Index

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Acanthobdella, Clitellata, 242–244

Acanthocephala

Platyhelminthes, 209

Syndermata, 224–225

Acanthomorpha, “bush at the top,” 419–421

Acari, mites and ticks, 299–301

Acercaria, 338–339, 340

Acidianus species, Sulfolobales, 56

Acidobacteria, 53

Acidophilic thermophiles, Archaea, 81

Acoelomorpha

apomorphy, 211

bilaterians, 203–204

flatworms, 210–211

Actinistia, chordates, 398

Actinobacteria, gram-positive bacteria, 51,

52

Actinopterygii

chordates, 396–397

diversity, 416–417, 559

rayfin fishes, 416

African populations, human gene trees, 28

Age. See Ghost lineage; Molecular clock

Agriculture, 11–12

Alderflies, Neuropterida, 351–352

Algae. See also Brown algae; Green algae;

Red algae

definition, 121–122

eukaryotes with plastids, 121

glaucocystophytes, 122

plastids evolution, 124–125

plastids of lineages from cyanobacteria, 122

species for food, 122

Allopatric speciation, sympatric and, 30–31

All-taxon biological inventory (ATBI),

global, 541–542

Alpha taxonomy, descriptive, 540

Alveolates, 64

Amblypygi, whip spiders, 305

Ambulacraria

deuterostome relationships, 367

Metazoan phylogeny, 378–380

monophyly, 366–367

on the Tree of Life, 558

phylogenetic relationships, 374

representative taxa, 366

Amitochondriate excavates, 61–62

Amniota, chordates, 400–401

Amniotes, 451, 452, 559

Amoebozoa, 67–68

Amphibia, 400, 430–432

Amphibians

Anura and Salientia, 438–439

basal frogs, 439–440

caecilians, 434–436

discoglossoids, 439–440

frogs, 437–438, 439, 440

geographic distribution, 435

Hyloidea, 441–442, 443

interrelationships of modern, 433–434

modern, 430–431

Neobatrachia, 441

nomenclature, 445

origin of tetrapods, 432–433

phyloinformatics, 445

Pipanura, 440–441

prospects for future, 444–445

Ranoidea, 442, 444

relationships among modern and

Paleozoic groups, 433

salamanders, 436–437

two-phase life history, 430

Amphilinidea, 220, 221

Amphineura, Mollusca, 262–263

Angiosperms

ABC model of floral organ identity, 162–

163, 164

angiosperm classes, 157–160

asterids, 160

Berberidopsidales, 159

carpels, 154, 162

Caryophyllales, 159

diversity, 163

double fertilization, 154, 161–162

endosperm formation, 161–162

eudicots, 158–160

evolution, 161–163

fossil record of early, 156–157

gaps in angiosperm phylogeny

knowledge, 160–161

564 Index

Angiosperms (continued)

Gunnerales, 159

gymnosperms and, 148

magnoliids, 157–158

major clades, 157–160

molecular vs. fossil ages, 157

monocots, 157

morphology and floral genes, 162–163

multigene analyses, 155

perianth, 162–163

phylogeny, 155–156, 160–161, 550

radiations in, phylogeny, 160

relationships, 556

root, 155–157

rosids, 159–160

Santalales, 159

Saxifragales, 160

sepals and petals, 162

synapomorphy, 154

Animals

basal, 554

Bremer support indices (BSI), 199

data set analysis of metazoans, 198

genealogy, 197

interrelationships, 197–198

nuclear small subunit (nSSU) ribosomal

DNA (rDNA), 171

phylogenetic tree, 172

phylogeny of new, 209, 210

Anisozygoptera, 336

Annelida

arthropods with, 238–239

Articulata, 238–239

characteristics, 237

Clitellata, 240–244

ecological importance, 237

economic importance, 245

gene sequences, 247–248

leeches, 237

morphological and molecular data,

240

oligochaetes, 237

phylogenetic analyses, 239–240

polychaetes, 237

principal groups, 237, 238

rooting, 246

segmentation, 237, 238

sister search, 238–239

swarming, 245

whirling disease, 237

worm or not, 239–240

Anthophyte hypothesis, vascular plants,

147, 148

Antibiotic resistance

lateral gene transfer (LGT), 88–89

superbugs, 89

Antibiotics, Streptomycetes and

Actinomycetes, 51

Ants, 12, 352, 540

Anura

frogs, 438–439

geographical distribution, 435

meaning, 430

Apes, close relatives, 518–519

Aphids, Buchnera, 21

Apicomplexa, 64, 123, 126

Aplacophora, 263–264

Apodida, holothurians, 376

Apodiformes, phylogenetic relationships,

476–477

Appendages, Gnathostomata, 394

Arabidopsis thaliana, 162

Aquificae, hyperthermophiles, 46

Arachnida, phylogeny, 296–299

Arachnids

Acari, 298, 300

Acariformes, 300

Acari or Acarina, 299–301

Amblypygi, 305

Buthidae, 308–309

camel spiders, 312

Chactidae, 310

Chaerilidae, 309–310

cladistic analysis, 297

diversity, 296, 297

Dyspnoi, 307

Elassommatina, 311–312

elongation factor, 298

Euchelicerata, 296

extinct orders, 297

fossils, 296, 312

harvestmen, 306–308

Holothyrans, 301

Iuridae, 310

Laniatores, 308

mites and ticks, 299–301

molecules and morphology, 312

Monogynaspida, 301

morphological analysis, 297–298

Opiliones, 306–308

Palpigrades, 302

Parasitiformes, 301

Phalangida, 307–308

Prostigmata, 300

Pseudoscorpiones, 310–312

Ricinulei, 301–302

Sarcoptiformes, 300–301

schizomids, 306

Scorpiones, 308–310

scorpions, 298, 308–310

Solifugae, 312

spiders, 302, 304–305

Trigynaspida, 301

Uropygi, 305–306

Uropygi–Schizomida doublet, 298

Vaejovidae, 310

whip scorpions, 305–306

whip spiders, 305

Araneae, spiders, 302–305

Araneoidea, spiders, 304

Araneomorphs, spiders, 304

Archaea

Archaeoglobus species, 57

Cenarchaeum group, 56–57

coherence, 91

Crenarchaeota, 55–57

deoxyribonucleic acid (DNA) replication,

54

description, 54

Desulfurococcales, 56

Euryarchaeota, 57–59

evolutionary structure, 81–82

extremophilic organisms, 59–60

genomics and phylogenetic analysis, 8

genomic sequencing, 59–60

Halobacteria, 57

in the Tree of Life, 45

Korarchaeota, 59

membrane lipids, 55

methanogens, 57–58

Nanoarchaeota, 59

newly discovered organisms, 14

phylogenetic domain of life, 77–79

phylogeny of, 82

prokaryotes, 43

RNA polymerases, 54

Sulfolobales, 56

Thermococci, 58

Thermoplasmata, 58–59

Thermoproteales, 56

universal tree, 78

Archaeal tree, support for deep branches, 55

Archaefructus sinensis, fossil record, 156–157

Archaeoglobus species, Euryarchaeota, 57

Archaeoglobus fulgidis, 91

Archetypes, ancestors, 197

Archezoa, 60, 69, 97

Archosauromorphs, relationships, 462

Archosaurs

birds, 463

crocodilians, 462

diapsids, 455–456

dinosaurs, 463

ornithodirans, 462–463

pterosaurs, 462–463

traits, 461

Ardipithecus ramidus, hominin, 521–522

Arenaviruses, human land use, 12–13

Arhynchobdellida, blood-feeding, 241

Arrow worms, Chaetognatha, 225–226

Arsenic, Chinese brake ferns, 22–23

Arthropods

annelid worms with, 238–239

characters, 287

Chelicerata, 283

cladistic analysis of crusteomorph, 327

cladogram of extant relationships, 285

Index 565

combined analyses, 290, 291

Crustacea, 283

current status, 287

developmental genetics, 324

diversity, 281

evolution of long-bodied articulate, 325

extinct lineages, 283–284, 291–292

fossil history, 283–284

geological history, 281

Hexapoda, 282

living taxa analysis, 287, 290

long-bodied, 324

Mandibulata, 284

monophyly vs. polyphyly, 285–286

morphological and molecular analysis,

287, 288, 289

Myriapoda, 282–283

relationships of classes, 284–285

relatives, 281–282

role of fossils, 287

Schizoramia vs. Mandibulata, 286

sensitivity plots for extant and extant +

extinct taxa, 290

taxa, 287

Tetraconata hypothesis, 284

Tracheata hypothesis, 284

Tracheata vs. Tetraconata, 286–287

Articulata, annelid worms with arthropods,

238–239

Ascomycota

characteristics, 173–174

dikaryomycetes, 172

generalized life cycle, 175

hyphae, 173

life cycle, 174–175

macroscopic and microscopic images, 174

nutrition, symbioses, and distribution,

175–176

phylogenetic relationships within, 176–

178

pleomorphy, 174

relationships among members, 177

relationships to other fungi, 176

reproduction, 172, 174–175

species, 172–173

symbioses, 175–176

Aspidogastrea, 221

Assembling the Tree of Life (ATOL)

