A dated phylogeny of the genus Pennantia (Pennantiaceae) based on whole chloroplast genome and nuclear ribosomal 18S–26S repeat region sequences

Abstract

Pennantia, which comprises four species distributed in Australasia, was the subject of a monographic taxonomic treatment based on morphological characters in 2002. When this genus has been included in molecular phylogenies, it has usually been represented by a single species, P. corymbosa J.R.Forst. & G.Forst., or occasionally also by P. cunninghamii Miers. This study presents the first dated phylogenetic analysis encompassing all species of the genus Pennantia and using chloroplast DNA. The nuclear ribosomal 18S–26S repeat region is also investigated, using a chimeric reference sequence against which reads not mapping to the chloroplast genome were aligned. This mapping of off-target reads proved valuable in exploiting otherwise discarded data, but with rather variable success. The trees based on chloroplast DNA and the nuclear markers are congruent but the relationships among the members of the latter are less strongly supported overall, certainly due to the presence of ambiguous characters in the alignment resulting from low coverage. The dated chloroplast DNA phylogeny suggests that Pennantia has diversified within the last 20 My, with the lineages represented by P. baylisiana (W.R.B.Oliv.) G.T.S.Baylis, P. endlicheri Reissek and P. corymbosa diversifying within the last 9 My. The analyses presented here also confirm previous molecular work based on the nuclear internal transcribed spacer region showing that P. baylisiana and P. endlicheri, which were sometimes considered synonyms, are not sister taxa and therefore support their recognition as distinct species.

A dated phylogeny shows Plio‐Pleistocene climates spurred evolution of antibrowsing defences in the New Zealand flora

“…Coprosma , Cantley et al ., 2016 and Teucrium , Salmaki et al ., 2016 ). Finally, the relationships among species within genera are also consistent with previous work (except for Muehlenbeckia , see next paragraph), some based on plastid DNA (Maurin, 2020b for Pennantia , Maurin & Smissen, 2021 for Corokia ); others on nuclear ribosomal markers (e.g. Gardner et al ., 2021 for Streblus ; Mitchell et al ., 2009 for Melicytus ; Appelhans et al ., 2014 for Melicope ) or based on morphological characters (e.g.…”

“…We reconstructed the phylogeny of our samples with RA x ML v.8.2.12 (Stamatakis, 2014 ), run on CIPRES (Miller et al ., 2010 ), following the guide by Maurin ( 2020 ). The search for the best ML tree was conducted with the following settings: 10 random alternative starting trees, 1000 bootstrap (BS) replicates, GTRGAMMA model, and fixing the sequence of Ranunculus sceleratus (Ranunculales) as an outgroup to the rest of the Eudicots.…”

“…The search for the best ML tree was conducted with the following settings: 10 random alternative starting trees, 1000 bootstrap (BS) replicates, GTRGAMMA model, and fixing the sequence of Ranunculus sceleratus (Ranunculales) as an outgroup to the rest of the Eudicots. From this best ML tree, we generated 1000 BS replicates to produce a dated phylogeny with a 95% confidence interval (CI) on the age at the nodes using tree PL (Smith & O’Meara, 2012 ), again following the guide by Maurin ( 2020 ). To calibrate the tree, we used 10 fossils assigned to internal nodes (all outside our study clades) and one secondary calibration for the root of the tree.…”

Elevation of Pennantia J.R.Forst. & G.Forst. sect. Dermatocarpus Miers (Pennantiaceae J.Agardh.) to subgenus rank

“…Subsequent phylogenetic analyses consistently showed well-supported lineages, where Pennantia cunninghamii is sister to the three members of section Pennantia (Keeling et al, 2004;Maurin, 2020). Keeling et al, (2004) showed 15% sequence divergence between Pennantia cunninghamii and the other three members under nrDNA ITS gene, while Maurin (2020) estimated the sister split within the last 20 My (vs. estimation of 4.2 Mya diversification between New Zealand, Three Kings/ Manawatawhi and Norfolk Island species) using whole chloroplast genome and 18S-26S nuclear ribosomal repeat sequences.…”

“…The position of the family with its sole genus, following its reinstatement by Kårehed (2001) is unequivocal (Maurin, 2020). All four species within the genus are well defined (Gardner & de Lange, 2002) and widely accepted (https://powo.science.…”