Evolution of habitat use by deep-sea mussels

Previous phylogenetic studies proposed that symbiont-bearing mussels of the subfamily Bathymodiolinae (Bivalvia: Mytilidae) invaded progressively deeper marine environments and evolved from lineages that decomposed wood and bone to specialized lineages that invaded cold-water hydrocarbon seeps and finally deep-sea hydrothermal vents. To assess the validity of the hypotheses, we examined two nuclear (18S and 28S rRNA) and two mitochondrial genes (COI and ND4) from a broad array of bathymodiolin species that included several recently discovered species from shallow hydrothermal seamounts. Bayesian phylogenetic analysis and maximum-likelihood estimates of ancestral character states revealed that vent species evolved multiple times, and that reversals in vent and seep habitat use occurred within the sampled taxa. Previous hypotheses regarding evolution from wood/bone-to-seeps/vents are supported in that mid-ocean hydrothermal vent species may represent a monophyletic group with one noticeable reversal. Earlier hypotheses about progressive evolution from shallow-to-deep habitats appear to hold with a few instances of habitat reversals.     

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     

Evolutionary relationships of deep-sea hydrothermal vent and cold-water seep clams (Bivalvia: Vesicomyidae): results from the mitochondrial cytochrome oxidase subunit I

Phylogenetic relationships among vesicomyid clams (Bivalvia: Vesicomyidae) and their placement within the order Heterodonta were examined using mitochondrial encoded cytochrome oxidase subunit I (COI) DNA sequences. The presently analyzed vesicomyids represent a recent monophyletic radiation that probably occurred within the Cenozoic. Nucleotide phylogenetic analyses resolved discrete clades that were consistent with currently recognized species: Calyptogena magnifica, C. ponderosa, Ectenagena extenta, C. phaseoliformis, Vesicomya cordata, Calyptogena n. sp. (Gulf of Mexico), C. kaikoi, C. nautilei, C. solidissima and C. soyoae (Type-A). However, specimens variously identified as: V. gigas, C. kilmeri, C. pacifica, and V. lepta comprised two “species complexes”, each composed of multiple evolutionary lineages. Most taxa are limited to hydrothermal-vent or cold-seep habitats, but the “vent” versus “seep” clams do not constitute separate monophyletic groups. Current applications of the generic names Calyptogena, Ectenagena, and Vesicomya are not consistent with phylogenetic inferences. Received: 24 July 1997 / Accepted: 22 August 1997     

Extreme mitochondrial DNA divergence within populations of the deep-sea gastropod Frigidoalvania brychia

The deep sea supports a diverse and highly endemic invertebrate fauna, the origin of which remains obscure. Little is known about geographic variation in deep-sea organisms or the evolutionary processes that promote population-level differentiation and eventual speciation. Sequence variation at the 16 S rDNA locus was examined in formalin-preserved specimens of the common upper bathyal rissoid Frigidoalvania brychia (Verrill, 1884) to examine its population genetic structure. The specimens came from trawl samples taken over 30 years ago at depths of 457-1,102 m at stations in the Northwest Atlantic south of Woods Hole, Massachusetts, USA. Near the upper boundary of its bathymetric range (500 m), extremely divergent haplotypes comprising three phylogenetically distinct clades (average uncorrected sequence divergence among clades ~23%, ~3% within clades) were found at stations separated by a maximum distance of ~80 km, suggesting the presence of high levels of intraspecific divergence or the possibility of morphologically cryptic species. Only one of these clades was found at two stations in the mid- to lower part of F. brychia's depth distribution (800-1,100 m), suggesting lower clade diversity with increasing depth, although among-sample divergence, with a single exception, was minimal. One station was genetically divergent from all others sampled, containing a unique suite of haplotypes including two found only at this site. Steep vertical selective gradients, major oceanographic changes during the late Cenozoic, and habitat fragmentation by submarine canyons might have contributed to an upper bathyal region that is highly conducive to evolutionary change.     