measuring progress, 548–549

symposium, 4, 545

Asterids, eudicots, 160

Asteroids

alternative phylogenetic hypotheses, 377

echinoderm relationships, 371, 375–376

fossils, 376

nerve arrangement, 371

phylogenetic relationships, 374

Atmospheric CO

2

, vascular plants, 138

Atrazine, tadpoles and frogs, 22

Australopiths

Australopithecus afarensis, 525

Australopithecus africanus, 523–524

Australopithecus anamensis, 525–526

Australopithecus bahrelghazali, 525

Australopithecus garhi, 526

fossils, 523–526

Kenyanthropus platyops, 526

Paranthropus aethiopicus, 524–525

Paranthropus boisei, 524

Paranthropus robustus, 524

Aves. See Birds, Neornithes

Avian relationships, challenge, 472–473

Bacillus-Clostridium group, Firmicutes, 51–

52

Backbone, chordates with, 392–393

Bacteria

Acidobacteria, 53

Actinobacteria, 51

Aquificae, 46

Bacteroides, 48–49

blue-green algae, 50–51

Chlamydiae, 49–50

Chlorobi, 49

Chloroflexi, 47–48

coherence, 91

Coprothermobacter, 53

cyanobacteria, 50–51

cytophagas, 48–49

Dienococci, 50

distributions of small subunit ribosomal

RNA sequences, 81

evolutionary structure, 79–80

Firmicutes, 51–52

flavobacteria, 48–49

flexibacteria, 48

gene expression, 45

general rules, 44

genomes, 44–45

genomics and phylogenetic analysis, 8

gram-positive, 51–52

green nonsulfur bacteria, 46–48

green sulfur bacteria group, 49

hyperthermophiles, 46

lateral gene transfer-induced artifacts, 46

motility, 44

photosynthesis, 45

phylogenetic divisions, 80

phylogenetic domain of life, 77–79

phylogenetic treatment by Woese, 45

Planctomycetes, 48, 99

prokaryotes, 43

Proteobacteria, 52–53

purple, 52–53

sizes, 44

Spirochaetes, 50

Sporomusa, 52

Thermotagae, 46

Thermus group, 50

Tree of Life, 45

universal tree, 78

Verrucomicrobia, 53

whole-genome sequencing, 46

Bacterial antibiotic resistance genes,

superbugs, 89

Bacterial phylogeny, ribosomal RNA, 98–99

Bacterial relationships, characters, 555

Bacterial symbionts, mitochondria and

chloroplasts, 78–79

Bacterial tree, support for deep branches, 47

Bacteroidetes, bacteria, 48–49

Ballistospory, 178

Basal animals, Tree of Life, 557

Basal clades, Tree of Life, 554

Basal Eucarya, Tree of Life, 556

Basal relationships, Actinopterygii, 416–417

Base, early-branching lineages, 99

Basidiomycota

ballistospory, 178

characteristics, 178

dikaryomycetes, 172

diversity, 181

ecology, 178–180

ectomycorrhizal symbiosis, 179–180

habitat, 178

Hymenomycetes, 179, 180–181

life cycle, 179, 180

phylogenetic relationships, 179

phylogeny, 180–181

plant parasitism, 180

reproduction, 172, 178

saprotrophy, 179, 180

species, 178

symbioses, 179–180

Batoidea, elasmobranchs, 414–415

Bees, Hymenoptera, 352

Beetles, 12, 349–351

Berberidopsidales, eudicots, 159

Bilateria, 201–202, 209, 210, 557

Bilaterians, acoelomorphs, 203–204

Biocomplexity, 19

Biodiversity, 20, 539, 540, 541–542

Biofilms, shaping environment, 21–22

Biogeochemical cycles, human health, 22

Biological control, 14

Biomineralization, Gnathostomata, 394

Birds. See also Neornithes

archosaurs, 463

dinosaurs, 470

Reptilia, 401–402

systematics, 468

Bivalvia

diversity and fossil history, 267

habitat, 260, 267

major groups, 267

morphology and biology, 265–267

BLAST analyses, 90–91

566 Index

Blood circulatory system, Euchordata, 389

Blood-letting, medicinal leech, 241

Blue-green algae, 50–51, 121

Boas, snakes, 460

Body plan, 370–371, 379

Bolivia, Machupo virus (MACV), 12–13

Bolivian hemorrhagic fever (BHF), 12

Bolyeriines, snakes, 460

Bone development, Gnathostomata, 394

Bony fishes, Osteichthyes, 396, 415

Bootstrap analysis, 77

Bottleneck, speciation, 28

Brachycera, dipterans, 357–358

Brain

chordates with, 388–389

Craniata, 390

Euchordata, 389

Gnathostomata, 393–394

Vertebrata, 392–393

Branchiobdellidans, 242–244

Brassicales, rosids, 159

Breathing, amphibians, 431

Brittlestars. See Ophiuroids

Brown algae, term, 121

Bryophytes

land plants, 133

life cycle, 140, 551

paraphyly, 549, 551

phylogeny, 550

vascular plants, 139

Buchnera, 21

Burgess Shale, crustaceans, 323–324

“Bush at the top”

Acanthomorpha and, 419–421

Percomorpha and, 421–423

Butterflies, Lepidoptera, 352–354

Caddisflies, Trichoptera, 354–355

Caecilians, amphibians, 434–436

Caenogastropoda, Gastropoda, 270

Caenorhabditis elegans, 19

Calcarea, sponges, 200

Calibration

ghost lineage, 504

molecular clock, 504–506

Calomys species, arenaviruses, 12–13

Cambrian, 322, 324

Camel spiders, Solifugae, 312

Canellales, magnoliids, 157–158

Caprimulgiformes, 476–477

Carpels, angiosperms, 154, 162

Casichelydians, turtles, 455

Catenulida, 213, 214

Caudata

alternative relationships, 436

geographical distribution, 435

salamanders, 436

tetrapods, 430

Caudofoveata, Aplacophora, 263

Cenarchaeum group, 56–57

Central nervous system, chordates, 387

Cephalochordata, chordates, 389–390

Cephalorhyncha, 228

Cephalopoda, 259, 271, 272

Cerambycidae, invasive species, 12

Cercomeromorphae, posterior hook, 217

Cercomonads, Cercozoa, 65

Cercozoa, 65, 66

Cestoda, gutless tapewormlike groups, 218–

219, 221

Cetacea, mammal phylogeny, 498–501

Chactidae, scorpions, 310

Chaerilidae, scorpions, 309–310

Chaetodermomorpha, Aplacophora, 263

Chaetognatha

apomorphy, 226

arrow worms, 225–226

phylogenetic problem, 203

Character evolution, 31–32

Charales, green algae, 132

Charophyceae, green algae, 128–129

Charophyta, chlorophytes, 129, 131

Chelicerata, arthropod, 283, 285

Chengjiang fauna, crustaceans, 323–324

Chernobyl nuclear power plant, sunflowers,

22

Chimaeras, 410–412, 415

Chimpanzee, 517, 518–519

Chitons, Mollusca, 262–263

Chlamydiae, bacteria, 49–50

Chlorarachniophytes

Cercozoa, 65

plastids evolution, 123

secondary plastids from green algae, 127

Chlorobi, bacteria, 49

Chloroflexi, green nonsulfur bacteria, 47–48

Chlorokybales, green algae, 131

Chlorophyceae, green algae, 129, 130

Chlorophyta, primary lineages, 129

Chloroplasts

bacterial symbionts, 78–79

heterokonts, 126

photosynthesis organelle, 121

Choanata, respiratory system, 398

Choanoflagellates, Opisthokonta, 199–200

Choanozoa, Opisthokonta, 68

Cholera, factors, 21

Chondrichthyes

cartilaginous fishes, 410–412

characters, 395

chordates, 395–396

Chordates

Actinistia, 398

Actinopterygii, 396–397

Amniota, 400–401

ancestry, 386

breathing, 398

central nervous system, 387

Cephalochordata, 389–390

characters, 386–388

Choanata, 398

Chondrichthyes, 395–396

Chordata, 386–388

coelacanths, 398

Craniata, 390–392

deuterostome relationships, 365–367

Dipnoi, 398–399

epigenesis, 385–386, 404

Euchordata, 388–389

fossils, 386

gene increases, 403

gill anatomy, 367

Gnathostomata, 393–395

hagfish, 392

hormonal glands, 387–388

lampreys, 393

lancelets, 389–390

lungfishes, 398–399

Mammalia, 402–403

Myxini, 392

notochord, 386–387

on the Tree of Life, 384, 558–559

ontogeny, 384–385, 404

Osteichthyes, 396

Petromyzontida, 393

phylogeny, 385

ray-finned fishes, 396–397

Reptilia, 401–402

Sarcopterygii, 397–398

sensory organs of head, 387

sharks and rays, 395–396

taxonomic names, ancestry, and fossils, 386

Tetrapoda, 399–400

tunicates or sea squirts, 388

turtles, lizards, crocodilians, and birds,

401–402

Urochordata, 388

Vertebrata, 392–393

Chromalveolate hypothesis, plastids

evolution, 123

Chromalveolates, 63–65, 125

Chromista, Chromalveolates, 63–64

Chromophytes, definition, 125

Chrysomelidae, 34

Chytridiomycota

animals and fungi, 171

asterospheres, 184

fungal species, 183–184

life cycle, 185

morphology, 185

phylogenetic relationships, 186–187

reproduction, 172, 183–184, 185

rumposome, 186

taxonomy, 184–185

ultrastructure, 185–186

zoospore, 185–186

Ciliates, alveolates, 64

Circulatory system

Craniata, 391

Euchordata, 389

Index 567

Mollusca, 255

Vertebrata, 393

Cladistic method, Hennig, 95, 469

Cladoxydopsidales, extinct, 149

Clams, Bivalvia, 265–267

Climate change, vascular plant radiation,

138

Clitellata, annelid subset, 240–244

Clock. See Molecular clock

Closed carpels, angiosperms, 162

Cnidarians, models for ancestors, 200

Coalescent theory, phylogenetic methods, 28

Cocculinida, Gastropoda, 270

Coelacanths, 398, 415

Coherence, stable core, 91

Coleochaetales, green algae, 131–132

Coleoidea, Cephalopoda, 272

Coleoptera, 349–351

Coliiformes, 477, 479–480

Collodictyonids, eukaryotes, 68

Colonization of land, green algae, 130–132

Colubroidea, snakes, 461

Comatulida, crinoids, 375

Community ecology, 33–35

Complexity hypothesis, small subunit (SSU)

