398
Index
SignalP, 57, 339, 341–342
Signal peptide, 341–342
Silica cell walls, 192
SILVA, 58, 153
Simple Sequence Repeat (SSR), 4–5, 76,
85–86, 215–218
Single cell genomics, 37, 40, 60, 290–291
Single cell isolation, 40, 44, 291
Single-nucleotide polymorphism (SNP), 75,
77–78, 80, 84–87, 93, 95–96, 215,
217–218, 223, 225, 254–255, 322
Singleton, 328–330, 365
Small subunit of ribosomal RNA (18S) /
large subunit of ribosomal RNA (18S),
10, 127
Social–ecological systems (SES) approach, 22
Sockeye, 259
Solasteridae, 19
Solea senegalensis, 222
Sorangium cellulosum, 48, 318
Sorcerer II, 189, 293, 296
Sparus aurata, 214, 221
Spatangus purpureus, 19
Speciation, 2–3, 81, 90–92, 152, 165, 196, 250,
260–261, 343
Species diversity, 2, 4, 6, 8, 13–14, 17, 22, 189
Spisula spp, 18
Sponge, 126, 136, 146, 149, 151–152, 288,
298, 306
Sporophyte, 200–201
Spot/feature, 82, 98, 150, 161, 182, 192,
196–197, 250, 263, 300, 346,
362–363, 366
Spotted green pufferfish, 214
Stable isotope, 40, 44, 299
Staphylothermus marinus F1, 294
Statistical electronic Northern blot (SteN),
328–330
Stomatopod larvae, 19
Stramenopiles, 182
Streptococcus agalactiae, 291
Stress, 97–99, 101–102, 104–105, 200, 221,
230, 234, 236–237, 242, 305
Strongylocentrotus purpuratus, 166
Suberites domuncula, 151–152
Substitution model, 131
Subtidal zone, 200
Subtracted library, 234
Sulfolobus solfataricus, 294
Supermatrix approach, 127–128
Supertree approach, 127
Support Vector Machine (SVM), 333–334, 366
Swiss-Prot, 56–58, 351–354
Syllida, 19
Synechococcus sp. PCC7942, 303
Synechococcus spp, 304
Synteny, 136, 167, 196, 220
Systematic error, 121, 125, 128, 132
T
Tachypleus tridentatus, 307
Tags, 58, 94, 222, 316, 322, 326, 350, 355, 357
Takifugu rubripes, 99, 214, 234, 252
Target, 5, 13, 16, 21, 35, 39–40, 42, 50, 81,
183, 195, 218, 239, 245, 263, 322
TC, 327, 329–330
Terebellidea, 19
Terminal restriction fragment length
polymorphism (TRFLP), 11
Tertiary endosymbiosis, 181
Tethya crypta, 288
TETRA, 53
Tetraodon nigroviridis, 214
Tetrapturus albidus, 19
Tetrapturus pfluegeri, 19
Tevnia jerichonana, 20
TGF, 152, 245
TGICL, 327, 329
Thalassiosira pseudonana, 185, 192, 304, 306
Theora fragilis, 19
Thermal history, 100
Thermococcus barophilus MP, 294
Thermococcus gammatolerans, 294
Thermococcus kodakaraensis, 294
Thermococcus onnurineus, 294
Thermococcus thioreducens, 289
Thermostability, 101
Thermotoga maritima MSB8, 295
Third Party annotation (TPA) sequence
database, 351
Thoracica, 19
Three-spined stickleback, 88, 214, 257, 260
Thunnu salbacares, 19
Thunnus alalunga, 19
Thunnus atlanticus, 19
Thunnus obsesus, 19
Thunnus thynnus, 19
TMHMM, 57
Total evidence, 124, 126
Toxins, 180, 190–191, 223, 238
Toxins, coastal ecosystems, 180, 199, 203
Trachuru picturatus, 18
Trachurus mediterraneus, 18
Trachurus sp., 20
Trachurus trachurus, 18
Transcription factor, 149–152, 155, 163,
168, 343
