Kathy Ann Miller

Morphometric and molecular analyses confirm two distinct species of Calliarthron (Corallinales, Rhodophyta), a genus endemic to the northeast Pacific

Gabrielson P.W., Miller K.A. and Martone P.T. 2011. Morphometric and molecular analyses confirm two distinct species of Calliarthron (Corallinales, Rhodophyta), a genus endemic to the northeast Pacific. Phycologia 50: 298–316. DOI: 10.2216/10-42.1 Phylogenetic analyses of rbcL sequences demonstrate that Calliarthron as currently constituted is paraphyletic. Calliarthron yessoense and C. latissimum from the northwest Pacific belong in Alatocladia and are conspecific. After the transfer of C. yessoense and C. latissimum, Calliarthron is monophyletic, known only from the northeast Pacific and comprises two species, C. cheilosporioides and C. tuberculosum, which are distinct morphologically, biogeographically and by molecular sequence. Sequence data for the types of C. regenerans and C. setchelliae confirm that they are heterotypic synonyms of C. tuberculosum. Lectotypes are designated for C. cheilosporioides, C. regenerans and C. setchelliae. A morphometric analysis shows that three measured characters reliably distinguish C. cheilosporioides from C. tuberculosum. Alatocladia is monophyletic, known only from the northwest Pacific and comprises two species, A. modesta and A. yessoensis, which are distinct morphologically, biogeographically and by molecular sequence. rbcL sequence data of the type species of Alatocladia, Bossiella, Calliarthron and Chiharaea confidently differentiate these genera with strong bootstrap support.

Minimally destructive sampling of type specimens of Pyropia (Bangiales, Rhodophyta) recovers complete plastid and mitochondrial genomes

Plant species, including algae and fungi, are based on type specimens to which the name of a taxon is permanently attached. Applying a scientific name to any specimen therefore requires demonstrating correspondence between the type and that specimen. Traditionally, identifications are based on morpho-anatomical characters, but recently systematists are using DNA sequence data. These studies are flawed if the DNA is isolated from misidentified modern specimens. We propose a genome-based solution. Using 4 × 4 mm2 of material from type specimens, we assembled 14 plastid and 15 mitochondrial genomes attributed to the red algae Pyropia perforata, Py. fucicola, and Py. kanakaensis. The chloroplast genomes were fairly conserved, but the mitochondrial genomes differed significantly among populations in content and length. Complete genomes are attainable from 19th and early 20th century type specimens; this validates the effort and cost of their curation as well as supports the practice of the type method.

Western Range Extension for Nereocystis luetkeana in the North Pacific Ocean

Discovery of a bed of Nereocystis luetkeana (Mertens f.) Postels et Ruprecht extends the know range of this species to Umnak Island, about 100 km west of Unalaska Island in the Eastern Aleutians

CHIHARAEA AND YAMADAIA (CORALLINALES, RHODOPHYTA) REPRESENT REDUCED AND RECENTLY DERIVED ARTICULATED CORALLINE MORPHOLOGIES 1

Phycologists have hypothesized that the diminutive fronds produced by species in the genera Chiharaea and Yamadaia, which are composed of comparatively few genicula and intergenicula, represent morphological intermediates in the evolution of articulated corallines from crustose ancestors. We test this “intermediate frond hypothesis” by comparing rbcL sequences from the generitype species Chiharaea bodegensis and Yamadaia melobesioides to sequences from other coralline genera. We demonstrate that Chiharaea includes two other NE Pacific species, Arthrocardia silvae and Yamadaia americana. Chiharaea species are characterized morphologically by inflated intergenicula and axial conceptacles with apical or acentric pores. Although relationships among the three species are unresolved, Chiharaea bodegensis, C. americana comb. nov., and C. silvae comb. nov. are distinguished from one another by DNA sequences, morphology, habitat, and biogeography. Chiharaea occurs together with Alatocladia, Bossiella, Calliarthron, and Serraticardia macmillanii in a strongly supported clade of nearly endemic north Pacific articulated coralline genera and species that have evolved relatively recently compared to other articulated corallines. In contrast, NW Pacific Yamadaia melobesioides belongs in a clade with Corallina officinalis, the generitype species of Corallina, and therefore we reduce Yamadia to a synonym of Corallina and propose Corallina melobesioides comb. nov. We reject the ‘intermediate frond hypothesis’ and conclude that Chiharaea and Yamadaia are recently derived taxa that evolved from articulated coralline ancestors and represent a reduction in the number of genicula and intergenicula.