ribosomal RNA, 91–92

Computational power, phylogenetic

analyses, 2

Computer science, tree assembly, 7–8

Concatenated data sets, deep phylogeny, 44

Coniferophyta, spermatophytes, 145

Conifers, association with gnetophytes, 147–

148

Conservation biology, 9–11, 35

Copepods, cholera bacterium host, 21

Coprothermobacter, thermophile, 53

Coraciiformes, phylogenetic relationships,

477, 479–480

Coral of life, Darwin, 117

Corvida, Passeriformes, 480–482

Craniata, characters, 390–391

Creationism, 94

Crenarchaeota

Archaea, 14, 55–57, 81–82

Cenarchaeum group, 56–57

Crinoids

cladogram, 376

echinoderm relationships, 371, 375

mitochondrial gene order, 373

phylogenetic relationships, 374

Crocodiles, archosaurs, 462

Crocodilians, Reptilia, 401–402

Crown, 84, 99

Crown Radiation, 60, 82–83

Crustacea, arthropods, 283, 290

Crustaceans

Burgess and Chengjiang faunas, 323–324

Cambrian, 322, 324

challenge of Cambrian, 322–323

cladistic analysis, 327

classic definition, 325, 326

developmental genetics, 324

fossils, 321–323

genetics, 324

long-bodied ancestor theory for

arthropods, 325

long-bodied arthropods, 324

long-standing assumptions, 325

molecules, 320–322

monophyly, 326–328

morphology, 319–320

morphology and function of second

antenna, 326

Orsten, 323

phylogenetic relationships, 319, 320

phylogenetic tree, 321

polyphyly, 326

Tree of Life, 319

Cryptobranchidae, salamanders, 436

Cryptodires, turtles, 455

Cryptomonads, plastids, 123, 125

Cryptophytes, 63–65, 125

Ctenophores, eumetazoan, 200

Cuculiformes, phylogenetic relationships,

477, 479–480

Cyanidiales, red algae, 122, 124

Cyanobacteria

bacteria, 50–51

chloroplasts, 78

photosynthesis, 121

phycobilisomes, 122

phylogenetic radiation, 84

plastids of algal lineages derived from,

122

Cycadophyta, spermatophytes, 145

Cycliophora, description, 225

Cyphophthalmi, arachnids, 306–308

Cytochrome c, phylogeny of eucaryotes, 96

Cytophagas, Bacteroidetes, 48–49

Dactylochirotida, holothurians, 376

Dactylopteriformes, Percomorpha, 423

Daddy longlegs, harvestmen, 306–308

Darwin

avian relationships, 468

coral of life, 117

creationism, 94

tangled bank, 18–19

The Origin of Species, 2, 94

theory of evolution, 95

Tree of Life, 1, 548

universal Tree of Life, 93

vision, 554

Databases, genomics, for Tree of Life, 15

Data partitioning, supertrees and

supermatrices, 496

Deinococci, Thermus group, 50

Dendrobatidae, neobatrachians, 442, 444

Dendrochirotida, holothurians, 376

Dengue fever, 20–21

Dentition, Amniota, 401

Deoxyribonucleic acid (DNA)

