Telling the Evolutionary Time: Molecular Clocks and the Fossil Record

assumptions 41–2
Bilateria origin dating 166–89
biotic signal 74–5, 76, 77
Cambrian explosion 41–8, 59
chordate origins 190–223
confidence intervals 52
Foraminifera 111–13
heterogeneity 74–7
land plants origin 124–33, 135, 136
mammalian/avian divergence 29–30
metazoans 31–2
Neornithes radiations 263–78
oldest 73–4
phylogenetic fuses 108, 111–13, 115
quality 66–90
tetrapods 224–62
see also ghost lineages/ranges
FreqRat 72, 79
frogs 225, 238–9
fungi, Snowball Earth events 28–37

Galliformes 267, 271–2, 273
Gallinuloides 272, 273
Galloanserae 270–3
gap analysis 69, 71, 196–7
gap excess ratio (GER) 81–2, 83, 199–200,
201, 202, 203, 204, 210
gastropods, ghost ranges 100
gene duplication 47–8
general time-reversible (GTR) model 55, 109
generation-time effect 6–7
Geon 5 167
ghost lineage durations (GLDs) 82
ghost lineages/ranges 81, 82, 83, 91–106, 197
chordate origins 197–9, 200, 203, 204,
206, 208
lissamphibians 245
globigerinids 110, 111
globins 6
Globorotalia
G. inflata 114
G. scitula 111
G. truncatulinoides 111, 113
globorotaliids 110, 111
glucose-6-phosphate dehydrogenase (G6pd) 7
glycerol-3-phosphate dehydrogenase (Gpdh) 7,
53

gnathostomes 191–2, 199, 207–9, 210–11

graptolites 97, 99, 102, 171

green algae 120

divergence times 135

transformation to land plants 122, 123

group sampling 72–3, 79

hagfishes 191, 195, 201, 206, 207, 210

Haikouella 193

Haikouichthys 207

halkieriids 178

hamamelids 143, 152

helcionellids 178

helicoplacoids 193

Hemichordata 180, 191, 193, 206

heterostracans 202, 203

hidden Markov models (HMM) 56

HKY85 model 55, 145

homoplasy 157, 236

Ichthyornis 265

Ichthyostega 42, 226, 228, 231

Illiciaceae 157

implied gap (IG) 82

independence, phylogenetics 79–80

index of dispersion 6

individual protein (IP) approach 48

invariant sites 56–7

jacknife support 160

Jukes-Cantor (JC69) model 54–5

Jurassic

angiosperm divergence 152, 157

Neornithes radiations 263

Kimberella 168

Lactoridaceae 155, 157

lag intervals 176, 177

Lamiales 155, 160

lampreys 191–2, 195, 201, 206, 207, 208, 210

law of large numbers 2, 7, 22

lepospondyls 225–6, 228, 236, 237–8

lignins 35

likelihood methods 52

Bayesian inference 57

Bilateria origins 170

292 INDEX

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