Molecular phylogeny of vestimentiferans collected around Japan, revealed by the nucleotide sequences of mitochondrial DNA

The phylogenetic relationships among local populations of undescribed vestimentiferan species that belong to the genera Lamellibrachia and Escarpia and had been collected at six sites around Japan were analyzed on the basis of the partial (1023 bp) nucleotide sequences of the mitochondrial gene for cytochrome oxidase I (COI), using a pogonophoran and a polychaete as outgroups. The identical amino acid sequence was deduced from the nucleotide sequence obtained from each of the vestimentiferans analyzed. The strong similarity among deduced amino acid sequences of COI suggested a close relationship between vestimentiferans and pogonophorans. On the basis of the phylogenetic relationships, the analyzed vestimentiferan populations were classified tentatively as five species. The genetic differentiation of vestimentiferans was suggested to occur bathymetrically as well as being a consequence of horizontal segregation. Two of these tentatively identified species inhabit both a hydrothermal area and a cold seep area, as is the case for some species of bivalves that belong to the genera Bathymodiolus and Calyptogena. Received: 28 August 1996 / Accepted: 2 October 1996     

Molecular taxonomy of vestimentiferans of the western Pacific and their phylogenetic relationship to species of the eastern Pacific. I. Family Lamellibrachiidae

Phylogenetic relationships among vestimentiferans in the family Lamellibrachiidae collected from ten sites in the western Pacific were analyzed on the basis of the nucleotide sequence of part of a mitochondrial gene for cytochrome oxidase I. The 103 individuals analyzed were tentatively classified into five species: namely, Lamellibrachia satsuma, three tentative species inhabiting Japanese waters and one tentative species from the Manus Basin. Phylogenetic analysis of the four tentative species, L. satsuma, and two lamellibrachiids, whose sequences had been reported previously, namely L. columna from the Lau Basin and L. barhami from the Oregon Margin and the Middle Valley, revealed that the lamellibrachiids from Japanese waters were not monophyletic. While two tentative species from Japanese waters and L. columna formed a monophyletic group, the other tentative species from Japanese waters was closely related to the tentative species from the Manus Basin. L. satsuma was shown to be phylogenetically distinct from other lamellibrachiids of the western Pacific. A lamellibrachiid that had been collected from the Nikko Seamount was also demonstrated to be L. sastuma.     

Phylogeny and biogeographic history of hake (genus Merluccius), inferred from mitochondrial DNA control-region sequences

 Phylogenetic analyses of the left domain of the mitochondrial DNA control-region sequence have been used to examine the relationships among species of the genus Merluccius (Rafinesque, 1810), and to compare these with hypotheses based on morphological, meristic and allozyme characters. Analysis of aligned sequences revealed that transition bias was much lower than in mammalian mtDNA, and that nucleotide composition of control-region sequences was biased toward A and T. We have roughly calibrated a molecular clock for the genus, based on the rise of the Isthmus of Panamá, which is believed to have created a barrier to dispersal between marine species of the Atlantic and Pacific Oceans. Our mtDNA-based phylogeny was highly congruent with allozyme-based phylogenies, but poorly so with a previously described phylogeny based on morphology. Specifically, our phylogeny resolved two well-supported principal clades, one of American (west Atlantic and east Pacific) species and the other of Euro–African (east Atlantic) species. This suggests an evolutionary history during which the ancestral lineage of Merluccius was divided between two geographic regions, with subsequent dispersal and vicariant events resulting in the evolution and distribution of extant taxa. However, the relationships between some taxa within the American clade could not be resolved. We suggest that this is consistent with an hypothesis of a rapid origin and radiation of these taxa. Received: 12 December 1998 / Accepted: 15 October 1999     

A systematic study of some Black Corals species (Antipatharia,Hexacorallia) based on rDNA internal transcribed spacers sequences

A phylogenetic analysis based on rDNA internal transcribed spacers (ITS) sequences was performed on 15 species of black corals assigned to the genera Antipathes, Stichopathes, Cirrhipathes, Rhipidipathes, Antipathella, Myriopathes and Cupressopathes recorded from the Messina Strait (Mediterranean Sea) and the Bunaken Marine Park (Celebes Sea, Indonesia). The phylogenetic analysis shows that the examined species are grouped in two main branches corresponding to the families Antipathidae-Aphanipathidae and Myriopathidae. While among the Myriopathidae species there is a very small genetic distance, the Antipathidae-Aphanipathidae clade shows a high degree of divergence between different genera. According to this study, the taxon Antipathes? sp. 3 characterised by a bush-like corallum without a well-defined axis, probably belongs to a new undescribed genus of the family Antipathidae.     

