Genetics September 2006

genetics@lists.oulu.fi

5 participants
6 discussions

Reija Laitisen visiitti
by Helmi Kuittinen 21 Sep '06

21 Sep '06

hei, Reija Laitinen Applied Biosystemsiltä tulee käymään tiistaina 26.9. klo 10. Jos haluatte tavata hänet, tulkaa genetiikan kahvihuoneeseen. t. Helmi Helmi Kuittinen Oulun yliopisto University of Oulu Biologian laitos Department of Biology PL 3000 P.O.Box 3000, 90014 University of Oulu 90014 Oulun yliopisto Finland email: Helmi.Kuittinen(a)oulu.fi tel. 358-(0)8-553 1803 fax 358-(0)8-553 1061

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[Fwd: Other: Software Arlequin ver 3.1]
by Tanja Pyhäjärvi 21 Sep '06

21 Sep '06

-------- Original Message -------- Subject: Other: Software Arlequin ver 3.1 Date: Thu, 21 Sep 2006 03:18:44 -0400 (EDT) From: evoldir(a)evol.biology.mcmaster.ca Reply-To: brian(a)helix.biology.mcmaster.ca To: tanja.pyhajarvi(a)oulu.fi Please note that a new version (3.1) of Arlequin is now available on http://cmpg.unibe.ch/software/arlequin3 Compared to version 3.01, Arlequin 3.1 includes several cosmetic and speed improvements, as well as bug corrections and additional features: Improvements ------------ * Locus-by-locus AMOVA can now be performed independently from conventional AMOVA. This can lead to faster computations for large sample sizes and large number of population samples. * Faster routines to handle long DNA sequences or large number of microsatellites. * Faster reading of input file. * Faster computation of demographic parameters from mismatch distribution. Improved convergence of least-square fitting algorithm. Additions: ---------- * Computations of population specific inbreeding coefficients and estimation of their significance level. * Output of the number of alleles as well as observed and expected heterozygosity per locus for all populations. * Computation of the Garza-Williamson statistic for MICROSAT data. * New sections are provided at the end of the result file, in order to report summary statistics computed for each population: - Basic properties of the samples (size, no. of loci, etc...) - Heterozygosity per locus - Number of alleles + total no. of alleles over all pops - Allelic range + total allelic range over all pops (for microsatellite data) - Garza-Williamson index (for microsatellite data) - Number of segregating sites, + total over all pops - Molecular diversity indices (theta values) - Neutrality tests summary statistics and p-values - Demographic parameters estimated from the mismatch distribution and p-values. * New shortcuts are provided in the left pane of the html result file for F-statistics bootstrap confidence intervals, population specific FIS, and summary of intra-population statistics. Bug corrections: ---------------- 1. Locus-by-locus AMOVA failed for on DNA sequences when corrections for multiple hits were selected. These corrections have been di 2. File conversion towards the Phylip format could not be done. 3. It was impossible to change the default significance level of 0.05 for highlighting significant genetic distances in output file. 4. Missing data identifier other than "?" was not accepted. 5. If a a project file (or the path to it) contained the letters "arb", then it was erroneously considered as a Batch file. 6. Reported confidence interval around FST were badly reported by the bootstrap procedure in case of a single group and no Individual Level taken into account. 7. Estimation of haplotype frequencies from distance matrix was not performed when "Conventional FST" option was selected. 8. Locus-by-locus AMOVA reported incorrect results for Genotypic data when individuals had missing data for only one of their gene copy at a given locus. 9. Reported number of indels differed according to the weight given to indels in the Option panel. This bug did not affect AMOVA computations. 10. For sequence data, a mixture of N's and missing data led to problems in identifying distinct DNA sequences from distance matrix, leading to slightly incorrect FST computations. 11. Exact test of population differentiation could not be performed when gametic phase was unknown. Now, this option has been restored, like in ver. 2. 12. Arlequin hanged when a given population was entered several times in the definition of group for the computation of genetic structure. Now, the error is simply flagged but the program does not hang. 13. For frequency data, it was impossible to use a predefined distance matrix. 14. Beta approximation of the significance of Tajima's D gave wrong results. This approximation has been suppressed and now we only report the significance level obtained from coalescent 15. Bad computation of inbreeding coefficients under the locus-by-locus AMOVA approach for genotypic data when phenotype frequencies were larger than one. The bug caused an overestimation of the local (FIS) and total (FIT) inbreeding level. For samples where phenotype frequencies were all set to 1, the inbreeding coefficients were correctly estimated. 16. Expected heterozygosity reported under HWE exact test section was inaccurately computed. This inaccuracy however did not affect the results of the HWE exact test, which does not use information on observed and expected heterozygosity. -- Laurent Excoffier Computational and Molecular Population Genetics (CMPG) Zoological Institute, University of Bern 6, Baltzerstrasse, CH-3012 Bern, Switzerland Tel: +41 31 631 30 31 Fax: +41 31 631 48 88 Email: laurent.excoffier(a)zoo.unibe.ch URL: http://cmpg.unibe.ch/people/excoffier.htm Laurent <laurent.excoffier(a)zoo.unibe.ch>

