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Cambridge University Press 978-1-107-02858-6 - Next Generation Systematics: The Systematics Association Special Volume 85 Edited by Peter D. Olson, Joseph Hughes and James A. Cotton Index More information

Index

1000 Fungal Genome Project, 221 ancient DNA, 7, 95, 179, 282–300 1000 genomes project, 310 analysis, 292 10k vertebrate genomes initiative, 49, 78 authenticity of, 292 16S rRNA. See ribosomal RNA laboratories, 291–2 18S rRNA. See ribosomal RNA ancient metagenomic analysis, 297 ancient RNA, 294, 297 28S rRNA. See ribosomal RNA Ancylostoma caninum,75 Animalia, 256 454 GLS Flx. See Roche 454 annotation. See genome annotation 454 Life Sciences. See Roche 454 Anopheles aegypti, 255 Anopheles gambiae, 47, 255 Abyss, 312 anthocyanin Acari, 36 biosynthetic pathway, 270 accessory genome, 113, 242 deposition, 268 Acyrthosiphon, 36, 39, 42, 256 pigments, 269 adaptation, 169 antibiotic resistance, 110, 242 Aegilops tauschii, 275 anti-malarial drug, 272 Agave, 275 Aphididae, 256 Agilent SureSelect, 142 Apiaceae, 277 Agitata, 197 apomorphic genes, 237 agriculturalism, 285 Applied Biosystems 5550 Genetic Analyzer, 43 alignment. See sequence alignment Apusozoa, 197 allelic variation, 285 Arabidopsis thaliana, 230, 271 allopolyploidy, 132, 275, 321 Arabis, 276 allotetraploid, 132, 275 Araliaceae, 273 Alps, 131 Archaea, 245, 295 alternative splicing, 249 archaebacteria, 306 Alzheimer’s disease, 273 archaeobotany, 282, 284, 286 Amaranthaceae, 272 archaeoepigenetic analyses, 298 Amaranthus hypochondriacus, 272 archaeogenetic analysis, 286, 288 Amazon, 169 archaeogenomics, 298 America, 105 Archaeognatha, 53 amino acid substitution matrix, 86 Arctotideae, 266 amoeboid organisms, 195 Área de Conservación Guanacaste, 176 AmpliconNoise, 94 aRNA, 298, See ancient RNA ancestral states, 265 Artemisia annua, 272 ancient biomolecules, 282, 293, 298 artemisinin, 272 ancient divergences, 316 arthropod, 29

© in this web service Cambridge University Press www.cambridge.org Cambridge University Press 978-1-107-02858-6 - Next Generation Systematics: The Systematics Association Special Volume 85 Edited by Peter D. Olson, Joseph Hughes and James A. Cotton Index More information

INDEX 337

Arthropoda, 252, 253, 256 Biomonitoring 2.0, 180, 186 Articulata, 317 bioprospecting, 186 Ascarididomorpha, 73 birds, 85 Ascaris suum, 72, 73, 75 birth–death process, 17, 44 Ascidia, 95 bitter melon, 273 Asia, 105 bivalves, 246 Asian carp, 187 BLAST, 16, 92–3, 139, 166, 238, 240, 242, 271 Asparagaceae, 275 expected values, 240 assembly. See genome assembly homology, 271 association mapping, 276 position-speciﬁc iterated, 240 association studies, 114 Blattaria, 30 Asteraceae, 264, 266, 272, 273, 275 Blattodea, 30, 40, 53 Australia, 105 Bombyx mori,47 autolysis, 289 bootstrap. See phylogenetic methods: bootstrapping Bacillus anthracis, 242 Botanical Society of the British Isles, 138 bacteria, 5, 101, 110, 163, 164, 243, 305, 306, 315 Brachionus plicatilis,88 hyperthermophilic, 245 Branchiopoda, 29 pan-genomes, 241 Brassicaceae, 273, 276 bacteriophages, 104, 245 Brevimastigomonas, 199 bacterivores, 200 Britain, 131 baker’s yeast, 224 British Columbia, 107 Baltic, 131 Brugia malayi, 75, 243 banana, 274 Bursaphelenchus xylophilus,75 barcoding. See DNA barcoding barley, 275, 284, 285, 286, 297 Caenorhabditis, 317 Barometer of Life, 183 Caenorhabditis briggsae, 75, 243 base composition. See DNA base composition Caenorhabditis elegans, 62, 70, 72, 73, 74, 76, Basic Local Alignment Search Tool. See BLAST 230, 232, 243 Bay of Bengal, 109 development of, 76 Bayesian, 71, 108, 166 Cambridge, 106 inference, 4 Campylobacter, 242 methods, 111 Canada, 107 phylogenetic analysis, 109 candidate gene, 147 BEAST, 108 Cap3, 92, 93 bee-ﬂy, 267 Carpathians, 131 Beijing Genomics Institute. See BGI CAT model. See substitution models Bellis perennis, 126 cave bear, 297 benthic macroinvertebrates, 182 Cavernomonas, 198, 201 BGI, 48, 155, 167, 170 CBD, 141 BGI-10K, 49 CBoL, 142, 143, See Consortium for the Barcode Bilateria, 253 of Life bioanalyzer, 293 cDNA, 2, 38, 114, 200 biodiversity, 14, 28, 62, 149, 154, 155, 160, 165, Cephalocarida, 29 166, 168, 169, 171 cercomonad, 196 analysis, 175 Cercomonas, 197, 198 assessment of, 124, 177 Cercozoa, 196, 207 crisis, 188 character mapping, 266 bioinformatics, 3, 6, 35, 89, 117, 154–65 Chelicerata, 29, 43 pipelines, 170, 171 chemosensory, 45 biological invasions, 187 Chlorophytum, 275 biological species concept, 196 Chromadoria, 65 BioMarKs, 207 ciliates, 195 biomolecular banks, 282, 288 CITES, 141 biomonitoring, 179, 186 cladogram, 161

