Benefits of alignment quality‐control processing steps and an Angiosperms353 phylogenomics pipeline applied to the Celastrales

Abstract

We examined the impact of successive alignment quality‐control steps on downstream phylogenomic analyses. We applied a recently published phylogenomics pipeline that was developed for the Angiosperms353 target‐sequence‐capture probe set to the flowering plant order Celastrales. Our final dataset consists of 158 species, including at least one exemplar from all 109 currently recognized Celastrales genera. We performed nine quality‐control steps and compared the inferred resolution, branch support, and topological congruence of the inferred gene and species trees with those generated after each of the first six steps. We describe and justify each of our quality‐control steps, including manual masking, in detail so that they may be readily applied to other lineages. We found that highly supported clades could generally be relied upon even if stringent orthology and alignment quality‐control measures had not been applied. But separate instances were identified, for both concatenation and coalescence, wherein a clade was highly supported before manual masking but then subsequently contradicted. These results are generally reassuring for broad‐scale analyses that use phylogenomics pipelines, but also indicate that we cannot rely exclusively on these analyses to conclude how challenging phylogenetic problems are best resolved.

Classification of the Celastrales Based on Integration of Genomic, Morphological, and Sanger-Sequence Characters

“…Simmons et al (2022) sampled two to eight species of the 18 genera for which we had reason to doubt monophyly based on previous phylogenetic analyses, wherein some of the genera were not well supported as monophyletic. These additional specimens enabled us to make the following 15 tests: whether Parnassia is distinct from Lepuropetalon ; whether Allocassine is distinct from Lauridia (e.g.…”

“…Incorporation of Published Data —The four most recent and taxonomically well-sampled phylogenetic analyses of Celastrales are Bacon et al (2016), Biral et al (2017), Zhu et al (2020), and Simmons et al (2022). Those first three studies already incorporated data from several earlier studies that relied primarily upon (i.e.…”

“…Foci of This Study —This study is a follow-up to Simmons et al (2022), who sampled all currently recognized genera within Celastrales using phylogenomic data from 340 genes. Their phylogenetic trees are useful for Celastraceae systematics given their impressive generic and nucleotide-character sampling.…”

“…In addition to sampling publicly available data in our phylogenetic analysis, we incorporate novel sequences for the taxa sampled by Simmons et al (2022) for eight gene regions that had been sampled by many previous phylogenetic studies within the family (i.e. 18S nrDNA, ITS nrDNA, 26S nrDNA, atpB , matK , rbcL , trnL intron, and trnL-F spacer).…”

“…18S nrDNA, ITS nrDNA, 26S nrDNA, atpB , matK , rbcL , trnL intron, and trnL-F spacer). We also scored morphological characters for the 11 taxa that Simmons et al (2022) newly sampled relative to previous studies. We incorporated all of these data into a supermatrix-based analysis, which is currently the most thorough phylogenetic study within Celastrales with respect to both taxon and character sampling.…”