Cox2-3 Spacer Research Articles

Tracing genetic variation of Gelidium canariense (Rhodophyta) based on new and historical collections

ABSTRACT Genetic sequencing of herbarium specimens provides invaluable information on species genetic history. However, several factors hinder the extraction of high-quality DNA from long-term preserved specimens. Our goal was to study the genetic variability of the endemic and habitat-forming macroalga Gelidium canariense over the last 40 years using the mitochondrial intergenic marker cox2-3 spacer. We also studied the genetic diversity at the mesoscale (<100 km), i.e. between two localities on the north coast of Tenerife and at the macroscale (>100 km) using specimens collected on the island of La Palma. We found the presence of the same haplotype at the same location for the last 40 years. This haplotype also coincided within populations of Puerto de la Cruz and Garachico (Tenerife Island) and between populations of different islands (Tenerife and La Palma). This study provides a baseline (i.e. extraction method, PCR protocol for cox2-3 spacer molecular marker, level of DNA degradation of herbarium samples) of the genetic characterization of G. canariense that can be used in future molecular studies to better understand the distribution of genetic diversity in this vulnerable species.

Molecular Assessment of Kappaphycus alvarezii Cultivated in Tarakan based on cox2-3 Spacer

The seaweed Kappaphycus alvarezii is a leading aquaculture commodity possessing high economic value that has been used as a raw material for various natural products, food, and pharmaceutical industries. The main challenge regarding its production, escpecially in Tarakan is the supply of superior seeds. Therefore, this study aims to obtain phylogenetic information and the cultivation performance of the selected seeds by identifying genetic sources based on molecular markers. DNA sequencing analysis was carried out using the molecular marker cox2-3 spacer on a collection comprising 16 cultivars from all over the country (Indonesia). The four haplotypes representing K. alvarezii to be cultivated in the city were produced by phylogenetic clustering and further molecular analysis using cox2-3 intergenic spacer mitochondrial DNA marker. These include the Kupang varieties and Natuna, also referred to as Lampung seedlings, which is a tissue culture plantlet used for development at SEAMEO-BIOTROP Bogor and propagated by the Lampung Marine Aquaculture Center (BBPBL), Tarakan. These varieties were genetically distances (pairwise comparisons based on mean Kimura 2-parameter model) ranging from 0.00-0.23 unit. The cultivation was carried out for 30 days in the waters of Tanjung Batu (Tj. Batu) Mamburungan, Tarakan, North Kalimantan, for 30 days. The result showed that the Natuna* as Lampung cultivar has superior performance compared to local cultivars (Takalar as Mamburungan Tanjung Batu, Tarakan, and Kupang). Furthermore, the genetic analysis with cox2-3 spacer markers had the potential as an effective seed selection tool for tracing genetic information in the development of superior seedlings in aquaculture activities.

Molecular Assessment of Kappaphycus alvarezii Cultivated in Tarakan based on cox2-3 Spacer

The seaweed Kappaphycus alvarezii is a leading aquaculture commodity possessing high economic value that has been used as a raw material for various natural products, food, and pharmaceutical industries. The main challenge regarding its production, escpecially in Tarakan is the supply of superior seeds. Therefore, this study aims to obtain phylogenetic information and the cultivation performance of the selected seeds by identifying genetic sources based on molecular markers. DNA sequencing analysis was carried out using the molecular marker cox2-3 spacer on a collection comprising 16 cultivars from all over the country (Indonesia). The four haplotypes representing K. alvarezii to be cultivated in the city were produced by phylogenetic clustering and further molecular analysis using cox2-3 intergenic spacer mitochondrial DNA marker. These include the Kupang varieties and Natuna, also referred to as Lampung seedlings, which is a tissue culture plantlet used for development at SEAMEO-BIOTROP Bogor and propagated by the Lampung Marine Aquaculture Center (BBPBL), Tarakan. These varieties were genetically distances (pairwise comparisons based on mean Kimura 2-parameter model) ranging from 0.00-0.23 unit. The cultivation was carried out for 30 days in the waters of Tanjung Batu (Tj. Batu) Mamburungan, Tarakan, North Kalimantan, for 30 days. The result showed that the Natuna* as Lampung cultivar has superior performance compared to local cultivars (Takalar as Mamburungan Tanjung Batu, Tarakan, and Kupang). Furthermore, the genetic analysis with cox2-3 spacer markers had the potential as an effective seed selection tool for tracing genetic information in the development of superior seedlings in aquaculture activities.

