From owner-evolution@net.bio.net Sun May 01 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!usc!usc!not-for-mail From: phelps@calvin.usc.edu (Charles V. Phelps) Newsgroups: bionet.molbio.evolution,sci.math,sci.physics Subject: Re: Thomas Ray -- where published? Date: 2 May 1994 11:32:23 -0700 Organization: University of Southern California, Los Angeles, CA Lines: 41 Sender: phelps@calvin.usc.edu Message-ID: <2q3gvn$on9@calvin.usc.edu> References: <2prmop$evl@news.u.washington.edu> <2ptb6c$la8@dux.dundee.ac.uk> NNTP-Posting-Host: calvin-f0.usc.edu Xref: biosci bionet.molbio.evolution:1664 sci.math:32064 sci.physics:36824 growe@mcs.dundee.ac.uk (Glenn Rowe) writes: >John Sidles (sidles@u.washington.edu) wrote: >: Dear netfolks >: At the Institute for Advanced Study, I heard Thomas Ray of the >: University of Delaware give a wonderfully interesting talk on >: his computer simulations of evolutionary processes. >: On consulting INSPEC, I have not been able to find any publications >: relating to this work. Nor in our UW library catalog. Can anyone >: point me toward a published article? Or even better, ftp-available >: code? I would like to share it with some of the Seattle area >The only published article that I am aware of is: >T.S. Ray, "An approach to the synthesis of life", in "Artificial Life >II; Proceedings of the workshop on artificial life, held Feb 1990 in >Santa Fe, New Mexico", editors C.G. Langton, C. Taylor, J.D. Farmer, >and S. Rasmussen; Published by Addison-Wesley, 1992. ISBN >0-201-52571-2 (paperback edition). I found two references to conference papers; however, only the abstracts were published. These are: Ray, T. S., "Artificial life: Ecology and evolution in digital organisms," 75th Annual Meeting of the Ecological Society of America on Perspectives in Ecology: Past, Present, and Future, Snowbird, Utah, July 29-August 2, 1990. Published in Bulletin of the Ecological Society of America, v. 71 (2 suppl.), 1990. Ray abstract on p. 295-296. Ray, T. S., "Artificial life: Ecology and evolution in digital organisms," Fourth International Congress of Systematic and Evolutionary Biology; College Park, MD, July 1-7, 1990, sponsored by University of Maryland and The Smithsonian Institute, p. 74. Charles Phelps Science & Engineering Library University of Southern California From owner-evolution@net.bio.net Mon May 02 23:00:00 1994 Newsgroups: bionet.molbio.evolution Path: biosci!agate!library.ucla.edu!news.ucdavis.edu!pbmac-11.ucdavis.edu!user From: mezwick@ucdavis.edu (Mike Zwick) Subject: Re: phage models Message-ID: Followup-To: bionet.molbio.evolution Sender: usenet@ucdavis.edu (News Guru) Organization: UC Davis Dept of Ecology and Evolution References: <2pnbdl$omt@canopus.cc.umanitoba.ca> <2poo23$9ji@canopus.cc.umanitoba.ca> <2q5mpf$17q@brachio.zrz.TU-Berlin.DE> Date: Tue, 3 May 1994 14:56:30 GMT Lines: 20 In article <2q5mpf$17q@brachio.zrz.TU-Berlin.DE>, joaccigh@w354zrz.zrz.tu-berlin.de (Joachim Dagg) wrote: > Because Mike complains about the proceeding of building models after > making experiments, that can explain the results, I cite H.R.Erwin: I wasn't complaining about making models afterwards, instead I was questioning the assertion that an optimality model a priori somehow predicted that phage formation should proceed in a specific sequence. The real scenaro was that someone did experiments and then later made a model. However, the predictions of the model cannot rule out that there may be other (perhaps hypothetical) types of phage that develop through a completely different mechanism (one that is not predicted by the model nor consistent with the parameters of the model). -- mike zwick mezwick@ucdavis.edu Department of Ecology and Evolution Center for Population Biology From owner-evolution@net.bio.net Mon May 02 23:00:00 1994 Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!news.cac.psu.edu!psuvm!imeg Organization: Penn State University Date: Tue, 3 May 1994 17:55:17 EDT From: Sudhir Kumar Message-ID: <94123.175517IMEG@psuvm.psu.edu> Newsgroups: bionet.software,bionet.molbio.evolution Subject: MEGA: Order info repost on request Lines: 286 Xref: biosci bionet.software:8080 bionet.molbio.evolution:1668 This document contains many pages, including 1. Cover letter 2. Order form (We no longer accept purchase orders) 3. Hardware and software requirements 4. Program upgrade policy 5. Functions in MEGA MEGA version 1.0, 1.01 September, 1993 To whom it may concern: A computer software called MEGA: Molecular Evolutionary Genetics Analysis has been developed. This software is for facilitating statistical studies of molecular evolution by using IBM compatible personal computers. It contains various methods of estimating evolutionary distances and three different methods of phylogenetic inference (UPGMA, neighbor-joining, and maximum parsimony) with either a standard-error test or a bootstrap test of topological differences. For the maximum parsimony method, new algorithms of the branch-and-bound and heuristic searches are implemented. MEGA also computes basic statistical quantities such as nucleotide and amino acid frequencies, transition/transversion bias, codon usage frequencies, number of variable sites, etc. In addition, advance on- screen sequence data and phylogenetic tree editors are included. Integrated and interactive designs, on-line context-sensitive helps, text-file editor, and other unique features make it easy to use MEGA. MEGA version 1.0 is distributed with a nominal fee to defray the cost of producing the user manual (140 pp.) and diskettes, and the mailing and handling expenses (see enclosed order form). However, for anyone who is unable to pay the fee for some reason, it will be provided free of charge after receiving a letter explaining the circumstances. MEGA will not be sent by electronic-mail because the accompanying manual cannot be included in this case. Technical questions and other inquires about MEGA should be directed to the senior author of the software. Please include your electronic-mail address, if any. Sincerely yours, Sudhir Kumar Koichiro Tamura Masatoshi Nei Telephone: (814) 863-7334 FAX: (814) 863-7336 E-mail: imeg@psuvm, imeg@psuvm.psu.edu MEGA ORDER FORM Cost* ----------------------------------------------------------------- Program No Charge User manual, diskette, shipping, and handling $ 15.00 For shipment outside North America add $10.00 _________ (We will use first class airmail) TOTAL _________ ----------------------------------------------------------------- * This cost can be waived if the circumstances for the inability to pay (e.g., lack of hard currencies in some countries) are explained. Diskette type desired: Please specify: [ ] 3.5" Diskette (1.44MB) [ ] DOS Version ...... [ ] 5.25" Diskette (1.2MB) [ ] Computer system... [ ] other (specify).... [ ] Do you use windows? Yes/No All orders must be prepaid in U.S. dollars. Return this form together with a check or money order payable to Penn State University at the following address. Purchase orders will not be accepted. Joyce White Institute of Molecular Evolutionary Genetics The Pennsylvania State University 328 Mueller Laboratory University Park, PA 16802 USA Telephone: (814)-863-7334 Fax: (814)-863-7336 E-mail: IMEG@PSUVM.PSU.edu, IMEG@PSUVM About the user: Name: ____________________________________________ Address: ____________________________________________ ____________________________________________ ____________________________________________ Telephone: _____________________ Fax: _________________ E-Mail: ____________________________________________ --------Hardware and Software------ IBM and IBM-compatible PCs, XTs, ATs, etc. Color/monochrome monitors. 640KB RAM memory. DOS version 3.3 or later. Hard disk with 2MB free. No extended or expanded memory required. No graphics adapters required. No math-chip required. Supports the keyboard as well as the mouse (not essential). ------- Program upgrade policy ---- Since MEGA is in its first version, there may be many software bugs in the program. We are considering to provide registered users a version where bugs reported in version 1.0 and 1.01 will be fixed. As you may notice from the order form, we are just trying to recover the cost of distributing MEGA only. So we are not in a position to provide many upgrades. In any case, we do not plan to include new methods in MEGA soon (for at least one year), and therefore the questions about upgrades may not be so pressing at this moment. -------Functions in MEGA------- Input Input data: DNA sequences RNA sequences Amino acid sequences Distance matrices Input formats: Interleaved sequences Non-interleaved sequences Upper-triangular distance matrix Lower-triangular distance matrix Choice of: Alignment gap symbol Missing-information site symbol Identical site symbol In-memory data editing features Selection: Desired OTUs Domains of sequences Individual sites and codons Codon positions Exclude/include missing information sites Exclude/include alignment gap sites Edit OTU labels Restore OTU labels Sequence data presentation Highlight: Variable sites Parsimony-informative sites Two-fold redundant sites Four-fold redundant sites Translate: Translation of nucleotide sequences into amino acid sequences Output: Formats: MEGA PAUP PHYLIP Publication Data subsets: Only variable sites Only parsimony-informative sites Amino acid sequences translated Codon positions Sequence statistics: Nucleotide and amino acid frequencies Nucleotide pair frequencies in pairwise comparisons Insertion-deletion frequencies Codon usage frequencies Relative synonymous codon usage (RSCU) values Variable sites in overlapping segments Variable sites in nonoverlapping segments Distance estimation Nucleotide substitutions Quantities: Number of nucleotide differences Nucleotide substitutions Transitional substitutions Transversional substitutions Transition/transversion ratio Distance measures: p-distance Jukes-Cantor distance Kimura 2-parameter distance Tajima-Nei distance Tamura distance Tamura-Nei distance Gamma distances Jukes-Cantor model Kimura 2-parameter model Tamura-Nei model Synonymous-nonsynonymous substitutions Genetic code tables: "Universal" Mammalian mitochondrial Drosophila mitochondrial Yeast mitochondrial Computation: Synonymous substitutions Nonsynonymous substitutions Average distances for all pairwise comparisons and standard errors Amino acid substitutions Distance measurers: Number of amino acid differences p-distance Poisson-correction distance Gamma distance Distance output: Control on: Page size Precision for distance output Distance q standard error formats Tree building and test Methods: Neighbor-joining (NJ) UPGMA Maximum parsimony (MP): Branch-and-bound search Heuristic search Statistical Tests: Bootstrap test: Neighbor-joining UPGMA Branch length test: Neighbor-joining Phylogeny editing: Tree re-rooting Swapping and flipping branches Consensus tree Condensed tree Phylogeny printing: Various printers Multiple page printouts Choice of fonts Choice of orientation Choice of page size Tree preview General functions File browsing File editing Exiting to DOS temporarily Context-sensitive Helps Error messages From owner-evolution@net.bio.net Mon May 02 23:00:00 1994 Path: biosci!agate!ihnp4.ucsd.edu!swrinde!emory!nigel.msen.com!zib-berlin.de!zrz.TU-Berlin.DE!w354zrz!joaccigh From: joaccigh@w354zrz.zrz.tu-berlin.de (Joachim Dagg) Newsgroups: bionet.molbio.evolution Subject: Re: Reply to Mike Zwick Date: 3 May 1994 14:23:43 GMT Organization: TUBerlin/ZRZ Lines: 21 Message-ID: <2q5mpf$17q@brachio.zrz.TU-Berlin.DE> References: <2pnbdl$omt@canopus.cc.umanitoba.ca> <2poo23$9ji@canopus.cc.umanitoba.ca> NNTP-Posting-Host: w354zrz.zrz.tu-berlin.de Because Mike complains about the proceeding of building models after making experiments, that can explain the results, I cite H.R.Erwin: "Modellers who seek predictive results are indeed asking the wrong question much of the time, and instead should be seeking insight into their system." ("The Dynamics of Peer Polities", 1990, named CambridgeText.ps + CambridgeFigs.ps at anonymous ftp-site `mason1.gmu.edu' under /herwin.) As I understand, the insight is, that you know what parts your model is built of (attractors, saddle-points, limit-circles... or: information, replication, mutation, selection... or: whatever). If you find a real pendant for all the parts, you can simulate what will happen, when a new attractor/selection/... occurs, two saddle-points/species/... merge and so on. That doesn't mean you can make any exact predictions about the future development of your system. Joachim (joaccigh@w250zrz.zrz.tu-berlin.de) From owner-evolution@net.bio.net Mon May 02 23:00:00 1994 Newsgroups: bionet.molbio.evolution Path: biosci!agate!ames!purdue!mozo.cc.purdue.edu!bilbo.bio.purdue.edu!MAIZE From: maize@bilbo.bio.purdue.edu Subject: Mol evol postdoc Sender: news@mozo.cc.purdue.edu (USENET News) Message-ID: Date: Tue, 3 May 1994 15:24:30 GMT Reply-To: maize@bilbo.bio.purdue.edu Organization: Purdue University, Dept. of Biological Sciences Lines: 28 I have just received two years of funding from the USDA for a project to study the molecular evolution of homeologous chromosomal domains in maize, sorghum and rice. The research focuses on two particular regions; that surrounding Adh1 of maize and the homologous region of sorghum and that between the A1 and Sh2 homeologues of maize, sorghum, and rice. This will be the first project to investigate the evolution of intergenic sequences in a plant nuclear genome. We have cloned over 500 kb of contiguous DNA surrounding maize Adh1 on YACs and have over 200 kb of homologous DNA from sorghum on BACs and cosmids. The A1 and Sh2 genes of maize are about 140 kb apart on a single YAC, while the A1 and Sh2 genes of sorghum are less than 80 kb apart on a single BAC. We also have lambda clones of rice A1 and Sh2 homologues. We have mapped transcripts, scaffold attachment sites, and repeat classes across these regions. We now plan to sequence over 200 kb of homeologous DNA from these regions to determine: (a) what is there and (b) how it has evolved since these three species diverged. I am looking for a postdoctoral fellow, with experience both in sequence generation and analysis, to take charge of this project. Funding will be available as of June 1. Interested candidates should contact me at "maize@bilbo.bio.purdue.edu" or at 317-494-4763 (phone) or (317) 496-1496 (FAX). Jeff Bennetzen _______________________________________________________________________ Phillip SanMiguel Purdue maize@bilbo.bio.purdue.edu Institute for Molecular "We'll do anything Bennetzen Lab Plant for funding." Science _______________________________________________________________________ From owner-evolution@net.bio.net Tue May 03 23:00:00 1994 Path: biosci!CGL.UCSF.EDU!elder From: elder@CGL.UCSF.EDU (Bruce Elder) Newsgroups: bionet.molbio.evolution Subject: Duck codon usage Date: 3 May 1994 17:00:00 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 11 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <199405040000.RAA25985@socrates.ucsf.EDU> NNTP-Posting-Host: