Georeferenced database of genetic diversity (GD)² User Manual
Contents
1. First line precise all markers to import a set of markers population spaces merker name P A He Ho Me Fa Las Etangs 1 1 020800 3 000309 0 390814 0 346156 1 750154 0 114689 M St German 2 raaa 1030800 3 000900 00746 0 346855 1 782838 0 112090 lsoryme Foniany 3 n 1 000800 2 875300 0 222509 0 381654 1 231103 0 060185 Jlenzyme La Tenpk 4 103080 287550 0376637 0 348719 1 960915 0 085394 leoryme Abbeyes 5 1 030000 287550 0 384383 0 312122 1 745320 0 172746 isozyme miners 22 1 02080 3 000300 O coaz Q 3215 8 1 302158 0 231732 s LE Available indices in GD Ho observed heterozygosity He expected heterozygosity P polymorphism rate A allelic diversity Hit Fis inbreeding coefficients Ne efficiency number of alleles III Administration The administration part of the web application is reachable from the menu Data in the GD database are organized in projects and datasets A dataset must contain data that are compatible that can be studied together It is recommanded to create a dataset for one study example all data that are involved in a publication subject A dataset belongs to a project Users can create a project and add to this project some datasets in order to insert data When data are imported in the database only the user s laboratory can access to these data by default If he want to share his data with another partner he can grant some rights to another laboratory ADMINISTRATION Dat2. Delete rights If you want to delete rights on data 1 Add rights When you click on Add rights we access to a form ADD RIGHTS Select data to share Available dataset s Oaks cpDNA Polymorphism Balkan Genotype data Diversity measures with Laboratory Then you can select the dataset the data type genotyping or diversity the partner laboratory These informations are validated by clicking on Save changes The chosen partner laboratory can access to the data from the viewer 2 Delete rights To delete rights on data click on Delete rights A list displays all laboratories for which you have eranted some rights according to dataset and data type DELETE RIGHTS Select rights to delete Laboratory Dataset Data type P2a Alterra Oaks cpDNA Polymorphism Balkan geno measures P2a Alterra Oaks cpDNA Polymorphism Balkan diversity measures P2a Alterra Oaks cpDNA Polymorphism Balkan diversity measure all markers Delete selected rights Back to administration menu We check in this list the rights to delete then we validate by clicking on Delete selected rights This deletion takes effect immediately 3 Change password To change your password click on Change password All informations about your account are displayed last name first name e mail etc Type re type your new password and click on the Save changes button Th
3. All available populations in the GD database can be displayed on a map fere pe e All available samples in the GD database can be displayed on a map Advanced search This function allows to search for a particular population in GD using different criteria Map obtained with function See all populations Norge m yA Norway S PS S konmar Wi Suomi Finland 3 LJ La Ja Latvia Lithuania Ve Netherignd s e eee Deutschian ace ie 1 Croatia italia Westerr nj EEIE e 4 inibi r C oogle dhi bM ate Polska Warszawa Poland a th f gt E 45 x eS Libya GS d o 1 Sse 2 pe o i 1 x c Fokes cartographiqui 12 Basarsoft Google MapIT MapLink OR oM Lietuva A TN e Vilnius K N E 5 Romania Romania cu eS a Te C CUm se TR e e gt aa w gt a lt Er 4 A P Arabia ry ta Em pis MME Tele Atlas Imagerie 2012 NASA TemaMetric Morocco Population Species latitude longitude Altitude Country Number of individuals canariensis 5 0 35 03 1260 Morocco 2 Pmo pinaster 5 1 33 87 Morocco 117 Bucci 2007 33870000 4030000 NA pinaster 4 03 33 87 0 Morocco 0 Pian Satellite M Population El Anasser b Advanced search This function allows to search for a particular population To do so the following items must be selected the category fungi
4. By clicking on it there is two possibilities export all data of the dataset export the previously displayed data EXPORT FILE INDIVIDUAL DATA Dataset name Oaks cpDNA Polymorphism Balkan PDF Export entire dataset esv Export visualized data csv The exportation s format is in CSV By clicking on the chosen option the exportation process is launched Are you sure This can take a while please see in My files to retrieve the file Annuler OK It s confirmed by a message on the top of the window The file iz in production The file is then available in My files section of the web application It can be downloaded or deleted DuC EU eae LC BIA BET BLU E wri jeudi 12 2012 GD MY FILES Files ready to download 3 Importation The GD database Georeferenced Database of Genetic Diversity comprises georeferenced passport data and genetic data Genetic data can be inserted at the individual level or at the population level For example 1f you have already allelic frequencies and diversity statistics available they can be inserted and will refer to the population level If you have single tree genotypic data they can be inserted at the individual level The importation function is accessible from the menu by clicking on Import data IMPORT DATA The GD database Georeferenced Database of Genetic Diversity comprises georeferenced passport data and genetic data
