Multiple modes of convergent adaptation in the spread of glyphosate-resistant
            <i>Amaranthus tuberculatus</i>

Kreiner, Julia M.; Giacomini, Darci A.; Bemm, Felix; Waithaka, Bridgit; Regalado, Julián; Lanz, Christa; Hildebrandt, Julia; Sikkema, Peter H.; Tranel, Patrick J.; Weigel, Detlef; Stinchcombe, John R.; Wright, Stephen I.

doi:10.1073/pnas.1900870116

Cited by 111 publications

(150 citation statements)

References 64 publications

(89 reference statements)

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“…Evolutionary rescue has been explored theoretically (e.g., Gomulkiewicz and Holt, 1995;Uecker and Hermisson, 2016;Anciaux et al, 2018) and observed repeatedly in both experiments (e.g., Bell and Gonzalez, 2009;Lindsey et al, 2013;Ramsayer et al, 2013) and in host-pathogen systems in nature (e.,g., Wei et al, 1995;Feder et al, 2016). More recently, a number of studies have used genetic data to suggest that evolutionary rescue has occurred in the wild, including crickets becoming song-less to avoid parasitoid flies (Pascoal et al, 2018, reviewed in McDermott, 2019, killifish deleting receptors to tolerate pollution (Oziolor et al, 2019), hares moulting brown instead of white to avoid predation in snowless winters (Jones et al, 2018), bats altering hibernation to survive white-nose syndrome (Gignoux-Wolfsohn et al, 2018), and tall waterhemp evolving herbicide resistance (Kreiner et al, 2019). In nearly all of these cases there is strong evidence of a recent selective sweep by a very beneficial allele.…”

Section: Discussionmentioning

confidence: 99%

Genetic signatures of evolutionary rescue by a selective sweep

Osmond

Coop

2019

Preprint

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AbstractOne of the most useful models in population genetics is that of a selective sweep and the consequent hitch-hiking of linked neutral alleles. While variations on this model typically assume constant population size, many instances of strong selection and rapid adaptation in nature may co-occur with complex demography. Here we extend the hitch-hiking model to evolutionary rescue, where adaptation and demography not only co-occur but are intimately entwined. Our results show how this feedback between demography and evolution determines – and restricts – the genetic signatures of evolutionary rescue, and how these differ from the signatures of sweeps in populations of constant size. In particular, we find rescue to harden sweeps from standing variance or new mutation (but not from migration), reduce genetic diversity both at the selected site and genome-wide, and increase the range of observed Tajima’s D values. For a given initial rate of population decline, the feedback between demography and evolution makes all of these differences more dramatic under weaker selection, where bottlenecks are prolonged. Nevertheless, it is likely difficult to infer the co-incident timing of the sweep and bottleneck from these simple signatures, never-mind a feedback between them. Temporal samples spanning contemporary rescue events may offer one way forward.

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Section: Discussionmentioning

confidence: 99%

Genetic signatures of evolutionary rescue by a selective sweep

Osmond

Coop

2019

Preprint

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“…Short-read, shotgun sequence data at a depth of~10X were generated from 23 male and 19 female A. tuberculatus plants from Illinois as part of an ecological study to better understand A. tuberculatus population structure (Kreiner et al 2018). The sequence reads produced by this protocol were 150-bp pairedend reads with an approximate insert length of 300 bp.…”

Section: In Silico Marker Testingmentioning

confidence: 99%

Sex-specific markers for waterhemp (Amaranthus tuberculatus) and Palmer amaranth (Amaranthus palmeri)

et al. 2019

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Waterhemp [Amaranthus tuberculatus (Moq.) J. D. Sauer] and Palmer amaranth (Amaranthus palmeri S. Watson) are troublesome weeds of row-crop production in the United States. Their dioecious reproductive systems ensure outcrossing, facilitating rapid evolution and distribution of resistances to multiple herbicides. Little is known, however, about the genetic basis of dioecy in Amaranthus species. In this work, we use restriction site-associated DNA sequencing (RAD-Seq) to investigate the genetic basis of sex determination in A. tuberculatus and A. palmeri. For each species, approximately 200 plants of each sex were sampled and used to create RAD-Seq libraries. The resulting libraries were separately bar-coded and then pooled for sequencing with the Illumina platform, yielding millions of 64-bp reads. These reads were analyzed to identify sex-specific and sex-biased sequences. We identified 345 male-specific sequences from the A. palmeri data set and 2,754 male-specific sequences in A. tuberculatus. An unexpected 723 female-specific sequences were identified in a subset of the A. tuberculatus females; subsequent research, however, indicated female specificity of these markers was limited to the population from which they were identified. Primer sets designed to specifically amplify male-specific sequences were tested for accuracy on multiple, geographically distinct populations of A. tuberculatus and A. palmeri, as well as other Amaranthus species. Two primer sets for A. palmeri and four primer sets for A. tuberculatus were each able to distinguish between male and female plants with at least 95% accuracy. In the near term, sex-specific markers will be useful to the A. tuberculatus and A. palmeri research communities (e.g., to predict sex for crossing experiments). In the long-term, this research will provide the foundational tools for detailed investigations into the molecular biology and evolution of dioecy in weedy Amaranthus species.

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“…Scott.) and Eleusine indica (L.) Gaertn . The next steps for the consortia will be to not only produce genomes for the identified priority weed species but to revisit and improve the genomes of weed species whose initial drafts were produced with earlier generation sequencing technology, are fragmented, are incomplete or are not presented as chromosome‐scale scaffolds.…”

Section: Introductionmentioning

confidence: 99%

A chromosome‐scale draft sequence of the Canada fleabane genome

Laforest

Martin

Bisaillon

et al. 2020

Pest Management Science

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Background: Due to the accessibility of underlying technologies the 'Omics', in particular genomics, are becoming commonplace in several fields of research, including the study of agricultural pests. The weed community is starting to embrace these approaches; genome sequences have been made available in the past years, with several other sequencing projects underway, as promoted by the International Weed Genome Consortium. Chromosome-scale sequences are essential to fully exploit the power of genetics and genomics.Results: We report such an assembly for Conyza canadensis, an important agricultural weed. Third-generation sequencing technology was used to create a genome assembly of 426 megabases, of which nine chromosome-scale scaffolds cover more than 98% of the entire assembled sequence. As this weed was the first to be identified with glyphosate resistance, and since we do not have a firm handle on the genetic mechanisms responsible for several herbicide resistances in the species, the genome sequence was annotated with genes known to be associated with herbicide resistance. A high number of ABC-type transporters, cytochrome P450 and glycosyltransferases (159, 352 and 181, respectively) were identified among the list of ab initio predicted genes.Conclusion: As C. canadensis has a small genome that is syntenic with other Asteraceaes, has a short life cycle and is relatively easy to cross, it has the potential to become a model weed species and, with the chromosome-scale genome sequence, contribute to a paradigm shift in the way non-target site resistance is studied.

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Multiple modes of convergent adaptation in the spread of glyphosate-resistant Amaranthus tuberculatus

Cited by 111 publications

References 64 publications

Genetic signatures of evolutionary rescue by a selective sweep

Genetic signatures of evolutionary rescue by a selective sweep

Sex-specific markers for waterhemp (Amaranthus tuberculatus) and Palmer amaranth (Amaranthus palmeri)

A chromosome‐scale draft sequence of the Canada fleabane genome

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