-
Transposition
production of copies that become inserted into new positions in the genome
-
haplotype
particular DNA sequence that differs by 1 or more mutations from homologous sequences
-
transition vs. transversion
- transition: substitution of a purine for purine or pyrimidine for pyrimidine
- transversion: substitutions of purines for pyrimidines or vice versa
-
synonymous mutations vs nonsynonymous
synonymous: no effect on amino acid sequence (in the coding regions)
non: result in amino acid substitutions
-
replication slippage
process that alters the nunber of short repeats in microsatelites
-
intragenic recombination
when homologous DNA sequences differ at two or more base pairs --> new DNA sequences
-
unequal crossing over
when two homologous chromosomes are not perfectly aligned --> (two normals and 1 deletion, 1 duplication)
-
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
-
Back mutation
mutation of a mutant allele back to the allele from which it arose
-
mutagens
mutation causing agents (UV light, X-ray, chemicals
-
polygenic variation
based on several or many different genetic loci
-
mutational variance of a character
teh increased variation in a population caused by new mutations in each generation
-
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
-
incomplete dominance
degree to which the heterozygote resembles one or the other homozygote
-
additive inheritance
if heterozygotes phenotype is precisely intermediate between those of the homozygotes
-
pleitropic mutations
affect more than one character
-
kinds of gene mutations
base pair substitutions (point mutations), insertions/deletions, replication slippage, recombination, transposable elements
-
Karyotype
description of its complement of chromosomes (number, shape, size, internal arrangement)
-
aneuploid
unbalanced chromosome complement - inviable/fails to develop correctly
-
Polyploidy
changes in the number of whole sets of chromosomes (more than two sets of homologous chromosomes)
-
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
-
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
-
reciprocal translocation
breakage and reunion of two nonhomologous chromosomes that result in an exchange of segements - fertility reduced by 50%
-
acrocetnric chromosomes vs. metacentric chromosomes
- acrocentric: centromeer is near one end
- metcentric: centromere inthe middle
-
chromosome fusion
two nonhomologous acrocentric chromosomes undergo reciprocal translocation -- create a metacentric chromosome
-
fission heterozygote
metacentric chromosome synapses with acrocentric chromosomes as a "trivalent"
-
possible alterations of karyotypes
polyploidy, chromosome rearrangement, inversions/translocations, fissions/fusions (all are changes in chromosome number!)
-
locus
a site on a chromosome (the gene that occupies a site)
-
allele
particular form of a gene
-
developmental noise
variation arisen from random events at the molecular level in an organism - like fluctuating assymetry
-
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)
-
norm of reaction
variety of different phenotypic states that can be produced by a signle gentoype under different environmental conditions (genotype x environmental interaction
-
sources of variation
environment, developmental noise, maternal effect, epigenetic inheritance
-
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
-
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!
-
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
-
polymorphism
presence in a population of two or more variants (alleles/haplotypes)
opposed to monomorphic
-
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
-
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
-
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)
-
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
-
quantitative variation
continuous, fits a normal distirbutino - due to variation at several loci
-
variation in a phenotypic character
sum of genetic variance and environmental variance
-
heritability
the proportion of the phenotypic variance that is genetic variance
-
geographic variation
differences among populations in different geographic areas
-
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
-
hybrid zone
region in which genetically distinct parapatric forms interbreed
-
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)
-
ecotypes
phenotypes associated with a particular habitat, often in a patchy mosaic pattern
-
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
-
phenograms
diagrams that show the relative difference among populations or species
-
nonadaptive evolution
random fluctuations in allele frequencies can result in replacement of old alleles by new ones
-
demes vs. metapopulation
- deme: small independent populations
- metapopulation: ensemble of such demes
-
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
-
bottlenecks
restrictions in size thorugh which populations may pass
founder effect: random genetic drift from a small number of founderes form a different population
-
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!
-
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
-
the most important levels of selection
individual and genetic selection - turnover is much quicker than for populations/species
-
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)
-
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
-
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)
-
adaptive trait
one that enhances fitness compared with at elast some alternative traits
-
preadaptation
feature that fortuitously serves a new function
-
exaptations
a preadaptation that has been co-opted to serve a new function
-
complexity of a feature shows what
probably evolved by natural selection
-
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
-
directional selection
increases the proportion of genotypes witha more extreme value of the trait
-
overdominant vs underdominant
if the heterozygote has greatest fitness or lowest fitness
-
stabilizing selection
an intermediate phenotype is fittest - does not alter teh mean, but may reduce variation
-
diversifying (disruptive) selection
- unlikely to be symmetrical - usually shifts the mean
- Two or more phenotypes are fitter than the intermediates between them
-
parthenogenetic populations
asexually reproducing (reproduce onece, all at the same time, and then die)
very easy to determine fitness of these
-
mean fitness
average fitness of individuals in a population relative to the fittest genotype
-
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)
-
directional selection
homozygote for an advantageous allele has a fitenss equal to or greater than that of the heterozygote or any other genotype
-
cost of adaptation/trade-off
advantageous traits often have side effects that are disadvantageous in some environments
-
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
-
how can gene flow contribute to genetic variation?