Molecular systematic and phylogenetic assessment of 34 calanoid copepod species of the Calanidae and Clausocalanidae

DNA sequences for a 639 bp region of mitochondrial cytochrome oxidase I (mtCOI) were determined for 34 species of ten genera in two families of calanoid copepods, including: Calanoides, Cosmocalanus, Meoscalanus, Nannocalanus, Neocalanus, and Undinula (family Calanidae); and Clausocalanus, Ctenocalanus, Drepanopus, and Pseudocalanus (family Clausocalanidae). MtCOI gene sequences proved to be diagnostic molecular systematic characters for accurate identification and discrimination of the species. Levels of mtCOI variation within species (range: 1-4%) were significantly less than those between species (9-25%). Higher levels of intraspecific variation (>2%) usually resulted from comparisons between ecologically distinct or geographically isolated populations. MtCOI sequence variation resolved evolutionary relationships among species of Clausocalanus, Neocalanus, and Pseudocalanus, although there was evidence of saturation at some variable sites. Phylogenetic relationships among 11 copepod genera (adding Calanus to the list above) were reconstructed using a 660 bp region of nuclear small-subunit 18S rRNA, a slowly evolving gene that showed no variability within a species and differed by <1-6% among the genera. The 18S rRNA molecular phylogeny was consistent with the accepted limits of the Calanidae and Clausocalanidae and clearly resolved relationships among genera within each family. This molecular systematic and phylogenetic study was part of the ZooGene project, an international partnership to create a DNA sequence database as a tool for uniform, molecularly based species identification of planktonic calanoid copepods and euphausiids.     

Quaternary geographical sibling speciation and population structuring in the Eastern Atlantic skates (suborder Rajoidea) Raja clavata and R. straeleni

The European Raja clavata and the South African R. straeleni are marine skates which exhibit highly conserved morphological and ecological traits. Owing to this, taxonomic and evolutionary relationships between the two taxa have not yet fully elucidated. Here, we have tested the hypothesis that restricted gene flow and genetic divergence between these taxa might be associated with climatic/oceanographic discontinuities by surveying genetic variation in ten geographical samples at control region (CR) and amplified fragment length polymorphism (AFLP) loci. The clustering of CR haplotypes in two reciprocally monophyletic clades consistent with taxon zoogeography and the significant AFLP F values between the European and South African populations indicated the two taxa as recently diverged peripatric sibling species. Within each species, significant spatial genetic heterogeneity among samples at both markers revealed population structuring. We argued that structured populations and isolated sibling species might represent two stages of geographical speciation.     

Phylogenetic relationship among several genera of Dictyotaceae (Dictyotales, Phaeophyceae) based on 18S rRNA and partial rbcL gene sequences

The partial sequences of the 18S rRNA gene and the rbcL gene, RuBisCo spacer region of representatives of the Dictyotaceae were determined and compared to resolve their phylogenetic relationships. A total of 1,861 base pairs of 18S rDNA sequences were aligned and examined. There was a high similarity of nucleotide sequences within the tribe Dictyoteae (99.4-99.6%) and the tribe Zonarieae (92.8-99.8%). The largest intergeneric divergence within the Dictyotaceae was 7.31%, between Dilophus and Zonaria. The aligned 422 bases of partial rbcL gene sequences gave a similar phylogenetic relationship among taxa to those of the 18S rDNA sequences, although our alignment covered less than 30% of the whole gene. All genera of Dictyotales consisted of several clades forming a polychotomy in MP trees based on partial rbcL gene sequences and on 18S rDNA sequences. The genera within the tribe Dictyoteae formed a clade, a Dictyota-Phacydictyon-Dilophus clade, while genera of the tribe Zonarieae formed four clades: Padina; Distromium-Lobophora-Zonaria; Spatoglossum-Lobospira; and Dictyopteris-Spatoglossum. All genera of the Dictyotaceae included in these sequence analyses are classified into five groups, which have little phylogenetic resolution among them. The genera classified in the tribe Zonarieae according to Womersley's criteria do not appear to be monophyletic, based on our analyses. Although not all genera of Dictyotaceae were analysed, our data suggest that the status of the meristem cells should not be a criterion for separating tribes within the family Dictyotaceae and that other hierarchical systems should be adopted to properly reflect phylogenetic relationships.     