classification for viruses, 108

double- and single-strand DNA viruses,

109

horizontal gene transfer for DNA viruses,

115

polymerases, 13–14

replication, 54

synthesis and enzymes, 115

viruses, 114

Dermaptera, Polyneoptera, 337

Desmognathinae, salamanders, 437

Desulfovibrio, Proteobacteria, 53

Desulfurococcales, 56, 57

Deuterostomes

18S rDNA analyses, 366–367

adult morphology, 367

Ambulacraria, 378–380

Bilateria, 209

bilaterians, 201

characters, 367

classes and relationships, 371–372

echinoderm body plan, 370–371

echinoderms, 369–370

enteropneusts, 368

gill anatomy, 367

hemichordate phylogeny and

classification, 369

hemichordates, 368

Hox gene duplications, 365

molecular evidence for echinoderm class

relationships, 372–375

monophyly of Ambulacraria, 366–367

on the Tree of Life, 558

pterobranchs, 368–369

radial nerve arrangement in echinoderms,

371

relationships, 365–367

relationships within echinoderm classes,

375–378

schematic of body axes, 370

taxa, 202

tricoelomate body organization, 367

Developmental genetics, crustaceans, 324

Devonian, fossil monilophytes, 143

Diapsids, lepidosaurs and archosaurs, 455–

456

Diatoms, microalgae, 126

Dicamptodontidae, salamanders, 437

Dicondylia, insects, 334–335

Dictyoptera, Polyneoptera, 337

Dictyostelidae, Mycetozoa, 67

Digenea, flatworms, 221–223

Dikaryomycetes, Ascomycota and

Basidiomycota, 172

Dimargaritales, Zygomycota, 182

Dinoflagellates

alveolates, 64

plastids, 123, 126–127

568 Index

Dinosaurs

archosaurs, 463

birds, 470

Diplomonads, 61, 97

Diplura, insect phylogeny, 332, 334

Dipnoi, chordates, 398–399

Diptera, insects, 330, 356–358

Discicristates, mitochondriate excavates, 62

Discoglossoids, frogs, 439–440

Diversity

geography, 33

phylogeny, 32–33

sister groups, 32–33

DNA hybridization

future, 484

phylogenetic analyses of Cetacea, 499–

500

tapestry, 470–472

tree, 470–472

DNA sequencing

avian systematics, 469–470

in systematics, 543–544

phylogenetic analysis, 545

Dobsonflies, Neuropterida, 351–352

Domains

Archaea, 81–82

Bacteria, 79–80

Eucarya, 82–83

prokaryotes, 95

three phylogenetic, of life, 77–79

universal tree, 78, 95

Double fertilization, angiosperms, 154, 161–

162

Double RNA viruses, recognized families,

109

Double-strand DNA viruses, recognized

families, 109

Drugs, lateral gene transfer, 88–89

Dyspnoi. Phalangida, 307

Ear, middle, Mammalia, 402

Early-branching lineages, crown and base,

99

Earth biodiversity, 20, 539–540

Ecdysozoans

apomorphy, 226

monophyly, 202–203

on the Tree of Life, 557–558

Protostomia, 209

relationships, 226, 227

Echinoderms

adult morphology, 367

amino acid and sequence data, 373, 375

asteroids, 371, 375–376

autamorphies, 370

body plan, 370–371, 379

classes and relationships, 371–372

crinoids, 371, 375

description, 369–370

echinoids, 372, 378

fossil record, 372, 380

gill anatomy, 367

holothurians, 372, 376

larval ecology, 379–380

mitochondrial gene order, 373, 375

ophiuroids, 371–372, 376–378

relationships, 365–367, 374, 375–378

representative ambulacrarian taxa, 366

ribosomal sequence data, 372–373

Echinoids

echinoderm relationships, 372, 378

fossils, 378

morphological and molecular

phylogenies, 379

phylogenetic relationships, 374

Ecological islands, 89

Ecology

community, 33–35

phylogenies, 27–28, 29

Economics, 13–14

Ecosystems approach, term, 19

Ectognatha, insects, 334

Ectomycorrhizal symbiosis, basidiomycetes,

179–180

Egg, Amniota, 401

Elasipodans, holothurians, 376

Elasmobranchs

galeomorph sharks, 413

sharks and rays, 412–415

squalomorphs, 413–414

Elassommatina, pseudoscorpions, 311–312

Eleutherozoa, 371, 373, 375

Ellipura, insects, 332, 334

Elopomorpha, Teleostei, 417, 418

Embiida, Polyneoptera, 338

Embryological studies, Mollusca, 257

Embryophytes, land plants, 121

Enamel, Sarcopterygii, 397

Endodermal derivatives, 391, 394

Endopterygota, term, 345

Endosperm formation, angiosperms, 161–

162

Endospore formers, Firmicutes, 51

Endosymbiont hypothesis, mitochrondria,

88

Endosymbiosis, phenomenon, 124–125

Endosymbiotic events, evolution of plastids,

123

Endosymbiotic plastids, 124

Entamoebae, Amoebozoa, 67

Entelegynes, 304, 305

Enteropneusts, 368

Entomophthorales, Zygomycota, 182

Environmental change

National Ecological Observation Network

(NEON), 23

organisms shaping, 21–22

Environmental health, virus evolution, 116

Eogastropoda, Gastropoda, 270

Epigenesis, chordates, 385–386, 404

Epiocheirata, pseudoscorpions, 311

Epiprocta, insects, 336

Epitoky, phenomenon, 245

Escaped transcript hypothesis, 110–111

Escherichia coli

Buchnera comparison, 21

genome sequence, 89–90

proteobacteria, 52

Eubacteria. See Bacteria

Eucarya

alveolates, 64

amitochondriate excavates, 61–62

Amoebozoa, 66–68

animal-fungus allies, 68

animals, 68

apicomplexa, 64

basal, Tree of Life, 556

Cercozoa, 65

chromalveolates, 63–65

Chromista, 63–64

ciliates, 64

Crown Radiation, 82–83

cryptophytes, 63–64

diagram of evolution, 83

dinoflagellates, 64

domain, 60–61

eukaryote root, 69

eukaryotic rRNA diversification, 84

evolutionary structure, 82–83

excavates, 61–63

Foraminifera, 65–66

fungi, 68

new additions, 68–69

Opisthokonta, 68

Pelobionts and Entamoebae, 67

phylogenetic domain of life, 77–79

Plantae, 65

Radiolaria, 65–66

support for deep branches in eukaryote

tree, 61

universal tree, 78

Eucaryotes, 83, 97, 99. See also Eukaryotes

Eucaryotic phylogeny, 99–102

Eucestoda, tapeworms, 220

Euchordata, chordates, 388–389

Eucrustacea, crustacean clade, 326

Eudicots, 158–160

Euglenoids, 125, 127

Euglenophytes, plastids evolution, 123

Eukaryotes. See also Eucaryotes

definition, 60

derivation, 43

diversity, 60–61, 125–126

on the Tree of Life, 556

Opisthokonta, 199

photosynthesis, 121

root, 69

Eukaryote tree, support for deep branches, 61

Eukaryotic genomes, viruses and, 115

Eumetabola, insects, 340

Index 569

Eumetazoa, relationships, 200–201

Euphyllophytes, vascular plants, 139, 140–

141, 143

Eupnoi, Phalangida, 307

Euryalina, ophiuroids, 376–377

Euryarchaeota

Archaea, 14, 81–82

Archaeoglobus species, 57

Halobacteria, 57

methanogens, 57–58

Thermoplasmata, 58–59

Eutheria, definition, 494

Evolutionary biology

draft of human genome, 25

macro- and microevolutionary

approaches, 25–27

phylogenetic studies in, 29

phylogenies, 27–28

Evolutionary distance, inferring

phylogenetic trees, 77

Evolutionary processes, within species, 28–30

Evolutionary theory, 10–11, 95

Excavates, 61–63

Feather stars, See Crinoids

Fecampiida, flatworms, 216–217

Feet, Tetrapoda, 399–400

Ferns

life cycle, 140

phylogeny, 144

Ferroplasma, Euryarchaeota, 58–59

Fertilization, double, angiosperms, 154,

161–162

File snakes, 460–461

Fin folds, Craniata, 391

Firmicutes, gram-positive bacteria, 51–52

Flatworms, Platyhelminthes, 213

Flaviviridae, source and cause of spread, 116

Flavobacteria, Bacteroidetes, 48–49

Fleas, Siphonaptera, 356

Flies, Diptera, 356–358

Floral genes, flowering plants, 162–163

Florideophycidae, red algae, 122, 124

Florideophytes, Plantae, 65

Flowering plants. See also Angiosperms;

Land plants; Vascular plants

Foraminifera, 65–66

Frogs

alternative phylogenies, 439

amphibians, 437–438

Anura and Salientia, 438–439

atrazine, 22

basal, 439–440

discoglossoids, 439–440

fossils, 438–439

Hyloidea, 441–442, 443

Neobatrachia, 441

Pipanura, 440–441

Ranoidea, 442, 444

Function, second antenna of crustaceans, 326

Fungi

Ascomycota, 172–178

Basidiomycota, 178–181

Chytridiomycota, 171, 184–187

fossils, 187–189

geologic time, 187–189

hyphae, 171

life histories, 172

on the Tree of Life, 557

Opisthokonta, 68

origins of major groups, 187–189

phylogenetic tree, 172, 173

reproduction, 172

symbioses, 171

Zygomycota, 182–183

Fьrbringer, birds, 468–469

Fusobacteria, 54

Galeomorphi, elasmobranchs, 412, 413

Galloanserae, phylogenetic relationships,

474–475

Gametophytes, 133, 139, 140

Gastropoda, 268–270

Gastrotricha, 211–212

Gekkotan lizards, scleroglossans, 457

Gene expression, bacteria, 45

Genes

chordates, 403

deep phylogeny, 77

encoding 3-hydroxy-3-methylglutaryl

coenzyme A reductase, 92

exchange, 93

floral, 162–163

mitochondrial origin, 97

phylogenies, 87–89

Gene therapy, animal viruses, 116

Genetic diversity, life, 79

Genetic engineering, polymerase chain

reaction (PCR), 19–20

Gene trees, 28–30, 87

Genome evolution, model, 94

Genomes

bacteria, 44–45

dinoflagellate plastid, 127

identification, impact, 541

parallel sequencing, 541

phylogenies, 87–88

plastids, 121

tree of, 93

Genomic diversity, 89–90

Genomic mapping, ultrafast, 541

Genomics

knowledge base, 8

tomatoes, 19

tree assembly, 7

Genomics databases, Tree of Life, 15

Genomic sequencing

Archaea, 59–60

infectious disease, 21

Genostomatidae, flatworms, 216–217

Geography, species diversity, 33

Ghost lineage

assumptions, 504–505

concept, 504

Placentalia, 504–509

Gill anatomy, hemichordates and

echinoderms, 367

Gills, Mollusca, 254–255

Ginkgophytes, spermatophytes, 145

Glaucocystophytes, 122

Glaucophytes, Plantae, 65

Glires

character data vs. clock estimates, 510

mammal phylogeny, 498

tree of relationships, 499

Global all-taxon biological inventory, 541–542

Global biodiversity mapping, 541, 542

Global rock bias, 510–511

Glomales, Zygomycota, 182–183

Glossata, lepidopterans, 353

Glossiphoniidae, 241, 242

Glossopterids, pteridosperms, 147

Glyceridae, polychaete group, 245

Gnathostomata

Acanthomorpha and “bush at the top,”

419–421

Actinopterygii, 416–417

appendages, 394

characterization, 410

characters, 393–394

Chondrichthyes, 410–412

chordates, 393–395

coelacanths, 415

genetic complexity, 393

Holocephalans, 415

living actinopterygian diversity, 416–417

lungfishes, 415

Osteichthyes, 415

Pan-Gnathostomata, 394–395

Percomorpha and “bush at the top,” 421–

423

relationships of extant lineages, 411

Sarcopterygii, 415

teleostean basal relationships, 417–419

Teleostei, 417

Gnathostomulida, 211

Gnetophyta, spermatophytes, 145

Gnetophyte hypothesis, vascular plants,

147, 148

Gorilla, great apes, 517, 518–519

Graminoids, monocots, 157

Gram-positive bacteria, phylogeny, 52

Greater Antilles, adaptive radiations, 34

Green algae

charophytes, 130

colonization of land, 130–132

diversity, 127–130

insertion, 100

orders, 131

paraphyly, 549, 551

570 Index

Green algae (continued)

phylogenetic relationships, 129

phylogeny, 128, 550

secondary plastids from, 127

streptophytes, 130–131, 549

terrestrial, 132–134

Green nonsulfur bacteria, 46–48

Green plants

phylogenetic relationships, 129, 549, 556

phylogenetic tree, 172, 550

transition to land, 551

Green sulfur bacteria, 49

Gunnerales, eudicots, 159

Gymnophiona, caecilians, 434, 435

Gymnosperm hypothesis, vascular plants,

147, 148

Gymnosperms, 145, 148

Gyrocotylidea, 219, 221

Haeckel, Ernest

father of phylogenetics, 468

phylogenetic tree, 1, 3

universal Tree of Life, 95

Haemadipsids, leeches, 241

Hagfish, Myxini, 392

Hair, chordates with, 402–403

Halobacteria, 22, 57

Hands, Tetrapoda, 399–400

Hangingflies, Metacoptera, 355–356

Hantaviruses, 9, 10

Haptophytes

chromalveolates, 63

plastids, 123, 125–126

Heart, Craniata, 391

Heart urchins, echinoids, 378

Heavy metals, plants for removal, 22

Helcionelloidea, Monoplacophora, 264

Heliozoa, eukaryotes, 68–69

Hemichordates

classification and phylogeny, 369

description, 368

deuterostome relationships, 365–367

enteropneusts, 368

phylogenetic relationships, 369, 374

pterobranchs, 368–369

representative ambulacrarian taxa, 366

Hennig, Willi

avian systematics, 469

cladistic method, 95

comparing characters of organisms, 553

Dicondylia name, 335

Diptera, 330

father of modern phylogenetics, 346

phylogenetic argumentation scheme, 3

phylogenetic relationships, 347, 552

Phylogenetic Systematics, 1

Stammbaumentwurf, 333

systematic ichthyology, 423

Hennigian approach, eucaryotic phylogeny,

100–101

Hepatitis viruses, classification, 108

Herpetosiphon, green nonsulfur (GNS)