net.bio.net Howdy, I was wondering if anyone out there in net-land could point me at a reference for codon usage in ducks. I think that any avian species (chicken??) will be close enough for jazz (but I have been wrong before!!). Thanks in advance. Bruce Elder elder@cgl.ucsf.edu From owner-evolution@net.bio.net Tue May 03 23:00:00 1994 Path: biosci!agate!dog.ee.lbl.gov!ihnp4.ucsd.edu!library.ucla.edu!psgrain!nntp.cs.ubc.ca!newsxfer.itd.umich.edu!jobone!lynx.unm.edu!SantaFe!bcv From: bcv@alife.santafe.edu (Bradley Venner) Newsgroups: bionet.molbio.evolution Subject: Re: Thomas Ray Date: 4 May 1994 00:19:14 GMT Organization: The Santa Fe Institute Lines: 1 Message-ID: <2q6pm2$pi@tierra.santafe.ede> NNTP-Posting-Host: alife.santafe.ede X-Newsreader: TIN [version 1.2 PL2] From owner-evolution@net.bio.net Tue May 03 23:00:00 1994 Path: biosci!agate!ames!elroy.jpl.nasa.gov!swrinde!cs.utexas.edu!howland.reston.ans.net!torn!news.ccs.queensu.ca!qucdn!forsdyke Organization: Queen's University at Kingston Date: Wed, 4 May 1994 12:02:32 EDT From: Message-ID: <94124.120232FORSDYKE@QUCDN.QueensU.CA> Newsgroups: bionet.molbio.evolution Subject: Genomic GC% in different species Lines: 3 Does anyone know if there is an exhaustive tabulation of genomic GC% accessible by Gopher, or in the paper literature? Sincerely, Don Forsdyke From owner-evolution@net.bio.net Tue May 03 23:00:00 1994 Newsgroups: bionet.molbio.evolution Path: biosci!agate!library.ucla.edu!europa.eng.gtefsd.com!howland.reston.ans.net!EU.net!ub4b!news.sri.ucl.ac.be!idefix.CS.kuleuven.ac.be!reks.uia.ac.be!derijkp From: derijkp@reks.uia.ac.be (Peter.DeRijk) Subject: DCSE 3.0 alignment editor for X-Windows Message-ID: <1994May4.164906.27643@reks.uia.ac.be> Organization: U.I.A. X-Newsreader: Tin 1.1 PL5 Date: Wed, 4 May 1994 16:49:06 GMT Lines: 162 [ Article crossposted from bionet.software ] [ Author was Peter.DeRijk ] [ Posted on Wed, 4 May 1994 16:46:26 GMT ] The multiple sequence alignment editor DCSE has been converted to X-windows, and is available for Silicon Graphics (IRIX). It uses the the great embedable language Tcl/Tk (Thanks, Dr. Ousterhout) for its interface. This way it is not only very easy to use, but also easily adaptable and extendable. Several interesting new features have been added (see attached readme file for more details). DCSE 3.0 is currently only available for SGI systems, but other systems will follow. We will be installing some PC's with Linux shortly, so this will most probably be the next. I also would like to do a port to Sun, but do not have acces to one at the moment. You can get DCSE v3.0 for X-Windows via anonymous ftp on uiam3.uia.ac.be (143.169.8.1). To get it, do the following: % ftp uiam3.uia.ac.be login as anonymous and give your email adress as a password. ftp> cd [.dcse] ftp> bin ftp> get TKDCSE-SGI-3_0.TAR_Z ftp> quit % mv TKDCSE-SGI-3_0.TAR_Z tkdcse=sgi-3.0.tar.Z % zcat tkdcse=sgi-3.0.tar.Z | tar xf - % cd tkdcse_home % install Then read the help, and follow further instructions. If you have problems with it, please contact me. Of course, if you think it is good, or have writen nice extensions to it, you may also contact me. Peter De Rijk derijkp@reks.uia.ac.be I have attached the readme file for DCSE 3.0 to this message. ================ readme =================== What is DCSE ------------ DCSE (Dedicated Comparative Sequence Editor) is a multiple alignment editor. It can be used to edit protein, DNA or RNA alignments. The structure of the molecules can be incorporated in the alignment. It is written in C, and it uses dynamic memory for most things. This means you can almost edit any size of alignment with it. It offers lots of features such as color display of characters and structure, automatic alignment relative to sequences already aligned with others, sequence grouping, sequence or pattern searching, marker system, checking of incorporated RNA structure, on-line hypertext help, macros, and a lot more. This new version of DCSE has an easy to use, yet flexible and programmable X-windows interface provided by the Tcl/Tk language. A complete on-line hypertext help system is provided. Although DCSE v3.0 is compatible with the older version of DCSE, its implementation is completely different. The core of DCSE is implemented as an object which can be controlled by giving commands to it from the Tcl language, an easy to learn, yet flexible, interpreted language. The interface is written as a Tcl program. This way the program can be easily customized, and batch jobs are even possible. This approach has several advantages: - the user can adapt the interface of DCSE completely to his own liking. - It is easy to create macros or programs wich extend DCSE. - external programs can also be controlled in Tcl, and seamlessly integerated. - Tcl/Tk exists for a great variety of computers, so porting should be simplified. Convers is a complementary program to DCSE which does things like converting between different file-formats. The new version has been written a set of commandline programs, which are controlled by a Tcl/Tk interface. Legalities ---------- DCSE is Copyright Peter De Rijk, University of Antwerp (UIA), 1993 You may give this application to anyone, via any medium, so long as it is delivered with ALL the supplied files and UNALTERED, and it is not supplied on a disc you are charging for (except for media and postage costs). I maintain copyright on all the material supplied and reserve the right to amend these conditions in cases where I deem misuse. Disclaimer This application is supplied free to everyone 'as is', I do not give any guarantee that it is free of bugs, or supply any warranty about its suitability for use. No liability will be accepted for any damage to or loss of data as a result of using this application. However, if there are any problems with it and you notify me of them, I will probably do my best to rectify them. Citation A paper has been written about DCSE and this is submitted to and accepted by CABIOS. If you have used the program to obtain results in a paper you've written, please cite the following reference: Peter De Rijk and Rupert De Wachter DCSE v2.54, an interactive tool for sequence alignment and secondary structure research. Comput. Applic. Biosci. Reprints of articles in which DCSE is mentioned would be welcomed. I will do my best to reply as fast as I can to any problems, etc. . However, the development of DCSE is not my only task, which is why my response might not be always as fast as you would like. System ------ This program has been tested on an Indigo with an R4000 and on one with an R3000. It should work on other Silicon Graphics machines as well. Installing the package ---------------------- Uncompress and untar the distribution in a suitable directory. This will produce a directory called tkdcse_home. Go into that directory, and start the program install. Then follow directions. zcat tkdcse-sgi-3.0.tar.Z | tar xf - cd tkdcse_home ./install The install program will give you more info on what to do to install DCSE. The programs can be started by typing 'tkdcse' or 'tkconvers' in a shell window. Bugs ---- If you are having problems with the program contact me. I will do my best to get it fixed. Please report any bugs you have found. If possible, state your machine's hardware and software configurations. Sending me a full description of the circumstances in which the bug occurs, possibly with the data it happened on, will help me tracking down a bug. If you have any suggestions, you can also make them to me. How to contact me ----------------- Peter De Rijk University of Antwerp (UIA) Department of Biochemistry Universiteitsplein 1 B-2610 Antwerp tel.: 32-03-820.23.16 fax: 32-03-820.22.48 E-mail: derijkp@reks.uia.ac.be From owner-evolution@net.bio.net Wed May 04 23:00:00 1994 Path: biosci!UNH.EDU!Thomas.D.Kocher From: Thomas.D.Kocher@UNH.EDU (Thomas D Kocher) Newsgroups: bionet.molbio.evolution Subject: Molecular Evolution texts Date: 5 May 1994 12:42:58 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 9 Sender: daemon@net.bio.net Distribution: bionet Message-ID: NNTP-Posting-Host: net.bio.net Are there any new Molecular Evolution texts about to be published out there? I'm looking for a new text for my senior/graduate level course in Molecular Evolution. Tom Kocher Dept. Zoology Univ. of New Hampshire From owner-evolution@net.bio.net Wed May 04 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!gatech!udel!news2.sprintlink.net!news.sprintlink.net!sundog.tiac.net!usenet.elf.com!rpi!batcomputer!ghost.dsi.unimi.it!univ-lyon1.fr!news From: duret@evoserv.univ-lyon1.fr (Laurent Duret) Newsgroups: bionet.molbio.evolution Subject: Re: Genomic GC% in different species Date: 5 May 1994 06:00:50 GMT Organization: Universite Claude Bernard - Lyon 1 Lines: 14 Distribution: world Message-ID: <2qa22i$6ar@cismsun.univ-lyon1.fr> References: <94124.120232FORSDYKE@QUCDN.QueensU.CA> Reply-To: duret@evoserv.univ-lyon1.fr NNTP-Posting-Host: evoserv.univ-lyon1.fr In article 120232FORSDYKE@QUCDN.QueensU.CA, writes: > Does anyone know if there is an exhaustive tabulation of genomic GC% > accessible by Gopher, or in the paper literature? > Sincerely, Don Forsdyke For a discussion of vertebrate genomes nucleotide composition, you may see Bernardi (1993) Gene 135:57-66 and references therein. Laurent Duret From owner-evolution@net.bio.net Wed May 04 23:00:00 1994 Path: biosci!THALAMUS.WUSTL.EDU!yamagatm From: yamagatm@THALAMUS.WUSTL.EDU (Yamagata =?ISO-2022-JP?B?GyRCOzM3QRsoQg==?=) Newsgroups: bionet.molbio.evolution Subject: Homolog/ortholog Date: 5 May 1994 07:49:13 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 8 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <9405051451.AA20816@thalamus.wustl.edu> NNTP-Posting-Host: net.bio.net How do you define a homolog, ortholog, or paralog? Family, superfamily, subfamily, cognate, counterpart, related, homologous, --Do you use other words for describing relationships among homologous genes? And, how would you use these words? Is there good references for how we can accurately distinguish these words? I know there is no simple answer for this. But, I would like to know how molecular evolutionalists are using these words. Thanks in advance. From owner-evolution@net.bio.net Wed May 04 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!eunet.no!nuug!EU.net!howland.reston.ans.net!cs.utexas.edu!usc!nic-nac.CSU.net!charnel.ecst.csuchico.edu!psgrain!nntp.cs.ubc.ca!unixg.ubc.ca!quartz.ucs.ualberta.ca!tribune.usask.ca!canopus.cc.umanitoba.ca!newsflash.concordia.ca!nstn.ns.ca!dal1!arlin From: arlin@ac.dal.ca Newsgroups: bionet.molbio.evolution Subject: Re: the common mode of bacterial motility Message-ID: <1994May5.193601.23827@dal1> Date: 5 May 94 19:36:00 -0300 References: <1994Apr21.190914.23337@dal1> Organization: Dalhousie University, Halifax, Nova Scotia, Canada Lines: 32 In article , lamoran@gpu.utcc.utoronto.ca (L.A. Moran) writes: > In article , > Jeff Lawrence wrote: >> >>While i agree that circular chromosomes are likely to be ancestral to the >>bacterial lineage, linear chromosomes and linear plasmids are widespread >>among bacterial taxa. Aside from Borrelia (Casjens Mol Micro, May 93), i >>can recall that Agrobacterium (J Bact, Dec 93) and Streptomyces (MGG, Nov >>93) also have linear chromosomes. I also recal sherwood casjens popping up Thanks for this list of my earlier oversights. > The common ancestor of all bacteria may have had circular chromromsome(s) but > whether the common ancestor of all life had linear or circular chromosome(s) > is an open question. (Assuming that the root of the universal tree falls > between prokaryotes and eukaryotes.) Circular chromosomes may still be a > derived character in prokaryotes. > > Larry Moran > Agreed. I'm not making alot of assumptions about the universal tree. The Iwabe-Gogarten tree, the Eocyte/Woese&Wolfe tree, the Gupta tree-- all of these trees have organisms with bacterial features (circular chromosomes, operons, etc) on *both* sides of the root, and thus if any of these trees are correct, the most recent common ancestor of all cells was likely to have been a bacterium _sensu latu_. If Larry's suggestion that euks may be an outgroup to bacteria _sensu latu_ is correct, then, as Larry suggests, circular chromosomes and other characteristic bacterial features may be derived states rather than primitive ones. Arlin From owner-evolution@net.bio.net Wed May 04 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!uknet!demon!news2.sprintlink.net!news.sprintlink.net!sundog.tiac.net!usenet.elf.com!rpi!batcomputer!ghost.dsi.unimi.it!univ-lyon1.fr!news From: duret@evoserv.univ-lyon1.fr (Laurent Duret) Newsgroups: bionet.molbio.evolution Subject: Re: Duck codon usage Date: 5 May 1994 15:58:49 GMT Organization: Universite Claude Bernard - Lyon 1 Lines: 15 Distribution: world Message-ID: <2qb53p$j2v@cismsun.univ-lyon1.fr> References: <199405040000.RAA25985@socrates.ucsf.EDU> Reply-To: duret@evoserv.univ-lyon1.fr NNTP-Posting-Host: evoserv.univ-lyon1.fr In article RAA25985@socrates.ucsf.EDU, elder@CGL.UCSF.EDU (Bruce Elder) writes: > > Howdy, > > I was wondering if anyone out there in net-land could point me at > a reference for codon usage in ducks. I think that any avian species > (chicken??) will be close enough for jazz (but I have been wrong before!!). see: "The compositional pattern of the avian genomes and their evolutionary implications" Kadi et al (1993) J. Mol. Evol. 37:544-551 Laurent Duret From owner-evolution@net.bio.net Thu May 05 23:00:00 1994 Path: biosci!news.cs.umb.edu!hsdndev!nmr-z.mgh.harvard.edu!nmr-z.mgh.harvard.edu!lfk From: lfk@receptor.mgh.harvard.edu (Lee F. (Frank) Kolakowski) Newsgroups: bionet.molbio.evolution Subject: Re: cladistics Date: 06 May 1994 21:40:14 GMT Organization: Mass. General Hospital, Renal Unit Lines: 44 Message-ID: References: <1994Apr26.193206.1597@honte.uleth.ca> <1994May6.193558.18710@muss.cis.mcmaster.ca> NNTP-Posting-Host: receptor.mgh.harvard.edu In-reply-to: g8713026@mcmail.cis.mcmaster.ca's message of Fri, 6 May 1994 19:35:58 GMT > In article <1994Apr26.193206.1597@honte.uleth.ca> std_dickout@hg.uleth.ca writes: >>I am taking a course in cladistics and am interested in information >>concerning the use of Maximum Parsimony and Distance analyses in the >>treatment of molecular data. Any reasons why you would choose one >>method over the other would be greatly appreciated. The generally accepted methods have been outlined by Bill Pearson earlier. The note to add to this discussion is the paper by Hillis and colleagues in the most recent Science (4/29). In this paper, the authors use combinations of simulations and know phylogenies to test the performance of UPGMA, NJ (Both distance methods) and Parsimony. The results show that weighted parsimony has the best performance curve, but in the tests used, all methods can work. So it is a philosophical and practical issue as to which method or methods to use. Some have said that they do not trust any single method, and that situations where significantly different results