From owner-population-bio@net.bio.net Sun May 05 23:00:00 1996 Path: biosci!biosci!not-for-mail From: syoung@unix5.netaxs.com (Resampling; syoung) Newsgroups: bionet.plants,bionet.info-theory,bionet.software,bionet.population-bio,bionet.molbio-evolution Subject: Short Course in Resampling Statistics (p04306) Followup-To: poster Date: 5 May 1996 19:24:53 -0700 Organization: Philadelphia's Complete Internet Provider Lines: 24 Sender: biohelp@net.bio.net Distribution: world Message-ID: <4m4guc$a0r@netaxs.com> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.plants:11180 bionet.info-theory:4114 bionet.software:15403 bionet.population-bio:1925 Course in Resampling Statistics An introduction to the "new statistics" of resampling will be offered June 3-5 in Washington, DC. Resampling - bootstrap, permutation, and other tests - has revolutionized the field of statistics. Resampling is now the method of choice for confidence limits, hypothesis tests, and other everyday inferential problems. Resampling is for both experts and non-statisticians. With resampling procedures you use the given sample data to repeatedly simulate hypothetical "re-samples", recalculating the statistic of interest. No "black-box" formulas will hide the underlying statistical procedure. This is an introductory course, with no specific pre- requisites, though a familiarity with basic probability and descriptive statistics will help. For information reply by email to: syoung@netaxs.com Resampling Project Fax: (703) 522-5846 From owner-population-bio@net.bio.net Fri May 10 23:00:00 1996 Path: biosci!internet!biosci!not-for-mail From: biohelp (BIOSCI Administrator) Newsgroups: bionet.population-bio Subject: IMPORTANT - BIOSCI Fundraising Update! Date: 11 May 1996 02:01:22 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 154 Sender: daemon@net.bio.net Distribution: world Message-ID: <199605110900.CAA24743@net.bio.net> NNTP-Posting-Host: net.bio.net BIOSCI is about halfway to its funding goal!! I'm interrupting the usual monthly posting of the BIOSCI miniFAQ to bring you up to date on BIOSCI fundraising progress, a topic of concern to your future use of this resource. Thank you in advance for taking the time to read this message carefully. Last year we announced that BIOSCI was going to adopt the U.S. Public Broadcasting System model to fund its operations after our DOE/NSF grant runs out later this year. Unlike PBS, we are not soliciting contributions from users; we are only selling ads on our Web pages solely to cover our operating costs. Our goal is to seek sponsorships until we build up an operating reserve of about $100,000 and then cease further promotions until we need to build the reserve back up. (The accountants among our readership will be familiar with the problem of deferred revenue which we can not safely utilize until ads have been displayed for a period of time.) We are only about halfway to our funding goal and need to raise further funds to avoid having to curtail services at net.bio.net. Fundraising is time-consuming, however, and we need your help as explained further below. Our operating costs consist of our network connection, phone lines, hardware maintenance (we will be getting newer and faster hardware soon!), plus 0.7 FTE of salaries covering UNIX systems admin, technical support, quality assurance, i.e., testing, of our system, and administrative costs (such as the time it takes to actually find/write/call potential sponsors and raise money!). Although the BIOSCI staff does get compensated for a portion of the work that they do, this project has always received a lot of free after-hours and "vacation" time labor, so we hope that no one will begrudge the time that we do charge to the project to serve you. All of the three part-time staff members, Dave Mack, Julie Lawrence, and myself, have full time day jobs and families in addition to working hard to keep this service running for all of you. Julie and Dave Mack are subcontractors for BIOSCI; my time that is charged to the project defrays a portion of my regular salary instead of adding to my income. Besides having to relocate the project, we were very busy this last year building new infrastructure such as our WWW hypermail interface to the system. This was released last December along with scores of WAIS indices for the newsgroups. Virtually everything is complete, although we do continue to find and fix bugs (many through your helpful feedback!). We are still having some problems with our WAIS indexing. The archives continue to grow rapidly. We are running over 100 indexes now versus three