Population structure of loggerhead turtle (Carettacaretta) nesting colonies in the Atlantic and Mediterranean as inferred from mitochondrial DNA control region sequences

Mitochondrial (mt) DNA control region sequences were analyzed for 249 Atlantic and Mediterranean loggerhead turtles (Carettacaretta Linnaeus, 1758) to elucidate nesting population structure and phylogeographic patterns. Ten haplotypes were resolved among individuals sampled between 1987 and 1993, from ten major loggerhead nesting areas in the region. Two distinct phylogenetic lineages were distinguished, separated by an average of 5.1% sequence divergence. Haplotype frequency comparisons between pairs of populations showed significant differentiation between most regional nesting aggregates and revealed six demographically independent groups, corresponding to nesting beaches from: (1) North Carolina, South Carolina, Georgia and northeast Florida, USA; (2) southern Florida, USA; (3) northwest Florida, USA; (4) Quintana Roo, Mexico; (5) Bahia, Brazil; and (6) Peloponnesus Island, Greece. The distribution of mtDNA haplotypes is consistent with a natal homing scenario, in which nesting colonies separated by a few hundred kilometers represent isolated reproductive aggregates. However, a strong exception to this pattern was observed in the first group defined by mtDNA data (North Carolina to northeast Florida), which included samples from four nesting locations spread across thousands of kilometers of coastline. These locations were characterized by a single haplotype in 104 out of 105 samples, providing inadequate resolution of population divisions. In view of the subdivisions observed elsewhere, we attribute the lack of differentiation between North Carolina and northeast Florida to recent colonization of these warm temperate coastlines (after the Wisconsin glaciation) not to ongoing gene flow among spatially distinct nesting locations. The relationships among observed haplotypes suggest a biogeographic scenario defined by climate, natal homing, and rare dispersal events. The redefined relationships among nesting aggregations in the western Atlantic region (southeastern USA and adjacent Mexico) prompt a reconsideration of management strategies for nesting populations and corresponding habitats in this region. Received: 28 October 1996 / Accepted: 24 October 1997     

Evolutionary relationships among deep-sea mytilids (Bivalvia: Mytilidae) from hydrothermal vents and cold-water methane/sulfide seeps

A protein electrophoretic survey of mytilids inhabiting deep-sea hydrothermal vents and cold-water methane/sulfide seeps revealed electromorph patterns diagnostic of 10 distinct species. From hydrothermal vents located at sites on the Galápagos Rift, the Mid-Atlantic Ridge, and the Mariana Back Arc Basin, we detected four species of mytilids. Six additional species were detected from three cold-water seep sides in the Gulf of Mexico. The patchy distribution and temporal stability of seeps may provide a greater opportunity for mytilid diversification and persistence than vent sites Nei's genetic distances (D) between species were relatively large (range: 0.528 to ) both within and among habitat types. This pronounced degree of genetic differentiation suggests a relatively ancient common ancestor for the group. Phylogenetic trees were generated using distance Wagner and parsimony analyses of allozyme and morphological characters. The tree topologies obtained from both methods support: (1) the hypothesis that a seep ancestor gave rise to the deep-sea hydrothermal vent mytilids, (2) a historical progression from shallow-water to deep-water habitats, and (3) a co-evolutionary progression from external to internal localization of bacterial symbionts. Whether the seep mytilid taxa constitute paraphyletic or polyphyletic groups remains unresolved. Our phylogenetic hypotheses also provide a benchmark for the phylogeny of mytilid bacterial symbionts.     

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     

Introgression and mitochondrial DNA heteroplasmy in the Baltic populations of mussels Mytilus trossulus and M. edulis

A strong clinal change in salinity occurs between the Baltic Sea and the North Sea, Atlantic Ocean, in the Danish Straits, where hybridization zone between mussels Mytilus edulis and M. trossulus has been reported. Eleven samples of mussels were studied from the Danish Straits and the inner Baltic Sea. Extensive introgression of M. edulis alleles from the North Sea into populations throughout the Baltic was ascertained for mitochondrial DNA (mtDNA) and two nuclear markers (ME15–16 and ITS). In the opposite direction, introgression of M. trossulus alleles into the M. edulis background was observed at the EFbis nuclear marker in populations from Kattegat (Danish Straits). While only M. edulis F (female) mtDNA was present in the Baltic, there were still strong differences in frequencies in the control region length variants between the Danish Straits and the inner Baltic samples, and weaker variation in coding region ND2–COIII haplotype frequencies. In the assays of the two mtDNA regions, various patterns of heteroplasmy were detected in 32% of all the studied individual mussels; this includes the presence of distinct, independently inherited M and F mitochondria in males, as well as the presence of two different distinguishable F genomes. The male-inherited M mtDNA genomes are quite common in the mussels from the Danish Straits, but very rare in males from the inner Baltic. Instead, a recombined control region variant (1r), which seems to have taken over the role of the M genome, was present in a number of specimens in the Baltic. Observations of heteroplasmy for two F genomes in some females and males confirm disruptions of the doubly uniparental inheritance mechanism in the hybrid Baltic Mytilus.     