are obtained, make to problem too difficult to approach. I myself am heartened as we have used a form of weighted parsimony we call "Accepted Mutation Parsimony" (AMP) to look at a complex 125 taxon problem. This is a protein sequence method which utilizes a weighting scheme derived from the aligned dataset. What do other people think about the MP vs NJ vs ML problem? Thanks -- Frank Kolakowski ======================================================================= O Email: lfk@receptor.mgh.harvard.edu O O kolakowski@helix.mgh.harvard.edu O O lfk@eastman1.mit.edu O O US Mail: Lee F. Kolakowski Renal Unit, 8th Flr. O O Massachusetts General Hospital Charlestown Navy Yard O O 149 13th Street FAX : 1-617-726-5669 O O Charlestown, MA 02129 Phone AT&T: 1-617-726-5666 O ======================================================================= O The home of the G-Protein-Coupled Receptor Database (GCRDb) O ======================================================================= From owner-evolution@net.bio.net Thu May 05 23:00:00 1994 Newsgroups: bionet.molbio.evolution Path: biosci!news.cs.umb.edu!hsdndev!yale!yale!yale.edu!news.yale.edu!news From: ALMASY@biomed.med.yale.edu (Laura Almasy) Subject: Re: Duck codon usage In-Reply-To: elder@CGL.UCSF.EDU's message of 3 May 1994 17:00:00 -0700 Message-ID: <1994May5.194352.28004@news.yale.edu> Sender: news@news.yale.edu (USENET News System) Nntp-Posting-Host: biomed.med.yale.edu Organization: Yale University References: <199405040000.RAA25985@socrates.ucsf.EDU> Date: Thu, 5 May 1994 19:43:52 GMT X-News-Reader: VMS NEWS 1.20 Lines: 22 In <199405040000.RAA25985@socrates.ucsf.EDU> elder@CGL.UCSF.EDU writes: > I was wondering if anyone out there in net-land could point me at > a reference for codon usage in ducks. I think that any avian species > (chicken??) will be close enough for jazz (but I have been wrong before!!). Try: K. Wada et. al. (1992) "Codon Usage" Nucleic Acids Research 20:2111-2118. The above article has codon usage tables for a variety of organisms, including not only chickens but ducks themselves. Hope it helps, Laura -------------------------------------------------------------------------------- Laura A. Almasy almasy@biomed.med.yale.edu Dept. of Genetics Yale University From owner-evolution@net.bio.net Thu May 05 23:00:00 1994 Path: biosci!agate!overload.lbl.gov!deh From: deh@s27w007.pswfs.gov (Dave Harry) Newsgroups: bionet.molbio.evolution Subject: Re: Molecular Evolution texts Date: 6 May 1994 20:24:56 GMT Organization: Dendrome, A Genome Database for Forest Trees Lines: 15 Distribution: bionet Message-ID: <2qe92o$2nl@overload.lbl.gov> References: NNTP-Posting-Host: s27w007.pswfs.gov Depending on the focus of your course, the following may or may not be of interest. I've been very impressed with the following text as an overview, although its emphasis may be too broad for your needs. Avise, John C. 1994 Molecular markers, natural history, and evolution Chapman and Hall, Pubs (ISBN 0-412-03781-5). David Harry Institute of Forest Genetics deh@s27w007.pswfs.gov USDA Forest Service, Pacific SW Station Phone: 510/559-6439 PO Box 245 FAX: 510/559-6499 Berkeley, CA 94701 From owner-evolution@net.bio.net Thu May 05 23:00:00 1994 Newsgroups: bionet.molbio.evolution Path: biosci!bcm!cs.utexas.edu!howland.reston.ans.net!torn!mcshub!muss.cis.mcmaster.ca!mcmail!g8713026 From: g8713026@mcmail.cis.mcmaster.ca (Anouk Behara) Subject: Re: cladistics Message-ID: <1994May6.193558.18710@muss.cis.mcmaster.ca> Sender: usenet@muss.cis.mcmaster.ca (News Database) Nntp-Posting-Host: mcmail.cis.mcmaster.ca Organization: McMaster University, Hamilton, Ontario, Canada References: <1994Apr26.193206.1597@honte.uleth.ca> Date: Fri, 6 May 1994 19:35:58 GMT Lines: 19 In article <1994Apr26.193206.1597@honte.uleth.ca> std_dickout@hg.uleth.ca writes: >I am taking a course in cladistics and am interested in information con >cerning the use of Maximum Parsimony and Distance analyses in the treatment >of molecular data. Any reasons why you would choose one method over the >\ >other would be greatly appreciated. > >Thank you >J.L. Burke If anyone does have references or ideas, could you please post them? I would also be interested in seeing some references etc. on the subject. Thank you -- ,~~_ Anouk Behara |/\ =_ _ ~ _( )_( )\~~ Department of Biology \,\ _|\ \~~~ Mcmaster University From owner-evolution@net.bio.net Thu May 05 23:00:00 1994 Path: biosci!agate!msuinfo!schmidt2.mph.msu.edu!user From: lepppaul@studentL.msu.edu (Paul W Lepp) Newsgroups: bionet.molbio.evolution Subject: Re: cladistics Followup-To: bionet.molbio.evolution Date: 6 May 1994 23:09:58 GMT Organization: MSU Lines: 29 Message-ID: References: <1994Apr26.193206.1597@honte.uleth.ca> <1994May6.193558.18710@muss.cis.mcmaster.ca> NNTP-Posting-Host: schmidt2.mph.msu.edu In article <1994May6.193558.18710@muss.cis.mcmaster.ca>, g8713026@mcmail.cis.mcmaster.ca (Anouk Behara) wrote: > In article <1994Apr26.193206.1597@honte.uleth.ca> std_dickout@hg.uleth.ca writes: > >I am taking a course in cladistics and am interested in information con > >cerning the use of Maximum Parsimony and Distance analyses in the treatment > >of molecular data. Any reasons why you would choose one method over the > >\ > >other would be greatly appreciated. > > > >Thank you > >J.L. Burke > > If anyone does have references or ideas, could you please post them? I > would also be interested in seeing some references etc. on the subject. > Frank Kolakowski already mentioned one good article by Hillis. Another by Huelsenbeck and Hillis is a great comparison of various methods versus various data sets. I found the paper cited below some work to get through, but well worth the effort. Happy hunting. Paul Lepp lepppaul@studentL.msu.edu J.P. Huelsenbeck and D.M. Hillis. 1993. Success of phylogenetic methods in the four-taxon case. Syst. Biol. 42(3):247-264. From owner-evolution@net.bio.net Fri May 06 23:00:00 1994 Newsgroups: bionet.molbio.evolution Path: biosci!agate!howland.reston.ans.net!gatech!swrinde!ihnp4.ucsd.edu!library.ucla.edu!news.ucdavis.edu!pbmac-5.ucdavis.edu!user From: tdlong@ucdavis.edu (Tony Long) Subject: Re: Fossil genetics Message-ID: Followup-To: bionet.molbio.evolution Sender: usenet@ucdavis.edu (News Guru) Organization: Center for Population Biology References: <7MAY94.04423854@biotek.arc.ab.ca> Date: Sat, 7 May 1994 18:04:54 GMT Lines: 41 In article , wgallin@gpu.srv.ualberta.ca (Warren Gallin) wrote: > an early biological determinant of mating incompatibility is probably > changes in chromosome structure, which will interfere with functional > meiosis. To see that, you would need a full karyotype analysis; I think > that is extremely unlikely. Most of the structural genes are not going to > confer mating incompatibility. What is your evidence for this? Sure there are a lot of karyotype differences between species, but such changes do not imply they are the cause of reproductive isolation. I suggest looking at recent work out of the Wu lab at University of Chicago (or any of the other labs doing work in this area) on reproductive isolation between species in the Drosophila group. This work suggests that a number of 'factors' are associated with reproductive isolation in these groups. As these factors are not cloned (not yet anyway) it is not clear if they represent structural or regulatory genes. Eitherway, at least in Drosphila, there is evidence that reproductive isolation can evolve before karyotype changes. Mileage may vary in other taxa. > you're suggesting, but I think it is in the realm of science fiction right now. > Warren Gallin, > Department of Zoology, University of Alberta > wgallin@gpu.srv.ualberta.ca Even if one had the sequence of the entire genome of an extinct species, the task of associating this variation with ANY phenotypic differences (be it isolation or nose size) between species would remain in the realm of science fiction. In order to map such loci one needs to associate DNA variation with phenotypic variation in the F2 (or a subsequent backcross) generation of a cross between the species. Of course in order to do this we would have to recreate the species in a Jurassic Park fashion ... or make transgenic animals that differ only in a candidate gene (this is possible in Drosophila). Tony Long Center for Population Biology U. C. Davis Davis, CA tdlong@ucdavis.edu From owner-evolution@net.bio.net Fri May 06 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!gatech!newsxfer.itd.umich.edu!nntp.cs.ubc.ca!unixg.ubc.ca!quartz.ucs.ualberta.ca!uapc.biology.ualberta.ca!wgallin From: wgallin@gpu.srv.ualberta.ca (Warren Gallin) Newsgroups: bionet.molbio.evolution Subject: Re: Fossil genetics Date: Sat, 7 May 94 16:04:48 GMT Organization: University of Alberta Lines: 36 Message-ID: References: <7MAY94.04423854@biotek.arc.ab.ca> NNTP-Posting-Host: uapc.biology.ualberta.ca X-Newsreader: VersaTerm Link v1.1.4 In Article <7MAY94.04423854@biotek.arc.ab.ca>, matlock@biotek.arc.ab.ca wrote: > Does anyone know where I could find more information about fossil DNA or >genetics? Eventually, I need to consider the following question bothering >me and a few friends: > > I use the definition that two animals are of the same species if they can >naturally mate and produce fertile offspring. > > How far back in time can we go before a species can no longer mate with >its ancestors. This is obviously a hypothetical question, since ancestral >species are usually extinct. But say we had genetic samples of homo habilis. >Can we compare their genes with ours and come to any conclusions about our >mating compatibility? I need to know where to look to find out if anyone >has done any work along these lines. > > I think paleontologists don't use the above species definition, since >they can only compare morphological or environmental characters. > > Please email your answers, as well as post if you think you should. The only information on molecular data from fossils that I am aware of are a few reports on collagen from bones and some of the DNA extracted from amber-embedded organisms. I think that we will never have sufficient DNA sequence from fossils to answer the question you are after. For one thing, an early biological determinant of mating incompatibility is probably changes in chromosome structure, which will interfere with functional meiosis. To see that, you would need a full karyotype analysis; I think that is extremely unlikely. Most of the structural genes are not going to confer mating incompatibility. Paleontologists go with morphological definitions of species because that is what their data will allow them. I wish we could get the data that you're suggesting, but I think it is in the realm of science fiction right now. Warren Gallin, Department of Zoology, University of Alberta wgallin@gpu.srv.ualberta.ca From owner-evolution@net.bio.net Fri May 06 23:00:00 1994 Newsgroups: bionet.molbio.evolution Path: biosci!agate!ihnp4.ucsd.edu!usc!nic-nac.CSU.net!charnel.ecst.csuchico.edu!rat!decwrl!tribune.usask.ca!kakwa.ucs.ualberta.ca!mercury.arc.ab.ca!biotek.arc.ab.ca!matlock From: matlock@biotek.arc.ab.ca Subject: Re: Fossil genetics Message-ID: <7MAY94.23213845@biotek.arc.ab.ca> Sender: news@arc.ab.ca (USENET News System) Nntp-Posting-Host: biotek.arc.ab.ca Organization: Alberta Research Council Date: Sat, 7 May 1994 23:21:38 GMT Lines: 24 Thanks to all who responded to my query. I think I have a better under- standing now of the problem. (I am a geologist, not educated in this complex biology stuff). So the way I see it, even if we had all the genetic samples from a species ancestor, there is no way you could say if it were still compatible with its descendants unless you built the organism and then tested one gene at at time. Is that about right? Put another way, even if you could unravel and map the DNA chains, you couldn't assign any function to them without extensive testing. You would have to test them in the manner of Tony Long's Drosophila candidate genes example. I hope you are forgiving of a geologists poor molecular biology terminology. For the record, I'd like to make clear that I never considered the Jurassic Park fictions when I formulated these thoughts. I was consider- ing comparing, for example, the compatibility of homo habilis with homo you-name-it. As a final note, I understand that there is a project out there to map all homo sapiens DNA. To my knowledge, it is far from complete, but it is a healthy, well-funded project. Is there anyone working in a similar manner with the fossil DNA of homo, or other genera? --John Vezina From owner-evolution@net.bio.net Fri May 06 23:00:00 1994 Newsgroups: bionet.molbio.evolution Path: biosci!agate!library.ucla.edu!psgrain!nntp.cs.ubc.ca!unixg.ubc.ca!quartz.ucs.ualberta.ca!kakwa.ucs.ualberta.ca!mercury.arc.ab.ca!biotek.arc.ab.ca!matlock From: matlock@biotek.arc.ab.ca Subject: Fossil genetics Message-ID: <7MAY94.04423854@biotek.arc.ab.ca> Sender: news@arc.ab.ca (USENET News System) Nntp-Posting-Host: biotek.arc.ab.ca Organization: Alberta Research Council Date: Sat, 7 May 1994 04:42:38 GMT Lines: 20 Does anyone know where I could find more information about fossil DNA or genetics? Eventually, I need to consider the following question bothering me and a few friends: I use the definition that two animals are of the same species if they can naturally mate and produce fertile offspring. How far back in time can we go before a species can no longer mate with its ancestors. This is obviously a hypothetical question, since ancestoral species are usually extinct. But say we had genetic samples of homo habilis. Can we compare their genes with ours and come to any conclusions about our mating compatibility? I need to know where to look to find out if anyone has done any work along these lines. I think paleontologists don't use the above species definition, since they can only compare morphological or environmental characters. Please email your answers, as well as post if you think you should. --John Vezina From owner-evolution@net.bio.net Sun May 08 23:00:00 1994 Path: biosci!agate!ihnp4.ucsd.edu!swrinde!gatech!newsxfer.itd.umich.edu!nntp.cs.ubc.ca!unixg.ubc.ca!quartz.ucs.ualberta.ca!uapc.biology.ualberta.ca!wgallin From: wgallin@gpu.srv.ualberta.ca (Warren Gallin) Newsgroups: bionet.molbio.evolution Subject: Re: Fossil genetics Followup-To: bionet.molbio.evolution Date: Mon, 9 May 94 15:27:56 GMT Organization: University of Alberta Lines: 58 Message-ID: References: <7MAY94.04423854@biotek.arc.ab.ca> NNTP-Posting-Host: uapc.biology.ualberta.ca X-Newsreader: VersaTerm Link v1.1.4 In Article , tdlong@ucdavis.edu (Tony Long) wrote: >In article , >wgallin@gpu.srv.ualberta.ca (Warren Gallin) wrote: >> an early biological determinant of mating incompatibility is probably >> changes in chromosome structure, which will interfere with functional >> meiosis. To see that, you would need a full karyotype analysis; I think >> that is extremely unlikely. Most of the structural genes are not going to >> confer mating incompatibility. > > What is your evidence for this? Sure there are a lot