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Two of the four currently recognised species of Phymatolithon in South Africa are P. repandum (type locality: Half Moon Bay, Port Philip Bay, Victoria, Australia) and P. ferox (type locality: Natal, KwaZulu-Natal, South Africa). Partial rbcL sequences of the lectotype of P. repandum and the holotype of P. ferox demonstrate that the former is not present in South Africa and does not belong in Phymatolithon, whereas the latter belongs in Phymatolithon, but that the name has been misapplied in South Africa. The correct name for the species, currently called P. repandum in South Africa, is P. ferox. Partial rbcL and psbA sequences of two of the current heterotypic synonyms of P. ferox, Lithothamnion prolixum and Lithothamnion prolixum f. plicatum, show that they are conspecific and do not belong in Phymatolithon. Lithothamnion prolixum is the basionym for the species currently, but incorrectly, called P. ferox in South Africa. Phymatolithon repandum and L. prolixum belong in an as yet undescribed genus. All heterotypic synonyms of currently recognised names of non-geniculate corallines that were placed in synonymy based on morpho-anatomy should not be accepted until confirmed by DNA sequencing.

A partial rbcL sequence from the type material of Spongites discoideus from southern Argentina showed that it was distinct from rbcL sequences of South African specimens to which that name had been applied based on morpho-anatomy. A partial rbcL sequence from an original syntype specimen, herein designated the lectotype, of Lithophyllum marlothii, type locality Camps Bay, Western Cape Province, South Africa, was identical to rbcL sequences of South African field-collected specimens assigned to S. discoideus. Based on phylogenetic analyses of rbcL and/or psbA sequences, both of these species belong in Pneophyllum and are transferred there as P. discoideum comb. nov. and P. marlothii comb. nov. The two species exhibit a distinct type of development where thick, secondary, monomerous disks are produced from thin, primary, dimerous crusts. Whether this type of development represents an example of convergent evolution or is characteristic of a clade of species within Pneophyllum remains to be resolved.

Caulacanthus okamurae is an invasive red alga that forms extensive mats in sheltered marine habitats around the world. To determine its genomic structure and genetic relationship to native and othe...

Current usage of the name Ulva lactuca, the generitype of Ulva, remains uncertain. Genetic analyses were performed on the U. lactuca Linnaean holotype, the U. fasciata epitype, the U. fenestrata holotype, the U. lobata lectotype, and the U. stipitata lectotype. The U. lactuca holotype is nearly identical in rbcL sequence to the U. fasciata epitype, a warm temperate to tropical species, rather than the cold temperate species to which the name U. lactuca has generally been applied. We hypothesize that the holotype specimen of U. lactuca came from the Indo-Pacific rather than northern Europe. Our analyses indicate that U. fasciata and U. lobata are heterotypic synonyms of U. lactuca. Ulva fenestrata is the earliest name for northern hemisphere, cold temperate Atlantic and Pacific species, with U. stipitata a junior synonym. DNA sequences from type specimens provide an unequivocal method for applying names to Ulva species. This article is protected by copyright. All rights reserved.

One of the earliest described non-geniculate coralline algae from the Arctic is Kjellman’s 1877 Lithophyllum arcticum. It has been classified successively in Lithothamnion and Mesophyllum and curre...

International audience; Non‐geniculate coralline algae are difficult to identify based solely on morpho‐anatomy. To address the systematics of several taxonomically challenging taxa, we analyzed DNA sequences of a short portion (118‐296 base pairs) of the 3’ end of the rbcL gene from three type specimens. The analyses revealed that Harveylithon munitum (basionym: Lithophyllum munitum), described in 1906 from Cave Cays, Exuma Chain, Bahamas, is conspecific with both Goniolithon accretum and Goniolithon affine, described in 1906 from Sand Key, Florida and in 1907 from Culebra Island, Puerto Rico, respectively. L. munitum and G. accretum were described in the same 1906 publication and have equal priority. We have selected the currently accepted and most commonly used name H. munitum to apply to this entity. Comparative analyses of rbcL, psbA, UPA, COI, and LSU sequences from contemporary field‐collected specimens revealed that H. munitum currently inhabits mesophotic rhodolith beds in the northwestern Gulf of Mexico, as well as the intertidal zone in the Florida Keys, Honduras, Atlantic Mexico, Caribbean Panama, and Guadeloupe, French West Indies. Species delimitation analyses reveal that the Western Atlantic and Australian H. munitum populations may be separate species. Two new species of Harveylithon from the northwestern Gulf of Mexico and one new species from the southwestern Gulf of Mexico, the Caribbean, and the Red Sea were also identified in the analyses and are described.

