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INDEX
aardvarks 191, 192
abominable snowman, see Yeti
adaptive radiation 99–101, 143–5, 191–6, 200, 207, 208, 210–12
Africa 42, 83, 84, 129, 130, 166, 189, 191–3, 197–200, 203, 210, 215–16, 217
Afrotheria theory 190–3
agouti-signaling protein 53
AIDS (Acquired Immune Deficiency Syndrome), see HIV virus
algae 150–2
Allen’s rule 218
alligators 37, 80
altruism 134
amphibians
general 7, 42, 68–71, 79, 80, 137–40, 173, 209, 219, 220
taxonomic genus Allobates 70,
Colostethus 70,
Dendrobates 69, 73,
Epipedobates 70,
Ichthyophis 208, 209,
Nasikabatrachus 200,
Philautus 208, 209,
Phyllobates 69, 73,
Uraeotyphus 209
Amphioxus 174
Andes Mountains 72, 73, 190
annelids 140, 175
Antarctica 159–62, 191, 198
antelopes 117, 123, 191, 210
antifreeze proteins 159
ants 69, 70, 101–4, 134, 135, 200
apes 118
see also chimpanzees, gorillas
aphids 104, 134
aposematic coloration, see warning coloration
Appalachian Mountains 138
Archaea 178, 179
Arctic region 161–62, 213
area cladogram 198
Argentina 19, 74, 86, 129
Aristotle 1, 129, 223
armadillos 192, 193
arthropods 175
see also invertebrates
ascidians 174
asexuality 1
see also parthenogenesis
Asia 48, 79, 80, 99, 100, 129, 216, 217
auklets 80
Australia 42, 49, 110, 115, 159, 191, 193–6, 198, 203, 210–12
bacteria
general 121, 154, 178, 179, 181, 186
see also Archaea
taxonomic genus Alcaligenes 122,
Desulfobacter 122,
Desulfomonile 122,
Desulfosarcina 122,
Desulfovibrio 122,
Desulfuromonas 122,
Escherichia 122,
Magnetospirillum 122,
Planctomyces 122,
Proteus 122,
Pseudomonas 122,
Rhodopila 122,
Rhodospirillum 122
badgers 45, 47, 111, 112, 116
barbets 20, 21–2
barnacles 204
bats 3, 12, 118–21, 192, 227
Bayesian methods 14
bears 44, 45, 46, 47, 111, 212–14, 215
bees 134
beetles 134
Bergmann’s rule 218–20
bettongs 115
bilateral symmetry 175–8
billfishes 162, 163, 164, 165
bills (avian) 19–22
biodiversity x, 8, 11, 73, 76
biodiversity hotspots 208
biogenetic law, see recapitulation
biogeography, see phylogeography
biological classification 1, 12, 44, 216, 218, 223
bipedality 114–17
birds
general 2, 6, 42, 47–8, 52, 54–68, 77–87, 104–7, 110, 129–31, 170, 193–6, 219, 220
taxonomic genus Agelaius 54,
Anas 58–62,
Anser 63,
Arenaria 19,
Aquila 45, 48,
Caladris 130,
Catharus 130–1,
Charadrius 19,
Coccyzus 84,
Collocalia 80,
Cyanocitta 55,
Ensifera 20,
Eutoxeres 20,
Gallus 79,
Haematopus 19,
Harpagornis 44, 47,
Heteronetta 84,
Hieraaetus 45, 48,
Hirundo 129,
Icterus 62,
Malimbus 80,
Mellisuga 20,
Molothrus 86,
Numenius 20,
Oenanthe 130,
Opisthocomus 154,
Piranga 54,
Pitohui 65,
Scaphidura 86,
Serinus 129,
Stercorarius 63,
Troglodytes 55,
Turdus 129
birds-nest soup 80
blackbirds 54, 192
blowholes 127
bonitos 164
Borneo 210, 211, 216
brood parasitism 84–7
brood pouch 93–5, 117, 141–3, 196
see also pipefishes, seahorses, viviparity
bushbaby 174
butterflies 66, 68, 71–6, 101–4
caecilians 208, 209
CAIC (computer software) 236
caimans 37
camels 123, 125
Caribbean region 143–5, 207
caterpillars 74, 75
catfishes 166
cats 45, 46, 49, 192
cattle 123, 125, 154
Central America 68, 129
cetaceans 122–8, 192
Ceylon, see Sri Lanka
chameleons 89, 107, 196–200