338 INDEX

Cleome, 273 Cryptocercus punctulatus,49 climate change, 164, 170, 188 Cucurbitaceae, 273 clonal, 102 cultivated crops, 285 Clostridium difficile, 106 Cupressaceae, 277 clustering algorithms, 182 Curculionidae, 40 Cnidaria, 246, 256 Cuvier, Georges, 317 Cnidium dubium, 277 cyanogenic glucosides, 274 CO1. See cytochrome oxidase 1 cyprinid, 88 coalescence, 207, 223 cytochrome oxidase 1, 4, 69, 70, 87, 88, 89, 95, coalescent process, 320–3 142, 159, 179, 181, 205 Codes of Nomenclature, 148 Czechoslovakia, 131 codon bias, 108 codon usage, 85 D1–D2 variable regions. See ribosomal RNA Coelomata, 317 Dactylorhiza, 132, 133 COI. See cytochrome oxidase 1 daisy, 264, 266 Coleoptera, 31, 36, 39, 40, 42, 49, 52 Daphnia, 35, 43, 235 collections Darwin, Charles, 184, 223 archaeobotanical, 290 data analysis, 170 herbarium, 282, 284, 286 data deluge, 220, 226 museum, 284 data repositories, 167 Collembola, 29, 38 data sharing, 167 Colugo, 297 data storage, 167–168 comparative biology, 7 dauer stage, 232 comparative genomics. See genomics: dbEST, 37 comparative Denoising, 155 compensatory base changes, 204 Dermaptera, 31, 33, 53 computational complexity, 20 deuterostomes, 86 computational costs, 168 developmental control genes, 230 concatenation, 316 developmental genetics, 264 consensus. See phylogenetic method: consensus developmental plasticity, 264 conservation, 50 diagenesis, 290 conservation genetics, 276 diagnostics, 87 conserved domains, 271 Dictyocaulus viviparus,75 Consortium for the Barcode of Life, 180, 210 Dicyema,88 contamination, 290, 291, 309 diploid, 132 bacterial, 295, 309 Diplura, 29 fungi, 292 Diptera, 31, 35, 36, 39, 40, 42, 44, 49, 52, 253 human, 291, 292 Dirofilaria immitis, 75, 77 microbial, 291 disabling mutations, 249 plant, 292 discordance, 19 soil bacteria, 292 disease management, 274 yeast, 309 diversification rates, 15 contig, 91–3, 312 DNA barcoding, 6, 7, 64, 66–70, 88, 123, 125, convergent evolution, 109, 195 135–49, 159, 169, 176, 179–82, 188, 210, Convolvulaceae, 273 275, 297 Conyza canadensis, 273 choice of locus, 67 Copepoda, 29 DNA base composition, 35, 73, 85, 164, 245, coprolites, 297 250, 308 core genome, 113 DNA fingerprinting, 125 Costa Rica, 176 DNA fragmentation, 290, 293, 294 cotton, 295 DNA hybridization, 95 crop domestication, 285 DNA methylation, 145, 298 crop species, 276, 299 DNA sequencing. See sequencing crustacea, 29, 43, 86 DNA-based identification, 136 cryptic species, 134, 135 DNAnexus, 169

