MOLECULAR EVIDENCE FROM nrDNA ITS SEQUENCES THAT LAMINARIOCOLAX (PHAEOPHYCEAE, ECTOCARPALES SENSU LATO) IS A WORLDWIDE CLADE OF CLOSELY RELATED KELP ENDOPHYTES

Marine brown algae living as endophytes in macroalgae are morphologically simple and their taxonomy is particularly difficult. A molecular phylogeny for endophytic taxa isolated from kelps and red algae, and for putative epiphytic and free-living relatives, was inferred from partial small subunit and complete internal transcribed spacer nuclear ribosomal DNA sequences. It has revealed the following results. (1) Three species of endophytes isolated from members of the Laminariales are closely related. They form a clade together with the epi-endophytic species Laminariocolax tomentosoides (Farlow) Kylin. Members of the clade possess uniseriate plurilocular sporangia, and they may form erect filaments. Laminariocolax eckloniae sp. nov., occurring in the South African host Ecklonia maxima (Osbeck) Papenfuss, is described. The new combinations, Laminariocolax aecidioides (Rosenvinge) comb. nov. and L. macrocystis (Peters) comb. nov., are proposed for two taxa previously classified in Gononema and Streblonema , respectively. (2) The genus Laminariocolax occurs worldwide in temperate areas, and the phylogeny of the taxa studied is in agreement with biogeographic distribution. (3) Laminariocolax belongs to the Ectocarpales sensu lato. The genus is more closely related to Chordaria than to Dictyosiphon, Ectocarpus, or Scytosiphon . (4) Two brown endophytes ( Streblonema spp.), isolated from red algae, are closely related to each other and may form a sister clade to Laminariocolax .     

A NEW BROWN ALGAL ORDER,ISHIGEALES (PHAEOPHYCEAE), ESTABLISHED ON THE BASIS OF PLASTID PROTEIN‐CODING rbcL,psaA, AND psbA REGION COMPARISONS1

The brown algal family Ishigeaceae currently includes a single genus, Ishige Yendo, with two species. The relationship of the family to other brown algal lineages is less studied in terms of their plastid ultrastructure and molecular phylogeny. We determined the sequences of rbcL from four samples of the two Ishige species and nine putative relatives and the psaA and psbA sequences from 37 representatives of the brown algae. Analyses of individual and combined data sets resulted in similar trees; however, the concatenated data gave greater resolution and clade support than each individual gene. In all the phylogenies, the Phaeophyceae was well resolved, the Ectocarpales being placed in a terminal position and the Ishigeaceae ending up in a basal position. From our ultrastructural study, we concluded that the pyrenoid is absent in the Ishigeaceae, despite the presence of a rudimentary pyrenoid in I. okamurae. These results suggest that the Ishigeaceae is an early diverging brown lineage. Our molecular and morphological data, therefore, lead us to exclude the Ishigeaceae from the Ectocarpales s.l., which have an elaborate pyrenoid, and to propose its own order Ishigeales ord. nov. The Ishigeales is distinguished by oligostichous structure of thalli, phaeophycean hairs formed within cryptostomata, unilocular sporangia transformed from terminal cortical cells, and plurilocular sporangia lacking sterile terminal cells. This study is the first to document the utility of the psaA and psbA sequences for brown algae and also the first report on the multigene phylogeny of the Phaeophyceae based on three protein‐coding plastid genes.     

A MOLECULAR ANALYSIS OF ANALIPUS AND RALFSIA (PHAEOPHYCEAE) SUGGESTS THE ORDER ECTOCARPALES IS POLYPHYLETIC1

We report partial 18S ribosomal DNA sequences of Analipus japonicus (Harvey) Wynne and Ralfsia fungiformis (Grunnerus) Setchell et Gardner. These sequences were compared with the corresponding sequences of 13 brown algae representing six phaeophycean orders: Dictyotales, Ectocarpales, Fucales, Laminariales, Sphacelariales, and Syringodermatales. These 15 brown algae included 10 ectocarpoids representing nine ectocarpacean (sensu Gabrielson et al. 1989) families: Chordariaceae, Dictyosiphonaceae, Ectocarpaceae, Elachistaceae, Heterochordariaceae, Leathesiaceae, Punctariaceae, Ralfsiaceae, and Scytosiphonaceae. We addressed the controversial taxonomic placement of A. japonicus and R. fungiformis in the Ectocarpales by analysis of DNA sequences. Neighbor-joining and maximum parsimony-inferred phylogenies provided evidence that A. japonicus and R. fungiformis are not closely associated with the other representatives of the Ectocarpales. Bootstrap analyses suggest polyphyly of the order Ectocarpales (sensu Gabrielson et al.). However, our analysis failed to resolve the phylogenetic relationship between A. japonicus and R. fungiformis. Our results suggest that the ectocarpoids are just as distantly related to A. japonicus and R. fungiformis as they are to members of the advanced orders Desmarestiales, Dictyotales, Fucales, Laminariales, Sphacelariales, and Syringodermatales.     