A new genetic lineage of Asparagopsis taxiformis (Rhodophyta) in the Mediterranean Sea: As the DNA barcoding indicates a recent Lessepsian introduction

Asparagopsis taxiformis(Delile) Trevisan is a red marine macroalga (Bonnemaisoniales, Rhodophyta) with high invasive potential and broad worldwide distribution. In the Mediterranean Sea,A. taxiformiswas reported before the opening of the Suez Canal and is comprised of two different cryptic lineages, named L2 and L3. As for the Israeli Mediterranean Sea (IMS),A. taxiformisbenthic populations have seemingly expanded with several large seasonal blooms recorded in recent years. However, neither ecology nor molecular substantial studies have been conducted for this particular geographical area. Increasing sampling intensity and geographical coverage may reveal new lineages or indicate human-mediated spread routes not only forA. taxiformisbut for macroalgae in general. This approach is particularly important in areas such as the eastern Mediterranean Sea, which experiences intense biological invasion on a global scale. In this study, randomly samples specimens (n = 30) ofA. taxiformisand preserved herbarium samples (n = 4) collected from the IMS in the past, were all barcoded and taxonomically identified using three molecular genetic markers (LSU,cox2-3 spacer, andrbcL). We found a cryptic lineage 4 (L4) ofA. taxiformisfirst reported here for the Mediterranean Sea, and previously described for the western Indo-Pacific and Hawaii. Herbarium samples confirmed the presence of L4 as early as 2013. Comparative assessment ofcox2-3 spacer marker indicates 100% similarity to sequenced L4 samples from Egypt in the Red Sea. The IMScox2-3 spacer sequences differed from previously sequenced samples from the Mediterranean Sea by 2.3% and 3.9% bp, compared to L3 and L2 Mediterranean populations, respectively. Morphological inspections indicate monoecious L4 gametophytes which are larger than the L4 population reported previously from Hawaii. Altogether, our results strongly indicate a Lessepsian migration route forA. taxiformisL4 with yet unknown consequences for the local marine ecosystems.

Phylogeny and genetic diversity of the Philippine eucheumatoid genus Mimica (Solieriaceae, Rhodophyta), and the proposal for Kappaphycopsis gen. nov. to include the anomalous species of Kappaphycus, K. cottonii

ABSTRACT The term ‘eucheumatoids’ designates a group of genera in the family Solieriaceae that are the source of some of the most valuable algal products in cultivation. While economically important in the tropics, much of its taxonomy is yet to be fully resolved. The eucheumatoid species Mimica arnoldii is a Batesian mimic of corals that was recently transferred to its own genus from Eucheuma based primarily on peculiarities of habit and a lack of medullary rhizoids, in contrast to the generitype Eucheuma denticulatum that has the latter. We studied the diversity of Mimica arnoldii from samples collected in the Philippines to determine their genetic variation, relationships to other eucheumatoids, and whether its two distinct morphological expressions, which have been named as varieties, are genetically different. We produced a phylogeny using a three-gene concatenated dataset, and used the variable mitochondrial cox2-3 spacer to determine intraspecific variation and the degree of correlation between sequence-variation and varietal status. Our results showed that Mimica is a distinct genus, and that intra-specific molecular data did not correspond to the morphology-based varieties, although it did correlate with geographical distribution. Our results also indicate that Kappaphycus, as presently circumscribed, contains species with (Kappahycus alvarezii, K. striatus and K. malesianus) and without (Kapppahycus cottonii) internal medullary hyphal core, and that K. cottonii is sister to the remaining Kappaphycus species. We thus propose Kappaphycopsis gen. nov. for K. cottonii for the species of Kappaphycus without internal medullary rhizoids (anaxiferous).

