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The Dynamics of Positive Selection on the Mammalian Tree. Carolin Kosiol Cornell University < email@example.com >. Joint with: Tomas Vinar, Rute Da Fonseca, Melissa Hubisz, Carlos Bustamante, Rasmus Nielsen and Adam Siepel. human. chimp. macaque. mouse. rat. dog. 0.05 subst/site.
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Joint with: Tomas Vinar, Rute Da Fonseca, Melissa Hubisz,
Carlos Bustamante, Rasmus Nielsen and Adam Siepel
0 i,j differ by > 1 nucleotide
ji, j synonymous transversion
j i, j synonymous transition
j i, j nonsynonymous transversion
j i, j nonsynonymous transition
< 1purifying selection
: transition/transversion rate ratio
j : equilibrium frequency of codon j
: nonsynonymous/synonymous rate ratio
(Goldman &Yang 1994,Yang et al. , 2000)
selection (ω<1) or neutral evolution (ω=1)
with alternative model additionally allowing
for positive selection (ω>1)
(Nielsen & Yang, 1998; Yang & Nielsen, 2002)
Branch and clade LRTs
Total: 544 positively selected genes (PSGs) identified
X =(X1, …XN) be the alignment data, with Xi alignment of ith gene
Z=(Z1,…,ZN) be the set of selection histories, with Zidenoting history of ith gene.
is set of switching parameters
Assume independence of genes X and histories Z, and conditional independence X and given Z. Thus,
(Beta distrib =1, =9)
(Likelihoods from codon models
assuming selection histories Zj)
(Product relevant switching prob)
Variables Z and are unobserved. We sample from the
joint posterior distribution
by a Gibbs sampler that alternates between sampling
each Zi conditional on Xi and previously sampled and
sampling conditional on a previously sampled Z.
(Puente et al, 2003)
PP = 0.82
Siepel Lab (Cornell)
Adam Siepel, Tomas Vinar, Brona Brejova,
Adam Diehl, Andre Luis Martins
Bustamante Lab (Cornell)
Carlos Bustamante,Adam Boyko, Adam Auton, Keyan Zhao,
Abra Brisbin, Kasia Bryc, Jeremiah Degenhardt,
Lin Li, Kirk Lohmueller, Weisha Michelle Zhu, Amit Indap
Nielsen lab (Berkeley)
Rute Da Fonseca
NIH and NSF for funding