Circumscription of the order Ectocarpales (Phaeophyceae): bibliographical synthesis and molecular evidence

Phylogenetic analyses of 27 brown algae including the type genera of the orders Chordariales, Dictyosiphonales, Ectocarpales sensu stricto, and Scytosiphonales, using partial SSU + LSU combined rDNA sequence data, supports a broadly circumscribed order Ectocarpales. This order is redefined to include taxa possessing an exserted, pedunculated pyrenoid. Previous then taxa were placed in the Ectocarpales sensu stricto, the Chordariales, the Dictyosiphonales, or the Scytosiphonales. Algae either lacking a pyrenoid, and sometimes included in the Ectocarpales (Tilopteridales, Ralfsiales sensu Nakamura), or which possess a non-pedunculated pyrenoid (such as those placed in the recently proposed order Scytothamnales, as well as Asteronema, Asterocladon and Bachelotia), are excluded from the Ectocarpales.     

Plastid Genome of <Emphasis Type="Italic">Dictyopteris divaricata</Emphasis> (Dictyotales,Phaeophyceae): Understanding the Evolution of Plastid Genomes in Brown Algae

Dictyotophycidae is a subclass of brown algae containing 395 species that are distributed worldwide. A complete plastid (chloroplast) genome (ptDNA or cpDNA) had not previously been sequenced from this group. In this study, the complete plastid genome of Dictyopteris divaricata (Okamura) Okamura (Dictyotales, Phaeophyceae) was characterized and compared to other brown algal ptDNAs. This plastid genome was 126,099 bp in size with two inverted repeats (IRs) of 6026 bp. The D. divaricata IRs contained rpl21, making its IRs larger than representatives from the orders Fucales and Laminariales, but was smaller than that from Ectocarpales. The G + C content of D. divaricata (31.19%) was the highest of the known ptDNAs of brown algae (28.94–31.05%). Two protein-coding genes, rbcR and rpl32, were present in ptDNAs of Laminariales, Ectocarpales (Ectocarpus siliculosus), and Fucales (LEF) but were absent in D. divaricata. Reduced intergenic space (13.11%) and eight pairs of overlapping genes in D. divaricata ptDNA made it the most compact plastid genome in brown algae so far. The architecture of D. divaricata ptDNA showed higher similarity to that of Laminariales compared with Fucales and Ectocarpales. The difference in general features, gene content, and architecture among the ptDNAs of D. divaricata and LEF clade revealed the diversity and evolutionary trends of plastid genomes in brown algae.     

Molecular phylogeny of Punctaria mageshimensis reveals evidence for its transfer to Spatoglossum as S. mageshimense (Dictyotales,Phaeophyceae)

Taxonomy of the little‐studied brown algal species Punctaria mageshimensis (Ectocarpales s.l.) was reexamined by molecular phylogeny and morphology. In the genetic analyses of newly collected specimens using plastid rbcL and psaA gene sequences, the specimens morphologically referable to P. mageshimensis were phylogenetically distant from Ectocarpales s.l. and were included in the clade of Spatoglossum (Dictyotales). Morphological reexamination of the type specimen and newly collected specimens confirmed its systematic position in Dictyotales: Branched thallus; cushion‐shaped rhizoidal holdfast occasionally forming secondary holdfast at the bottom of the thallus; many discoidal plastids without pyrenoid per cell; tetrasporangium‐like reproductive structures with dark, homogeneous cell content; occurrence of hair tufts. Genetically P. mageshimensis was most related to a reported sequence of Spatoglossum asperum, but P. mageshimensis was considerably different from S. asperum as well as other known Spatoglossum species in the deep habitat and in having scarcely‐branched lanceolate and considerably thickened thallus. In conclusion, we propose the transfer of P. mageshimensis to Spatoglossum as S. mageshimense comb. nov.     