chevrotains 123, 125
chickadees 62
chickens 77–80, 178
chimpanzees 2, 49, 50, 187, 188, 201, 203
China 79
chirality 28
chloroplast (cp) DNA
evolutionary origins of 183
general description of 9, 10
civets 45, 49
cladistics, see also maximum parsimony
history and methods 223–8
terms and concepts 225, 226
cleidoic egg 77–80, 137
clonal reproduction, see parthenogenesis
clutch-size rule 218
c-myc (proto-oncogene) 39
cnidarians 175, 204–7
codfishes 161
coelacanth 42–4
co-evolution 101–7
see also brood parasitism, commensalism, Müllerian mimicry, mutualism, pollination, protocooperation, social parasitism
commensalism 150
Comoros Islands 197, 199
conservation, see biodiversity
continental drift 159, 190–1, 197–200
copepods 204
copperhead snakes 158
corals 175, 204–7
coral snakes 156, 158
correlated character states 233–8
see also independent contrasts
cottonmouth snakes 158
countercurrent heat exchanger 163
cowbirds 86–7
crabs 28, 34–5, 36, 98–101, 208
creationism 170
Cretaceous 41
crocodiles 37, 79, 80, 87
crows 47, 195
cryptic colorations 52, 53–4, 68
cryptic species 73–6, 103, 143, 204–5, 208, 216
Cuba 144, 145, 146, 211
cuckoos 84
cytochrome c 8
cytochrome oxidase 74
cytoplasmic genomes 9–10
see also chloroplast DNA, mitochondrial DNA
Darwin, Charles 1, 2, 6, 91, 170
Darwin, Erasmus 1
David, Père Armand 44, 47
de Buffon, Comte 1
deer 47, 123, 125
delayed implantation 110–13
dinosaurs 80, 191
DNA barcoding 76
DNA forensics 173, 188
see also cryptic species
DNA hybridization 13, 45, 193–4, 195
DNA repair 178–80
Dobzhansky, Theodosius 3
dogs 45, 46, 48, 192
Dollo’s law 25–8, 30, 34, 140
donkeys 50
doves 84
ducks 47, 58–62, 79, 82, 84
eagles 47–8, 49
ear bones 220
echinoderms 140, 173, 175
echolocation 120, 124, 128
ectothermy 162, 218
eels 166
egg, see cleidoic egg, oviparity
egg dumping, see brood parasitism
electrical currents 160–2, 168
elephantfishes 166–8
elephants 123, 191, 192, 215–18
elephant shrews 191, 192
embryonic diapause, see delayed implantation
endangered species 104
endophyte 184
endosymbiosis 183
endothermy 162–5, 218–20
epidemiology 187
Era of Genomics 218, 221
Europe 104, 111, 129, 130, 193, 203, 214, 215
eusociality 134–5, 136
eyes 14, 91, 118, 150, 163, 165, 170–4, 196
fairy wrens 193, 194, 195
fantails 194, 195
fermentation (in foregut) 153–6
filefishes 132
fishers 112
fishes
general 7, 22–5, 42–4, 68, 80, 90–8, 110, 131–4, 159–68, 169–70, 172, 178, 181, 208
taxonomic genus Auxis 164,
Balistes 133,
Batheropterois 171,
Boleopthalmus 171,
Carcharodon 165,
Chilomycterus 133,
Chloropthalmus 171,
Coryphaena 164,
Coryphopterus 171,
Cyclothone 171,
Dormitator 171,
Electrophorus 166,
Eleotris 171,
Euthynnus 164,
Eviota 171,
Fusigobius 171,
Gambusia 92,
Gasterochisma 164,
Gasterosteus 162, 163,
Gempylus 164,
Gobiodon 171,
Gobionellus 171,
Gobiosoma 171,
Gonostoma 171,
Heterandria 92,
Hippocampus 93,
Istiophorus 164,
Katsuwonus 192,
Lampanyctus 171,
Latimeria 42,
Lepidocybium 164,
Lepomis 96, 133,
Lophogobius 171,
Makaira 164,
Monocanthus 133,
Neoceratodis 42,
Neogobius 171,
Neoheterandria 92,
Parvilax 171,
Phallichthys 92,
Poecilia 92, 96,
Poeciliopsis 91, 92, 110,
Priapella 97,
Priapichthys 92,