Index
SignalP, 57, 339, 341–342
Signal peptide, 341–342
Silica cell walls, 192
SILVA, 58, 153
Simple Sequence Repeat (SSR), 4–5, 76,
85–86, 215–218
Single cell genomics, 37, 40, 60, 290–291
Single cell isolation, 40, 44, 291
Single-nucleotide polymorphism (SNP), 75,
77–78, 80, 84–87, 93, 95–96, 215,
217–218, 223, 225, 254–255, 322
Singleton, 328–330, 365
Small subunit of ribosomal RNA (18S) /
large subunit of ribosomal RNA (18S),
10, 127
Social–ecological systems (SES) approach, 22
Sockeye, 259
Solasteridae, 19
Solea senegalensis, 222
Sorangium cellulosum, 48, 318
Sorcerer II, 189, 293, 296
Sparus aurata, 214, 221
Spatangus purpureus, 19
Speciation, 2–3, 81, 90–92, 152, 165, 196, 250,
260–261, 343
Species diversity, 2, 4, 6, 8, 13–14, 17, 22, 189
Spisula spp, 18
Sponge, 126, 136, 146, 149, 151–152, 288,
298, 306
Sporophyte, 200–201
Spot/feature, 82, 98, 150, 161, 182, 192,
196–197, 250, 263, 300, 346,
362–363, 366
Spotted green pufferfish, 214
Stable isotope, 40, 44, 299
Staphylothermus marinus F1, 294
Statistical electronic Northern blot (SteN),
328–330
Stomatopod larvae, 19
Stramenopiles, 182
Streptococcus agalactiae, 291
Stress, 97–99, 101–102, 104–105, 200, 221,
230, 234, 236–237, 242, 305
Strongylocentrotus purpuratus, 166
Suberites domuncula, 151–152
Substitution model, 131
Subtidal zone, 200
Subtracted library, 234
Sulfolobus solfataricus, 294
Supermatrix approach, 127–128
Supertree approach, 127
Support Vector Machine (SVM), 333–334, 366
Swiss-Prot, 56–58, 351–354
Syllida, 19
Synechococcus sp. PCC7942, 303
Synechococcus spp, 304
Synteny, 136, 167, 196, 220
Systematic error, 121, 125, 128, 132
T
Tachypleus tridentatus, 307
Tags, 58, 94, 222, 316, 322, 326, 350, 355, 357
Takifugu rubripes, 99, 214, 234, 252
Target, 5, 13, 16, 21, 35, 39–40, 42, 50, 81,
183, 195, 218, 239, 245, 263, 322
TC, 327, 329–330
Terebellidea, 19
Terminal restriction fragment length
polymorphism (TRFLP), 11
Tertiary endosymbiosis, 181
Tethya crypta, 288
TETRA, 53
Tetraodon nigroviridis, 214
Tetrapturus albidus, 19
Tetrapturus pfluegeri, 19
Tevnia jerichonana, 20
TGF, 152, 245
TGICL, 327, 329
Thalassiosira pseudonana, 185, 192, 304, 306
Theora fragilis, 19
Thermal history, 100
Thermococcus barophilus MP, 294
Thermococcus gammatolerans, 294
Thermococcus kodakaraensis, 294
Thermococcus onnurineus, 294
Thermococcus thioreducens, 289
Thermostability, 101
Thermotoga maritima MSB8, 295
Third Party annotation (TPA) sequence
database, 351
Thoracica, 19
Three-spined stickleback, 88, 214, 257, 260
Thunnu salbacares, 19
Thunnus alalunga, 19
Thunnus atlanticus, 19
Thunnus obsesus, 19
Thunnus thynnus, 19
TMHMM, 57
Total evidence, 124, 126
Toxins, 180, 190–191, 223, 238
Toxins, coastal ecosystems, 180, 199, 203
Trachuru picturatus, 18
Trachurus mediterraneus, 18
Trachurus sp., 20
Trachurus trachurus, 18
Transcription factor, 149–152, 155, 163,
168, 343