Lecture 18.doc

3 Pages
Unlock Document

University of Toronto St. George
Ecology & Evolutionary Biology
Stephen Wright

Lecture 18: • Questions About the Genomics of Adaptation  What fraction of the differences between humans and chimps are adaptive, deleterious and neutral  What genes were involved  What type of changes drove adaptation (protein, regulatory, gene duplication) • Where is the signal of positive selection?  Basic patterns of human diversity consistent with strong effects of history and weak purifying selection on human genome  Where is the signal for adaptation AKA positive selection? • Evidence for Adaptive Protein Evolution:  Ka/Ks >1 provides evidence for adaptive evolution, however this type of positive selection GENOME WIDE is rare  However Ka/Ks <1 could still mean that positive selection is acting in parts of the gene  Polymorphisms within species and divergence between species to test for adaptive evolution. There is some fixed differences between species since coalescence and polymorphisms within species • Kimura Neutral Theory Revised:  Uo= neutral mutation rate, t is the time  Thus the rate of molecular evolution will be 2Uot for two genes  Uo=FouT, where Fo is the fraction of sites that are neutral, and uT is the total mutation rate  Divergence is the fraction of neutral sites and the mutation rate factor into determining substitution rates  Understanding Ka/Ks:  If synonymous sites are completely neutral, Fo=1 and Ks=2uTt  Under Kimura’s neutral model, NS sites are either constrained by strong purifying selection or are neutral  Ka/Ks=(2FouTt)/(2uTt)=Fo = 0.23 from H-C divergence, NS sites that are neutral. 20% of AA mutations are neutral  The amount of diversity is determined by θ=4Neu0, same as 4NeFouT, however since Fo is 1 under the neutral theory then UT =Uo  θa/ θs=(4(Ne)FoUt)/(4NeUT)  Divergence of NS to Sand polymorphism of NS to S, then they should be the same ratio as they are determined by what the proportion of AA changes are neutral • Testing for the action of Selection: Using P and D:  Looking at a single species and their polymorphism data and also their divergence to an out-group  Under neutral theory, the amount of P and D (fixed differences) should be correlated, since both depend on the neutral mutation rate (F0UT)  If AA evolution is neutral, the ratio of AA polymorphisms to S polymorphism should be equal to the ratio of AA D to S D.  Pa/Ps = Da/Ds: McDonald-Kreitman test • Neutral Theory (Strong purifying selection): Pa/Ps =Da/Ds • Positive Selection: Da/Ds > Pa/Ps, as NS changes are happening faster than we expect under Kimura’s positive model. Excess of AA fixation between species as advantageous mutations spend less time as polymorphism and show elevated fixation • Weak Purifying Selection: Da/Ds < Pa/Ps, as deleterious mutations will be found as polymorphisms but selection will prevent them from getting fixed • McDonald-Kreitman Approach to testing Neutrality:  Neutral Model: N
More Less

Related notes for EHJ352H1

Log In


Don't have an account?

Join OneClass

Access over 10 million pages of study
documents for 1.3 million courses.

Sign up

Join to view


By registering, I agree to the Terms and Privacy Policies
Already have an account?
Just a few more details

So we can recommend you notes for your school.

Reset Password

Please enter below the email address you registered with and we will send you a link to reset your password.

Add your courses

Get notes from the top students in your class.