I–24 INDEXinferring phylogenies, 35–38
rejoining of branches, 38–39
similarity versus relationship, 33–34
Tree of Life concept, 28–33
Phylogenetics
estimating time of divergence, 42–43
evidence for evolution, 580
historical biogeography and, 476
inferring the history of character
evolution, 41–42
patterns of evolution, 43–51
practical applications, 585
rejoining of branches, 38–39
studies of diversity, 502–507
studies of infectious diseases, 592
Phylogenies
biological evolution and, 18
of cells, 41
defined, 33
difficulties in estimating, 404–409, 410
distinguished from gene trees, 406, 407
of genes, 39–40
inferring, 35–38, 402–404
introduction, 401–402
lineage-through-time plots, 506–507, 508
methods for estimating, 409–416
overview of phylogenetic trees, 33–35 (see
also Phylogenetic trees)
patterns of diversification, 50–51
testing the validity of, 414
using in classification, 424–426
using to date evolutionary events, 416–
417, 418
using to discover the history of genes and
cultures, 417–419, 420
using to reconstruct ancestors, 419, 421
using to study adaptations with the
comparative method, 421–423
Phylogeny matching, 322–323, 324
Phylogeography, 480, 481
Physalaemus, 222
Physalaemus pustulosus (túngara frog), 222 ,
252
Physalis, 380, 381
Physical barriers, allopatric speciation and,
235–238
Physical constraints, 390
Piciformes, 425
Pierinae, 330
Pierine butterflies, 524
Pieris rapae (cabbage white butterfly), 524
Pigeons, 471
Pigs, 42, 408 , 461
Pikas, 408
Pilosa, 461
Pima people, 556
“Pin” flowers, 87, 88
Pinaroloxias inornata, 29
Pines, 491, 504
Pinker, Steven, 558
Pinus flexilis (limber pine), 322, 323
Pinus longaeva (bristlecone pine), 275, 276
Pitcher plant (Sarracenia purpurea), 59
Pitcher-plant mosquito (Wyeomyia smithii), 59
Pithecophaga jefferyi (Philippine eagle), 572Pitx1 gene, 47, 382, 383
Placenta, 383
Placental mammals, 458 , 461
Placidochromis, 214
Placoderms, 445
Planktonic foraminiferans, 452
Plant species diversity
effects of diversity on, 508
key adaptations and, 503–504
latitudinal diversity gradient, 485
limits to, 507
speciation rate and, 504, 505
Plants
abortion of seeds, 307
adaptive design of leaves, 68, 69
co-option in, 380, 381
colonization of land, 447
competition with relatives and dispersal,
204–205
convergent evolution in, 49, 405 , 470
cytoplasmic male sterility, 312–313
dispersal and disjunct distributions, 478,
479
dispersal and range limits, 482
dispersal and species distribution, 479–480
diversification in the Mesozoic, 453–454
early reproduction in growing
populations, 280
epigenetic mutations, 97
evolution in the Paleozoic, 446
evolution of multicellularity, 440
evolution of plant–herbivore interactions,
325–326, 329–330
experimental analysis of animal
pollination, 69, 70
genome size, 365
inheritance of somatic mutations, 94
iteroparity, 285
latitudinal diversity gradient, 485
number of offspring, 286, 287
numbers of protein-coding genes, 346
phenotypic plasticity and differences
between populations, 198
phylogenetic niche conservatism, 484
phylogeography, 480, 481
semelparity, 282–283, 284
sequential hermaphroditism, 286–287
speciation by polyploidy, 232, 233
species richness, 491, 492
sympatric speciation, 240, 241
trends in self-fertilization, 537–538
vicariance and geographic distribution,
477, 478
See also Angiosperms; Flowers
Plasmodial slime molds, 440
Plasmodium, 120, 346
Plate tectonics, 432–433
Plato, 9
Platypus, 461
Platyrrhine primates (Platyrrhini), 470, 472
Platyspiza crassirostris, 29
Plectrohyla clade, 486
Pleiotropy
antagonistic, 281
definition and description of, 92, 93evolution of reproductive isolating barriers
by, 228
evolvability and, 386–388
female choice and, 258, 259
genetic correlations and, 116, 153–154
Pleistocene epoch, 433, 434 , 459, 463–465
Pleistophora intestinalis, 332, 333
Pleobionts, 440
Plesiomorphic characters, 44–45
Plethodon, 48 , 471
Plethodon caddoensis, 471
Plethodontidae, 524–525
Plethodontinae, 48
Pleuromaria, 526
Pliocene epoch, 434 , 459, 462
Poaceae, 460
Podarcis muralis (European wall lizard), 483
Podiceps cristatus (great crested grebe), 306
Podisma pedestris, 202
Podospora anserina, 38
Poecilia reticulata. See Guppy
Point mutations, 89
Poison dart frog (Epipedobates trivittatus), 305
Policing
evolution of multicellularity and, 316
of noncooperators, 310
Polistes gallicus (paper wasp), 309
Political organization, phylogenetic analyses
of, 419, 420
Pollen
male-male competition, 260
self-incompatibility and, 269
Pollination
experimental analysis of animal
pollination, 69, 70
orchids and euglossine bees, 248, 249
by pseudocopulation, 74
Pollinator isolation, 221
Polydactyly, 173
Polygamous species, 70–71
Polygenic traits, 135
Polygyny, 568
Polymerase chain reaction (PCR), 585
Polymorphic equilibrium, 121–122
Polymorphic loci, defined, 82
Polymorphisms
patterns in the genome, 174–176
See also DNA polymorphisms
Polyphyletic taxa, 32, 425, 426
Polyploidy
description and types of, 350
genome size and, 365
reproductive isolation in plants, 225
speciation by, 232–233
Polytomy, 38
Pomacanthidae, 71
Pongidae, 426
Pongo, 408 , 426
Pongo pygmaeus. See Orangutan
Poplars (Populus), 277
Popper, Karl, 584
Population bottlenecks, 173
Population density, evolution of, 281–287
Population genetics, 585
Population growth rate, evolution of, 281–28727_EVOL4E_INDEX.indd 24 3/22/17 2:01 PM