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Santos, S.R. Chapter 23: From one to many: the population genetics of cnidarian-Symbiodinium symbioses. Invited book chapter in Springer volume "The Cnidaria, past, present and future. The world of Medusa and her sisters" Eds. Goffredo, S. & Dubinsky, Z. in press



Li, Y., K.M. Kocot, N.V. Whelan , S.R. Santos, D.S. Waits, D.J. Thornhill, K.M. Halanych. Phylogenomics of tubeworms (Siboglinidae, Annelida) and comparative performance of supermatrix versus multispecies-coalescent and Bayesian-Concordance approaches. Zoological Scripta. in press



Havird, J.C., R.T. Mitchell, R.P. Henry, S.R. Santos. Salinity-induced changes in gene expression from anterior and posterior gills of Callinectes sapidus (Crustacea: Portunidae) with implications for crustacean ecological genomics. Comparative Biochemistry and Physiology - Part D: Genomics and Proteomics. in press



Havird, J.C., S.R. Santos. Invited SICB Symposium Contribution: Here we are, but where do we go? A systematic review of crustacean transcriptomic studies from 2014-2015. Integrative and Comparative Biology. in press



Havird, J.C., S.R. Santos. Invited SICB Symposium Contribution: Developmental transcriptomics of the Hawaiian anchialine shrimp Halocaridina rubra Holthuis, 1963 (Crustacea: Atyidae). Integrative and Comparative Biology. in press



Selkoe, K.A., O.E. Gaggiotti, E.A. Treml, J.L.K. Wren, M.K. Donovan, Hawai'i Reef Connectivity Consortium (Santos, S.R. - among additional authors), R.J. Toonen. 2016. The DNA of coral reef biodiversity - predicting and protecting genetic diversity of reef assemblages. Proceedings of the Royal Society of London B. 283: 20160354. Request Reprint



Waits, D.S., S.R. Santos, D.J. Thornhill, Y. Li, K.M. Halanych. 2016. Evolution of sulfur binding in hemoglobin in Siboglinidae (Annelida) with special reference to bone-eating worms, Osedax. Journal of Molecular Evolution. 82:219-229. (Featured Cover Article) Request Reprint



Justice, J.L., D.A. Weese, S.R. Santos. 2016. Phylogenetic utility, and variability in structure and content, of complete mitochondrial genomes among genetic lineages of the Hawaiian anchialine shrimp Halocaridina rubra Holthuis 1963 (Atyidae:Decapoda). Mitochondrial DNA. 27:2710-2718. Request Reprint



Learman, D.R., M.W. Henson, J.C. Thrash, B. Temperton, P.M. Brannock, S.R. Santos, A.R. Mahon, K.M. Halanych. 2016. Biogeochemical and microbial variation across 5500 km of Antarctic surface sediment implicates organic matter as a driver of benthic community structure. Frontiers in Microbiology. 7:284. Request Reprint



Weese, D.A., Y. Fujita, S.R. Santos. 2016. Looking for needles in a haystack: Molecular identification of anchialine crustacean larvae from the Shiokawa Spring, Okinawa, Japan. Journal of Crustacean Biology. 36:61-67. Request Reprint



Havird, J.C., R.C. Vaught, D.A. Weese, S.R. Santos. 2015. Reproduction and development in Halocaridina rubra Holthuis, 1963 (Crustacea: Atyidae) clarifies larval ecology in the Hawaiian anchialine ecosystem. The Biological Bulletin. 229:134-142. Request Reprint



Helms, B.S., R.C. Vaught, S.K. Suciu, S.R. Santos. 2015. Cryptic diversity within two endemic crayfish species of the Southeastern US revealed by molecular genetics and geometric morphometrics. Hydrobiologia. 755:283-298. (Featured Cover Article) Request Reprint



Havird, J.C., K.M. Kocot, P.M. Brannock, J.T. Cannon, D.S. Waits, D.A. Weese, S.R. Santos, K.M. Halanych. 2015. Reconstruction of cyclooxygenase evolution in animals suggests variable, lineage-specific duplications and homologs with low sequence identity. Journal of Molecular Evolution. 80:193-208. Request Reprint



Li, Y., K.M. Kocot, C. Schander, S.R. Santos, D.J. Thornhill, K.M. Halanych. 2015. Mitogenomics reveals phylogeny and dramatic size variations of control regions in the deep-sea family Siboglinidae (Annelida). Molecular Phylogenetics and Evolution. 85:221-229. Request Reprint



Whelan, N.V., K.M. Kocot, S.R. Santos, K.M. Halanych. 2014. Nemertean toxin genes revealed through transcriptome sequencing. Genome Biology and Evolution. 6:3314-3325. Request Reprint



