Archive of newsgroup
Archive of messages in the Genetics 453 newsgroup
From joe@evolution.genetics.washington.edu Fri Feb 7 23:13:41 PST 1997
Article: 20 of uwash.class.genet453
Path: news.u.washington.edu!evolution.genetics.washington.edu!joe
From: joe@evolution.genetics.washington.edu (Joe Felsenstein)
Newsgroups: uwash.class.genet453
Subject: Hello
Date: 8 Jan 1997 14:29:27 GMT
Organization: University of Washington Genetics
Lines: 14
Message-ID: <5b0b07$6vp@nntp3.u.washington.edu>
NNTP-Posting-Host: evolution.genetics.washington.edu
Summary: Introduction
This newsgroup is now ready for business.
I am asked by C&C to remind you that you are not to abuse the use of
this newsgroup in any of a variety of ways.
If you have functional questions about the course, or any question at all
about the lecture material, please post here and I will try to answer, or
you can answer each other.
By the way, I also hope to announce office hours very soon, as soon as I
can find any. It will probably be on Thursdays early afternoon.
--
Joe Felsenstein joe@genetics.washington.edu (IP No. 128.95.12.41)
Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA
From joe@evolution.genetics.washington.edu Fri Feb 7 23:14:33 PST 1997
Article: 21 of uwash.class.genet453
Path: news.u.washington.edu!evolution.genetics.washington.edu!joe
From: joe@evolution.genetics.washington.edu (Joe Felsenstein)
Newsgroups: uwash.class.genet453
Subject: Office hours and web page
Date: 13 Jan 1997 18:58:21 GMT
Organization: University of Washington Genetics
Lines: 10
Message-ID: <5be0kd$50d@nntp3.u.washington.edu>
NNTP-Posting-Host: evolution.genetics.washington.edu
Summary: Now available
The class web page is now available. It is, as we announced, at
http://weber.u.washington.edu/~genetics/courses/genet453/1997/genet453.html
I will have office hours every Thursday from 2-3 in my office (J253 HSB).
This is right down the hall from the lecture room. I will, however, be
away on January 16.
---
Joe Felsenstein joe@genetics
Department of Genetics, Box 357360
From joe@evolution.genetics.washington.edu Fri Feb 7 23:19:08 PST 1997
Article: 22 of uwash.class.genet453
Path: news.u.washington.edu!evolution.genetics.washington.edu!joe
From: joe@evolution.genetics.washington.edu (Joe Felsenstein)
Newsgroups: uwash.class.genet453
Subject: Office hours (revised)
Date: 22 Jan 1997 19:02:15 GMT
Organization: University of Washington Genetics
Lines: 8
Message-ID: <5c5o7n$95v@nntp3.u.washington.edu>
NNTP-Posting-Host: evolution.genetics.washington.edu
Summary: Half an hour later
The office hours for this class have been changed to 2:30-3:30 Thursdays.
This is to avoid conflict with a seminar that I am attending. Thus they
are half an hour later than previously announced.
--
Joe Felsenstein joe@genetics.washington.edu (IP No. 128.95.12.41)
Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA
From jonmac@u.washington.edu Fri Feb 7 23:19:24 PST 1997
Article: 23 of uwash.class.genet453
Path: news.u.washington.edu!root
From: jonmac@u.washington.edu (Jonathan McBride)
Newsgroups: uwash.class.genet453
Subject: first student to post a message
Date: Tue, 28 Jan 1997 05:09:23 GMT
Organization: University of Washington
Lines: 8
Message-ID: <32ee88e4.19068096@news.u.washington.edu>
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I've been checking the news group for a week now and no one has posted
a message, so I thought I would start things off.
I don't really have anything to say, just that I downloaded the simul8
program this afternoon and everything went well.
From joe@evolution.genetics.washington.edu Fri Feb 7 23:15:10 PST 1997
Article: 24 of uwash.class.genet453
Path: news.u.washington.edu!evolution.genetics.washington.edu!joe
From: joe@evolution.genetics.washington.edu (Joe Felsenstein)
Newsgroups: uwash.class.genet453
Subject: Re: first student to post a message
Date: 28 Jan 1997 07:21:59 GMT
Organization: University of Washington Genetics
Lines: 16
Message-ID: <5ck9en$k7e@nntp3.u.washington.edu>
References: <32ee88e4.19068096@news.u.washington.edu>
NNTP-Posting-Host: evolution.genetics.washington.edu
Summary: Hooray
In article <32ee88e4.19068096@news.u.washington.edu>,
Jonathan McBride wrote:
>
>I've been checking the news group for a week now and no one has posted
>a message, so I thought I would start things off.
