Molecular ecology publications

Maas, Paula A.Y., O'Mullan, Gregory D., Lutz, Richard A., Vrijenhoek, Robert C., (1999). Genetic and morphometric characterization of mussels (Bivalvia: Mytilidae) from Mid-Atlantic hydrothermal vents. Biological Bulletin, 196: 265-272.
Peek, Andrew S., Gaut, Brandon S., Feldman, Robert A., Barry, James P., Kochevar, Randall E., Lutz, Richard A., Vrijenhoek, Robert C., (2000). Neutral and nonneutral mitochondrial genetic variation in deep sea clams from the family Vesicomyidae. Journal of Molecular Evolution, 50: 141-153.
O'Mullan, G.D., P.A.Y. Maas, R.A. Lutz, R.C. Vrijenhoek, (2001). A hybrid zone between hydrothermal vent mussels (Bivalvia: Mytilidae) from the Mid-Atlantic Ridge. Molecular Ecology, 10: 2819–2831.
Guinot, Danièle., Hurtado, Luis Alberto, Vrijenhoek, R. C., (2002). New genus and species of brachyuran crab from the southern East Pacific Rise (Crustacea Decapoda Brachyura Bythograeidae). Comptes Rendus Biologies, 325: 1119–1128.
Mateos, M., Sanjur,O.I., Vrijenhoek, Robert C., (2002). Historical biogeography of the livebearing fish genus Poeciliopsis (Poeciliidae: Cyprinodontiformes). Evolution, 56: 972–984.
Mateos, M., Vrijenhoek, Robert C., (2002). Ancient versus reticulate origin of a hemiclonal lineage. Evolution, 56: 985–992.
Van Dover, C. L., German, C.R., Speer, K.G., Parson, L.M., Vrijenhoek, R. C., (2002). Evolution and biogeography of deep-sea vent and seep invertebrates. Science, 295: 1253–1257.
Goffredi, S.K., Hurtado, L.A., Hallam, S., Vrijenhoek, R.C., (2003). Evolutionary relationships of deep-sea vent and seep clams (Mollusca: Vesicomyidae) of the ‘pacifica/lepta’ species complex. Marine Biology, 142: 311–320.
Hurtado, L. A., M. Mateos, R.A. Lutz, R.C. Vrijenhoek, (2003). Coupling of bacterial endosymbiont and host mitochondrial genomes in the hydrothermal vent clam Calyptogena magnifica. Applied and Environmental Microbiology, 69: 2058-2064.
Won, Y., Hallam, S.J. , G.D. O'Mullan, I.L. Pan, K.R. Buck, R.C. Vrijenhoek, (2003). Environmental acquisition of thiotrophic endosymbionts by deep-sea mussels of the genus Bathymodiolus. Applied and Environmental Microbiology, 69: 6785-6792.
Won, Y., Hallam, S.J. , G.D. O'Mullan, R.C. Vrijenhoek, (2003). Cytonuclear disequilibrium in a hybrid zone involving deep-sea hydrothermal vent mussels of the genus Bathymodiolus. Molecular Ecology, 12: 3185-3190.
Won, Y., C.R. Young, R.A. Lutz, R.C. Vrijenhoek, (2003). Dispersal barriers and isolation among deep-sea mussel populations (Mytilidae: Bathymodiolus) from eastern Pacific hydrothermal vents. Molecular Ecology, 12: 169-184.
Goffredi, S.K., Paull, C.K. , Fulton-Bennett, K. , Hurtado, L.A. , Vrijenhoek, R.C. , (2004). Unusual benthic fauna associated with a whale fall in Monterey Canyon, California.. Deep Sea Research I, 51: 1295-1306.
Goffredi, S.K., A. Warén, V.J. Orphan, C.L. VanDover, R.C. Vrijenhoek, (2004). Novel forms of structural integration between microbes and a Hydrothermal Vent Gastropod from the Indian Ocean.. Applied and Environmental Microbiology, 70: 3082-3090.
Hurtado, L.A., R.A. Lutz, R.C. Vrijenhoek, (2004). Distinct patterns of genetic differentiation among annelids of eastern Pacific hydrothermal vents.. Molecular Ecology, 13: 2603-2615.
