Genome-wide scans of selection highlight the impact sof biotic and abiotic constraints in natural populations of the model grass<i>Brachypodium distachyon</i>

Bourgeois, Yann; Stritt, Christoph; Walser, Jean‐Claude; Gordon, Sean P.; Vogel, John P.; Roulin, Anne

doi:10.1101/246090

Cited by 9 publications

(16 citation statements)

References 99 publications

(120 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The fact that genes involved in immunity escaped this trend suggests an important role of biotic constraints in maintaining diversity even in bottlenecked populations. This confirms the resilience of this type of adaptive variation to demographic perturbations (Bourgeois, Stritt, et al, 2018;Oliver & Piertney, 2012).…”

Section: Balancing Selection Maintains Diversity At Immune and Devesupporting

confidence: 78%

“…We followed a procedure similar in spirit to a previous study (Bourgeois, Stritt, et al, 2018). We trained the algorithm using a set of 3,000 coalescent simulations using the discoal simulator (Schrider & Kern, 2016), modelling changes in population sizes inferred from a previous SMC++ analysis ( Figure 1b; Bourgeois, Ruggiero, et al, 2019;Terhorst, Kamm, & Song, 2016; Method S1).…”

Section: Genome Scan Using Diplos/hicmentioning

confidence: 99%

See 1 more Smart Citation

Selection at behavioural, developmental and metabolic genes is associated with the northward expansion of a successful tropical colonizer

Bourgeois

Boissinot

2019

Molecular Ecology

Self Cite

View full text Add to dashboard Cite

What makes a species able to colonize novel environments? This question is key to understand the dynamics of adaptive radiations and ecological niche shifts, but the mechanisms that underlie expansion into novel habitats remain poorly understood at a genomic scale. Lizards from the genus Anolis are typically tropical, and the green anole (Anolis carolinensis) constitutes an exception since it expanded into temperate North America from subtropical Florida. Thus, we used the green anole as a model to investigate signatures of selection associated with colonization of a new environment, namely temperate North America. To this end, we analysed 29 whole‐genome sequences, covering the entire native range of the species. We used a combination of recent methods to quantify both positive and balancing selection in northern populations, including FST outlier methods, machine learning and ancestral recombination graphs. We naively scanned for genes of interest and assessed the overlap between multiple tests. Strikingly, we identified many genes involved in behaviour, suggesting that the recent successful colonization of northern environments may have been linked to behavioural shifts as well as physiological adaptation. Using a candidate genes strategy, we determined that genes involved in response to cold or behaviour displayed more frequently signals of selection, while controlling for local recombination rate, gene clustering and gene length. In addition, we found signatures of balancing selection at immune genes in all investigated genetic groups, but also at genes involved in neuronal and anatomical development.

show abstract

Section: Balancing Selection Maintains Diversity At Immune and Devesupporting

confidence: 78%

Section: Genome Scan Using Diplos/hicmentioning

confidence: 99%

Selection at behavioural, developmental and metabolic genes is associated with the northward expansion of a successful tropical colonizer

Bourgeois

Boissinot

2019

Molecular Ecology

Self Cite

View full text Add to dashboard Cite

show abstract

“…The fact that genes involved in immunity escaped this trend suggests an important role of biotic constraints in maintaining diversity even in bottlenecked populations. This confirms the resilience of this type of adaptive variation to demographic perturbations (Oliver and Piertney 2012; Bourgeois et al 2018b).…”

Section: Discussionsupporting

confidence: 76%

Selection at behavioral, developmental and metabolic genes is associated with the northward expansion of a successful tropical colonizer

Bourgeois

Boissinot

2018

Preprint

Self Cite

View full text Add to dashboard Cite

23What makes a species able to colonize novel environments? This question is key to understand 24 the dynamics of adaptive radiations and ecological niche shifts, but the mechanisms that underlie 25 expansion into novel habitats remain poorly understood at a genomic scale. Lizards from the 26 genus Anolis are typically tropical and the green anole (Anolis carolinensis) constitutes an 27 exception since it expanded into temperate North America from subtropical Florida. Thus, we 28 used the green anole as a model to investigate signatures of selection associated with 29 colonization of a new environment, namely temperate North America. To this end, we analyzed 30 29 whole genome sequences, representing the entire genetic diversity of the species. We used a 31 combination of recent methods to quantify both positive and balancing selection in northern 32 populations, including FST outlier methods, machine learning and ancestral recombination 33graphs. We naively scanned for genes of interest and assessed the overlap between multiple tests.34 Strikingly, we identified many genes involved in behavior, suggesting that the recent successful 35 colonization of northern environments may have been linked to behavioral shifts as well as 36 physiological adaptation. These results were robust to recombination, gene length and clustering. 37

show abstract

“…B. distachyon is a model species for monocotyledons and a close relative of major cereal crops (Brkljacic et al, 2011), so arguably it can be useful to understand adaptations in both cultivated and wild grass species. B. distachyon has an excellent reference genome (The International Brachypodium Consortium, 2010), and importantly, for the work described in the highlighted paper (Bourgeois et al, 2018), there are whole genome sequences available (Gordon et al, 2017) for 44 natural accessions from the Mediterranean region, with 6 million single nucleotide polymorphisms (SNPs). In the highlighted paper, Bourgeois et al (2018) set out to use these Brachypodium datasets to identify genomic regions under positive selection.…”

mentioning

confidence: 99%

“…B. distachyon has an excellent reference genome (The International Brachypodium Consortium, 2010), and importantly, for the work described in the highlighted paper (Bourgeois et al, 2018), there are whole genome sequences available (Gordon et al, 2017) for 44 natural accessions from the Mediterranean region, with 6 million single nucleotide polymorphisms (SNPs). In the highlighted paper, Bourgeois et al (2018) set out to use these Brachypodium datasets to identify genomic regions under positive selection. Soft and hard sweeps are two different ways by which positive selection acts (Mitchell-Olds et al, 2007).…”

mentioning

confidence: 99%

Using Brachypodium distachyon natural populations to uncover genomic regions under selection

McCormick¹

2018

The Plant Journal

View full text Add to dashboard Cite

Genome-wide scans of selection highlight the impact sof biotic and abiotic constraints in natural populations of the model grassBrachypodium distachyon

Cited by 9 publications

References 99 publications

Selection at behavioural, developmental and metabolic genes is associated with the northward expansion of a successful tropical colonizer

Selection at behavioural, developmental and metabolic genes is associated with the northward expansion of a successful tropical colonizer

Selection at behavioral, developmental and metabolic genes is associated with the northward expansion of a successful tropical colonizer

Using Brachypodium distachyon natural populations to uncover genomic regions under selection

Contact Info

Product

Resources

About