Genetic stock structure of the swordfish (Xiphias gladius ) inferred by PCR-RFLP analysis of the mitochondrial DNA control region

Restriction fragment length polymorphism (RFLP) analysis was performed on PCR amplified DNA fragments containing the control region of the swordfish (Xiphias gladius Linnaeus, 1758) mitochondrial DNA. A total of 456 individuals comprising 13 local samples (six Pacific, three Atlantic, the Mediterranean Sea, two Indian Ocean and the Cape of Good Hope) were surveyed with four endonucleases (Alu I, Dde I, Hha I and Rsa I), yielding a total of 52 composite genotypes. Within-sample genotypic diversity (H) was high ranging from 0.702 to 0.962 with a value of 0.922 for the pooled sample. Significant geographic variation in the frequencies of genotypes and restriction patterns was revealed. The Mediterranean sample was highly distinct from all other samples. Further, Rsa I digestion revealed high levels of polymorphism in all but the Mediterranean samples, indicating that exogenous swordfishes rarely enter that body of water. Heterogeneity between the North and South Atlantic samples was significant, both of which differed from those of the Pacific. In contrast, the Indian Ocean samples were not significantly different from the samples of South Atlantic and Pacific. Genetic differentiation among the Pacific samples was low. The results indicate that the world-wide swordfish population is genetically structured not only among, but also within ocean basins and suggest that gene flow is restricted despite the absence of geographic barriers. Received: 28 August 1996 / Accepted: 2 October 1996     

Low levels of global genetic differentiation and population expansion in the deep-sea teleost <Emphasis Type="Italic">Hoplostethus atlanticus</Emphasis> revealed by mitochondrial DNA sequences

The orange roughy Hoplostethus atlanticus is a well-known commercial species with a global distribution. There is no consensus about levels of connectivity among populations despite a range of techniques having been applied. We used cytochrome c oxidase subunit I (COI) and cytochrome b sequences to study genetic connectivity at a global scale. Pairwise Φ_ST analyses revealed a lack of significant differentiation among samples from New Zealand, Australia, Namibia, and Chile. However, low but significant differentiation (Φ_ST = 0.02–0.13, P < 0.05) was found between two Northeast Atlantic sites and all the other sites with COI. AMOVA and the haplotype genealogy confirmed these results. The prevalent lack of genetic differentiation is probably due to active adult dispersal under the stepping-stone model. Demographic analyses suggested the occurrence of two expansion events during the Pleistocene period.     

Phylogenetic relationships of deep-sea mussels of the genus<Emphasis Type="Italic"> Bathymodiolus</Emphasis> (Bivalvia: Mytilidae)

We examined phylogenetic relationships among three Bathymodiolus species in Japanese waters and Bathymodiolus spp. from the Manus Basin by two different approaches. Two-dimensional gel electrophoresis allowed us to compare 263–407 (average=318) proteins, giving comprehensive information on genetic distances among the species. The neighbor-joining tree presented two clusters: (1) B. japonicus and B. platifrons and (2) B. septemdierum and B. sp. Members of the first cluster contain methanotrophic endosymbiotic bacteria and members of the second cluster contain thioautotrophic endosymbionts. DNA sequencing of a fragment (415 bp) of mitochondrial cytochrome c oxidase subunit I (COI) provided a neighbor-joining tree with the same topology as that derived from protein analysis. Inspection of intraspecific variation in COI in B. japonicus and B. platifrons revealed no genetic differentiation between mussel populations of either species from cold-water seeps versus hydrothermal vents, suggesting high adaptability of these Bathymodiolus species to deep-sea chemosynthetic environments. Our results indicated genetic exchanges between mussels from distant localities, suggesting that a limited dispersal capability of the larvae is not the likely factor leading to speciation events in these Bathymodiolus species.Communicated by T. Ikeda, Hakodate     

Phylogenetic relationships among species of Calyptogena (Bivalvia: Vesicomyidae) collected around Japan revealed by nucleotide sequences of mitochondrial genes

Phylogenetic relationships among the seven species of deep-sea giant clams Calyptogena (Bivalvia: Vesicomyidae) collected around Japan were examined using parts of nucleotide sequences of mitochondrial genes for cytochrome oxidase I (COI) and cytochrome oxidase III (COIII) and the encoded amino acid sequences. The seven species were C. soyoae (Sagami Bay), C. fausta (Suruga Bay), C. kaikoi (Nankai Trough), C. nautilei (Nankai Trough), C. phaseoliformis (Japan Trench), C. solidissima (Minami-Ensei Knoll, Okinawa Trough) and Calyptogena sp. (Iheya Ridge, Okinawa Trough). A clear phylogenetic split was observed between one group of three species (C. kaikoi, C. phaseoliformis and C. fausta) and the remaining species. This clustering corresponds to the two previously described subgenera within the genus Calyptogena (Calyptogean and Ectenagena) with the exception of the placement of C. nautilei, which had been placed in the subgenus Ectenagena. Genetic distances between two haplotypes of C. soyoae were 0.043 for the COI region and 0.055 for the COIII region, and three amino acid substitutions were detected with the COIII region. Calyptogena sp. from the Iheya Ridge could be distinguished from one of the two haplotypes (type A) of C. soyoae by only a single nucleotide substitution, a result that suggests that Calyptogena sp. of the Iheya Ridge diverged from C. soyoae after the two haplotypes had diverged, and it is now isolated from C. soyoae in Sagami Bay.     