of karyotype >differences between species, but such changes do not imply they are the >cause of reproductive isolation. I suggest looking at recent work out of >the Wu lab at University of Chicago (or any of the other labs doing work in >this area) on reproductive isolation between species in the Drosophila >group. This work suggests that a number of 'factors' are associated with >reproductive isolation in these groups. As these factors are not cloned >(not yet anyway) it is not clear if they represent structural or regulatory >genes. Eitherway, at least in Drosphila, there is evidence that >reproductive isolation can evolve before karyotype changes. Mileage may >vary in other taxa. > >> you're suggesting, but I think it is in the realm of science fiction right now. > Even if one had the sequence of the entire genome of an extinct species, >the task of associating this variation with ANY phenotypic differences (be >it isolation or nose size) between species would remain in the realm of >science fiction. In order to map such loci one needs to associate DNA >variation with phenotypic variation in the F2 (or a subsequent backcross) >generation of a cross between the species. Of course in order to do this >we would have to recreate the species in a Jurassic Park fashion ... or >make transgenic animals that differ only in a candidate gene (this is >possible in Drosophila). Actually I was thinking of the case of horses and donkeys. I agree that this isn't the only cause, but neither is Drosophila necessarily representative of other species. As I recall some of that is based on the presence of an intracellular bacterium. In general, karyotypic changes that lead to non-functional meiosis will necessarily lead to reproductive isolation. The point is that karyotype changes are common; I don't know if some of the other factors occur as widely. Karyotype differences (in particular translocations that lead to acentric or dicentric chromosomes on recombination) are effective blocks to interbreeding. Whether they are the first cause of isolation is open to study for any species. When I said that most of the strucrual genes are not going to confer compatibility, I think I was on firm ground. Note, I was not saying that structural genes won't do it, I said most of them have nothing to do with it. A small sample of genomic sequence (which is all you are likely to get from a fossil sample, is unlikely to have the genes that are associated with reproductive isolation, even if you knew what you were looking for, which we both agree we don't. Warren Gallin, Department of Zoology, University of Alberta wgallin@gpu.srv.ualberta.ca From owner-evolution@net.bio.net Sun May 08 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!xlink.net!scsing.switch.ch!swidir.switch.ch!univ-lyon1.fr!news From: duret@evoserv.univ-lyon1.fr (Laurent Duret) Newsgroups: bionet.software,bionet.molbio.evolution Subject: Homologous Vertebrate Genes Data Base: new release Date: 9 May 1994 13:07:58 GMT Organization: Universite Claude Bernard - Lyon 1 Lines: 62 Distribution: world Message-ID: <2qlcje$9q7@cismsun.univ-lyon1.fr> Reply-To: duret@evoserv.univ-lyon1.fr NNTP-Posting-Host: evoserv.univ-lyon1.fr Xref: biosci bionet.software:8154 bionet.molbio.evolution:1687 ANNOUNCEMENT ================================================================================ HOVERGEN Homologous Vertebrate Genes Data Base Release 6 (May 9 1994) from GenBank Release 82 (April 15 1994) ================================================================================ The new release is available by anonymous FTP at biom3.univ-lyon1.fr (134.214.100.42) in the directory /pub/hovergen HOVERGEN is a database of homologous vertebrate genes. HOVERGEN allows one to easily select sets of homologous genes among a given set of vertebrate species. HOVERGEN corresponds to all nuclear vertebrate sequences of GenBank, with some data corrected, clarified, or completed, notably to address the problem of redundancy. Coding sequences have been classified in gene families. Protein multiple alignments and phylogenetic trees have been calculated for each family. Sequences and related information have been structured in an ACNUC database. A program named "query" allows to make complex selections in the ACNUC database according to any information clearly declared (keywords, bibliography, taxonomy, etc.). Selection criteria can be combined with boolean operators. A graphical interface has been developed to visualize and edit trees. Genes are displayed in color, according to their taxonomy. Users have directly access to all information attached to sequences (either from GenBank or specific of HOVERGEN), or multiple alignments simply by clicking on genes. This graphical tool gives thus a rapid and simple access to all data necessary to interpret homology relationships between genes: phylogenetic trees of gene families, taxonomy, GenBank information and protein multiple alignments. HOVERGEN is particularly useful for: - comparative sequence analysis - phylogeny - molecular evolution studies More generaly, HOVERGEN gives an overall view of what is known about a particular gene family. Laurent Duret Laboratoire de Biometrie, Genetique et Biologie des Populations URA CNRS 243 Universite Claude Bernard - Lyon I 43, Bd du 11 Novembre 1918 F-69622 Villeurbanne cedex Tel: +33 72.44.81.42 E-mail: duret@biomserv.univ-lyon1.fr From owner-evolution@net.bio.net Sun May 08 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!cs.utexas.edu!pirates.cs.swt.edu!swrinde!news.uh.edu!imb.imb.uh.edu!george From: george@imb.imb.uh.edu (George Fox) Newsgroups: bionet.molbio.evolution Subject: Schedule for Gordon Conference on Origin of Life Date: 9 May 1994 16:38 CST Organization: IMB Research Cluster Lines: 93 Distribution: world Message-ID: <9MAY199416381070@imb.imb.uh.edu> NNTP-Posting-Host: gfox.imb.uh.edu News-Software: VAX/VMS VNEWS 1.41 GORDON RESEARCH CONFERENCE ON THE ORIGIN OF LIFE Salve Regina University, Newport, Rhode Island August 21-26, 1994 David J. Des Marais, Chairman; Gerald F. Joyce, Vice Chairman This meeting addresses several aspects of origin of life studies, including the early history and environment of earth, prebiotic chemistry, and the geologic and molecular biological record of early evolution. A session on early Mars is also included! A single fee ($465., if paid before July 31) covers registration, room and board for the entire meeting. To obtain a registration form please send a request to the Gordon Research Conference Office (tel.: 401-783-4011, FAX: 401-783-3372) or to D. Des Marais (tel. 415-604-3220, FAX: 415-604-1088, email: david_desmarais@qmgate.arc.nasa.gov). Monday AM: External controls on the early environment; S. Chang, discussion leader J. Cronin Organic chemistry of the early solar system: recent molecular and isotopic analyses of meteorites V. Oberbeck Meteorite impacts and the origin and early evolution of life Y. Zhang History of mantle/crust exchange of volatiles Monday PM: RNA World; G. Joyce, discussion leader A. Schwartz Testing candidates for a pre-RNA world R. Green Defining the minimal requirements for the peptidyl transferase reaction of the ribosome Tuesday AM: Iron and sulfur transformations; H. Holland, discussion leader G. Wachterhauser The iron-sulfur world in Vitro K. Stetter Hyperthermophilic communities in deep terrestrial and submarine environments: the iron-sulfur world in Vivo D. Canfield The early geologic record of iron and sulfur biogeochemistry Tuesday PM: The role of phosphate; D. Canfield, discussion leader G. Arrhenius Phosphate - an early choice H. Holland Marine phosphate and atmospheric O2 Wednesday AM: Mars; J. Rummel, discussion leader J. Farmer Exopaleontology and the search for a fossil record on Mars J. Wisdom Orbital obliquity history of Mars and Earth C. McKay Earth analogs to past life on Mars Wednesday PM: Early phylogeny; A. Knoll, discussion leader A. Lazcano Rooting the tree of life: what came before the last common ancestor? S. Barns Novel Archaeal lineages from a natural microbial population Thursday AM: Photosynthesis; R. Castenholz, discussion leader B. Pierson Physiological ecology and the evolution of diversity among ancient photosynthetic bacteria R. Blankenship Evolution of photosynthetic reaction centers A. Knoll The Precambrian record of photosynthetic organisms Thursday PM: Early biosphere: the rock record; B. Simoneit, discussion leader D. Lowe Life on an early warm (hot?) earth R. Summons Molecular fossils: the nature and quality of the record in Archean and Proterozoic sediments Friday AM: Prebiotic chemistry: membranes, microenvironments and light S. Miller, discussion leader A. Pohorille Structure and functions of the earliest membrane systems: computer simulations D. Deamer Membrane permeability and encapsulated catalysts P. Braterman Photochemistry of iron(II)-containing systems in prebiotic reduction and synthesis From owner-evolution@net.bio.net Sun May 08 23:00:00 1994 Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!europa.eng.gtefsd.com!darwin.sura.net!jhunix.hcf.jhu.edu!NewsWatcher!user From: Hieter@jhuigf.med.jhu.edu (Hieter Lab) Newsgroups: bionet.molbio.evolution Subject: human cDNAs that can complement yeast mutants Followup-To: bionet.molbio.evolution Date: Mon, 09 May 1994 15:39:37 -0500 Organization: Johns Hopkins University Lines: 49 Message-ID: NNTP-Posting-Host: 128.220.56.46 I am interested in finding all examples where HUMAN cDNAs can complement yeast (S. cerevisiae) mutations. Below are those that I have found so far. Please write back ASAP with any that you might know of that I missed. Please include references if available. Thanks, Stuart T. YEAST MUTANT Human gene cdc9 DNA ligase I hap2 human hap2 vdac HVDAC1 and 2 rbp1 hFKB12 srm1/prp20 RCC1 (rescues ts, not null) pro3 P5C reductase cdc28 P34CDC2 cdc28 CDK2 cdc28 CDK3 nmt1 NMT (rescues ts or null) cpr1 oxidoreductase cim5 MSS1 pfk? Phosphofructokinase, muscle cki1 choline kinase gst1 GST1-Hs or GSPT1 nop1 fibrillarin rad6 HHR6A, HHR6B arf1 /arf2 ARF5 or ARF6 gal1 galactokinase cdc24 p21rap1A cdc42-1 or cdc24-4 G25K pde1,2 HCP1 ura1 dihydroorotate dehydrogenase abf2 MTTF1 cdc34 HUMCDC34H cks1 CKShs1 or CKShs2 smd1 snRNP D1 ade5, 7, or 8 GART cdc8 dTMP kinase cyc1 cytochrome c glc3 HGBE cln1,2,&3 Cyclin D1/PRAD1/CCND1 From owner-evolution@net.bio.net Sun May 08 23:00:00 1994 Newsgroups: bionet.software,bionet.molbio.evolution Path: biosci!agate!howland.reston.ans.net!torn!utnut!utgpu!lamoran From: lamoran@gpu.utcc.utoronto.ca (L.A. Moran) Subject: Re: Homologous Vertebrate Genes Data Base: new release Message-ID: Organization: UTCC Public Access References: <2qlcje$9q7@cismsun.univ-lyon1.fr> Date: Mon, 9 May 1994 15:55:56 GMT Lines: 29 Xref: biosci bionet.software:8156 bionet.molbio.evolution:1689 In article <2qlcje$9q7@cismsun.univ-lyon1.fr>, Laurent Duret wrote: > > ANNOUNCEMENT >================================================================================ > HOVERGEN > Homologous Vertebrate Genes Data Base > > Release 6 (May 9 1994) > > from GenBank Release 82 (April 15 1994) > >================================================================================ > >The new release is available by anonymous FTP at > > biom3.univ-lyon1.fr (134.214.100.42) > >in the directory > /pub/hovergen > It would be helpful to know what machines this program (database?) runs on and what software is required. Laurence A. Moran (Larry) From owner-evolution@net.bio.net Mon May 09 23:00:00 1994 Path: biosci!PSUVM.PSU.EDU!sws4 From: sws4@PSUVM.PSU.EDU ("Stephen W. Schaeffer") Newsgroups: bionet.molbio.evolution Subject: Re: Fossil genetics Date: 10 May 1994 05:40:48 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 33 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <18429.sws4@psuvm.psu.edu> Reply-To: NNTP-Posting-Host: net.bio.net > Actually I was thinking of the case of horses and donkeys. I agree that >this isn't the only cause, but neither is Drosophila necessarily >representative of other species. As I recall some of that is based on the >presence of an intracellular bacterium. In general, karyotypic changes that >lead to non-functional meiosis will necessarily lead to reproductive >isolation. The point is that karyotype changes are common; I don't know if >some of the other factors occur as widely. Karyotype differences (in >particular translocations that lead to acentric or dicentric chromosomes on >recombination) are effective blocks to interbreeding. Whether they are the >first cause of isolation is open to study for any species. The genetics of hybrid sterility in Drosophila that Tony Long mentions is observed when species of the melanogaster subgroup, D. simulans, D. seychellia, and D. mauritiana, are crossed. The reproductive isolation caused by an intracellular bacterium was observed when D. simulans was crossed to D. simulans from separate geographic populations (Hoffman, Turelli, and Simmons, 1986 Evolution 40:692-701). Perhaps intracellular bacteria are important in some cases of reproductive isolation, but the work of Jerry Coyne, Allen Orr, and Chung-I Wu have mapped genes on all major chromosomes of Drosophila that contribute to hybrid sterility. Karytypic changes are not always associated with reproductive isolation. Populations of D. pseudoobscura and D. subobscura have chromosomal inversions segregating on one or more of their chromosomes. These inversions suppress recombination in inversion heterozygotes but there is no evidence that these have caused reproductive isolation. The limited comparisons of genetic maps among species of Drosophila do show that chromosomes have been translocated in Drosophila evolution. These data, however, cannot be used to suggest that the translocations caused the many speciation events in Drosophila. Stephen W. Schaeffer Institute of Molecular Evolutionary Genetics The Pennsylvania State University From owner-evolution@net.bio.net Mon May 09 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!xlink.net!scsing.switch.ch!swidir.switch.ch!univ-lyon1.fr!news From: duret@evoserv.univ-lyon1.fr (Laurent Duret) Newsgroups: bionet.molbio.evolution Subject: Re: Homologous Vertebrate Genes Data Base: Date: 10 May 1994 08:45:16 GMT Organization: Universite Claude Bernard - Lyon 1 Lines: 49 Distribution: world Message-ID: <2qnhis$3ca@cismsun.univ-lyon1.fr> References: Reply-To: duret@evoserv.univ-lyon1.fr NNTP-Posting-Host: evoserv.univ-lyon1.fr In article Izw@gpu.utcc.utoronto.ca, lamoran@gpu.utcc.utoronto.ca (L.A. Moran) writes: > In article <2qlcje$9q7@cismsun.univ-lyon1.fr>, > Laurent Duret wrote: > > > > ANNOUNCEMENT > >================================================================================ > > HOVERGEN > > Homologous Vertebrate Genes Data Base > > > > Release 6 (May 9 1994) > > > > from GenBank Release 82 (April 15 1994) > > > >================================================================================ > > > >The new release is available by anonymous FTP at > > > > biom3.univ-lyon1.fr (134.214.100.42) > > > >in the directory > > /pub/hovergen > > (...) > > It would be helpful