genome analysis of field-collected specimens to study evolution of Cry resistance demonstrates the potential and need for a more holistic approach to examining pest adaptation to changing agricultural practices.

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Section: Discussionmentioning

confidence: 99%

Genome evolution in an agricultural pest following adoption of transgenic crops

Fritz

Hamby

Taylor

et al. 2020

Preprint

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“…In the few cases where reproductive isolation has been demonstrated, it can result either as a by-product of divergent adaptation to different habitats or ecological niches that lead to assortative mating preferences (Rundle et al, 2000;Boughman, 2001), or from ecological selection that puts hybrids at a fitness disadvantage and may lead to reinforcement (Rundle and Schluter, 1998;Lackey and Boughman, 2017). Previous work on crosses of sympatric benthic and limnetic stickleback demonstrated that hybrids are not at any intrinsic disadvantage, but they may perform worse than either of the parental types in the parental niche (Schluter, 1994(Schluter, , 1995(Schluter, , 2003Schluter et al, 1996;Hatfield and Schluter, 1999;Vamosi et al, 2000;Jones et al, 2006;Gow et al, 2007;Arnegard et al, 2014;Laurentino et al, 2020). This opens the possibility that hybrids could invade novel (non-parental) niches if the opportunity arises.…”

Section: How Stickleback Diversifymentioning

confidence: 99%

Threespine Stickleback in Lake Constance: The Ecology and Genomic Substrate of a Recent Invasion

et al. 2021

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Invasive species can be powerful models for studying contemporary evolution in natural environments. As invading organisms often encounter new habitats during colonization, they will experience novel selection pressures. Threespine stickleback (Gasterosteus aculeatus complex) have recently colonized large parts of Switzerland and are invasive in Lake Constance. Introduced to several watersheds roughly 150 years ago, they spread across the Swiss Plateau (400–800 m a.s.l.), bringing three divergent hitherto allopatric lineages into secondary contact. As stickleback have colonized a variety of different habitat types during this recent range expansion, the Swiss system is a useful model for studying contemporary evolution with and without secondary contact. For example, in the Lake Constance region there has been rapid phenotypic and genetic divergence between a lake population and some stream populations. There is considerable phenotypic variation within the lake population, with individuals foraging in and occupying littoral, offshore pelagic, and profundal waters, the latter of which is a very unusual habitat for stickleback. Furthermore, adults from the lake population can reach up to three times the size of adults from the surrounding stream populations, and are large by comparison to populations globally. Here, we review the historical origins of the threespine stickleback in Switzerland, and the ecomorphological variation and genomic basis of its invasion in Lake Constance. We also outline the potential ecological impacts of this invasion, and highlight the interest for contemporary evolution studies.

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“…Compared with our database, finding out growth-related functional annotation and molecular mechanisms are both shared in the GH/IGF axis and its downstream signaling pathways. However, these studies have focused on gene function and its integrated signal pathways; by contrast, transcripts identified using a transcriptome profile may influence target traits through various genes [ 84 , 85 , 86 ].…”

Section: Discussionmentioning

confidence: 99%

Development of EST-Molecular Markers from RNA Sequencing for Genetic Management and Identification of Growth Traits in Potato Grouper (Epinephelus tukula)

Hsu

Chiu

Lee

et al. 2021

Biology

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The accuracy and efficiency of marker-assisted selection (MAS) has been proven for economically critical aquaculture species. The potato grouper (Epinephelus tukula), a novel cultured grouper species in Taiwan, shows large potential in aquaculture because of its fast growth rate among other groupers. Because of the lack of genetic information for the potato grouper, the first transcriptome and expressed sequence tag (EST)-derived simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers were developed. Initially, the transcriptome was obtained from seven cDNA libraries by using the Illumina platform. De novo transcriptome of the potato grouper yielded 51.34 Gb and 111,490 unigenes. The EST-derived SSR and SNP markers were applied in genetic management, in parentage analysis, and to discover the functional markers of economic traits. The F1 juveniles were identified as siblings from one pair of parents (80 broodstocks). Fast- and slow-growth individuals were analyzed using functional molecular markers and through their association with growth performance. The results revealed that two SNPs were correlated with growth traits. The transcriptome database obtained in this study and its derived SSR and SNP markers may be applied not only for MAS but also to maintain functional gene diversity in the novel cultured grouper.

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Genomic release-recapture experiment in the wild reveals within-generation polygenic selection in stickleback fish

Cited by 26 publications

References 58 publications

Genome evolution in an agricultural pest following adoption of transgenic crops

Genome evolution in an agricultural pest following adoption of transgenic crops

Threespine Stickleback in Lake Constance: The Ecology and Genomic Substrate of a Recent Invasion

Development of EST-Molecular Markers from RNA Sequencing for Genetic Management and Identification of Growth Traits in Potato Grouper (Epinephelus tukula)

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