Rouse, G.W., S.K. Goffredi, R.C. Vrijenhoek, (2004). Osedax: Bone-eating marine worms with dwarf males.. Science, 305: 668-671.
Smith, P.J., S.M. McVeagh, Y.J. Won, R.C. Vrijenhoek, (2004). Genetic heterogeneity among New Zealand species of hydrothermal vent mussels (Mytilidae: Bathymodiolus). Marine Biology, 144: 537-545.
Goffredi, S.K., Orphan, V.J., Rouse, G.W., Jahnke, L., Embaye, T., Turk, K., Lee, R., Vrijenhoek, R.C., (2005). Evolutionary innovation: A bone-eating marine symbiosis. Environmental Microbiology, 7: 1369-1378.
Mateos, M., Vrijenhoek, R.C., (2005). Independent origins of allotriploidy in the fish genus Poeciliopsis. Journal of Heredity, 96: 32-39.
Goffredi, S.K., Jones, W.J., Scholin, C.A., Marin III, R., Vrijenhoek, R.C., (2006). Molecular detection of marine invertebrate larvae. Marine Biotechnology, 8: 149-160.
Hey, R., Massoth, G., Vrijenhoek, R.C., Rona, P., Lupton, J., Butterfield, D., (2006). Hydrothermal vent geology and biology at Earth's fastest spreading rates. Marine Geophysical Researches, 27: 1249-1262.
Johnson, S.B, Young, C.R., Jones, W.J., Warén, A, Vrijenhoek, R.C., (2006). Migration, isolation, and speciation of hydrothermal vent limpets (Gastropoda; Lepetodrilidae) across the Blanco Transform Fault. Biological Bulletin, 210: 140-157.
Jones, J., Won, Y.J., Maas, P.A.Y., Smith, P.J., Lutz, R.A., Vrijenhoek, R.C., (2006). Evolution of habitat use by deep-sea mussels. Marine Biology, 148: 841-851.
Vrijenhoek, R.C., (2006). Polyploid hybrids: Multiple origins of a treefrog species. Current Biology, 16: 245-247.
Braby, C.E., Rouse, G.W., Johnson, S.B., Jones, W.J., Vrijenhoek, R.C., (2007). Bathymetric and temporal variation among Osedax boneworms and associated megafauna on whale-falls in Monterey Bay, California. Deep-Sea Research Part I, 54: 1773-1791.
Goffredi, S.K., Johnson, S.B., Vrijenhoek, R.C., (2007). Genetic and potential function of microbial symbionts associated with newly discovered species of Osedax polychaete worms. Applied and Environmental Microbiology, 73: 2314-2323.
Vrijenhoek, R.C., Duhaime, M., Jones, W.J., (2007). Subtype variation among bacterial endosymbionts of tubeworms (Annelida: Siboglinidae) from the Gulf of California. Biological Bulletin, 212: 180-184.
Goffredi, S.K., Jones, W.J., Erhlich, H., Springer, A., Vrijenhoek, R.C., (2008). Epibiotic bacteria associated with the recently discovered Yeti crab, Kiwa hirsuta. Environmental Microbiology, 10: 2623-2634.
Johnson, S.B., Warén, A., Vrijenhoek, R.C., (2008). DNA barcoding of Lepetodrilus limpets reveals cryptic species. Journal of Shellfish Research, 27: 43-51.[43:Dbollr]2.0.Co;2
Jones, W.J., Johnson, S.B., Rouse, G.W., Vrijenhoek, R.C., (2008). Marine worms (genus Osedax) colonize cow bones. Proceedings of the Royal Society B, 275: 387-391.
Rouse, G.W., Worsaae, K., Johnson, S.B., Jones, W.J., Vrijenhoek, R.C., (2008). Acquisition of dwarf male "harems" by recently settled females of Osedax roseus n. sp. (Siboglinidae; Annelida). Biological Bulletin, 214: 67-82.
Turcotte, M.M., Pires, M.N., Vrijenhoek, R.C., Reznick, D.N., (2008). Maternal provisioning in livebearing fish species and their hybrids (Poeciliidae: Poeciliopsis). Functional Ecology, 22: 1118-1124.
Vrijenhoek, R.C., Collins, P.C., Van Dover, C.L., (2008). Bone-eating marine worms: Habitat specialists or generalists?. Proceedings of the Royal Society B, 275: 1963-1964.
