Utility of psbA and nSSU for phylogenetic reconstruction in the Corallinales based on New Zealand taxa

Evolutionary history of the Corallinales (Corallinophycidae, Rhodophyta) inferred from nuclear, plastidial and mitochondrial genomes

“…1) shows that specimens of M. erubescens from New Zealand are more closely related to M. lichenoides (lineage D) from France (Channel Sea) than to specimens of M. erubescens from the type-locality (Brazil), or from the South-Pacific Ocean (Vanuatu, Fiji) (lineage C). Broom et al (2008) already highlighted the cryptic diversity of M. erubes-cens and our results confirm that this morpho-species has been overlooked. These findings thus warrant a thorough study of the species from various geographical locations combining morpho-anatomic observations and molecular phylogenies (inferred from a more variable marker than the SSU) to better delineate species frontiers within this complex.…”

“…This was likely due to its length (here 2502 bp) as well as its phylogenetic signal. In a recent study Broom et al (2008) stated that psbA has considerable potential as a marker for the Corallinales because it is easily amplified and considerably more variable than SSU. COI is another gene that has recently been used to assess subfamilial relationships within the Corallinales (Walker et al, 2009) and this marker, selected as the DNA-barcode for the Rhodophyta, is currently widely se-quenced by the barcode community to populate the Barcode Of Life Database (Ratnasingham and Hebert, 2007).…”

“…We therefore recommend that LSU, rather than SSU sequences, be used to pursue further phylogenetic inferences within the Corallinales. However, considering that psbA sequences (1) are easy to amplify, (2) only require two sequencing reactions (one forward, one reverse), (3) can be aligned unambiguously and (4) provide significant phylogenetic signal in recent and deep branching (Broom et al, 2008), focusing on the use of new plastid-ial sequences other than LSU sequences, might also be an attractive strategy to access coralline algal relationships in future analyses. The studies of sub-datasets (built with the SlowFaster software, Kostka et al, 2008), where fast-evolving sites were removed, showed that our alignments were not affected by phylogenetic noise.…”

“…Broom et al (2008) only found the monophyly of Hapalidiaceae with their worldwide dataset based on SSU sequences (BS(Neighbour-Joining analyse) = 99, BS(ML) = 91, Posterior probabilities for Bayesian analyses = 1.00). In Fig.…”

“…In addition, all the coralline algal phylogenies published until 2008 were inferred from a single marker, the SSU. Broom et al (2008) proposed the plastidial gene psbA (encoding for the D1 protein of photosystem II) as a novel marker to be used in combination with SSU data to improve the phylogenetic resolution within the order. Walker et al (2009) also showed the relevance of using a mitochondrial marker to get new insights into the genetic diversity at a lower taxonomic level; i.e.…”