bacteria, 47, 48

Heterokonts, 123, 125–126

Heterotachy, long-branch attraction (LBA)

artifacts, 98

Hexapoda, 282, 290, 330

Higher land birds, phylogenetic

relationships, 477, 479–480

Hirudo medicinalis, medicinal leech, 241

Historical demography, Oporornis tolmiei,

29, 30

Holocephalans, chimaeras, 415

Holometabola

Coleoptera, 349–351

defining characteristic, 345

Diptera, 356–358

evolutionary history, 345, 359

future prospects, 358–359

Hymenoptera, 352

insects, 340

interordinal phylogeny, 346–349

Lepidoptera, 352–354

lineages, 345–346

main divisions, 346

Mecoptera, 355–356

Neuropterida, 351–352

orders and common names, 346

phylogenetic hypotheses of relationships,

347

Siphonaptera, 356

sister-group relationships, 347–348

species, 345

Strepsiptera, 349, 358

superordinal groups in insect phylogeny,

348

Trichoptera, 354–355

Holothurians

echinoderm relationships, 372, 376

fossils, 376

morphological and molecular

phylogenies, 378

nerve arrangement, 371

phylogenetic relationships, 374

Holothyrans, 301

Hominini, hominins, modern humans, 517

Hominins. See also Human origins

alternate taxonomies, 521

Ardipithecus ramidus, 521–522

Australopithecus afarensis, 525

Australopithecus africanus, 523–524

Australopithecus anamensis, 525–526

Australopithecus bahrelghazali, 525

Australopithecus garhi, 526

Homo clade, 526–531

Homo antecessor, 531

Homo erectus, 528–529

Homo ergaster, 530–531

Homo habilis, 530

Homo heidelbergensis, 529–530

Homo neanderthalensis, 527–528

Homo rudolfensis, 531

Homo sapiens, 526–527

human fossil record, 520

Kenyanthropus platyops, 526

modern terminology, 517–518

Orrorin tugenensis, 522–523

Paranthropus aethiopicus, 524–525

Paranthropus boisei, 524

Paranthropus robustus, 524

phylogeny, 531–532

primitive, 521–523

proposed taxonomy, 522

Sahelanthropus tchadensis, 523

Homo sapiens, 517, 526–527

Horizontal gene transfer, DNA viruses, 115

Hormonal glands, chordates, 387–388

Hornworts, 129, 133, 134

Horsehair worms, Nematomorpha, 227–228

Horsetails, phylogeny, 144

Hox genes, 365, 370

Human gene tree, major histocompatibility

complex (MHC), 28

Human genome, 19, 25

Human health

infectious diseases, 21–23

viruses, 8–9, 115–116

Human immunodeficiency viruses (HIV),

115, 116

Human land use, rodents and arenaviruses,

12–13

Human origins. See also Hominins

alternate hominin taxonomies, 521

ancestral differences, 519–520

australopiths, 523–526

close relatives, 518–519

hominin in fossil record, 520

hominin or panin lineage, 520

Homo clade, 526–531

Homo sapiens, 517, 526–527

phylogeny of hominin, 531–532

primitive hominins, 521–523

scale, 518

singularities, 517

taxonomy of living higher primates, 518

terminology, 517–518

traditional “premolecular” taxonomy,

518

Human pathogens, microorganisms, 20

Hummingbirds, phylogenetic relationships,

476–477

Huxley, Thomas Henry, avian classification,

468

3-Hydroxy-3-methylglutaryl coenzyme A

reductase

BLAST analyses, 90–91

phylogeny of genes encoding, 92

Hylidae, node name, 442

Hyloidea, neobatrachians, 441–443

Hymenoptera, holometabolous insects, 352

Index 571

Hyperthermophiles, bacteria, 46

Hyphae, 171, 173

Ichthyology, systematic, Hennig, 423

Immune system, Gnathostomata, 394

Immunodeficiency viruses, phylogeny, 116

Indels, character as phylogenetic marker, 101

Infectious diseases, 20–21, 51, 116

Information processing, eukaryotes, 60

Insects

Acercaria, 338–339

basal phylogenetic relationships, 335

characters, 340–341

cladograms, 334, 340

classifications, 330–331

Dicondylia, 334–335

Ectognatha, 334

Eumetabola, 340

evolution, 332, 334

fossils, 330

Hexapoda vs. Insecta, 330

hypotheses of relationships, 333

morphological evidence, 340–341

Neoptera, 336

number of species, 330

origin and sister group, 331–332

phylogeny, 332, 334

Polyneoptera, 336–338

Pterygota, 335–336

relationships among Polyneoptera, 337

superordinal groups in phylogeny, 348

Zoraptera, 339–340

Interdisciplinary research, Tree of Life, 15

Internal skeleton, Craniata, 390

International Committee on Taxonomy of

Viruses, 107

International effort, tree construction, 15

Jakobids, mitochondriate excavates, 62–63

Jaws, chordates with, 393–395

Jaw worms, Gnathostomulida, 211

Kenyanthropus platyops, australopith, 526

Kinorhyncha, species, 228

Korarchaeota, Archaea, 14, 59, 81–82

Labiata hypothesis, insects, 332

Lacewings, Neuropterida, 351–352

Lamellibranchs, Bivalvia, 265–267

Lampreys, Petromyzontida, 393

Lancelets, Cephalochordata, 389–390

Land birds, phylogenetic relationships, 477,

479–480

Land colonization, green algae, 130–132

Land plants. See also Angiosperms; Vascular

plants

differences in nonvascular and vascular,

139, 140

embryophytes, 121

phylogenetic tree, 172

phylogeny, 11, 550

terrestrial green algae, 132–134

tracheophytes, 133–134

Large subunit (LSU), ribosomes, 43

Larval stages, Mollusca, 257

Last universal common ancestor (LUCA),

96–97

Lateral gene transfer

frequent trading, 44

how much exchange, 90–91, 93

3-hydroxy-3-methylglutaryl coenzyme A

reductase, 92

phylogenetic relationships, 93

superbugs, drugs, and, 88–89

Thermoplasma acidophilum, 58

universal tree challenge, 96

Lateral line, Amniota, 401

Latino virus (LAT), Bolivia, 12

Leaf beetles, 28, 34

Lecithoepitheliata, flatworms, 214, 215

Leeches

annelid group, 237, 238

Clitellata, 240–244

description, 239

microsurgical importance, 242

morphological and molecular data, 240

phylogenetic relationships, 244

terrestrial, 241–242

Leeching, 241

Lentiviridae, phylogeny, 116

Lepidoptera, 352–354

Lepidosaurs, 455–456

Lesser Antilles, species sorting, 34

Lignophytes, vascular plants, 145, 147–148

Limbed marine snakes, 459–460

Limbs, Tetrapoda, 399

Lipids, Archaea, 55

Lissamphibia-, 431

Lithophora, 215

Liverworts, 129, 133, 134

Lizards

lepidosaurs, 456

Reptilia, 401–402

squamates, 456–458

Lobefin fishes, Sarcopterygii, 415

Lobe fins, chordates with, 397–398

Lobosa, Amoebozoa, 66–68

Locomotion, Choanata, 398

Long-branch attraction, 98, 99

Longhorn beetles, invasive species, 12

Long-terminal-repeat retrotransposons,

112

Lophotrochozoa

bilaterians, 201, 202

on the Tree of Life, 557

Protostomia, 209

Loricifera, species, 228

Lungfishes, 398–399, 415

Lungs, chordates with, 396

Lycophytes, vascular plants, 139–140, 142

MacGillivray’s warbler, historical

demography, 29, 30

Machupo virus (MACV), Bolivia, 12–13

Macroevolution, 25–27

Macrolepidoptera, species, 354

Macrostomorpha, phylogenetic analyses,

214

Magnoliids, 157–158

Major histocompatibility complex (MHC),

tree for human genes, 28

Mammalia

characteristics, 490

characters, 402–403, 495–496

classification, 491, 494–495

data partitioning, 496

generic-level extinction within, 492, 493

in the Tree of Life, 511

Marsupialia, 491, 494

Monotremata, 491, 494

Placentalia, 491, 494

phylogenetics, 490–491, 495

rates for different genes, 506

supermatrices of extinct or extant taxa,

497

supertrees and supermatrices, 496, 503–

504

tribospheny, 498

tripartite division, 491, 494

Mammaliaformes, 494, 497–498

Mammal phylogeny

agreement subtree for extinct + extant

whale supermatrix, 503

assumptions of ghost lineage analysis,

504–505

Cetacea, 498–501

clock model calibration, 504–506

divergence times for Placentalia, 506–510

extant whale-artiodactylan supermatrix,

501–502

extinct + extant whale supermatrix, 502

Glires, 498, 510

heterogeneity in rates for different genes,

506

molecular clock analyses, 504–506

Mammals. See Mammalia

Mandibulata, 284, 286

Marsupialia

divergence time, 508

mammal clade, 491, 494

split between, and Placentalia, 509

Membrane lipids, Archaea, 55

Mesotheles, spiders, 302

Metabolic capacity, Craniata, 391

Metabolic pathways, 14

Metacoptera, holometabolous insects, 355–

356

Metatheria, definition, 494

Metazoan phylogeny, Ambulacraria, 378–

380

Metazoans, 198, 199–200

572 Index

Methanogens, Euryarchaeota, 57–58