Vrijenhoek, R.C., Johnson, S.B., Rouse, G.W., (2008). Bone-eating Osedax females and their "harems" of dwarf males are recruited from a common larval pool. Molecular Ecology, 17: 4535-4544.
Young, C.R., Fujio, S., Vrijenhoek, R.C., (2008). Directional dispersal between mid-ocean ridges: Deep-ocean circulation and gene flow in Ridgeia piscesae. Molecular Ecology, 17: 1718-1731.
Rouse, G.W., Wilson, N.G., Goffredi, S.K., Johnson, S.B., Smart, T., Widmer, C., Young, C.M., Vrijenhoek, R.C., (2009). Spawning and development in Osedax boneworms (Siboglinidae, Annelida). Marine Biology, 156: 395-405.
Scholin, C., Doucette, G., Jensen, S., Roman, B., Pargett, D., Marin III, R., Preston, C., Jones, W., Feldman, J., Everlove, C., Harris, A., Alvarado, N., Massion, E., Birch, J., Greenfield, D., Vrijenhoek, R.C., Mikulski, C., Jones, K, (2009). Remote detection of marine microbes, small invertebrates, harmful algae and biotoxins using the Environmental Sample Processor (ESP). Oceanography, 22: 158-167.
Vrijenhoek, R.C., (2009). Cryptic species, phenotypic plasticity, and complex life histories: Assessing deep-sea faunal diversity with molecular markers. Deep-Sea Research Part II, 56: 1713-1723.
Audzijonyte, A., Vrijenhoek, R.C., (2010). Three nuclear genes for phylogenetic, SNP and population genetic studies of molluscs and other invertebrates. Molecular Ecology Resources, 10: 200-204.
Audzijonyte, A., Vrijenhoek, R.C., (2010). When gaps really are gaps: Statistical phylogeography of hydrothermal vent invertebrates. Evolution, 64: 2369-2384.
Johnson, S.B., Warén, A, Lee, R., Kanno, Y., Kaim, A., Davis, A., Strong, E., Vrijenhoek, R.C., (2010). Rubyspira, new genus and two new species of bone-eating deep-sea snails with ancient habits. Biological Bulletin, 219: 166-177.
Lundsten, L., Schlining, K.L., Frasier, K., Johnson, S.B., Kuhnz, L., Harvey, J., Clague, G., Vrijenhoek, R.C., (2010). Time-series analysis of six whale-fall communities in Monterey Canyon, California, USA. Deep-Sea Research Part I, 57: 1573-1584.
Ryan, J.P., Johnson, S.B., Sherman, A.D., Rajan, K., Py, F., Thomas, H., Harvey, J.B.J., Bird, L., Paduan, J.D., Vrijenhoek, R.C., (2010). Mobile autonomous process sampling within coastal ocean observing systems. Limnology and Oceanography: Methods, 8: 394-402.
Clague, G.E., Jones, W.J., Paduan, J.B., Clague, D.A., Vrijenhoek, R.C., (2011). Phylogeography of Acesta clams from submarine seamounts and escarpments along the western margin of North America. Marine Ecology, 33: 75-87.
Coykendall, D.K., Johnson, S.B., Karl, S.A., Lutz, R.A., Vrijenhoek, R.C., (2011). Genetic diversity and demographic instability in Riftia pachyptila tubeworms from eastern Pacific hydrothermal vents. BMC Evolutionary Biology, 11: 96.
Rouse, G.W., Goffredi, S.K., Johnson, S.B., Vrijenhoek, R.C., (2011). Not whale-fall specialists, Osedax worms also consume fishbones. Biology Letters, 7: 736-739.
Thaler, A.D., Zelnio, K., Saleu, W., Schultz, T.F., Carlsson, J., Cunningham, C., Vrijenhoek, R.C., Van Dover, C.L., (2011). The spatial scale of genetic subdivision in populations of Ifremeria nautilei, a hydrothermal-vent gastropod from the southwest Pacific. BMC Evolutionary Biology, 11: .
