Differential patterns of connectivity in Western Pacific hydrothermal vent metapopulations: A comparison of biophysical and genetic models.

Hydrothermal ecosystems face threats from planned deep-seabed mining activities, despite the fact that patterns of realized connectivity among vent-associated populations and communities are still poorly understood. Since populations of vent endemic species depend on larval dispersal to maintain connectivity and resilience to habitat changes, effective conservation strategies for hydrothermal ecosystems should include assessments of metapopulation dynamics. In this study, we combined population genetic methods with biophysical models to assess strength and direction of gene flow within four species of the genus Alviniconcha (A. boucheti, A. kojimai, A. strummeri and A. hessleri) that are ecologically dominant taxa at Western Pacific hydrothermal vents. In contrast to predictions from dispersal models, among-basin migration in A. boucheti occurred predominantly in an eastward direction, while populations within the North Fiji Basin were clearly structured despite the absence of oceanographic barriers. Dispersal models and genetic data were largely in agreement for the other Alviniconcha species, suggesting limited between-basin migration for A. kojimai, lack of genetic structure in A. strummeri within the Lau Basin and restricted gene flow between northern and southern A. hessleri populations in the Mariana back-arc as a result of oceanic current conditions. Our findings show that gene flow patterns in ecologically similar congeneric species can be remarkably different and surprisingly limited depending on environmental and evolutionary contexts. These results are relevant to regional conservation planning and to considerations of similar integrated analyses for any vent metapopulations under threat from seabed mining.

Range extensions of Pacific bone-eating worms (Annelida, Siboglinidae, Osedax).

First described in 2004 off California, Osedax worms are now known from many of the world's oceans, ranging from 10 to over 4000 m in depth. Currently, little is known about species ranges, since most descriptions are from single localities. In this study, we used new sampling in the north-eastern Pacific and available GenBank data from off Japan and Brazil to report expanded ranges for five species: Osedaxfrankpressi, O.knutei, O.packardorum, O.roseus and O.talkovici. We also provided additional DNA sequences from previously reported localities for two species: Osedaxpriapus and O.randyi. To assess the distribution of each species, we used cytochrome c oxidase subunit I (COI) sequences to generate haplotype networks and assess connectivity amongst localities where sampling permitted. Osedaxfrankpressi, O.packardorum, O.priapus, O.roseus and O.talkovici all had one or more dominant COI haplotypes shared by individuals at multiple localities, suggesting high connectivity throughout some or all of their ranges. Low ΦST values amongst populations for O.packardorum, O.roseus and O.talkovici confirmed high levels of gene flow throughout their known ranges. High ΦST values for O.frankpressi between the eastern Pacific and the Brazilian Atlantic showed little gene flow, reflected by the haplotype network, which had distinct Pacific and Atlantic haplotype clusters. This study greatly expands the ranges and provides insights into the phylogeography for these nine species.

Speciation of pelagic zooplankton: Invisible boundaries can drive isolation of oceanic ctenophores.

The study of evolution and speciation in non-model systems provides us with an opportunity to expand our understanding of biodiversity in nature. Connectivity studies generally focus on species with obvious boundaries to gene flow, but in open-ocean environments, such boundaries are difficult to identify. Due to the lack of obvious boundaries, speciation and population subdivision in the pelagic environment remain largely unexplained. Comb jellies (Phylum Ctenophora) are mostly planktonic gelatinous invertebrates, many of which are considered to have freely interbreeding distributions worldwide. It is thought that the lobate ctenophore Bolinopsis infundibulum is distributed throughout cooler northern latitudes and B. vitrea warmer. Here, we examined the global population structure for species of Bolinopsis with genetic and morphological data. We found distinct evolutionary patterns within the genus, where B. infundibulum had a broad distribution from northern Pacific to Atlantic waters despite many physical barriers, while other species were geographically segregated despite few barriers. Divergent patterns of speciation within the genus suggest that oceanic currents, sea-level, and geological changes over time can act as either barriers or aids to dispersal in the pelagic environment. Further, we used population genomic data to examine evolution in the open ocean of a distinct lineage of Bolinopsis ctenophores from the North Eastern Pacific. Genetic information and morphological observations validated this as a separate species, Bolinopsis microptera, which was previously described but has recently been called B. infundibulum. We found that populations of B. microptera from California were in cytonuclear discordance, which indicates a secondary contact zone for previously isolated populations. Discordance at this scale is rare, especially in a continuous setting.