A study of the genetic relationships within and among wolf packs using DNA fingerprinting and mitochondrial DNA

Summary DNA fingerprinting and mitochondrial DNA analyses have not been used in combination to study relatedness in natural populations. We present an approach that involves defining the mean fingerprint similarities among individuals thought to be unrelated because they have different mtDNA genotypes. Two classes of related individuals are identified by their distance in standard errors above this mean value. The number of standard errors is determined by analysis of the association between fingerprint similarity and relatedness in a population with a known genealogy. We apply this approach to gray wolf packs from Minnesota, Alaska, and the Northwest Territories. Our results show that: (1) wolf packs consist primarily of individuals that are closely related genetically, but some packs contain unrelated, non-reproducing individuals; (2) dispersal among packs within the same area is common; and (3) short-range dispersal appears more common for female than male wolves. The first two of these genetically-based observations are consistent with behavioral data on pack structure and dispersal in wolves, while the apparent sex bias in dispersal was not expected.USA Offprint requests to: N. Lehman at the present address     

The importance of methane and thiosulfate in the metabolism of the bacterial symbionts of two deep-sea mussels

Undescribed hydrocarbon-seep mussels were collected from the Louisiana Slope, Gulf of Mexico, during March 1986, and the ultrastructure of their gills was examined and compared to Bathymodiolus thermophilus, a mussel collected from the deep-sea hydrothermal vents on the Galápagos Rift in March 1985. These closely related mytilids both contain abundant symbiotic bacteria in their gills. However, the bacteria from the two species are distinctly different in both morphology and biochemistry, and are housed differently within the gills of the two mussels. The symbionts from the seep mussel are larger than the symbionts from B. thermophilus and, unlike the latter, contain stacked intracytoplasmic membranes. In the seep mussel three or fewer symbionts appear to be contained in each host-cell vacuole, while in B. thermophilus there are often more than twenty bacteria visible in a single section through a vacuole. The methanotrophic nature of the seep-mussel symbionts was confirmed in ¹⁴C-methane uptake experiments by the appearance of label in both CO₂ and acid-stable, non-volatile, organic compounds after a 3 h incubation of isolated gill tissue. Furthermore, methane consumption was correlated with methanol dehydrogenase activity in isolated gill tissue. Activity of ribulose-1,5-biphosphate (RuBP) carboxylase and ¹⁴CO₂ assimilation studies indicate the presence of either a second type of symbiont or contaminating bacteria on the gills of freshly captured seep mussels. A reevaluation of the nutrition of the symbionts in B. thermophilus indicates that while the major symbiont is not a methanotroph, its status as a sulfur-oxidizing chemoautotroph, as has been suggested previously, is far from proven.     

Structure and migration corridors in Pacific populations of the Swordfish Xiphius gladius, as inferred through analyses of mitochondrial DNA

 The swordfish Xiphias gladius is a migratory oceanic species distributed in sub-tropical and temperate waters worldwide. Studies utilizing mitochondrial DNA (mtDNA) have demonstrated genetic subdivision between ocean basins, as well as within the Atlantic basin. However, there has been no support of population subdivision within the Pacific. We sequenced 629 base pairs of the control region for 281 swordfish collected in the Pacific. A rate heterogeneity parameter, alpha, was found to be 0.201, indicating substantial variation in mutation rate within the control region of swordfish. Hierarchical analysis of molecular variance supported significant genetic structuring among Pacific populations. Northern and southern populations in the western Pacific were significantly divergent, while populations in the east appeared to be genetically continuous. Regression analysis supported a correlation of genetic differentiation with geographic distance along a U-shaped corridor of gene flow. These results reveal a pelagic biogeographic pattern heretofore unrecognized in the Pacific, and reject the null hypothesis that Pacific populations of swordfish are unstructured and comprise only a single homogeneous stock. Received: 10 November 1998 / Accepted: 4 February 2000     

Molecular phylogeny of Ostracoda (Crustacea) inferred from 18S ribosomal DNA sequences: implication for its origin and diversification

