1. Transposition
    production of copies that become inserted into new positions in the genome
  2. haplotype
    particular DNA sequence that differs by 1 or more mutations from homologous sequences
  3. transition vs. transversion
    • transition: substitution of a purine for purine or pyrimidine for pyrimidine
    • transversion: substitutions of purines for pyrimidines or vice versa
  4. synonymous mutations vs nonsynonymous
    synonymous: no effect on amino acid sequence (in the coding regions)

    non: result in amino acid substitutions
  5. replication slippage
    process that alters the nunber of short repeats in microsatelites
  6. intragenic recombination
    when homologous DNA sequences differ at two or more base pairs --> new DNA sequences
  7. unequal crossing over
    when two homologous chromosomes are not perfectly aligned --> (two normals and 1 deletion, 1 duplication)
  8. Recurrent mutation
    reapeated origin of a particular mutation (number of independent origins per gene copy per generation -

    this is a measure of hte rate at which a particular mutation occurs
  9. Back mutation
    mutation of a mutant allele back to the allele from which it arose
  10. mutagens
    mutation causing agents (UV light, X-ray, chemicals
  11. polygenic variation
    based on several or many different genetic loci
  12. mutational variance of a character
    teh increased variation in a population caused by new mutations in each generation
  13. homeotic selector genes
    determine the basic body plan of an organism (distinct identity on each segment of the developing body) by having regulating gnes - homeotic mutatiosn
  14. incomplete dominance
    degree to which the heterozygote resembles one or the other homozygote
  15. additive inheritance
    if heterozygotes phenotype is precisely intermediate between those of the homozygotes
  16. pleitropic mutations
    affect more than one character
  17. kinds of gene mutations
    base pair substitutions (point mutations), insertions/deletions, replication slippage, recombination, transposable elements
  18. Karyotype
    description of its complement of chromosomes (number, shape, size, internal arrangement)
  19. aneuploid
    unbalanced chromosome complement - inviable/fails to develop correctly
  20. Polyploidy
    changes in the number of whole sets of chromosomes (more than two sets of homologous chromosomes)
  21. auto vs. allopolyploid
    auto: union of unreduced gametes of the same species - usually results in aneuploid gametes

    allopolyploid: union of unreduced gametes by hyrbidization between closely related species - usually result in normal segregation of pairs
  22. pericentric vs. paracentric inversions
    pericentric - it includes the centromere

    paracentric - it does not include the centromere

    alignment of the inverted chromosomes requires a loop! - cross over - inviable
  23. reciprocal translocation
    breakage and reunion of two nonhomologous chromosomes that result in an exchange of segements - fertility reduced by 50%
  24. acrocetnric chromosomes vs. metacentric chromosomes
    • acrocentric: centromeer is near one end
    • metcentric: centromere inthe middle
  25. chromosome fusion
    two nonhomologous acrocentric chromosomes undergo reciprocal translocation -- create a metacentric chromosome
  26. fission heterozygote
    metacentric chromosome synapses with acrocentric chromosomes as a "trivalent"
  27. possible alterations of karyotypes
    polyploidy, chromosome rearrangement, inversions/translocations, fissions/fusions (all are changes in chromosome number!)
  28. locus
    a site on a chromosome (the gene that occupies a site)
  29. allele
    particular form of a gene
  30. developmental noise
    variation arisen from random events at the molecular level in an organism - like fluctuating assymetry
  31. epigenetic inheritance
    phenotypic differences that are not based on DNA sequence differences are transmitted among generations of dividing cells and sometimes from parents to offspring (genomic imprinting of parental origin like DNA methylation - gene memory)
  32. norm of reaction
    variety of different phenotypic states that can be produced by a signle gentoype under different environmental conditions (genotype x environmental interaction
  33. sources of variation
    environment, developmental noise, maternal effect, epigenetic inheritance
  34. Hardy Weinberg principle
    Whatever intial genotype frequencies for two alleles may be, after one generation of random mating, genotype frequencies witll be p squared, 2pq and q squared
  35. Hardy Weinberg assumptions
    • 1. Mating is random (population must be panmitic)
    • 2. Population is indefinitely large (no genetic drift)
    • 3. no gene flow or migration from other populations
    • 4. no mutation
    • 5. all individuals have equal probabilities of survival and reproduction (no natural selection)
    • If nto all met --> evolutionary change within populations!
  36. inbreeding
    form of nonrandom mating - mate with relatives - genes with identical descent - self-fertilization!