>
>I don't really have anything to say, just that I downloaded the simul8
>program this afternoon and everything went well.
Congratulations on being first! I *had* wondered whether student *could*
post. Now I know. Anyone with further experiences with simul8 should
post here.
--
Joe Felsenstein joe@genetics.washington.edu (IP No. 128.95.12.41)
Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA
From jonmac@u.washington.edu Fri Feb 7 23:15:26 PST 1997
Article: 25 of uwash.class.genet453
Path: news.u.washington.edu!root
From: jonmac@u.washington.edu (Jonathan McBride)
Newsgroups: uwash.class.genet453
Subject: simul8
Date: Wed, 29 Jan 1997 05:31:46 GMT
Organization: University of Washington
Lines: 16
Message-ID: <32eede73.3089022@news.u.washington.edu>
NNTP-Posting-Host: cs207-22.student.washington.edu
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I've been fiddling around with the simul8 program tonight and I
discovered that what Professor Felsenstein said was right (I guess
that is why he is the professor). I ran 20 simulation with the
fitnesses all equal and the beginning gene frequency at 0.5 but with a
migration rate of 0.5 also. From the first 10 runs, I only got "a"
fixed twice (so I was a little skeptical of the program). But in the
next 10 runs the "a" allele was fixed 6 more times. I suppose that
if I would have kept doing simulations, it would have evened out so
that half would be fixed at "A" and the other half would be fixed at
"a".
I do have one question, though, why is the gene frequeny of
the immigrating population not a variable that affects this scenetio?
Intuatively it seems like it should be. Is it just assumed to be the
same as in the main population?
jonmac@u.washigton.edu
From joe@evolution.genetics.washington.edu Fri Feb 7 23:16:05 PST 1997
Article: 26 of uwash.class.genet453
Path: news.u.washington.edu!evolution.genetics.washington.edu!joe
From: joe@evolution.genetics.washington.edu (Joe Felsenstein)
Newsgroups: uwash.class.genet453
Subject: Re: simul8
Date: 29 Jan 1997 08:53:30 GMT
Organization: University of Washington Genetics
Lines: 24
Message-ID: <5cn36a$min@nntp3.u.washington.edu>
References: <32eede73.3089022@news.u.washington.edu>
NNTP-Posting-Host: evolution.genetics.washington.edu
Summary: Migration, how it works
In article <32eede73.3089022@news.u.washington.edu>,
Jonathan McBride wrote:
> I do have one question, though, why is the gene frequeny of
>the immigrating population not a variable that affects this scenetio?
>Intuatively it seems like it should be. Is it just assumed to be the
>same as in the main population?
By the "immigrating population" I think you mean the population that is the
source of the migrants. I guess I didn't make it clear that when there are
(say) 8 populations, and a migration rate of m = 0.1, that means that
0.10 of the individuals in each population come from a random mixture of
all 8 populations. That is, each migrant in effect is drawn at random
>from the species as a whole.
Thus migration makes the populations' gene frequencies get closer to each
other, not to some source population's gene frequencies.
There are other ways to model migration, and in the Mac version that I
demonstrated in class, there are ways you can do the source-population
case, but iin Simul8 it's done only one way, they way described above.
--
Joe Felsenstein joe@genetics.washington.edu (IP No. 128.95.12.41)
Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA
From jonmac@u.washington.edu Thu Feb 27 07:16:47 PST 1997
Article: 27 of uwash.class.genet453
Path: news.u.washington.edu!root
From: jonmac@u.washington.edu (Jon McBride)
Newsgroups: uwash.class.genet453
Subject: migration
Date: Sun, 09 Feb 1997 19:31:18 GMT
Organization: University of Washington
Lines: 20
Message-ID: <32fe224b.1304965@news.u.washington.edu>
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I was just playing around with the simul 8 program again and I was
experimenting by progressively increasing the migration rate. The
degree to which the respective populations changed relative to each
other (differentiated) decreased as the migration rate increased. I
kept the population size the same. I was trying to think of an
explanation for this observation, and I would like to know if it is a
sound interpretation or not.
