Curious bivalves: Systematic utility and unusual properties of anomalodesmatan mitochondrial genomes.

Mitogenomic trees for Bivalvia have proved problematic in the past, but several highly divergent lineages were missing from these analyses and increased representation of these groups may yet improve resolution. Here, we add seven new sequences from the Anomalodesmata and one unidentified semelid species (Bryopa lata, Euciroa cf. queenslandica, Laternula elliptica, Laternula truncata, Lyonsia norwegica, Myadora brevis, Tropidomya abbreviata, "Abra" sp.). We show that relationships in a mitogenomic tree for the Class are improved by the addition of seven anomalodesmatans from this highly divergent clade, but are still not completely consistent with relationships recovered in studies of nuclear genes. We suggest that some anomalous relationships (for instance the non-monophyly of Bivalvia) may be partially explained by compositional heterogeneity in the mitogenome and suggest that the addition of more taxa may help resolve both this effect and possible instances of long branch attraction. We also identify several curious features about anomalodesmatan mitogenomes. For example, many protein-coding gene boundaries are poorly defined in marine bivalves, but particularly so in anomalodesmatans, primarily due to non-conserved boundary sequences. The use of transcriptomic and genomic data together enabled better definition of gene boundaries, the identification of possible pseudogenes and suggests that most genes are translated monocistronically, which contrasts with many other studies. We also identified a possible case of gene duplication of ND5 in Myadora brevis (Myochamidae). Mitogenome size in the Anomalodesmata ranges from very small compact molecules, with the smallest for Laternula elliptica (Laternulidae) only 14,622bp, to Bryopa lata (Clavagellidae) which is at least 31,969bp long and may be >40,000bp. Finally, sampled species show a high degree of sequence divergence and variable gene order, although intraspecific variation in Laternula elliptica is very low.

New digeneans (Opecoelidae) from hydrothermal vent fishes in the south eastern Pacific Ocean, including one new genus and five new species.

A new genus and five new species of digeneans are reported from fishes at hydrothermal vent sites in the South East Pacific Rise region. Biospeedotrema n. gen. (Opecoelidae: Stenakrinae) is distinguished from other stenakrines by the more or less symmetrical testicular configuration, with the uterus passing between the testes, sometimes distinctly into the post-testicular region. Biospeedotrema jolliveti n. gen., n. sp. from Ventichthys biospeedoi (Ophidiidae) is distinguished by the vitelline fields which extend only slightly into the post-testicular region, the intestinal bifurcation is dorsal to the ventral sucker, the genital pore is slightly dextrally submedian or median, the cirrus sac is short and the caeca are broad and overlap the testes, usually reaching into the post-testicular region. Biospeedotrema parajolliveti n. sp. from Thermichthys hollisi differs from Biospeedotrema jolliveti in being squat, always just wider than long, the tegument is wrinkled, the testes are lobate, and the caeca only just reach to the testes. Biospeedotrema biospeedoi n. sp. from T. hollisi differs from its congeners in its body-shape, uterine extent posterior to the testes and the small vitellarium. Caudotestis ventichthysi n. sp. (Opecoelidae: Stenakrinae) from V. biospeedoi is distinguished from its five congeners in various combinations of caecal length, cirrus sac length, internal seminal vesicle shape, vitelline extent and distribution, forebody length and egg-size. Buticulotrema thermichthysi n. sp. (Opecoelidae: Opecoelininae) from T. hollisi (Bythitidae) is distinguished from its only congener by its very long, very strongly muscular oesophagus, bifurcating dorsally to the posterior part of the ventral sucker, the long, narrow pars prostatica and distal male duct and the sinistral genital pore at the level of the pharynx. The phylogenetic position for three of these species, Buticulotrema thermichthysi, Biospeedotrema jolliveti and Biospeedotrema biospeedoi, is assessed based on ssrDNA and lsrDNA sequences, which verify the position of these species in the Opecoelidae. 

Cenozoic climate change and diversification on the continental shelf and slope: evolution of gastropod diversity in the family Solariellidae (Trochoidea).

