1 Genomics in the Discovery and Monitoring
27
Dasmahapatra KK, Mallet J (2006) DNA barcodes: recent successes and future prospects. Heredity
97:254–255
Deagle BE, Bax N, Hewitt CL, Patil JG (2003) Development and evaluation of a PCR-based test
for detection of Asterias (Echinodermata : Asteroidea) larvae in Australian plankton samples
from ballast water. Mar Freshwat Res 54:709–719
DeLey P, DeLey IT et al (2005) An integrated approach to fast and informative morphological
vouchering of nematodes for applications in molecular barcoding. Phil Trans R Soc London B
360:1945–1958
DeLong EF (2005) Microbial community genomics in the ocean. Nat Rev Microbiol 3:459–469
DeLong EF and Karl DM (2005) Genomic perspectives in microbial oceanography. Nature
437:336–342
de Tomaso AW, Weissman IL (2003) Construction and characterization of large-insert genomic
libraries (BAC and fosmid) from the Ascidian Botryllus schlosseri and initial physical mapping
of a histocompatibility locus. Mar Biotechnol (NY) 5(2):103–115
Díez B, Pedrós-Alío C, Massana R (2001) Study of genetic diversity of eukaryotic picoplankton in
different oceanic regions by small-subunit rRNA gene cloning and sequencing. Appl. Environ
Microbial 67:2932–2941
Dinsdale EA, Pantos O et al (2008) Microbial ecology of four coral atolls in the Northern Line
Islands. PLoS ONE 3(2):e1584
Doi RH, Igarashi RT (1965) Conservation of ribosomal and messenger ribonucleic acid cistrons in
Bacillus species. J Bacteriol 90:384–390
Dubnau D, Smith I, Morell P, Marmur J (1965) Gene conservation in Bacillus species. I.
Conserved genetic and nucleic acid base sequence homologies. Proc Natl Acad Sci USA 54(2):
491–498
Duffy JE, Stachowicz JJ (2006) Why biodiversity is important to oceanography: potential roles
of genetic, species, and trophic diversity in pelagic ecosystem processes. Mar Ecol Prog Ser
311:179–189
Eisen JA (2007) Environmental shotgun sequencing: Its potential and challenges for studying the
hidden world of microbes. PLoS Biol 5:e82
Eller G, Töbe K, Medlin LK (2007) A set of hierarchical FISH probes for the Haptophyta and a
division level probe for the Heterokonta. J Plank Res 29:629–640
Evans KM, Wortley AH, Mann DG (2007) An assessment of potential diatom “Barcode” genes
(cox1, rbcL, 18S and ITS rDNA) and their effectiveness in determining relationships in
sellaphora (Bacillariophyta). Protist 158:349–364
Floyd R, Abebe E et al (2002) Molecular barcodes for soil nematode identification. Mol Ecol
11(4):839–850
Fox CJ, Taylor MI et al (2008) Mapping the spawning grounds of Noth Sea cod (Gadus morhua)
by direct and indirect means. Proc R Soc Lond 275:1543–1548
Fox CJ, Taylor CJ, Pereyra R, Willasana MI, Rico C (2005) TaqMan DNA technology confirms
likely overestimation of cod (Gadus morhua L.) egg abundance in the Irish Sea: Implications
for the assessment of the cod stock and mapping of spawning areas using egg-based methods.