Atolla reynoldsi sp. nov. (Cnidaria, Scyphozoa, Coronatae, Atollidae): A New Species of Coronate Scyphozoan Found in the Eastern North Pacific Ocean.

We have observed and collected unusual specimens of what we recognize as undescribed types of the genus Atolla over the past 15 years. Of these, there appear to be three potentially different types. One of these has now been genetically sequenced and compared both morphologically and molecularly with five other Atolla species that have been found in the eastern Pacific. This new variant is so morphologically distinct from other previously described Atolla species that we believe it can be described as a new species, Atolla reynoldsi sp. nov. This species along with two additional types may comprise a new genus. It is also clear that a more accurate and diagnostic morphological key for the genus Atolla needs to be developed. This paper will also provide some potential starting points for a new key to the genus.

Hidden diversity of Ctenophora revealed by new mitochondrial COI primers and sequences.

The mitochondrial gene cytochrome-c-oxidase subunit 1 (COI) is useful in many taxa for phylogenetics, population genetics, metabarcoding, and rapid species identifications. However, the phylum Ctenophora (comb jellies) has historically been difficult to study due to divergent mitochondrial sequences and the corresponding inability to amplify COI with degenerate and standard COI "barcoding" primers. As a result, there are very few COI sequences available for ctenophores, despite over 200 described species in the phylum. Here, we designed new primers and amplified the COI fragment from members of all major groups of ctenophores, including many undescribed species. Phylogenetic analyses of the resulting COI sequences revealed high diversity within many groups that was not evident from more conserved 18S rDNA sequences, in particular among the Lobata (Ctenophora; Tentaculata; Lobata). The COI phylogenetic results also revealed unexpected community structure within the genus Bolinopsis, suggested new species within the genus Bathocyroe, and supported the ecological and morphological differences of some species such as Lampocteis cruentiventer and similar undescribed lobates (Lampocteis sp. "V" stratified by depth, and "A" differentiated by colour). The newly designed primers reported herein provide important tools to enable researchers to illuminate the diversity of ctenophores worldwide via quick molecular identifications, improve the ability to analyse environmental DNA by improving reference libraries and amplifications, and enable a new breadth of population genetic studies.

Allopatric and Sympatric Drivers of Speciation in Alviniconcha Hydrothermal Vent Snails.

Despite significant advances in our understanding of speciation in the marine environment, the mechanisms underlying evolutionary diversification in deep-sea habitats remain poorly investigated. Here, we used multigene molecular clocks and population genetic inferences to examine processes that led to the emergence of the six extant lineages of Alviniconcha snails, a key taxon inhabiting deep-sea hydrothermal vents in the Indo-Pacific Ocean. We show that both allopatric divergence through historical vicariance and ecological isolation due to niche segregation contributed to speciation in this genus. The split between the two major Alviniconcha clades (separating A. boucheti and A. marisindica from A. kojimai, A. hessleri, and A. strummeri) probably resulted from tectonic processes leading to geographic separation, whereas the splits between co-occurring species might have been influenced by ecological factors, such as the availability of specific chemosynthetic symbionts. Phylogenetic origin of the sixth species, Alviniconcha adamantis, remains uncertain, although its sister position to other extant Alviniconcha lineages indicates a possible ancestral relationship. This study lays a foundation for future genomic studies aimed at deciphering the roles of local adaptation, reproductive biology, and host-symbiont compatibility in speciation of these vent-restricted snails.

Zooplankton biogeographic boundaries in the California Current System as determined from metabarcoding.