Recent expeditions have revealed high levels of biodiversity in the tropical deep-sea, yet little is known about the age or origin of this biodiversity, and large-scale molecular studies are still few in number. In this study, we had access to the largest number of solariellid gastropods ever collected for molecular studies, including many rare and unusual taxa. We used a Bayesian chronogram of these deep-sea gastropods (1) to test the hypothesis that deep-water communities arose onshore, (2) to determine whether Antarctica acted as a source of diversity for deep-water communities elsewhere and (3) to determine how factors like global climate change have affected evolution on the continental slope. We show that although fossil data suggest that solariellid gastropods likely arose in a shallow, tropical environment, interpretation of the molecular data is equivocal with respect to the origin of the group. On the other hand, the molecular data clearly show that Antarctic species sampled represent a recent invasion, rather than a relictual ancestral lineage. We also show that an abrupt period of global warming during the Palaeocene Eocene Thermal Maximum (PETM) leaves no molecular record of change in diversification rate in solariellids and that the group radiated before the PETM. Conversely, there is a substantial, although not significant increase in the rate of diversification of a major clade approximately 33.7 Mya, coinciding with a period of global cooling at the Eocene-Oligocene transition. Increased nutrients made available by contemporaneous changes to erosion, ocean circulation, tectonic events and upwelling may explain increased diversification, suggesting that food availability may have been a factor limiting exploitation of deep-sea habitats. Tectonic events that shaped diversification in reef-associated taxa and deep-water squat lobsters in central Indo-West Pacific were also probably important in the evolution of solariellids during the Oligo-Miocene.

Global diversification of mangrove fauna: a molecular phylogeny of Littoraria (Gastropoda: Littorinidae).

The genus Littoraria is one of very few molluscan groups that are closely associated with mangroves. We document its global evolutionary radiation and compare biogeographic patterns with those of mangrove plants, based on phylogenetic and fossil evidence. Using sequences from three genes (nuclear 28S rRNA, mitochondrial 12S rRNA and COI) we reconstruct a phylogeny of 37 of the 39 living morphospecies. Six monophyletic subgenera are defined (Bulimilittorina, Lamellilitorina, Littoraria, Palustorina, Protolittoraria, Littorinopsis) and we synonymize L. coccinea and L. glabrata. A deep division between Palustorina from the Indo-West Pacific and Littoraria from the Atlantic and Eastern Pacific is estimated by a Bayesian relaxed-clock method to be of Middle Eocene to Palaeocene age (43.2-62.7 Ma), which far predates the Early Miocene (18 Ma) closure of the Tethyan Seaway; this, as in mangrove plants, may reflect vicariance by climatic cooling, rather than tectonic processes. The age of Littoraria angulifera in the Atlantic is, however, consistent with Early Miocene vicariance of a Tethyan ancestor. We infer that speciation events are mainly of Miocene or older age, and that diversification has not been driven by depletion of mangrove habitats during recent glacial intervals. Parsimonious reconstruction of ancestral habitats suggests that the genus has inhabited mangrove or wood substrates since its origin, while the rock-dwelling habit of the four members of Protolittoraria is derived. Three species span the Eastern Pacific Barrier, and one is amphi-Atlantic, consistent with a long larval phase of up to 10 weeks. Allopatric speciation is inferred, but usually with subsequent range overlap. Ovoviviparity (interpreted as an adaptation to life in mangroves) has arisen twice.

Mudwhelks and mangroves: the evolutionary history of an ecological association (Gastropoda: Potamididae).

Most of the 29 living species of Potamididae show a close association with mangroves. The trees provide the snails with shelter, protection from predators, a solid substrate and sometimes food. Using sequences from three genes (nuclear 18S rRNA and 28S rRNA, mitochondrial COI) we derive a molecular phylogeny and recognize six living genera (Terebralia, Telescopium, Tympanotonos, Cerithidea, Cerithideopsis, Cerithideopsilla). The oldest modern genera (Terebralia, Cerithideopsis) appeared in the Tethyan realm in the Middle Eocene, shortly after the origin of mangrove trees. Whereas most potamidid genera are now restricted to either the Indo-West Pacific (IWP) or to the eastern Pacific plus Atlantic (EPA), sister clades of Cerithideopsis survive in both realms. Based on a reinterpretation of the fossil record (particularly of the monotypic Tympanotonos and extinct Potamides), and parsimonious reconstruction of ancestral habitats, we suggest that the living potamidids are an adaptive radiation that has always been closely associated with mangroves. The specialized tree-climbing groups Cerithidea and Cerithideopsis were independently derived from mud-dwelling ancestors. Cerithideopsilla cingulata (a species complex in the IWP) and 'Potamides' conicus (in the Mediterranean and Indian Ocean) form a single clade within the genus Cerithideopsilla. This refutes the hypothesis that 'P.'conicus is the sole relict of the Tethyan Potamides that has occurred in the Mediterranean region since the Palaeocene. Instead, the phylogeny and fossil record suggest that an ancestor of Cerithideopsilla conica with planktotrophic larvae dispersed from the IWP to the Mediterranean in the Middle Miocene, that its direct development evolved in the Mediterranean during the Pliocene, and that it reinvaded the Indian Ocean during the Plio-Pleistocene.

