Re: Computer simulations of population genetics --
- From: "ErikW" <bryophyta@xxxxxxxxxxx>
- Date: Mon, 18 Dec 2006 14:54:30 -0500 (EST)
Perplexed in Peoria wrote:
<inmanh@xxxxxxxxxx> wrote in message news:elpudp$2cpv$1@xxxxxxxxxxxxxxxxxxxxxx
Walter ReMine wrote:
Computer simulations of population genetics --
I am seeking to survey the computer simulations of population genetics
that run forward in time, and that realistically model mutation rates
(with harmful and beneficial mutations), under selection and
reproduction. That is, the simulated offspring receive mutations,
followed by selection and sexual reproduction to form the next
generation. Any simulations that meet this general specification are
requested. Especially simulations from an academic, commericial, or
industrial setting, or simulations that have resulted in published
papers, or that are widely known.
Please direct me to those by providing the name of the simulation, a
person to contact, or a reference to a paper. There is quite a variety
of these simulations, and I don't want to miss any.
Wowww. This gives the impression that you have no idea of the size of
this field (these fields) and no idea where to start. Are you familiar
with search engines such as Google and citeseer?
These will direct you to published works primarily on the genetic
algorithm side -- ie (theory of) technical applications for
engineering/design purposes, more so than scientific population
genetics studies -- but you seem to be asking for that.
At a guess, between 1,000 and 10,000 papers per year published in this
area, so when you say you don't want to miss any ....
If you Google "site:citeseer.ist.psu.edu genetic algorithm" you get
28,300 hits
If you Google "site:citeseer.ist.psu.edu evolutionary simulation" you
get 4,600 hits
I tried the second suggested Google and was charmed to find one of the
top ten hits being a paper titled "Simulation models as opaque thought
experiments". That pretty well sums it up, IMHO.
I've seen a pretty good smattering of papers based on pop-gen simulations.
The simulation code is rarely published along with the opaque thoughts
that summarize the results. Instead, there is the standard 'contact the
lead author' citation.
By contrast, sequence based phylogeny papers almost always use named,
standard, public-domain software products with more useful citations in
the Materials and Methods section. There are manuals, names of contact
persons for support, and (most impressive to an ex-software producer)
release numbers and revision histories.
Why the difference? Is it fair to say that the phylogeny people are doing
real science, whereas the pop-gen people are only experimenting with their
own opaque thoughts?
I have some disagreements with this I think, especially after reading
the full abstract of the opaque thought model paper. It refers mainly
to Artificial Life simulations, AFAICT, which, in my opinion doesn't
belong in traditional pop gene simulations, whereas you seem to refer
to the latter. Standard pop gen simulations are done with published and
usually fairly standard models like various forms of the coalescent and
are really quite easy to understand. The insights that they bring are
also fairly straight forward to interpret. Coalesent simulations are
also used to generate distributions for hypothesis testing and
parameter estimates of real data.
So I don't think it's fair to say that refering to populatoin genetics
whereas it might be regarding AL-simulations
On the other hand there are probably loads of pop-gen simulations where
I am left more in the dark.
Turning to the presumed (?) topic of this thread, here's a link to a
simulation paper concerning the cost of natural selection (Nunney
2003):
http://www.sekj.org/PDF/anz40-free/anz40-185.pdf
The model is rather clearly described and a quick look tells me that
two of the assumptions of Haldane's model that I consider interesting
(admittedly my understanding of this topic is limited) are not
explored, namely all loci are unlinked and independent. Instead he
focussed on other factors. But all in all real science :P
Btw, maybe someone knowledgable/interested person can comment on the
paper?
ErikW
.
- References:
- Computer simulations of population genetics --
- From: Walter ReMine
- Computer simulations of population genetics --
- Prev by Date: Article: Comets hold life chemistry clues
- Next by Date: Re: Computer simulations of population genetics --
- Previous by thread: Re: Computer simulations of population genetics --
- Next by thread: Re: Computer simulations of population genetics --
- Index(es):
Relevant Pages
|