PHYLOGENETIC RELATIONSHIPS OF THE BROWN ALGAL ORDERS ECTOCARPALES, CHORDARIALES, DICTYOSIPHONALES, AND TILOPTERIDALES (PHAEOPHYCEAE) BASED ON RUBISCO LARGE SUBUNIT AND SPACER SEQUENCES

Phylogenetic relationships among 23 species of morphologically simple brown algae belonging to the Ectocarpales sensu stricto , Chordariales, Dictyosiphonales, and Tilopteridales sensu stricto , Phaeophyceae (Fucophyceae), were analyzed using chloroplast-encoded RUBISCO large subunit gene sequences ( rbc L) and the associated RUBISCO spacer sequences. Comparison of the observed and expected sequence divergence at the three codon positions of rbc L showed that the level of mutational saturation within the brown algae is minor. Thus, rbc L is well suited for phylogenetic studies in this group. Unweighted parsimony analyses and a neighbor-joining distance analysis were performed using unambiguously aligned rbc L sequences from the above four orders, one marine raphidophyte and two Tribophyceae (Xantophyceae). Polyphyly of Tilopteridales sensu lato (i.e. including Dictyosiphonales) is verified; we therefore recommend the use of Tilopteridales in the strict sense. The Ectocarpales, Chordariales, and Dictyosiphonales are paraphyletic with respect to each other, forming a highly interwoven clade. A separate parsimony analysis of the RUBISCO spacer as well as a combined rbc L and spacer analysis supported the close relationship among the latter three orders, adding to the evidence that they should be subsumed into the Ectocarpales sensu lato.     

RESOLVING EVOLUTIONARY RELATIONSHIPS AMONG THE BROWN ALGAE USING CHLOROPLAST AND NUCLEAR GENES1

The brown algae are one of the largest and most important groups of primary producers in benthic coastal marine environments. Despite their biological importance, consensus regarding their taxonomic or evolutionary relationships remains elusive. Our goal was to produce a taxon‐rich two‐gene (rbcL and LSU rDNA) phylogeny. Key species were sequenced to represent each order and family in the analyses across all 19 orders and ～40 families, including selected outgroups Schizocladiophyceae and Xanthophyceae. Our results are in sharp contrast to traditional phylogenetic concepts; the Ectocarpales are not an early diverging clade, nor do the Fucales diverge early from other brown algae. Rather, Choristocarpus is sister to the remaining brown algae. Other groups traditionally considered to have primitive features are actually recently diverged lineages, turning traditional phylogenetic concepts upside down. Additionally, our results allow for the assessment, in the broadest context, of many of the historical and more recent taxonomic changes, resulting in several emended groups along with proposals for two new orders (Onslowiales, Nemodermatales) and one new family (Phaeosiphoniellaceae).     

Molecular phylogeny of Zeacarpa (Ralfsiales,Phaeophyceae) proposing a new family Zeacarpaceae and its transfer to Nemodermatales

Zeacarpa leiomorpha is a crustose brown alga endemic to South Africa. The species has been tentatively placed in Ralfsiaceae, but its ordinal assignment has been uncertain. The molecular phylogeny of brown algae based on concatenated DNA sequences of seven chloroplast and mitochondrial gene sequences (atpB, psaA, psaB, psbA, psbC, rbcL, and cox1) of taxa covering most of the orders revealed the most related phylogenetic relationship of Z. leiomorpha to Nemoderma tingitanum (Nemodermatales) rather than Ralfsiaceae (Ralfsiales). Morphologically, Zeacarpa and Nemoderma share crustose thallus structure and multiple discoidal chloroplasts without pyrenoids in each cell, however, the formation of lateral unilocular zoidangia in tufts in loose upright filaments in Zeacarpa is distinctive in brown algae. Considering the relatively distant genetic divergence between the two taxa, comparable to that among families or orders in representative brown algae, in addition to the above‐mentioned unique morphological features, we propose the classification of Zeacarpa in a new family Zeacarpaceae in the order Nemodermatales.     