Importance of macroalgal fields as coral reef fish nursery habitat in north-west Australia

Macroalgal fields are a feature of the shallow tropical benthos, yet their importance for coral reef fish population dynamics remains poorly understood. The abundance of fish recruits was recorded using underwater visual census at six macroalgal and 11 coral reef sites in the Montebello and Barrow Islands. Surveys identified 6,935 individual recruit fish from 105 species, 54 genera and 20 families. Of these, 1,401 recruits from 48 species, 31 genera and 14 families were observed in macroalgal sites. Sixteen of the 105 recruit species (15.2 %) were observed exclusively at macroalgal sites. Forty-two (87.5 %) of these species have been observed as adults on adjacent coral reefs. Species composition of fish recruits differed significantly between the two habitats. Corallivore, small omnivore and zooplanktivore recruits had significantly higher numbers in the coral sites, while the results clearly demonstrate that juveniles, within the genera Lethrinus and Choerodon, as well as large algal croppers, are predominantly found at macroalgal (74–100 %) rather than coral-dominated sites. High-canopy macroalgae cover was positively correlated with abundance of these taxa, particularly Lethrinids (r ² = 0.40). This study is the first to highlight the important attributes of tropical macroalgal fields and suggests that they have a similar role to seagrass meadows as essential juvenile habitat, thus warranting greater attention in conservation planning and ecological studies.     

Development of clade-specific Symbiodinium primers for quantitative PCR (qPCR) and their application to detecting clade D symbionts in Caribbean corals

We developed quantitative PCR (qPCR) assays to distinguish each of the four clades (A–D) of dinoflagellate endosymbionts (genus Symbiodinium) commonly found in Caribbean corals. We applied these primer sets, which target portions of the multi-copy ribosomal DNA (rDNA) gene family, to assess the presence/absence of symbionts in clade D (as indicated by the detection of clade D DNA). We detected these symbionts in five of six Caribbean host species/genera (21% of samples analyzed, N = 10 of 47 colonies), from which clade D had rarely or never been observed. This suggests that Symbiodinium in clade D are present in a higher diversity of coral species than previously thought. This qPCR-based approach can improve our understanding of the total microbial diversity associated with corals, particularly in hosts thought to be relatively specific, and has many other potential applications for studies of coral reef ecology and conservation.     

Vacuolate-attached filaments: highly productive Ridgeia piscesae epibionts at the Juan de Fuca hydrothermal vents

Vacuolate sulfur bacteria with high morphological similarity to vacuolate-attached filaments previously described from shallow hydrothermal vents (White Point, CA) were found at deep-sea hydrothermal vents. These filamentous bacteria grow in dense mats that cover surfaces and potentially provide a significant source of organic carbon where they occur. Vacuolate-attached filaments were collected near vents at the Clam Bed site of the Endeavour Segment of the Juan de Fuca Ridge and from the sediment surface at Escanaba Trough on the Gorda Ridge. A phylogenetic analysis comparing their 16S rRNA gene sequences to those collected from the shallow White Point site showed that all vacuolate-attached filament sequences form a monophyletic group within the vacuolate sulfur-oxidizing bacteria clade in the gamma proteobacteria. Abundance of the attached filaments was quantified over the length of the exterior surface of the tubes of Ridgeia piscesae worms collected from the Clam Bed site at Juan de Fuca yielding a per worm average of 0.070 ± 0.018 cm³ (n = 4). In agreement with previous results for White Point filaments, anion measurements by ion chromatography showed no detectable internal nitrate concentrations above ambient seawater (n = 9). For one R. piscesae tube worm “bush” at the Easter Island vent site, potential gross epibiont productivity is estimated to be 15 to 45× the net productivity of the worms.     