    • Inbreeding Coefficient: probability that a random pair of gene copies are identical by descent = F
    • As F increases you get less heterozygosity
  37. polymorphism
    presence in a population of two or more variants (alleles/haplotypes)

    opposed to monomorphic
  38. inbreeding depression
    because a lot of genetic variation is concealed until the organism is homozygous - and inbreeding causes an increase in homozygosity --> reduced fitness

    lower viabilities for homozygotes coudl indicate the prsence of recessive deleterious alleles
  39. genetic hitchhiking
    any factor that caused a change in the frequencies of an allele at one location would result in a correlated change at the other locus (have A1B1 or A2B2, an increase in A1 would cause an increase in B1)

    associations between alleles
  40. linkage disequilibrium vs. equilibrium
    disequilibrium: association of two alleles at two or more loci more frequently (or less) than predicted by their individual frequencies - common in asexual populations (little recombination)

    equilibrium: teh association of two alleles at two or more loci at teh frequency predicted by their individual frequency - not linked (recombination brings loci to equilibrium)
  41. Why do we find linkage disequilibrium if recombination breaks it up?
    nonrandom mating, new mutation in LD with alleles associated with it (not broken down until recombination), recently formed union of two populations, recombination could be very low/nonexistent, genetic drift, natural selection if two or more gene combos are more fit than recombinant genotypes

    Usually in panmictic sexually reproducing organisms - loci are in linkage equilbrium
  42. quantitative variation
    continuous, fits a normal distirbutino - due to variation at several loci
  43. variation in a phenotypic character
    sum of genetic variance and environmental variance
  44. heritability
    the proportion of the phenotypic variance that is genetic variance
  45. geographic variation
    differences among populations in different geographic areas
  46. sympatric populations vs. parapatric vs allopatric
    • s; populations that have overlapping geographic distributions (occupy same area and frequently encounter each other)
    • para: populationswith adjacent but nonoverlapping ranges that come into contact
    • allo: populations with separated distributions
  47. hybrid zone
    region in which genetically distinct parapatric forms interbreed
  48. cline
    gradual change in a character or in allele frequencies over geographic distance (Bergmann's rule: adaptive geographic varaition from natural selection - body size increases iwth increasing latitude)
  49. ecotypes
    phenotypes associated with a particular habitat, often in a patchy mosaic pattern
  50. gene flow
    populations exchanging genes with one anotehr - homogenizes the species of a population (all to same allele frequencies)

    founder effects - same genes

    greater among more mobile organisms
  51. phenograms
    diagrams that show the relative difference among populations or species
  52. nonadaptive evolution
    random fluctuations in allele frequencies can result in replacement of old alleles by new ones
  53. demes vs. metapopulation
    • deme: small independent populations
    • metapopulation: ensemble of such demes
  54. effective population size
    • number of individuals that reproduces - the number at which genetic drift actually works at
    • can be smaller b/c of variation in progeny number, a non 1:1 sex ratio, generations overlapping, natural selection, fluctuations in population size
  55. bottlenecks
    restrictions in size thorugh which populations may pass

    founder effect: random genetic drift from a small number of founderes form a different population
  56. Neutral theory of molecular evolution
    the great majority of those mutations that are fixed are effectively neutral with respect to fitness and are fixed by genetic rif

    degree of sequence differen ce can serve as a molecular clock!