Coralline red algae in the non-geniculate genera Clathromorphum, Phymatolithon and Lithothamnion are important benthic ecosystem engineers in the photic zone of the Arctic and Subarctic. In these regions, the systematics and biogeography of Clathromorphum and Phymatolithon have mostly been resolved whereas Lithothamnion has not, until now. Seventy-three specific and infraspecific names were given to Arctic and Subarctic Lithothamnion specimens in the late 19th and early 20th century by Frans R. Kjellman and Mikael H. Foslie. DNA sequences from 36 type specimens, five historical specimens, and an extensive sampling of recent collections resulted in the recognition of four Arctic and Subarctic Lithothamnion species, L. glaciale, L. lemoineae, L. soriferum and L. tophiforme. Three genes were sequenced, two plastid-encoded, rbcL and psbA, and the mitochondrial encoded COI-5P; rbcL and COI-5P segregated L. glaciale from L. tophiforme but psbA did not. Partial rbcL sequences obtained from type collections enabled us to correctly apply the earliest available names and to correctly place the remainder in synonymy. We were unable to sequence another 22 type specimens, but all of these are more recent names than those that are now applied. It is difficult to identify these species solely on morpho-anatomy as they can all occur as encrusting corallines or as maerl (rhodoliths). We demonstrate the importance of sequencing historical type specimens by showing that the recently proposed North-east Atlantic L. erinaceum is a synonym of one of the earliest published Arctic species of Lithothamnion, L. soriferum, itself incorrectly placed in synonymy under L. tophiforme based on morpho-anatomy. Based on sequenced specimens, we update the distributions and ecology of these species.

International audience; Lithophyllum species in the Mediterranean Sea function as algal bioconstructors, contributing to the formation of biogenic habitats such as coralligenous concretions. In such habitats, thalli of Lithophyllum, consisting of crusts or lamellae with entire or lobed margins, have been variously referred to as either one species, L. stictiforme, or two species, L. stictiforme and L. cabiochiae, in the recent literature. We investigated species diversity and phylogenetic relationships in these algae by sequencing three markers (psbA and rbcL genes, cox2,3 spacer), in conjunction with methods for algorithmic delimitation of species (ABGD and GMYC). Mediterranean subtidal Lithophyllum belong to a well‐supported lineage, hereby called the L. stictiforme complex, which also includes two species described from the Atlantic, L. lobatum and L. searlesii. Our results indicate that the L. stictiforme complex consists of at least 13 species. Among the Mediterranean species, some are widely distributed and span most of the western and central Mediterranean, whereas others appear to be restricted to specific localities. These patterns are interpreted as possibly resulting from allopatric speciation events that took place during the Messinian Salinity Crisis and subsequent glacial periods. A partial rbcL sequence from the lectotype of L. stictiforme unambiguously indicates that this name applies to the most common subtidal Lithophyllum in the central Mediterranean. We agree with recent treatments that considered L. cabiochiae and L. stictiforme conspecific. The diversity of Lithophyllum in Mediterranean coralligenous habitats has been substantially underestimated, and future work on these and other Mediterranean corallines should use identifications based on DNA sequences.

Although complete mitogenomic data have been widely applied in human and other animal population studies, they are extremely limited for florideophycean red algal populations. Gelidiella fanii is a recently described rhodophyte, previously misidentified as G. acerosa, a cosmopolitan agar-yielding species from tropical to subtropical waters. To decipher patterns in genetic diversity and geographic distribution for G. fanii, we obtained 10 complete mitogenomes including two outgroups, G. acerosa and G. flabella. The mitogenomes ranged in size from 25,223 bp to 25,281 bp and had 48 genes, which are similar in general structure, gene order and content, and presence of a group II intron. Phylogenomic analysis revealed that G. fanii was monophyletic and clearly separate from G. acerosa. The range of G. fanii was extended from Southeast Asia and northern Australia to Eritrea, Juan de Nova Island, and Kenya in the west, and to Hawai‘i and Tetiaroa Atoll to the east. Haplotype network analysis of cox1 revealed seven geographically structured groups: Southeast Asia, Kenya/Juan de Nova Island, Indonesia, northern Australia, the Philippines, Tetiaroa Atoll, and Hawai‘i. This regional structure has likely resulted from the separation and isolation of an ancient widespread population during the Pleistocene. This study demonstrates that mitogenome sequencing is a powerful genotyping tool for studies of genetic diversity, biogeography, and conservation of economically valuable marine algal species.