Within the southern California Current ecosystem there are two well-documented breaks in marine community structure at Point Conception and Punta Eugenia. We explored the presence of similar breaks in a diverse zooplankton community through metabarcoding of mixed net tow tissue samples collected during an expedition from Monterey to Baja California in February of 2012. We recovered a high diversity of species as well as patterns of species presence that align with their previously documented ranges in this region. We found a clear break at Punta Eugenia in overall zooplankton community structure, while Point Conception was weakly linked to changes in community structure. We analyzed this dataset through two parallel bioinformatic pipelines to examine the robustness of these results. Our overall conclusions were consistent across both pipelines, however there were differences in species detection. This study illustrates the utility of metabarcoding analysis on mixed tissue samples for recovering known patterns of diversity, as well as allowing elucidation of broad patterns of community differentiation across many groups of organisms.

Host hybridization as a potential mechanism of lateral symbiont transfer in deep-sea vesicomyid clams.

Deep-sea vesicomyid clams live in mutualistic symbiosis with chemosynthetic bacteria that are inherited through the maternal germ line. On evolutionary timescales, strictly vertical transmission should lead to cospeciation of host mitochondrial and symbiont lineages; nonetheless, examples of incongruent phylogenies have been reported, suggesting that symbionts are occasionally horizontally transmitted between host species. The current paradigm for vesicomyid clams holds that direct transfers cause host shifts or mixtures of symbionts. An alternative hypothesis suggests that hybridization between host species might explain symbiont transfers. Two clam species, Archivesica gigas and Phreagena soyoae, frequently co-occur at deep-sea hydrocarbon seeps in the eastern Pacific Ocean. Although the two species typically host gammaproteobacterial symbiont lineages marked by divergent 16S rRNA phylotypes, we identified a number of clams with the A. gigas mitotype that hosted symbionts with the P. soyoae phylotype. Demographic inference models based on genome-wide SNP data and three Sanger sequenced gene markers provided evidence that A. gigas and P. soyoae hybridized in the past, supporting the hypothesis that hybridization might be a viable mechanism of interspecific symbiont transfer. These findings provide new perspectives on the evolution of vertically transmitted symbionts and their hosts in deep-sea chemosynthetic environments.

An inordinate fondness for Osedax (Siboglinidae: Annelida): Fourteen new species of bone worms from California.

We incorporate DNA sequences from a comprehensive sampling of taxa to provide an updated phylogeny of Osedax and discuss the remarkable diversity of this clade of siboglinids. We formally describe 14 new species of Osedax from Monterey Bay, California, USA, raising the total number of properly named Osedax species to 25. These new species had formerly been recognized by informal names in various publications, and on GenBank. The descriptions document the occurrence of dwarf males in five of the new species. The distribution for the 19 species of Osedax known to occur in Monterey Bay across depths from 385 to 2898 meters and various bone substrates is documented. The exploitation of extant bird and marine turtle bones by Osedax is reported for the first time.

Population subdivision of hydrothermal vent polychaete Alvinella pompejana across equatorial and Easter Microplate boundaries.

BACKGROUND: The Equator and Easter Microplate regions of the eastern Pacific Ocean exhibit geomorphological and hydrological features that create barriers to dispersal for a number of animals associated with deep-sea hydrothermal vent habitats. This study examined effects of these boundaries on geographical subdivision of the vent polychaete Alvinella pompejana. DNA sequences from one mitochondrial and eleven nuclear genes were examined in samples collected from ten vent localities that comprise the species' known range from 23°N latitude on the East Pacific Rise to 38°S latitude on the Pacific Antarctic Ridge. RESULTS: Multi-locus genotypes inferred from these sequences clustered the individual worms into three metapopulation segments - the northern East Pacific Rise (NEPR), southern East Pacific Rise (SEPR), and northeastern Pacific Antarctic Ridge (PAR) - separated by the Equator and Easter Microplate boundaries. Genetic diversity estimators were negatively correlated with tectonic spreading rates. Application of the isolation-with-migration (IMa2) model provided information about divergence times and demographic parameters. The PAR and NEPR metapopulation segments were estimated to have split roughly 4.20 million years ago (Mya) (2.42-33.42 Mya, 95 % highest posterior density, (HPD)), followed by splitting of the SEPR and NEPR segments about 0.79 Mya (0.07-6.67 Mya, 95 % HPD). Estimates of gene flow between the neighboring regions were mostly low (2 Nm < 1). Estimates of effective population size decreased with southern latitudes: NEPR > SEPR > PAR. CONCLUSIONS: Highly effective dispersal capabilities allow A. pompejana to overcome the temporal instability and intermittent distribution of active hydrothermal vents in the eastern Pacific Ocean. Consequently, the species exhibits very high levels of genetic diversity compared with many co-distributed vent annelids and mollusks. Nonetheless, its levels of genetic diversity in partially isolated populations are inversely correlated with tectonic spreading rates. As for many other vent taxa, this pioneering colonizer is similarly affected by local rates of habitat turnover and by major dispersal filters associated with the Equator and the Easter Microplate region.

