Search

We present the complete chloroplast genome sequence of an endophytic Ostreobium sp. isolated from a 19th-century coralline red algal specimen from St. Croix, U.S. Virgin Islands. The chloroplast genome is 84,848 bp in length, contains 114 genes, and has a high level of gene synteny to other Ostreobiaceae.

Here, we present the complete chloroplast genome sequence of Toxicodendron diversilobum , western poison oak, from Pacific Grove, California. The genome is 159,543 bp in length, contains 133 genes, and has a high level of gene synteny to other species of Toxicodendron .

Partial rbcL sequences were obtained from the type specimens of Lithophyllum coarctatum and L. gardineri. Both species were variably assigned to either Hydrolithon or Porolithon during the last two centuries, with L. coarctatum, from the tropical eastern Indian Ocean currently considered a synonym of L. gardineri from the tropical western Indian Ocean. Phylogenetic analyses show that both belong in Porolithon and that they are distinct species despite their morpho-anatomical similarities, including a columnar morphology. Porolithon epiphyticum sp. nov., from the same locality as P. coarctatum, Cocos-Keeling Islands, is the first reported epiphytic species in the genus. Eight of the currently recognized 15 species of Porolithon have had their type specimens sequenced to correctly apply names, including the generitype specimen. DNA sequencing provides independent confirmation that the morpho-anatomical character of the presence of horizontal fields of trichocytes without intervening vegetative cells is diagnostic for Porolithon. The generitypes of the four genera classified in the subfamily Metagoniolithoideae, Dawsoniolithon, Floiophycus, Harveylithon, and Metagoniolithon as well as Hydrolithon in the subfamily Hydrolithoideae, have not been sequenced. The taxonomic and nomenclatural uncertainties in each of these genera are discussed.

Here, we present the complete chloroplast genomes of Quercus × morehus , Q. wislizeni , and Q. kelloggii from California. The genomes are 161,119 to 161,130 bp and encode 132 genes. Quercus × morehus and Q. wislizeni are identical in sequence but differ from Q. kelloggii by three indels and eight SNPs.

Species of Ulva Linnaeus are nearly impossible to identify using morpho-anatomy due to their simple thallus structure and phenotypic plasticity. The current solution to this problem is to sequence ...

The taxonomic status of species assigned to the marine red algal genus Osmundea from Pacific North America has not been critically studied. We analyzed the complete organellar genomes of an isotype specimen of O. sinicola and conducted a genetic comparison of rbcL and COI-5P markers based on 15 specimens of Laurencia scrippsensis, O. crispa, and O. sinicola collected from California, the Gulf of California, and Pacific Baja California, including their type specimens. The mitogenome of O. sinicola was 25,021 bp in length and contained 44 genes, and the plastid genome was 171,419 bp with 225 genes. Both genomes show a high level of gene synteny with previously published organellar chromosomes from the Rhodomelaceae. Phylogenetic analysis of the rbcL and COI-5P genes identified two distinct clades, one containing the isotype of O. sinicola, and the other included the isotype of O. crispa and holotype of Laurencia scrippsensis. These data show that L. scrippsensis is a heterotypic synonym of O. crispa, rather than of O. sinicola. They support the recognition of two species, O. crispa from Monterey, California to Baja California Sur, and O. sinicola from Baja California Sur to the Gulf of California. California specimens identified as O. sinicola are misidentified O. crispa. Reports of O. sinicola from outside this range based on morpho-anatomy require confirmation by DNA sequencing. These genetic results highlight the need further analyses of type material from the Rhodomelaceae.

Here, we present the complete chloroplast genomes of

Here, we present the chloroplast genome sequence of Quercus agrifolia Née, the California live oak, an ecologically important oak species along the coast of California. The genome is 161,283 bp in length, encodes 132 genes, and has a high level of gene synteny to other Fagaceae.