An essential suite of coral reef ecosystem engineers is coralline red algae. Among these, the smooth, encrusting Porolithon onkodes has historically been considered the most important and common reef building species worldwide. We assess P. onkodes biodiversity by performing a genomic analysis of the lectotype specimen collected in 1892 from the Tami Islands, Gulf of Huon, east of New Guinea. Comparisons of DNA sequences from the lectotype specimen to those deposited in GenBank and to newly generated sequences from both field-collected and historical specimens demonstrate that at least 20 distinct species are passing under P. onkodes. We hypothesize that there were multiple evolutionary drivers including ecophysiology, hydrodynamic regimes, and biotic interactions as well as historical biogeography, which resulted in this high diversity of smooth, encrusting Porolithon species throughout the tropics. Our results emphasize the need to document the biodiversity, ecophysiology, and habitats of these tropical, reef-building algae in light of climate change and ocean acidification.

The current identification of crustose coralline algae from North Carolina is based on a few morphoanatomical studies from the last century. We reassessed the type specimens of the two Lithophyllum species historically reported from offshore communities in North Carolina, L. intermedium with a Caribbean Sea type locality and L. subtenellum with an Atlantic southern France type locality, using scanning electron microscopy images and diagnostic rbcL sequences. Neither of the sequences generated from the type specimens matched rbcL sequences from contemporary specimens collected from subtidal North Carolina epibenthic communities. On the basis of analyses of rbcL and other loci (psbA, UPA, and COI), we instead found L. atlanticum, recently described from Brazil, and L. searlesii sp. nov. from Onslow Bay, North Carolina. These sequence data show that L. atlanticum is related to northeast Pacific species, whereas L. searlesii is related to Mediterranean species.

Palmaria decipiens (Reinsch) R.W.Ricker is a ecologically important red seaweed restricted to high latitudes of the southern hemisphere. Here, we contribute to the bioinformatics and evolut...

Plastid-encoded rbcL and psbA sequences from branched, Caribbean Sea Lithophyllum specimens indicate that four species are present, not one. Short (263 base pairs) rbcL sequences from an isolectotype of L. kaiseri (Gulf of Suez) and the holotypes of L. congestum, L. daedaleum and L. platyphyllum (Caribbean Sea) show that L. congestum and L. daedaleum are conspecific with L. kaiseri, the last having nomenclatural priority. Lithophyllum platyphyllum, currently considered a synonym of L. congestum, is recognised as a valid species. Lithophyllum stictaeforme, originally described from the Mediterranean Sea, is not conspecific with L. kaiseri (as L. congestum) as previously suggested. Lithophyllum neocongestum sp. nov. and L. pseudoplatyphyllum sp. nov. are proposed. Together with L. platyphyllum, these three branched species are so far endemic to the Caribbean Sea. This is the first report, documented by DNA sequence data, of a coralline species (L. kaiseri) widespread through the tropical Indo-West Pacific Oceans, Red Sea and Caribbean Sea.

The filamentous marine red alga Ceramium cimbricum was described from Denmark, but the name has since been applied to populations worldwide. To determine if C. cimbricum from the Pacific is conspecific with C. cimbricum from the Atlantic, we (1) deciphered an authentic rbcL sequence for the lectotype specimen of C. cimbricum, (2) performed phylogenetic analysis on Pacific and Atlantic C. cimbricum, and (3) assembled and analyzed the complete mitochondrial and plastid genomes of specimens of C. cimbricum from Denmark and California. The lectotype sequence of C. cimbricum was unique and fully resolved with other Atlantic Ceramium species, however, the specimens of C. cimbricum from Denmark, Norway, California, Oregon, and Korea formed a clade with Pacific species. The plastid and mitochondrial genomes of C. cimbricum from Denmark and California were similar in length and gene content, differing by only 67 SNPs and nine gaps for the plastid, and by 100 SNPs and 31 gaps for the mitochondrial genomes. These results support the continued application of the name C. cimbricum to specimens from Denmark, and warrant the naming of a new species, Ceramium sungminbooi sp. nov., native to Asia and introduced to the northeastern Pacific and Europe.

