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59 Cards in this Set

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Mutation

the creation of a new allele.

Substitution

replacement of an allele in a population.

Neutral mutations

at the molecular level most evolutionary changes are not caused by natural selection but by random drift of mutant alleles that are neutral. Neutral mutations are changes in the DNA sequence that are neither beneficial nor detrimental to the ability of the organism to survive and reproduce. In pop. genetics, mutations in which, natural selection does not affect the spread of mutation in a species are called neutral mutations.

Neutral theory

Replacement of an allele by a new allele. Depends on mutation rate, more mutation generates more mutants, shorter generations results in more mutations, smaller pop are more greatly affected by drift. Genetic variation in a pop is determined by an increase in mutation and a decrease in pop size.

Nearly neutral theory

neutral mutation rate (v) should vary among species as a function of gen time. Over any time interval, more neutral mutations should occur in species with short gen times than in species with long gen times.

Synonymous vs. nonsynonymous substitutions

syn - these are sometimes called silent substitutions (not always silent though), and what happens is that one nucleotide base in a codon is changed so that the amino acid that it would code for is still the same as the amino acid that it codes for now.


non syn - this is a nucleotide substitution that will change the amino acid that the codon codes for, thus changing the protein that is produced.

linkage

This means that two alleles are most likely going to be inherited together as a unit, when they are separated the offspring with the seperate alleles are called recombinants. These alleles are close together and less likely to be separated, they are linked.

fixation

Pop genetics, is the change in a gene pool from a situation where there exists at least two variants of a particular gene, to a gene pool where there is only one allele.

hitchhiking

the change in frequency of an allele that is caused by linkage to a positively or negatively selected allele at another locus.

hitchhiking related to fixation

when the mutations that are linked to an advantageous mutation goes to fixation, where it replaces an ancestrial allele completely.

hitchhiking related to extinction

when the mutations on the same chromosome as the one that underwent hitchhiking is eliminated from the pop. This is background selection, which is a type of purifying negative selection of linked deleterious alleles.

haplotype

a set of DNA variations, or polymorphisms that tend to be inherited together. Can refer to a combination of a group of alleles on the same chromosome.

linkage equilibrium

if two traits/loci are in linkage equilibrium it means that they are inherited independently in each generation. Linkage disequilibrium would equal 0. The frequencies of the haplotypes are the same value that they would be if they were combined at random.

linkage disequilibrium

certain alleles of each gene are inherited together more often than would be expected by chance, so the traits are linked. It could also mean that the traits are so beneficial in their environment that the offspring with both alleles will have an increased fitness. Causes include the selection of multilocus genotypes, drift, and the mixing of pops with different allele frequencies.

Imbreeding depression

the reduced biological fitness in a given pop as a result of inbreeding. This is why endangered species can die out so fast, inbreeding brings out deleterious recessive alleles and the species will not survive.

Substitutions vs. mutations

sub - the replacement of and old allele with a new one.


mut - new alleles are created.

Red Queen hypothesis

A species must constantly adapt and evolve to pass on genes to the next generation, the competing species will in tern adapt in order to compete with the other species. ex: parasite and host are constantly adapting to each other.

Substitution rate

the rate at which one allele is replaced by a new allele, it depends on the size of a pop or the likeihood that an allele shows up by selection.

Would rates of divergence be lower for nonsynonymous substitutions than for syn substitutions?

Rates of divergence would be lower for nonsyn because of functional constraints and lower substitution rates.

sexual vs. asexual

asexual - generates offspring that are genetically identical to the parent


sexual - two parents contribute genetic info to produce diverse offspring.


asexual pops will overrun pops that undergo sexual reproduction, however they are more suseptible to changing environements.

Muller's Ratchet

functionally important genes may be lost when an organism's genes are transferred vertically, without recombination from sex. This applies to any deleterious mutation that occurs when an organism (bacteria) is transmitted to the offspring.

genetic load

the difference between the fitness of a genotype in a pop and the fitness of the abserved average in a pop. Pops with a low genetic load will be healthier, have fitness that is less dispersed, and have offspring that are more likely to survive and make babies.

continuous variation

variations in phenotypic traits (weight and height) that are distributed in a bell curve/continuum instead of categories.

blending inheritance

the (incorrect) theory that traits from two parents will create an intermediate trait in the offspring.

segregation and independent assortment

law of segregation - states that the alleles of a given locus segregate into separate gametes.


law of independent assortment- states that the alleles of one gene sort into gametes independently of the alleles of another gene.