previously and any systems crashes cause greater havoc with the indexing than before! We are still working to fix this as fast as our resources permit and appreciate your patience, but we have been able to automate a lot of the infrastructure to reduce labor as compared to past requirements. We have also implemented new software to make moderation of BIOSCI/bionet newsgroups much easier and combat the growing problem of Internet junk mail and USENET "spamming." About 20% of our groups are now moderated, many of them by the BIOSCI staff! This, for example, made a major difference last year in the quality of content in our EMPLOYMENT/bionet.jobs.offered newsgroup which many commercial concerns and recruiting firms are using **without charge** to recruit candidates for positions in the biological sciences. We are also now in a position to have sponsors for individual newsgroups as you will have noticed if you have visited http://www.bio.net/ and clicked on "Access the BIOSCI/bionet newsgroups" recently. So, how can you help?? ---------------------- As noted above it can take a lot of time to contact potential sponsors if I have to do it all myself. Our request is quite simple. You can do two important things which will take very little time for you individually. First, please use our WWW system at http://www.bio.net/ to access the archives. You can now post or reply to messages via your Web browser. Your usage helps attract sponsors. If you contact any of our sponsors, please be sure to thank them for supporting BIOSCI. It is critical for them to get this feedback if they are to continue their sponsorship for the long term. Second, if you work for a company or organization that provides products or services of interest to the biology community, please pass this message on to your marketing or marketing communications department or other appropriate group. Please ask them to help support BIOSCI by sponsoring our Web site and explain the uses and benefits of the system to the biology community. If they are interested, they can then contact us for further information at our tech support address, biosci-help@net.bio.net. Our hope is to quickly raise several large corporate/institutional sponsors on our heavily-used WWW locations (some stats appended below), and then end this sponsorship campaign so that our resources can continue to be used for service provision, not fundraising. Many of our specialty newsgroup WWW archives are still used by small communities of scientists (and they haven't been heavily promoted yet). While these may be valuable niche markets to some advertisers, it will generate more labor and overhead having to find these sponsors, fairly price the locations, and deal with lots of smaller sponsorships than fewer mid-to large sponsors. We are striving to keep our operation as lean and efficient as possible since we are not trying to make careers out of running BIOSCI. We are trying if at all possible to avoid the administrative overhead entailed with processing lots of small payments to reach our fundraising goals. I'd like to thank all of you for your help in advance. In helping us, you are also helping yourselves, not only in keeping this resource available for all of the both large and small research communities that we serve, but also by alleviating the need for us to go back and compete with researchers for tight grant dollars! We promised NSF when we were awarded the BIOSCI grant that we would carry out this mission to make the service self-supporting. With your help, we will succeed in continuing BIOSCI's work into its second decade. Thank you very much! Sincerely, Dave Kristofferson BIOSCI/bionet Manager biosci-help@net.bio.net A list of our prime WWW sponsorship locations follow. Please contact us for further details. ---------------------------------------------------------------------- The overall BIOSCI WWW pages are currently visited by users from close to 5500 unique computer hosts per week. Web servers only log the Internet computer/host name and frequently more than one individual can connect to us from a particular host. Main home page, http://www.bio.net, visited recently by about 2100 unique hosts per week Main Newsgroups archives page, http://www.bio.net/archives.html, visited recently by about 1200 Unique hosts per week BIO-JOURNALS archive page, http://www.bio.net/BIO-JOURNALS.html, visited recently by about 1000 unique hosts per week. EMPLOYMENT archive pages: http://www.bio.net:80/hypermail/EMPLOYMENT/ and monthly header pages, visited recently by about 800 unique hosts per week. Address database search