INDEX 339

domestication, 286 evo-devo, 7, 8, 229, 264, 265, 270, 271, 272 genes, 284 evolution syndrome traits, 283, 284 real-time, 284, 289 trait loci, 285 evolutionarily signiﬁcant units, 207, 208 traits, 284 evolutionary developmental biology. Doolittle, R. F., 237 See evo-devo Dorylaimia, 65, 75 evolutionary ecology, 229 Drosophila, 35, 37, 44, 45, 46, 235, 239, 247, 251, evolutionary novelty, 229 252, 254 Evolutionary Placement Algorithm, 166 Drosophila melanogaster, 230, 241, 243, 253 exon, 37 segmentation, 230 expressed sequence tag. See EST drug resistance, 109, 113 extinction risks, 183

early hominins, 300 Fabaceae, 274, 276 Ecdysozoa, 63, 317, 318 Felsenstein Zone, 22 Echinococcus,90 field taxonomy, 146 Echinococcus canadensis, 92, 93 fieldwork, 124, 128 ecologists, 137 field biologists, 125, 139, 141, 143, 145 ecology, 7, 129, 147, 149 field naturalist, 135, 138 ecological adaptation, 324 field-based sequencing, 142, 146, 147, 148, ecological observatories, 164 149, 157 ecological selection, 206 field-based sequencing device. See Economic Botany Collection, 287 sequencing: palmtop sequencer ecosystems, 154, 162, 168 file formats, 311 functioning, 185 bam, 311 ecotypes, 204 bcf, 311 Ectognatha, 29 Bed, 311 effective population size, 323 cram, 311 eggplant, 276 Fasta, 311 Embioptera, 30, 31, 42 Fastq, 311 emergent properties, 185 gff, 311 endogenous endonucleases, 289 gtf, 311 Endopterygota, 31, 253 sam, 311 Enoplea, 78 vcf, 311 Enoplia, 65, 75 Filosa, 196 Enoplida, 75 FISH, 85, 88, See fluorescent in situ hybridization enterobacteria, 245 fish gut microbiota, 187 Entognatha, 29 fitness, 110 environmental microbiology, 202 flagellates, 195 environmental selection, 285 flavonoids, 268 Eocercomonas, 198, 201 flax, 287 Ephemeroptera, 53 florets, 267 epidemiology, 102, 106 flow cytometry, 131, 145 epigenetics, 145 Flowsim, 91, 93 Escherichia coli, 108, 114, 163, 232, 242, 246 Fluidigm access array, 142 EST, 16, 37, 38, 45, 70, 243, 244, 247, 272, 275 fluorescent in situ hybridization, 203 databases of, 71 food quality, 284 ESTs, 34, 37 food security, 283 ESUs. See evolutionarily significant units Formicidae, 39, 244 eubacteria, 306 forward genetics, 232 Eukaryota, 253 fossil record, 282 Eumetazoa, 253 founder genes, 253 Euphorbiaceae, 273 fruit quality traits, 273 Europe, 105, 108, 129, 131, 132, 134 functional annotation, 166 Euryarchaeota, 255 functional genomics, 114

340 INDEX

fungi, 7, 221 Genome 10 K Project, 221 metabolism evolution, 224 genome annotation, 44, 50, 72, 95, 114, 163, 166, 167 GAL. See galactose pathway artefacts, 247 galactose pathway, 224 RNA-seq and, 114 gamma distribution, 318 genome assembly, 16, 48, 50, 72, 77, 92, 93, 103, gastropods, 246 157, 167 GC content. See DNA base composition algorithms, 312 Genbank, 40, 124, 125, 139, 140, 141, 147, 205, assembly graph, 313 219, 222, 256 De Bruijn graph assembler, 312 gene de novo, 114, 313 cytochrome b, 283 draft, 160 cytochrome P450, 272 reference guided, 313 LpoB, 246 scaffolding, 312 Nv-osk, 241 software, 93, 312 Nwgl, 245 genome evolution, 42 oskar, 239, 241 genome finishing, 160 pbf, 285 genome rearrangement, 73 pbf1, 286 genome reduction, 42 Poldi, 249 genome sequencing, 39, 42, 77, 78 su1, 285, 286 choice of targets, 48, 50, 53, 76 tb1, 285, 286 large-scale initiatives, 54, 76, 77 vrs1, 285 pre-publication availability, 76 gene clusters, 224 genome size, 39, 131 gene discovery, 272 genome-wide association studies, 234 gene duplication, 15, 17, 36, 42, 44, 314, 321 genomic selection, 276 tandem, 44 genomics gene evolution comparative, 101, 103, 157, 305 de novo, 248 evolutionary, 305 duplication, 248 phylogenomics. See phylogenomics horizontal gene transfer, 248 genotype–phenotype gap, 225 reshuffling, 248 genotyping, 308 retrotransposition, 248 glissomonad, 196 gene expression, 46, 47, 166 Globodera pallida,75 gene expression homology, 271 Glycine max,17 gene expression patterns, 271 GMYC, 209, 210, See generalized mixed gene families, 17, 19, 36, 44, 314 Yule-coalescent gene flow, 161, 323 Google, 169 gene homology networks, 270 Gorteria diffusa, 264, 265–9 gene loss, 17, 36, 44, 45, 321 Gorteriinae, 265–9 gene motifs, 271 Gossypium, 296 gene networks, 270 GPS, 124, 138, 140, 145 gene order, 21, 85, 87 Group B Streptococcus, 242 gene silencing, 266 Grylloblattodea, 30 gene tree, 18, 19, 33, 66, 315, 320 GTR. See substitution models gene tree parsimony, 19, 36 GWAS. See genome-wide association studies generalized mixed Yule-coalescent, 207 Gymnadenia, 131, 132, 145 genetic code, 87 gyrA, 109 genetic drift, 161, 250 genome Haemonchus contortus,75 architecture, 224, 226 Haemophilus influenzae, 101 assembly, 311 Haliotis asinine, 247 filtering, 308 Hallwachs, Winnie, 176 reduction, 308 haploid, 73 reference, 293, 307, 308, 313 Harpegnathos,36