The aphid Chaetosiphon fragaefolii Cockerell, 1901 is an agricultural pest and known vector of strawberry viruses. To better understand its biology and systematics, we performed a genomic analysis on C. fragaefolii collected from Quinalt strawberry plants from Pacific Grove, Monterey county, California, USA using Oxford Nanopore and Illumina sequencing. The resulting data were used to assemble the aphids complete mitogenome. The mitogenome of C. fragaefolii is 16,108 bp in length and contains 2 rRNA, 13 protein-coding, and 22 tRNA genes (GenBank accession number LC590896). The mitogenome is similar in content and organization to other Aphididae. Phylogenetic analysis of the C. fragaefolii mitogenome resolved it in a fully supported clade in the tribe Macrosiphini. Analysis of the cox1 barcode sequence of C. fragaefolii from California found exact and nearly identical sequences to C. fragaefolii and Chaetosiphon thomasi Hille Ris Lambers, 1953, suggesting the two species are conspecific.

Gigartina skottsbergii is the currently accepted name for the large, peltate species of Gigartinaceae distributed in Argentina, Chile, and along the Antarctic Peninsula. However, phylogenetic analyses of DNA sequences for more than twenty years indicate that two species are passing under the name G. skottsbergii, and both DNA sequences and morpho-anatomy indicate that the species are assignable to an undescribed genus. To formally validate the new genus and species, we performed next generation sequencing (NGS) on the lectotype material of G. skottsbergii to document its genetic identity and obtained its complete mitogenome and partial plastid genome. Phylogenetic analysis of rbcL and cox1 sequences of the lectotype along with recent collections of G. skottsbergii from southern South America and Antarctica, confirmed the generic distinction and the presence of two morphologically similar taxa. We propose Sarcopeltis gen. nov., containing the generitype S. skottsbergii comb. nov. from southern South America, and S. antarctica sp. nov. from the Antarctic Peninsula. Sarcopeltis is characterized by the following suite of features: 1) peg-like secondary haptera that adhere to the substratum, 2) absence of an envelope surrounding each cystocarp, 3) presence of extensive, terminal, tubular gonimoblast filaments that fuse with surrounding vegetative cells, and 4) tetrasporangia formed from secondary filaments entirely in the medulla. This study demonstrates that genetic analysis of type material, together with recently obtained DNA sequences from field collected specimens, can provide clear and objective taxonomic conclusions.

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.

Here, we present the chloroplast genome sequence of Quercus agrifolia Née, the California live oak, an ecologically important oak species along the coast of California. The genome is 161,283 bp in length, encodes 132 genes, and has a high level of gene synteny to other Fagaceae.

Amorpha californica var. napensis Jeps. 1925, the Napa false indigo, is a threatened shrub endemic to northern California. Here the complete chloroplast genome of topotype material of var. napensis was assembled and characterized to contribute to the bioinformatics, systematics, and conservation of this variety. The chloroplast genome (GenBank accession OK274088) is 158,294 base pairs (bp) in length, encodes 130 genes including 85 protein-coding, 37 tRNA, 8 rRNA, and shows a high-level of gene synteny to other Papilionoideae. Phylogenetic analysis fully resolved var. napensis in a clade with A. fruticosa L. and A. roemeriana Scheele, sister to the Dalbergieae. The newly sequenced chloroplast genome shows that the genetic differences between var. napensis and Amorpha californica Nutt. var. californica are greater than the variation observed between var. napensis and many other Amorpha spp. sequences deposited in GenBank. These data suggest that var. napensis should be elevated to full species rank.

The aphid Chaetosiphon fragaefolii Cockerell, 1901 is an agricultural pest and known vector of strawberry viruses. To better understand its biology and systematics, we performed a genomic analysis on C. fragaefolii collected from Quinalt strawberry plants from Pacific Grove, Monterey county, California, USA using Oxford Nanopore and Illumina sequencing. The resulting data were used to assemble the aphids complete mitogenome. The mitogenome of C. fragaefolii is 16,108 bp in length and contains 2 rRNA, 13 protein-coding, and 22 tRNA genes (GenBank accession number LC590896). The mitogenome is similar in content and organization to other Aphididae. Phylogenetic analysis of the C. fragaefolii mitogenome resolved it in a fully supported clade in the tribe Macrosiphini. Analysis of the cox1 barcode sequence of C. fragaefolii from California found exact and nearly identical sequences to C. fragaefolii and Chaetosiphon thomasi Hille Ris Lambers, 1953, suggesting the two species are conspecific.

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...

