molec evo quiz 7

what does absolute time estimation allow for

to connect biological and geological history

phylogenies with branch lengths proportion to time provide

more information about evolutionary history than unrooted trees with branch lengths in units of subsitution/sites

problems with fossil record

biased towards organisms that fossilize well

geological processes destroy them

gaps and missing data

molecular clock

mutations accumulate in proteins in a linear relationship to species divergence time

zuckerkandl and pauling (molec clock)

rate of evolution is approximately constant over time in all lineages

changes within a protein are clock like and sequence divergence measures elapsed time

original molec clock hypothesis

for one protein evolutionary rate is constant across lineages

does not claim different proteins change at the same rate

does not claim evolution is gradual at the phenotypic level

molecular clock is predicted by

neutral theory

in small populations there are — number of new mutants but — probability of fixation

lower higherin

in large populations there are — number of new mutants but — probability of fixation

higher , lower

neutral theory

evolutionary rate is independet of population size and there is a constant neutral rate of evolution

relative rate test evaluates

whether molecular clock holds for a given taxa and sequence

is there a global molecular clock

no, rates differ among mammalian orders and within them, humans are slowest primates. evertyhing has to accomodate rate variation

why is the clock not constant (selectionist explanation)

rate reflects the strength and direction of selection which varies with the enviornment and life hsitory

why is the clock not constant (neutralist explanation)

rate reflects the mutation rate which varies for mechanical reasons

generation time, efficinecy of dna repair, and metabolic rate

strict global clock model

one rate parameter for the whole tree

substution ratei s constant over time

(not true known from relative rate test)

relaxed clocks

every branch has its own rate drawn from distirbution

uncorrelated relaxed clock

each barnch draws indepdendelty, usually from log normalau

autocorrelated relaxed clock

substitution rate evovle gradually over time. closely related lienages have similar rates.

autocorrelated relaxed clock says rate is —- uncorrelated says its —-

heritated, not heritable

where are clocks the hardest

extremes

over short intervals mutations are counted not substitutions

over long intervals you undercount because of saturation

clock calibration

a fossil fixes the age of one node it sites on

every other node is dated by propagating outwards

propagation needs an assumption about how the rate behaves between calibrated node and everywhere else