Complete mitochondrial genome of the headwater livebearer, Poeciliopsis monacha: the mother of clones.

The sexually reproducing fish, Poeciliopsis monacha (Actinopterygii, Cyprinodontiformes, Poeciliidae), is the maternal ancestor of six hybrid biotypes that reproduce clonally. The gene content and order of its 16,818 bp mitochondrial genome is virtually identical with that of other sexually reproducing poeciliid fishes, providing no evidence for a mitochondrial involvement in the origins of all-female reproduction.

Larvae from deep-sea methane seeps disperse in surface waters.

Many species endemic to deep-sea methane seeps have broad geographical distributions, suggesting that they produce larvae with at least episodic long-distance dispersal. Cold-seep communities on both sides of the Atlantic share species or species complexes, yet larval dispersal across the Atlantic is expected to take prohibitively long at adult depths. Here, we provide direct evidence that the long-lived larvae of two cold-seep molluscs migrate hundreds of metres above the ocean floor, allowing them to take advantage of faster surface currents that may facilitate long-distance dispersal. We collected larvae of the ubiquitous seep mussel "Bathymodiolus" childressi and an associated gastropod, Bathynerita naticoidea, using remote-control plankton nets towed in the euphotic zone of the Gulf of Mexico. The timing of collections suggested that the larvae might disperse in the water column for more than a year, where they feed and grow to more than triple their original sizes. Ontogenetic vertical migration during a long larval life suggests teleplanic dispersal, a plausible explanation for the amphi-Atlantic distribution of "B." mauritanicus and the broad western Atlantic distribution of B. naticoidea. These are the first empirical data to demonstrate a biological mechanism that might explain the genetic similarities between eastern and western Atlantic seep fauna.

A hybrid zone between Bathymodiolus mussel lineages from eastern Pacific hydrothermal vents.

BACKGROUND: The inhabitants of deep-sea hydrothermal vents occupy ephemeral island-like habitats distributed sporadically along tectonic spreading-centers, back-arc basins, and volcanically active seamounts. The majority of vent taxa undergo a pelagic larval phase, and thus varying degrees of geographical subdivision, ranging from no impedance of dispersal to complete isolation, often exist among taxa that span common geomorphological boundaries. Two lineages of Bathymodiolus mussels segregate on either side of the Easter Microplate, a boundary that separates the East Pacific Rise from spreading centers connected to the Pacific-Antarctic Ridge. RESULTS: A recent sample from the northwest flank of the Easter Microplate contained an admixture of northern and southern mitochondrial haplotypes and corresponding alleles at five nuclear gene loci. Genotypic frequencies in this sample did not fit random mating expectation. Significant heterozygote deficiencies at nuclear loci and gametic disequilibria between loci suggested that this transitional region might be a 'Tension Zone' maintained by immigration of parental types and possibly hybrid unfitness. An analysis of recombination history in the nuclear genes suggests a prolonged history of parapatric contact between the two mussel lineages. We hereby elevate the southern lineage to species status as Bathymodiolus antarcticus n. sp. and restrict the use of Bathymodiolus thermophilus to the northern lineage. CONCLUSIONS: Because B. thermophilus s.s. exhibits no evidence for subdivision or isolation-by-distance across its 4000 km range along the EPR axis and Galápagos Rift, partial isolation of B. antarcticus n. sp. requires explanation. The time needed to produce the observed degree of mitochondrial differentiation is consistent with the age of the Easter Microplate (2.5 to 5.3 million years). The complex geomorphology of the Easter Microplate region forces strong cross-axis currents that might disrupt self-recruitment of mussels by removing planktotrophic larvae from the ridge axis. Furthermore, frequent local extinction events in this tectonically dynamic region might produce a demographic sink rather than a source for dispersing mussel larvae. Historical changes in tectonic rates and current patterns appear to permit intermittent contact and introgression between the two species.

