The Dynamics of Positive Selection on the Mammalian Tree
description
Transcript of The Dynamics of Positive Selection on the Mammalian Tree
![Page 1: The Dynamics of Positive Selection on the Mammalian Tree](https://reader036.fdocuments.net/reader036/viewer/2022062410/5681591e550346895dc646ad/html5/thumbnails/1.jpg)
1
The Dynamics of Positive Selection on the Mammalian Tree
Carolin KosiolCornell University
Joint with: Tomas Vinar, Rute Da Fonseca, Melissa Hubisz,Carlos Bustamante, Rasmus Nielsen and Adam Siepel
![Page 2: The Dynamics of Positive Selection on the Mammalian Tree](https://reader036.fdocuments.net/reader036/viewer/2022062410/5681591e550346895dc646ad/html5/thumbnails/2.jpg)
2
6 high-quality genomes of eutherian mammals
16529 human / chimp / macaque / mouse / rat / dog orthologous genes.
544 genes identified to be under positive selection using codon models.
Positive selection in six mammalian genomes
0.05
subst/site
human
macaque
mouse
rat
dog
chimp
![Page 3: The Dynamics of Positive Selection on the Mammalian Tree](https://reader036.fdocuments.net/reader036/viewer/2022062410/5681591e550346895dc646ad/html5/thumbnails/3.jpg)
3
Qij
=
0 i, j differ by > 1 nucleotide
j i, j synonymous transversion
j i, j synonymous transition
j i, j nonsynonymous transversion
j i, j nonsynonymous transition
(Goldman &Yang 1994,Yang et al. , 2000)
where : transition/transversion rate ratioj : equilibrium frequency of codon j : nonsynonymous/synonymous rate ratio
Codon models
< 1 purifying selection = 1 neutral evolution > 1 positive selection
![Page 4: The Dynamics of Positive Selection on the Mammalian Tree](https://reader036.fdocuments.net/reader036/viewer/2022062410/5681591e550346895dc646ad/html5/thumbnails/4.jpg)
4
• Based on continuous-time Markov models of codon evolution
• Compare null model allowing for negative
selection (ω<1) or neutral evolution (ω=1)
with alternative model additionally allowing
for positive selection (ω>1)
• Both models allow ω to vary across sites
• Can have foreground branches with PS and background branches without
• Applied separately to each gene
(Nielsen & Yang, 1998; Yang & Nielsen, 2002)
Branch-Site LikelihoodRatio Tests (LRTs)
![Page 5: The Dynamics of Positive Selection on the Mammalian Tree](https://reader036.fdocuments.net/reader036/viewer/2022062410/5681591e550346895dc646ad/html5/thumbnails/5.jpg)
5Total: 544 positively selected genes (PSGs) identified
10 18 7 10
chimp macaquehuman hominid
400
Branch and clade LRTs
6156 21 24
primateclade
primatebranch
rodentclade
rodentbranch
![Page 6: The Dynamics of Positive Selection on the Mammalian Tree](https://reader036.fdocuments.net/reader036/viewer/2022062410/5681591e550346895dc646ad/html5/thumbnails/6.jpg)
6
Co-evolution in complement immunity
P<0.05
FDR<0.05
![Page 7: The Dynamics of Positive Selection on the Mammalian Tree](https://reader036.fdocuments.net/reader036/viewer/2022062410/5681591e550346895dc646ad/html5/thumbnails/7.jpg)
7
29-1 = 511 possible selection histories on the 9 branch
mammalian phylogeny
![Page 8: The Dynamics of Positive Selection on the Mammalian Tree](https://reader036.fdocuments.net/reader036/viewer/2022062410/5681591e550346895dc646ad/html5/thumbnails/8.jpg)
8
• Many of the likelihoods of the 511 models might be very similar or identical.
• Models are not nested.
• Bayesian analysis looks at distribution of selection histories.
• Bayesian analysis allows “soft” (probabilistic) choices of selection histories.
• We can compute prevalence of selection on individual branches and clades that considers uncertainty of selection histories.
Why Baysian Model Selection?
![Page 9: The Dynamics of Positive Selection on the Mammalian Tree](https://reader036.fdocuments.net/reader036/viewer/2022062410/5681591e550346895dc646ad/html5/thumbnails/9.jpg)
9
Two evolutionary modes:
Selected
Non-selected
Parameters describing the switching process:
b,G : probability that gene gains positive selection on
branch b
b,L : probability that gene loses positive selection on
branch b
Bayesian Switching Model
![Page 10: The Dynamics of Positive Selection on the Mammalian Tree](https://reader036.fdocuments.net/reader036/viewer/2022062410/5681591e550346895dc646ad/html5/thumbnails/10.jpg)
10
X =(X1, …XN) be the alignment data, with Xi alignment of ith gene
Z=(Z1,…,ZN) be the set of selection histories, with Zi denoting 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,
Bayesian Switching Model
![Page 11: The Dynamics of Positive Selection on the Mammalian Tree](https://reader036.fdocuments.net/reader036/viewer/2022062410/5681591e550346895dc646ad/html5/thumbnails/11.jpg)
11
Mapping selection histories to switches (cont.)