Molecular surveys are leading to the discovery of many new cryptic species of marine algae. This is particularly true for red algal intertidal species, which exhibit a high degree of morphological convergence. DNA sequencing of recent collections of Gelidium along the coast of California, USA, identified two morphologically similar entities that differed in DNA sequence from existing species. To characterize the two new species of Gelidium and to determine their evolutionary relationships to other known taxa, phylogenomic, multigene analyses, and morphological observations were performed. Three complete mitogenomes and five plastid genomes were deciphered, including those from the new species candidates and the type materials of two closely related congeners. The mitogenomes contained 45 genes and had similar lengths (24,963-24,964 bp). The plastid genomes contained 232 genes and were roughly similar in size (175,499-177,099 bp). The organellar genomes showed a high level of gene synteny. The two Gelidium species are diminutive, turf-forming, and superficially resemble several long established species from the Pacific Ocean. The phylogenomic analysis, multigene phylogeny, and morphological evidence confirms the recognition and naming of two new species, describe herein as G. gabrielsonii and G. kathyanniae. On the basis of the monophyly of G. coulteri, G. gabrielsonii, G. galapagense, and G. kathyanniae, we suggest that this lineage likely evolved in California. Organellar genomes provide a powerful tool for discovering cryptic intertidal species and they continue to improve our understanding of the evolutionary biology of red algae and the systematics of the Gelidiales.

Genomic analysis of the invasive marine snail Batillaria attramentaria from Elkhorn Slough, Moss Landing, California, USA using 150 bp paired-end Illumina sequences resulted in the assembly of its complete mitogenome. The mitogenome is 16,095 bp in length and contains 2 rRNA, 13 protein-coding, and 22 tRNA genes (GenBank Accession MN557850). Gene content and organization of B. attramentaria are identical to the Turritellidae and Pachychilidae. The phylogenetic analysis of B. attramentaria resolves it in a fully supported clade with these same two families in the superfamily Cerithioidea. Nucleotide BLAST searches of the Elkhorn Slough cox1 gene of B. attramentaria yielded identical sequences from invasive populations from California and British Columbia, and native populations from northeastern and central Japan. These data show that mitogenome sequencing is a useful tool for studying the classification and phylogenetic history Cerithioidea.

Rupicola peruvianus Latham, known as the Andean Cock-of-the-Rock or locally as Tunqui, is distributed in the Andean cloud forests of South America from Venezuela to Bolivia. Here, we contribute to ...

Lessonia spicata (Suhr) Santelices is the most ecologically and economically important kelp from Pacific South America. Here, we contribute to the bioinformatics and evolutionary systematics of the species by performing high throughput sequencing on L. spicata from Valparaiso, Chile. The L. spicata complete mitogenome is 37,097 base pairs (bp) in length and contains 66 genes (GenBank accession MK965907), the complete plastid genome is 130,305 bp and has 173 genes (accession MK965908), and the data assembled 7,630 bp of the nuclear ribosomal cistron (accession MK965909). The organellar genomes are similar in structure and content to others published from the Laminariales.

Genomic analysis of the kelp fly Fucellia costalis (Family Anthomyiidae) from Asilomar beach, Pacific Grove, California, resulted in the assembly of its complete mitogenome. The mitogenome is 16,17...

Genomic analysis of the marine alga Corallina chilensis from Tomales Bay, California, USA, resulted in the assembly of its complete mitogenome (GenBank accession number MK598844) and plastid genome...