Genetic diversity and demographic instability in Riftia pachyptila tubeworms from eastern Pacific hydrothermal vents.

BACKGROUND: Deep-sea hydrothermal vent animals occupy patchy and ephemeral habitats supported by chemosynthetic primary production. Volcanic and tectonic activities controlling the turnover of these habitats contribute to demographic instability that erodes genetic variation within and among colonies of these animals. We examined DNA sequences from one mitochondrial and three nuclear gene loci to assess genetic diversity in the siboglinid tubeworm, Riftia pachyptila, a widely distributed constituent of vents along the East Pacific Rise and Galápagos Rift. RESULTS: Genetic differentiation (F(ST)) among populations increased with geographical distances, as expected under a linear stepping-stone model of dispersal. Low levels of DNA sequence diversity occurred at all four loci, allowing us to exclude the hypothesis that an idiosyncratic selective sweep eliminated mitochondrial diversity alone. Total gene diversity declined with tectonic spreading rates. The southernmost populations, which are subjected to superfast spreading rates and high probabilities of extinction, are relatively homogenous genetically. CONCLUSIONS: Compared to other vent species, DNA sequence diversity is extremely low in R. pachyptila. Though its dispersal abilities appear to be effective, the low diversity, particularly in southern hemisphere populations, is consistent with frequent local extinction and (re)colonization events.

Not whale-fall specialists, Osedax worms also consume fishbones.

Marine annelid worms of the genus Osedax exploit sunken vertebrate bones for food. To date, the named species occur on whale or other mammalian bones, and it is argued that Osedax is a whale-fall specialist. To assess whether extant Osedax species could obtain nutrition from non-mammalian resources, we deployed teleost bones and calcified shark cartilage at approximately 1000 m depth for five months. Although the evidence from shark cartilage was inconclusive, the teleost bones hosted three species of Osedax, each of which also lives off whalebones. This suggests that rather than being a whale-fall specialist, Osedax has exploited and continues to exploit a variety of food sources. The ability of Osedax to colonize and to grow on fishbone lends credibility to a hypothesis that it might have split from its siboglinid relatives to assume the bone-eating lifestyle during the Cretaceous, well before the origin of marine mammals.

A remarkable diversity of bone-eating worms (Osedax; Siboglinidae; Annelida).

BACKGROUND: Bone-eating Osedax worms have proved to be surprisingly diverse and widespread. Including the initial description of this genus in 2004, five species that live at depths between 25 and 3,000 m in the eastern and western Pacific and in the north Atlantic have been named to date. Here, we provide molecular and morphological evidence for 12 additional evolutionary lineages from Monterey Bay, California. To assess their phylogenetic relationships and possible status as new undescribed species, we examined DNA sequences from two mitochondrial (COI and 16S rRNA) and three nuclear genes (H3, 18S and 28S rRNA). RESULTS: Phylogenetic analyses identified 17 distinct evolutionary lineages. Levels of sequence divergence among the undescribed lineages were similar to those found among the named species. The 17 lineages clustered into five well-supported clades that also differed for a number of key morphological traits. Attempts to determine the evolutionary age of Osedax depended on prior assumptions about nucleotide substitution rates. According to one scenario involving a molecular clock calibrated for shallow marine invertebrates, Osedax split from its siboglinid relatives about 45 million years ago when archeocete cetaceans first appeared and then diversified during the late Oligocene and early Miocene when toothed and baleen whales appeared. Alternatively, the use of a slower clock calibrated for deep-sea annelids suggested that Osedax split from its siboglinid relatives during the Cretaceous and began to diversify during the Early Paleocene, at least 20 million years before the origin of large marine mammals. CONCLUSION: To help resolve uncertainties about the evolutionary age of Osedax, we suggest that the fossilized bones from Cretaceous marine reptiles and late Oligocene cetaceans be examined for possible trace fossils left by Osedax roots. Regardless of the outcome, the present molecular evidence for strong phylogenetic concordance across five separate genes suggests that the undescribed Osedax lineages comprise evolutionarily significant units that have been separate from one another for many millions of years. These data coupled with ongoing morphological analyses provide a solid foundation for their future descriptions as new species.