page, http://www.bio.net/addrsearch.html, visited recently by about 450 unique hosts per week. Methods newsgroup archive pages, http://www.bio.net:80/hypermail/METHDS- REAGNTS/ and monthly header pages, visited recently by about 350 unique hosts per week. Ads can also be displayed on various combinations of other BIOSCI/bionet newsgroups. Please contact us at biosci-help@net.bio.net for details. ---------------------------------------------------------------------- From owner-population-bio@net.bio.net Sat May 11 23:00:00 1996 Newsgroups: bionet.population-bio Path: biosci!agate!howland.reston.ans.net!newsfeed.internetmci.com!usenet.logical.net!news.telenet.net!news From: "Larry C. Watkins" Subject: (no subject) Sender: news@telenet.net Message-ID: Date: Sun, 12 May 1996 23:16:51 GMT X-Nntp-Posting-Host: dialup034.telenet.net Content-Transfer-Encoding: 7bit Content-Type: text/plain; charset=us-ascii Mime-Version: 1.0 X-Mailer: Mozilla 1.22 (Windows; U; 16bit) Organization: Watkins Natural History Books Lines: 8 I have just published catalogue no. 75 which contains over 500 used and out of print natural history books. The list contains some titles in population biology. If anyone would like a copy of the catalogue, send me your mailing address. Watkins Natural History Books Dolgeville, NY 13329 From owner-population-bio@net.bio.net Mon May 13 23:00:00 1996 Path: biosci!rutgers!csn!nntp-xfer-1.csn.net!magnus.acs.ohio-state.edu!lerc.nasa.gov!purdue!yuma!usenet From: engcc@aol.com Newsgroups: bionet.population-bio Subject: Re: (no subject) Date: 14 May 1996 20:01:28 GMT Organization: Colorado State University, Fort Collins, CO 80523 Lines: 10 Message-ID: <4naoqo$1sci@yuma.ACNS.ColoState.EDU> References: NNTP-Posting-Host: scirpus.cemml.colostate.edu Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 1.1N (Windows; I; 16bit) To: bearsend@telenet.net Yes, Please send me your latest catalog. Mick Castillo box 1684 Fort Collins, CO 80522 mickc@cnr.colostate.edu From owner-population-bio@net.bio.net Thu May 16 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!sgigate.sgi.com!swrinde!howland.reston.ans.net!news-e2a.gnn.com!newstf01.news.aol.com!newsbf02.news.aol.com!not-for-mail From: latenimg22@aol.com (LatenImg22) Newsgroups: bionet.population-bio Subject: Population Models Date: 17 May 1996 15:13:26 -0400 Organization: America Online, Inc. (1-800-827-6364) Lines: 2 Sender: root@newsbf02.news.aol.com Message-ID: <4nij4m$ien@newsbf02.news.aol.com> Reply-To: latenimg22@aol.com (LatenImg22) NNTP-Posting-Host: newsbf02.mail.aol.com I am looking for population models and lifestyle impact models - anyone have one or know where I can get one? From owner-population-bio@net.bio.net Tue May 21 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!elroy.jpl.nasa.gov!swrinde!newsfeed.internetmci.com!cdc2.cdc.net!news.texas.net!nntp.primenet.com!news.asu.edu!usenet From: jml@asu.edu (John M. Lynch) Newsgroups: bionet.population-bio Subject: Finches and Morphological Evolution Date: Wed, 22 May 1996 16:35:10 GMT Organization: Arizona State University Lines: 21 Message-ID: <31a34223.108207295@news.asu.edu> NNTP-Posting-Host: ppp2-04.inre.asu.edu X-Newsreader: Forte Agent .99e/32.201 In 1988, Stuart Pimm wrote an article for Trends in Evolution and Ecology (TREE 3, 290-291), describing research by another party which showed rapid morphological change in a finch introduced to a south Pacific island. Unfortunately, the library here at ASU doesn't have that volume of TREE, Can anyone provide me with the reference to the _original_ study. Much obliged, John ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + John M. Lynch + Phn: (602) 965 6747+ + + Fax: (602) 965 9100+ + Faculty Associate ++++++++++++++++++++++ + Interdisciplinary Humanities Program + + Arizona State University + + Tempe, AZ 85287-0302, USA + + + + Personal Web Page: http://www.public.asu.edu/~jmlynch + + PGP Key on web page + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-population-bio@net.bio.net Wed May 22 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!newsfeed.pitt.edu!nntp.club.cc.cmu.edu!clpgh.org!panzar From: panzar@clpgh.org (Robin Panza) Newsgroups: bionet.population-bio Subject: Re: Finches and Morphological Evolution Message-ID: <1996May23.101743.5085@clp2> Date: 23 May 96 10:17:43 -5 References: <31a34223.108207295@news.asu.edu> Organization: Carnegie Library of Pittsburgh Lines: 17 In article <31a34223.108207295@news.asu.edu>, jml@asu.edu (John M. Lynch) writes: > In 1988, Stuart Pimm wrote an article for Trends in Evolution and Ecology (TREE > 3, 