Analysis of Phrynosoma blainvillii Gray from Marina, Monterey County, California, using 150 bp paired-end Illumina sequences (Illumina, San Diego, CA) resulted in the assembly of its complete mitogenome. The mitogenome is 16,946 bp in length and contains a putative origin of light strand replication (OL), control region, 22 tRNA, 2 rRNA, and 13 protein-coding genes. Its content and organization are similar to other Squamata. Phylogenetic analysis of P. blainvillii resolves it in a clade with P. sherbrookei Nieto-Montes de Oca, Arenas-Moreno, Beltrán-Sánchez & Leaché, sister in position to Uma notata Baird. Mitochondrial marker analysis of P. blainvillii from Marina shows that it belongs to a coastal Santa Lucia Mountain Range haplogroup that is distinct from other populations of P. blainvillii in California.

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.

The classification of species originally assigned to the marine red algal genus Coeloseira G.J. Hollenberg remains univestigated using molecular data. Paired-end 36 bp Illumina sequences (Illumina Inc, San Diego, CA) were generated from a specimen of Coeloseira compressa G. J. Hollenberg and used to assemble the partial mitochondrial and complete plastid genomes. The mitogenome is 25,391 bp in length and contains 46 genes, and the plastome is 176,291 bp with 233 genes. Both organellar genomes show high gene synteny with previously published Florideophyceae. Comparison of organellar and nuclear phylogenetic markers (rbcL, CO1, LSU) of C. compressa to other genera in the Champiaceae supports its removal from Gastroclonium Kützing and the reinstatement of the name Coeloseira compressa.

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.

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 other non-native populations of C. okamurae, high-throughput sequencing analysis was performed on an introduced specimen from Bennett Slough, Moss Landing, California, USA. Assembly of 23,146,595 filtered 150 bp paired-end Illumina sequencing reads yielded its complete mitogenome (GenBank accession MT193839) and plastid genome (GenBank accession MT193838). The mitogenome is 25,995 bp in length and contains 50 genes. The plastid genome is 173,516 bp and contains 234 genes. Comparison of the organellar chromosomes to other Gigartinales revealed a high-level of gene synteny. BLAST analysis of marker sequences (rbcL, cox1, cox2) of C. okamurae from Moss Landing identified four identical DNA sequences: one from a specimen from a native population of C. okamurae from South Korea and three from specimens representing invasive populations from France, Spain, and the USA. These genetic results confirm the presence of C. okamurae in central California, USA, and represent the first complete mitogenome and plastid genome from the Caulacanthaceae.

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.

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 the bioinformatics and evolutionary systematics of the Cotingidae by performing high-throughput sequencing analysis on R. peruvianus from Luya, Amazonas, Peru. The R. peruvianus mitogenome is 17,035 base pairs (bp) in length and contains 37 genes (GenBank accession No. MN602289). The mitogenome is similar in structure and content to published mitogenomes from the neognathid orders Passeriformes and Falconiformes. Phylogenomic analysis of the R. peruvianus mitogenome situates it in a clade with the Pipridae, sister to the Tyrannidae. We anticipate that further mitogenome sequencing of the parvorder Tyrannida will improve the phylogenetic resolution and our understanding of the evolutionary history of this taxon.

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.

Recent genetic studies of the Bangiales (Rhodophyta) led to the resurrection of the marine red algal genus Wildemania De Toni. To gain a better understanding of the phylogenetic history of this genus and its plastid genome structure, the holotype specimen of Wildemania schizophylla (Hollenberg) S. C. Lindstrom was analyzed using next generation sequencing technology. The plastid genome of W. schizophylla is 193,008 bp in length and contains 249 genes, including 47 ribosomal, 34 tRNA, 29 photosystem, 27 open reading frames, 25 hypothetical proteins, 10 phycobiliprotein, 8 ATP synthase, and 8 cytochrome b/f complex genes. The plastid genome shows similar organization and content to other Bangiaceae, except that it lacks the typical 16S and 23S ribosomal RNA repeat. Phylogenetic analysis of the W. schizophylla plastid genome against other Bangiaceae places W. schizophylla in a robustly supported position, intermediate between Porphyra C. Agardh and Pyropia J. Agardh. These data support the recent re...

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.

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 ...

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...