QTL mapping

Quantitative trait loci are stretches of DNA containing or linked to genes that underlie a quantitative trait.

Quantitative traits

traits that are controlled by one or more genes and the environment. ex: height, you can have tall parents, but you could have been calcium deficient. Or short parents but tons of calcium.

genetic marker

gene or DNA sequence with a known location on a chromosome that can be used to identify individuals or species, can be described as a variation.

Broad sense vs. narrow sense heritability

broad - the ratio of genetic variance/total phenotypic variance.


narrow - the ratio of additive genetic variance/total phenotypic variance.

LOD score

(logarithm of the odds score) measure of how likely an outcome is for a given recombination frequency relative to free recombination. High freq of association allele to phenotype = reject null.

Adaptation

a feature produced by natural selection in the context of its current function.

exaptation

evolves early but is used advantageously for something else later on. ex: feathers on dinos and eventually feathers on wings, same trait but used for running in dinos and flying in birds.

panselection

when people try to explain everything in terms of adaptation.

sexual dimorphism

difference in males and females in a species.

fundimental assymetry of sex

higher investment from one sex in terms of producing offspring (females making the babies), females are generally more selective of their mates (limited reproductive potential), male spends energy on looking pretty to attract female (limited reproductive opportunity).

Intrasexual selection

when member of the same gender and species compete for the opposite gender mates. ex: sperm competition = sneaky fishes, infanticide = lions killing other males cubs.

Intersexual selection

the female chooses the male. The males develop courtship rituals, dancing, decor, plumage.

good gene hypothesis

- handicap hypothesis - the ability to survive despite the cost and display.


- parasite hypothesis - has the energy to make a big display, must be resistant to parasites.


- developmental stability - more symmetry = good for offspring.

sexy son hypothesis

- males are just sexy and are displaying sexiness so when they mate with the females they will produce sexy offspring.


- only limit being the cost of ornament becoming too much.

sociobiology

at least some part of behavior is heritable, most behavior is polygenic, meaning it is influenced by more than one gene. It is also influenced by the environment.

Altruism

the behavior of one individual (A) in a species, to increase the fitness of another individual (b) in the same species. This decreases the fitness of individual (A).


reasons for this


1. group selection - the food of the species


2. inclusive fitness/kin selection - you are related so some genes get passed down even if they are not yours.


3. reciprocal altruism - they will do the same thing for you.

can pops be the target of selection?

Yes the social spiders showed us that specific phynotype frequencies shaped the overall fitness of the species as a pop.

kin selection

direct fitness - you produce babies


indirect fitness - your relative produces babies.

relatedness

(r) the probability that alleles are identical by descent.


Hamilton's rule


B(r)-C>0


B=benefit to recipient


r=relatedness


C=cost to actor

neutral theory as Null

dN/dS=1 neutral selection


dN/dS<1 negative selection


dN/dS>1 positive selection

genetic drift

this can be brought about by migration and isolating populations, alleles can disappear or become more prominent, but it is important to remember that it is a random process that does not produce adaptations.

Stuff about large pops

Large pops have more mutations, but fixation by drift is less likely in large pops. Neutral

Stuff about small pops

drift is stronger in small pops, but fewer new mutations. Neutral

Observation - rates of divergence in absolute time roughly independent of generation time.


Why wouldn't we expect this to be true.

shorter generations should mean more mutations.

organisms with short gen times have __________ _______________

larger populations

organisms with long gen times have __________ ______________

small populations,


drift is more effective at fixing new alleles, so selection is less important. Balances out in absolute time.

Synonymous not necessarily silent

availability of tRNAs might differ, affects translation.

group selection

for the good of the species

a gene for altruistic behavior is likely to spread if...

Br-C>0

Pleiotrophy

genes with multiple effects.

phenotypic plasticity

the plasticity of phenotypes in different conditions, the environment will influence the phynotypes slightly.

causes of disequilibrium

1. fitness of an allele may depend of genotype at another loci


2. drift - new mutations are in disequilibrium


3. a mixture of pops with different allele frequencies.

What does sex do to pops in linkage disequilibrium?

Sex reduced linkage disequilibrium

What does inbreeding do to heterozygosity?

In a small pop inbreeding increases homo and leads to less hetero.