Host preference of a symbiotic flatworm in relation to the ecology of littoral snails

Some polyclads associate with other marine invertebrates such as gastropods, but how these associations evolve is not well understood. This study examined the relationships between a polyclad, Stylochoplana pusilla, and six species of snails in 10 eulittoral sites in Mutsu Bay, northern Japan, in 2010 and 2011. Of the six potential host snail species, Monodonta labio was present at all sites and the prevalence of S. pusilla in the snails’ mantle cavities overall was 82.6 %. Four other snail species occurred at five or six sites in comparable densities, but of these, only Chlorostoma turbinatum and Omphalius rusticus had S. pusilla in their mantle cavities (prevalence of 42.0 and 15.4 %). A congener of M. labio, Monodonta neritoides, occurred at only one site and had no S. pusilla. The mantle, which provides habitat space for S. pusilla, was proportionally the longest in M. labio. In laboratory experiments, the flatworms preferentially entered M. labio over other snail species with the same mantle length. Observed vertical distributions of snails in the littoral zone indicate that M. labio is present in the eulittoral at both high and low tides, while C. turbinatum and O. rusticus are usually found in the sublittoral. In an evolutionary sense, the relationship between S. pusilla and its host may have developed as a mechanism for the flatworm to avoid predation by living in the eulittoral and to avoid desiccation by establishing commensal relationships with certain snails.     

Ecological niche similarities of Peponapis bees and non-domesticated Cucurbita species

Peponapis bees are considered specialized pollinators of Cucurbita flowers, a genus that presents several species of economic value (squashes and pumpkins). Both genera originated in the Americas, and their diversity dispersion center is in Mexico. Ten species of Peponapis and ten species of Cucurbita (only non-domesticated species) were analyzed considering the similarity of their ecological niche characteristics with respect to climatic conditions of their occurrence areas (abiotic variables) and interactions between species (biotic variables). The similarity of climatic conditions (temperature and precipitation) was estimated through cluster analyses. The areas of potential occurrence of the most similar species were obtained through ecological niche modeling and summed with geographic information system tools. Three main clusters were obtained: one with species that shared potential occurrence areas mainly in deserts (P. pruinosa, P. timberlakei, C. digitata, C. palmata, C. foetidissima), another in moist forests (P. limitaris, P. atrata, C. lundelliana, C. o. martinezii) and a third mainly in dry forests (C. a. sororia, C. radicans, C. pedatifolia, P. azteca, P. smithi, P. crassidentata, P. utahensis). Some species with similar ecological niche presented potential shared areas that are also similar to their geographical distribution, like those occurring predominantly on deserts. However, some clustered species presented larger geographical areas, such as P. pruinosa and C. foetidissima suggesting other drivers than climatic conditions to shape their distributions. The domestication of Cucurbita and also the natural history of both genera were considered also as important factors.     

Molecular evidence for multiple lineages in the gorgonian family Plexauridae (Anthozoa: Octocorallia)

Octocorals are diverse and abundant on many marine hard substrates, and, within this group, members of the family Plexauridae are an important component of tropical reef assemblages, especially in the Caribbean. To understand historical relationships within this large and diverse assemblage, and to test the monophyly of the family and some of its genera, DNA sequences of two mitochondrial loci (msh1 and ND2, ~1,185 bp) were analyzed from 46 species in 21 genera from deep and shallow waters in the tropical western Atlantic and in the tropical western and eastern Pacific (plus 9 taxa in the closely related Gorgoniidae and 1 species of the more distantly related Alcyoniidae). Five strongly supported clades were recovered. Three large clades correspond roughly to the Plexauridae, Paramuriceidae, and Gorgoniidae, and two smaller clades were comprised of taxa previously assigned to several families. Astrogorgia sp. did not group with any of the clades. The mutual relationships among the five clades remain unclear. Several genera previously regarded as unrelated appear to be grouped among the three families; e.g. Hypnogorgia sp. (Paramuriceidae) falls within a clade consisting of both Pacific and Atlantic Muricea spp. (Plexauridae), while Swiftia sp., Scleracis sp., and an Atlantic Thesea sp. (all Paramuriceidae) group with the gorgoniids. In several instances, genera containing Atlantic and Pacific species were recovered as monophyletic (Muricea spp., Bebryce spp.). However, in at least three cases (Echinomuricea spp., Thesea spp., Villogorgia spp.), placement of Atlantic and Pacific species in the same genus may reflect convergence of sclerite morphology. The results indicate a strong need for reexamination of octocoral taxonomy using a combination of molecular, morphological, and chemical evidence.Electronic Supplementary Material Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s00227-005-1592-y.Communicated by J.P. Grassle, New Brunswick     