Priolepis 171,
Puntius 208,
Ruvettus 164,
Sarda 164,
Sauridia 171,
Scomber 164,
Scomberomorus 164,
Scopelengys 171,
Sphoeroides 133,
Sphyraena 164,
Stenobranchius 171,
Stenoptyx 171,
Symbolophorus 171,
Synechogobius 171,
Syngnathus 93,
Synodus 171,
Tetrapterus 164,
Thunnus 164, 165,
Trachinocephalus 171,
Triacanthus 133,
Trichiurus 164,
Xiphias 164, 165,
Xiphophorus 96, 97
flatworms, see platyhelminths
fleas 32
flightlessness 32–4, 47
fluoroacetate 65
flying fishes 22, 23, 24
folivory 232, 233
forensics, see DNA forensics
fossil DNA 20, 47–8
foster parentage, see brood parasitism
foxes 45, 48–51, 159
francolins 79
frequency-dependent selection 27, 30
frogs 66, 68–71, 137, 174, 200, 208, 209
see also amphibians
fruitflies, see Drosophila under Invertebrates
fungi
general 9, 150–2
taxonomic genus Arthonia 151, 152,
Dictyonema 151, 152,
Lecanora 151, 152,
Multiclavula 150, 151,
Omphalina 150, 151
Galápagos
Islands 210
finches 232, 233
Garden of Eden model 203
gazelles 123
geckos 107, 110
gene flow 140
Generelle Morphologie der Organismen 6, 7
genetic drift ix, 4, 57
gene trees (as distinct from species trees) 5, 16, 38
see also mitochondrial DNA
genomes (structures of) 8–9, 11
see also Human Genome Project
gharials 36–9
gill brooding 143
giraffes 123, 125
Gloger’s rule 218, 221
glycoproteins, see antifreeze proteins
gnatcatchers 62, 195
goats 123
Gondwanaland 191, 193, 196, 198, 200–4
gorillas 3, 45, 49, 50
goshawk 49
granivory 232, 233
grebes 80, 84
Greece 79
Greenland 129, 130
grouse 79
guineafowl 79
gulls 64
guppies 96–8
gypsy elements, see transposable elements
Haeckel, Ernst 6–7, 23
Haiti 189
halfbeak fishes 22–3, 24
Hawaiian Islands 148–9, 210–12
Hennig, Willi 224
hermaphroditism 169, 170
hibernation 120, 129
Himalayan Mountains 48, 190, 198
hippopotamuses 123, 124, 125
Hispaniola 144, 146
HIV viruses 187–9
hoatzins 154
holoparasite 184
homeothermy, see endothermy
homeotic genes 25, 30, 177
homobatrachotoxin 66
Homo sapiens , see humans
honeycreepers 149, 212
honeyeaters 194, 195
honeyguides 20, 84
horizontal gene transfer 154, 180–9
see also endosymbiosis
horses 8, 45, 50, 51, 117, 123, 191
Hox genes 177
Human Genome Project 178
humans 2, 4, 10, 11, 45, 49, 50, 134, 169, 173, 174, 178, 179, 187–9, 200–4
hummingbirds 20, 104–7
hybridization 68, 108, 210, 214, 218
hydras 175
hyenas 45, 51
hyraxes 191, 192
icefishes 160–2
immunological comparisons 45
inclusive fitness 134
incubation 82
see also brood parasitism, viviparity
independent contrasts 233–8
Indian Ocean 42, 197, 198, 199, 200
Indian subcontinent 37, 191, 197, 198–200, 207–9, 210
Indonesia 37
insectivory 232, 233
introgression, see hybridization
invertebrates
general 2, 25–35, 52, 66, 71–6, 98–104, 105, 110, 134–5, 143, 145–50, 172, 174–8, 181, 204–5
taxonomic genus Alpheus 136,
Armases 100,
Astraptes 74,
Caradina 208,
Drosophila 34, 173, 174, 181–3, 212,
Erythranthe 105–7,
Euhadra 25, 30, 31,
Euphilotes 102,
Favia 205, 206,
Glaucopsyche 102,
Heliconius 66, 71–3,
Iolana 102,
Maculinea 101–4,
Metopaulias 98,
Montastrea 205, 206,
Myrmica 101–4,
Otnjukovia 102,
Pachygrapsus 100,
Phengaris 102, 103,
Pseudophilotes 102,
Scolymia 205, 206,
Sesarma 98,