if it keeps reintroducing deleterious alleles that are selected against in the population
-
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
-
balancing selection
keeps a lot of the genetic variation - maintains polymorphism (heterozygote advantage, antagonistic selection, frequency dependent selection,
-
antagonistic selection
opposing forces of natural selection - usually does not keep polymorphism
-
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
-
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
-
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
-
inverse frequency depenent selection
teh rarer a phenotype is in the population the greater its fitness
shift toward a stable equilibrium value
-
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!!
-
heterozygote disadvantage
heterozygote has lower fitness than either homozygote (underdominance) (initially more frequent allele will be fixed by selection)
-
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)
-
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)
-
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
-
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
-
QTL mapping
quantitative trait loci - use these regions as markers
-
phenotypuic variance
sum of genetic variance and environmental variance
-
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
-
faster than neutral rate of trait divergence means....
slower thatn entural rate of trait divergence means...
- directional selection!
- stabilizing selection!
-
truncation selection
imposes selection by breeding only those organisms with a certain state of a character
-
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
-
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
-
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
-
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
-
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)
-
phenotypic plasticity
a signel genotype may produce radically different phenotypes in response to environmental stimuli (norms of reaction)
-
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)
-
genetic assimilation
a character state that initialy developed in response to teh environment had become genetically determined
-
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
-
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
-
life histories
age specific probabilities of survival and reproducitve success characteristic of a species
-
optimality theory
which state of some charcter, among a specified set of plausible states would maximize individual fitness, subject to specified constraints
-
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
-
semelparous life history
females reproduce once and then die
-
iteroparous species
females reproduce more than once
-
constraints on the maximization of fiteness
phlogenetic constriaints, physiological/genetic constraints (like trade-offs - antagonistic pleiotriopy)
-
antagonistic pleiotropy
results from a trade-off, genotypes manifest an inverse relationship between different components of fitness
-
senescence
aging - why does this occur - selective advantage of an enhanced probability of survival declines with age
-
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)
-
reprouctive effort in iteroparous species vs. semelparaous
mroe effor t for the semelparaous species!
-
optimal clutch size
number of offspring that yields the greatest number of surviving offspring
-
delayed onset of reproduction is most likely in species iwth low/high rates of adult survival?
high
-
isogamous species
the uniting cells are the same size (they have mating types but not distinct species)
-
dioecious species
individduals are either female or male
-
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)
-
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)
-
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
-
reason for asexual organisms high rate of extinction?
slower adaptation!
-
sex ratio
proportion of males
-
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
-
incest avoidance
avoidance of mating with relatives
inbreeding increases homozygosity and is often accompanied by inbreeding depression
-
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)
-
sexual selection
differences among individuals of a sex in the number or reproductive capacity of mates they obtain
- contests between males
- female choice
-
arms race in sexual selection
evolution of ever more extreem traits by male contest (directional selection for bigger, faster, display features)
-
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
-
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
-
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!)
-
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
-
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
-
way males inflict harm on their mates
semen toxicity, forced copulation,
-
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)
-
anisogamous species
distinct sexes (eggs/sperm)
can be dioecious (us) or hermaphroditic
-
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
-
sexual dimorphism
differences in males/females traits
-
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)
-
brood parasitism
conflict! a female lays eggs in other females nests in addition to her own
-
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)
-
ESS
evolutionary stabel strategy
-
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)
-
cooperation vs. altruism
- cooperation: provides a benefit to the other individuals and the actor
- altruism: enhances fitness of other individuals but lowers their fitness
-
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
-
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
-
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
-
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
-
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
-
two factors under which kin selection can happen
- 1) able to distinguish related from unrelated
- 2) if individuals are associated with kin
-
trait group selection
altruism evolves by group selection -multilevel selection can influence trait evolution!
-
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
-
parental care trade off
will increase reproductive fitness BUT it comes at a cost (energy and time)
-
infanticide
males that replace a mated male kill existing offpsring of his mates - females become more fertile - have his own offpsring
-
abortion/killing of own offspring
a way to adaptively regulate brood size
-
siblicide
to get more food!
-
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)
-
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
-
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
-
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)
-
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
-
mutualism
interaction in which two genetic entities enhance each other's fitness - any advantage to one party provides an advantage to the otehr
-
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)
|
|