Marine worms (genus Osedax) colonize cow bones.

Bone-eating worms of the genus Osedax colonized and grew on cow bones deployed at depths ranging from 385 to 2893m in Monterey Bay, California. Colonization occurred as rapidly as two months following deployment of the cow bones, similar to the time it takes to colonize exposed whalebones. Some Osedax females found on the cow bones were producing eggs and some hosted dwarf males in their tubes. Morphological and molecular examinations of these worms confirmed the presence of six Osedax species, out of the eight species presently known from Monterey Bay. The ability of Osedax species to colonize, grow and reproduce on cow bones challenges previous notions that these worms are 'whale-fall specialists.'

Genetic diversity and potential function of microbial symbionts associated with newly discovered species of Osedax polychaete worms.

We investigated the genetic diversity of symbiotic bacteria associated with two newly discovered species of Osedax from Monterey Canyon, CA, at 1,017-m (Osedax Monterey Bay sp. 3 "rosy" [Osedax sp. MB3]) and 381-m (Osedax Monterey Bay sp. 4 "yellow collar") depths. Quantitative PCR and clone libraries of 16S rRNA gene sequences identified differences in the compositions and abundances of bacterial phylotypes associated with the newly discovered host species and permitted comparisons between adult Osedax frankpressi and juveniles that had recently colonized whalebones implanted at 2,891 m. The newly discovered Osedax species hosted Oceanospirillales symbionts that are related to Gammaproteobacteria associated with the previously described O. frankpressi and Osedax rubiplumus (S. K. Goffredi, V. J. Orphan, G. W. Rouse, L. Jahnke, T. Embaye, K. Turk, R. Lee, and R. C. Vrijenhoek, Environ. Microbiol. 7:1369-1378, 2005). In addition, Osedax sp. MB3 hosts a diverse and abundant population of additional bacteria dominated by Epsilonproteobacteria. Ultrastructural analysis of symbiont-bearing root tissues verified the enhanced microbial diversity of Osedax sp. MB3. Root tissues from the newly described host species and O. frankpressi all exhibited collagenolytic enzyme activity, which covaried positively with the abundance of symbiont DNA and negatively with mean adult size of the host species. Members of this unusual genus of bone-eating worms may form variable associations with symbiotic bacteria that allow for the observed differences in colonization and success in whale fall environments throughout the world's oceans.

Migration, isolation, and speciation of hydrothermal vent limpets (Gastropoda; Lepetodrilidae) across the Blanco Transform Fault.

The Sovanco Fracture Zone and Blanco Transform Fault separate the Explorer, Juan de Fuca, and Gorda ridge systems of the northeastern Pacific Ocean. To test whether such offsets in the ridge axis create barriers to along-axis dispersal of the endemic hydrothermal vent animals, we examined the genetic structure of limpet populations previously identified as Lepetodrilus fucensis McLean, 1988 (Gastropoda, Lepetodrilidae). Mitochondrial DNA sequences and patterns of allozyme variation revealed no evidence that the 150-km-long Sovanco Fracture Zone impeded gene flow between the Explorer and Juan de Fuca populations. In contrast, the 450-km-long Blanco Transform Fault separates the limpets into highly divergent northern and southern lineages that we recognize as distinct species. We describe southern populations from the Gorda Ridge (Seacliff) and Escanaba Trough as Lepetodrilus gordensis new species and refer northern populations from the Explorer and Juan de Fuca ridge systems to L. fucensis sensu stricto. The species are similar morphologically, but L. gordensis lacks a sensory neck papilla and has a more tightly coiled teleconch. To assess the degree of isolation between these closely related species, we used the Isolation with Migration method to estimate the time of population splitting, effective sizes of the ancestral and derived populations, and rates of migration across the Blanco Transform Fault.