Analysis of chloroplast genomes and a supermatrix inform reclassification of the Rhodomelaceae (Rhodophyta)

Abstract

With over a thousand species, the Rhodomelaceae is the most species-rich family of red algae. While its genera have been assigned to 14 tribes, the high-level classification of the family has never been evaluated with a molecular phylogeny. Here, we reassess its classification by integrating genome-scale phylogenetic analysis with observations of the morphological characters of clades. In order to resolve relationships among the main lineages of the family we constructed a phylogeny with 55 chloroplast genomes (52 newly determined). The majority of branches were resolved with full bootstrap support. We then added 266 rbcL, 125 18S rRNA gene and 143 cox1 sequences to construct a comprehensive phylogeny containing nearly half of all known species in the family (407 species in 89 genera). These analyses suggest the same subdivision into higher-level lineages, but included many branches with moderate or poor support. The circumscription for nine of the 13 previously described tribes was supported, but the Lophothalieae, Polysiphonieae, Pterosiphonieae and Herposiphonieae required revision, and five new tribes and one resurrected tribe were segregated from them. Rhizoid anatomy is highlighted as a key diagnostic character for the morphological delineation of several lineages. This work provides the most extensive phylogenetic analysis of the Rhodomelaceae to date and successfully resolves the relationships among major clades of the family. Our data show that organellar genomes obtained through high-throughput sequencing produce well-resolved phylogenies of difficult groups, and their more general application in algal systematics will likely permit deciphering questions about classification at many taxonomic levels.

Widely distributed red algae often represent hidden introductions, complexes of cryptic species or species with strong phylogeographic structure

“…Xiphosiphonia pennata , S. spinifera, and S. dendroidea are placed in a tribe (Pterosiphonieae) with high morphological variation ranging from filiform to foliose species (Díaz‐Tapia et al. ). The body plan of both species is filiform, among the simplest observed in the tribe, and morphological stasis is a plausible explanation for their similarity.…”

“…In the tribe Herposiphonieae all species are very similar in morphology, with limited differences in their body plans (Díaz‐Tapia et al. ) and the cryptic diversity in H. tenella might result from morphological stasis or developmental constraints.…”

“…Three species of Xiphosiphonia and Dipterosiphonia were selected as the respective outgroups for the Symphyocladia and Herposiphonia trees based on our phylogenomic analyses of the major lineages of the Rhodomelaceae (Díaz‐Tapia et al. ).…”

Organellar genomics: a useful tool to study evolutionary relationships and molecular evolution in Gracilariaceae (Rhodophyta)

“…, Díaz‐Tapia et al. ). Those data also facilitated the investigation of other aspects of red algal genomes, including gene synteny and horizontal gene transfers (Yang et al.…”

Plasmid‐Associated Organelle Genome Evolution In Red Algae

“…2016a, Díaz‐Tapia et al. ). Since the rise of high‐throughput sequencing (HTS) technologies, massive organelle genome databases have become available to better understand the evolutionary history of eukaryotes.…”