to know what machines this program (database?) runs on > and what software is required. > > Laurence A. Moran (Larry) > > > Hovergen runs on Sun workstations under SunOS or Solaris. Interested people should get and read the README file on our ftp server "biom3.univ-lyon1.fr" in the directory /pub/hovergen. Laurent Duret Laboratoire de Biometrie, Genetique et Biologie des Populations URA CNRS 243 Universite Claude Bernard - Lyon I 43, Bd du 11 Novembre 1918 F-69622 Villeurbanne cedex Tel: +33 72.44.81.42 E-mail: duret@biomserv.univ-lyon1.fr From owner-evolution@net.bio.net Mon May 09 23:00:00 1994 Path: biosci!agate!spool.mu.edu!howland.reston.ans.net!pipex!sunic!EU.net!uunet!panix!zip.eecs.umich.edu!newsxfer.itd.umich.edu!jobone!lynx.unm.edu!news.cs.indiana.edu!babbage.ece.uc.edu!ucbeh!rogstad From: rogstad@ucbeh.san.uc.edu Newsgroups: bionet.molbio.evolution Subject: JOB: EPA POSTDOC: PLANT POPULATION GENETICS Message-ID: <1994May9.231355.7301@ucbeh> Date: 9 May 94 23:13:55 EST Distribution: world Organization: University of Cincinnati Lines: 29 POSTDOCTORAL POSITION: PLANT MOLECULAR POPULATION GENETICIST Oak Ridge Institute of Science and Education Research Fellowship tenable at the Department of Biological Sciences, University of Cincinnati, and sponsored by the U.S. Environmental Protection Agency Environmental Monitoring Systems Laboratory - Cincinnati. The position is available immediately and is funded for two years, although application for extension will be expected. The research involves all or part of the following: * Investigations, utilizing DNA variation, of effects of anthropogenic disturbance on population genetics of selected plant species. * Learning, and developing further, methods to investigate genetic diversity of selected plant species. This may involve the use of microsatellite, minisatellite, RFLPS, or RAPD analyses. * Working with statistical analyses to optimize methods for data analysis. * Collecting and analyzing DNA variation of field samples from impacted and control field sites. QUALIFICATIONS: Applicants must have a Ph.D. degree by the time of appointment. Individuals with extensive experience in molecular population genetics including field botany skills, plant DNA extraction, RFLP Southern hybridization techniques, PCR methodology, and data analysis will be preferred. APPLICATION: Send curriculum vitae, brief statement of research experience and goals, and list of three references (with phone numbers) to S. Rogstad, Biological Sciences ML6, University of Cincinnati, Cincinnati, OH 45229-0006. From owner-evolution@net.bio.net Mon May 09 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!torn!news.ccs.queensu.ca!qucdn!malboobi Organization: Queen's University at Kingston Date: Sun, 8 May 1994 11:06:52 EDT From: Message-ID: <94128.110652MALBOOBI@QUCDN.QueensU.CA> Newsgroups: bionet.molbio.evolution,bionet.molbio.methds-reagnts Subject: Re: TA microsatellite References: <94120.121152IO01072@MAINE.MAINE.EDU> Lines: 21 Xref: biosci bionet.molbio.evolution:1695 bionet.molbio.methds-reagnts:14107 Dear Netters: I am screening A. thaliana genomic library with a heterologous probe. By screening about 160'000 plaques(!), I have got 9 independent clones. These clones are purified to homogeneity by 3-5 time screening. All washes were to high stringency. To double check that these (or at least one of them) are corresponding to the right gene and not other related genes (i.e. other members of a gene family), I do the following test primarily. That is, I made a southern blot of A. thaliana genomic DNA digested by 3 different restriction enzymes. Then, I hybridize the original probe (which was used for screening) and the probe made from the whole insert (9-17 Kb) of the isolated clones. I expected that the banding pattern of the S. blots of the isolated clones to be similar (or include) that of the S. blot probed with the screening probe. This did not happened for any of the isolated clones. Any advice or comment regarding this problem is greatly appreciated. Thanks. Ali My E-Mail Address is: malboobi@qucdn.queensu.ca From owner-evolution@net.bio.net Mon May 09 23:00:00 1994 Newsgroups: bionet.molbio.evolution Path: biosci!daresbury!trane.uninett.no!eunet.no!nuug!EU.net!howland.reston.ans.net!vixen.cso.uiuc.edu!uchinews!quads!ecec From: ecec@quads.uchicago.edu (Eric Cabot) Subject: Re: Fossil genetics Message-ID: <1994May10.190847.28487@midway.uchicago.edu> Sender: news@uchinews.uchicago.edu (News System) Reply-To: ecec@midway.uchicago.edu Organization: University of Chicago References: Date: Tue, 10 May 1994 19:08:47 GMT Lines: 46 In article wgallin@gpu.srv.ualberta.c a (Warren Gallin) writes: [in reference to hybrid sterility being due to kayrotypic changes] > Actually I was thinking of the case of horses and donkeys. I agree that It is unfortunate that this impression persists in biological lore. I recall that we of the Wu lab were quite horrified to read in the new GRE test booklet that the correct answer to the question "Why are the offspring of closely related species sterile?" was "chromosomal incompatibility". >this isn't the only cause, but neither is Drosophila necessarily >representative of other species. As I recall some of that is based on the I think that this discussion serves as a useful reminder that the basis of hybrid sterility may be either genic or chromosomal. Geneotypic effects leading to reproductive isolation need not be structural or even have anything to do with meiosis, for that matter. Consider, for example, cases of geneic differences with behavioral or morphological manifestations that cause reproductive isolation. >presence of an intracellular bacterium. In general, karyotypic changes that >lead to non-functional meiosis will necessarily lead to reproductive >isolation. The point is that karyotype changes are common; I don't know if >some of the other factors occur as widely. Karyotype differences (in >particular translocations that lead to acentric or dicentric chromosomes on >recombination) are effective blocks to interbreeding. Whether they are the >first cause of isolation is open to study for any species. It doesn't necessarily follow that chromosomal changes are going to cause isolation, though. (For elaboration see Steve Schaeffer's post elsewhere in this thread). In fact some rearrangements or aberations are so severe that it is hard to envision how the first individuals with the new arrangements found any compatible mates. You raise an interesting point about the first causes of isolation. We found lots of genetic factors causing hybrid sterility between D. simulans and its relatives but still have no idea which, if any, of them were responsible for the original isolation and which, if any, "merely" represent the accumulation of mutations (or the rarefication of ancestral polymorphisms for that matter) after the species diverged. Eric Cabot elmo@helix.nih.gov From owner-evolution@net.bio.net Mon May 09 23:00:00 1994 Path: biosci!agate!spool.mu.edu!howland.reston.ans.net!EU.net!Austria.EU.net!newsfeed.ACO.net!info.univie.ac.at!lab8486.abc.univie.ac.at!ma From: ma@ABC.univie.ac.at (Manuel Simon) Newsgroups: bionet.molbio.evolution Subject: Re: human cDNAs that can complement yeast mutants Date: Tue, 10 May 1994 18:16:55 Organization: Inst. Biochemistry and Molecular Cell Biology Lines: 21 Message-ID: References: NNTP-Posting-Host: lab8486.abc.univie.ac.at X-Newsreader: Trumpet for Windows [Version 1.0 Rev A] In article Hieter@jhuigf.med.jhu.edu (Hieter Lab) writes: >From: Hieter@jhuigf.med.jhu.edu (Hieter Lab) >Subject: human cDNAs that can complement yeast mutants >Date: Mon, 09 May 1994 15:39:37 -0500 >I am interested in finding all examples where HUMAN cDNAs can complement >yeast (S. cerevisiae) mutations. Below are those that I have found so far. >Please write back ASAP with any that you might know of that I missed. >Please include references if available. >Thanks, >Stuart T. High, I think also the ras2 can be functionally complemented by human cDNA. Manuel From owner-evolution@net.bio.net Mon May 09 23:00:00 1994 Path: biosci!agate!spool.mu.edu!torn!news.ccs.queensu.ca!qucdn!malboobi Organization: Queen's University at Kingston Date: Mon, 9 May 1994 11:19:34 EDT From: Message-ID: <94129.111934MALBOOBI@QUCDN.QueensU.CA> Newsgroups: bionet.molbio.evolution,bionet.molbio.methds-reagnts Subject: Genomic library screening-help References: <94120.121152IO01072@MAINE.MAINE.EDU> <94128.110652MALBOOBI@QUCDN.QueensU.CA> Lines: 20 Xref: biosci bionet.molbio.evolution:1696 bionet.molbio.methds-reagnts:14108 Dear Netters: I am screening A. thaliana genomic library with a heterologous probe. By screening about 160'000 plaques(!), I have got 9 independent clones. These clones are purified to homogeneity by 3-5 time screening. All washes were to high stringency. To double check that these (or at least one of them) are corresponding to the right gene and not other related genes (i.e. other members of a gene family), I do the following test primarily. That is, I made a southern blot of A. thaliana genomic DNA digested by 3 different restriction enzymes. Then, I hybridize the original probe (which was used for screening) and the probe made from the whole insert (9-17 Kb) of the isolated clones. I expected that the banding pattern of the S. blots of the isolated clones to be similar (or include) that of the S. blot probed with the screening probe. This did not happened for any of the isolated clones. Any advice or comment regarding this problem is greatly appreciated. Thanks. Ali From owner-evolution@net.bio.net Tue May 10 23:00:00 1994 Newsgroups: bionet.molbio.evolution Path: biosci!agate!howland.reston.ans.net!darwin.sura.net!hearst.acc.Virginia.EDU!murdoch!dayhoff.med.Virginia.EDU!wrp From: wrp@dayhoff.med.Virginia.EDU (William R. Pearson) Subject: Re: Homolog/ortholog Message-ID: Sender: usenet@murdoch.acc.Virginia.EDU Organization: University of Virginia References: <9405051451.AA20816@thalamus.wustl.edu> Distribution: bionet Date: Tue, 10 May 1994 14:57:57 GMT Lines: 31 In article <9405051451.AA20816@thalamus.wustl.edu>, Yamagata =?ISO-2022-JP?B?GyRCOzM3QRsoQg==?= wrote: >How do you define a homolog, ortholog, or paralog? Family, superfamily, >subfamily, cognate, counterpart, related, homologous, --Do you use other >words for describing relationships among homologous genes? And, how would >you use these words? Is there good references for how we can accurately >distinguish these words? I know there is no simple answer for this. But, >I would like to know how molecular evolutionalists are using these words. >Thanks in advance. Homolog (homologous) - shares a common ancestor ortholog - differences between two "orthologous" proteins reflect a speciation event - mouse alpha-hemoglobin and human alpha-hemoglobin differ because of the divergence of the lines leading to mice and humands paralog - differences reflect gene duplication events, e.g. human beta-hemoglobin and mouse alpha-hemoglobin. An evolutionary tree based on chimpanzee alpha-globin, human beta-globin, and mouse beta-globin would put humans much closer to mice than chimps. This definition is available in any textbook on molecular evolution. The superfamily/family/subfamily hierarchy was defined by Dayhoff. Typically members of a subfamily are more than 80% identical, family > 50%, and superfamily < 50%. (Meth. Enz. 1990 183:37) Bill Pearson From owner-evolution@net.bio.net Tue May 10 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!xlink.net!scsing.switch.ch!swidir.switch.ch!univ-lyon1.fr!news From: duret@evoserv.univ-lyon1.fr (Laurent Duret) Newsgroups: bionet.molbio.evolution Subject: Re: human/yeast complementation Date: 11 May 1994 06:32:54 GMT Organization: Universite Claude Bernard - Lyon 1 Lines: 11 Distribution: world Message-ID: <2qpu6m$19k@cismsun.univ-lyon1.fr> Reply-To: duret@evoserv.univ-lyon1.fr NNTP-Posting-Host: evoserv.univ-lyon1.fr There's also UEF upstream element factor: Moncollin V. et al. (1990) Nucl. Acids Res. 18:4817-4823 Laurent Duret Laboratoire de Biometrie - Lyon - France From owner-evolution@net.bio.net Tue May 10 23:00:00 1994 Path: biosci!agate!alliance.hip.berkeley.edu!user From: mdhouse@mendel.berkeley.edu (Martin Latterich) Newsgroups: bionet.n2-fixation,bionet.clamydomonas,bionet.immunology,bionet.molbio.evolution,bionet.molbio.hiv,bionet.molbio.yeast,bionet.mycology,bionet.parasitology,bionet.protista,bionet.virology,sci.bio,sci.med Subject: CALL FOR DISCUSSION: MICROBIOLOGY/bionet.microbiology Followup-To: bionet.general Date: Tue, 10 May 1994 20:30:54 -0800 Organization: Howard Hughes Medical Institute Lines: 40 Message-ID: NNTP-Posting-Host: alliance.hip.berkeley.edu Xref: biosci bionet.immunology:1346 bionet.molbio.evolution:1699 bionet.molbio.hiv:375 bionet.molbio.yeast:1089 bionet.mycology:549 bionet.parasitology:146 bionet.protista:84 bionet.virology:531 sci.bio:8597 sci.med:37045 (NB: This is a copy of a letter posted to bionet.general which maybe of interest to the readership of this newsgroup. To save bandwidth, please follow up to the bionet.general copy of this letter.) Hi netters: I'd like to invite anyone interested in the establishment of a new newsgroup, "bionet.microbiology", to participate in a discussion concerning the main direction/goals. This discussion will take place on bionet.general. A number of other people and I felt the need for a newsgroup with the main focus on microbiology. Recent developments in the field have shown that there is an active, popular interest in this particular discipline (The issue of Science from April 15 this year immediately jumps into my mind), and it would be nice to have a forum specifically devoted to any aspects concerning microbiology. This would allow the discussion of old and new ideas, problems and recent developments in the field, finding quick help/pointers to methodologies, strains, etc. I have proposed a draft-proposal for such a newsgroup, and I'd be eternally grateful for any suggestions and input to make this proposal a better one. In general I hope that bionet.microbiology will become a place for scientists and interested non-scientists to communicate and find help and new ideas. If you have any helpful comments and/or suggestions, please feel free to post them to bionet.general or send them to me via e-mail. Microbiologically, Dr. Martin Latterich Howard Hughes Medical Institute and Dptm. of Molecular and Cell Biology University of California, Berkeley, CA 94706 USA Tel.: (510) 624-6171 (W) (510) 913-6027 (H) FAX: (510) 642-7846 e-mail: mdhouse@mendel.berkeley.edu From owner-evolution@net.bio.net Wed May 11 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!gatech!willis1.cis.uab.edu!maze.dpo.uab.edu!bcrf.microbio.uab.edu!Lefkowitz From: Lefkowitz@orion.cmc.uab.edu (Elliot Lefkowitz) Newsgroups: bionet.molbio.evolution Subject: Transition/Transversion Ratios Date: Thu, 12 May 94 14:50:46 GMT Organization: University of Alabama Lines: 21 Message-ID: NNTP-Posting-Host: bcrf.microbio.uab.edu X-Newsreader: VersaTerm Link v1.1.4 It seems to be taken as given in the