Cryptic diversity and phylogeographic patterns in the Asparagopsis armata species complex (Bonnemaisoniales, Rhodophyta) from New Zealand

ABSTRACT Molecular techniques have become important tools to investigate cryptic diversity and phylogeographic patterns. Mitochondrial markers have revealed that the temperate red alga Asparagopsis armata contains two cryptic clades. The A. armata species complex is native to Australia and New Zealand and has been introduced around the world, particularly to Europe. Previous sequencing has focused on A. armata outside of its native range, and there are few sequences available from Australia and New Zealand. Our study investigated cryptic diversity and phylogeographic patterns for over 60 individuals from 7 locations around New Zealand using the mitochondrial cox2-3 spacer and plastid rbcL markers, and found that both cryptic clades within A. armata (L1 and L2) can be found in New Zealand. For the first time, our study has revealed haplotype variation (A and B) within each of the two cryptic A. armata clades. Asparagopsis armata L1A has been found in Australia, Europe and South Africa and is the only invasive lineage currently known, while A. armata haplotype L1B is found throughout New Zealand. In addition, A. armata L2A has been found only in Australia, and A. armata L2B has a southern distribution in New Zealand. The two mitochondrial lineages from New Zealand (L1B and L2B) were found to coexist in several locations. Further work is needed to characterize any differences in the morphology, physiology and biochemistry of the four genetically distinct mitochondrial lineages within the two cryptic clades, as well as their geographic and ecological distributions.

Betaphycus gelatinus and B. philippinensis (Gigartinales, Rhodophyta) are conspecific

Due to lack of definitive differences in phenotypic characters, earlier taxonomic work questioned the separation between Betaphycus gelatinus and B. philippinensis. To date, no attempt has been made to clarify their species boundaries. To investigate whether the two names constitute distinct species, an organellar marker-based phylogenetic approach (rbcL, COI-5P, and cox2-3 spacer) was performed using molecular species discrimination methods (ABGD, SPN, GMYC, and PTP/bPTP). Concordant with observed and published morphological data, the molecular results revealed that B. gelatinus is indistinguishable from B. philippinensis. The name B. philippinensis is thus relegated to synonymy with B. gelatinus.

Unmasking a cryptic ethnotaxon: a case study on the identity of Dermonema virens (Nemaliales, Rhodophyta) in the Philippines

Indigenous knowledge on seaweed utilisation in the Philippines is common; with the coastal natives of the country’s northern region regarded as the most knowledgeable. Dependence on use of vernacular seaweed names valorises traditional wisdom, however, this is prone to taxonomic ambiguities. Such is the case for cryptic seaweed ethnotaxa whose accurate taxonomic recognition largely falls short. Known in the northern Philippines as an edible seaweed, the taxonomy of Salingongo or Kaññungu remains ambiguous. Molecular analysis based on plastid rbcL gene sequences revealed the identity of Salingongo/Kaññungu as Dermonema virens. Due to lack of any available mitochondrial DNA sequences for D. virens in GenBank, the COI-5P and cox2-3 spacer sequences generated from this study did not permit species recognition. The newly sequenced mtDNA accessions therefore served, otherwise, as the database representing the first mtDNA sequence reference for D. virens. The use of D. virens as an edible seaweed in the Philippines further reinforces the extensive overlap of traditional knowledge with regard to seaweed utilisation between the indigenous people from Taiwan and the northern Philippines. The case study presented here underpins the utility of molecular analysis, along with morphological evaluation, as a key combinatory tool for unmasking the diversity of seaweed ethnotaxa.

Phenotypic and mtDNA variation in Philippine Kappaphycus cottonii (Gigartinales, Rhodophyta)

