Re: [R-sig-phylo] simulate Ne changes on a given phylogeny

[Jacob Berv]

Yes, this has come up in my reading…but there do seem to be situations where 
’nearly neutral’ substitutions can be negatively or positively associated with 
population size:

From Lanfear 2014 Population size and the rate of evolution:

"Putting aside variation in the mutation rate, we largely expect the total rate 
of evolution to be negatively correlated with Ne if slightly deleterious 
mutations dominate evolution, and to be positively correlated with Ne if 
advantageous mutations dominate evolution.”
"On the other hand, any process that leads to an association between Ne and 
mutation rates will cause a similar association between Ne and neutral and 
effectively neutral substitution rates. These processes could include effects 
such as the evolution of mutation rates, and the co-variation of Ne with 
life-history traits such as generation time”

I think I need to read more about how to simulate these different kinds of 
demographic scenarios.

I suppose the question is, what is the more likely null hypothesis? That 
mutation rates can change extremely rapidly? Or that demographic fluctuations 
(pop size, generation time) can induce changes in the detectable substitution 
rate among lineages. 

Jake



> On Oct 17, 2015, at 11:21 PM, Liam J. Revell  wrote:
> 
> Hi Jacob.
> 
> Can I add the somewhat boring & probably obvious comment that under the 
> neutral theory of molecular evolution the substitution rate is independent of 
> the effective population size?
> 
> All the best, Liam
> 
> Liam J. Revell, Associate Professor of Biology
> University of Massachusetts Boston
> web: http://faculty.umb.edu/liam.revell/
> email: liam.rev...@umb.edu
> blog: http://blog.phytools.org
> 
> On 10/17/2015 11:01 PM, Jacob Berv wrote:
>> Hmmm that seems somewhat indirect but might work… I’ll look into that.
>> 
>> To give you more information - I’m actually trying to come up with a way to 
>> test the idea that substitution rate shifts detected with a relaxed 
>> molecular clock (BEAST) may be driven by changes in effective population 
>> size. Simulating data for particular scenarios, and then running that 
>> simulated data through BEAST could be a useful way to test some explicit 
>> hypotheses I’m interested in. But I have to simulate the data first.
>> 
>> Jake
>> 
>> 
>>> On Oct 17, 2015, at 10:40 PM, Brian O'Meara  wrote:
>>> 
>>> Dick Hudson's ms software can simulate gene trees along a species tree or 
>>> network with migration, changing population size, etc. The package phyclust 
>>> can call ms. You could then just simulate nucleotides on these gene trees.
>>> 
>>> Best,
>>> Brian
>>> 
>>> ___
>>> Brian O'Meara
>>> Associate Professor
>>> Dept. of Ecology & Evolutionary Biology
>>> U. of Tennessee, Knoxville
>>> http://www.brianomeara.info 
>>> 
>>> Postdoc collaborators wanted: http://nimbios.org/postdocs/ 
>>> 
>>> Calendar: http://www.brianomeara.info/calendars/omeara 
>>> 
>>> On Sat, Oct 17, 2015 at 10:12 PM, Jacob Berv 
>>> > 
>>> wrote:
>>> Dear R-sig-phylo,
>>> 
>>> I have a somewhat general simulation question and I was hoping someone on 
>>> here might have some insight.
>>> 
>>> I’m trying to figure out if it’s possible to simulate nucleotide sequence 
>>> data (an arbitrary number of neutral loci under a multi species coalescent 
>>> model), on an ultrametric input topology (where tips represent species), 
>>> with user defined changes in effective population size at the start and end 
>>> of a particular internal branch. In my searching I’ve come across some 
>>> software by Deren Eaton (https://github.com/dereneaton/simLoci 
>>>  
>>> >> >) that looks like it might do what 
>>> I want - but I’m not sure. It looks like I can specify migration events 
>>> between taxa, but perhaps not population size changes on internal branches. 
>>> There are many other applications for simulating sequence data but I am not 
>>> familiar with any of them. Any thoughts would be appreciated!
>>> 
>>> Thanks,
>>> 
>>> Jacob Berv
>>> 
>>> Ph.D. Student
>>> Lovette Lab
>>> Cornell Laboratory of Ornithology
>>> 
>>> 
>>> [[alternative HTML version deleted]]
>>> 
>>> ___
>>> R-sig-phylo mailing list - R-sig-phylo@r-project.org 
>>> 
>>> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo 
>>> 
>>> Searchable archive at 
>>> http://www.mail-archive.com/r-sig-phylo@r-project.org/ 
>>> 
>> 
>> Jacob Berv
>> 
>> Ph.D. Student
>> Lovette Lab
>> Cornell Laboratory 

Re: [R-sig-phylo] simulate Ne changes on a given phylogeny

[Santiago Sánchez]

Hi Jacob,

You might want to check Joseph Heled's python package biopy 
(https://code.google.com/p/biopy), I know it has some simulation capabilities. 
Also check Z. Yang's program MCMCcoal, I know some people have used it for 
simulation analyses in BPP.

Cheers,
Santiago

Sent from my iPhone
___
R-sig-phylo mailing list - R-sig-phylo@r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
Searchable archive at http://www.mail-archive.com/r-sig-phylo@r-project.org/