literature discussing nucleotide sequence mutagenesis, that transition mutations generally predominate over tranversions. What I have missed in all the papers that take this as an axiom is any reference to a publication that rigorously examined this question. Can anyone point me to such a reference? Is there sufficient evidence to conclude that transitions do predominate over transversions, or were these conclusions reached (and then taken as gospel) by analysis of a much too limited dataset? Elliot ****************************************** * Elliot J. Lefkowitz, Ph.D. * * University of Alabama * * Biological Computing Resource Facility * * Department of Microbiology * * Birmingham, AL 35294-2170 * * * * Lefkowitz@orion.cmc.uab.edu * ****************************************** From owner-evolution@net.bio.net Wed May 11 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!noc.near.net!usenet.uchc.edu!L.Sumoy From: Sumoy@mbcg.uchc.edu (L. Sumoy) Newsgroups: bionet.molbio.evolution,bionet.molbio.methds-reagnts Subject: Re: Genomic library screening-help Date: 12 May 1994 13:29:57 GMT Organization: Univ of CT Health Center Lines: 17 Sender: -Not-Authenticated-[4842] Message-ID: <2qtb0l$9r3@threed.uchc.edu> References: <94120.121152IO01072@MAINE.MAINE.EDU> <94128.110652MALBOOBI@QUCDN.QueensU.CA> <94129.111934MALBOOBI@QUCDN.QueensU.CA> NNTP-Posting-Host: upholt.uchc.edu X-Posted-From: InterNews 1.0@threed.uchc.edu. Xdisclaimer: No attempt was made to authenticate the sender's name. Xref: biosci bionet.molbio.evolution:1703 bionet.molbio.methds-reagnts:14183 > I am screening A. thaliana genomic library with a heterologous probe. >(...) > banding pattern on the S. blots whole insert (9-17 Kb) of the isolated clones used as probe not matching that obtained with the screening probe >(...) Ali Your inserts should hybridize with the bands recognized by the probe used in the screening if they correspond to the right thing. You would also expect, that since the inserts are up to 17 kb long, they would hybridize to extra bands. If the hybridization conditions were right you probably saw a single band per restriction digest on genomic southerns with the screening probe (you could see more than a single band if the probe is a cDNA comprised of multiple exons spliced together or if there are restriction sites for the enzyme used in the digestion of the genomic DNA within your probe). Hope this helps. Lauro From owner-evolution@net.bio.net Wed May 11 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!noc.near.net!transfer.stratus.com!bigboote.WPI.EDU!wpi.WPI.EDU!jbagshaw From: jbagshaw@wpi.WPI.EDU (Joseph C. Bagshaw) Newsgroups: bionet.molbio.evolution,bionet.molbio.methds-reagnts Subject: Re: TA microsatellite Date: 12 May 1994 13:14:57 GMT Organization: Worcester Polytechnic Institute Lines: 37 Message-ID: <2qta4h$kfd@bigboote.WPI.EDU> References: <94120.121152IO01072@MAINE.MAINE.EDU> <94128.110652MALBOOBI@QUCDN.QueensU.CA> NNTP-Posting-Host: wpi.wpi.edu Xref: biosci bionet.molbio.evolution:1702 bionet.molbio.methds-reagnts:14182 In article <94128.110652MALBOOBI@QUCDN.QueensU.CA> writes: >Dear Netters: > I am screening A. thaliana genomic library with a heterologous probe. By >screening about >160'000 plaques(!), I have got 9 independent clones. These clones are purified >to homogeneity by 3-5 >time screening. All washes were to high stringency. To double check that these >(or at least one of them) >are corresponding to the right gene and not other related genes (i.e. other >members of a gene family), I >do the following test primarily. That is, I made a southern blot of A. thaliana >genomic DNA digested by >3 different restriction enzymes. Then, I hybridize the original probe (which was >used for screening) and >the probe made from the whole insert (9-17 Kb) of the isolated clones. I >expected that the banding >pattern of the S. blots of the isolated clones to be similar (or include) that >of the S. blot probed with >the screening probe. This did not happened for any of the isolated clones. Any >advice or comment >regarding this problem is greatly appreciated. Thanks. Ali >My E-Mail Address is: malboobi@qucdn.queensu.ca Ali, If I understand your question correctly, you are using the same approach we use in my lab to verify clones of genomic DNA. It is essential, especially with inserts as big as yours, that the DNA for the genomic digest is from the _same plant_ as the DNA used to construct the library. Even that might not work if the gene you've cloned is highly polymorphic. If the two DNA samples are from different individuals, your chances of finding the same restriction patterns are reduced. Good luck. Joe Bagshaw From owner-evolution@net.bio.net Mon May 16 23:00:00 1994 Newsgroups: bionet.molbio.evolution Path: biosci!bcm!cs.utexas.edu!swrinde!ihnp4.ucsd.edu!library.ucla.edu!news.ucdavis.edu!pbmac-5.ucdavis.edu!user From: tdlong@ucdavis.edu (Tony Long) Subject: Re: Fossil genetics Message-ID: Followup-To: bionet.molbio.evolution Sender: usenet@ucdavis.edu (News Guru) Organization: Center for Population Biology References: <199405171401.HAA09692@net.bio.net> Distribution: bionet Date: Tue, 17 May 1994 17:03:20 GMT Lines: 35 In article <199405171401.HAA09692@net.bio.net>, DRAND@BROWNVM.BROWN.EDU ("David M. Rand") wrote: > > Further comments on single gene vs. chromosomal changes in speciation: > > What seems to be interesting about this issue is that there are different > lineages where karyotypic changes seem to be common and play a major role > in isolation, whereas other lineages have all sorts of rearragements with > little evidence for isolation (see above comments by Steve Schaeffer and Eric (other stuff deleted) I guess I still don't see the evidence that the karyotype changes are the cause of isolation or simply a correlate! Once species are reproductively isolated it seems likely that karyotype changes will occur in the independent lineages. Proving these changes are the cause of isolation is an entirely different problem. The only way of doing this is to find species that are relatively early in the speciation process and see if karyotype changes are already prevalent. Even this evidence, unfortunately is only correlative. The great promise of single (or few) gene theories of reproductive isolation was that hey were testable. Species can be transformed with the candidate gene and the the hypothesis actually tested in a rigorous manner (i.e., gene from species A in species B rescues AB hybrids). These days in molecular genetics of Drosophila this is the standard. That is if you claim to have cloned a new homeotic mutant it better rescue a homeotic phenotype when transformed into a mutant background. Should we as evolutionists set our standards any lower?? Tony Long Center for Population Biology U. C. Davis Davis, CA tdlong@ucdavis.edu From owner-evolution@net.bio.net Mon May 16 23:00:00 1994 Path: biosci!BROWNVM.BROWN.EDU!DRAND From: DRAND@BROWNVM.BROWN.EDU ("David M. Rand") Newsgroups: bionet.molbio.evolution Subject: Re: Fossil genetics Date: 17 May 1994 07:01:11 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 31 Sender: daemon@net.bio.net Distribution: bionet Message-ID: <199405171401.HAA09692@net.bio.net> NNTP-Posting-Host: net.bio.net Further comments on single gene vs. chromosomal changes in speciation: What seems to be interesting about this issue is that there are different lineages where karyotypic changes seem to be common and play a major role in isolation, whereas other lineages have all sorts of rearragements with little evidence for isolation (see above comments by Steve Schaeffer and Eric Cabot). It is important here to distinguish between inversions and translocations of whole chromosome arms. The latter should have more effect. M. J. D. White studied orthopterans (Grasshoppers, crickets etc.) and was the strongest proponent of "chromosomal" speciation. Robert Baker from Texas has also written about the important role of chromosomal changes in mammalian speciation. I may be wrong, but most of these well documented cases involve transolcations rather than inversions. It would be interesting to some Coyne-Orr-Wu et al studies in Orthopterans to see what the relative contributions of single-gene, gene interatcions and chromosomal changes play in the isolation of species. Obviously the genetics of most grasshoppers and crickets are sufficiently primitive that it is almost impossible to do this. So, in short, while Eric Cabot and other Wu lab-mates were disturbed to find that the answer to the GRE question about species isolation is "chromosomal changes", the issue really depends on what the other possible answers were (e.g., "unhappy childhood?" or "bad attitiude?" or "point mutation?", or "none of the above?") For some groups, chromosomal changes IS the best answer David M. Rand Department of Ecology and Evolutionary Biology Brown University David_Rand@brown.edu From owner-evolution@net.bio.net Tue May 17 23:00:00 1994 Newsgroups: bionet.molbio.evolution Path: biosci!bcm!cs.utexas.edu!convex!darwin.sura.net!news.Vanderbilt.Edu!NewsWatcher!user From: sticknbd@miranda.cc.vanderbilt.edu (B Stickney) Subject: a question concerning ds RNAS Message-ID: Followup-To: bionet.molbio.evolution Sender: news@news.vanderbilt.edu Nntp-Posting-Host: 160.129.125.10 Organization: Department of Pathology Date: Wed, 18 May 1994 23:36:41 GMT Lines: 24 It is my understanding that a cell commits suicide if there are double-stranded RNAs present inside. This is alleged to reflect a give-it-up strategy in case of viral infection, so that the spread of the virus is inhibited. However, I believe most RNA viri are of the retrovirus class. As such they would not be generating any ds-RNA (RNA->DNA->RNA, rather than RNA->RNA). I believe also that there are only a limited number of known RNA viri that do not have reverse transcriptase activity. Therefore, can one assume that this strategy was so effective that those viri employing the ds-RNA phenotype just went (mostly) extinct, and this adamant reaction is vestigial? What could explain this strong reaction to ds-RNA? Was this type of viri more common in times past? Is there some other explanation? Periferally, what is the explanation for the existance of reverse transcriptase in eukaryotes? Are we looking at viral contamination here, a leftover gene from some infection, or is there some use to eukaryotes for reverse transcriptase? sticknbd@miranda.cc.vanderbilt.edu From owner-evolution@net.bio.net Wed May 18 23:00:00 1994 Newsgroups: bionet.molbio.evolution Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!copperhead.bio.indiana.edu!jlogsdon From: John Logsdon Subject: Biocomputing Position (PostDoc or Tech) - Mol Evol & Parallel Comp Message-ID: X-Xxmessage-Id: X-Xxdate: Thu, 19 May 1994 11:45:51 GMT Sender: news@usenet.ucs.indiana.edu (USENET News System) Nntp-Posting-Host: copperhead.bio.indiana.edu Organization: Department of Biology / Indiana University X-Newsreader: Nuntius Version 1.2 Date: Thu, 19 May 1994 21:37:25 GMT Lines: 54 Biocomputing Position (Molecular Evolution & Parallel Computing) We seek an individual with strong computer skills and a background/interest in biology to fill a full-time research position in the Department of Biology at Indiana University. This position is open as either a **entry-level computer technician** or a **biocomputing post-doctoral scientist**. It is currently funded for two years at full-time pay, with pay commensurate with the skills and experience of the applicant, but the possibility exists for the continuation of the position after the current two year term has expired. The position will be roughly half-time creating, maintaining, and analyzing a molecular sequence database, and half-time developing and implementing parallel computing in biology. The database project is an outgrowth of a laboratory research project on the molecular evolution of introns. The parallel computing project will involve diverse biological projects ranging from phylogenetic analyses to ecological simulations. The position will involve development of new software, modification of existing tools, and responsibility for system administration on a parallel-processing UNIX workstation. Qualifications: Bachelors degree or greater in computer science or biology. Proficiency in the UNIX environment is essential. At least 2 years programming experience - language requirements include C or C++ and familiarity with FORTRAN. Familiarity with system administration and parallel processing environments and programming experience in windowing systems (X, Macintosh) are desirable. Molecular biology software and database experience are a plus. Location: The IU Department of Biology is located in Bloomington, Indiana. Bloomington is a pleasant, small community in the rolling hills of southern Indiana, and has an active cultural life stimulated by IU's excellent music and liberal arts programs. IU is well-known in biocomputing because of the IUBio archive created and administered by Dr. Don Gilbert. In addition, there are two other biocomputists, and a strong commitment to biocomputing in the department. We are an equal opportunity employer, and encourage women and minority applicants. The successful applicant will be selected on the basis of their skills and qualifications. Applicants should submit a detailed curriculum vitae, a list of references (including phone numbers), and salary requirements to: Dr. Jeffrey D. Palmer Department of Biology Jordan Hall Indiana University Bloomington, IN 47405 812- 855-6705 (FAX) Electronic communication should be directed to jlogsdon@bio.indiana.edu. From owner-evolution@net.bio.net Wed May 18 23:00:00 1994 Path: biosci!BCRSSU.AGR.CA!RAMPITSCH From: RAMPITSCH@BCRSSU.AGR.CA Newsgroups: bionet.molbio.evolution Subject: Re: a question concerning dsRNAs Date: 19 May 1994 15:48:26 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 58 Sender: daemon@net.bio.net Distribution: world Message-ID: <01HCJ80MN5YA003152@GW.AGR.CA> NNTP-Posting-Host: net.bio.net Hello: I have a few comments to make on the following argument: >Subj: a question concerning ds RNAS >It is my understanding that a cell commits suicide >if there are double-stranded RNAs present inside. >This is alleged to reflect a give-it-up strategy in >case of viral infection, so that the spread of the >virus is inhibited. However, I believe most RNA viri >are of the retrovirus class. As such they would not The retroviruses form a very small subset of the RNA viruses. There are dozens of groups of RNA viruses which have no DNA intermediate in both the animal and plant viruses. Also some groups have a dsRNA genome; infact the vast majority of plant viruses have a RNA genome. >be generating any ds-RNA (RNA->DNA->RNA, rather >than RNA->RNA). I believe also that there are only >a limited number of known RNA viri that do not have >reverse transcriptase activity. Therefore, can one Actually there are a limited number of RNA viruses that do have reverse transcriptase activity; most don't. >assume that this strategy was so effective that those >viri employing the