Reconstructing the complex evolutionary history of mobile plasmids in red algal genomes

The integration of foreign DNA into algal and plant plastid genomes is a rare event, with only a few known examples of horizontal gene transfer (HGT). Plasmids, which are well-studied drivers of HGT in prokaryotes, have been reported previously in red algae (Rhodophyta). However, the distribution of these mobile DNA elements and their sites of integration into the plastid (ptDNA), mitochondrial (mtDNA), and nuclear genomes of Rhodophyta remain unknown. Here we reconstructed the complex evolutionary history of plasmid-derived DNAs in red algae. Comparative analysis of 21 rhodophyte ptDNAs, including new genome data for 5 species, turned up 22 plasmid-derived open reading frames (ORFs) that showed syntenic and copy number variation among species, but were conserved within different individuals in three lineages. Several plasmid-derived homologs were found not only in ptDNA but also in mtDNA and in the nuclear genome of green plants, stramenopiles, and rhizarians. Phylogenetic and plasmid-derived ORF analyses showed that the majority of plasmid DNAs originated within red algae, whereas others were derived from cyanobacteria, other bacteria, and viruses. Our results elucidate the evolution of plasmid DNAs in red algae and suggest that they spread as parasitic genetic elements. This hypothesis is consistent with their sporadic distribution within Rhodophyta.

Research note: First report of the Japanese species Grateloupia lanceolata (Halymeniaceae, Rhodophyta) from California, USA

The Japanese red alga Grateloupia lanceolata (Okamura) Kawaguchi was discovered in southern California at Santa Catalina Island in spring 2003 and April 2008 and in central California at the mouth of the Elkhorn Slough in Moss Landing in May, June and July of 2008. The morphology of thalli from both localities agrees with published figures. Sequences from the rbcL gene and the nuclear marker, internal transcribed spacer‐1 from Californian G. lanceolata were identical to those from two specimens of G. lanceolata introduced to the Thau Lagoon, Mediterranean France and a specimen from Japan. It is likely that the import of oysters for mariculture played a role in its introduction into California.

Resolving cryptic species of Bossiella (Corallinales, Rhodophyta) using contemporary and historical DNA

PREMISE OF THE STUDY Phenotypic plasticity and convergent evolution have long complicated traditional morphological taxonomy. Fortunately, DNA sequences provide an additional basis for comparison, independent of morphology. Most importantly, by obtaining DNA sequences from historical type specimens, we are now able to unequivocally match species names to genetic groups, often with surprising results. METHODS We used an integrative taxonomic approach to identify and describe Northeast Pacific pinnately branched species in the red algal coralline genus Bossiella, for which traditional taxonomy recognized only one species, the generitype, Bossiella plumosa. We analyzed DNA sequences from historical type specimens and modern topotype specimens to assign species names and to identify genetic groups that were different and that required new names. Our molecular taxonomic assessment was followed by a detailed morphometric analysis of each species. KEY RESULTS Our study of B. plumosa revealed seven pinnately branched Bossiella species. Three species, B. frondescens, B. frondifera, and B. plumosa, were assigned names based on sequences from type specimens. The remaining four species, B. hakaiensis, B. manzae, B. reptans, and B. montereyensis, were described as new to science. In most cases, there was significant overlap of morphological characteristics among species. CONCLUSIONS This study underscores the pitfalls of relying upon morpho-anatomy alone to distinguish species and highlights our likely underestimation of species worldwide. Our integrative taxonomic approach can serve as a model for resolving the taxonomy of other plant and algal genera.