Mol Ecol 14:879–884
Fuchs BM, Spring S et al (2007) Characterization of a marine gammaproteobacterium capable of
aerobic anoxygenic photosynthesis. Proc Natl Acad Sci U S A 104(8):2891–2896
Gescher C, Metfies K, Frickenhaus S, Knefelkamp B, Wiltshire K, Medlin LK (2008) Feasibility
of assessing the community composition of prasinophytes at the helgoland roads sampling site
with a DNA microarray. Appl Environ Microbiol 74:5305–5316
Giovannoni SJ, Britschgi TB, Moyer CL et al (1990) Genetic diversity in sargasso sea bacterloplankton. Nature (London) 345:60–63
Goffredi SK, Jones WJ, Scholin CA, Marin R, Vrijenhoek RC (2006) Molecular detection of
marine invertebrate larvae. Mar Biotech 8:149–160
Gómez A, Wright PJ, Lunt DH et al (2007) Mating trials validate the use of DNA barcoding to
reveal cryptic speciation of a marine bryozoan taxon. Proc R Soc B 274:199–207
27
Dasmahapatra KK, Mallet J (2006) DNA barcodes: recent successes and future prospects. Heredity
97:254–255
Deagle BE, Bax N, Hewitt CL, Patil JG (2003) Development and evaluation of a PCR-based test
for detection of Asterias (Echinodermata : Asteroidea) larvae in Australian plankton samples
from ballast water. Mar Freshwat Res 54:709–719
DeLey P, DeLey IT et al (2005) An integrated approach to fast and informative morphological
vouchering of nematodes for applications in molecular barcoding. Phil Trans R Soc London B
360:1945–1958
DeLong EF (2005) Microbial community genomics in the ocean. Nat Rev Microbiol 3:459–469
DeLong EF and Karl DM (2005) Genomic perspectives in microbial oceanography. Nature
437:336–342
de Tomaso AW, Weissman IL (2003) Construction and characterization of large-insert genomic
libraries (BAC and fosmid) from the Ascidian Botryllus schlosseri and initial physical mapping
of a histocompatibility locus. Mar Biotechnol (NY) 5(2):103–115
Díez B, Pedrós-Alío C, Massana R (2001) Study of genetic diversity of eukaryotic picoplankton in
different oceanic regions by small-subunit rRNA gene cloning and sequencing. Appl. Environ
Microbial 67:2932–2941
Dinsdale EA, Pantos O et al (2008) Microbial ecology of four coral atolls in the Northern Line
Islands. PLoS ONE 3(2):e1584
Doi RH, Igarashi RT (1965) Conservation of ribosomal and messenger ribonucleic acid cistrons in
Bacillus species. J Bacteriol 90:384–390
Dubnau D, Smith I, Morell P, Marmur J (1965) Gene conservation in Bacillus species. I.
Conserved genetic and nucleic acid base sequence homologies. Proc Natl Acad Sci USA 54(2):
491–498
Duffy JE, Stachowicz JJ (2006) Why biodiversity is important to oceanography: potential roles
of genetic, species, and trophic diversity in pelagic ecosystem processes. Mar Ecol Prog Ser
311:179–189
Eisen JA (2007) Environmental shotgun sequencing: Its potential and challenges for studying the
hidden world of microbes. PLoS Biol 5:e82
Eller G, Töbe K, Medlin LK (2007) A set of hierarchical FISH probes for the Haptophyta and a
division level probe for the Heterokonta. J Plank Res 29:629–640
Evans KM, Wortley AH, Mann DG (2007) An assessment of potential diatom “Barcode” genes
(cox1, rbcL, 18S and ITS rDNA) and their effectiveness in determining relationships in
sellaphora (Bacillariophyta). Protist 158:349–364
Floyd R, Abebe E et al (2002) Molecular barcodes for soil nematode identification. Mol Ecol
11(4):839–850
Fox CJ, Taylor MI et al (2008) Mapping the spawning grounds of Noth Sea cod (Gadus morhua)
by direct and indirect means. Proc R Soc Lond 275:1543–1548
Fox CJ, Taylor CJ, Pereyra R, Willasana MI, Rico C (2005) TaqMan DNA technology confirms
likely overestimation of cod (Gadus morhua L.) egg abundance in the Irish Sea: Implications
for the assessment of the cod stock and mapping of spawning areas using egg-based methods.
Mol Ecol 14:879–884
Fuchs BM, Spring S et al (2007) Characterization of a marine gammaproteobacterium capable of
aerobic anoxygenic photosynthesis. Proc Natl Acad Sci U S A 104(8):2891–2896
Gescher C, Metfies K, Frickenhaus S, Knefelkamp B, Wiltshire K, Medlin LK (2008) Feasibility
of assessing the community composition of prasinophytes at the helgoland roads sampling site
with a DNA microarray. Appl Environ Microbiol 74:5305–5316
Giovannoni SJ, Britschgi TB, Moyer CL et al (1990) Genetic diversity in sargasso sea bacterloplankton. Nature (London) 345:60–63
Goffredi SK, Jones WJ, Scholin CA, Marin R, Vrijenhoek RC (2006) Molecular detection of
marine invertebrate larvae. Mar Biotech 8:149–160
Gómez A, Wright PJ, Lunt DH et al (2007) Mating trials validate the use of DNA barcoding to
reveal cryptic speciation of a marine bryozoan taxon. Proc R Soc B 274:199–207