Sesarmoides 99, 100,
Sigapatella 28, 30–4,
Sinia 102,
Streblospio 140–3,
Synalpheus 135, 136,
Tetragnatha 148–50,
Tisbe 204,
Trochita 27, 28, 30, 32,
Turanana 102,
Zegalerus 28, 34–5
jacamars 20
Jamaica 98, 100, 144, 146
jays 55, 195
jellyfishes 175
jumping genes, see transposable elements
kangaroos 45, 47, 112, 114–17
kingfishers 62, 80
kiwis 47
Lamarck, Jean-Baptiste 1
langurs 154, 156
lateral gene transfer, see horizontal gene transfer
lecithotrophy 91, 140–3
lemurs 118, 200
lice 32
lichens 150–2
life cycles 137–43
life-history traits 82, 122, 143
see also life cycles
limbs (evolutionary loss of) 39–42
limpets 26–8
Linnaeus, Carolus 1, 223
live-bearing, see viviparity
lizards 39, 80, 87, 89, 107–10, 143–5, 146, 169, 218
see also reptiles
lobsters 34
lorises 118
lungfishes 42–4
lysozymes 154–6
MacClade (computer software) 230
mackerels 162, 163, 164
Madagascar 199, 210
magnetotaxis 121
magpies 64, 195
Malaysia 37
mammals
general 2, 8, 42, 44–6, 48–51, 52–4, 110–13, 114–21, 122–8, 170, 172, 190–3, 194–6, 212–20, 227,
see also humans
taxonomic genus Ailuropoda 44, 45, 47–8,
Ailurus 44, 47–8,
Balaenoptera 127,
Bos 154,
Cercocebus 187,
Chaetodipus 52,
Circopithecus 188,
Elephas 210, 216,
Heterocephalus 134,
Hypsiprymnodon 115,
Kogia 124,
Lontra 111,
Loxodonta 210, 216,
Mandrillus 188,
Mus 53,
Mustela 111,
Pan 187 (see also chimpanzees) 187,
Physeter 124,
Presbytis 154,
Spilogale 111,
Ursus 44, 45, 47, 212–14
mandrills 188
mangabeys 187, 188
Margoliash, Emanuel 8–9, 11
marlins, see billfishes
martens 112
maternity analysis, see parentage analysis
matrotrophy 91
maximum likelihood 14, 105, 231–3
maximum parsimony 14, 62, 105, 228–30, 231, 232
see also cladistics
medicine 187
melanism 53–4, 63–5
melanocortin-1 receptor 53, 64
Mesozoic Era 3, 6, 191, 193
metaphors (of phylogeny) 3–8
Mexico 19
mice 52–4, 55, 174, 178, 191
microsatellite markers 217
migration 129–31
Milne-Edwards, Alphonse 45, 47
mimic thrushes 82, 195
minks 112
mites 69, 181
mitochondrial (mt) DNA
general description of 9–10
origins in evolution of 181–3
use of, in particular phylogeny reconstructions 23, 24, 28, 31, 32, 37, 40, 43, 49, 50, 54, 55, 63, 70, 71, 72, 73, 74, 75, 87, 90, 91, 93, 94, 100, 103, 108, 116, 119, 124, 130, 138, 139, 141, 142, 145, 148, 162, 163, 164, 168, 185, 186, 200, 202, 203, 205, 208, 210, 214, 216
moas 45, 47
molecular clocks 3, 9, 91, 100, 189, 198, 202
molecular paleontology, see fossil DNA
molecular technologies 3, 4, 10, 11–12, 13
mole-rats 134
moles 191
mollusks 27, 34–5, 140, 172, 175, 204
see also snails, octopuses, squids
mongooses 45, 49
monkeys 118, 154, 187, 188
monkeyflowers 105–7
monogamy 94, 95
moon snails 27
morels 150
mosasaurs 41
molds 150
MRBAYES (computer software) 14
Müllerian mimicry 66, 71–3
mushrooms 150
mutation ix, 4, 108, 177, 187
mutualism 102, 103, 107, 150
see also co-evolution, symbiosis
nad1 gene 185, 186
natural selection ix, 1, 4, 19, 20, 47–8, 53, 57, 69, 88, 105, 112–13, 120, 123, 148, 154, 155, 167, 172, 220
needlefishes 22–5
nematodes 173, 174, 175
nemerteans 173, 174
neonatal crawling 117
nests 80–4, 145
neutralism (ecological) 150
New Caledonia 210, 216
New Guinea 65, 66, 203, 210, 211, 214