Members of the carrageenan-producing seaweeds of the genus Kappapphycus have a complicated taxonomic history particularly with regard to species identification. Many taxonomic challenges in this group have been currently addressed with the use of mtDNA sequences. The phylogenetic status and genetic diversity of one of the lesser known species, Kappaphycus cottonii, have repeatedly come into question. This study explored the genetic variation in Philippine K. cottonii using the mtDNA COI-5P gene and cox2-3 spacer sequences. The six phenotypic forms in K. cottonii did not correspond to the observed genetic variability; hinting at the greater involvement of environmental factors in determining changes to the morphology of this alga. Our results revealed that the Philippine K. cottonii has the richest number of haplotypes that have been detected, so far, for any Kappaphycus species. Our inferred phylogenetic trees suggested two lineages: a lineage, which exclusively includes K. cottonii and another lineage comprising the four known Kappaphycus species: K. alvarezii, K. inermis, K. malesianus, and K. striatus. The dichotomy supports the apparent synamorphy for each of these lineages (the strictly terete thalli, lack of protuberances, and the presence of a hyphal central core in the latter group, while the opposite of these morphologies in K. cottonii). These findings shed new light on understanding the evolutionary history of the genus. Assessing the breadth of the phenotypic and genetic variation in K. cottonii has implications for the conservation and management of the overall Kappaphycus genetic resources, especially in the Philippines.

Advancing the taxonomy of economically important red seaweeds (Rhodophyta)

ABSTRACTThe cultivation of red seaweeds for food (nori), agar and carrageenans is the basis of a valuable industry. However, taxonomic knowledge of these cultivated seaweeds and their wild relatives has not kept pace with advances in molecular systematics despite the fundamental importance of being able to identify commercially important species and strains, discover cryptic and endemic taxa and recognize non-native species with potentially damaging diseases and epiphytes. This review focuses on molecular taxonomic advances in the cultivated red algae with the highest commercial value globally: Eucheuma and Kappaphycus, Porphyra sensu lato and Gracilaria. All three groups are similarly taxonomically challenging: speciose, morphologically plastic, with poorly resolved species boundaries. Eucheuma and Kappaphycus are frequently misidentified and the molecular markers cox2-3 spacer, cox1 and RuBisCO spacer have helped in understanding phylogenetic relationships and identifying new species and haplotypes. In Porphyra sensu lato (Bangiales) species identification and phylogenetic relationships were highly problematic until a taxonomic revision based on a two-gene phylogeny (18S and rbcL) resulted in nine genera of bladed species. Pyropia, with at least 89 species, three in nori cultivation, has potential for new commercial evaluation. In Gracilaria sensu lato, earlier efforts to resolve species-level taxonomy and generic descriptions were superseded by application of molecular tools, including DNA sequences of the RuBisCO spacer, rbcL gene, 18S and the ITS region. Studies of these cultivated red algal genera highlight the need for a robust taxonomy, a more standardized approach to the molecular markers used and a comprehensive dataset for each representative species. Current work on DNA-based species delimitation, the emergence of high throughput sequencing, multi-gene phylogenies, publication of whole genomes (e.g. Porphyra umbilicalis) and genomes in the pipeline (e.g. Gracilaria) are increasingly improving our understanding of phylogenomic relationships and species relationships. This knowledge, in turn, can then be applied to improving red seaweed aquaculture.

Taxonomical Synonymy of Red Seaweed Gracilaria foliifera (Forsskal) Borgesen, 1932 with Gracilaria corticata J. Agardh, 1852 based on Multi-Local Phylogeny

In this study, we assessed taxonomical position of Gracilaria corticata J. Agardh and Gracilaria foliifera (Forsskal) Borgesen collected from various locations along Indian coastline by combined morphological and multi-local molecular approaches. The species were indistinguishable based on morphological features which were previously claimed by various authors as diagnosing traits for the two species.These taxa were polyphyletic in our phylograms based either on chloroplast DNA rbcL-rbcS or mitochondrial DNA Cox2-3 spacer sequences. A clade consisting of Gracilaria corticata and Gracilaria foliifera was indeed monophyletic and strongly supported, resolving the conspecificity of these two taxa. Based on article 11 of ICN, the principle of taxonomic priority, the binomen Gracilaria corticata is valid and preferable. Gracilaria foliifera nomen rejiciendum is therefore a synonym of the valid binomen Gracilaria corticata.