Harvey, J.B.J., Ryan, J.P., Marin III, R., Preston, C.M., Alvarado, N., Scholin, C.A., Vrijenhoek, R.C., (2012). Robotic sampling, in situ monitoring and molecular detection of marine zooplankton. Journal of Experimental Marine Biology and Ecology, 413: 60-70.
Salathé, R.M., Vrijenhoek, R.C., (2012). Temporal variation and lack of host specificity among bacterial endosymbionts of Osedax bone worms (Polychaeta: Siboglinidae). BMC Evolutionary Biology, 12: 189.
Harvey, J.B.J., Djunaedi, A.F., Vrijenhoek, R.C., (2013). Validation of a sandwich hybridization assay for marine copepod detection. Journal of Experimental Marine Biology and Ecology, 446: 306-310.
Johnson, S.B., Won, Y-J, Harvey, J.B.J., Vrijenhoek, R.C., (2013). A hybrid zone between Bathymodiolus mussel lineages from eastern Pacific hydrothermal vents. BMC Evolutionary Biology, 13: 21.
Stiller, J., Rousset, V., Pleijel, F., Chevaldonne, P., Vrijenhoek, R.C., Rouse, G.W., (2013). Phylogeny, biogeography and systematics of hydrothermal vent and methane seep Amphisamytha (Ampharetidae, Annelida), with descriptions of three new species. Systematics and Biodiversity, 11: 35-65.
Arellano, S.M., Van Gaest, A.L., Johnson, S.B., Vrijenhoek, R.C., Young, C.M., (2014). Larvae from deep-sea methane seeps disperse in surface waters. Proceedings of the Royal Society B, 281: .
Goffredi, S.K., Yi, H., Zhang, Q., Klann, J.E., Struve, I.A., Vrijenhoek, R.C., Brown, C.T., (2014). Genomic versatility and functional variation between two dominant heterotrophic symbionts of deep-sea Osedax worms. The ISME Journal, 8: 908-924.
Zhang, H., Geller, J.B., Vrijenhoek, R.C., (2014). Genetic diversity in native and introduced populations of the amethyst gem clam Gemma gemma (Totten, 1834) from the U.S. east and west coasts. Biological Invasions, 16: 2725-2735.
Breusing, C., Johnson, S.B., Tunnicliffe, V., Vrijenhoek, R.C. , (2015). Population structure and connectivity in Indo-Pacific deep-sea mussels of the Bathymodiolus septemdierum complex. Conservation Genetics , 16: 1415-1430.
Liu, H., Cai, S., Zhang, H., Vrijenhoek, R.C., (2015). Complete mitochondrial genome of hydrothermal vent clam Calyptogena magnifica. Mitochondrial DNA : 1-3.
Rouse, G. W., Wilson, N. G., Carvajal, J. I., Vrijenhoek, R. C., (2015). New deep-sea species of Xenoturbella and the position of Xenacoelomorpha. Nature, 530: 94-97.
Rouse, G.W., Wilson, N.G., Worsaae, K., Vrijenhoek, R.C., (2015). A dwarf male reversal in bone-eating worms. Current Biology, 25: 236-241.
Zhang, H., Johnson, S.B., Flores, V.R., Vrijenhoek, R.C., (2015). Intergradation between discrete lineages of Tevnia jerichonana, a deep-sea hydrothermal vent tubeworm. Deep-Sea Research Part II: Topical Studies in Oceanography, 121: 53-61.
Breusing, C., Biastoch, A., Drews, A., Metaxas, A., Jollivet, D., Vrijenhoek, R. C., Bayer, T., Melzner, F., Sayavedra, L., Petersen, J. M., Dubilier, N., Schilhabel, M. B., Rosenstiel, P., Reusch, T. B., (2016). Biophysical and population genetic models predict the presence of “phantom” stepping stones connecting Mid-Atlantic Ridge vent ecosystems. Current Biology, 26: 2257-2267.
Jang, S. J., Park, E., Lee, W. K., Johnson, S. B., Vrijenhoek, R. C., Won, Y. -J., (2016). Population subdivision of hydrothermal vent polychaete Alvinella pompejana across equatorial and Easter Microplate boundaries. BMC Evolutionary Biology, 16: 235.
Breusing, C., Vrijenhoek, R. C., Reusch, T. B., (2017). Widespread introgression in deep-sea hydrothermal vent mussels. BMC Evolutionary Biology, 17: 10.