newts 137
New Zealand 45, 47–8, 198, 210, 211, 214
North America 48, 52, 85, 86, 105, 110, 111, 129, 130, 138, 141, 191, 214, 215
see also United States
nuclear genes (in phylogeny estimation) 10, 24, 32, 39, 40, 43, 103, 119, 120, 124, 138, 139, 168, 186, 202, 205, 216, 217
see also DNA, hybridization, immunological comparisons, microsatellite markers, ribosomal DNA
nuthatches 193, 195
Occam’s razor 228
octopuses 172, 174
okapis 123
orioles 62, 63, 64, 80, 195
ostriches 45, 47
otters 45, 111, 112
out-of-Africa model 202–3
oviparity 77–80, 88–90, 137
see also cleidoic egg, life cycles
owls 53
pademelons 116
paedomorphosis 23–5
Panamanian land bridge 100, 190
pandas 44–6
Paraguay 19
parasitic plants 184–7
pardalotes 194, 195
parentage analysis (genetic) 95
parsimony, see maximum parsimony
parthenogenesis 107–10, 169
partridges 79, 82
paternity analysis, see parentage analysis
PAUP (computer software) 14
pax6 gene 172–4
peafowl 95
peccaries 123, 125
penguins 159
penicillin 65
petrels 62, 80
pheasants 57, 79
Philippine Islands 210, 214
photosynthesis 150
phylogenetic character mapping
general approach 15–17, 18
limitations 16–17
Phylogenetic Systematics 224
phylogenetic trees
definitions and properties of 5
general diagrams of 6, 7
reconstruction methods for 13–14
phylogeography 72, 143, 190–218
pigs 8, 123, 125
pipefishes 93–5
pitohuis 65–8
placenta 91–2, 93
planktotrophy 34, 98, 140–3
plants
general 9, 104–7, 110, 181, 184–7, 210–12
taxonomic genus Hampea 74,
Mimulus 105, 106,
Rafflesia 186,
Scaevola 210–12,
Tetrastigma 184,
Trigonia 74
plate tectonics, see continental drift
platyfish 96–8
platyhelminths 172, 173, 174, 175
Pleistocene
ice ages 90, 129, 159, 207, 210, 214
land bridges 209
Pliocene 159
poikilothermy, see ectothermy
poisons, see toxins, venoms
polecats 112
pollination 20, 21–2, 52, 105–7, 184
polyandry 95
polychaetes 88, 140–3
polygamy 94, 95
polymerase chain reaction 44, 47
Polynesians 45, 47
population bottleneck 216
porpoises, see cetaceans
potoroos 116
pouch-brooding, see brood pouch
pre-existing bias (in female choice) 96
pregnancy, see viviparity
primates 2, 51, 118–20, 122, 187–9, 192, 193, 200
see also apes, chimpanzees, gorillas, humans, monkeys
protocooperation 150
pterodactyls 3
Puerto Rico 144, 146
puffbirds 20
pufferfish 131–4
quail 79, 82, 174
quantitative traits 233–8
rabbits 191, 193
raccoons 31, 45, 46
radial symmetry 174–8
rafting (as overseas dispersal mechanism) 200
rails 45, 47
rat-kangaroos, see kangaroos
rattlesnakes 156, 158
rays 88, 166
recapitulation 23–5
recombinant DNA 173
recombination (genetic) 4, 108
reptiles
general 36–42, 79, 80, 87–90, 107–10, 137, 143–5, 155–9, 196–200, 227
taxonomic genus Anolis 143–5, 146,
Cnemidophorus 108–10,
Gavialis 37,
Heteronotia 110,
Lacerta 89,
Tomistoma 37
reticulate evolution, see horizontal gene transfer, hybridization
retroposons 124
retroviruses, see HIV viruses
rhinoceroses 50, 123
ribbonworms, see nemerteans
ribosomal DNA 51, 121, 150, 210
ricefishes 22, 24
Rocky Mountains 190
rodents 191, 192, 193, 200
see also mice
roundworms, see nematodes
sailfishes, see billfishes
salamanders 137–40, 218
sandpipers 130
saprobes 150, 152
