RADseq dataset with 90% missing data fully resolves recent radiation of Petalidium (Acanthaceae) in the ultra‐arid deserts of Namibia

Abstract

Deserts, even those at tropical latitudes, often have strikingly low levels of plant diversity, particularly within genera. One remarkable exception to this pattern is the genus Petalidium (Acanthaceae), in which 37 of 40 named species occupy one of the driest environments on Earth, the Namib Desert of Namibia and neighboring Angola. To contribute to understanding this enigmatic diversity, we generated RADseq data for 47 accessions of Petalidium representing 22 species. We explored the impacts of 18 different combinations of assembly parameters in de novo assembly of the data across nine levels of missing data plus a best practice assembly using a reference Acanthaceae genome for a total of 171 sequence datasets assembled. RADseq data assembled at several thresholds of missing data, including 90% missing data, yielded phylogenetic hypotheses of Petalidium that were confidently and nearly fully resolved, which is notable given that divergence time analyses suggest a crown age for African species of 3.6–1.4 Ma. De novo assembly of our data yielded the most strongly supported and well‐resolved topologies; in contrast, reference‐based assembly performed poorly, perhaps due in part to moderate phylogenetic divergence between the reference genome, Ruellia speciosa, and the ingroup. Overall, we found that Petalidium, despite the harshness of the environment in which species occur, shows a net diversification rate (0.8–2.1 species per my) on par with those of diverse genera in tropical, Mediterranean, and alpine environments.

Practical considerations for plant phylogenomics

“…This has led to considerable debate as to whether RAD-seq can be accurately applied to deeper phylogenetic scales (Rubin et al, 2012;Cariou et al, 2013). Although it is now clear from empirical applications that RAD-seq can provide significant phylogenetic information over even tens of millions of years divergence (Eaton and Ree, 2013;Escudero et al, 2014;Eaton et al, 2015Eaton et al, , 2017McVay et al, 2017;Tripp et al, 2017;Vargas et al, 2017), the more relevant concern is the scale at which missing data make this method no longer economical compared to alternatives.…”

Phylogenomics supported by geometric morphometrics reveals delimitation of sexual species within the polyploid apomicticRanunculus auricomuscomplex (Ranunculaceae)

“…The application of phylogenomic methods provides a magnitude more loci compared to traditional genetic markers and can resolve relationships of taxa with less than few million (or even less than 100.000) years of divergence (Pellino & al., 2013; Tripp & al., 2017; Tomasello et al, in subm.). Currently, two main approaches are used in species-level systematics: Target enrichment and restriction site-associated DNA sequencing (RADseq; and the similar Genotyping-by-Sequencing = GBS method).…”

“…Target enrichment (i.e., nuclear genes selected out of a reference genome) is most useful for diverged species and genus-wide relationships (Folk & al., 2015; Schmickl & al., 2016; Tomasello, 2018). RADseq has repeatedly proven its efficiency in resolving intraspecific relationships, phylogenies of closely related species, but also within genera (relationships between less than 100.000 and more than 50 Mya years; (Baird & al., 2008; Hipp & al., 2014; Cavender-Bares & al., 2015; Tripp & al., 2017; Wagner & al., 2018; Pätzold & al., 2019). Although RADseq yields much more loci and SNPs than target enrichment, it is considered to become less informative with increasing species divergence due to increasing mutations in enzyme cutting sites leading to loss of loci (Rubin & al., 2012; Eaton & al., 2017).…”

Congruent species delimitation of two controversial gold‐thread nanmu tree species based on morphological and restriction site‐associated DNA sequencing data

“…This technique can produce a vast number of short sequences from various genomic DNA loci and was designed originally as a tool for finding single-nucleotide polymorphisms (SNPs) for population genetic structural inference, linkage mapping, association study, and other intraspecific genomic analyses (Miller et al, 2007;Baird et al, 2008). Recently, RAD-seq has also been used to resolve phylogenetic relationships of diverse lineages including polyploids (e.g., Rubin et al, 2012;Eaton & Ree, 2013;Wagner et al, 2013;Wang et al, 2013;Escudero et al, 2014;Hipp et al, 2014;Takahashi et al, 2014;Qi et al, 2015;Ree & Hipp, 2015;Takahashi & Moreno, 2015;Boucher et al, 2016;Takahashi & Sota, 2016;Fitz-Gibbon et al, 2017;Tripp et al, 2017).…”