Complete large subunit ribosomal RNA sequences from the heterokont algae ochromonas danica, nannochloropsis salina, and tribonema aequale, and phylogenetic analysis

The large subunit ribosomal RNA sequences from the heterokont algae Ochromonas danica, Nannochloropsis salina, and Tribonema aequale were determined. These sequences were combined with small subunit ribosomal RNA sequences in order to carry out a phylogenetic analysis based on neighbor-joining, maximum parsimony, and maximum likelihood methods. Our results indicate that heterokont fungi and heterokont algae each are monophyletic, and confirm that they together form a monophyletic group called ``stramenopiles.' Within the heterokont algae, the eustigmatophyte Nannochloropsis salina either clusters with the chrysophyte Ochromonas danica or forms a sister group to a cluster comprising the phaeophyte Scytosiphon lomentaria and the xanthophyte Tribonema aequale. The alveolates were identified as the closest relatives of the stramenopiles, but the exact order of divergence between the eukaryotic crown taxa could not be established with confidence. Received: 22 November 1996 / Accepted: 14 February 1997     

Reinstatement of Myelophycus caespitosus (Scytosiphonaceae,Phaeophyceae) from Japan

Reinstatement of Myelophycus caespitosus Kjellman (Ectocarpales s.l., Phaeophyceae) described from western Japan is proposed based on the comparisons of DNA sequences of Japanese Myelophycus specimens, the type specimen of Chordaria simplex and lectotypified specimen of Myelophycus caespitosus. In the genetic analyses using mitochondrial cox1 and cox3, chloroplast atpB, psbA and rbcL DNA sequences, the specimens morphologically referable to M. simplex formed two distinct clades (clade‐1 and clade‐2) supported by high statistical values. Clade‐1 was distributed on the western coast of Japan (Honshu, Shikoku and Kyushu) from the Kii Peninsula to Tsushima and the Pacific coast of Aomori, northeastern Honshu, and clade‐2 on the Pacific coast of central Honshu from Sanriku to the Kii Peninsula. Based on the cox3 DNA sequences and the location of the type locality at Shimoda, Izu Peninsula, clade‐2 was concluded to correspond to true M. simplex. There were no recognizable differences in the representative morphological features (height and diameter of sporophytes and gametophytes, number of cells comprising cortical, subcortical and medullary layers, thickness of plurilocular gametangia, or length and diameter of unilocular zoidangia) between the specimens included in the two taxa. Analyses of the specimens of the two taxa, including sympatric populations on the Kii Peninsula, using a nuclear genetic marker ocm3 did not suggest any genetic exchanges between the two taxa. On the other hand, cox3 gene sequence of the voucher specimen of Myelophycus caespitosus collected from Goto, Kyushu, western Japan housed in the UPS herbarium was included in clade‐1. In conclusion, we propose the reinstatement of M. caespitosus and to lectotypify the specimen in UPS. Korean Myelophycus specimens reported from Cheju Island and Wando were considered to belong to M. caespitosus based on the reported rbcL sequences.     

Complete Plastid Genome Sequence of the Brown Alga Undaria pinnatifida

In this study, we fully sequenced the circular plastid genome of a brown alga, Undaria pinnatifida. The genome is 130,383 base pairs (bp) in size; it contains a large single-copy (LSC, 76,598 bp) and a small single-copy region (SSC, 42,977 bp), separated by two inverted repeats (IRa and IRb: 5,404 bp). The genome contains 139 protein-coding, 28 tRNA, and 6 rRNA genes; none of these genes contains introns. Organization and gene contents of the U. pinnatifida plastid genome were similar to those of Saccharina japonica. There is a co-linear relationship between the plastid genome of U. pinnatifida and that of three previously sequenced large brown algal species. Phylogenetic analyses of 43 taxa based on 23 plastid protein-coding genes grouped all plastids into a red or green lineage. In the large brown algae branch, U. pinnatifida and S. japonica formed a sister clade with much closer relationship to Ectocarpus siliculosus than to Fucus vesiculosus. For the first time, the start codon ATT was identified in the plastid genome of large brown algae, in the atpA gene of U. pinnatifida. In addition, we found a gene-length change induced by a 3-bp repetitive DNA in ycf35 and ilvB genes of the U. pinnatifida plastid genome.     

Utility of rbcS gene as a novel target DNA region for brown algal molecular systematics

The usefulness of molecular phylogenetic studies has increased remarkably as the quantity and quality of available DNA sequences has increased. When compared with the progress that has occurred in angiosperms and animals, there have been relatively few target DNA regions identified for use in taxonomic studies of brown algae. Therefore, in this study, we developed a new set of primers to amplify Rubisco small subunit (rbcS) gene sequences and determined the rbcS gene sequences of various species of brown algae including those belonging to Dictyotales, Ectocarpales, Fucales and Sphacelariales. The level of sequence variations in the rbcS gene varied according to the brown algal lineages. When focusing on the relationship of species within the genus Sargassum, the rbcS gene sequences provided useful information regarding the phylogenetic relationship among sections of the subgenus Bactrophycus. Based on the broad applicability and phylogenetic utility of the rbcS gene, we suggest that the sequence be used as a new target region for the molecular systematics of brown algae.     

