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Question 1

what is tree reconciliation used for

Answer 1

why two phylogenies dont match

Question 2

p elements and trees

Answer 2

by looking aty clades see a random element in a clade that doesnt have p eleements. This shows recent entry of P elements into D melanogaster

Question 3

why can tree reconciliation be cmplicated?

Answer 3

duplications
sorting events (extinction)
cannot say which is more likely so have to calculate probabilities

Question 4

what are genealogies?

Answer 4

the study of families and the tracing of their lineages and history.

Question 5

what is coalescent process?

Answer 5

ancestry of this sample is traced backwards in time to the point where these two lineages coalesce in their MRCA. Coalescent theory seeks to estimate the expectation of this time period and its variance.

Question 6

what is coalescent theory?

Answer 6

retrospective stochastic model of population genetics that relates genetic diversity in a sample to demographic history of the population from which it was taken. That is, it is a model of the effect of genetic drift, viewed backwards in time, on the genealogy of antecedents.

Question 7

what is time back to MRCA?

Answer 7

-4N generations

Question 8

do larger pops have shorter or longer coalesce times?

Answer 8

longer

takes longer to get back to lca

Question 9

what different scenarious can you see on coalesce trees?

Answer 9

balancing selection - split into Y earlier
negative selection (flattened tops)
positive selection at single locus/population bottleneck single splits into lots

REMEBER SHAPES

Question 10

what does neutral drift in growing population versus static population look like?

Answer 10

growing-longer ends

static is still

Question 11

what does exponential growth look like

Answer 11

lengthened ends (out of proportion ends)

Question 12

what does population constant over time look like

Answer 12

normal length ends relative to rest (in proportion)