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

[Rob Lanfear]

Hi Jake,

Weighing in late here, and just with an opinion on your last question.

In my opinion, it is unlikely that the mutation probability per generation
would change very rapidly. On the assumption that it is already somewhere
near some limit (e.g. the drift barrier that Lynch proposed, or some other
limit), then a rapid change would require the fixation of some alleles of
large effect, which is unlikely.

However, the mutation rate per year could change relatively rapidly, e.g.
because the generation time can change with demography. (E.g., higher
offspring survival leads to a shorter generation time, all else being
equal).

Finally, I think it's highly likely that demographic fluctuations influence
the substitution rate, independently of the mutation rate, via their
influence on the strength of genetic drift. Pretty much all the theoretical
and empirical results point in that direction, for non-neutral mutations.

Cheers,

Rob

On 19 October 2015 at 03:04, Jacob Berv 
wrote:

> 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/ <
> http://nimbios.org/postdocs/>
> >>> Calendar: http://www.brianomeara.info/calendars/omeara <
> http://www.brianomeara.info/calendars/omeara>
> >>> On Sat, Oct 17, 2015 at 10:12 PM, Jacob Berv <
> jakeberv.r.sig.ph...@gmail.com >
> 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
>  <
> https://github.com/dereneaton/simLoci <
> https://github.com/dereneaton/

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

[Jacob Berv]

Wow this is awesome - it totally works! Thanks! This is a hugely useful tool! 

Jake

> On Oct 22, 2015, at 12:35 PM, Santiago Sánchez  
> wrote:
> 
> Hi Jacob,
> 
> There is a package named OutBreakTools (
> https://cran.r-project.org/web/packages/OutbreakTools/index.html) that
> includes a function named "read.annotated.nexus". It will retrieve all
> metadata from trees produced by BEAST/TreeAnnotator. I found particularly
> useful that you can also import "raw" posterior trees with their metadata.
> I've tried it on species trees from *BEAST and it works well. In contrast
> to "read.beast" from phyloch, "read.annotated.nexus" will associate
> metadata to edges (e.g. edge number), rather than nodes.
> 
> Cheers,
> Santiago
> 
> -- 
> Santiago Sánchez-Ramírez, PhD
> Department of Ecology and Evolutionary Biology, University of Toronto
> Department of Natural History (Mycology), Royal Ontario Museum
> 100 Queen's Park
> Toronto, ON
> M5S 2C6
> Canada
> Other email: santiago.sanc...@mail.utoronto.ca
> Tel. 416-586-8025
> Website: https://sites.google.com/site/santiagosnchezrmirez/
> 
>   [[alternative HTML version deleted]]
> 
> ___
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> https://stat.ethz.ch/mailman/listinfo/r-sig-phylo
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Jacob Berv

Ph.D. Student
Lovette Lab
Cornell Laboratory of Ornithology

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

[Santiago Sánchez]

Hi Jacob,

There is a package named OutBreakTools (
https://cran.r-project.org/web/packages/OutbreakTools/index.html) that
includes a function named "read.annotated.nexus". It will retrieve all
metadata from trees produced by BEAST/TreeAnnotator. I found particularly
useful that you can also import "raw" posterior trees with their metadata.
I've tried it on species trees from *BEAST and it works well. In contrast
to "read.beast" from phyloch, "read.annotated.nexus" will associate
metadata to edges (e.g. edge number), rather than nodes.

Cheers,
Santiago

-- 
Santiago Sánchez-Ramírez, PhD
Department of Ecology and Evolutionary Biology, University of Toronto
Department of Natural History (Mycology), Royal Ontario Museum
100 Queen's Park
Toronto, ON
M5S 2C6
Canada
Other email: santiago.sanc...@mail.utoronto.ca
Tel. 416-586-8025
Website: https://sites.google.com/site/santiagosnchezrmirez/

[[alternative HTML version deleted]]

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

[Jacob Berv]

On a related note- does anyone know of a function or package that can parse and 
store all of the metadata associated with nodes and branches from a BEAST 
output file? read.beast from phyloch will parse all of the data associated with 
internal nodes, but not with terminal branches (for example, substitution rate 
information). I emailed the developer of that tool and he indicated this was by 
design (though he may be able to offer a solution).

Jake

> On Oct 18, 2015, at 12:04 PM, Jacob Berv  
> wrote:
> 
> 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 
 mailto:jakeberv.r.sig.ph...@gmail.com>> 
 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
 Cornel

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 
>>> mailto:jakeberv.r.sig.ph...@gmail.com>> 
>>> 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 of Ornithology
>> 
>> 
>>  [[alternative HTML version deleted]]
>> 
>> ___

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

[Liam J. Revell]

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 mailto:jakeberv.r.sig.ph...@gmail.com>> 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]]

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Jacob Berv

Ph.D. Student
Lovette Lab
Cornell Laboratory of Ornithology


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

[Jacob Berv]

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 of Ornithology


[[alternative HTML version deleted]]

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

[Brian O'Meara]

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 <
> 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]]
>
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> Searchable archive at
> http://www.mail-archive.com/r-sig-phylo@r-project.org/

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

[Jacob Berv]

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]]

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