An unidentified marine red algal species classified in Pyropia J. Agardh was discovered from Monterey, CA. Morphological, barcode, and complete mitochondrial genome analysis of the alga support its recognition as a new species, Pyropia nitida sp. nov. The species is a high-intertidal, winter annual that is lanceolate in shape, monostromatic, and dioecious. Based on CO1 sequences, P. nitida is closely allied with the P. nereocystis clade. The mitogenome of P. nitida is 35 313 bp in length and contains 53 genes, including two ribosomal RNAs, 24 transfer RNAs, four ribosomal proteins, two ymfs, four ORFs, and 17 genes involved in electron transport and oxidative phosphorylation. The results support the recognition of P. nitida as distinct from the morphologically similar P. lanceolata.

Nothogenia fastigiata has been reported to exhibit great morphological variability and has been considered to be widely distributed in the Southern Hemisphere. To test its current circumscription, sequences from type material of N. fastigiata and other species currently synonymized with it were compared to those from recent collections of this and other species in the genus. Eight distinct species previously subsumed under the name N. fastigiata were identified. Multiple specimens from southern Chile and a single specimen from Campbell Island (subantarctic New Zealand) were conspecific with type material of N. fastigiata from the Falkland Islands. For other species, molecular analyses of recent collections using the nuclear ITS1-5.8S-ITS2 region of the ribosomal cistron, the chloroplast rbcL and psbA genes and the mitochondrial COI gene indicated a strong geographic pattern to species relationships. Other specimens identified as N. fastigiata from Chile represented up to five species, including N. chilensis and N. fragilis, based on sequences of type material; these Chilean species occurred on a monophyletic branch. We also recognized N. lingula comb. nov. from Tasmania, which is closely related to N. fastigiata, based on sequences of type material. Specimens from mainland New Zealand identified as N. fastigiata fell into a distinct clade with New Zealand N. pulvinata and represented a previously undescribed species, described here as N. neilliae sp. nov. Another New Zealand species, N. pseudosaccata, was distantly related to N. variolosa from Auckland Island and other subantarctic islands south of New Zealand. The New Zealand species were more closely related to South African N. erinacea and N. ovalis than to species of Nothogenia from Chile, including N. fastigiata, although bootstrap support for this interpretation was weak. These genetic data demonstrate that matching DNA sequences from archival Nothogenia material to modern specimens can be used to identify and define new and old cryptic species.

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.

Fucus spiralis L. is a broadly distributed monoecious intertidal seaweed. The specific status of F. spiralis however is debatable. Here, we contribute to the bioinformatics and systematics of F. spiralis by analysing the complete mitochondrial and plastid genomes of a specimen from California, U.S.A. The F. spiralis mitogenome is 36,396 base pairs (bp) in length and contains 67 genes, and the plastid genome is 125,066 bp in length and contains 171 genes. The F. spiralis genomes are 99.7% and 99.8% similar in nucleotide sequence to F. vesiculosus, and support the revised classification of F. spiralis to Fucus vesiculosus var. spiralis.

A large number of invasive marine invertebrates are recognized from Elkhorn Slough (ES), California. One of these species in the slough is treated as Hymeniacidon sinapium (Family Halichondriidae) but its species identity is in doubt pending molecular confirmation. The purpose of this investigation was to confirm the presence of H. sinapium in ES, determine its distribution in the slough, and compare its genetic diversity to others in California and worldwide. To address these goals, 23 specimens of Hymeniacidon were analyzed using DNA sequences of the nuclear rDNA internal transcribed spacers (ITS1 + ITS2) and the 5.8S exon. The sequences were compared against those of H. sinapium from: San Diego and Tomales Bay in California; Japan; and South Korea. All ES sequences were found to be nearly identical to the other H. sinapium sequences, differing by only 1-3 nucleotides. ES specimens displayed five unique genotypes: three showed intragenomic polymorphisms (IGPs) in the ITS1 region (positions 155, 181, and 195). These data conclusively document the presence of H. sinapium in ES as well as define the species to a relatively narrow portion of its eastern shores (~4 km long). Since the genetic diversity of H. sinapium in ES is higher than that reported worldwide, its presence in ES is likely the result of multiple introductions. One of the IGPs in ES was found to be the most abundant and was widely distributed in the slough: an indication that it may be spreading.