Multiple origins of anaerobic ciliates with hydrogenosomes within the radiation of aerobic ciliates.

Some ciliates live anaerobically and lack mitochondria, but possess hydrogenosomes: organelles that contain hydrogenase and produce hydrogen. The origin of hydrogenosomes has been explained by two competing hypotheses: (i) they are biochemically modified mitochondria; or (ii) they are derived from endosymbiotic association(s) of ciliates and anaerobic eubacteria that possessed the hydrogenosome biochemistry. Phylogenetic analyses of representative aerobic, and anaerobic hydrogenosomal ciliates using host nuclear SSU rDNA sequences indicate a minimum of three, but more likely four, separate origins of hydrogenosomes. Whereas this does not refute either hypothesis, the implausibility of multiple convergent endosymbioses gives further support to the view that hydrogenosomes in ciliates derive from an existing organelle, which ultrastructural evidence suggests is the mitochondrion. Our results indicate a considerable potential for physiological-biochemical plasticity among a group of predominantly aerobic eucaryotes, and provide a phylogenetic framework to further refine and test hypotheses of the origins of the hydrogenosomal enzymes.

Use of the PCR and fluorescent probes to recover SSU rRNA gene sequences from single cells of the ciliate protozoon Spathidium.

A two-stage heminested PCR approach was developed to amplify small subunit (SSU) rDNA sequences, via two overlapping fragments, from single cells of microbial eucaryotes. The method was evaluated using the ciliate protozoon Spathidium when PCR products were obtained from nine of 10 cells tested. Southern blotting demonstrated that all fragments contained the same sequence in a region of SSU rDNA which is normally highly variable between species. A fluorescent oligonucleotide probe was used to demonstrate that this sequence also occurred in fixed cells of Spathidium. Fixatives containing mercuric salts preserved cell shape and allowed probe binding with little background autofluorescence. The Spathidium sequence is closely related to that from the haptorid Homalozoon vermiculare.

Phylogenetic relationships among karyorelictids and heterotrichs inferred from small subunit rRNA sequences: resolution at the base of the ciliate tree.

Ciliate protozoa are among the most diverse and complex cells that have been described. Ciliates are characterized by nuclear dimorphism, possessing a macronucleus and a micronucleus which share the same cytoplasm. An understanding of the evolution of ciliate diversity depends upon knowledge of their phylogeny. In this study we attempted to resolve some of the relationships at the base of the ciliate tree by determining the phylogenetic position of a sample of heterotrich and hypothesized primitive karyorelictid ciliates. Karyorelictids are considered primitive because they possess a "simple" form of nuclear dualism whereby the macronucleus does not divide once it has differentiated from a micronucleus. We micromanipulated cells of two heterotrichs, Spirostomum ambiguum and Gruberia sp., and two karyorelictids, Loxodes magnus and Tracheloraphis sp., and amplified their small subunit (SSU) rDNA using PCR. The primary structure of the SSU rDNA was determined for each species and used to infer their positions in the ciliate phylogenetic tree. The results indicate, with strong support, that the aerobic heterotrichs and the karyorelictids sampled constitute a monophyletic group. The most parsimonious interpretation of the form of nuclear dimorphism in karyorelictids is that it is derived from the general condition as found in its sister group the aerobic heterotrichs. The two anaerobic heterotrichs, Metopus contortus and Metopus palaeformis, comprise a distinct clade, so that the subclass Heterotrichia, as currently conceived, is not a monophyletic group. The complex mouth architecture which characterizes all heterotrichs must be reassessed in light of this finding.

The use of rRNA sequences and fluorescent probes to investigate the phylogenetic positions of the anaerobic ciliate Metopus palaeformis and its archaeobacterial endosymbiont.

The polymerase chain reaction (PCR) was used to amplify small-subunit ribosomal DNA from the anaerobic ciliated protozoon Metopus palaeformis, and from its uncultured endosymbiotic bacteria. This was accomplished directly from total DNA extracted from protozoa without prior isolation or enrichment for symbiont cells. The double-stranded amplification products were precipitated and directly sequenced using the linear PCR reaction. Fluorescent oligonucleotide probes were designed and used in whole-cell hybridizations to provide direct visual evidence that the sequences originated from the host ciliate and from the endosymbiont. Phylogenetic analysis of the Metopus palaeformis sequence consistently placed it as a deep-branching lineage near the root of the ciliate tree. However, the present data were insufficient to resolve the detailed relationship between Blepharisma and Metopus and thus to determine if the heterotrichs are mono- or paraphyletic. Phylogenetic analysis of the symbiont partial sequence clearly demonstrated that it is an archaeobacterium and that it is closely related to, but distinct from, Methanobacterium formicicum.