INDEX 341

Helicos Heliscope, 299 insects, 5, 28–54, 253 Hemiptera, 36, 39, 40, 42, 44, 49, 52 insertion sequences, 102 Hennig, 31 insertion–deletion events, 276, 315 Heteromita globosa, 197 insulin, 257 Heterorhabditis, 64, 75 interdisciplinary, 168 heterotrophs, 196 internal transcribed spacer. See ribosomal RNA heuristics, 20 inter-retrotransposon amplified polymorphism, Hexapoda, 29, 38 287 hexapods, 29 introgression, 19, 23, 223, 321 hidden Markov model, 315 intron, 37, 72 high-throughput sequencing, 159 invariant sites, 318 HiSeq. See Illumina HiSeq invasive plant, 276 historical samples, 290 Ion Torrent, 3 HMM. See hidden Markov model PGM, 43, 106 Holometabola, 31, 37, 40, 43 Proton, 106 Holozoa, 253 iPhy, 71 homoplasy, 46, 73, 109, 110, 111 Ipomoea batatas, 273 homopolymer regions, 203, 206 IRAP. See inter-retrotransposon amplified honey bee, 247 polymorphism horizontal gene transfer, 111, 224, 257 Isoptera, 48 horseweed, 273 ITS. See ribosomal RNA Hosta, 275 ITS1. See ribosomal RNA Hox genes, 170 ITS2. See ribosomal RNA Hubble, Edwin, 257 Ixodes, 36, 43 human genome, 244 Human Genome Project, 167 Janzen, Dan, 176 human gut microbiome, 178 Jatropha curcas, 273 Human Microbiome project, 167 Joint Genome Institute, 221 Huperzia serrata, 272 Juncaceae, 276 Huperziaceae, 272 Juncus effusus, 276 hybridization, 19, 23, 223 Juniperus tibetica, 277 hybridization capture, 297 junk DNA, 296 Hydra, 235, 246 hydrolysis, 291 Kew Gardens, 287 hydrolytic depurination, 290 k-mer, 312 Hymenoptera, 31, 36, 37, 39, 40, 42, 44, 48, 49, 52 La Réunion island, 234 large subunit ribosomal RNA. See ribosomal i5k, 49, 78, 221 RNA Illumina, 43, 70, 72, 160 large-scale genomics intitatives, 49 GAII, 103 lateral gene transfer, 240, 257, 315, 318, 321 HiSeq, 67, 155 Lepidoptera, 31, 36, 39, 40, 42, 49, 52 HiSeq 2000, 94, 95, 168 LGT. See lateral gene transfer HiSeq 2500, 43, 72, 160 lice. See Phthiraptera MiSeq, 43, 67, 91, 106 likelihood, 4, 15, 20, 71, 105, 166 NextSeq, 43 limb regeneration, 247, 256 in situ hybridization, 265 lineage sorting, 223, 322 incomplete lineage sorting, 19, 22 lineage-through-time plot, 208 incongruence, 19, 22 Linephithema,36 indels. See insertion–deletion events LINEs, 219 Indian Ocean, 232 linkage maps, 276 indicator taxa, 186 Linnaean classification, 299 industrial revolution, 287 Linnaean species, 177 infectious diseases, 187 Linnean binomial, 126–9 Insecta. See insects LINUX, 72