Morphological and Taxonomic Interpretation of <Emphasis Type="Italic">Orestovia</Emphasis> and <Emphasis Type="Italic">Schuguria</Emphasis>, Enigmatic Devonian Plants from Russia

A detailed study of the external and internal surfaces of the cuticle of Orestovia and Schuguria using scanning electron microscopy and confocal laser microscopy has shown that the structures formerly interpreted as stomata or reproductive organs are most likely to be gland cells producing mucilage. Each structure represents a single large cell with a complex aperture on the external wall. In addition, a reproductive organ similar to multilocular sporangia known in brown algae of the order Ectocarpales has been found in attachment to a compression fossil of Orestovia. These data suggest similarity of the genera studied with brown algae.     

The phylogenetic position of the subantarctic marine macroalga Desmarestia chordalis (Phaeophyceae) inferred from nuclear ribosomal ITS sequences

The phylogenetic position of the subantarctic brown macroalga Desmarestia chordalis was inferred from nuclear ribosomal DNA internal transcribed spacer sequences, which were compared with published homologous sequences of putative relatives. According to the molecular data, D. chordalis is closely related to the Antarctic species D. menziesii, and more distantly related to other taxa of similar morphology, i.e. Antarctic D. anceps and northern hemisphere D. aculeata. Accepted: 2 August 1999     

Deceptive Desmas: Molecular Phylogenetics Suggests a New Classification and Uncovers Convergent Evolution of Lithistid Demosponges

Reconciling the fossil record with molecular phylogenies to enhance the understanding of animal evolution is a challenging task, especially for taxa with a mostly poor fossil record, such as sponges (Porifera). ‘Lithistida’, a polyphyletic group of recent and fossil sponges, are an exception as they provide the richest fossil record among demosponges. Lithistids, currently encompassing 13 families, 41 genera and >300 recent species, are defined by the common possession of peculiar siliceous spicules (desmas) that characteristically form rigid articulated skeletons. Their phylogenetic relationships are to a large extent unresolved and there has been no (taxonomically) comprehensive analysis to formally reallocate lithistid taxa to their closest relatives. This study, based on the most comprehensive molecular and morphological investigation of ‘lithistid’ demosponges to date, corroborates some previous weakly-supported hypotheses, and provides novel insights into the evolutionary relationships of the previous ‘order Lithistida’. Based on molecular data (partial mtDNA CO1 and 28S rDNA sequences), we show that 8 out of 13 ‘Lithistida’ families belong to the order Astrophorida, whereas Scleritodermidae and Siphonidiidae form a separate monophyletic clade within Tetractinellida. Most lithistid astrophorids are dispersed between different clades of the Astrophorida and we propose to formally reallocate them, respectively. Corallistidae, Theonellidae and Phymatellidae are monophyletic, whereas the families Pleromidae and Scleritodermidae are polyphyletic. Family Desmanthidae is polyphyletic and groups within Halichondriidae – we formally propose a reallocation. The sister group relationship of the family Vetulinidae to Spongillida is confirmed and we propose here for the first time to include Vetulina into a new Order Sphaerocladina. Megascleres and microscleres possibly evolved and/or were lost several times independently in different ‘lithistid’ taxa, and microscleres might at least be four times more likely lost than megascleres. Desma spicules occasionally may have undergone secondary losses too. Our study provides a framework for further detailed investigations of this important demosponge group.     

A molecular-assisted floristic survey of crustose brown algae (Phaeophyceae) from Malaysia and Lombok Island,Indonesia based on rbcL and partial cox1 genes

