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78

 

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

 

77

 

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

 

76

 

Titus, B.M., M. Daly, J. Macrander, A. Del Rio, S.R. Santos, N.E. Chadwick. Contrasting abundance and contribution of clonal proliferation to the population structure of the corkscrew sea anemone Bartholomea annulata in the tropical Western Atlantic. Invertebrate Biology. in press

 

75

 

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

 

74

 

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

 

73

 

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. 19:34-44. Request Reprint

 

72

 

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

 

71

 

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

 

70

 

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

 

69

 

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

 

68

 

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

 

67

 

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

 

66

 

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

 

65

 

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

 

64

 

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

 

63

 

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

 

62

 

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

 

61

 

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

 

60

 

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

 

59

 

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

 

58

 

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

 

57

 

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

 

56

 

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

 

55

 

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

 

54

 

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

 

53

 

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

 

52

 

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

 

51

 

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.

 

50

 

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

 

49

 

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

 

48

 

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

 

47

 

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

 

46

 

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

 

45

 

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

 

44

 

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

 

43

 

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

 

42

 

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

 

41

 

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

 

40

 

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

 

39

 

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

 

38

 

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

 

37

 

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

 

36

 

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

 

35

 

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

 

34

 

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

 

33

 

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

 

32

 

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

 

31

 

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

 

30

 

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

 

29

 

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

 

28

 

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

 

27

 

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

 

26

 

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

 

25

 

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

 

24

 

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

 

23

 

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

 

22

 

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

 

21

 

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

 

20

 

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

 

19

 

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

 

18

 

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

 

17

 

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

 

16

 

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

 

15

 

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

 

14

 

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

 

13

 

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.

 

12

 

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

 

11

 

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

 

10

 

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

 

9

 

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

 

8

 

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

 

7

 

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

 

6

 

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

 

5

 

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

 

4

 

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

 

3

 

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

 

2

 

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

 

1

 

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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