342 INDEX

Loa loa,75 microbial eukaryotes, 207 Lolium perenne, 274 microﬂuidic, 164 long non-coding RNAs, 251 microRNA, 46–48, 219, 298 long-branch attraction, 38, 86 Microstegium vimineum, 276 long-term ecological research, 185 minicollagen, 256 Lotus corniculatus, 274 Mira, 92, 93 LSU. See ribosomal RNA miRNA. See microRNA LTR-retrotransposons, 274 missing data, 15, 16, 17, 18 LTT. See lineage-through-time plot missing links, 299 lycophyte, 272 mitochondrial genomes, 33, 35, 70, 84–9, 93 lycopodium alkaloid biosynthesis, 272 annotation of, 95 Lythraceae, 277 genome structure, 88 mitogenomics, 72, 84, 95 maize, 244, 284, 285, 290 mitogenomes. See mitochondrial genomes Malvaceae, 274 MLST. See multi-locus sequence typing mammals, 85 mobile genetic elements, 104, 110, 113, 114 mammoth, 283, 296 mobile phones, 138 DNA, 297 molecular archaeobotany, 283 Mantophamatodea, 30 molecular clock, 111, 283 Map of Life, 183 molecular dating, 108, 109 mapping, 103 molecular evolution, 102 markers molecular operational taxonomic units, 67, 68, DNA barcode, 179 204 microsatellite, 276 molecular phylogenetics phylogenetic, 306 substitution models, 73 RAD-Tags, 219 molecular systematics, 125, 147 ribosomal, 179 history of, 4 sequence tagged site, 274 methods. See phylogenetic methods simple sequence repeat, 273 molecular typing, 102 SNP. See single nucleotide polymorphism Mollusca, 86, 246 maternal inheritance, 296 Momordica charantia, 273 matK, 142, 143 monophyletic, 134 maximum likelihood. See likelihood Moore’s law, 222 maximum parsimony. See parsimony morphology, 129, 131, 134, 141, 147, 161, 164 Mecoptera, 30, 31 morphological characters, 30, 33, 62 Medicago sativa, 276 morphometrics, 132, 134 Megaloptera, 30, 31 morphospecies, 175 MEGAN, 166 most recent common ancestor. See MRCA Megapalpus capensis, 267 moth, 274 meiofauna, 62, 66, 69, 159 MOTU. See molecular operational taxonomic Meloidogyne,75 units mesozoan, 88 MRCA, 108 Metabolomonas, 198 mRNA, 33, 35, 37, 70, 163, 169 metadata, 167 MRSA, 106, 109, See Staphylococcus aureus metagenome, 163, 164, 166, 167 mtDNA, 84, 94, 95 metagenomics, 6, 157, 161, 165, 166, 219, 292, multi-locus sequence typing, 102 294, 295 multispecies coalescence methods, 322 large-scale initiatives, 156 Musa, 274 metagenomic enrichment, 297 Musa acuminata cv. ‘Calcutta 4’, 274 Metaseiulus,36 mutagenesis, 115 metasystematics, 183 mutation, 250 metatranscriptomics, 163, 165 mutation rate, 102, 107 Metazoa, 253 Mycobacterium abscessus, 106 Methanopyrus kandlerii, 245 Mycobacterium tuberculosis, 102, 107, 110 microarrays, 114, 160 Mycoplasma genitalium, 101

INDEX 343

Myriapoda, 29, 36 orchids, 129, 130, 132, 138, 139, 140 myxozoans, 256 orders of insects, 30 ORFans. See taxonomically restricted genes nacre formation, 247 orphan genes. See taxonomically restricted Namibia, 266 genes NanoDrop 2000, 94 orthologs, 35, 36, 70, 314 Nasonia, 36, 45, 241 algorithms for identifying, 314 National Center for Biotechnology information. identifying, 314 See NCBI single copy, 314 natural historians, 137, 138 OrthoMCL, 314 natural mutants, 269 Orthoptera, 36, 40, 42 natural selection, 109, 160, 161 Oryza,16 genome-wide scans, 324 OTUs. See operational taxonomic units NCBI, 76, 205, 271 Oxford Nanopore, 157 ncRNA, 115 GridION, 157 Neanderthal, 296 MinION, 43, 144–6, 157 genome, 297 Oxyuridomorpha, 73 Necator americanus,75 nematodes, 5, 62–78, 175, 181, 182, 232, 243, 317 Paciﬁc Biosciences, 157 protein space, 244 Paclitaxel, 272 Nematomorpha, 63 palaeogenome, 296 Nematostella, 235 palaeopolyploidy, 275 NEON project, 164, 165 Paleoptera, 54 Neotylenchinae, 64 palmtop barcoding. See sequencing palmtop neural network, 169 sequencer Neuroptera, 31 Panagrellus redivivus,75 Newbler, 92, 93 Panax ginseng, 273 Nigritella, 131 Pancrustacea, 253 Nobel prize, 2 pan-genome, 113, 242, 243 non-coding RNA, 115 Paracercomonas, 198 non-genic regions, 251 parallel evolution, 109 non-synonymous sites, 108 paralogs, 44, 275 novel gene evolution, 248 Paraneoptera, 40, 43, 54 nuclear copies of mitochondrial genes. See parasites, 77, 195, 309 NUMTs eukaryotic, 306 nuclear genome, 74 evolution of parasitism, 63, 64 nucleic acid integrity, 295 parataxon, 148 Nucleocercomonas, 199 parataxonomists, 137, 146, 148 nucleotide composition. See DNA base Paraview, 170 composition parC, 116 nucleotide diversity, 90 parE, 116 NUMTs, 84 Parhyale, 235 parsimony, 15, 19, 20, 105 Odonata, 40, 53 gene tree. See gene tree parsimony Olea, 273 pathogenicity, 101, 221 Oleaceae, 273 pathogens, 101, 102, 110, 117, 300, 309 oligonucleotide ‘baits’, 307 bacterial, 306 Oligostraca, 29 plant, 286 olive, 273 viral, 306 OMA, 314 PCR. See polymerase chain reaction Onchocercinae, 73, 74 pea, 274 operational taxonomic units, 162, 165, 178, 179, pea aphid. See Acyrthosiphon 182, 204, 207, 210 Pediculus, 39, 45 Opisthokonta, 253 Pentastomida, 29 optical mapping, 157, 313 periculin genes, 246