Nucleotide sequences for the 18S rDNA of 17 ostracod species, representing 4 extant orders and 12 superfamilies, were determined and compared with known sequences of other crustaceans. Resulting molecular phylogenetic trees based on maximum-likelihood, maximum-parsimony, and neighbor-joining methods consistently indicated that the Podocopida plus Platycopida forms a monophyletic group, but did not indicate monophyly of the Ostracoda consisting of the four orders, Podocopida, Platycopida, Kirkbyocopida, and Myodocopida. The tree topology and the crustacean fossil record suggest that the lineage of podocopidans and platycopidans, that of kirkbyocopidans, and that of myodocopidans should have separately been established already in the Cambrian, although there is no ostracod fossil record in that time period. Close relationships between the Bythocytheroidea and Cytheroidea and among the Macrocypridoidea, Pontocypridoidea, and Cypridoidea can safely be postulated, but other relationships among podocopidan and platycopidan superfamilies could not be resolved from the 18S rDNA data. The polychotomous relationship among five lineages of the podocopidan and platycopidan superfamilies, i.e. Cytherelloidea, Bairdioidea, Darwinuloidea, Bythocytheroidea plus Cytheroidea, and Macrocypridoidea plus Pontocypridoidea plus Cypridoidea, suggests that common ancestors of those lineages diverged from each other rapidly in short intervals in the early Paleozoic.     

Phylogeny of Opsanus spp. (Batrachoididae) inferred from multiple mitochondrial-DNA sequences

 Species of the toadfish genus Opsanus are increasingly used as experimental organisms in biomedicine and evolutionary/ecological physiology. Despite their importance, little is known of the phylogenetic relationships among Opsanus species. DNA sequence data for portions of the mitochondrial 12S rRNA, cytochrome oxidase I and cytochrome b genes were generated and analyzed from the four recognized Opsanus species and three outgroup taxa. Results of these analyses indicate an evolutionarily rapid divergence of three lineages within the genus. O. beta and O. pardus were resolved within the same lineage, and could not be distinguished with these mitochondrial sequence data. These data and paleoclimatic theory support a hypothesis of speciation based on the formation of allopatric populations during periods of elevated water temperature in the northern Caribbean. Received: 6 July 1999 / Accepted: 15 March 2000     

Global population structure of albacore (Thunnus alalunga) inferred by RFLP analysis of the mitochondrial ATPase gene

The genetic population structure of the highly migratory albacore (Thunnus alalunga) was investigated using restriction fragment length polymorphism (RFLP) analysis of the mitochondrial ATPase gene amplified by the polymerase chain reaction (PCR). 620 individuals comprising 13 geographically distant samples (ten Pacific, two Atlantic and the Cape of Good Hope) were surveyed between 1991 and 1994 with two restriction endonucleases (Mse I and Rsa I), resulting in seven haplotypes. No heterogeneity was observed in the distribution of haplotypes among the ten samples from the North and South Pacific, nor among the samples from North and South Atlantic and Cape of Good Hope. However, highly significant heterogeneity was evident among Atlantic and Pacific samples. Higher haplotypic diversity (h) was observed in the Pacific samples (0.59 to 0.69) than in the Atlantic and Cape samples (0.22 to 0.43). These results suggest greater gene flow between albacore of the northern and southern hemispheres (within oceans) than between the Atlantic and Pacific Oceans.     

Incorporation of organic aggregates by marine mussels

Two marine mussels, Geukensia demissa (Dillwyn) and Mytilus edulis (L.) collected in 1990 in Old Silver Beach, Falmouth, Massachusetts, incorporated nitrogen when fed ¹⁵N-labelled organic aggregates produced from dissolved organic nitrogen released by the brown sea-weed Fucus vesiculosis. Uptake of ¹⁵N on the aggregate diet was linear over the course of 24 h, and unincorporated ¹⁵N was eliminated from the gut after 48 h. Both species of mussels incorporated approximately five times more N when they were fed organic aggregates than when they were fed either ¹⁵N-labelled dissolved organic material (DOM) or particulate detritus, both of which were also derived from the seaweed. Nitrogen uptake was greatest in controls fed the diatom Thalassiosira weissflogii; mussels fed phytoplankton incorporated seven times more nitrogen than those fed aggregates. However, aggregates could supply an estimated 7 to 14% of the N requirements for both mussels, whereas DOM or particulate detritus could only supply 1 to 3%. These data provide evidence that a food web pathway exists from primary producer to released dissolved organic nitrogen to microbial organic aggregate to metazoan consumer, and, further, that it can be more important in a detrital food web than either particulate detritus or DOM.