Cannon, J.T., K.M. Kocot, D.S. Waits, D.A. Weese, B.J. Swalla, S.R. Santos, K.M. Halanych. 2014. Phylogenomic resolution of the hemichordate and echinoderm clade. Current Biology. 24:2827-2832. Request Reprint



Havird, J.C., R.C. Vaught, J.R. Weeks, Y. Fujita, M. Hidaka, S.R. Santos, R.P. Henry. 2014. Taking their breath away: Metabolic responses to low-oxygen levels in anchialine shrimps (Crustacea: Atyidae and Alpheidae). Comparative Biochemistry and Physiology - Part A: Molecular & Integrative Physiology. 178:109-120. Request Reprint



Santos, S.R. 2014. Invited Contribution: News and Views: Perspective: Expanding the population genetic perspective of cnidarian-Symbiodinium symbioses. Molecular Ecology. 23:4185-4187. Request Reprint



Havird, J.C., S.R. Santos. 2014. Genomic Resources Note: Transcriptomic resources for five shrimp (Crustacea: Atyidae and Alpheidae) species from the anchialine ecosystem. Molecular Ecology Resources. 14:1322. Request Reprint



Vaught, R.C., J.C. Havird, S.R. Santos. 2014. Genetic lineage and environmental conditions as drivers of chromatosome variation in the anchialine shrimp Halocaridina rubra Holthuis 1963 (Atyidae:Decapoda). Journal of Crustacean Biology. 34:647-657. Request Reprint



Havird, J.C., S.R. Santos, R.P. Henry. 2014. Osmoregulation in the Hawaiian anchialine shrimp Halocaridina rubra (Crustacea: Atyidae): expression of ion transporters, mitochondria-rich cell proliferation, and hemolymph osmolality during salinity transfers. Journal of Experimental Biology. 217:2309-2320. Request Reprint



Weigert, A., C. Helm, M. Meyer, B. Nickel, D. Arendt, B. Hausdorf, S.R. Santos, K.M. Halanych, G. Purschke, C. Bleidorn, T.H. Struck. 2014. Illuminating the base of the annelid tree using transcriptomics. Molecular Biology and Evolution. 31:1391-1401. Request Reprint



Santos, S.R. 2014. Genomic Resources Note: Complete mitochondrial and partial nuclear genomes for the jack species Caranx ignobilis (Forsskål, 1775) and C. melampygus (Cuvier, 1833) (Perciformes:Carangidae) from the High Hawaiian Islands. Molecular Ecology Resources. 14:435-436. Request Reprint



Havird, J.C., S.R. Santos. 2014. Performance of single and concatenated sets of mitochondrial genes at inferring metazoan relationships relative to full mitogenome data. PLoS One. 9:e84080. Download article directly from PLoS One website



GIGA Community of Scientists (Santos, S.R. - among additional authors). 2014. The Global Invertebrate Genomics Alliance (GIGA): developing community resources to study diverse invertebrate genomes. Journal of Heredity. 105:1-18. (Featured Cover Article) Editor's Pick Jan. 2014: Request Reprint



Kirk, N.L., R. Ritson-Williams, M.A. Coffroth, M.W. Miller, N.D. Fogarty, S.R. Santos. 2013. Tracking transmission of apicomplexan symbionts in diverse Caribbean corals. PLoS One. 8:e80618. Download article directly from PLoS One website



Weese, D.A., Y. Fujita, S.R. Santos. 2013. Multiple colonizations lead to cryptic biodiversity in an island ecosystem: comparative phylogeography of anchialine shrimp species in the Ryukyu Archipelago, Japan. The Biological Bulletin 225:24-41. (Featured Cover Article) Editor's Pick Sept. 2013: Free Download from Biol. Bull.



Thornhill, D.J., Y. Xiang, D.T. Pettay, M. Zhong, S.R. Santos. 2013. Population genetic data of a model symbiotic cnidarian system reveal remarkable symbiotic specificity and vectored introductions across ocean basins. Molecular Ecology 22:4499-4515. (Featured Perspectives article by Christian R. Voolstra) Request Reprint



Havird, J.C. J.R. Weeks, S. Hau, S.R. Santos. 2013. Invasive fishes in the Hawaiian anchialine ecosystem: investigating potential predator avoidance by endemic organisms. Hydrobiologia 716:189-201. (Featured Cover Article) Request Reprint



Kirk, N.L., D.J. Thornhill, D.W. Kemp, W.K. Fitt, S.R. Santos. 2013. Ubiquitous associations and a peak fall prevalence between apicomplexan symbionts and reef corals in Florida and the Bahamas. Coral Reefs 32:847-858. Request Reprint