ds-RNA phenotype just went (mostly) >extinct, and this adamant reaction is vestigial? What >could explain this strong reaction to ds-RNA? Was >this type of viri more common in times past? Is there >some other explanation? It is possible to isolate dsRNA from plant tissue infected with many kinds of RNA viruses. Whether this is artefactual is not known for sure as far as I know; these dsRNAs are intermediates of RNA replication. Many plant cells survive in the presence of this dsRNA intermediate. >Periferally, what is the explanation for the existance >of reverse transcriptase in eukaryotes? Are we looking >at viral contamination here, a leftover gene from some >infection, or is there some use to eukaryotes for reverse >transcriptase? >sticknbd@miranda.cc.vanderbilt.edu Regards, ------------------------------------------------------------------------------ Chris Rampitsch | RAMPITSCH@BCRSSU.AGR.CA Dept. Plant Science, Univ. of BC | Phone (604) 494-7711 Vancouver, British Columbia | Fax (604) 494-0755 Canada V6T 2A2 _/\_ ---------------------------------- __\ /__ ---------------------------------- \__ __/ || From owner-evolution@net.bio.net Wed May 18 23:00:00 1994 Newsgroups: bionet.molbio.evolution Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!vixen.cso.uiuc.edu!usenet.ucs.indiana.edu!copperhead.bio.indiana.edu!jlogsdon From: John Logsdon Subject: Re: Biocomputing Position (PostDoc or Tech) - Mol Evol & Parallel Comp Message-ID: X-Xxmessage-Id: X-Xxdate: Thu, 19 May 1994 12:12:21 GMT Sender: news@usenet.ucs.indiana.edu (USENET News System) Nntp-Posting-Host: copperhead.bio.indiana.edu Organization: Department of Biology / Indiana University X-Newsreader: Nuntius Version 1.2 References: Date: Thu, 19 May 1994 22:03:56 GMT Lines: 7 In article John Logsdon, jlogsdon@bio.indiana.edu writes: >Applicants should submit a detailed curriculum vitae, a list of >references (including phone numbers), and salary requirements to: Please note that applications should be submitted as soon as possible. Those received by July 1 1994 will be assured consideration. From owner-evolution@net.bio.net Thu May 19 23:00:00 1994 Newsgroups: bionet.molbio.evolution Path: biosci!agate!usenet.ins.cwru.edu!gatech!swrinde!pipex!uknet!EU.net!uunet!newsflash.concordia.ca!pavo.concordia.ca!dl_tato From: dl_tato@pavo.concordia.ca (DAN THE FUNKY MOOSE MAN) Subject: KT-extinction Message-ID: <20MAY199400303121@pavo.concordia.ca> News-Software: VAX/VMS VNEWS 1.41 Sender: usenet@newsflash.concordia.ca (USENET News System) Nntp-Posting-Host: pavo1.concordia.ca Organization: Concordia University Date: Fri, 20 May 1994 05:30:00 GMT Lines: 12 Hello, I hope U don't mind not having to do with mol. biol. but this was the closest group to evolution... unless someone can tell me about another? .. anyway can anyone tell me where I can get anything to do with K-T extincton and how mammals evolved from it.... also how the early primates evolved into modern man?.... if someone has some info on of his/her own or can lead me to some.. please re by whatever means ....thanx. da MoOsE/Dan e-mail: dl_tato@pavo.concordia.ca From owner-evolution@net.bio.net Fri May 20 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!sunic!EU.net!uunet!newsflash.concordia.ca!canopus.cc.umanitoba.ca!xia From: xia@cc.umanitoba.ca (Xuhua Xia) Newsgroups: bionet.molbio.evolution Subject: Ontogeny & Phylogeny V Date: 21 May 1994 22:11:12 GMT Organization: The University of Manitoba Lines: 114 Message-ID: <2rm0u0$fsj@canopus.cc.umanitoba.ca> NNTP-Posting-Host: mira.cc.umanitoba.ca Keywords: ontogeny, phylogeny, development, evolution ================================================================== Human ontogeny is simply a matter of enzymatic transformation of groceries. --------- Dobzhansky (I forgot the original wording, and might have cited wrong.) =================================================================== Ontogeny & Phylogeny: We need molecular biology Let me first share with you some of my experience accumulated while attending a neurobiology symposium called Altschul Symposium held in University of Saskaschewan at Saskatoon. Most basic studies presented are descriptive, i.e., documenting what gene is expressed where and when, and what would happen when a particular gene fails to express where and when it normally should. I suspect that most of modern-day biologists would be offended when their research is labelled as descriptive. If this is indeed the case, let me hurriedly add that a good description of a biological pattern almost always leads to new insight. For example, one French biologist showed in the symposium that a homeotic mutation in the mouse led to several extra skeletal elements which had not mammalian equivelents, but had counterparts in reptiles. No one would doubt the evolutionary significance of this description. In this and the following 3 or 4 postings I will talk about a few powerful techniques in molecular biology that can be used to describe ontogeny in relation to the study of ontogeny and phylogeny. In consideration of those readers with a computer or engineering background, I will limit one method per posting, and only the conceptual aspect of the method and its utility will be illustrated. This posting will focus on subtraction hybridization. Let us digress a bit to talk about a cDNA library. A cDNA library represents a set of mRNA species present in a particular body part (or a particular cell) at a particular developmental stage. Such a library can be written as: L = {gene1, gene2, gene3, ......, geneN} Suppose we now make a cDNA library from a gorilla embryo at one embryonic stage, and another cDNA library from a chipanzee embryo at the same stage. Now we have L(gorilla) = {Ggene1, Ggene2, ......, GgeneN1}; and L(chimp) = {Cgene1, Cgene2, ......, CgeneN2}. Subtraction hybridization is a technique that tells us what gene is present in L(gorillar) but absent in L(chimp), and vice versa. In addition, available data also allow us to have an approximate answer to the intersection of the two sets. The following data matrix is then generated: ================================================================= Genes Species at equivalent embryonic stage --------------------------------------------------------- gorilla chimp human . . . . gene1 1 1 1 gene2 1 1 0 gene3 1 0 1 gene4 0 1 1 . . . . . . . . . . . . geneN 1 1 0 ================================================================= Such a data set will tell us the difference between gorilla and chimp, between chimp and human and between human and gorilla. It is most likely that there will be no difference among them during early ontogeny, but then, at embryonic stage ES5, say, a gene or a gene group sets gorilla aside from chimp and human. Then, at ES9, say, another gene or gene group arises in the chimp and sets chimp and human apart. Isn't this nice! Once we get a series of cDNA libraries fron gorilla, chimp and human at different ontogenetic stages, further insights can arise. For example, if the chimp library at embryonic week 5 is most similar to the human library at embryonic week 7, then we can infer that the hypothetical "neoteny gene" responsible for human evolution must have already come into operation before embryonic week 7 in human ontogeny. The table below suggest that this gene might be expressed at embryonic stage 3. If we knock out genes expressed at embryonic stage 3 one by one, then we may find one particular gene, when knocked out, cause accelerated development of the human embryo...... We can then knock out such genes in cows to reduce their lengthy misery of pregnancy. (I think I can write a good science fiction based on this.) ================================================================= Embryonic Embryonic weeks stage ------------------------------------------------------- gorilla chimp human . . . . 1 1 1 1 2 2 2 2 3 3 3 3 4 4 4 5 5 5 5 7 6 6 6 10 . . . . . . . . . . . . N . . . ================================================================= (to be continued) -- ==================================================================== Xuhua Xia University of Manitoba xia@ccu.umanitoba.ca From owner-evolution@net.bio.net Fri May 20 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!pipex!zaphod.crihan.fr!jussieu.fr!univ-lyon1.fr!news From: robinson@evol10.univ-lyon1.fr (Marc Robinson) Newsgroups: bionet.molbio.evolution Subject: Re: KT-extinction Date: 21 May 1994 15:49:37 GMT Organization: Universite Claude Bernard - Lyon 1 Lines: 17 Distribution: world Message-ID: <2rlaih$995@cismsun.univ-lyon1.fr> References: <20MAY199400303121@pavo.concordia.ca> Reply-To: robinson@evol10.univ-lyon1.fr NNTP-Posting-Host: evol10.univ-lyon1.fr In article 20MAY199400303121@pavo.concordia.ca, dl_tato@pavo.concordia.ca (DAN THE FUNKY MOOSE MAN) writes: > > > Hello, I hope U don't mind not having to do with mol. biol. but this > was the closest group to evolution... unless someone can tell me about another? > ... anyway can anyone tell me where I can get anything to do with K-T extincton > and how mammals evolved from it.... also how the early primates evolved into > modern man?.... if someone has some info on of his/her own or can lead me > to some.. please re by whatever means ....thanx. > da MoOsE/Dan > > e-mail: dl_tato@pavo.concordia.ca > you should try sci.bio.evolution From owner-evolution@net.bio.net Fri May 20 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!usc!elroy.jpl.nasa.gov!lll-winken.llnl.gov!fnnews.fnal.gov!nntp-server.caltech.edu!fennel.bio.caltech.edu!user From: schwarze@starbase1.caltech.edu (Erich Schwarz) Newsgroups: bionet.software,bionet.molbio.evolution Subject: PAUP 3.1 -- the Forbidden Program? Followup-To: bionet.software Date: 21 May 1994 02:45:10 GMT Organization: Div. of Biology, Caltech Lines: 11 Distribution: world Message-ID: NNTP-Posting-Host: fennel.bio.caltech.edu Xref: biosci bionet.software:8254 bionet.molbio.evolution:1712 Does anybody out there know of any lawful means of obtaining (e.g. buying) PAUP 3.1? I have had a miserable time trying (and failing) to get it from either its author (swofford@onyx.si.edu) or from its former distributor (the Illinois Natural History Survey.) Replies by e-mail would be preferred (heck, *any* helpful replies would be preferred.) Thanks. --Erich Schwarz / schwarze.ccomail@starbase1.caltech.edu From owner-evolution@net.bio.net Sun May 22 23:00:00 1994 Path: biosci!agate!howland.reston.ans.net!EU.net!uknet!daresbury!not-for-mail From: "JAMES O. MCINERNEY" Newsgroups: bionet.molbio.evolution Subject: Course in molecular analysis of fish pathogens Date: 23 May 1994 16:46:12 +0100 Lines: 62 Sender: daemon@mserv1.dl.ac.uk Distribution: bionet Message-ID: <2rqj44$pma@mserv1.dl.ac.uk> Original-To: mol-evol@dl.ac.uk The following message was given to me and I was asked to forward it t= o this to this newsgroup -----------------------------cut here--------------------------------= ---------- NUCLEIC ACID TECHNIQUES FOR THE ANALYSIS OF FISH PATHOGENS:=20 DETECTION, CHARACTERISATION AND EVOLUTION August 7th - August 17th, 1994 Department of Microbiology, University College Galway, Ireland This intensive practical course is designed to provide a training in = the=20 use of nucleic acid techniques for the analysis of bacterial and vira= l=20 pathogens of fish. It is aimed at scientists wishing to expand their = research=20 to include this area or younger scientists entering this field. No di= rect=20 experience is required. This course is sponsored in part by the Europ= ean=20 Commission (AIR Programme), University College Galway and BioResearch= Ireland. This is a residential course, without exception, and there is a char= ge of=20 IR=A3550 towards board and lodging. The course will cover the following techniques. Nucleic acids isolation, Southern/Northern blotting,=20 Gene cloning, DNA sequencing,=20 Polymerase Chain Reaction,=20 Reverse Transcriptase-PCR, DNA probes, 16S ribosomal RNA Sequencing and Analysis, Ribotyping, in situ hybridisation, Random Amplification of Polymorphic DNA,=20 Gene Amplification from Environmental Samples,=20 Gene Amplification from Fish Tissues. The practical work will be supplemented by lectures given by=20 University College Galway staff and invited speakers.=20 There are no formal application forms but applicants should send= =20 a copy of their CV together with a short outline of their interest to= =20 Dr. Richard Powell,=20 Course Director,=20 Department of Microbiology,=20 University College Galway,=20 Ireland. Tel: 353-91-24411 (ext 2404) Fax: 353-91-257= 00 Closing date for applications is 8th July 1994. From owner-evolution@net.bio.net Mon May 23 23:00:00 1994 Newsgroups: bionet.molbio.evolution Path: biosci!daresbury!trane.uninett.no!eunet.no!nuug!EU.net!howland.reston.ans.net!sol.ctr.columbia.edu!usenet.ucs.indiana.edu!sunflower.bio.indiana.edu!gilbertd From: gilbertd@sunflower.bio.indiana.edu (Don Gilbert) Subject: Re: 18S rRNA Alignments Message-ID: Sender: news@usenet.ucs.indiana.edu (USENET News System) Nntp-Posting-Host: sunflower.bio.indiana.edu Organization: Biology, Indiana University - Bloomington References: <199405241616.MAA06475@evol.biology.duq.edu> Date: Tue, 24 May 1994 21:31:18 GMT Lines: 29 Here are a couple of Internet resources for rRNA which may be of interest to your topic: Gopher to rdpgopher.life.uiuc.edu for the Ribosomal Database project archive. This archive includes sequences, alignments, secondary structures and phylo trees for large and small subunit ribosomal RNA from many species. This is the work of (& citation for): Niels Larsen, Gary J. Olsen, Bonnie L. Maidak, Michael J. McCaughey, Ross Overbeek, Thomas J. Macke, Terry L. Marsh and Carl R. Woese: The ribosomal database project. _Nucleic Acids Research_, Vol. 21 Supplement, p.3021-3023, 1993. Gopher or ftp to ftp.bio.indiana.edu:/molbio/rnase-p for the ribonuclease P sequence database archive, including a compilation of sequences, sequence alignments, secondary structures, and other information. This is the work of James W. Brown, Elizabeth Haas, and Norman Pace. I know that Pace's lab here uses secondary structure information in making alignments. I couldn't give you any details on it though. The RDP project produces a number of alignments, which I think take into account secondary structures. The ref above and at the archive may include details. -- Don -- -- d.gilbert--biocomputing--indiana u--bloomington--gilbertd@bio.indiana.edu From owner-evolution@net.bio.net Mon May 23 23:00:00 1994 Path: biosci!QMRELAY.MAIL.CORNELL.EDU!warren_lamboy From: warren_lamboy@QMRELAY.MAIL.CORNELL.EDU ("Warren Lamboy") Newsgroups: bionet.molbio.evolution Subject: Methods of phylogeny recons Date: 24 May 1994 12:19:59 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 24 Sender: daemon@net.bio.net Distribution: world Message-ID: <94May24.152037edt.579038-2@cornell.edu> NNTP-Posting-Host: net.bio.net Subject: Time:14:58 OFFICE MEMO Methods of phylogeny reconstruction Date:24/05/1994 To those interested in phylogeny reconstruction: The communications concerning phylogeny reconstruction that