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

• Published in: Ecology and evolution Vol. 7; no. 19; pp. 7920 - 7936
• Main Authors: Tripp, Erin A., Tsai, Yi‐Hsin Erica, Zhuang, Yongbin, Dexter, Kyle G.
• Format: Journal Article
• Language: English
• Published: England John Wiley & Sons, Inc 01-10-2017; John Wiley and Sons Inc
• Subjects: Acanthaceae; Alpine environments; Aridity; Assembly; Best practice; de novo assembly; desert; Desert environments; Deserts; Divergence; Genomes; Missing data; Nucleotide sequence; Original Research; Petalidium; Phylogenetics; Phylogeny; Plant diversity; Radiation; RADseq; reference‐based assembly; speciation; Species; stacks; United States > US; Namibia; Angola; RADseq; reference‐based assembly; de novo assembly; desert; stacks; speciation
• ISSN: 2045-7758; 2045-7758
• DOI: 10.1002/ece3.3274

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.
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. Using RADseq loci, we constructed a phylogenomic hypothesis for this radiation and explored the impacts of 18 different combinations of assembly parameters via both de novo and reference‐based approaches. The reference‐based assembly performed poorly compared to most de novo assemblies. Our results indicate a crown age for African species of 3.6–1.4 Ma. Despite the harshness of the environment in which species of Petalidium occur, this lineage has diversified at a net rate on par with those of diverse genera in tropical, Mediterranean, and alpine environments.