Interspecific systematics in the red algal order Sporolithales remains problematic. To re-evaluate its species, DNA analyses were performed on historical type material and recently collected specimens assigned to the two genera Sporolithon and Heydrichia. Partial rbcL sequences from the lectotype specimens of Sporolithon ptychoides (the generitype species) and Sporolithon molle, both from El Tor, Egypt, are exact matches to field-collected topotype specimens. Sporolithon crassum and Sporolithon erythraeum also have the same type locality; material of the former appears to no longer exist, and we were unable to PCR amplify DNA from the latter. A new species, Sporolithon eltorensis, is described from the same type locality. We have not found any morpho-anatomical characters that distinguish these three species. No sequenced specimens reported as S. ptychoides from other parts of the world represent this species, and likely reports of S. ptychoides and S. molle based on morpho-anatomy are incorrect. A partial rbcL sequence from the holotype of Sporolithon dimotum indicates it is not a synonym of S. ptychoides, and data from the holotype of S. episporum confirm its specific recognition. DNA sequences from topotype material of Heydrichia woelkerlingii, the generitype species, and isotype material of Heydrichia cerasina confirm that these are distinct species; the taxon reported to be H. woelkerlingii from New Zealand is likely an undescribed species. Type specimens of all other Sporolithon and Heydrichia species need to be sequenced to confirm that they are distinct species; morpho-anatomical studies have proved inadequate for this task.

An unknown species of marine sea lettuce was observed forming green tides consecutive years from 2014 to 2016 in Seaside, California. This Ulva sp. was similar in thallus size and shape to U. expansa. To confirm this identification, whole genome sequencing was performed on the bloom-forming species of Ulva and the holotype specimen of U. expansa. The complete green tide Ulva mitogenome is 64,143 bp in length, contains 65 genes, and displays high gene synteny with U. pertusa Kjellman. The mitogenome was incomplete for the holotype of U. expansa, but the analysis yielded the mitoexome, plastid, and nuclear genetic markers. These data verify that the native U. expansa is responsible for the blooms in central California.

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.

Analysis of the marine black prickleback Xiphister atropurpureus Kittlitz using 76 bp paired-end Illumina sequences resulted in the assembly of its complete mitogenome. The mitogenome is 16,518 bp in length and contains an origin of light strand replication (OL), control region, 22 tRNA, 2 rRNA, and 13 protein-coding genes. Content and organization of the X. atropurpureus mitogenome is consistent with other teleost. Phylogenetic analysis of X. atropurpureus resolves it in a clade with another member of the Stichaeidae, Chirolophis japonicus Herzenstein.

Next generation sequence data were generated and used to assemble the complete plastomes of the holotype of Membranoptera weeksiae, the neotype (designated here) of M. tenuis, and a specimen examined by Kylin in making the new combination M. platyphylla. The three plastomes were similar in gene content and length and showed high gene synteny to Calliarthron, Grateloupia, Sporolithon, and Vertebrata. Sequence variation in the plastome coding regions were 0.89% between M. weeksiae and M. tenuis, 5.14% between M. weeksiae and M. platyphylla, and 5.18% between M. tenuis and M. platyphylla. We were unable to decipher the complete mitogenomes of the three species due to low coverage and structural problems; however, we assembled and analyzed, the cytochrome oxidase I, II, and III loci and found that M. weeksiae and M. tenuis differed in sequence by 1.3%, M. weeksiae and M. platyphylla by 8.4%, and M. tenuis and M. platyphylla by 8.1%. Evaluation of standard marker genes indicated that sequences from the rbcL, RuBisCO spacer, and CO1 genes closely approximated the pairwise genetic distances observed between the plastomes of the three species of Membranoptera. A phylogenetic tree based on rbcL sequences showed that M. tenuis and M. weeksiae were sister taxa. Short rbcL sequences were obtained from type specimens of M. dimorpha, M. multiramosa, and M. edentata and confirmed their conspecificity with M. platyphylla. The data support the recognition of three species of Membranoptera occurring south of Alaska: M. platyphylla, M. tenuis, and M. weeksiae. This article is protected by copyright. All rights reserved.

Ion Proton data was used to assemble the complete mitochondrial genome from the holotype specimen of Wildemania schizophylla (29,156 bp). The mitogenome contains 50 genes, including 2 ribosomal RNA, 23 transfer RNA, 4 ribosomal proteins, 2 ymfs, 3 open reading frames (ORFs), and 19 genes involved in cellular respiration. Although gene synteny is conserved, the mitogenome of W. schizophylla is significantly smaller due to the lack of large intronic ORFs present in the cytochrome oxidase locus of other Bangiales. The results support the recognition of Wildemania as distinct from Porphyra, and demonstrate that small amounts of type material are suitable for genomic studies.