If the migration rate is high (say 0.8) between 8 populations of 1000,
isn't it the same as having a population of nearly 8000? If there is
complete migration (1.0) it would be exactly the same because the
whole idea of a subpopulation is meaningless. So, in a way, one could
think of migration as a restriction that is placed on a population of
individuals to limit the extent that they breed (m = 1-r) and, in
effect, creating subpopulations. Then one would expect, as I observed
in the simulation, the differentiation of the simulated populations to
be small.
Jon McBride
jonmac@u.washigton.edu
From joe@evolution.genetics.washington.edu Thu Feb 27 07:17:13 PST 1997
Article: 28 of uwash.class.genet453
Path: news.u.washington.edu!evolution.genetics.washington.edu!joe
From: joe@evolution.genetics.washington.edu (Joe Felsenstein)
Newsgroups: uwash.class.genet453
Subject: Re: migration
Date: 10 Feb 1997 06:27:20 GMT
Organization: University of Washington Genetics
Lines: 36
Message-ID: <5dmf48$4g2@nntp3.u.washington.edu>
References: <32fe224b.1304965@news.u.washington.edu>
NNTP-Posting-Host: evolution.genetics.washington.edu
Summary: Yup
Keywords: migration, population genetics
In article <32fe224b.1304965@news.u.washington.edu>,
Jon McBride wrote:
>I was just playing around with the simul 8 program again and I was
>experimenting by progressively increasing the migration rate. The
>degree to which the respective populations changed relative to each
>other (differentiated) decreased as the migration rate increased. I
>kept the population size the same. I was trying to think of an
>explanation for this observation, and I would like to know if it is a
>sound interpretation or not.
Very sound. It's what you expect. When m is zero, they wander off
independently. When m is large, theye act like parts of one big
population. In that case they have almost the same gene frequency
at all times.
>If the migration rate is high (say 0.8) between 8 populations of 1000,
>isn't it the same as having a population of nearly 8000? If there is
>complete migration (1.0) it would be exactly the same because the
>whole idea of a subpopulation is meaningless.
Correct.
>So, in a way, one could
>think of migration as a restriction that is placed on a population of
>individuals to limit the extent that they breed (m = 1-r) and, in
>effect, creating subpopulations. Then one would expect, as I observed
>in the simulation, the differentiation of the simulated populations to
>be small.
Well, you would expect that, but I don't find it any clearer than just
thinking about migration. But 30 years in the field may have warped
my idea of what is clear ...
--
Joe Felsenstein joe@genetics.washington.edu (IP No. 128.95.12.41)
Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA
From jonmac@u.washington.edu Thu Feb 27 07:17:35 PST 1997
Article: 29 of uwash.class.genet453
Path: news.u.washington.edu!root
From: jonmac@u.washington.edu (Jon McBride)
Newsgroups: uwash.class.genet453
Subject: Re: migration
Date: Mon, 24 Feb 1997 05:35:22 GMT
Organization: University of Washington
Lines: 26
Message-ID: <331227a5.344421@news.u.washington.edu>
References: <32fe224b.1304965@news.u.washington.edu> <5dmf48$4g2@nntp3.u.washington.edu>
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On 10 Feb 1997 06:27:20 GMT, joe@evolution.genetics.washington.edu
(Joe Felsenstein) wrote:
>In article <32fe224b.1304965@news.u.washington.edu>,
>Jon McBride wrote:
>>So, in a way, one could
>>think of migration as a restriction that is placed on a population of
>>individuals to limit the extent that they breed (m = 1-r) and, in
>>effect, creating subpopulations. Then one would expect, as I observed
>>in the simulation, the differentiation of the simulated populations to
>>be small.
>
>Well, you would expect that, but I don't find it any clearer than just
>thinking about migration. But 30 years in the field may have warped
>my idea of what is clear ...
>
You're right. Just thinking about migration is easier and more clear,
but the only way to truly grasp a concept is to be able to apply the
information one already knows to a new explanation. The more a
concept is processed by the mind, and the more aspects of that concept
one considers, the clearer it actually is.