Microalgae, diatoms, 126

Microbial world, 79

Microevolution, emergence of synthesis, 25–

27

Microorganisms, 22, 540

Microsurgery, leeches, 242

Middle ear, Mammalia, 402

Mites, 299–301

Mitochondria, 78–79, 88

Mitochondrial gene order, echinoderms,

373, 375

Mitochondriate excavates, 62–63

Modern humans. See Human origins

Molecular clock

calibration, 505–506

divergences, 510

Molecular data

angiosperms, 157

anthropods, 290

avian systematics, 469–470

combined analysis of insects, 334

crustaceans, 320–322

echinoderm classes, 372–373

hemichordates, 369

ophiuroids, 377–378

phylogenetic analysis for arthropods, 287,

289

turtles, 454

Molecular phylogeny

models, 87–88

phylogenetic trees, 76–77

sequencing data, 86–88

slow-fast (SF) method, 98–99

substitutions, 97–98

Zygomycota, 183

Molecular sequencing, crustaceans, 323

Mollusca

annelids and, 253

characters, 254–257

developments, 257, 272–274

diversity, 257, 258

feeding types in major clades, 260

fossil history, 252, 258

future, 272–274

habitats and habits, 252, 258–260

major groups, 252–253

morphological features, 252

outline of major groups, 260–261

phylogenetic relationships, 254, 257, 557

phylogenetic scenarios and hypotheses, 253

plesiomorphic character states, 256

possible mollusks, 261–262

problems remaining, 272–274

publications, 273–274

research effort on major living taxa, 273

respiration and ventilation, 254–255

sister taxa, 261

spiralian taxon, 253–254

Tree of Life branch, 260–261

Molluscan taxa, higher

Aplacophora, 263–264

Bivalvia, 265–267

Cephalopoda, 271–272

Gastropoda, 268–270

Monoplacophora, 264

Polyplacophora, 262–263

Rostroconchia, 267–268

Scaphopoda, 265

Monilophytes, vascular plants, 141–143,

144

Monocots, angiosperms, 157

Monogenea, flatworms, 218, 219

Monoplacophora, description, 264

Monotremata, mammal clade, 491, 494

Morphology

Acanthobdella and branchiobdellidans,

243

Aplacophora, 263

Bivalvia, 265–267

Cephalopoda, 271

Chytridiomycota, 185

crustaceans, 319–320

echinoderm classes, 373

eumetazoans, 200–201

flowering plants, 162–163

Gastropoda, 268–269

hemichordates and echinoderms, 367

hypotheses of insect relationships, 333

insects, 340–341

Monoplacophora, 264

phylogenetic analysis for arthropods, 287,

288

Polyplacophora, 262

Scaphopoda, 265

second antenna of crustaceans, 326

spermatophyte diversity, 147

turtles, 454

Mosses, 133, 134, 140

Moths, Lepidoptera, 352–354

Motility, Bacteria, 44

Muscular systems, 391, 393

Myriapoda, 282–283, 285, 290

Myxini, chordates, 392–393

Myzostomida, species and morphology,

225

Nanoarchaeota, Archaea, 59

National Ecological Observation Network

(NEON), 23

National Science Foundation, Tree of Life,

18

Neanderthals, 527–528

Nematoda, 19, 209, 226–227

Nematoida, 228

Nematomorpha, 227–228

Nemertea, ribbonworms, 223–224

Neoaves

phylogenetic hypothesis, 478

relationships within, 473, 475

resolving relationships, 472–473

uncertainty, 483

Neobatrachia, frogs, 441

Neocortex, Mammalia, 402

Neodermata, 217, 218

Neomeniomorpha, Aplacophora, 263–264

Neoptera, relationships, 336

Neornithes. See also Birds

basal relationships of modern birds, 473

birds and dinosaurs, 470

challenge, 484–485

conceptual roadblocks, 485

cuculiforms, coraciiforms, and piciforms,

479

current status, 482–484

DNA hybridization, 470–472

future, 484

Galloanserae, 474–475

hypothesis for avian higher level

relationships, 483

Palaeognathae, 473–474

Passeriformes, 480–482

phylogenetic relationships, 475–480, 482

phylogenetic tree, 474

resolving avian relationships, 472–473

systematics, 468

tapestry, 470–472

Nephroposticophora, worms, 220

Nervous system, Mollusca, 255, 257

Neural crest, Craniata, 390–391

Neuropterida, holometabolous insects, 351–

352

Nightjars, phylogenetic relationships, 476–

477

Nitrospira, bacteria, 54

Nonvascular plants, morphology and life

cycle, 139, 140

North American birds, speciation, 30

Notochord, chordates, 386–387

Nuclear dualism, term, 64

Nuclear phylogeny, algae, 121

Nuclear small subunit (nSSU) ribosomal

DNA (rDNA), 171, 172

Olfactory system, Mammalia, 402–403

Oligochaetes, 237–239

Ontogeny, chordates, 384–385, 404

Oomycetes, 63, 126

Ophiurina, 377

Ophiuroids, 371–372, 374, 376–378

Ophraella, 28, 31–32

Opiliones, harvestmen, 306–308

Opisthokonta, 68, 100, 199

Oporornis tolmiei, historical demography, 29,

30

Orangutan, 517, 518–519

Organismal, genome, and gene phylogenies,

87

Origin of Species, 2, 94

Orrorin tugenensis, hominin, 522–523

Index 573

Orsten, crustaceans, 323, 324, 325

Orthogastropoda, Gastropoda, 270

Osteichthyes, 396, 415

Owls, phylogenetic relationships, 476–477

Paddlefishes, Actinopterygii, 416

Palaeognathae, phylogenetic relationships,

473–474

Palaeoptera hypothesis, 335

Palola viridis, delicacy, 244

Palpatores, paraphyly, 307

Palpigrades, micro-whip scorpions, 302

Pan, great ape, 517, 518–519

Pan-, definition, 386

Pan-Actinistia, 398

Pan-Actinopterygii, 397

Pan-Amniota, 401

Pan-Amphibia, 400

Pan-Cephalochordata, 389–390

Pan-Choanata, 398

Pan-Chondrichthyes, 395–396

Pan-Chordata, 388

Pan-Craniata, 391–392

Pancrustacea, crustacean-containing clade,

326

Pan-Dipnoi, 399

Pan-Euchordata, 389

Pan-Gnathostomata, 394–395

Panin, lineage, 520

Pan-Mammalia, 403

Pan-Myxini, 392

Pan-Osteichthyes, 396

Pan-Petromyzontida, 393

Pan-Reptilia, 401–402

Pan-Sarcopterygii, 397–398

Pan-Urochordata, 388

Pan-Vertebrata, 393

Paranthropus aethiopicus, 524–525

Paranthropus boisei, 524

Paranthropus robustus, 524

Paraphyly, 549, 560

Parareptiles, 453

Partitioning data, 496

Passerida, Passeriformes, 480–482

Pathogenicity islands, genes, 89

Pedomorphosis, amphibians, 431

Pelecypoda, Bivalvia, 265–267

Pelobatoidea, 440, 441

Pelobionts, Amoebozoa, 67

Pelodytidae, definition, 441

Penicillium, domestication, 172

Perching birds, phylogenetic relationships,

480–482

Percomorpha

Acanthomorpha, 419

“bush at the top,” 421–423

Teleostei, 417

Perianth, sepals and petals, 162–163

Petals, flower, 162–163

Petromyzontida, chordates, 393

Pharyngeal arch, Craniata, 391

Pharyngeal skeleton, Choanata, 398

Photodegradation, plastids, 125

Photosynthesis

cyanobacteria, 45, 51

eukaryotes, 121

green sulfur bacteria, 49

vascular plants, 138

Phractamphibia-, 431

Phycoplast, cell division, 130

PhyloCode, 551

Phylogenetic analyses

biological control, 14

conservation planning, 10–11

evolutionary biology and ecology, 29

hantaviruses, 9

invasive species, 12

major developments, 2

operating procedure, 546

supermatrices of extinct or extant taxa,

497

vicariance biogeography, 33

Phylogenetic methods, 28–30

Phylogenetic publications, 545–546

Phylogenetic relationships

comparative analysis, 553–554

corn to wild relatives, 12

definition, 1

discoveries of paraphyly, 549

gene transfers, 93

methods for inference, 77

Zimmermann, Walter, 1, 3

Phylogenetic systematics, tree assembly, 7

Phylogenetic Systematics, Hennig, 1

Phylogenetic theory, 1, 346

Phylogenetic trees

among-sites rate variation, 101

Haeckel, Ernest, 3

molecular phylogeny, 76–77

time and Tree of Life, 83–84

Phylogeny

analysis of papers, 545–546

diversity, 32–33

evolutionary biology, 27–28

impact of molecular, 95

in textbooks, 26

molecular, 76–77, 86–88

organismal, genome, and gene

relationships, 87

publications, 26, 545–546

Phylogeography, intraspecific phylogeny,

28–29

Phyloinformatics, 445, 559

Phylotyping, gene sequencing, 90

Piciformes, phylogenetic relationships, 477,

479–480

Picrophilus, Euryarchaeota, 58–59

Pigmentation, haptophytes, 126

Pipanura, frogs, 440–441

Pipidae, definition, 441

Pipoidea, definition, 441

Placentalia

calculating age using ghost lineages, 506,

510

character sampling, 509

divergence times, 506–510

ghost lineage concept, 504

mammal clade, 491, 494

Planctomycetes, bacteria, 48, 99

Plantae, 65

Plant evolution, vascular, 148–149

Plants, 171, 556 (see also Angiosperms;