Saturn's Magnetic Field and Magnetosphere.

The Pioneer Saturn vector helium magnetometer has detected a bow shock and magnetopause at Saturn and has provided an accurate characterization of the planetary field. The equatorial surface field is 0.20 gauss, a factor of 3 to 5 times smaller than anticipated on the basis of attempted scalings from Earth and Jupiter. The tilt angle between the magnetic dipole axis and Saturn's rotation axis is < 1 degrees , a surprisingly small value. Spherical harmonic analysis of the measurements shows that the ratio of quadrupole to dipole moments is < 10 percent, indicating that the field is more uniform than those of the Earth or Jupiter and consistent with Saturn having a relatively small core. The field in the outer magnetosphere shows systematic departures from the dipole field, principally a compression of the field near noon and an equatorial orientation associated with a current sheet near dawn. A hydromagnetic wake resulting from the interaction of Titan with the rotating magnetosphere appears to have been observed.

Jupiter's Magnetic Field. Magnetosphere, and Interaction with the Solar Wind: Pioneer 11.

The Pioneer 11 vector helium magnetometer provided precise, contititious measurements of the magnetic fields in interplanetary space, inside Jupiter's magnetosphere, and in the near vicinity of Jupiter. As with the Pioneer 10 data, evidence was seen of the dynanmic interaction of Jupiter with the solar wind which leads to a variety of phenomena (bow shock, upstream waves, nonlinear magnetosheath impulses) and to changes in the dimension of the dayside magnetosphere by as much as a factor of 2. The magnetosphere clearly appears to be blunt, not disk-shaped, with a well-defined outer boundary. In the outer magnetosphere, the magnetic field is irregular but exhibits a persistent southward component indicative of a closed magnetosphere. The data contain the first clear evidence in the dayside magnetosphere of the current sheet, apparently associated with centrifugal forces, that was a donminatnt feature of the outbound Pionieer 10 data. A modest westward spiraling of the field was again evident inbound but not outbound at higher latitudes and nearer the Sun-Jupiter direction. Measurements near periapsis, which were nearer the planet and provide better latitude and longitude coverage than Pioneer 10, have revealed a 5 percent discrepancy with the Pioneer 10 offset dipole mnodel (D(2)). A revised offset dipole (6-parameter fit) is presented as well as the results of a spherical harmonic analysis (23 parameters) consisting of an interior dipole, quadrupole, and octopole and an external dipole and quadrupole. The dipole moment and the composite field appear moderately larger than inferred from Pioneer 10. Maximum surface fields of 14 and 11 gauss in the northern and southern hemispheres are inferred. Jupiter's planetary field is found to be slightly more irregular than that of Earth.

Magnetic field of jupiter and its interaction with the solar wind.

Jupiter's magnetic field and its interaction with the magnetized solar wind were observed with the Pioneer 10 vector helium magnetometer. The magnetic dipole is directed opposite to that of the earth with a moment of 4.0 gauss R(J)(3) (R(J), Jupiter radius), and an inclination of 15 degrees lying in a system III meridian of 230 degrees . The dipole is offset about 0.1 R(J) north of the equatorial plane and about 0.2 R(J) toward longitude 170 degrees . There is severe stretching of the planetary field parallel to the equator throughout the outer magnetosphere, accompanied by a systematic departure from meridian planes. The field configuration implies substantial plasma effects inside the magnetosphere, such as thermal pressure, centrifugal forces, and differential rotation. As at the earth, the outer boundary is thin, nor diffuse, and there is a detached bow shock.

Whole body response of the moon to electromagnetic induction by the solar wind.

A comparison has been made of the interplanetary magnetic field as measured both by Apollo 12 on the lunar surface and by Explorer 35 in orbit around the moon. Two examples are given, one of a step change in the field vector and another of a sinusoidally varying field. A large response measured on the surface is attributed to confinement of the induced field lines between the streaming solar plasma and the high-conductivity interior. A steep bulk electrical conductivity gradient in the lunar crust is implied, with a confining layer roughly 100 kilometers deep.

Apollo 12 magnetometer: measurement of a steady magnetic field on the surface of the moon.

The Apollo 12 magnetometer has measured a steady magnetic field of 36 +/- 5 gammas on the lunar surface. Surface gradient measurements and data from a lunar orbiting satellite indicate that this steady field is localized rather than global in its extent. These data suggest that the source is a large, magnetized body which acquired a field during an epoch in which the inducing field was much stronger than any that presently exists at the moon.