2022
DOI: 10.24823/ejb.2022.409
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Abstract: Hybrid capture with baits has proven to be a rich source of genetic data for many genera. The depth of information provided allows resolution of rapid radiations and of deep phylogenetic patterns. Retrieved data can also be used for population genetic studies and analysis of functional genetic diversity. To gain a better understanding of the evolutionary patterns across this large, diverse and fascinating genus through phylogenetics, population genetics and sequence analysis, we have designed and tested a set … Show more

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Cited by 4 publications
(4 citation statements)
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“…Several automated pipelines using the software above have been developed to exploit target capture data following a reference‐based mapping approach (Fér and Schmickl, 2018), a de novo assembly approach (Yang and Smith, 2014), or a combination of both (Johnson et al, 2016) (Table 1). The usage of those different pipelines is intensively discussed in the literature (Fér and Schmickl, 2018; Herrando‐Moraira et al, 2018; Andermann et al, 2020; Michel et al, 2022). Although intended to facilitate data analysis, care should be taken with the one‐size‐fits‐all approach, especially for users who are not comfortable using command lines.…”
Section: Target Capturementioning
confidence: 99%
“…Several automated pipelines using the software above have been developed to exploit target capture data following a reference‐based mapping approach (Fér and Schmickl, 2018), a de novo assembly approach (Yang and Smith, 2014), or a combination of both (Johnson et al, 2016) (Table 1). The usage of those different pipelines is intensively discussed in the literature (Fér and Schmickl, 2018; Herrando‐Moraira et al, 2018; Andermann et al, 2020; Michel et al, 2022). Although intended to facilitate data analysis, care should be taken with the one‐size‐fits‐all approach, especially for users who are not comfortable using command lines.…”
Section: Target Capturementioning
confidence: 99%
“…We designed two versions of a bespoke Begonia bait set (Michel et al, 2022); the second version differed by 96 genes that were replaced after they performed poorly at sequence capture in early experiments. The phylogeny was constructed using data assembled to genes common to both versions of the bait set.…”
Section: Nuclear Phylogeneticsmentioning
confidence: 99%
“…This uses a very conservative assembly method to minimise the mapping of paralogues, and a conservative consensus method that removes ambiguous sites due to allele variants. This is the same pipeline as the 'basic' one described by Michel et al (2022). The concatenated alignment of 1235 genes contained 234,578 parsimony-informative characters, and 75% of the bases were constant.…”
Section: Nuclear Phylogeneticsmentioning
confidence: 99%
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