    most of the variation we observe at the molecular level has little effect on fitness!
  57. Mconald-Kreitman test for selection
    replacement substitutions that are advantageous will be fixed more rapidly - they will spend less time in a polymorphic state than selectively neutral synonymous changes do - contribute less to polymorphic variation
  58. the most important levels of selection
    individual and genetic selection - turnover is much quicker than for populations/species
  59. selection of versus slectionfor
    there may be incidental selectionof other features that are correlated with those features that are selected for (select for small size, selecttion of red balls)
  60. selfish genetic elements
    transmitted at a higher rate than the rest of an individuals genome and are detrimental (not advantageous at least) to teh organism
  61. altruistic trait
    a feature that reuces the fitness of an individual that bears it for the benefit of hte population or species (can't evolve by individual selection - group selection only to increase chance that their alleles will spread)
  62. adaptive trait
    one that enhances fitness compared with at elast some alternative traits
  63. preadaptation
    feature that fortuitously serves a new function
  64. exaptations
    a preadaptation that has been co-opted to serve a new function
  65. complexity of a feature shows what
    probably evolved by natural selection
  66. comparative method
    way of inferring the adaptive significance of a feature - compare sets of species to pose or test hypotheses on adaptation and other evolutionary phenomena
  67. directional selection
    increases the proportion of genotypes witha more extreme value of the trait
  68. overdominant vs underdominant
    if the heterozygote has greatest fitness or lowest fitness
  69. stabilizing selection
    an intermediate phenotype is fittest - does not alter teh mean, but may reduce variation
  70. diversifying (disruptive) selection
    • unlikely to be symmetrical - usually shifts the mean
    • Two or more phenotypes are fitter than the intermediates between them
  71. parthenogenetic populations
    asexually reproducing (reproduce onece, all at the same time, and then die)

    very easy to determine fitness of these
  72. mean fitness
    average fitness of individuals in a population relative to the fittest genotype
  73. coefficient of selection
    amount by which the fitness of a genotype differs from the reference genotype (selection of teh fitter genotype, or measurement of the selection against the less fit genotype)
  74. directional selection
    homozygote for an advantageous allele has a fitenss equal to or greater than that of the heterozygote or any other genotype
  75. cost of adaptation/trade-off
    advantageous traits often have side effects that are disadvantageous in some environments
  76. how do deleterious alleles stay in the population?
    balance between the rate at which it is elminated by selection and teh rate at which it is introduced by mutation/gene flow

    proportional to mutation rate, inversely proportional to strength of selection
  77. how can gene flow contribute to genetic variation?
    if it keeps reintroducing deleterious alleles that are selected against in the population
  78. factors responsible for wealth of variation
    1) recurrent mutation 2) gene flow of locally deleterious alleles from other populations where they are selected for 3) selective neutrality 4) maintenance of polymorphism by natural selection
  79. balancing selection
    keeps a lot of the genetic variation - maintains polymorphism (heterozygote advantage, antagonistic selection, frequency dependent selection,
  80. antagonistic selection
    opposing forces of natural selection - usually does not keep polymorphism
  81. temporal and spatial variation
    a fluctuating environment may favor different genotypes in different generations

    different genotypes may be best adapted to different microhabitats or resources
  82. soft vs. hard selection
    soft: when teh number of survivors in a patch of a particular microenvironment is determiend by competition for a lmiting resource

    hard: liklihood of survival depends on absolute fitness, not on density of the competitors
  83. frequency dependent selection
    maintains polymorphisms, the fitenss of a genotype depends on teh genotype frequencies in the population

    often seen when genotypes competet for limiting resources
  84. inverse frequency depenent selection
    teh rarer a phenotype is in the population the greater its fitness

    shift toward a stable equilibrium value
  85. positive frequency dependent selection
    fitness of a genotype is greater the more frequent it is in the population

    whichever allele is initally more frequent will be fixed!!
  86. heterozygote disadvantage
    heterozygote has lower fitness than either homozygote (underdominance) (initially more frequent allele will be fixed by selection)
  87. can allele frequencies cross an adaptive valley?
    usually teh can't because a population cannot become worse just to get better (two peaks)

    it will if teh population is so low that allele frequencies are changed a lot by genetic drift --> peak shift (depends on population size and difeerent in mean fiteness between teh valley and initially occupied peak)
  88. positive directional selection effect on variation at closely related linked sites
    by hitchiking the variation is reduced!