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Graduate School Positions at FGSPB (fwd)
by Marjut Kreivi 14 Sep '06

14 Sep '06

4-year PhD graduate school positions AVAILABLE AT THE FINNISH GRADUATE SCHOOL IN PLANT BIOLOGY, starting January 1, 2007 Positions are open for graduate students with a background in plant biology or related field. Applicants should have a master's degree or equivalent, or be expected to complete their studies before starting their PhD training in January 2007. Matching funds student positions are also available, where the student is a full member of the graduate school but their salary comes from another source. PhD studies are to be carried out under the supervision of one of the group leaders from the FGSPB, and progress is monitored by a yearly follow-up group. The Finnish Graduate School in Plant Biology is a national graduate school administered by the University of Helsinki. It is financed by the Ministry of Education and the Academy of Finland. The director of the graduate school is Tapio Palva (University of Helsinki) and the vice director is Eva-Mari Aro (University of Turku). The graduate school aims to train scientific researchers in molecular plant biology including molecular biology and genomics, biochemistry, developmental biology, pathology and biotechnology. PhD training includes a national and international teaching program, participation in courses and meetings within and outside Finland and cooperation with other graduate schools. Monthly salary is 1619 EURO. This is based on level 2 of the demands chart for teaching and research personnel in the new salary system of Finnish universities. A personal work performance component of the system is to be phased in gradually subject to negotiations with the student's supervisor and follow-up group. Salary costs of the graduate students as defined by the Ministry of Education (27400 EURO/year) will be shared equally between FGSPB and the supervisor of the student with FGSPB remaining the employer. Applications in English must be completed using the online application form. For more information please see: http://www.helsinki.fi/bioscience/fgspb/english/application.htm or contact Karen Sims-Huopaniemi karen.sims-huopaniemi(a)helsinki.fi Closing date for applications is 8 October 2006, 23.59 (local Helsinki time). ----------------------------------------- This message was sent to you by FinBioNet Anita Tienhaara Institute of Biotechnology P.O.Box 56 (Viikinkaari 9) FIN-00014 University of Helsinki, Finland tel +358-9-191 59656 fax +358-9-191 59550 email anita.tienhaara(a)helsinki.fi www.biocenter.helsinki.fi/finbionet/

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Genetiikan seminaarit/Genetics seminars
by Helmi Kuittinen 08 Sep '06

08 Sep '06

Hei, tämän syksyn ensimmäinen genetiikan seminaari on 14.9. klo 12.15 PT302:ssa. Cristina Lopez-Gallego (University of New Orleans/Brown University) puhuu aiheesta: "Adaptive genetic divergence between populations from native and disturbed habitats in a rainforest Cycad (Gymnosperm)" Tervetuloa! Seuraavat seminaarit ovat 28.9. Prof. Pekka Pamilo (Oulun yliopisto): NUMTs in the honeybee genome 23.11. MSc Timo Knürr (Oulun yliopisto): Migration, selection and clines in adaptive variation of budset timing in Pinus sylvestris. Yleistä seminaareista: Genetiikan seminaarit ovat tutkijoiden, opettajien ja vierailijoiden vapaamuotoisia tutkimus- ja tutkimussuunnitelmaesitelmiä tai keskustelua ajankohtaisista aiheista. 10 osallistumista (kuuntelua) raportteineen (1-2 sivua) on 2 op (1ov). Soveltuu etenkin jatko-opiskelijoille. Opintosuoritusmerkinnän saa minulta. Syksyyn mahtuu vielä lisää seminaareja. Ilmoita jos haluat pitää seminaarin tai luoksesi on tulossa esitelmähaluinen vierailija. ------------------------------------------------- We´ll have this autumn´s first Genetics seminar September 14, at 12.15 in PT302. Cristina Lopez-Gallego (University of New Orleans/Brown University) will talk about "Adaptive genetic divergence between populations from native and disturbed habitats in a rainforest Cycad (Gymnosperm)" Wellcome! Next seminars are 28.9. Prof. Pekka Pamilo (University of Oulu): NUMTs in the honeybee genome 23.11. MSc Timo Knürr (University of Oulu): Migration, selection and clines in adaptive variation of budset timing in Pinus sylvestris. General information about the seminars: Visitors, researchers, graduate students and advanced masters students can give informal seminars in this series. Participation and reporting 10 seminars is worth 2 op (1 ov) (753630S). Recommended especially for graduate students. Please let me know if you or your visitor is interested in giving a talk. regards, Helmi Kuittinen Oulun yliopisto University of Oulu Biologian laitos Department of Biology PL 3000 P.O.Box 3000, 90014 University of Oulu 90014 Oulun yliopisto Finland email: Helmi.Kuittinen(a)oulu.fi tel. 358-(0)8-553 1803 fax 358-(0)8-553 1061