Phylogeography of the freshwater red alga Setacea puiggariana (Rhodophyta, Batrachospermales) in Brazil

:Phylogeography of Setacea puiggariana, which is widely distributed in southern and south-eastern Brazil, with few records in South America and Africa, was investigated based on mitochondrial genetic markers: the cox2-3 spacer and the barcode region of cox1 gene. Ten stream segments were sampled across the known geographic distribution in Brazil, with a total of 65 individuals sequenced for the cox2-3 spacer and 30 for cox1. Six cox2-3 and eight cox1 haplotypes were observed among the individuals analyzed. Two haplotypes were found in one location for cox2-3 spacer, with all other locations having just one haplotype. Each of the cox1 haplotypes was found in a distinct location. Haplotype networks showed one haplotype occurring in most locations in southern and south-eastern Brazil for cox2-3 and revealed a relatively complex structure for cox1, with the same haplotype represented by individuals from two distant locations of southern and south-eastern Brazil. The low divergence observed among the Brazilian haplotypes supported the recognition of all collections as a single species, for both markers considering the geographic range sampled (maximum distance ~ 1000 km) as compared with previous studies at similar or broader geographic scales (> 2500 km). This study confirmed the general pattern found in Batrachospermales: that little variation is typically observed within a location and that most populations have one, rarely two haplotypes. In addition, we found no evidence of higher genetic divergences with increased geographic distance among haplotypes, which has also been reported in members of the Batrachospermales.

Ecology and pathology of Phytophthora ITS clade 3 species in forests in western Oregon, USA

ABSTRACTPhytophthora species are widespread and diverse in forest ecosystems, but little is known about their ecology. We explore ecological attributes of the closely related clade 3 species that occur sympatrically in western North American forests. We address the population structure, pathology, and epidemiology of P. ilicis, P. nemorosa, P. pluvialis, P. pseudosyringae, and P. psychrophila. Phytophthora species were isolated from plant tissues, rainwater falling through the forest canopy, streams, and soils in forests in western Oregon. Species identifications were based on morphology in culture with molecular confirmation using COX spacer and internal transcribed spacer (ITS) sequences. All five clade 3 Phytophthora species are present in western Oregon forests, although P. ilicis (only 1 forest isolate) and P. psychrophila (only 12 isolates) are apparently rare. P. ilicis is known only from holly in horticultural situations and once from a naturalized seedling in an urban forest. The known distribution of P. nemorosa in forest settings coincides with the ranges of its principle hosts, tanoak and myrtlewood, in Oregon and California. Although it is regularly identified from streams within the tanoak range, it has not been recovered from streams beyond that range. P. pluvialis is primarily associated with Douglas-fir canopies. It was identified from scattered locations throughout western Oregon in rain traps beneath Douglas-fir plantations and from diseased needles. P. pseudosyringae is also isolated from tanoak and myrtlewood in southwest Oregon and California, but its distribution, in streams at least, extends throughout much of western Oregon. P. psychrophila in Oregon is known only from rain traps beneath tanoak trees. Little intraspecific variation was detected in the nuclear rDNA ITS of clade 3 species. Variation in the mitochondrial COX spacer region was more frequent, with 2 to 10 haplotypes identified in the clade 3 species, for which we had multiple isolates.

Population genetic analyses are consistent with the introduction of Ceramium secundatum (Ceramiaceae, Rhodophyta) to Narragansett Bay, Rhode Island, USA.

During ongoing DNA barcode (COI-5P) surveys of the macroalgal flora along the northwest Atlantic coast, we discovered a population of Ceramium secundatum in Narragansett Bay, Rhode Island, USA. This species is regarded as common and widespread in the northeast Atlantic, ranging from Norway to Morocco, but until now has not been reported from the western Atlantic. Several lines of evidence suggest that C.secundatum may be introduced to Narragansett Bay: (1) despite extensive collecting, specimens have only been obtained from a limited geographic range in the northwest Atlantic; (2) three other nonindigenous seaweed species are reportedly introduced in this region, which is thought to be a consequence of shipping; and (3) this species is introduced to South Africa and New Zealand. To investigate this suspected introduction, we applied population genetic analyses (using the cox2-3 spacer) to compare the Narragansett Bay C.secundatum population to native populations in the Republic of Ireland and the United Kingdom. Collectively, analyses of biogeographical and molecular data indicate that C.secundatum is likely introduced to Narragansett Bay. The implications of this discovery are discussed.