sauries 24
scrub-birds 194, 195
sea anemones 175
sea cows 191
seahorses 93–5
sea lions 45, 47
seals 45, 47–8, 111, 159
sea squirts 173
sea urchins 174, 175, 204
segmented worms, see annelids
selection, see natural selection, sexual selection
sensitivity analysis 62
sex-biased gene expression 55
sex-determination mode 168–70
sex-role reversal 93, 94
sexual dichromatism 54–62
sexual dimorphism 95
see also sexual dichromatism
sexual selection 19, 57–8, 64, 94, 96–8
Seychelle Islands 197, 199, 200
sharks 88, 165, 166
sheep 123, 125
shorebirds 19–20
shrews 191
see also elephant shrews
shrikes 64, 195
shrimp 34, 36, 134–5, 136, 208
Siberia 130, 215
sibling species, see cryptic species
silverswords 212
Simpson, George Gaylord 4
SINEs (short interspersed elements) 128
sitellas 193, 194, 195
skunks 45, 46, 47, 111, 112
sloths 192, 193
snails 25–30, 31
snakes 39, 41–2, 68, 80, 87, 107, 156–9, 200, 208, 218
see also reptiles
social parasitism 101–4
Socotra 211
South America 21, 42, 66, 68, 71, 73, 84, 129, 130, 159, 166, 191, 198
sparrows 79, 82, 195
speciation 143
see also adaptive radiation, cryptic species
spiders 145–50, 200
squid 173, 174
Sri Lanka 207, 209, 210
starfish 175, 176
stick insects, see walkingsticks
sunbirds 62, 64
sunfish 133
swallows 82–4, 129
swordfishes, see billfishes
swordtails 96–8
symbiosis 102, 150–2, 187
see also co-evolution, endosymbiosis, pollination
systematics, see biological classification
tanagers 54, 57, 195
tapirs 50, 123
tarsiers 118
Tasmanian wolf 196
taxonomy, see biological classification
tenrecs 191
termites 69, 134, 135
Tertiary 101
The Origin of Species 6, 170
thermogenic organs 163
thornbills 193, 194, 195
thrushes 130–1, 195
toads 137
Tongo 211, 215–18
toucans 19–22
toxins 65–8, 158
see also venoms
transposable elements 181–3
treecreepers 193, 194, 195
Tree of Life ix, 4, 7–8, 11, 108, 183
TREE-PUZZLE (computer software) 14
triggerfishes 132
truffles 150
tunas 8, 162–3, 164, 165
turkeys 79, 82
turtles 79, 80, 87, 169, 218, 219, 220
type I statistical error 234, 236
type II statistical error 234, 236
unisexuality, see parthenogenesis
United States 74, 189
see also North America
venoms 156–9
see also toxins
vicariance 144
see also phylogeography
vireos 64
virgin birth, see parthenogenesis
viruses 181, 186
see also HIV viruses
viviparity 3, 87–95
walkingsticks 30–4
wallabies 115, 116
walruses 45
warblers 62, 64, 79, 82, 193, 195
warning coloration 52, 65–73
wasps 134
W-chromosome, see sex-determination mode
weasels 45, 46, 47, 111, 112
weaver birds 80, 83, 84, 195
webs (of spiders) 145–50
whales, see cetaceans
whelks 27
whistlers 194, 195
wings 2–3, 12, 25, 28, 30–4, 45, 65–8, 73, 120, 166, 177, 224, 226, 227, 228
wolverines 45, 112
wolves 45, 196
woodchucks 196
woodpeckers 20
woodswallows 194, 195
worms 176, 204
see also annelids, nematodes, nemerteans, platyhelminths, polychaetes
worm shells 27
wrens 55
see also fairy wrens
X-chromosome 202
see also sex-determination mode
Y-chromosome 202, 204
see also sex-determination mode
yeasts 8, 150, 178, 179
Yeti 45, 48–51
Z-chromosome, see sex-determination mode
zebrafish 174
zebras 50
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