Evolution

production of copies that become inserted into new positions in the genome

particular DNA sequence that differs by 1 or more mutations from homologous sequences

• transition: substitution of a purine for purine or pyrimidine for pyrimidine
• transversion: substitutions of purines for pyrimidines or vice versa

synonymous: no effect on amino acid sequence (in the coding regions)

non: result in amino acid substitutions

process that alters the nunber of short repeats in microsatelites

when homologous DNA sequences differ at two or more base pairs --> new DNA sequences

when two homologous chromosomes are not perfectly aligned --> (two normals and 1 deletion, 1 duplication)

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

mutation of a mutant allele back to the allele from which it arose

mutation causing agents (UV light, X-ray, chemicals

based on several or many different genetic loci

teh increased variation in a population caused by new mutations in each generation

determine the basic body plan of an organism (distinct identity on each segment of the developing body) by having regulating gnes - homeotic mutatiosn

degree to which the heterozygote resembles one or the other homozygote

if heterozygotes phenotype is precisely intermediate between those of the homozygotes

affect more than one character

base pair substitutions (point mutations), insertions/deletions, replication slippage, recombination, transposable elements

description of its complement of chromosomes (number, shape, size, internal arrangement)

unbalanced chromosome complement - inviable/fails to develop correctly

changes in the number of whole sets of chromosomes (more than two sets of homologous chromosomes)

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 - it includes the centromere

paracentric - it does not include the centromere

alignment of the inverted chromosomes requires a loop! - cross over - inviable

breakage and reunion of two nonhomologous chromosomes that result in an exchange of segements - fertility reduced by 50%

• acrocentric: centromeer is near one end
• metcentric: centromere inthe middle

two nonhomologous acrocentric chromosomes undergo reciprocal translocation -- create a metacentric chromosome

metacentric chromosome synapses with acrocentric chromosomes as a "trivalent"

polyploidy, chromosome rearrangement, inversions/translocations, fissions/fusions (all are changes in chromosome number!)

a site on a chromosome (the gene that occupies a site)

particular form of a gene

variation arisen from random events at the molecular level in an organism - like fluctuating assymetry

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)

variety of different phenotypic states that can be produced by a signle gentoype under different environmental conditions (genotype x environmental interaction

environment, developmental noise, maternal effect, epigenetic inheritance

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

• 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!

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

presence in a population of two or more variants (alleles/haplotypes)

opposed to monomorphic

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

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

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)

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

continuous, fits a normal distirbutino - due to variation at several loci

sum of genetic variance and environmental variance

the proportion of the phenotypic variance that is genetic variance

differences among populations in different geographic areas

• 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

region in which genetically distinct parapatric forms interbreed

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)

phenotypes associated with a particular habitat, often in a patchy mosaic pattern

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

diagrams that show the relative difference among populations or species

random fluctuations in allele frequencies can result in replacement of old alleles by new ones

• deme: small independent populations
• metapopulation: ensemble of such demes

• 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

restrictions in size thorugh which populations may pass

founder effect: random genetic drift from a small number of founderes form a different population

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!

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

individual and genetic selection - turnover is much quicker than for populations/species

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)

transmitted at a higher rate than the rest of an individuals genome and are detrimental (not advantageous at least) to teh organism

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)

one that enhances fitness compared with at elast some alternative traits

feature that fortuitously serves a new function

a preadaptation that has been co-opted to serve a new function

probably evolved by natural selection

way of inferring the adaptive significance of a feature - compare sets of species to pose or test hypotheses on adaptation and other evolutionary phenomena

increases the proportion of genotypes witha more extreme value of the trait

if the heterozygote has greatest fitness or lowest fitness

an intermediate phenotype is fittest - does not alter teh mean, but may reduce variation

• unlikely to be symmetrical - usually shifts the mean
• Two or more phenotypes are fitter than the intermediates between them

asexually reproducing (reproduce onece, all at the same time, and then die)

very easy to determine fitness of these

average fitness of individuals in a population relative to the fittest genotype

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)

homozygote for an advantageous allele has a fitenss equal to or greater than that of the heterozygote or any other genotype

advantageous traits often have side effects that are disadvantageous in some environments

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

if it keeps reintroducing deleterious alleles that are selected against in the population