Phillips, M.J., T.J. Page, M. de Bruyn, J.A. Huey, W.F. Humphreys, J.M. Hughes, S.R. Santos, D.J. Schmidt, J.M. Waters. 2013. The linking of plate tectonics and evolutionary divergences (Reply to Bauza-Ribot et al.). Current Biology 23:R603-R605. Request Reprint



Weese, D.A., Y. Fujita, M. Hidaka, S.R. Santos. 2012. The long and short of it: Genetic variation and population structure of the anchialine atyid shrimp Caridina rubella on Miyako-jima, Japan. Journal of Crustacean Biology 32:109-117. Request Reprint



Kocot, K.M., J.T. Cannon, C. Todt, M.R. Citarella, A.B. Kohn, A.Meyer, S.R. Santos, C. Schander, L.L. Moroz, B. Lieb, K.M. Halanych. 2011. Phylogenomics reveals deep molluscan relationships. Nature. 477:452-457. Download article directly from Nature website



Stephens, J.D., S.R. Santos, D.R. Folkerts. 2011. Genetic differentiation, structure, and a transition zone among populations of the pitcher plant moth Exyra semicrocea: Implications for conservation. PLoS One. 6:e22658. Download article directly from PLoS One website



Roopin, M., D.J. Thornhill, S.R. Santos, N.E. Chadwick. 2011. Ammonia flux, physiological parameters, and Symbiodinium diversity in the anemonefish symbiosis on Red Sea coral reefs. Symbiosis. 53:63-74. (Featured Cover Article) Request Reprint



Santos, S.R., D.A. Weese. 2011. Invited Contribution: Rocks and Clocks: Linking geologic history and rates of genetic differentiation in anchialine organisms. Hydrobiologia. 677:54-63. Request Reprint



Santos, S.R., Y. Xiang, A.W. Tagawa. 2011. Population structure and comparative phylogeography of jack species (Caranx ignobilis and C. melampygus) in the high Hawaiian Islands. Journal of Heredity. 102:47-54. PDF Supplementary Materials Raising Islands feature by Jan TenBruggencate



Thornhill, D.J., K. Doubleday, D.W. Kemp, S.R. Santos. 2010. Host hybridization alters specificity of cnidarian-dinoflagellate associations. Marine Ecology Progress Series. 420:113-123. Request Reprint



Betancur-R, R., A. Acero P., H. Duque-Caro, S.R. Santos. 2010. Phylogenetic and morphologic analyses of a coastal fish reveals a marine biogeographic break of terrestrial origin in the southern Caribbean. PLoS One. 5:e11566. Download article directly from PLoS One website



Russ, A., S.R. Santos, C. Muir. 2010. Genetic population structure of an anchialine shrimp, Metabetaeus lohena (Crustacea: Alpheidae), in the Hawaiian Islands. Revista de Biologia Tropical. 58:159-170. PDF



Santos, S.R., J. Toyoshima, R.A. Kinzie III. 2009. Invited Contribution: Spatial and temporal dynamics of symbiotic dinoflagellates (Symbiodinium:Dinophyta) in the perforate coral Montipora capitata. Galaxea JCRS. 11:139-147. PDF



Thornhill, D.J., Y. Xiang, W.K. Fitt, S.R. Santos. 2009. Reef endemism, host specificity and temporal stability in populations of symbiotic dinoflagellates from two ecologically dominant Caribbean corals. PLoS One. 4:e6262. Featured Weekly Image in EveryOne, the PLoS One Community Blog Download article directly from PLoS One website



Cummings, S.P., P. Gyaneshwar, P. Vinuesa, F.T. Farruggia, M. Andrews, D. Humphry, G.N. Elliott, A. Nelson, C. Orr, D. Pettitt, G.R. Shah, S.R. Santos, H.B. Krishnan, D. Odee, F.M.S. Moreira, J.I. Sprent, J.P.W. Young, E.K. James. 2009. Nodulation of Sesbania species by Rhizobium (Agrobacterium) strain IRBG74 and other rhizobia. Environmental Microbiology. 11:2510-2525. PDF



Kirk, N.L., J.P Andras, C.D Harvell, S.R Santos, M.A. Coffroth. 2009. Population structure of Symbiodinium sp. associated with the common sea fan, Gorgonia ventalina, in the Florida Keys across distance, depth, and time. Marine Biology. 156:1609-1623. Request Reprint  Supplementary Materials at Marine Biology Website



