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 103 publications

(141 citation statements)

References 64 publications

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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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“…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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“…The high degree of synteny and collinearity preserved among the Angiosperms can offer insights into the genomic origin(s) of the eccDNA replicon. The eccDNA replicon was aligned to two the closely related species grain amaranth ( Amaranthus hypochondriacus ) and water-hemp ( Amaranthus tuberculatus ), each with a haploid chromosome number (n=16) and pseudochromosome-scale reference assemblies, (Lightfoot et al, 2017; Kreiner et al, 2019). Both comparator genome assemblies have a single copy of the EPSPS gene located near the middle of scaffold 5 (Figure 3).…”

Section: Resultsmentioning

confidence: 99%