    if an advantageous mutation is fixed by selection - all variation in teh gene is eliminated by a selective sweep

    if advantageous mutation is at intermediate frequency - see LD b/c teh mutation is still associated with apricular nucleotides at linked sites (correlated iwth one anotehr then)
  89. background selection
    purifying selection against deleterious mutations reduces neutral polymorphism at closely linked sites

    when a copy of a deleterious mutation is elminitated from a population, selectively netural mutations linked to it are eliniated as well
  90. signatures, or imprints of selection
    proportion of functional changes (nonsynonymous vs synonymous), reduced sequency diversity (selective sweep reduces heterozygosity), long haplotypes and linkage disequilibrium

    high LD with normal recombination is likely to indicate a young allele
  91. QTL mapping
    quantitative trait loci - use these regions as markers
  92. phenotypuic variance
    sum of genetic variance and environmental variance
  93. response to selection
    change in mean character state of one generation as a result of selection in the previous generation

    enabled by the additive genetic variance (when alleles have additive effects, teh expected average penotype of a brood of offspring equals thea verage of their parents phenotypes)

    greater response to selection with a greater heritability
  94. faster than neutral rate of trait divergence means....
    slower thatn entural rate of trait divergence means...
    • directional selection!
    • stabilizing selection!
  95. truncation selection
    imposes selection by breeding only those organisms with a certain state of a character
  96. selection plateau
    when organisms stopped responding to selection - irregularities in artificial selection are due to teh origin and fixation of new mutations with large effects
  97. why would a selection platueau and a decline when selection is relaxed occur in seletion experiments?
    natural selection! it opposes artificial selection. The selected trait is extreme values ahve lower fitness
  98. how does quantitative genetic variation stay in the population?
    • variable selection:fluctuation in teh optimal phenotype from oen generation to anotehr
    • gene flow between populations with different optimal phenotypes

    mutation-selection balance: balance between erosion of variation by stabilizing selection and input of new variation by mutation
  99. how do correlated features occur (correlated evolution?)
    • correlated selection: selection favors soem combo of charcter states over otehrs
    • genetic correlations: genetic differences taht affect both characters, they evolve in concert! can enhance or slwo the rate of adaptive evolution --> b/c of LD among genes, or b/c of pleiotropy, or b/c of natural selection which may favor modifier alleles that can alter and mitigate the deleterious effects of other alleles
  100. what happens when there is a conflict between teh genetic correlation of characters and directional selection of those characters?
    the two characters may evolve to their optimum only slowly (may evolve temporarily in a maladaptive direction)
  101. phenotypic plasticity
    a signel genotype may produce radically different phenotypes in response to environmental stimuli (norms of reaction)
  102. canalization
    developmental system evovles so that it resists environmental influnces on teh phenotype - when teh adaptive norm of reaction is a constant phenotype (buffered against alterations by teh environment)
  103. genetic assimilation
    a character state that initialy developed in response to teh environment had become genetically determined
  104. phenotypic integration hhypothesis
    functionally related characteristics should be genetically correlated with another: they shoudl reamin coordinated even as they vary within species and as they evolve
  105. constraints on eveolution - why not perfect adaptation?
    • gene flow from populations adapted to a different environment
    • amount of genetic variance? and variance among individual characters?
    • genetic correlations - more variation for some combos of traits that for others
    • environment may change so fast taht evolution cannot keep pace with the moving optimum
  106. life histories
    age specific probabilities of survival and reproducitve success characteristic of a species
  107. optimality theory
    which state of some charcter, among a specified set of plausible states would maximize individual fitness, subject to specified constraints
  108. evolutionary stable strategy
    strategy such that if all the members of a population adopt it, then no mutatn strategy could invatde under teh influnce of natural selection
  109. semelparous life history
    females reproduce once and then die
  110. iteroparous species
    females reproduce more than once
  111. constraints on the maximization of fiteness
    phlogenetic constriaints, physiological/genetic constraints (like trade-offs - antagonistic pleiotriopy)
  112. antagonistic pleiotropy
    results from a trade-off, genotypes manifest an inverse relationship between different components of fitness
  113. senescence
    aging - why does this occur - selective advantage of an enhanced probability of survival declines with age
  114. 2 hypotheses for senescence
    • 1) muattion accumulation: genetic variation in fitness-related traits should be greater in late age classes - more likely to have deleterious muatations in later age class b/c selection against them is weaker
    • 2) antagonistic pleiotropy: genetic trade offs - senescence is jsut a cost of reproduction ( a trait that allows early repoproduction may be disadvantageous to us later in life)
  115. reprouctive effort in iteroparous species vs. semelparaous
    mroe effor t for the semelparaous species!
  116. optimal clutch size
    number of offspring that yields the greatest number of surviving offspring
  117. delayed onset of reproduction is most likely in species iwth low/high rates of adult survival?
  118. isogamous species
    the uniting cells are the same size (they have mating types but not distinct species)
  119. dioecious species
    individduals are either female or male
  120. asexual reproduction can be carried out by... (3 types)
    • vegetative propagation: offpsring from a group of cells
    • parthenogenesis : from a single cell
    • apomixis (offspring develops from an unfertilized egg)
  121. disadvantages to sexual reproduction
    the cost of sex compared to asexual reproduction (get all genotypes handed down) and good combos of genes are broken down by recombination (LD is reduced)
  122. Muller's Ratchet
    how in asexually producing organisms, the amount of mutations keeps increasing and the process is irreversible

