An empirical assessment of a single family‐wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae

Abstract

2019. An empirical assessment of a single family-wide hybrid capture locus set at multiple evolutionary timescales in Asteraceae. Applications in Plant Sciences 7(10): e11295. PREMISE:Hybrid capture with high-throughput sequencing (Hyb-Seq) is a powerful tool for evolutionary studies. The applicability of an Asteraceae family-specific Hyb-Seq probe set and the outcomes of different phylogenetic analyses are investigated here. METHODS:Hyb-Seq data from 112 Asteraceae samples were organized into groups at different taxonomic levels (tribe, genus, and species). For each group, data sets of non-paralogous loci were built and proportions of parsimony informative characters estimated. The impacts of analyzing alternative data sets, removing long branches, and type of analysis on tree resolution and inferred topologies were investigated in tribe Cichorieae. RESULTS:Alignments of the Asteraceae family-wide Hyb-Seq locus set were parsimony informative at all taxonomic levels. Levels of resolution and topologies inferred at shallower nodes differed depending on the locus data set and the type of analysis, and were affected by the presence of long branches. DISCUSSION:The approach used to build a Hyb-Seq locus data set influenced resolution and topologies inferred in phylogenetic analyses. Removal of long branches improved the reliability of topological inferences in maximum likelihood analyses. The Astereaceae Hyb-Seq probe set is applicable at multiple taxonomic depths, which demonstrates that probe sets do not necessarily need to be lineage-specific.

Generic boundaries in subtribe Saussureinae (Compositae: Cardueae): Insights from Hyb‐Seq data

“…Continued. Jones & al., 2019), tribe , and genus level (Herrando-Moraira & al., 2018;. For Saussureinae, this method also allowed to recover a well-supported phylogeny.…”

“…In recent years, most phylogenomic studies conducted on Compositae have succesfully employed the Hyb‐Seq technique based on 1061 COS loci, at family (Mandel & al., 2014, 2015, 2017, 2019; Jones & al., 2019), tribe (Herrando‐Moraira & al., 2019; Siniscalchi & al., 2019), and genus level (Herrando‐Moraira & al., 2018; Thapa & al., 2019). For Saussureinae, this method also allowed to recover a well‐supported phylogeny.…”

“…Vouchers and accession numbers are detailed in Appendix 1. From the total sampling (167), 97 individuals were newly sequenced in this study, and the remaining 70 were obtained from raw reads sequenced on previous studies (Mandel & al., 2014, 2019; Herrando‐Moraira & al., 2018, 2019; Jones & al., 2019) (see suppl. Table S2).…”

Enabling evolutionary studies at multiple scales in Apocynaceae through Hyb‐Seq

“…Target capture sequencing of nuclear genes is one approach that facilitates large-scale phylogenomic studies of non-model organisms (Lemmon and Lemmon, 2013;Dodsworth et al, 2019). In plants, this approach has clarified evolutionary relationships in multiple lineages (e.g., Mandel et al, 2015;Fisher et al, 2016;Heyduk et al, 2016;Léveillé-Bourret et al, 2018;Boutte et al, 2019;Couvreur et al, 2019;Herrando-Moraira et al, 2019;Bagley et al, 2020). Obtaining data from many nuclear genes facilitates the use of species tree methods based on the multispecies coalescent model (Mirarab and Warnow, 2015;Edwards et al, 2016) and provides data sets of the size required to address problems that have been unsolvable using traditional molecular systematics approaches (e.g., Léveillé-Bourret et al, 2018;Herrando-Moraira et al, 2019), or even whole plastome data (e.g., Straub et al, 2014).…”

“…In plants, this approach has clarified evolutionary relationships in multiple lineages (e.g., Mandel et al, 2015;Fisher et al, 2016;Heyduk et al, 2016;Léveillé-Bourret et al, 2018;Boutte et al, 2019;Couvreur et al, 2019;Herrando-Moraira et al, 2019;Bagley et al, 2020). Obtaining data from many nuclear genes facilitates the use of species tree methods based on the multispecies coalescent model (Mirarab and Warnow, 2015;Edwards et al, 2016) and provides data sets of the size required to address problems that have been unsolvable using traditional molecular systematics approaches (e.g., Léveillé-Bourret et al, 2018;Herrando-Moraira et al, 2019), or even whole plastome data (e.g., Straub et al, 2014). This method allows sufficient flexibility to design probes in conserved regions that flank more variable intron and intergenic regions, providing sequence data that are useful for comparative analysis of distantly related species, among closely related species within a genus, or even within a single species (Weitemier et al, 2014(Weitemier et al, , 2019Crowl et al, 2017;Peng et al, 2017;Villaverde et al, 2018;de la Harpe et al, 2019;Jones et al, 2019).…”