Boyd, R.S., M.A. Wall, S.R. Santos, M.A. Davis. 2009. Variation of morphology and elemental concentrations in the California nickel hyperaccumulator Streptanthus polygaloides (Brassicaceae). Northeastern Naturalist. 16:21-38. Request Reprint



Weese, D.A., S.R. Santos. 2009. Genetic identification of source populations for an aquarium-traded invertebrate. Animal Conservation. 12:13-19. (Featured Cover Article) Request Reprint



Kocot, K.M., S.R. Santos. 2009. Secondary structural modeling of the second internal transcribed spacer (ITS2) from Pfiesteria-like dinoflagellates (Dinophyceae). Harmful Algae. 8:441-446. PDF  Supplementary Materials



Thornhill, D.J., K.T. Fielman, S.R. Santos, K.M. Halanych. 2008. Siboglinid-bacteria endosymbiosis: A model system for studying symbiotic mechanisms. Communicative & Integrative Biology. 1:1-4.  PDF



Craft, J.D., A.D. Russ, M.N. Yamamoto, T.Y. Iwai Jr., S. Hau, J. Kahiapo, C.T. Chong, S. Ziegler-Chong, C. Muir, Y. Fujita, D.A. Polhemus, R.A. Kinzie III, S.R. Santos. 2008. Islands under islands: The phylogeography and evolution of Halocaridina rubra Holthuis, 1963 (Crustacean: Decapoda: Atyidae) in the Hawaiian archipelago. Limnology and Oceanography. 53:675-689.  PDF  Supplementary Material #1  Supplementary Material #2



Thornhill, D.J., T.C. LaJeunesse, S.R. Santos. 2007. Measuring rDNA diversity in eukaryotic microbial systems: How intragenomic variation, pseudogenes, and PCR artifacts confound biodiversity estimates. Molecular Ecology. 16:5326-5340.  PDF  Supplementary Materials  Download datasets



Ivey, J.L., S.R. Santos. 2007. The complete mitochondrial genome of the Hawaiian anchialine shrimp Halocaridina rubra Holthuis, 1963 (Crustacea: Decapoda: Atyidae). Gene. 394:35-44. PDF  View genome  Download datasets



Hunter, R.L., T.C. LaJeunesse, S.R. Santos. 2007. Structure and evolution of the rDNA internal transcribed spacer (ITS) region 2 in the symbiotic dinoflagellates (Symbiodinium, Dinophyta). Journal of Phycology. 43:120-128. PDF  Supplementary Materials  Download datasets



Kuguru, B., G. Winters, S. Beer, S.R. Santos, N.E. Chadwick. 2007. Adaptation strategies of the corallimorpharian Rhodactis rhodostoma to irradiance and temperature. Marine Biology. 151:1287-1298. PDF



Humphry, D.R., M. Andrews, S.R. Santos, E.K. James, L.V. Vinogradova, L. Perin, V.M. Reis, S.P. Cummings. 2007. Phylogenetic assignment and mechanism of action of a crop growth promoting Rhizobium radiobacter strain used as a biofertiliser on graminaceous crops in Russia. Antonie van Leeuwenhoek. 91:105-113. PDF



Cummings, S.P., D.R. Humphry, S.R. Santos, M. Andrews, E.K. James. 2006. The potential and pitfalls of exploiting nitrogen fixing bacteria in agricultural soils as a substitute for inorganic fertiliser. Environmental Biotechnology. 2:1-10. PDF



Coffroth, M.A., C.F. Lewis, S.R. Santos, J.L. Weaver. 2006. Environmental populations of the symbiotic dinoflagellate, Symbiodinium (Freudenthal), can initiate symbioses with reef cnidarians. Current Biology. 16:R985-R987. PDF  Supplementary Materials



Santos, S.R. 2006. Patterns of genetic connectivity among anchialine habitats: a case study of the endemic Hawaiian shrimp Halocaridina rubra on the Island of Hawaii. Molecular Ecology. 15:2699-2718. PDF



Moran, N.A., P.H. Degan, S.R. Santos, H.E. Dunbar, H. Ochman. 2005. The players in a mutualistic symbiosis: Insects, bacteria, viruses and virulence genes. Proceedings of the National Academy of Sciences USA. 102:16919-16926. PDF  Supporting data set



Coffroth, M.A., S.R. Santos. 2005. Invited Review: Genetic diversity of symbiotic dinoflagellates in the genus Symbiodinium. Protist. 156:19-34. PDF



Ochman, H., S.R. Santos. 2005. Exploring microbial microevolution with microarrays. Infection, Genetics and Evolution. 5:103-108. PDF