290-291), describing research by another party which showed rapid > morphological change in a finch introduced to a south Pacific island. > Unfortunately, the library here at ASU doesn't have that volume of TREE, Can > anyone provide me with the reference to the _original_ study. The research is by (Peter?) Grant, a long-term series of studies on Galapagos Finches (which introduced themselves to the Galapagos Islands and then diversified). He has recently published a popular book on the work, titled "The Beak of the Finch" and available in most book stores. It probably has citations for the original papers by himself and his students. Robin Panza panzar@clp2.clpgh.org Section of Birds, Carnegie Museum of Natural History 4400 Forbes Ave., Pittsburgh PA 15213 From owner-population-bio@net.bio.net Thu May 23 23:00:00 1996 Path: biosci!rutgers!csn!nntp-xfer-1.csn.net!dimensional.com!winternet.com!nntp.primenet.com!news.asu.edu!usenet From: jml@asu.edu (John M. Lynch) Newsgroups: bionet.population-bio Subject: Re: Finches and Morphological Evolution Date: Thu, 23 May 1996 22:31:05 GMT Organization: Arizona State University Lines: 25 Message-ID: <31a4e6db.97697019@news.asu.edu> References: <31a34223.108207295@news.asu.edu> <1996May23.101743.5085@clp2> NNTP-Posting-Host: ppp1-14.inre.asu.edu X-Newsreader: Forte Agent .99e/32.201 On 23 May 96 10:17:43 -5, panzar@clpgh.org (Robin Panza) wrote: :The research is by (Peter?) Grant, a long-term series of studies on Galapagos :Finches (which introduced themselves to the Galapagos Islands and then :diversified). He has recently published a popular book on the work, titled :"The Beak of the Finch" and available in most book stores. It probably has :citations for the original papers by himself and his students. Actually, I managed to omit a piece of evidence that would have clarified my original post. The island wasn't the Galapagos - it was Layasa (spelling ?). -jml ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + John M. Lynch + Phn: (602) 965 6747+ + + Fax: (602) 965 9100+ + Faculty Associate ++++++++++++++++++++++ + Interdisciplinary Humanities Program + + Arizona State University + + Tempe, AZ 85287-0302, USA + + + + Personal Web Page: http://www.public.asu.edu/~jmlynch + + PGP Key on web page + ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ From owner-population-bio@net.bio.net Fri May 24 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!newsfeed.sunet.se!news01.sunet.se!sunic!news99.sunet.se!umdac!pelle.ekbot.umu.se!pelle From: pelle@ekbot.umu.se (Pelle Ingvarsson) Newsgroups: bionet.population-bio Subject: Re: Finches and Morphological Evolution Date: Fri, 24 May 1996 16:03:19 LOCAL Organization: University of Umea Lines: 19 Message-ID: References: <31a34223.108207295@news.asu.edu> <1996May23.101743.5085@clp2> NNTP-Posting-Host: pelle.ekbot.umu.se X-Newsreader: Trumpet for Windows [Version 1.0 Rev B final beta #4] >The research is by (Peter?) Grant, a long-term series of studies on Galapagos >Finches (which introduced themselves to the Galapagos Islands and then >diversified). He has recently published a popular book on the work, titled >"The Beak of the Finch" and available in most book stores. It probably has >citations for the original papers by himself and his students. Sorry, but Peter Grant did not write "The beak of the Finch", Jonathan Weiner did. Peter Grant did, however, write a book called "Ecology and Evolution of Darwin's Finches" published in 1987 (Princeton UP). He also co-wrote a book with his wife Rosemary Grant called "Evolutionary Dynamics of a Natural Population: The Large Cactus Finch of the Galapagos" published in 1990 (U of Chicago Press). -Pelle ---------------- Dept. Of Ecological Botany University of Umea SWEDEN From owner-population-bio@net.bio.net Mon May 27 23:00:00 1996 Path: biosci!daresbury!nntp-trd.UNINETT.no!nntp.uio.no!Norway.EU.net!EU.net!usenet1.news.uk.psi.net!uknet!tank.news.pipex.net!pipex!usenet.eel.ufl.edu!bofh.dot!news.alt.net!newspost1.alt.net!usenet From: J Buchheim Newsgroups: bionet.population-bio Subject: Re: Odyssey Expeditions Scholarship Date: Tue, 28 May 1996 00:15:36 -0700 Organization: Odyssey Expeditions Lines: 23 Message-ID: <31AAA817.4479@edisto.cofc.edu> References: <960517191049_493323919@emout14.mail.aol.com> Mime-Version: 1.0 Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit X-Mailer: Mozilla 3.0b4 (Win95; I) Odyssey Expeditions is a nonprofit marine science and diver training program offering Tropical Marine Biology Voyages on a liveaboard research vessel in the British Virgin Islands. Two programs are avialable this summer