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Kakkukahvit
by Soile Finne 08 Sep '06

08 Sep '06

Heip! Tarjoan tänään kakkukahvit viran saamisen kunniaksi PT:n kahvihuoneessa klo. 13.00. Hi! Coffee and cake in coffeeroom today 13.00 pm. Soile

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Fwd: VL: Huoltottiedote
by Tuulikki Pakonen 07 Sep '06

07 Sep '06

>Subject: VL: Huoltottiedote >Date: Thu, 7 Sep 2006 08:45:32 +0300 >X-MS-Has-Attach: yes >X-MS-TNEF-Correlator: >Thread-Topic: Huoltottiedote >Thread-Index: AcbRs7L75UPdM7rCSvKnx79JBC24lAAjLS/w >From: "Raija Ukkola" <Raija.Ukkola(a)oulu.fi> >To: <tuulikki.pakonen(a)oulu.fi>, <niilo.rankka(a)oulu.fi> >Cc: "Erja Heiskari" <Erja.Heiskari(a)oulu.fi>, > "Arto Haverinen" <Arto.Haverinen(a)oulu.fi> >X-Spam-Checker-Version: SpamAssassin 2.63 (2004-01-11) on sun3.oulu.fi >X-Spam-Level: >X-Spam-Status: No, hits=-4.9 required=5.0 tests=BAYES_00 autolearn=ham > version=2.63 > > Hei! > >----Välitättekö tämän tiedon perinnöllisyystieteelle! >Yst.terv. >Raija Ukkola >Ylivirastomestari >085533035 >0407045670 >raija.ukkola(a)oulu.fi > > > > >Tervehdys! > >Ohessa IV-kanavapuhdistusosastomme tiedote huoltotöistä >perinnöllisyystieteenlaitoksella.KO.alueella on Medivire tutkinut >hengitysteiden osalta oireilevaa yliopiston henkilökuntaa.Edellisen >johdosta Senaatti-kiinteistön toimeksiannosta puhdistamme ao.alueen >ilmanvahtolaitoksen. > >Terveisin > >ISS Palvelut Oy >Oulu-Kainuu >Tekniset Palvelut >Projektipäällikkö >Jukka Myllykoski > >040 861 0105 >jukka.myllykoski(a)iss.fi >---------------------- Edelleen lähettänyt: Jukka Myllykoski/cl/fi/ISS >pvm: 06.09.2006 15:49 --------------------------- > >MAIL >Postisanoma > > > Lähettäjä: Teemu Säkkinen , pvm: 06.09.2006 08:22 > > Vastaanotta kari.kaijalainen(a)senaatti.fi > jat: > > Tiedoksi: Jukka Myllykoski/cl/fi/ISS@ISS, tuomo.kukkone(a)ouka.fi > > > > > Otsikko: Kanava puhdistus tiedoite > > > > > >Tervehdys. >Ohessa kanavapuhdistustiedote koskien Perinnöllisyystieteenlaitosta. > >Olisitko Jukka ystävällinen ja jakaisit tiedotteen sähköpostilla käyttäjille. > >Käymme liputtamassa tilat tänään. > >(See attached file: Tiedote oyo-pt.doc) > >Teemu Säkkinen palveluohjaaja - Tekniset palvelut ISS Palvelut Oy - PL 135 >- Mallastie 1 - 90520 OULU - Finland >e-mail: teemu.sakkinen(a)iss.fi - Puh: 02051 40042 >Faksi: 02051 57050 - www.iss.fi > > > > >

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Genetics September 2006