Santos, S.R., H. Ochman. 2004. Identification and phylogenetic sorting of bacterial lineages using universally conserved genes and proteins. Environmental Microbiology. 6:754-759.PDF  Download datasets



Santos, S.R. 2004. Comments on the article of Gou et al. (2003, J. Exp. Mar. Biol. Ecol. 296, 135-144): Phylogenetic analysis of a free-living strain of Symbiodinium isolated from Jiaozhou Bay, P.R. China. Journal of Phycology. 40:395-397. PDF



Takabayashi, M., S.R. Santos, C.B. Cook. 2004. Mitochondrial DNA phylogeny of the symbiotic dinoflagellates (Symbiodinium, Dinophyta). Journal of Phycology. 40:160-164. PDF



Santos, S.R., T.L. Shearer, A.R. Hannes, M.A. Coffroth. 2004. Fine-scale diversity and specificity in the most prevalent lineage of symbiotic dinoflagellates (Symbiodinium, Dinophyceae) of the Caribbean. Molecular Ecology. 13:459-469. PDF



Francino, M.P., S.R. Santos, H. Ochman. 2003. Phylogenetic Relationships of Bacteria with Special Reference to Endosymbionts and Enteric Species. For: M. Dworkin (Editor-in-Chief), The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community, 3rd edition, release 3.13, May 12, 2003. Springer-Verlag, New York.



Santos, S.R., R.A. Kinzie III, K. Sakai, M.A. Coffroth.  2003. Molecular characterization of nuclear small subunit (18S)-rDNA pseudogenes in a symbiotic dinoflagellate (Symbiodinium, Dinophyta). Journal of Eukaryotic Microbiology. 50:417-421. PDF



Santos, S.R., C. Gutierrez-Rodriguez, M.A. Coffroth. 2003. Phylogenetic identification of symbiotic dinoflagellates via length heteroplasmy in domain V of chloroplast large subunit (cp23S)-rDNA sequences. Marine Biotechnology. 5:130-140. (Featured Cover Article) PDF



Santos, S.R., C. Gutierrez-Rodriguez, H.R. Lasker, M.A. Coffroth. 2003. Symbiodinium sp. associations in the gorgonian Pseudopterogorgia elisabethae in the Bahamas: high levels of genetic variability and population structure in symbiotic dinoflagellates. Marine Biology. 143:111-120. PDF  Supplementary Materials



Ochman, H., S.R. Santos. 2003. Eyeing bacterial genomes. Current Opinion in Microbiology. 6:109-113. PDF



Santos, S.R., M.A. Coffroth. 2003. Molecular genetic evidence that dinoflagellates belonging to the genus Symbiodinium Freudenthal are haploid. The Biological Bulletin. 204:10-20. (Featured Cover Article) PDF



Santos, S.R., D.J. Taylor, R.A. Kinzie III, K. Sakai, M.A. Coffroth. 2002. Evolution of length variation and heteroplasmy in the chloroplast rDNA of symbiotic dinoflagellates (Symbiodinium, Dinophyta) and a novel insertion in the universal core region of the large subunit rDNA. Phycologia. 41:311-318. (Featured Cover Article) PDF



Santos, S.R., D.J. Taylor, R.A. Kinzie III, M. Hidaka, K. Sakai, M.A. Coffroth. 2002. Molecular phylogeny of symbiotic dinoflagellates inferred from partial chloroplast large subunit (23S)-rDNA sequences. Molecular Phylogenetics and Evolution. 23:97-111. PDF



Kinzie, R.A. III, M. Takayama, S.R. Santos, M.A. Coffroth. 2001. The adaptive bleaching hypothesis: Experimental tests of critical assumptions. The Biological Bulletin. 200:51-58. PDF



Coffroth, M.A., S.R. Santos, T.L. Goulet. 2001. Early ontogenetic expression of specificity in a cnidarian-algal symbiosis. Marine Ecology Progress Series. 222:85-96. PDF



Santos, S.R., D.J. Taylor, M.A. Coffroth. 2001. Genetic comparisons of freshly isolated vs. cultured symbiotic dinoflagellates: Implications for extrapolating to the intact symbiosis. Journal of Phycology. 37:900-912. PDF



Larned, S.T., S.R. Santos. 2000. Light- and nutrient-limited periphyton in low order streams of Oahu, Hawaii. Hydrobiologia. 432:101-111. PDF



Santos, S.R. 1995. Ultraviolet radiation: helpful or harmful to growth of  cultured zooxanthellae? In Gulko, D. and Jokiel, P.L. [Eds.] Ultraviolet Radiation and Coral Reefs. HIMB Technical Report No. 41, Hawaii, pp. 165-169. PDF

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