Seeing stars: a molecular and morphological investigation into the evolutionary history of Odontasteridae (Asteroidea) with description of a new species from the Galapagos Islands

Odontasteridae (Asteroidea: Echinodermata) (Verrill in Am J Sci, 1899) is placed within Valvatida, a derived assemblage of sea stars. Odontasterids are found in the Southern, Atlantic, and Pacific Oceans and are concentrated in high southern latitudes. To date, the phylogenetic and evolutionary history of Odontasteridae as a whole has not been rigorously examined. We conducted molecular and morphological phylogenetic analyses of Odontasteridae to assess the interrelationships among and within recognized genera. We used mitochondrial 16S and cytochrome c oxidase subunit I molecular markers and 29 external morphological characters in an attempt to reconstruct the evolutionary history of the group. Generally, our results indicate that traditionally used external skeletal characters are not representative of phylogenetic history of Odontasteridae. We can conclude that species present in high latitudes in the Southern Hemisphere (i.e., Southern Ocean) are the most derived taxa. Additionally, mtDNA data suggest unrecognized lineages of odontasterids are present in high southern latitudes. A new species Odontaster cynthiae sp. nov. is described from the Galapagos Islands.     

The mudsnail genus Hydrobia s.s. in the northern Atlantic and western Mediterranean: a phylogenetic hypothesis

The mudsnail taxon Hydrobia s.l. plays a major role in numerous ecological and parasitological studies. Yet, its taxonomy is confusing and its biogeography is poorly understood. A principal problem is that taxa of Hydrobia s.l. belong to morphostatic radiations – widely allopatric species radiations with little or no habitat diversification and a low level of anatomical change. So far, three morphostatic radiations can be identified within Hydrobia s.l.: Hydrobia s.s., Peringia, and Ventrosia. These radiations are identical with the putative genera of Hydrobia s.l. The purpose of the paper is to infer phylogenetic relationships within one of these radiations, Hydrobia s.s. in the northern Atlantic and western Mediterranean. A total of 22 populations, including topotypical populations of five commonly used taxa, were studied genetically using partial sequences of the mitochondrial cytochrome c oxidase subunit I gene. Based on molecular data and the species concept we define, the following species and subspecies were identified: Hydrobia acuta acuta (Draparnaud, 1805) [=H. minoricensis (Paladilhe, 1875)], H. acuta neglecta Muus, 1963, and H. glyca (Servain, 1880) (=H. joossei van Aartsen, Menkhorst and Gittenberger, 1984). One population from Djerba, Tunisia (Hydrobia sp. A) and one population from Mallorca, Spain (Hydrobia sp. B) are genetically distinct from all other taxa studied here. Both populations potentially represent new species. Due to the fact that only one population each has been studied, and so the degree of variation within these two taxa cannot be assessed, a final decision regarding their species level cannot yet be made. Received: 6 October 1999 / Accepted: 12 September 2000     

Phylogenetic relationships within the Octocorallia (Cnidaria: Anthozoa) based on nuclear 18S rRNA sequences