344 INDEX

permafrost, 295 inhibition, 179 petal spot, 268 long, 35, 86, 88, 94 development, 264 multiplex, 297 Phasmatodea, 30, 31, 40 primers, 70, 86, 87, 88, 162, 182 phenlypropanoids, 274 qPCR, 265 phenotype, 102, 147 Polyneoptera, 33 Phlegmariurus carinatus, 272 polyphyletic, 134 Phthiraptera, 30 polyploidy, 17, 42, 133, 275, 296 PhyloBayes, 74 population genetics, 19, 134 phylodiversity. See phylogenetic diversity population genomics, 88, 160, 161, 322 phylodynamics, 108, 113 population size, 109, 161 phylogenetic diversity, 40, 50, 51, 52, 53 pplacer, 166 phylogenetic incongruence, 316 primates, 251 phylogenetic methods, 4 Pristionchus, 232 Bayesian inference, 316 Pristionchus pacificus, 75, 232 bootstrapping, 19, 20, 222, 223, 316, 317 professional taxonomists, 139, 146, 148 consensus, 20, 31, 321, 322 progenitor sequences, 248 maximum likelihood, 316 prokaryotes. See bacteria parsimony, 316 promoter regions, 114, 250 phylogenetic substitution models. See protein supercoiling, 245 substitution models protist, 7, 164, 204 phylogenomics, 8, 14, 15, 23, 31, 35, 36, 71, 109, DNA barcoding, 210 204, 219, 305, 314, 317 ecology, 195 phylogeography, 108, 148 systematics, 195 phylostratigraphy, 225, 252, 254 taxonomy, 195 phylostratum, 253 protogenes, 250 phylotranscriptomics, 70 Protostomia, 253 phylotypic stage, 225 Protura, 29 picobiliphytes, 164 Pscoptera, 30 Pinctada maxima, 247 pseudogenes, 224 Pisum sativum, 274 pseudogenization, 44, 249 plantain, 274 Psocodea, 30, 39, 52 plants, 8, 142 Puccinia graminis subsp. graminicola, 274 plasmids, 104 pulse field gel electrophoresis, 104 plastid, 164 Platanthera, 129, 130, 131 QC. See quality control Platyhelminthes, 170 QIIME, 161 Plecoptera, 31, 53 QTL. See quantitative trait loci plsC, 116 quality control, 308 Poa, 275 filtering, 315 Poaceae, 274, 275, 276 Quality Index for Predicted Proteins, 244 pocket sequencers. See sequencing: palmtop quantitative trait loci, 274, 275 sequencer quickly evolving species, 316 Pogonmyrmex,36 quinolone, 109 polar bear, 296 pollinators, 270 RAD. See sequencing polyethylene glycol, 288 Raphidioptera, 30, 31 polymer consolidation, 288 rapid evolution, 255 polymerase chain reaction, 2, 4, 63, 67, 69, 86, rare genomic changes, 219 115, 142, 159, 160, 169 rarefaction, 161 artefacts, 203 rat, 249 chimaeras, 66, 69, 162, 182, 203, 205 rate heterogeneity, 85 enrichment, 297 rbcl, 4, 142, 143, See rubisco error rate, 67 RdDM. See RNA-directed DNA methylation