Mitogenomes from type specimens, a genotyping tool for morphologically simple species: ten genomes of agar-producing red algae

DNA sequences from type specimens provide independent, objective characters that enhance the value of type specimens and permit the correct application of species names to phylogenetic clades and specimens. We provide mitochondrial genomes (mitogenomes) from archival type specimens of ten species in agar-producing red algal genera Gelidium and Pterocladiella. The genomes contain 43–44 genes, ranging in size from 24,910 to 24,970 bp with highly conserved gene synteny. Low Ka/Ks ratios of apocytochrome b and cytochrome oxidase genes support their utility as markers. Phylogenies of mitogenomes and cox1+rbcL sequences clarified classification at the genus and species levels. Three species formerly in Gelidium and Pterocladia are transferred to Pterocladiella: P. media comb. nov., P. musciformis comb. nov., and P. luxurians comb. and stat. nov. Gelidium sinicola is merged with G. coulteri because they share identical cox1 and rbcL sequences. We describe a new species, Gelidium millariana sp. nov., previously identified as G. isabelae from Australia. We demonstrate that mitogenomes from type specimens provide a new tool for typifying species in the Gelidiales and that there is an urgent need for analyzing mitogenomes from type specimens of red algae and other morphologically simple organisms for insight into their nomenclature, taxonomy and evolution.

A novel phylogeny of the Gelidiales (Rhodophyta) based on five genes including the nuclear CesA, with descriptions of Orthogonacladia gen. nov. and Orthogonacladiaceae fam. nov.

Although the Gelidiales are economically important marine red algae producing agar and agarose, the phylogeny of this order remains poorly resolved. The present study provides a molecular phylogeny based on a novel marker, nuclear-encoded CesA, plus plastid-encoded psaA, psbA, rbcL, and mitochondria-encoded cox1 from subsets of 107 species from all ten genera within the Gelidiales. Analyses of individual and combined datasets support the monophyly of three currently recognized families, and reveal a new clade. On the basis of these results, the new family Orthogonacladiaceae is described to accommodate Aphanta and a new genus Orthogonacladia that includes species previously classified as Gelidium madagascariense and Pterocladia rectangularis. Acanthopeltis is merged with Gelidium, which has nomenclatural priority. Nuclear-encoded CesA was found to be useful for improving the resolution of phylogenetic relationships within the Gelidiales and is likely to be valuable for the inference of phylogenetic relationship among other red algal taxa.

PHYLOGEOGRAPHY OF CUTLERIA CYLINDRICA (CUTLERIALES, PHAEOPHYCEAE) IN NORTHEASTERN ASIA, AND THE IDENTITY OF AN INTRODUCED POPULATION IN CALIFORNIA1

Cutleria cylindrica Okamura was described from Japan in 1902 and has been reported only from northwestern Asia until its relatively recent discovery in California, USA, and Baja California, Mexico. To clarify the genetic relationships within and among the disjunct populations, we carried out a molecular phylogenetic study, as well as the examination of sex ratio and the life‐history patterns, of populations in Japan, Korea, and California. Based on the DNA sequences of mitochondrial genes cox2, cox3, the open reading frame (ORF) region, and the spacer between cox3 and ORF, a total of 23 haplotypes were detected in the 85 individuals from 20 localities in Japan, Korea, and California. All localities in Japan and Korea included multiple haplotypes, but only a single haplotype was found in California. There was a positive relationship between distance and genetic divergence in Japan and Korea. The single haplotype found in California was the same as one occurring in Japan (Aomori Pref. and Fukuoka Pref.) and Korea (Daedaepo, Pusan). Both male and female gametophytes were distributed in most northeastern Asian populations. Only female gametophytes, developing parthenogenetically from female gametes, were found in California and Aomori Pref., Japan. On the basis of these results, we conclude that the disjunct population of C. cylindrica in California originated from a relatively recent introduction from Japan and shares its origin with the parthenogenetic population in the Tsugaru Strait.