We determined the nuclear 18S rRNA sequences for 41 species of octocorals and used these to address the validity of the historical ordinal divisions and the current subordinal divisions within the subclass Octocorallia. We also explored the phylogenetic affinities of the species Dendrobrachia paucispina, which was originally classified in the order Antipatharia (subclass Ceriantipatharia) although polyp structure indicates it belongs in the subclass Octocorallia. Trees constructed using maximum likelihood techniques are incongruent with the current and historical taxonomy of the Octocorallia. There appeared to be three major clades of octocorals. The first clade included most, but not all, pennatulaceans as a monophyletic group. The second clade contained 21 species, representing all major octocoral groups other than pennatulaceans. The third clade contained members from three suborders of the Alcyonacea and one member of the Pennatulacea. These data could not be used to distinguish the branching order of the three major clades. The species D. paucispina had a close affinity with the genera Corallium and Paragorgia (Alcyonacea: Scleraxonia), although its morphology suggests it is more similar to the genus Chrysogorgia (Alcyonacea: Calcaxonia). The morphological character of dimorphism (the presence of both autozooids and siphonozooids within a single colony) corresponded loosely with the topology of the most likely trees, and a single origin of dimorphism could not be rejected. Despite sampling from the majority of families within the Octocorallia, many of the relationships within this group remain ambiguous. Received: 16 June 2000 / Accepted: 14 September 2000     

Taxonomic revisions in the marine biflagellate fungi: The ultrastructural evidence

The ultrastructure of the genera Althornia, Aplanochytrium, Japonochytrium, Schizochytrium and Thraustochytrium is described, and all are regarded as members of the new order Thraustochytriales Sparrow. Species considered are Althornia crouchii, Aplanochytrium kerguelensis, Hyalochlorella marina, Japonochytrium sp., Schizochytrium aggregatum, Thraustochytrium kinnei and T. striatum. All but H. marina are, on ultrastructural evidence, related genera, and some speculative suggestions are made about possible interrelationships both between the species discussed, between the Thraustochytriales and Labyrinthulales, and between these two and other major taxa.     

Vertical zonation of endosymbiotic zooxanthellae within a population of the intertidal sea anemone,Anthopleura uchidai

Intertidal organisms commonly form zonation bands along the shore. Environmental stressors often determine the vertical position of each zonation band. These stressors may similarly affect the distribution pattern of endogenous species in their intertidal hosts. To evaluate this possibility, we investigated the distribution pattern of endosymbiotic zooxanthellae in the genus Symbiodinium in a population of the intertidal sea anemone Anthopleura uchidai. We used molecular genetics to identify the Symbiodinium clades and found that A. uchidai has two clades of Symbiodinium, clades A and F. These Symbiodinium clades were disproportionally distributed along the vertical gradient of the intertidal shore. Anemones on the upper shore exclusively possessed clade F Symbiodinium while clade A Symbiodinium became dominant in the sea anemones on the lower shore. Photosynthesis activity assays showed that these Symbiodinium clades had similar net productivities at 23.3 and 31.8 °C at all irradiance levels. At 35 °C, however, clade A Symbiodinium exhibited substantially lower net productivities than clade F Symbiodinium, demonstrating that these Symbiodinium clades have distinct tolerances to thermal stress. These results suggest that the thermal gradient across tidal height is a major factor shaping the zonation pattern of Symbiodinium clades in A. uchidai.     

Phylogeny and biogeography of Sicydiinae (Teleostei: Gobiidae) inferred from mitochondrial and nuclear genes

In the Indo-Pacific area, the Caribbean region and West Africa, insular systems are colonised by particular Gobiids of the Sicydiinae subfamily. These species spawn in freshwater, the free embryos drift downstream to the sea where they undergo a planktonic phase, before returning to rivers to grow and reproduce; an amphidromous lifestyle. These gobies are the biggest contributors to the diversity of fish communities in insular systems and have the highest levels of endemism, yet their phylogeny has not been explored before with molecular data. To understand the phylogeny and the biogeography of this subfamily, sequences from the mitochondrial 16S rDNA and cytochrome oxidase I and from the nuclear rhodopsin gene were obtained for 50 Sicydiinae specimens of seven genera. Our results support the monophyly of the subfamily and of all the genera except Sicyopus, which is polyphyletic. Five major clades were identified within this subfamily. One clade clusters Sicyopterus and Sicydium as sister genera, one contains the genus Stiphodon split into two different groups, two other clades include only Sicyopus (Smilosicyopus) and Cotylopus, respectively, and the last clade groups Akihito, Lentipes and Sicyopus (Sicyopus). As a result, the subgenus Smilosicyopus is elevated herein as a genus. A molecular dating approach helps the interpretation of these phylogenetic results in terms of amphidromy and biogeographical events that have allowed the Sicydiinae to colonise the Indo-Pacific, West African and Caribbean islands.