INDEX 345

rDNA. See ribosomal RNA rubisco, 179 read mapping, 114 rye, 275 recombination, 110, 111, 169, 182, 250 ryegrass, 274 detection of, 111 hotspots, 111 Saccharomyces cerevisiae, 224, 225, 250, 317 recorder eﬀect, 177 Saccharomyces kudriavzevii, 224 reduced-representation. See sequencing salamanders, 247 reference genome, 101, 104, 157, 164, 165–7 Salmonella enterica, 108, 113, 114, 115 regulatory genes, 266, 270 Salmonella Typhi, 115, 116 Remipedia, 29 Salvia sclarea, 274 repeat junctions, 275 sampling repeats. See repetitive DNA artefacts, 202 repetitive DNA, 36, 72, 103, 182, 275, 295, chimaeras, 202 296, 312 destructive, 290 repetitive elements. See repetitive DNA environmental, 200 reproductive isolation, 148 maximum information content, 177 restriction sites, 308 voucher, 184 restriction-site Associated DNA sequencing. See Sanger, Frederick, 3, 257 sequencing satellite model organisms, 230 reverse genetics, 232, 324 saturated, 35 Rhabdias bufonis,66 scaﬀolds, 157 Rhabditida, 75, 78 Scandinavia, 131 Rhabditina, 78 scarab beetle, 232 Rhabditomorpha, 73 secondary metabolite pathways, 274 rhinoceros, 296 secondary metabolites, 274 ribosomal proteins, 38 secondary structure ribosomal RNA, 4, 5, 31, 85, 89, 162, 163, 169, RNA, 95 170, 257, 297, 306 self-organizing maps, 164 16S rRNA, 163, 164, 179, 255 sequence alignment, 4, 15, 16, 17, 18, 66, 71, 92, 18S rRNA, 30, 51–3, 63–70, 163, 165, 196–200, 93, 103, 111, 276 203, 205, 207 accuracy, 315 28S rDNA, 205 algorithms, 315 D1-D2 variable regions, 205 gold standard, 315 ITS, 16, 17, 18, 129–32, 142, 143, 145, 179, 180, guide tree, 315 197, 199, 205, 297 invariant sites, 318 ITS1, 198, 205 multiple, 314 ITS2, 130, 204, 205 partitioning, 318 secondary structure, 206 rate of evolution, 318 V4 variable region, 205 unreliable sites, 315 V9 variable region, 205 sequence divergence, 16 rifampicin, 110 Sequence Read Archive, 40 RNA-directed DNA methylation, 298 sequencing RNAi, 46 capillary. See sequencing: Sanger RNA-polymerase, 110 chimaera. See polymerase chain reaction: RNA-seq, 2, 8, 114, 275, 276, 308, 309 chimaeras directional, 115 cost of, 1, 72, 95, 144, 145, 155 Roche 454, 38, 46, 67, 68, 69, 70, 88, 89, 94, 103, depth of, 202 155, 160, 162, 202, 203, 205, 207, 209, 272, environmental, 6, 7, 160, 165, 167, 168, 273, 274, 275, 276 199–204 Romanomermis culicivorax,75 errors, 64, 67, 69, 91, 144, 155, 158, 162 rotifer, 88 EST, 305 rpoA, 110 Illumina, 160, 203, 273 rpoB, 110 large-scale initiatives, 156 rpoC, 110 magnetic, 159 rRNA. See ribosomal RNA multiplex, 88

