The present classification of the Delesseriaceae retains the essential features of Kylin's system, which recognizes two subfamilies Delesserioideae and Nitophylloideae and a series of "groups" or tribes. In this study we test the Kylin system based on phylogenetic parsimony and distance analyses inferred from two molecular data sets and morphological evidence. A set of 72 delesseriacean and 7 additional taxa in the order Ceramiales was sequenced in the large subunit rDNA and rbc L analyses. Three large clades were identified in both the separate and combined data sets, one of which corresponds to the Delesserioideae, one to a narrowly circumscribed Nitophylloideae, and one to the Phycodryoideae, subfam. nov., comprising the remainder of the Nitophylloideae sensu Kylin. Two additional trees inferred from rbc L sequences are included to provide broader coverage of relationships among some Delesserioideae and Phycodryoideae. Belonging to the Delesserioideae are the Caloglosseae with Caloglossa ; an expanded Hemineureae that includes Hemineura , Patulophycus , Marionella , Laingia , Botryocarpa , and Pseudophycodrys ; the Delesserieae with Delesseria and Membranoptera ; the Apoglosseae with Apoglossum and a group of southern hemisphere species presently placed in Delesseria that belong in Paraglossum ; the Hypoglosseae with Hypoglossum , Branchioglossum , Zellera , and Bartoniella ; and the Grinnellieae with Grinnellia. The revised Nitophylloideae contains the Nitophylleae with Nitophyllum , Valeriemaya , Polyneuropsis , and Calonitophyllum and the Martensieae with Opephyllum and Martensia. A new subfamily, Phycodryoideae, is proposed to include the Phycodryeae with Phycodrys , Polyneura , Nienburgia , Cladodonta , Heterodoxia , and Womersleya ; the Cryptopleureae with Cryptopleura , Hymenena , Acrosorium , and Botryoglossum ; the Myriogrammeae with Myriogramme and Haraldiophyllum ; and the Schizoserideae with Schizoseris , Neuroglossum , Drachiella , Abroteia , and species from South America placed in Platyclinia. This research promotes the correlation of molecular and morphological phylogenies.

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A multi-gene (SSU, LSU, psbA, and COI) molecular phylogeny of the family Corallinaceae (excluding the subfamilies Lithophylloideae and Corallinoideae) showed a paraphyletic grouping of six monophyletic clades. Pneophyllum and Spongites were reassessed and recircumscribed using DNA sequence data integrated with morpho-anatomical comparisons of type material and recently collected specimens. We propose Chamberlainoideae subfam. nov., including the type genus Chamberlainium gen. nov., with C. tumidum comb. nov. as the generitype, and Pneophyllum. Chamberlainium is established to include several taxa previously ascribed to Spongites, the generitype of which currently resides in Neogoniolithoideae. Additionally we propose two new genera, Dawsoniolithon gen. nov. (Metagoniolithoideae), with D. conicum comb. nov. as the generitype and Parvicellularium gen. nov. (subfamily incertae sedis), with P. leonardi sp. nov. as the generitype. Chamberlainoideae has no diagnostic morpho-anatomical features that enable one to assign specimens to it without DNA sequence data, and it is the first subfamily to possess both Type 1 (Chamberlainium) and Type 2 (Pneophyllum) tetra/bisporangial conceptacle roof development. Two characters distinguish Chamberlainium from Spongites: tetra/biasporangial conceptacle chamber diameter (<300 μm in Chamberlainium vs. >300 μm in Spongites) and tetra/bisporangial conceptacle roof thickness (<8 cells in Chamberlainium vs. >8 cells in Spongites). Two characters also distinguish Pneophyllum from Dawsoniolithon: tetra/bisporangial conceptacle roof thickness (<8 cells in Pneophyllum vs. >8 cells in Dawsoniolithon) and thallus construction (dimerous in Pneophyllum vs. monomerous in Dawsoniolithon).

BackgroundObtaining strongly supported phylogenies that permit confident taxonomic and evolutionary interpretations has been a challenge in algal biology. High-throughput sequencing has improved the capacity to generate data and yields more informative datasets. We sequenced and analysed the chloroplast genomes of 22 species of the order Nemaliales as a case study in the use of phylogenomics as an approach to achieve well-supported phylogenies of red algae.ResultsChloroplast genomes of the order Nemaliales are highly conserved, gene-dense and completely syntenic with very few cases of gene loss. Our ML estimation based on 195 genes recovered a completely supported phylogeny, permitting re-classification of the order at various taxonomic levels. Six families are recognised and the placement of several previously contradictory clades is resolved. Two new sub-orders are described, Galaxaurineae and Nemaliineae, based on the early-branching nature and monophyly of the groups, and presence or absence of a pericarp. Analyses of subsets of the data showed that >90 % bootstrap support can be achieved with datasets as small as 2500 nt and that fast and medium evolving genes perform much better when it comes to resolving phylogenetic relationships.ConclusionsIn this study we show that phylogenomics is an efficient and effective approach to investigate phylogenetic relationships. The six currently circumscribed Nemaliales families are clustered into two evolutionary lineages with strong statistical support based on chloroplast phylogenomic analyses. The conserved nature of red algal chloroplast genomes is a convenient and accessible source of data to resolve their ancient relationships.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-016-0772-3) contains supplementary material, which is available to authorized users.