Land plants; Vascular plants)

Plastids

dinoflagellates and apicomplexans, 126–127

genomes, 121

glaucocystophytes, 122

hypothesis for endosymbiotic events in

evolution, 123

origins of primary, 124–125

secondary from red algae, 125–126

Platyhelminthes, 209, 213, 214

Poliovirus, phylogenetic analysis, 20

Polychaetes

anatomical diversity, 246

annelid group, 237, 238

cladistic analyses, 247

delicacy Palola viridis, 244

description, 239

families and groups, 245

morphological and molecular data, 240

paraphyletic taxa, 246–247

systematics, 245–246

Polycladida, flatworms, 214

Polymerase chain reaction (PCR)

genetic engineering, 19–20

phylogenetic analysis, 545

sequencing small subunit rRNA, 44

technology, 13–14

Polyneoptera, 336–338

Polyplacophora, 262–263

Polysporangiophytes, 141

Pongo, great apes, 517, 518–519

Population genetic model, quasi-species

concept, 108

Population genetic theory, phylogenetic

methods, 28

Populations, estimating historical, 28

Population thinking, systematics, 469

Priapulida, worms, 228

Primary endosymbiosis, evolution of

plastids, 123

Primates, relatives, 518–519 (see also

Human origins)

Primitive hominins

Ardipithecus ramidus, 521–522

Orrorin tugenensis, 522–523

Sahelanthropus tchadensis, 523

Primitive reptiles, 453

Primordial hypothesis, 110, 111

574 Index

Progymnosperms, 145, 146

Prokaryotes, 20, 43, 95–96

Prolecithophora, interrelationships, 216

Proseriata, marine worms, 215

Proteobacteria, 52–53, 78

Protostomia, 201–202, 209, 210

Prototheria, definition, 494

Pseudoscorpions, 310–312

Pteridosperms, 146, 147

Pterobranchs, hemichordates, 368–369

Pterosaurs, archosaurs, 462–463

Pterygota, insects, 335–336

Public health, 13, 115–116

Publications, phylogenetic, 545–546

Purple bacteria, Proteobacteria, 52–53

Pythons, snakes, 460

Raccoons, relationship to skunk and weasel,

8

Radiolaria, 65–66

Ranoidea, neobatrachians, 441, 442, 444

Rayfin fishes, Actinopterygii, 396–397, 416

Rays

Chondrichthyes, 395–396, 410–412

elasmobranchs, 412–415

Recombination, viral lineages, 116

Reconstruction artifacts, 97–98, 100

Red algae, 121, 122–126

Regressive hypothesis, virus origins, 111

Relative apparent synapomorphy analysis

(RASA), 99

Replicated sister-group, comparison

method, 32–33

Reptiles

alethinophidians, 460

amniotes, 451

archosaurs, 461–463

barometer for systematics, 463–464

birds, 463

boas and pythons, 460

bolyeriines, 460

Colubroidea, 461

crocodilians, 462

details of analyses, 464

diapsids, 455–456

dinosaurs, 463

file snakes, 460–461

lepidosaurs, 456

macrostomatans, 460

ornithodirans, 462–463

parareptiles and other primitive, 453

pterosaurs, 462–463

relationships and temporal duration, 452

relationships between extant, 453

relationships between fossil and living

archosauromorphs, 462

simultaneous analysis approach, 464

snakes, 458–461

squamates, 456–458

theropod-bird transition, 463

total evidence approach, 464

turtles, 453–455

vipers, 461

Xenopeltidae, 460

Reptilia, 401–402, 451, 452

Reverse-transcribing, DNA-RNA viruses,

109, 112–114

Reverse transcriptase, 110, 115

Revertospermata, flatworms, 216–217

Rhabditophora, diversity, 213–214

Rhabdocoela, 216, 217

Ribbonworms, Nemertea, 223–224

Ribonucleic acid (RNA)

classification for viruses, 108

Picorna-like supergroup, 112, 113

polymerases, 54

single- and double-strand RNA viruses,

109–110

viruses, 111–112

Ribosomal RNA (rRNA)

bacterial phylogeny, 98–99

construction of universal, 95

universal Tree of Life based on, 97

Ribosomal RNA (rRNA) tree

bacterial portion of tree, 96–97

impact of long-branch attraction (LBA),

99

last universal common ancestor (LUCA),

96–97

relative apparent synapomorphy analysis

(RASA), 99

Ribosomes, 43, 91

Ricinuleids, arachnida, 301–302

Rosids, eudicots, 159–160

Rostroconchia, description, 267–268

Rotifera, Syndermata, 224–225

Roundworms, Nematoda, 226–227

Sabin oral vaccine, poliovirus, 20

Sahelanthropus tchadensis, hominin, 523

St. Louis encephalitis virus, human health, 9

Salamanders, 436–437

Salientia, frogs, 438–439

Santalales, eudicots, 159

Saprophytic islands, 89

Saprotrophy, Basidiomycota, 179, 180

Sarcopterygii

characters, 397

chordates, 397–398

lobefin fishes and tetrapods, 415

Sawfishes, batoids, 414

Sawflies, Hymenoptera, 352

Saxifragales, eudicots, 160

Scalidophora, 228

Scaphopoda, description, 265

Schizogamous epitoky, palolo worm, 245

Schizomids, arachnids, 306

Schizoramia, 286

Scorpionflies, Metacoptera, 355–356

Scorpions

palpigrades, 302

pseudoscorpions, 310–312

Scorpiones, 308–310

whip, 305–306

Sea cucumbers. See Holothurians

Sea lilies. See Crinoids

Sea slugs, plastid retention, 125

Sea squirts, chordates, 388

Sea urchins. See Echinoids

Second antenna, morphology and function,

326

Secondary endosymbiosis, 123, 125

Secondary plastid, 127

Seed, definition, 146

Seed ferns, term, 147

Seed plants, phylogeny, 146, 550

Segmentation, 237, 238, 389

Selection, antibiotic resistance, 88

Senses

amphibians, 431

Euchordata, 389

Gnathostomata, 393–394

Vertebrata, 392–393

Sensory organs, Craniata, 390

Sensory organs of head, chordates, 387

Sepals, flower, 162–163

Sexual selection, evolutionary processes, 29–

30

Sharks

Chondrichthyes, 395–396, 410–412

elasmobranchs, 412–415

Shell, turtles, 453

Shell morphology, Mollusca, 260

Shikimate pathway, metabolic, 14

Shotgunning method, genomics, 541

Silicea, sponges, 200

Single-strand DNA viruses, recognized

families, 109

Single-strand RNA viruses, 109–110

Sin Nombre virus (SNV), human health, 8–9

Siphonaptera, holometabolous insects, 356

Skeleton

Amniota, 401

Craniata, 390

Gnathostomata, 394

Osteichthyes, 396

Skippers, Lepidoptera, 352–354

Skull

Gnathostomata, 394

Tetrapoda, 399

turtles, 453

Skunk, relationship to raccoon and weasel, 8

Slime molds, Mycetozoa, 67

Slow-fast (SF) method, 98–99

Small subunit (SSU)