Studies on the crustose brown algae are relatively few despite a long history of studies conducted since the 1800s, with temperate species forming the bulk of these studies. There is a need for more focus on crustose brown algae particularly in the tropics as they are generally different from those in the temperate regions. Taxonomic confusion arising from morphological simplicity largely dependent on the reproductive structures and overlap in morpho-anatomical features among species necessitates the use of molecular techniques. This study is dedicated to a better understanding of the diversity of these understudied algae in the Indo–Malay region. Specimens collected from Peninsular Malaysia, Sabah (Borneo) and Lombok Island in Indonesia were identified using molecular markers from the plastid rubisco large subunit (rbcL) and mitochondrial cytochrome c oxidase subunit 1 (cox1) genes in tandem with morphology and anatomy. Three Mesospora spp., two putative Diplura spp. and the cosmopolitan Neoralfsia expansa were identified in this study, including a new record of Mesospora negrosensis for Malaysia. Despite their morpho-anatomical similarities, Mesospora and Diplura occur in widely divergent clades within the brown algae, the former in the Mesosporaceae in the Ralfsiales, the latter in an unclassified clade sister to the Ishigeales. All six species occurred both in Malaysia and Lombok Island except for M. elongata and M. negrosensis, respectively. The rbcL marker performed better in the elucidation of phylogeny among the brown algal orders, whereas cox1-5′ is more suited as a barcoding marker for species level identification.     

Origin, diversification, and evolution of Samolus valerandi (Samolaceae, Ericales)

The almost cosmopolitan distribution of Samolus valerandi is unique in the genus Samolus L. (Samolaceae), which also includes 12–15 taxa with distributions restricted to smaller areas of the Southern Hemisphere. Recent molecular phylogenetic studies based on chloroplast and nuclear DNA sequences showed that the widespread S. valerandi and the North American S. parviflorus are both part of a strongly supported clade, together with the North American S. vagans, S. spathulatus, and S. latifolius. To better understand the origin, distribution, and diversification of S. valerandi and to clarify the relationships within this clade, we performed molecular phylogenetic analyses based on the plastid trnS-G intergenic spacer and the nuclear ribosomal ITS region. We have also sought further support for relationships by examining flower and leaf characters. On the basis of new results, we propose that S. valerandi, S. parviflorus, and S. vagans are considered as part of a widespread “species complex”, with its centre of diversity in North America. No clear vicariance patterns were found regarding the phylogeography of S. valerandi, which thus seems to have dispersed secondarily to various places around the world, possibly as a result of human activities.     

The phylogenetic position of the Prolecithophora (Rhabditophora, 'Platyhelminthes')

Complete 18S ribosomal DNA (rDNA) sequences and partial 28S rDNA sequences from a selection of rhabditophoran taxa were obtained and used in combination with literature data to determine the phylogenetic position of the Prolecithophora and of two families sometimes included in the Prolecithophora, the Urastomidae and the Genostomatidae. The results are largely compatible with earlier molecular studies when supported clades are considered, and adjusting for the denser taxonomic sampling of this study. The position of the Proseriata is not compatible with the taxon Seriata, which is rejected. The Rhabdocoela excluding the Fecampiida and the Neodermata is monophyletic. The phylogenetic position of the Neodermata cannot be determined, but its placement is not compatible with the proposed taxa Revertospermata and Mediofusata Kornakova & Joffe, 1999, which are rejected. The Urastomidae and the Genostomatidae in all analyses group with the Fecampiida, and it is our recommendation that these taxa be included in the Fecampiida. The amended Fecampiida always group separately from the Prolecithophora sensu stricto , the Rhabdocoela, and the Neodermata. Our analyses reveal the existence of a strongly supported clade consisting of Prolecithophora + Tricladida + the amended Fecampiida, and we propose the name Adiaphanida for this clade. Tentatively the sister group of the Prolecithophora is a clade consisting of the Tricladida + amended Fecampiida.     

Phylogeny of the Northeast Pacific brown algal (Phaeophycean) orders as inferred from 18S rRNA gene sequences

Partial 18S rRNA gene sequences have been determined for thirteen brown algae representing nine Northeast Pacific brown algal orders: Chordariales, Desmarestiales, Dictyosiphonales, Dictyotales, Ectocarpales, Fucales, Scytosiphonales, Sphacelariales and Syringodermatales. These sequences were compared with published sequences from a kelp (Laminariales), a xanthophyte and a bacillariophyte. A preliminary phylogeny generated by the neighbor-joining phylogeny inference method indicated that the class Phaeophyceae is a monophyletic group in relation to the xanthophyte and the bacillariophyte. Further, bootstrap analysis of the phylogeny consistently grouped together all the representatives belonging to the orders Ectocarpales, Chordariales, Dictyosiphonales and Scytosiphonales and separated them from the representatives belonging to the other brown algal orders. These results offer valuable insights into the controversial brown algal orders' phylogeny and provide additional data to the phylogenetic relationship study among the chromophyte classes.