Analysis of the cox2-3 spacer region for population diversity and taxonomic implications in rhodolith-forming species (Rhodophyta: Corallinales)

Coralline red algae demonstrate phenotypic plasticity related to environmental factors, rendering their identification difficult. The cox2-3 spacer is a mitochondrial marker widely used for phylogeographic studies and discrimination between closely related species in red algae; however, cox2-3 spacer sequence data for coralline algae are still limited. In this study we substantially increase the number of cox2-3 spacer sequences available for coralline algae, exploring their usefulness for different types of molecular investigations in coralline algae (DNA barcoding and phylogeography), with emphasis on rhodolith-forming species. Specimens from North Atlantic Europe, the Caribbean region and the Gulf of California (Mexico) were sequenced and two datasets were built, one for the subfamily Lithophylloideae and one for the Melobesioideae. Our results suggest the utility of cox2-3 spacer as barcoding marker for coralline algae with a slight variation in the barcode gap depending in the way gaps in the alignment are treated. Analyses on both datasets found a barcode gap or separation between intra and interspecific divergence (p distance and ABGD analysis) while some inconsistencies were evident when the results were compared with morphology-based classification. Using the cox2-3 spacer region, the morphospecies Lithophyllum margaritae from the Gulf of California revealed the existence of two well-supported clades, with the possibility of respectively five and two additional species; haplotype networks for Phymatolithon calcareum and P. purpureum revealed similar patterns when Mediterranean and NW Europe specimens were analysed, and P. calcareum was shown to consist of a single population in NW Europe. Based on our analyses the marker cox2-3 spacer has strong potential applications for studies of phylogeography and DNA barcoding in coralline algae after understanding its variation.

Cryptic diversity in the euryhaline red alga Caloglossa ogasawaraensis (Delesseriaceae, Ceramiales)

:Caloglossa ogasawaraensis is one of the most widespread species of its genus, having been reported from marine to freshwater habitats in tropical to temperate regions of both hemispheres. Because little phenotypic variation has been reported for this species, we investigated genetic, physiological, and/or morphological variations in 18 strains of C. ogasawaraensis isolated from 14 countries. The combined data of plastid-encoded ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) gene and its spacer, nuclear-encoded large subunit (LSU) rDNA, and mitochondrion-encoded cox spacer region suggested that this species is divided into three groups; Group I contains Australian, Melanesian, and Micronesian strains; Group II includes strains from western Pacific coasts, Micronesia, and Madagascar; and Group III consists eastern Pacific–Atlantic and Malaysian strains. Considering wide distribution range and close genetic similarity within the groups, a long-distance dispersal event does not seem to be rare in this species. Growth of the strains was compared between brackish (salinity = 8) and seawater (salinity = 32) media; most Group I strains grew well in both brackish and seawater media; whereas, all the Group II strains showed better growth in the brackish medium. Morphological analyses of the strains incubated under the same conditions revealed that the Group III strains had wider rhizoids than the other strains. However, this feature was highly variable and easily affected by environmental and algal conditions. Although such morphological and physiological variations suggest speciation of the three phylogenetic groups, more clear-cut features are required to describe them as distinct morpho-species.

Molecular systematics of four endemic Batrachospermaceae (Rhodophyta) species in China with multilocus data

Four endemic Batrachospermaceae species in China, Batrachospermum hongdongense Xie & Feng, Batrachospermum longipedicellatum Hua & Shi, Kumanoa curvata (Shi) Vis et al., and Kumanoa intorta (Jao) Entwisle et al., were analyzed with multilocus data in order to assess their phylogenetic placement. Multilocus molecular data from one nuclear gene (the ribosomal SSU), one chloroplast gene (rbcL), and two mitochondrial genes (COI and the cox2-3 spacer) as well as morphological studies were used to determine the phylogenetic relationships of these endemic species within the Batrachospermales. Batrachospermum hongdongense and B. longipedicellatum had previously been placed in Batrachospermum section Batrachospermum, but based on the data from this study they should be transferred into section Helminthoidea. Kumanoa curvata and K. intorta clearly belong to the newly established genus Kumanoa.