ribosomes, 43

rRNA data, 43–44

Index 575

SSU rRNA as universal molecular

chronometer, 87, 91

Small subunit (SSU) rRNA sequences, 77–

79, 81

Snakeflies, Neuropterida, 351–352

Snakes

adaptations for predation, 458–459

lepidosaurs, 456

macrostomatans, 460

modern snakes, 458–461

relationships, 459

squamates, 456–458

Software, challenges, 8

Solar-powered sea slugs, plastids, 125

Solenogastres, Aplacophora, 263–264

Solifugae, camel spiders, 312

Somatic metamerism, segmentation, 237

Speciation, 28, 30–31

Species, 28–30, 540

Spermatophyte, diversity, 147

Spiders, 302, 304–305, 312

Spirochaetes, bacteria, 50

Sponges, monophyly, 200

Sporomusa, bacteria, 52

Squalomorphi, elasmobranchs, 412, 413–

414

Squamates

details of analyses, 464

lizards and snakes, 456–458

relationships, 457

Stable core, 87, 91–92

Stammbaumentwurf, Hennig, 333

Starfishes. See Asteroids

Statistician approach, eucaryotic phylogeny,

100

Stingrays, batoids, 414–415

Stramenopiles, 63, 125–126

Strepsiptera, 349, 358

Strigiformes, phylogenetic relationships,

476–477

Substitutions, molecular phylogeny, 97–98,

99

Sulfolobales, Crenarchaeote, 56, 57

Sunflowers, Chernobyl cleanup, 22

Superbugs, 88–89

Supermatrices

extant whale-artiodactylan, 501, 504

extinct + extant whale, 500, 502

mammals, 503

morphology, 496

whales, 498–503

Superordinal groups, insect phylogeny, 348

Supertrees, 496, 503

Swarming, annelids, 245

Swifts, phylogenetic relationships, 476–477

Symbiosis islands, 89

Sympatric speciation, allopatric and, 30–31

Syndermata, rotifers and thorny-headed

worms, 224–225

Systematics

discovery of species, 540

in biology, 539

methods and approaches, 543–544

redefinition, 469

reptiles as barometer, 463–464

study of spiders, 540–541

Tree of Life, 542

Tadpoles, atrazine, 22

Tadpole-shaped larva, chordates, 388

Tangled bank, Darwin, 18–19

Tapestry, DNA hybridization, 470–472

Taxonomic names

changes, 551–552

nomenclatural systems, 539, 551

Taxonomy, 518, 521–522, 551–552

Taxon sampling, crown placentals, 509

Teeth with enamel, Sarcopterygii, 397

Teleostei, relationships, 417–419, 420

Tergomya, Monoplacophora, 264

Terrestrial chordates, 400–401

Tertiary endosymbiosis, evolution of

plastids, 123

Tetraconata

arthropod relationships, 285

hypothesis, 284

sensitivity plots, 290

Tracheata vs., 286–287

Tetrapoda, 399–400, 415

Tetrapodous locomotion, Choanata, 398

Tetrapods, amphibians and origin of, 432–

433

Theria, mammal crown clade, 494, 510

Thermococci, Archaea, 58

Thermoplasma acidophilum, lateral gene

transfer, 58

Thermoplasmata, Euryarchaeota, 58–59

Thermoproteales, Crenarchaeota, 56, 57

Thermotogae, hyperthermophiles, 46

Thorny-headed worms, Syndermata, 224–

225

Thread worms, Nematoda, 226–227

Ticks, 299–301

Tiger mosquito, 20–21

Time-reversible model, among-site rate

variation, 98

Tomatoes, genome, 19

Tracheata, 284, 286–287, 290

Tracheophytes, 133, 134, 140, 551

Tree

deep branches of bacterial, 47

international effort for construction, 15

reconstruction artifacts, 97–98

TreeBASE, 548, 551

Tree of Life

agriculture, 11–12

applications, 546, 554

assembling talent, 18

benefits, 15

challenges, 7, 484–485

conservation, 9–11

construction of universal, 95

DNA sequencing, 543–544

economics, 13–14

enabling technology and challenges, 7–8

evolutionary theory, 10–11

excluding viruses from discussion, 108,

110

genetics, 543–544

human health, 8–9

human land use, 12–13

infectious diseases, 21

integration of viruses and, 107, 114–115

interdisciplinary fields, 15

invasive species, 12

major groups of organisms, 554

ongoing synthesis, 554

perspectives, 559

phylogenic relationships, 552

position of root, 44

practical outcomes, 554

progress against paraphyly, 560

shape, 20

small subunit rRNAs defining, 44

summary tree, 560

systematics, 542

time and, 83–84

universal, 93

value, 4

Tree thinking, 3, 469

Trematoda, flukes, 220, 222

Tribospheny, term, 498

Trichoptera, holometabolous insects, 354–

355

Tricladida, 215–216

Triconodonts, 497–498

Trimerophytes

lignophyte precursor, 145

phylogeny, 143, 146

vascular plants, 140–141

Trochozoa, 202, 239

Trogoniformes, phylogenetic relationships,

477, 479–480

Tryblidia, Monoplacophora, 264

Tuataras, lepidosaurs, 456

Tunicates, chordates, 388

Turtles, 401–402

anatomical studies, 453–455

Ultrafast genomic mapping, 541

Ultrastructural approach, green algae, 128

Ultrastructural types, eukaryotes, 60

Ultrastructure, Chytridiomycota, 185–

186

Unguiphora, 215

Universal marker, ribosomal RNA (rRNA),

96

576 Index

Universal molecular chronometer, 87, 91

Universal Tree of Life

challenges, 96

Darwin, 93, 95

living species, 542

ribosomal RNA (rRNA), 97

root, 77–78, 95

simplified, 102

value for society, 7

Urastomidae, flatworms, 216–217

Urochordata, chordates, 388

Uropygi, whip scorpions, 305–306

Uropygi–Schizomida doublet, arachnids,

298

Vaccine development, viruses, 116

Vascular plants. See also Angiosperms; Land

plants

anthophyte hypothesis, 147, 148

associations with fungi, 138–139

bryophyte and tracheophyte life cycles,

140

carboniferous, 138

euphyllophytes, 139, 140–141, 143

extinctions, 149

fossils, 148–149

gnetophyte hypothesis, 147, 148

gnetophytes and conifers, 147–148

gymnosperm hypothesis, 147, 148

hypotheses of relationships among extant

lineages of seed plants, 147

land plant lineages, 139

lignophytes, 145, 147–148

lycophytes, 139–140

monilophytes, 141–143

morphology and life cycle, 139, 140

photosynthesis, 138

phylogeny, 141, 146, 148–149, 550

radiation and climate change, 138

rhyniophytes, 139

trimerophytes, 140–141, 143

zosterophytes, 139–140

Verrucomicrobia, 53

Vertebrata

chordates, 392–393

genetic complexity, 392

on the Tree of Life, 558–559

Vertebrates, estimates, 540

Vipers, snakes, 461

Viruses

challenges, 116

classes and recognized families, 109–110

common features, 108

description, 107, 108

DNA, 109, 114

double RNA, 109

escaped transcript hypothesis, 110–111

eukaryotic genomes, 115

evolution, 114–115

evolutionary history, 116–117

exclusion from Tree of Life discussions,

108, 110

hepatitis, 108

hypotheses for origins, 111, 112

individual and public health, 115–116

integration of, and Tree of Life, 107, 114–

115

International Committee on Taxonomy of

Viruses, 107

management practices and virus

phylogeny, 116

origins, 110–111

phylogenetic hypothesis, 113

phylogenies, 111

primordial hypothesis, 110

regressive hypothesis, 111

reverse transcriptases and transition from

RNA to DNA, 115

RNA, 109–112

Single-strand DNA, 109

winning form and lifestyles, 107

Vomeronasal organ, Tetrapoda, 399

Wasps, Hymenoptera, 352

Waterbirds, 475–476, 477

Water lilies, fossil and modern, 156

Waterways, assessment, 22

Watson and Crick, DNA molecule, 519

Weasel, relationship to skunk and raccoon, 8

Web of Life, 1

West Nile virus, 9, 10, 116

phylogenetic analyses, 9

phylogenetic relationship to New York

strain, 10

Whales

extant whale-artiodactylan supermatrix,

501, 504

extinct + extant whale supermatrix, 500,

502

supermatrices, 500, 503

Whip scorpions, 305–306

Whip spiders, 305

Woese, Carl, 45, 77

World Health Organization (WHO), dengue

fever reemerging, 20

Worms

Acanthocephala, 224–225

Acoelomorpha, 210–211

Amphilinidea, 220, 221

Annelida, 237

arrow worms, 225–226

Aspidogastrea, 221

Catenulida, 213, 214

Cercomeromorphae, 217

Cestoda, 218–219

Chaetognatha, 225–226

Cycliophora, 225

Digenea, 221–223

Ecdysozoa, 226

Eucestoda, 220

Fecampiida, 216

Gastrotricha, 211–212

Genostomatidae, 216

Gnathostomulida, 211

Gyrocotylidea, 219, 221

horsehair, 227–228

Kinorhyncha, 228

Lecithoepitheliata, 215

Loricifera, 228

Macrostomorpha, 214

Monogenea, 218, 219

Myzostomida, 225

Nematoda, 226–227

Nematomorpha, 227–228

Nemertea, 223–224

Neodermata, 217, 218

Nephroposticophora, 220

Platyhelminthes, 213

Polycladida, 214

Priapulida, 228

Prolecithophora, 216

Proseriata, 215

Revertospermata, 216–217

Rhabditophora, 213–214

Rhabdocoela, 216, 217

ribbonworms, 223–224

Rotifera, 224–225

round, 226–227

Syndermata, 224–225

thorny–headed, 224–225

thread, 226–227

Trematoda, 220, 222

Tricladida, 215–216

Urastomidae, 216

Xenoturbellida, 213

Xenoturbellida, worm, 213

Yellow fever, 20–21

Zimmermann, Walter, phylogenetic

research, 1, 3

Zinc-rich waters, microorganisms, 22

Zoraptera, insects, 339–340

Zosterophytes, vascular plants, 139–140

Zygomycota

characteristics, 182–183

Dimargaritales, 182

Entomophthorales, 182

generalized life cycle, 183

Glomales, 182

life cycle, 182–183

molecular phylogenies, 183

Mucorales, 182

phylogenetic relationships, 183

reproduction, 172, 182

scanning electron micrographs, 184

Zoopagales, 182

Zygoptera, insects, 336

Zygopteridales, 149