Unraveling coevolutionary dynamics using ecological genomics

Cornille, Amandine; Ebert, Dieter; Stukenbrock, Eva H.; Vega, Ricardo C. Rodrí­guez de la; Tiffin, Peter; Croll, Daniel; Tellier, Aurélien

doi:10.1016/j.tig.2022.05.008

Cited by 4 publications

(5 citation statements)

References 86 publications

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“…In addition, adaptation to different abiotic environmental conditions independent of the host plant such as fluctuations in humidity or temperature could have played role. Environmental heterogeneity including both biotic and abiotic factors, reduced levels of gene flow and selection varying in space can drive coevolutionary dynamics (Amandine et al., 2022). At the local scale, such selection regimes can generate locally adapted populations (Croll & McDonald, 2016; Gandon & Nuismer, 2009; Laine, 2005).…”

Section: Discussionmentioning

confidence: 99%

“…Given the joint effects of biotic (e.g. host genotype) and abiotic factors driving selection across a pathogen species range, disentangling coevolutionary dynamics is challenging (Amandine et al., 2022). Understanding whether coevolution between a pathogen with its host is driven by arms race or trench warfare dynamics would require first ascertaining whether a particular locus is indeed selected due to host–pathogen interactions.…”

Section: Discussionmentioning

confidence: 99%

“…This could be the result of selection in the past, neutral genetic processes or stochastic events. The findings of both unique and shared regions under selection across populations may also be explained by asynchronous coevolutionary cycles with different populations being at different stages (Amandine et al., 2022). Complex signatures of selection regimes underscore the multidimensional nature of the coevolutionary process and were called ‘the geographic mosaic of coevolution’ by Thompson (2005).…”

Section: Discussionmentioning

confidence: 99%

“…Additionally, the relative strength of selection versus stochastic processes such as genetic drift largely depends on the N e of a given population (Charlesworth, 2009). To improve our understanding of antagonistic coevolutionary dynamics in spatially and genetically complex biological systems, analyses should cover multiple populations and closely related species to assess demographic processes simultaneously (Amandine et al., 2022).…”

Section: Introductionmentioning

confidence: 99%

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Two‐speed genomes of Epichloe fungal pathogens show contrasting signatures of selection between species and across populations

Treindl,

Stapley,

Croll

et al. 2023

Molecular Ecology

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Antagonistic selection between pathogens and their hosts can drive rapid evolutionary change and leave distinct molecular footprints of past and ongoing selection in the genomes of the interacting species. Despite an increasing availability of tools able to identify signatures of selection, the genetic mechanisms underlying coevolutionary interactions and the specific genes involved are still poorly understood, especially in heterogeneous natural environments. We searched the genomes of two species of Epichloe plant pathogen for evidence of recent selection. The Epichloe genus includes highly host‐specific species that can sterilize their grass hosts. We performed selection scans using genome‐wide SNP data from seven natural populations of two co‐occurring Epichloe sibling species specialized on different hosts. We found evidence of recent (and ongoing) selective sweeps across the genome in both species. However, selective sweeps were more abundant in the species with a larger effective population size. Sweep regions often overlapped with highly polymorphic AT‐rich regions supporting the role of these genome compartments in adaptive evolution. Although most loci under selection were specific to individual populations, we could also identify several candidate genes targeted by selection in sweep regions shared among populations. The genes encoded small secreted proteins typical of fungal effectors and cell wall‐degrading enzymes. By investigating the genomic signatures of selection across multiple populations and species, this study contributes to our understanding of complex adaptive processes in natural plant pathogen systems.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Two‐speed genomes of Epichloe fungal pathogens show contrasting signatures of selection between species and across populations

Treindl,

Stapley,

Croll

et al. 2023

Molecular Ecology

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“…Logically, this process can be expected to trigger coevolutionary dynamics. The research challenge that remains is to evaluate whether coevolutionary dynamics are a common force maintaining polymorphism and diversity in populations and communities where interference competition is frequent [ 3 , 13 ].…”

Section: Introductionmentioning

confidence: 99%

The evolutionary ecology of fungal killer phenotypes

2023

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Ecological interactions influence evolutionary dynamics by selecting upon fitness variation within species. Antagonistic interactions often promote genetic and species diversity, despite the inherently suppressive effect they can have on the species experiencing them. A central aim of evolutionary ecology is to understand how diversity is maintained in systems experiencing antagonism. In this review, we address how certain single-celled and dimorphic fungi have evolved allelopathic killer phenotypes that engage in antagonistic interactions. We discuss the evolutionary pathways to the production of lethal toxins, the functions of killer phenotypes and the consequences of competition for toxin producers, their competitors and toxin-encoding endosymbionts. Killer phenotypes are powerful models because many appear to have evolved independently, enabling across-phylogeny comparisons of the origins, functions and consequences of allelopathic antagonism. Killer phenotypes can eliminate host competitors and influence evolutionary dynamics, yet the evolutionary ecology of killer phenotypes remains largely unknown. We discuss what is known and what remains to be ascertained about killer phenotype ecology and evolution, while bringing their model system properties to the reader's attention.

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Toward Ecologically Relevant Genetics of Interactions Between Host Plants and Plant Growth‐Promoting Bacteria

Duflos,

Vailleau,

Roux

2024

Advanced Genetics

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The social movement to reduce reliance on pesticides and synthesized fertilizers and the growing global demand for sustainable food supplies require the development of eco‐friendly and sustainable agricultural practices. In line, plant growth‐promoting bacteria (PGPB) can participate in creating innovative agroecological systems. While the effectiveness of PGPB is highly influenced by abiotic conditions and microbe–microbe interactions, beneficial plant–PGPB interactions can also highly depend on both host and PGPB genotype. Here, the state of the art on the extent of natural genetic variation of plant–PGPB interactions and the underlying genetic architecture, in particular in Arabidopsis thaliana is reviewed. Extensive natural plant genetic variation in response to PGPB is associated with a polygenic architecture and genetic pathways rarely mentioned as being involved in the response to PGPB. To date, natural genetic variation within PGPB is little explored, which may in turn allow the identification of new genetic pathways underlying benefits to plants. Accordingly, several avenues to better understand the genomic and molecular landscape of plant–PGPB interactions are introduced. Finally, the need for establishing thorough functional studies of candidate genes underlying Quantitative Trait Loci and estimating the extent of genotype‐by‐genotype‐by‐environment interactions within the context of realistic (agro‐)ecological conditions is advocated.

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Unraveling coevolutionary dynamics using ecological genomics

Cited by 4 publications

References 86 publications

Two‐speed genomes of Epichloe fungal pathogens show contrasting signatures of selection between species and across populations

Two‐speed genomes of Epichloe fungal pathogens show contrasting signatures of selection between species and across populations

The evolutionary ecology of fungal killer phenotypes

Toward Ecologically Relevant Genetics of Interactions Between Host Plants and Plant Growth‐Promoting Bacteria

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