Jon McBride
jonmac@u.washigton.edu
From jonmac@u.washington.edu Thu Feb 27 07:18:24 PST 1997
Article: 30 of uwash.class.genet453
Path: news.u.washington.edu!root
From: jonmac@u.washington.edu (Jon McBride)
Newsgroups: uwash.class.genet453
Subject: phylogenetic trees
Date: Mon, 24 Feb 1997 05:41:50 GMT
Organization: University of Washington
Lines: 15
Message-ID: <331328a1.596429@news.u.washington.edu>
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This may be a silly question, but I will ask it anyway...
Last Wednesday when Dr. Rodrigo was lecturing about phylogenetic trees
he defined a clade as a group of taxa who exclusively share a common
ancestor. By that definition, clades have varying degrees of
specificity. It seems (in principle) that one could define an entire
phylogenetic tree as a clade because in order to be in a tree, all of
the organisms must have shared a common ancestor at one point. So I
guess my question is: do clades apply to all sections of a
phylogenetic tree, or just to the terminal branches as he illustrated
in his example?
Jon McBride
jonmac@u.washigton.edu
From joe@evolution.genetics.washington.edu Thu Feb 27 07:18:38 PST 1997
Article: 31 of uwash.class.genet453
Path: news.u.washington.edu!evolution.genetics.washington.edu!joe
From: joe@evolution.genetics.washington.edu (Joe Felsenstein)
Newsgroups: uwash.class.genet453
Subject: Re: phylogenetic trees
Date: 24 Feb 1997 18:09:36 GMT
Organization: University of Washington Genetics
Lines: 23
Message-ID: <5eslh0$oif@nntp3.u.washington.edu>
References: <331328a1.596429@news.u.washington.edu>
NNTP-Posting-Host: evolution.genetics.washington.edu
Summary: Clades apply to all
In article <331328a1.596429@news.u.washington.edu>,
Jon McBride wrote:
>Last Wednesday when Dr. Rodrigo was lecturing about phylogenetic trees
>he defined a clade as a group of taxa who exclusively share a common
>ancestor. By that definition, clades have varying degrees of
>specificity. It seems (in principle) that one could define an entire
>phylogenetic tree as a clade because in order to be in a tree, all of
>the organisms must have shared a common ancestor at one point. So I
>guess my question is: do clades apply to all sections of a
>phylogenetic tree, or just to the terminal branches as he illustrated
>in his example?
A clade is a part of a phylogeny consisting of an ancestor and all its
descendants. Thus the descendants of the first vertebrate to
become terrestrial are a clade. But if you leave out the bats, birds,
whales, say, then the remainder isn't a clade.
An entire phylogeny is a clade. It isn't a notion just confined to
terminal branches.
--
Joe Felsenstein joe@genetics.washington.edu (IP No. 128.95.12.41)
Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA
From jonmac@u.washington.edu Fri Mar 28 06:20:47 PST 1997
Article: 32 of uwash.class.genet453
Path: news.u.washington.edu!root
From: jonmac@u.washington.edu (Jon McBride)
Newsgroups: uwash.class.genet453
Subject: horses and donkeys
Date: Tue, 11 Mar 1997 01:37:07 GMT
Organization: University of Washington
Lines: 14
Message-ID: <3324b530.22016375@news.u.washington.edu>
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O.K., I have a question about what yo where talking about last Friday
in class. I was thinking last weekend about what you had said about
trans-species offspring. For example, a horse and a donkey produce a
mule (I think that is how it goes anyway) that is unable to reproduce.
Is the reason a mule is sterile because it is unlikely that a mule's
gametes will get a least one copy of each chromosome since after
chromosome segregation, there will most likely be
duplication/deficiency problems? I was trying to think of a real life
case to illustrate the point you were trying to make, was I successful
or is this just a coincidence?
Jon McBride
jonmac@u.washigton.edu
From joe@evolution.genetics.washington.edu Fri Mar 28 06:21:02 PST 1997
Article: 33 of uwash.class.genet453
Path: news.u.washington.edu!evolution.genetics.washington.edu!joe
From: joe@evolution.genetics.washington.edu (Joe Felsenstein)
Newsgroups: uwash.class.genet453
Subject: Re: horses and donkeys
Date: 12 Mar 1997 17:53:25 GMT
Organization: University of Washington Genetics
Lines: 28
Message-ID: <5g6qil$e0a@nntp3.u.washington.edu>
References: <3324b530.22016375@news.u.washington.edu>
NNTP-Posting-Host: evolution.genetics.washington.edu
Summary: Maybe ...