(0,0) (0,1)
(1,1) (1,1)(1,1)
(1,1)
(1,1)
Gain of pos. selection (0,1) : nbG
Absence of gain of pos. selection (0,0) : 1- nbG
Loss of pos. selection (0,1) : nbL
Absence of loss pos. selection (1,1) : 1- nbL
![Page 12: The Dynamics of Positive Selection on the Mammalian Tree](https://reader036.fdocuments.net/reader036/viewer/2022062410/5681591e550346895dc646ad/html5/thumbnails/12.jpg)
12
Bayesian Switching model
![Page 13: The Dynamics of Positive Selection on the Mammalian Tree](https://reader036.fdocuments.net/reader036/viewer/2022062410/5681591e550346895dc646ad/html5/thumbnails/13.jpg)
13
Putting everything together …
with
(Beta distrib =1, =9)
(Product relevant switching prob)
(Likelihoods from codon models
assuming selection histories Zj)
![Page 14: The Dynamics of Positive Selection on the Mammalian Tree](https://reader036.fdocuments.net/reader036/viewer/2022062410/5681591e550346895dc646ad/html5/thumbnails/14.jpg)
14
Gibbs sampling
Variables Z and are unobserved. We sample from the joint posterior distribution
by a Gibbs sampler that alternates between samplingeach Zi conditional on Xi and previously sampled and sampling conditional on a previously sampled Z.
![Page 15: The Dynamics of Positive Selection on the Mammalian Tree](https://reader036.fdocuments.net/reader036/viewer/2022062410/5681591e550346895dc646ad/html5/thumbnails/15.jpg)
15
Inferred Rates of Gain and Loss
gain loss
![Page 16: The Dynamics of Positive Selection on the Mammalian Tree](https://reader036.fdocuments.net/reader036/viewer/2022062410/5681591e550346895dc646ad/html5/thumbnails/16.jpg)
16
Episodic selection on the mammalian tree
• Most genes appear to have switched between evolutionary modes multiple times.
• Posterior expected number of modes switches 1.6 (0.6 gains, 1.0 loses)
• An expected 95% of PSGs have experienced at least once, 53% at least twice.
• These observations are qualitatively in agreement with Gillespie’s episodic molecular clock.
![Page 17: The Dynamics of Positive Selection on the Mammalian Tree](https://reader036.fdocuments.net/reader036/viewer/2022062410/5681591e550346895dc646ad/html5/thumbnails/17.jpg)
17
Inferred Number of Genes Under Positive Selection
(281-333)
(213-292)
(255-325)
(204-278)(357-426)
(338-382)
(32-62) (234 -327)
(219-257)
(183-232)(119-162)
(318-360)
![Page 18: The Dynamics of Positive Selection on the Mammalian Tree](https://reader036.fdocuments.net/reader036/viewer/2022062410/5681591e550346895dc646ad/html5/thumbnails/18.jpg)
18
Complement components C7 and C8B
• Components C7 and C8B encode proteases in the membrane attack complex
• Differences in complement proteases are thought to explain certain differences in immune responses of humans and rodents.
C7: PP=0.98 C8B: PP=0.93
(Puente et al, 2003)
![Page 19: The Dynamics of Positive Selection on the Mammalian Tree](https://reader036.fdocuments.net/reader036/viewer/2022062410/5681591e550346895dc646ad/html5/thumbnails/19.jpg)
19
Glycoprotein hormones GGA
• CGA is alpha subunit of
chorionic gonadotropin,
luteinizing hormone,
follicle stimulating, and thyroid
stimulating hormone.
• The alpha subunits of 4 hormones are identical, however,
their beta chains are unique and confer biological specificity.
• Beta subunits CGB1 and CGB2 are thought to have
originated from gene duplication in the common ancestor of
humans and great apes.
PP = 0.82
![Page 20: The Dynamics of Positive Selection on the Mammalian Tree](https://reader036.fdocuments.net/reader036/viewer/2022062410/5681591e550346895dc646ad/html5/thumbnails/20.jpg)
20
Summary and Future Work
• Bayesian analysis allows the study of patterns and the episodic nature of positive selection on the mammalian tree.
• Most probable selection histories can be identified for individual genes.
• Ideally, we like to model mode switches in continuous time.
• Compare functions of genes with high and low expected number of switches.
• Is the selection history predictive of function?
![Page 21: The Dynamics of Positive Selection on the Mammalian Tree](https://reader036.fdocuments.net/reader036/viewer/2022062410/5681591e550346895dc646ad/html5/thumbnails/21.jpg)
21
Resource
http://compgen.bscb.cornell.edu/projects/mammal-psg/
![Page 22: The Dynamics of Positive Selection on the Mammalian Tree](https://reader036.fdocuments.net/reader036/viewer/2022062410/5681591e550346895dc646ad/html5/thumbnails/22.jpg)
22
Thanks
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)Rasmus NielsenRute Da Fonseca
NIH and NSF for funding