Using RAD seq for reconstructing phylogenies of highly diverged taxa: A test using the tribe Scandiceae (Apiaceae)

Abstract

The angiosperm Apiaceae tribe Scandiceae includes four major clades—subtribes Daucinae, Ferulinae, Torilidinae, and Scandicinae—that originated ca. 20 Mya. Although all four subtribes are highly supported in molecular analyses, and morphological data indicate a sister relationship between Daucinae and Torilidinae, their branching order has not been resolved using standard Sanger multilocus data. Therefore, in this study, we test the utility of genomic RAD seq data in resolving deep phylogenetic relationships (up to 20 Mya) in Apiaceae subfamily Apioideae, with special emphasis on tribe Scandiceae using 12 representative species. We used two bioinformatic pipelines, pyRAD and RADIS (based on STACKS), to assemble RAD seq data and we tested the influence of various combinations of parameters on the robustness of the inferred tree topologies. Although different data processing approaches produced alignments with various amounts of missing data, they converged to two well‐supported topologies, irrespective of the phylogenetic method applied. Highly supported trees showed Scandicinae as sister to all other clades and indicated that Daucinae and Torilidinae are sister groups, thus confirming the relationship inferred from morphology. We conclude that the RAD seq method can be successfully used to resolve deep relationships formed 20 Mya within Apiaceae. We provide recommendations for parameter settings in RADIS and pyRAD for the analysis of taxa that have accumulated considerable genomic divergence.

Towards a new classification of Muscidae (Diptera): a comparison of hypotheses based on multiple molecular phylogenetic approaches

“…Moreover, R2 reads had very low quality terminal part, especially in one of the libraries. According to ipyrad developers [see discussion on Gitter 25 September 2020 (https://gitter.im/dereneaton/ipyrad)] and from our experience (Piwczyński et al ., 2021), the exclusion of R2 reads usually do not influence the final result. Typical RAD‐seq dataset generated by HiSeq platforms contains reads that are 50–100 bp long.…”

ISSRseq: An extensible method for reduced representation sequencing

“…(Acanthaceae); however, the number of SNPs included in their data matrices (1,568–53,792, depending on parameter choice) was only greater than that recovered using ISSRseq when the missingness cut‐off was greater than 60%. While variable SNP recovery may be relatively less of a concern for phylogenetic applications (Eaton et al., 2017; Piwczyński et al., 2020; Tripp et al., 2017), they are known to negatively impact estimation of population genetic parameters. For example, missing data are known to bias estimation of effective population size ( N e ) and the inbreeding coefficient ( F is ; Marandel et al., 2020).…”

ISSRseq: an extensible method for reduced representation sequencing

“…(Acanthaceae), however the number of SNPs included in their data matrices (1,568 to 53,792, depending on parameter choice) was only greater than that recovered using ISSRseq when the missingness cutoff was greater than 60%. While variable SNP recovery may be relatively less of a concern for phylogenetic applications (Eaton et al, 2017; Tripp et al, 2017; Piwczyński et al, 2020), they are known to negatively impact estimation of population genetic parameters. For example, missing data are known to bias estimation of effective population size (N e ) and the inbreeding coefficient (F is ; Marandel et al, 2020).…”