    this is an advantage for sex b/c recombination creates new combinations of alleles - wont' add up the mutations, selection will favor those progeny with combos of favorable alleles
  123. reason for asexual organisms high rate of extinction?
    slower adaptation!
  124. sex ratio
    proportion of males
  125. local mate competition
    sons compete with one another in a local group founded by their mother --> founding female's genes can be propagated best by producing mostly daughters
  126. incest avoidance
    avoidance of mating with relatives

    inbreeding increases homozygosity and is often accompanied by inbreeding depression
  127. why would selfing be advantageous?
    save energy and resources, produce highly fit homozygous genotype (rarely), protect against outbreeding depression (gene flow/recombination), reproductive assurace (certain to produce some seeds by selfing)
  128. sexual selection
    differences among individuals of a sex in the number or reproductive capacity of mates they obtain

    • contests between males
    • female choice
  129. arms race in sexual selection
    evolution of ever more extreem traits by male contest (directional selection for bigger, faster, display features)
  130. why would females prefer features that are probably disadvantageous to the male?
    • 1) direct benefits: nutrition, superior terioty, parental care (recognize superior providers by some feature that is correlated with their ability to provide)
    • 2) indirect benefits: runaway sexual selection, good gene models
    • 3) sensory bias
  131. runaway sexual selection
    sons of females that choose a male trait have improved mating success b/c they inhereit the trait that made their fathers appealing to their mothers - snowball effect

    increase in male trait is accompanied by increase in frequency of hte female preference for that trait by hitchhiking

    offspring are superior with respect to mating success
  132. good genes model
    females choose males with high genetic quality

    female preference for male indicator traits should be most likely to evolve if the trait is a condition dependent indicator of fitness (can have the trait b/c they are in good physiological condition!)
  133. sensory bias
    female preference for a trait can evolve before the preferred male trait

    may be more stimulating just because of the organization of the sensory system
  134. antagonistic coevolution
    genes that govern male versus female characters may conflict

    change in male character --> neutralized or paried by evolution of a female character --> chain reaction
  135. way males inflict harm on their mates
    semen toxicity, forced copulation,
  136. chase away sexual selection
    females evolve resistance to males inducements to mate - their resistance causes males to overcome the females reluctance (may get more elaborate traits to induce them to mate)
  137. anisogamous species
    distinct sexes (eggs/sperm)