for high school and college students. Academic credit and dive certifications are included. Each voyage is three weeks in duration and all equipment is provided. Research activities include investigations on the ecology of tube dwelling blennys in order to understand more about the limited larval fish recruitment vs. limited shelter hypothesis on determinants of community structure of reef fishes. We currently have four positions available for our voyages. In order to fill these vacancies as soon as possible, we are offering tuition scholarships to qualified applicants. Scholarships will reduce the all inclusive tuition and fees from $3500 to $2600 (That is a three week liveaboard dive trip and educational program at an unbelievably low cost). Potential scholarship applicants should contact us as soon as possible to reserve a berth. For more information, please visit our web site at http://www.odyssey.ycg.org or call (803)670-8767. Jason Buchheim director, Odyssey Expeditions mailto:buchheim@edisto.cofc.edu From owner-population-bio@net.bio.net Tue May 28 23:00:00 1996 Newsgroups: bionet.population-bio,sci.stat.edu Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!howland.reston.ans.net!vixen.cso.uiuc.edu!uchinews!not-for-mail From: leen@mail.bsd.uchicago.edu (Lee Newberg) Subject: Q: Compare Allele or Genotype Distributions X-Nntp-Posting-Host: bio-3.bsd.uchicago.edu Message-ID: Followup-To: bionet.population-bio Keywords: Chi Square, Allele, Genotype Sender: news@midway.uchicago.edu (News Administrator) Organization: U Chicago, Biological Sciences Division, Academic Computing Date: Wed, 29 May 1996 13:22:53 GMT Lines: 25 Xref: biosci bionet.population-bio:1944 sci.stat.edu:8801 I am writing software to teach population genetics to high school students. The laboratory revolves around the TPA-25 locus on Human chromosome 8 which is an ALU insertion point. There are two alleles and three genotypes. (The trait is not expressed so that would be one phenotype, I guess.) Among other things, the students are encouraged to compare two subsets of the data against each other using a chi-square test to see if the differences between the populations are "due to chance." My question is this: Should the comparison be between the two allele distributions or between the two genotype distributions? Since there are two allele types I could write a two-by-two matrix, with the rows labeled by allele type and with a column for each subset, and run the chi-square test on that with one degree of freedom. Alternatively, I could write a three-by-two matrix, with the rows labeled by genotype and with a column for each subset, and run the chi-square test on that with two degrees of freedom. Which makes more sense biologically and statistically? >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>Lee Newberg lee-newberg@uchicago.edu http://http.bsd.uchicago.edu/~l-newberg/ From owner-population-bio@net.bio.net Wed May 29 23:00:00 1996 Path: biosci!MCZ.HARVARD.EDU!dmw From: dmw@MCZ.HARVARD.EDU (Daniel Weinreich) Newsgroups: bionet.population-bio Subject: Re: Q: Compare Allele or Genotype Distributions Date: 30 May 1996 08:41:57 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 37 Sender: daemon@net.bio.net Distribution: world Message-ID: References: <1996May30.103719.5112@clp2> NNTP-Posting-Host: net.bio.net On 30 May 1996, Robin Panza wrote: > In article , leen@mail.bsd.uchicago.edu > (Lee Newberg) writes: > > Which makes more sense biologically and statistically? > The genotype distribution is simply a derivative of the allele > distribution, so you don't have any more degrees of freedom. You've > *calculated* the number of heterozygotes. If you had actually sampled a > population and determined each phenotype, then you could look at the > distribution of phenotypes and compare it to the distribution in another > determined sample. If I remember the original post, the student *will* have actual genotype frequencies, and thus would *not* be calculating them from H-W model > Run the chi-square on allele distributions. Nevertheless I agree with the conclusion because it seems to me that heterogeneity in genotype frequencies could be due *either* to population substructure *or* to differential deviation from H-W equilibrium. In other words, the pi's and qi's could be equal across popluations (thus no support for population substructure) while at the same time the two populations could be violating H-W assumptions to different degrees, giving different values of D, H and R. Anyone else care to chime in? Dan. ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Daniel M. Weinreich email: dmw@mcz.harvard.edu Harvard University usmail: 26 Oxford Street Museum of Comparative Zoology Cambridge, MA 02138 voice: (617) 495-1954 fax: (617) 495-5846 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ From owner-population-bio@net.bio.net Wed May 29 23:00:00 1996 Path: biosci!bcm.tmc.edu!pendragon!news.msfc.nasa.gov!newsfeed.internetmci.com!in1.uu.net!newsfeed.pitt.edu!nntp.club.cc.cmu.edu!clpgh.org!panzar From: panzar@clpgh.org (Robin Panza) Newsgroups: bionet.population-bio Subject: Re: Q: Compare Allele or Genotype Distributions Message-ID: <1996May30.103719.5112@clp2> Date: 30 May 96 10:37:19 -5 References: Followup-To: bionet.population-bio Organization: Carnegie Library of Pittsburgh Lines: 13 In article , leen@mail.bsd.uchicago.edu (Lee Newberg) writes: > Which makes more sense biologically and statistically? The genotype distribution is simply a derivative of the allele distribution, so you don't have any more degrees of freedom. You've *calculated* the number of heterozygotes. If you had actually sampled a population and determined each phenotype, then you could look at the distribution of phenotypes and compare it to the distribution in another determined sample. Run the chi-square on allele distributions. Robin P. panzar@clp2.clpgh.org From owner-population-bio@net.bio.net Thu May 30 23:00:00 1996 Path: biosci!rutgers!uwm.edu!math.ohio-state.edu!howland.reston.ans.net!swrinde!sgigate.sgi.com!news.msfc.nasa.gov!newsfeed.internetmci.com!in2.uu.net!newsfeed.pitt.edu!wpilib From: wpilib+@pitt.edu (Richard F Ulrich) Newsgroups: bionet.population-bio,sci.stat.edu Subject: Re: Q: Compare Allele or Genotype Distributions Date: 31 May 1996 15:28:06 GMT Organization: University of Pittsburgh Lines: 36 Message-ID: <4on366$7hn@usenet.srv.cis.pitt.edu> References: NNTP-Posting-Host: unixs-eval.cis.pitt.edu X-Newsreader: TIN [version 1.2 PL2] Xref: biosci bionet.population-bio:1947 sci.stat.edu:8830 < lee-newberg@uchicago.edu > Lee Newberg (leen@mail.bsd.uchicago.edu) wrote: : I am writing software to teach population genetics to high : school students. The laboratory revolves around the TPA-25 : locus on Human chromosome 8 which is an ALU insertion point. : There are two alleles and three genotypes. (The trait is not : expressed so that would be one phenotype, I guess.) Among other : things, the students are encouraged to compare two subsets of : the data against each other using a chi-square test to see if : the differences between the populations are "due to chance." ... and goes on to ask whether testing should be by counts of ALLELES or counts of GENOTYPES? If the counts of GENOTYPES are the same, then the counts of alleles would have to come out the same, too, so the hypotheses are a bit different. No one has claimed expertise here, so I will offer what I recollect from some genetics class, 15+ years ago: Starting from a statistician's preference for "independence" being assured, the counts of alleles would be regarded suspiciously - but if you are looking at the evolution of a population, then what "survives" to be passed on is the allele. I am sure that a consequence of this logic was that counts of alleles were sometimes used in statistical tests, and in statistical modeling. Maybe someone else will have more specific details to add. Hope this helps. Rich Ulrich, biostatistician wpilib+@pitt.edu Western Psychiatric Inst. and Clinic Univ. of Pittsburgh From owner-population-bio@net.bio.net Fri May 31 23:00:00 1996 Path: biosci!rutgers!uwm.edu!newsfeed.internetmci.com!tank.news.pipex.net!pipex!usenet1.news.uk.psi.net!uknet!uknet!bhamcs!news.ox.ac.uk!abr20.linacre.ox.ac.uk!user From: yan.wong@new.ox.ac.uk (yan wong) Newsgroups: bionet.population-bio Subject: Re: Q: Compare Allele or Genotype Distributions Date: Sat, 01 Jun 1996 11:38:43 +0000 Organization: Plant Sciences, Oxford Lines: 15 Distribution: world Message-ID: References: <1996May30.103719.5112@clp2> NNTP-Posting-Host: abr20.linacre.ox.ac.uk In article , dmw@MCZ.HARVARD.EDU (Daniel Weinreich) wrote: > If I remember the original post, the student *will* have actual genotype > frequencies, and thus would *not* be calculating them from H-W model > > > Run the chi-square on allele distributions. Surely if you were using frequencies, a Chi-squared contingency table would be inappropriate. You should have actual counts, which would mean using genotype distributions. I suppose that you could calculate the number of gene copies present (2 x homozygotes + 1 x heterozygotes), but I'm not sure how many independent point this would count as.