Assessing the use of mitochondrial cox1 gene and cox2-3 spacer for genetic diversity study of Malaysian Gracilaria changii (Gracilariaceae, Rhodophyta) from Peninsular Malaysia

Advances in DNA-based genetic markers provide the essential tools in measurement of genetic diversity relating to the evolution, biogeography, and systematics of red algae by exploiting genetic variation in the entire genome of organisms. The understanding of genetic diversity in Gracilaria changii (Gracilariaceae, Rhodophyta) will provide valuable information for conservation, plant breeding management, and strain selection for cultivation. However, information of intraspecific genetic variation is still rudimentary. In this study, two mitochondrial encoded markers, cytochrome oxidase subunit 1 (cox1) and intergenic spacer between the cytochrome oxidase subunits 2 and 3 (cox2-3 spacer) were used to investigate genetic diversity in 40 individuals of G. changii collected from 11 different geographically distinct populations from Peninsular Malaysia. Seven distinct mitochondrial haplotypes were identified with the cox1 gene and three mitochondrial haplotypes with the cox2-3 spacer. Intraspecific nucleotide differences ranged from 0 to 6 bp for the cox1 and 0–4 bp for the cox2-3 spacer, respectively. This is the first report comparing the suitability of mitochondrial markers of the cox1 gene and the cox2-3 spacer for genetic diversity studies on G. changii. The present study showed that the cox1 gene is a potential molecular marker to infer intraspecific genetic variation in red macroalgae. The cox1 marker is more variable compared to the cox2-3 spacer and revealed genetic variation and phylogeographic structure for this ecologically and economically important species.

Molecular and morphological variation of the red alga Spyridia filamentosa (Ceramiales, Rhodophyta) in the Hawaiian Archipelago

Conklin K.Y. and Sherwood A.R. 2012. Molecular and morphological variation of the red alga Spyridia filamentosa (Ceramiales, Rhodophyta) in the Hawaiian Archipelago. Phycologia 51: 347–357. DOI: 10.2216/10-26.1Genetic information is proving to be important in conservation and management efforts that involve cryptic species and their role in native ecosystem restoration. Previous molecular studies have demonstrated that the red alga Spyridia filamentosa consists of several cryptic species. Spyridia filamentosa is considered to be a native species in Hawai‘i and was recently used in preliminary seagrass meadow restoration efforts in Maunalua Bay, O‘ahu. It became necessary to understand the genetic diversity of this species in the Islands and determine if there are relationships between any molecular clades of S. filamentosa and anatomical characters that might be useful (e.g. sediment capture) in habitat remediation. Both molecular and morphological (determinate branch cell dimensions) analyses revealed the presence of multiple S. filamentosa clades in Hawai‘i. Nuclear [partial LSU (large subunit)] sequence and determinate branch cell data recovered two broad lineages (I and II), which are known worldwide. The mitochondrial sequence (cox2-3 spacer) data further separated samples into five distinct clades and indicated that S. filamentosa arrived in Hawai‘i on at least six occasions. These results aided decisions made concerning preliminary experiments involved in seagrass habitat remediation and emphasized the importance of genetically evaluating cryptic species that are being considered for use in native ecosystem restoration or conservation.

A molecular and morphological investigation of Batrachospermum arcuatum (Batrachospermales, Rhodophyta) in China

Batrachospermum arcuatum specimens were analysed from seven stream segments in North China. Morphological characteristics were observed and cluster analysis was used to evaluate the divergence among thalli from. Sequence data of the rbcL gene (chloroplast gene) and cox2-3 spacer region (mitochondrial gene) were also utilized to evaluate genetic variation in specimens among stream segments. The specimens from four of the streams were monoecious, while the individuals at the other three locations were dioecious. Cluster analysis showed that the monoecious specimens were not separated from the dioecious specimens, based on morphology, but rather the specimens were grouped by geographical closeness and habitat similarity. Likewise, the combined analyses of rbcL and the cox2-3 spacer data from provided more evidence that breeding system (monoecy vs. dioecy) is not a good morphological character to distinguish species.