    can be dioecious (us) or hermaphroditic
  138. Why sex? )3 reasons)
    • 1) siblings would be in less direct competition (not exactly identical)
    • 2) counteracting deleterious mutations
    • 3) adaptation to fluctuating , unpredictable environmental conditions
  139. sexual dimorphism
    differences in males/females traits
  140. Mating System/Parental Care system
    no parental care -->
    females care -->
    males care -->
    both care -->
    • promiscous
    • polygyny
    • polyandry
    • monogamy (with some extra pair copulation, brood parasitism)
  141. brood parasitism
    conflict! a female lays eggs in other females nests in addition to her own
  142. Hawk vs. Dove strategies
    • Hawk: escalates conflict until injured or wins (an ESS if teh fitness from a winning contest is greater than the cost of injury)
    • Dove: retreats as soon as possible (never an ESS)
  143. ESS
    evolutionary stabel strategy
  144. accessor strategy
    the individual escalates the conflict if it judges the opponent to be smaller but retereats if opponent is larger (mostly is an ESS)
  145. cooperation vs. altruism
    • cooperation: provides a benefit to the other individuals and the actor
    • altruism: enhances fitness of other individuals but lowers their fitness
  146. delayed benefit of cooperative behavior
    like when a dominant male takes on another male to make a team for coordinated displays, but the subordinant male must wait till the dominant one dies to get any mating
  147. reciprocity
    if X profits Y then Y will later profit X

    tehre must be repeated interactions, the organisms must remember each other, the benefits must be great enough to outweight the cost of helping

    appears to be uncommon
  148. transactional model of reproductive skew
    dominant individuals gain from the assitance of helpers and they pay those helpers by letting them reproduce a littme mroe than if they were alone
  149. inclusive fitness
    effect on the individual with it (direct) and teh fitness of other individuals that cary copies of the same allele (indirect) --> kin selection
  150. Hamiltons rule
    • kin selection
    • an altruistic trait can increase in frequency if the benefit from teh donor's relatives (weighted by their relationship) esceeds the cost of the trait to the donor's fitness
  151. two factors under which kin selection can happen
    • 1) able to distinguish related from unrelated
    • 2) if individuals are associated with kin
  152. trait group selection
    altruism evolves by group selection -multilevel selection can influence trait evolution!
  153. green beard model
    an allele for altruism can increase in frequency if the bearer can recognize other individuals that carry the same allele - whether or not they are closely related
  154. parental care trade off
    will increase reproductive fitness BUT it comes at a cost (energy and time)
  155. infanticide
    males that replace a mated male kill existing offpsring of his mates - females become more fertile - have his own offpsring
  156. abortion/killing of own offspring
    a way to adaptively regulate brood size
  157. siblicide
    to get more food!
  158. parent-offpsring conflict
    offpsring try to obtain as much resources from a parent (often much more than waht is optimal for the parent to give to them)
  159. eusocial animals
    nearly/completely sterile individuals rear the offspring of reproductive individuals (usually their parents)

    workers control who becomes a queen or a worker

    animals are haplodiploid (females from fertilized eggs, males are haploid) --> more productive for workers to deote energy to rear reproductive sisters than to have daughters
  160. genetic conflict
    conflicts between different genes as an outcome of selection at the gene level (when a gene has a transmission advantage over other genes)

    genes can evolve to counteract the effect of selfish genes at anotehr locus

    ex: opposing hormones between fetus and mom
  161. horizontal transmission effects on the cooperation
    their fitness does nto depend don teh reproductive success of the individual host - selection favors genotyupes iwth a high reproductive rate even if it kills the host (parasite)
  162. vertical tranmission effect on organization/cooperation
    symbiont and host are chained togheter and the success of the symbionts depends on teh fitness of the host- restrained reproduction is favored - mutualism
  163. mutualism
    interaction in which two genetic entities enhance each other's fitness - any advantage to one party provides an advantage to the otehr
  164. why homosexuals still in teh population?
    may have been helpers - were tolerated as logn as they played a socially expected procreative role (may have been as reproductive as heterosexuals)
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