In article <3324b530.22016375@news.u.washington.edu>,
Jon McBride wrote:
>Is the reason a mule is sterile because it is unlikely that a mule's
>gametes will get a least one copy of each chromosome since after
>chromosome segregation, there will most likely be
>duplication/deficiency problems?
I used to hear this asserted regularly. Apparently donkeys have 62
chromosomes (diploid number) and horses have 64. The chromosomes
differ in numerous ways. People used to say that this was the reason
for the sterility of the mule and the hinny (one is donkey male x
horse female, the other is the other way 'round). But more recently
I dimly recall having heard that this is not the reason.
The reference that seems to be the one to read is:
Chandley, A. C., R. Jones, H. M. Dott, W. R. Allen, and R. V. Short. 1974.
Meiosis in interspecific equine hybrids, I: The male mule (E. asinus X
E. caballus) and hinny (E. caballus X E. asinus). Cytogenetics and
Cell Genetics 13: 330-341.
If you get a chance to look at it (it should be in Health Sciences Library)
let me know what it says on this point. Recent textbooks avoid the earlier
claim, and I'm a bit swamped and unable to take time to go read this.
--
Joe Felsenstein joe@genetics.washington.edu (IP No. 128.95.12.41)
Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA
From joe@evolution.genetics.washington.edu Fri Mar 28 06:21:21 PST 1997
Article: 34 of uwash.class.genet453
Path: news.u.washington.edu!evolution.genetics.washington.edu!joe
From: joe@evolution.genetics.washington.edu (Joe Felsenstein)
Newsgroups: uwash.class.genet453
Subject: Review session and final exam
Date: 12 Mar 1997 17:55:27 GMT
Organization: University of Washington Genetics
Lines: 9
Message-ID: <5g6qmf$e12@nntp3.u.washington.edu>
NNTP-Posting-Host: evolution.genetics.washington.edu
Summary: When they are
The review session will be this Friday, March 14, in J280 (the usual lecture
room) at 3:30-4:30.
The final exam will, as previously announced, be in J280 at 2:30-4:30 on
Wednesday, March 19.
--
Joe Felsenstein joe@genetics.washington.edu (IP No. 128.95.12.41)
Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA
From joe@evolution.genetics.washington.edu Fri Mar 28 06:21:57 PST 1997
Article: 35 of uwash.class.genet453
Path: news.u.washington.edu!evolution.genetics.washington.edu!joe
From: joe@evolution.genetics.washington.edu (Joe Felsenstein)
Newsgroups: uwash.class.genet453
Subject: Picking up your exam
Date: 21 Mar 1997 18:07:03 GMT
Organization: University of Washington Genetics
Lines: 9
Message-ID: <5guio7$9i9@nntp3.u.washington.edu>
NNTP-Posting-Host: evolution.genetics.washington.edu
Summary: Monday in J205
We will have the exams available for pickup by Monday. They will be in
J205 HSB (the Genetics Department Office).
I will post and put on the web site the grade distribution. Am thinking
about what to do about a Key to the exam.
----
Joe Felsenstein joe@genetics.washington.edu (IP No. 128.95.12.41)
Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA
From joe@evolution.genetics.washington.edu Fri Mar 28 06:22:19 PST 1997
Article: 36 of uwash.class.genet453
Path: news.u.washington.edu!evolution.genetics.washington.edu!joe
From: joe@evolution.genetics.washington.edu (Joe Felsenstein)
Newsgroups: uwash.class.genet453
Subject: Key for exam
Date: 24 Mar 1997 20:18:03 GMT
Organization: University of Washington Genetics
Lines: 7
Message-ID: <5h6nhr$i0@nntp3.u.washington.edu>
NNTP-Posting-Host: evolution.genetics.washington.edu
Summary: in J205, you can copy
A rudimentary key for the final exam is available in J205 HSB (the Genetics
Office) from the secretary at the front desk, Bill, who will allow
you to copy it. There wasn't enough bulletin board space to post it.
--
Joe Felsenstein joe@genetics.washington.edu (IP No. 128.95.12.41)
Dept. of Genetics, Univ. of Washington, Box 357360, Seattle, WA 98195-7360 USA