have appeared in this forum over the past few weeks (and today) have finally induced me to make a comment. I think that it is safe to say that there is still a great deal of honest scientific disagreement about the "best" methods of phylogeny reconstruction. Assuming that most workers are familiar with the cladistic side of the issue, as exemplified by the many papers published in journals such as Cladistics and Systematic Biology, I would also recommend that those who are interested in a deeper understanding of the complex issues involved also consult the thoughtful works by M. Nei and coworkers, R.R. Sokal and associates, and F.J. Rohlf and collaborators. Warren Frank Lamboy "The truth you believe in and cling to makes you unavailable to hear anything new." - Pema Chodron From owner-evolution@net.bio.net Mon May 23 23:00:00 1994 Path: biosci!next.duq.edu!garey From: garey@next.duq.edu (Jim Garey) Newsgroups: bionet.molbio.evolution Subject: 18S rRNA Alignments Date: 24 May 1994 09:29:49 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 16 Sender: daemon@net.bio.net Distribution: world Message-ID: <199405241616.MAA06475@evol.biology.duq.edu> NNTP-Posting-Host: net.bio.net I need some information on the mysterious "taking secondary structure into account" when creating multiple alignments of 18S rRNA genes. My educated guess on the process is to mark known stem sequences on one sequence in the alignment, ie human, and then look for palindromic sequences in similar regions of the other sequences in the alignment and adjust the alignment to match them with the known stem. Is this how it is done? does anyone have any good references for this? Can anyone direct me to references containing good information on known 18S secondary structures (I am interested in yeast and animals)? Thanks in advance for the help. Jim Garey garey@next.duq.edu From owner-evolution@net.bio.net Mon May 23 23:00:00 1994 Newsgroups: bionet.molbio.evolution,sci.anthropology,sci.research,sci.bio,soc.college.grad Path: biosci!agate!ihnp4.ucsd.edu!swrinde!sgiblab!news.cs.indiana.edu!noose.ecn.purdue.edu!mozo.cc.purdue.edu!npirs!pneel From: pneel@CERIS.Purdue.EDU (Paul Neel) Subject: E-mail ? Drs. Brothers or Ring Message-ID: <1994May24.133123.8502@CERIS.Purdue.EDU> Organization: Center for Environmental and Regulatory Information Systems, Purdue University Date: Tue, 24 May 1994 13:31:23 GMT Lines: 10 Xref: biosci bionet.molbio.evolution:1717 sci.anthropology:5340 sci.research:2397 sci.bio:8886 soc.college.grad:4266 Can anyone provide an e-mail (or any mail) address for either Dr. Leslie Brothers or Dr. Brian Ring at the UCLA Brain Research Institute or the Sepulveda VA Medical Center. Information much appreciated. (By e-mail if you can.) Thanks Paul Neel From owner-evolution@net.bio.net Mon May 23 23:00:00 1994 Path: biosci!news.cs.umb.edu!hsdndev!nmr-z.mgh.harvard.edu!nmr-z.mgh.harvard.edu!lfk From: lfk@receptor.mgh.harvard.edu (Lee F. (Frank) Kolakowski) Newsgroups: bionet.software,bionet.molbio.evolution Subject: Re: Tree construction: parsimony versus distance-based Followup-To: bionet.molbio.evolution Date: 24 May 1994 16:47:43 GMT Organization: Mass. General Hospital, Renal Unit Lines: 65 Distribution: world Message-ID: References: <940524105834.20405ccd@scri.fsu.edu> NNTP-Posting-Host: receptor.mgh.harvard.edu In-reply-to: STRELETS@SCRI.FSU.EDU's message of 24 May 1994 07:58:00 -0700 Xref: biosci bionet.software:8284 bionet.molbio.evolution:1719 On 24 May 1994 07:58:00 -0700, STRELETS@SCRI.FSU.EDU ("VICTOR B. STRELETS") said: > Both parsimony and distance-based methods are completely wrong > and can be used only for approximate estimations of tree > topology. They are based on homology (similarity) evaluations. > In the best cases, for SUBsequences. Read the recent Science paper by David Hillis and colleagues. Parsimony and other methods are *not neccesarially correct*, but can often provide useful analyses as to a process that has left no fossils. What do you suppose, that molecular phylogentics is going to wait for zillions of higher order characters while genome efforts are speeding a long a millions of bases per year? > Any discussions about parsimony or distance-based methods are > applicable only for multiple alignments (good fast food for > experimentators). Implications to the evolutionary consequences > as well as attempts to find/explain correlations between > "phylogenetic" trees and archeological (real evolution) facts > seemed to be incorrect and in some cases even pseudo-scientific. Like all science, when it is practiced by uninformed untrained individuals, it is garbage. When the questions posed are thought about carefully, molecular phylogenetics is *good* science. It is all up to the practictioner. > And even for multiple alignments, similarity comparisons does > not work well: remember need to exclude gap penalties, recent > findings of structure similarity without same at sequence level > (so many such regions are present in 3D-align database files > which contain these alignments) etc. > Nothing to discuss - take any method if you do alignments > or generally reconstruct ALL results way if you > try to build something evolutionary. What does this mean? We need trees for lots of different purposes, not just for the evolution of life. Trees are good ways of classifying gene families, functional propoerties, sequences, organisms, planets. The method has to suit the problem. Are you flat out saying that you do not trust sequence dervived trees for displaying the factual evolutionary processes? If so good, because, I dont think anyone should do quite that. Do trees provide a reasonable assesment of some biologically relevant processes? Yes. There are lots of points to this discussion, and as such I have redirected followups to bionet.molbio.evolution. -- Frank Kolakowski ======================================================================== O Email: lfk@receptor.mgh.harvard.edu O O kolakowski@helix.mgh.harvard.edu O O lfk@eastman1.mit.edu O O US Mail: Lee F. Kolakowski Renal Unit, 8th Flr. O O Massachusetts General Hospital Charlestown Navy Yard O O 149 13th Street FAX : 1-617-726-5669 O O Charlestown, MA 02129 Phone AT&T: 1-617-726-5666 O ======================================================================== O The home of the G-Protein-Coupled Receptor Database (GCRDb) O O Email help to gcrdb@receptor.mgh.harvard.edu and in WWW format at O OGCRDb-WWWO ======================================================================== From owner-evolution@net.bio.net Mon May 23 23:00:00 1994 Path: biosci!KIMURA.STANFORD.EDU!jeisen From: jeisen@KIMURA.STANFORD.EDU (Jonathan Andrew Eisen) Newsgroups: bionet.molbio.evolution Subject: Re:18S rRNA Alignments Date: 24 May 1994 16:45:57 -0700 Organization: BIOSCI International Newsgroups for Molecular Biology Lines: 48 Sender: daemon@net.bio.net Distribution: world Message-ID: <9405242346.AA13227@Kimura.Stanford.EDU> NNTP-Posting-Host: net.bio.net Jim Garey asks about sequence alignments of rRNA A few citations for using secondary structure information for the alignment of rRNA primary sequences are R. Gutell et al. Prog. Nucl. Acids Res. Mol. Biol. 32:155-216 Woese, C et al. 1983. Microbiol. Rev. 47:621-669. Neefs et al. 1990. Nucl. Acids. Res. 18:2237-2317. Essentially the way it is done (or at least the way I've done it) is to align highly conserved regions of primary structure first. Then new sequences can be overlayed onto the modeled secondary structure of a known sequence (such as E. coli). Nucleotides at identical regions of the secondary structure can then be aligned in the primary structure. Of course you can run into lots of problems such as differences in secondary structure. For a simple example - if you have three sequences - 1 2 3 G A A A G A A G G A G A G A G A G A G G-C G-C G-C T-A A-T A-T A-T A-T A-T The position of the gap (due to the extra nucleotide in 3) may be somewhat hard to determine. 1 ATGAGA-AGGCAT 1 ATGAGA-AGGCAT 2 AAGAAA-GGGCTT or 2 AAGAAAG-GGCTT 3 AAGAAAGAGGCTT 3 AAGAAAGAGGCTT It gets worse with more sequences> Usually, regions like these are left out of phylogenetic reconstructions because of the difficulty in the alignment. But they do not constitute the majority of sites. Jonathan A. Eisen Department of Biological Sciences Stanford, CA 94305-5020 jeisen@kimura.stanford.edu From owner-evolution@net.bio.net Tue May 24 23:00:00 1994 Path: biosci!barrnet.net!well!mjbrauer From: mjbrauer@well.sf.ca.us (Matthew J. Brauer) Newsgroups: bionet.molbio.evolution,bionet.general,bionet.drosophila Subject: Re: the recent advertisement Date: 25 May 1994 19:32:31 GMT Organization: The Whole Earth 'Lectronic Link, Sausalito, CA Lines: 23 Message-ID: <2s094f$l9u@nkosi.well.com> References: <1994May25.103624.4739@Princeton.EDU> NNTP-Posting-Host: well.sf.ca.us X-Newsreader: NN version 6.5.0 #1 (NOV) Xref: biosci bionet.molbio.evolution:1728 bionet.general:9307 bionet.drosophila:406 mattweed@edith.Princeton.EDU (Matthew Weed) writes: >I suggest that you send email to the person who posted >the recent thigh cream ad, and also send to postmaster >at his machine. His address is:keogh@anshar.shadow.net >send also to: postmaster@anshar.shadow.net. >Both addresses work, at least I haven't gotten any bounced >mail since my response two days ago. >Matt >-- >"It may not be true, as Lincoln Supposed, that you can't fool all of the >people all of the time, but you can fool enough of them to rule a large >country." Will and Ariel Durant: _The Lessons of History_ 1969. >mattweed@edith.princeton.edu MPA candidate/WWS:95, (609)258-8236 Actually, this might no longer be a good idea. This joker (so I heard) included a .forward file in his home directory, sending all mail to an innocent user. Apparently his account has been pulled already. From owner-evolution@net.bio.net Tue May 24 23:00:00 1994 Newsgroups: bionet.molbio.evolution,bionet.general,bionet.drosophila Path: biosci!daresbury!trane.uninett.no!sunic!EU.net!howland.reston.ans.net!usc!elroy.jpl.nasa.gov!lll-winken.llnl.gov!fnnews.fnal.gov!att-in!princeton!edith!mattweed From: mattweed@edith.Princeton.EDU (Matthew Weed) Subject: the recent advertisement Message-ID: <1994May25.103624.4739@Princeton.EDU> Originator: news@nimaster Sender: news@Princeton.EDU (USENET News System) Nntp-Posting-Host: edith.princeton.edu Organization: Princeton University Date: Wed, 25 May 1994 10:36:24 GMT Lines: 15 Xref: biosci bionet.molbio.evolution:1727 bionet.general:9304 bionet.drosophila:405 I suggest that you send email to the person who posted the recent thigh cream ad, and also send to postmaster at his machine. His address is:keogh@anshar.shadow.net send also to: postmaster@anshar.shadow.net. Both addresses work, at least I haven't gotten any bounced mail since my response two days ago. Matt -- "It may not be true, as Lincoln Supposed, that you can't fool all of the people all of the time, but you can fool enough of them to rule a large country." Will and Ariel Durant: _The Lessons of History_ 1969. mattweed@edith.princeton.edu MPA candidate/WWS:95, (609)258-8236 From owner-evolution@net.bio.net Tue May 24 23:00:00 1994 Newsgroups: bionet.molbio.evolution Path: biosci!daresbury!trane.uninett.no!eunet.no!nuug!EU.net!howland.reston.ans.net!spool.mu.edu!torn!utnut!utgpu!lamoran From: lamoran@gpu.utcc.utoronto.ca (L.A. Moran) Subject: Re: 18S rRNA Alignments Message-ID: Organization: UTCC Public Access References: <9405242346.AA13227@Kimura.Stanford.EDU> <2rvll9$jhu@charm.magnus.acs.ohio-state.edu> Date: Wed, 25 May 1994 16:01:05 GMT Lines: 29 In article <2rvll9$jhu@charm.magnus.acs.ohio-state.edu>, Diane Stothard wrote: >It is ESSENTIAL to take secondary structure into account when aligning rRNA >genes! (It should be essential when aligning any gene sequence except >structures are not known for many proteins.) If you do not align your sequences >based on secondary structure, you cannot verify that you are actually comparing >homologous sites. If you are not comparing homologous sites, you cannot say >ANYTHING about the evolutionary relationship between the sequences you are >analyzing! > You are making the assumption that secondary structure is more highly conserved than primary structure. This is only an assumption. Evolutionary relationships are based on accumulated differences in the nucleotide sequence of homologous genes and this affects the amino acid sequence of the protein. A mutation (variation) could give rise to a primary sequence that results in an altered secondary structure. That variation could become fixed in the population if the changed secondary structure is not selected against. Two proteins can have similar amino acid sequences but different secondary structures in some regions. There are several examples of proteins that have similar secondary structures but are not homologous - or at least do not seem to have a common ancestor. Laurence A. Moran (Larry) From owner-evolution@net.bio.net Tue May 24 23:00:00 1994 Path: biosci!agate!usenet.ins.cwru.edu!lerc.nasa.gov!magnus.acs.ohio-state.edu!dstothar From: dstothar@magnus.acs.ohio-state.edu (Diane Stothard) Newsgroups: bionet.molbio.evolution Subject: Re: 18S rRNA Alignments Date: 25 May 1994 14:00:09 GMT Organization: The Ohio State University Lines: 9 Distribution: world Message-ID: <2rvll9$jhu@charm.magnus.acs.ohio-state.edu> References: <9405242346.AA13227@Kimura.Stanford.EDU> NNTP-Posting-Host: beauty.magnus.acs.ohio-state.edu It is ESSENTIAL to take secondary structure into account when aligning rRNA genes! (It should be essential when aligning any gene sequence except structures are not known for many proteins.) If you do not align your sequences based on secondary structure, you cannot verify that you are actually comparing homologous sites. If you are not comparing homologous sites, you cannot say ANYTHING about the evolutionary relationship between the sequences you are analyzing! Diane From owner-evolution@net.bio.net Tue May 24 23:00:00 1994 Newsgroups: bionet.molbio.evolution Path: biosci!agate!howland.reston.ans.net!pipex!sunic!EU.net!ub4b!idefix.CS.kuleuven.ac.be!reks.uia.ac.be!derijkp From: derijkp@reks.uia.ac.be (Peter.DeRijk) Subject: Re: 18S rRNA Alignments Message-ID: <1994May25.105213.26890@reks.uia.ac.be> Organization: U.I.A. X-Newsreader: Tin 1.1 PL5 References: <199405241616.MAA06475@evol.biology.duq.edu> Date: Wed, 25 May 1994 10:52:13 GMT Lines: 37 Jim Garey (garey@next.duq.edu) wrote: : : I need some information on the mysterious "taking secondary structure : into account" when creating multiple alignments of 18S rRNA genes. : My educated guess on the process is to mark known stem sequences on : one sequence in the alignment, ie human, and then look for : palindromic sequences in similar regions of the other sequences in : the alignment and adjust the alignment to match them with the known : stem. Is this how it is done? : In an alignment both primary and secondary structure should be similar in a certain region. It is easy to align very conserved areas on basis of primary structure alone. In the more variable areas the alignm