The origins of the Bronze Age Minoan and Mycenaean cultures have puzzled archaeologists for more than a century. We assembled genome-wide data from nineteen ancient individuals, including Minoans from Crete, Mycenaeans from mainland Greece, and their eastern neighbours from southwestern Anatolia. We show that Minoans and Mycenaeans were genetically similar, having at least three quarters of their ancestry from the first Neolithic farmers of western Anatolia and the Aegean1,2, and most of the remainder from ancient populations like those of the Caucasus3 and Iran4,5. However, the Mycenaeans differed from Minoans in deriving additional ancestry from an ultimate source related to the hunter-gatherers of eastern Europe and Siberia6–8, introduced via a proximal source related to either the inhabitants of either the Eurasian steppe1,6,9 or Armenia4,9. Modern Greeks resemble the Mycenaeans, but with some additional dilution of the early Neolithic ancestry. Our results support the idea of continuity but not isolation in the history of populations of the Aegean, before and after the time of its earliest civilizations.

The field of molecular paleontology has recently made significant contributions to anthropology and biology. Hundreds of ancient DNA studies have been published, but none has targeted fossil coralline algae. Using regions of the SSU gene, we analyzed rDNA from fossil coralline algae of varying ages and states of preservation from Spain, Papua New Guinea (PNG), and the Great Barrier Reef (GBR). Specimens from PNG, GBR, and some localities from Spain did not contain endogenous ancient DNA. Reproducible sequence data were obtained from specimens ∼550 years old from near Cadiz, Spain, and from rocky-shore deposits in Carboneras, Almeria Province of Spain (∼78,000 years before present [YBP]). Based on BLAST searches and a phylogenetic analysis of sequences, an undescribed coralline alga belonging to the Melobesioideae was discovered in the Carboneras material as well as the following coralline genera: Jania, Lithophyllum, Lithothamnion, Mesophyllum, and Phymatolithon. DNA from fleshy brown and red macroalgae was also discovered in the specimens from Carboneras. The coralline algae identified using molecular techniques were in agreement with those based on morphological methods. The identified taxa are common in the present-day southeastern Spain littoral zone. Amino acid racemization, concentration ratios, and specific concentrations failed to show a correlation between biomolecular preservation and PCR amplification success. Results suggest that molecular investigations on fossil algae, although limited by technical difficulties, are feasible. Validity of our results was established using authentication criteria and a self-critical approach to compliance.

The complete genome sequence from a nonhemolytic strain of Streptococcus agalactiae from the oral cavity of a canine was assembled. The genome is 2,165,968 bp, contains 2,055 genes, and is classified as group B streptococcus (GBS) serotype V, strain 1. A comparison to other S. agalactiae sequences shows high gene synteny with human and bovine strains.

Ancient DNA methodologies can be applied in the investigation of the genetics of extinct populations. A search for beta thalassemia mutations was performed on 49 Minoan individuals from the Bronze Age who were living in the island of Crete approximately 4000 Years Before Present (YBP). Standard precautionary measures were employed in the laboratory to ensure authenticity of the DNA extracted from the ancient bones, resulting in the successful analysis of DNA of 24 Minoans. DNA sequencing focused on the Intervening Sequence 1 (IVS-1) of the beta globin gene and its splicing junctions. 63% of the thalassemia mutations observed among modern Cretans reside in beta IVS-1. None of the Minoan individuals carried one of the IVS-1 mutations known to cause beta thalassemia; however, only one was expected to be observed if the average frequency of beta thalassemia heterozygotes in the Minoan population was the same with that of modern day Cretans (7.6%). One individual contained a C to G substitution in position 91 of the IVS-1, located 40 bp 5′ to the intron 1/exon 2 junction. Functional studies indicated that the mutation did not affect mRNA splicing or stability, and most likely represented an innocent single nucleotide polymorphism.

Analysis of Phrynosoma blainvillii Gray from Marina, Monterey County, California, using 150 bp paired-end Illumina sequences (Illumina, San Diego, CA) resulted in the assembly of its complete mitogenome. The mitogenome is 16,946 bp in length and contains a putative origin of light strand replication (OL), control region, 22 tRNA, 2 rRNA, and 13 protein-coding genes. Its content and organization are similar to other Squamata. Phylogenetic analysis of P. blainvillii resolves it in a clade with P. sherbrookei Nieto-Montes de Oca, Arenas-Moreno, Beltran-Sanchez & Leache, sister in position to Uma notata Baird. Mitochondrial marker analysis of P. blainvillii from Marina shows that it belongs to a coastal Santa Lucia Mountain Range haplogroup that is distinct from other populations of P. blainvillii in California.