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

keeps a lot of the genetic variation - maintains polymorphism (heterozygote advantage, antagonistic selection, frequency dependent selection,

opposing forces of natural selection - usually does not keep polymorphism

a fluctuating environment may favor different genotypes in different generations

different genotypes may be best adapted to different microhabitats or resources

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

maintains polymorphisms, the fitenss of a genotype depends on teh genotype frequencies in the population

often seen when genotypes competet for limiting resources

teh rarer a phenotype is in the population the greater its fitness

shift toward a stable equilibrium value

fitness of a genotype is greater the more frequent it is in the population

whichever allele is initally more frequent will be fixed!!

heterozygote has lower fitness than either homozygote (underdominance) (initially more frequent allele will be fixed by selection)

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)

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)

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

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

quantitative trait loci - use these regions as markers

sum of genetic variance and environmental variance

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

• directional selection!
• stabilizing selection!

imposes selection by breeding only those organisms with a certain state of a character

when organisms stopped responding to selection - irregularities in artificial selection are due to teh origin and fixation of new mutations with large effects

natural selection! it opposes artificial selection. The selected trait is extreme values ahve lower fitness

• 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

• 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

the two characters may evolve to their optimum only slowly (may evolve temporarily in a maladaptive direction)

a signel genotype may produce radically different phenotypes in response to environmental stimuli (norms of reaction)

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)

a character state that initialy developed in response to teh environment had become genetically determined

functionally related characteristics should be genetically correlated with another: they shoudl reamin coordinated even as they vary within species and as they evolve

• 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

age specific probabilities of survival and reproducitve success characteristic of a species

which state of some charcter, among a specified set of plausible states would maximize individual fitness, subject to specified constraints

strategy such that if all the members of a population adopt it, then no mutatn strategy could invatde under teh influnce of natural selection

females reproduce once and then die

females reproduce more than once

phlogenetic constriaints, physiological/genetic constraints (like trade-offs - antagonistic pleiotriopy)

results from a trade-off, genotypes manifest an inverse relationship between different components of fitness

aging - why does this occur - selective advantage of an enhanced probability of survival declines with age

• 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)

mroe effor t for the semelparaous species!

number of offspring that yields the greatest number of surviving offspring

high

the uniting cells are the same size (they have mating types but not distinct species)

individduals are either female or male

• vegetative propagation: offpsring from a group of cells
• parthenogenesis : from a single cell
• apomixis (offspring develops from an unfertilized egg)

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)

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

slower adaptation!

proportion of males

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

avoidance of mating with relatives

inbreeding increases homozygosity and is often accompanied by inbreeding depression

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)

differences among individuals of a sex in the number or reproductive capacity of mates they obtain

• contests between males
• female choice

evolution of ever more extreem traits by male contest (directional selection for bigger, faster, display features)

• 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

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

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!)

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

genes that govern male versus female characters may conflict

change in male character --> neutralized or paried by evolution of a female character --> chain reaction

semen toxicity, forced copulation,

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)

distinct sexes (eggs/sperm)

can be dioecious (us) or hermaphroditic

• 1) siblings would be in less direct competition (not exactly identical)
• 2) counteracting deleterious mutations
• 3) adaptation to fluctuating , unpredictable environmental conditions

differences in males/females traits

• promiscous
• polygyny
• polyandry
• monogamy (with some extra pair copulation, brood parasitism)

conflict! a female lays eggs in other females nests in addition to her own

• 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)

evolutionary stabel 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: provides a benefit to the other individuals and the actor
• altruism: enhances fitness of other individuals but lowers their fitness

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

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

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

effect on the individual with it (direct) and teh fitness of other individuals that cary copies of the same allele (indirect) --> kin selection

• 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

• 1) able to distinguish related from unrelated
• 2) if individuals are associated with kin

altruism evolves by group selection -multilevel selection can influence trait evolution!

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

will increase reproductive fitness BUT it comes at a cost (energy and time)

males that replace a mated male kill existing offpsring of his mates - females become more fertile - have his own offpsring

a way to adaptively regulate brood size

to get more food!

offpsring try to obtain as much resources from a parent (often much more than waht is optimal for the parent to give to them)

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

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

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)

symbiont and host are chained togheter and the success of the symbionts depends on teh fitness of the host- restrained reproduction is favored - mutualism

interaction in which two genetic entities enhance each other's fitness - any advantage to one party provides an advantage to the otehr

may have been helpers - were tolerated as logn as they played a socially expected procreative role (may have been as reproductive as heterosexuals)