346 INDEX

sequencing (cont.) species identiﬁcation, 124 multiplexing, 103 species richness, 182, 186 nanopore, 144 species tree, 19, 33, 66, 84 palmtop sequencer, 123, 124, 137, 139, Sphaerulariidae, 64 143, 144 Spiruria, 64, 70, 74 platforms. See also Illumina, Roche, Paciﬁc Spirurina, 73 Biosciences, Ion Torrent, Oxford Spiruromorpha, 73 Nanopore, Helicos, Applied Biosystems split network, 31 platforms, comparison of, 158 SplitsTree, 32 pooled samples, 95 Sporozoa, 195 RAD, 267, 274, 275, 276 SSU. See ribosomal RNA reduced-representation, 305, 307, 313 Staphylococcus aureus, 104, 108, 114, Sanger, 3, 4, 67, 88, 95, 125, 155, 159, 202, 242 219, 297 staple crops, 286 short-read, 307 Steinernema,64 shotgun, 292, 294, 295 Strepsiptera, 31, 39, 53 single-cell, 78, 163, 164 Streptococcus agalactiae, 242 single-molecule, 3, 144, 157, 159, 299 Streptococcus pneumoniae, 102, 111, tags, 308 112, 113 targetted, 5, 142, 160 stress-resistant plants, 272 taxonomic assignment, 166 Strigamia,36 technology, 6, 125, 155 Strongyloidoidomorpha, 64 transcriptome. See transcriptome Strongylomorpha, 64, 70 whole-genome, 71, 147, 307 substitution models, 4, 86, 319 shell evolution, 247 Bayesian MCMC, 320 Shigella, 109, 163 CAT model, 319 short interfering RNA, 298 covarion, 320 signature proteins, 255 general Markov, 320 simulation, 91–93, 170 General Time Reversible, 318 SINEs, 219 Jukes–Cantor, 318 single nucleotide polymorphism, 103, 108, mixture models, 320 110, 111, 168, 275, 276, 291, 293, 296, substitution rate, 107 308, 309 supermatrix, 15, 16, 19, 20, 316, 319, 321 single-molecule sequencing. See sequencing: super-spreader, 107 single-molecule supertree, 16, 19, 321 Siphonaptera, 30, 31 surrogate taxa, 186 siRNA. See short interfering RNA sweet potato, 273 size of phylogenetic trees, 13, 14 Switzerland, 277 small RNAs, 43, 46 symplesiomorphy, 252 small subunit ribosomal RNA. See ribosomal synapomorphy, 46, 87, 252 RNA:18s rRNA synapomorphic genes, 239 SNP. See single nucleotide polymorphism synonymous sites, 108 SOAPdenovo, 312 systematic error, 320 Solanaceae, 276 systems biology, 186 Solanum melongena, 276 SOLiD, 43 T4 bacteriophages, 245 Sonneratia, 277 Taenia, 92, 93 South Africa, 266 tapeworms, 89 South America, 105 Tara Oceans, 167 Southern Tibetan Plateau, 277 Tardigrada, 30 species circumscription, 126–35, 140, 141, target enrichment, 296, 297 147–9 Tasmanian tiger, 296 molecular, 143 Taxaceae, 272 species description, 126 Taxol, 272 species diversity, 40, 161 taxon delimitation, 196

INDEX 347

taxonomically restricted genes, 8, 17, 257 trnL-F, 143 classification, 239 trophic structure, 185 evolution, 248, 250 tuberculosis, 107 functional significance, 244 turfgrass, 274 origins, 248 Tylenchomorpha, 70 sampling error, 240 Typha minima, 277 similarity threshold, 240 Typhaceae, 277 systematics of, 252 ubiquity of, 241 ultra-barcoding, 274 taxonomically unique sequences. See uncultured, 166, 169 taxonomically restricted genes universal barcoding gene, 210 taxonomy, 6, 124–8, 135–7, 147, 148 universal primers, 203 Codes of Nomenclature, 126 unstable taxa, 316 taxonomic impediment, 137 untranslated regions. See UTRs taxonomic lumping, 199 UTRs, 115 taxonomic splitting, 199 Taxus mairei, 272 V4 variable region. See ribosomal RNA TB. See tuberculosis V9 variable region. See ribosomal RNA Tenebrionidae, 40 vaccine, 111 terpenoids, 274 variable number tandem repeats, 102, 104 Tetranychus,36 Vavilov Institute, 287 Thailand, 104, 106 vectorial capacity, 221 Theobroma, 274 Velvet, 312 ThermoFidelase sequencing kit, 246 Vibrio cholerae, 109 third generation sequencing, 299 viral genomes, 243, 245 Thysanoptera, 40 viral transfer, 243 ToL. See tree of life virosphere, 243 tooth fragments, 295 virus reservoirs, 243 Topo V, 245 viruses, 164 topoisomerase, 245 VisTrails, 170 total evidence, 321 VNTRs. See variable number tandem repeats TraDIS. See transposon directed insertion-site voucher specimen, 95, 139–41 sequencing Tragopogon miscellus, 275 wasp, 241 transcriptome, 16, 37, 43, 49, 70, 71, 74, 114 waterlogged timber, 288 transcriptomics, 8, 45, 70, 166, 270, 272, 273 wheat, 275, 284, 286, 290 comparative, 271 whole genome duplication, 17, 42 transmission, 108, 110 whole genome sequencing. See sequencing: transposable elements, 37 whole-genome transposon directed insertion-site sequencing, wiki, 76 115 Wilson, Edward O., 175 transposons, 104 Woese, Carl, 255 tree of life, 23, 219–26, 318 WormBase, 77 tree-thinking, 221 Tremula, 197 yeast, 239, 317 Tribolium castaneum, 42, 235 Yersinia pestis, 295 Trichinella spiralis,75 Trichoptera, 31, 40 Zootermopsis nevadensis,39 Trichuris,75 Zoraptera, 31, 33, 53 tRNA, 85, 95 Zygaena filipendulae, 274