Goffredi, S. K., Johnson, S. B., Tunnicliffe, V., Caress, D., Clague, D., Escobar, E., Lundsten, L., Paduan, J. B., Rouse, G., Salcedo, D. L., Soto, L. A., Spelz-Madero, R., Zierenberg, R., Vrijenhoek, R., (2017). Hydrothermal vent fields discovered in the southern Gulf of California clarify role of habitat in augmenting regional diversity. Proceedings of the Royal Society B, 284: .
Georgieva, M.N., Paull, C. K., Little, C.T.S., McGann, M., Sahy, D., Condon, D., Lundsten, L., Pewsey, J., Caress, D.W., Vrijenhoek, R. C., (2019). Discovery of an extensive deep-sea fossil serpulid reef associated with a cold seep, Santa Monica Basin, California. Frontiers in Marine Science, 6: .
Breusing, C., Johnson, S.B., Tunnicliffe, V., Clague, D.A., Vrijenhoek, R.C., Beinart, R.A., (2020). Both allopatric and ecological processes contribute to speciation in Alviniconcha hydrothermal vent snail. Molecular Biology and Evolution, 37: .


Upper-ocean systems
Acoustical ocean ecology
Acoustic instruments
Acoustic fingerprinting
Acoustic community ecology
Acoustics in the news
Biological oceanography
Global modes of sea surface temperature
Krill hotspots in the California Current
Nitrate supply estimates in upwelling systems
Chemical sensors
Chemical data
Land/Ocean Biogeochemical Observatory in Elkhorn Slough
Listing of floats
SOCCOM float visualization
Periodic table of elements in the ocean
Biogeochemical-Argo Report
Profiling float
Interdisciplinary field experiments
Ecogenomic Sensing
Genomic sensors
Field experiments
Harmful algal blooms (HABs)
Water quality
Environmental Sample Processor (ESP)
ESP Web Portal
In the news
Ocean observing system
Midwater research
Midwater ecology
Deep-sea squids and octopuses
Food web dynamics
Midwater time series
Respiration studies
Zooplankton biodiversity
Seafloor processes
Revealing the secrets of Sur Ridge
Exploring Sur Ridge’s coral gardens
Life at Sur Ridge
Mapping Sur Ridge
Biology and ecology
Effects of humans
Ocean acidification, warming, deoxygenation
Lost shipping container study
Effects of upwelling
Faunal patterns
Previous research
Technology development
High-CO2 / low-pH ocean
Benthic respirometer system
Climate change in extreme environments
Station M: A long-term observatory on the abyssal seafloor
Station M long-term time series
Monitoring instrumentation suite
Sargasso Sea research
Antarctic research
Geological changes
Arctic Shelf Edge
Continental Margins and Canyon Dynamics
Coordinated Canyon Experiment
CCE instruments
CCE repeat mapping data
Monterey Canyon: A Grand Canyon beneath the waves
Submarine volcanoes
Mid-ocean ridges
Magmatic processes
Volcanic processes
Explosive eruptions
Hydrothermal systems
Back arc spreading ridges
Near-ridge seamounts
Continental margin seamounts
Non-hot-spot linear chains
Eclectic seamounts topics
Margin processes
Hydrates and seeps
California borderland
Hot spot research
Hot-spot plumes
Magmatic processes
Volcanic processes
Explosive eruptions
Volcanic hazards
Hydrothermal systems
Flexural arch
Coral reefs
ReefGrow software
Eclectic topics
Submarine volcanism cruises
Volcanoes resources
Areas of study
Bioluminescence: Living light in the deep sea
Microscopic biology research
Open ocean biology research
Seafloor biology research
Automated chemical sensors
Methane in the seafloor
Volcanoes and seamounts
Hydrothermal vents
Methane in the seafloor
Submarine canyons
Earthquakes and landslides
Ocean acidification
Physical oceanography and climate change
Ocean circulation and algal blooms
Ocean cycles and climate change
Past research
Molecular ecology
Molecular systematics
SIMZ Project
Bone-eating worms
Gene flow and dispersal
Molecular-ecology expeditions
Ocean chemistry of greenhouse gases
Emerging science of a high CO2/low pH ocean