5. FOR ALLELIC HAPLOTY PIC FREQUENCIES Marker name RFLP FEM1562002526 Alleles haplo1 gt BEMOHZIES hapio11 gt NES hapios gt SXedOd2 hapios gt HEHE Fullscreen Sverige Sweden a oras N on way Suomi Finland H 4 Festi j stonia Latvija ta VU A a Lithuania a A Belarus A Ireland Eire SELETO Poland nte PI a O Slovensko PR sive akia v P Hungary d J Romania Hrvatska zx RS Rom 1 Croatia T ti s Cp nia Italia gi MEET italy OPI SUEDE Head Bulgaria T HEE gt M orgon T Populations in Dataset s Species Quercus Quercus Quercus Quercus Aisenay Quercus Aistersheim Quercus Algsja Finland Altenplathow Altenpl Anr chte Abt 32A B C Quercus Quercus Quercus Apriki Quercus Apriki 3993 Quercus Apriki413 Letland Quercus Arcachon Quercus Ares Quercus Arnsberg Quercus Arnsberg Abt438A Quercus be Benapyck Ma A oH YkpaiHa AS ut Georgia Caspian sA 1 coors eg y A Azerbaijan NB if all alleles or haplotypes are not selected in the form in the pie chart the black parts will represent the proportion of non selected alleles b Plot genotypic frequencies The display of genotypic frequencies is realised for a given marker and genotype s So must be selected acategory one or more genus one or more species Genoty
6. Genetic data can be inserted at the Individual level or at the population level Some basic rules a insert populations before their individuals a insert markers before the concerned data a insert populations and their individuals before their data rAdd Data Add Populations Samples Add populations and or samples to GD Add Individuals Add individuals to GD Add Markers Add markers to GD Add Genetic Data Add genotyping or diversity data to GD The importation concerns the following items populations samples individuals markers genetic data Some basic rules before inserting new data insert populations before their individuals insert markers before the concerned data insert populations and their individuals before their data populations population level data individuals individual level data All items upstream the arrows must be inserted before the items downstream the arrows 1 Import populations samples By clicking on Add Populations Samples we access to a simple form just select the csv file and click on insert to upload the populations IMPORT POPULATIONS SAMPLES Select your CSV file Parcouri PS Parcourir Insert The csv file is presented below File format informations smt pm jus pm Fobledo P 10 90 TR m Mandatory columns species long longitude
7. View View Stamser 89 robur 11 0 47 5 660 Austria 76 individual E sas individuals SEA E SE data nS View KG K ssen robur autochthonous 12 4 47 68 600 Austria 6 individual ae individuals TES ee C YET data pais View KG Ebbs rtplatz robur autochthonous 12 24 47 65 470 Austria 2 individual individuals EEE data ess View Kaisertal Kufstein robur autochthonous E221 47 61 650 Austria 3 ET LES individual individuals EU SS data View View KG Thiersee Pirchmoos robur autochthonous 12 05 47 61 770 Austria 2 E individual individuals gE TR data Vica View KG Kirchdorf robur autochthonous 12 45 47 56 690 Austria 5 TAI individual ESSE individuals um c See your populations From this part of the application you can also visualized the populations that you have inserted To do so the following items must be selected the category fungi insects or trees if you want a population or a sample check boxes population or sample See your populations Category Trees 3 Population a Sample O NB The display for populations can change according the level zoom When the number of populations to display is large one icon actually represents several populations The information window who displays by clicking on the icon will contain a list with the eight first populations and the complete number of populations left All the populations can be displayed if you further focus on the icon 2 Genetic data
8. aggregated diversity statistics on a Google earth interface map Data can also be exported in different formats to be used for data analysis by different software packages Population Populations on a map This part enables access to all functions concerning populations stored in GD Genetic Data Genetic data on a map The genetic part comprises functionalities regarding the genetic data single tree genotypes or aggregated diversity statistics allelic frequencies diversity parameters stored for populations Dataset summary Data are organized in projects and datasets A dataset must contain data that are compatible that can be studied together It is recommanded to create a dataset for one study Markers This part enables access to all markers available in GD a Population part This part enables access to all functions concerning populations stored in GD b Genetic Data part The genetic part comprises functionalities regarding the genetic data single tree genotypes or aggregated diversity statistics allelic frequencies diversity parameters stored for populations dataset summary and markers These two categories are also available using the Viewer menu Populations and sample on a map See all populations All available populations in the GD database can be displayed on a map Seeall samples All avai
9. insects or trees the genus one or more the species one or more if you want a population or a sample check boxes population or sample Click on the Select species button to display results Advanced search Category Trees e Select category Choose one or more genus Castanopsis Cedrus Cupressus Cyclobalanopsis Fagus Fraxinus Juniperus Lithocarpus Picea Pinus Quercus rehderiana resinosa E robur E rubra NE rugosa a Sample O Choose one or more species Population From this first selection two lists are obtained They permit to select some populations to display on a map to select countries so that all populations located in the country can be displayed Select some populations Anzing Apriki Apriki399 Apriki413 Letland Aramil Arcachon Or select some countries Austria A E Bielorussia Bosnia Bosnia and Herzegovina Ares Ariundle Arnsberg Croatia Arnsberg Abt438A Arnsberg Herdringen Arnsberg Stadt Arnsberg Stadt Arnsberg Stadt Arnsberg Stadt Under the map like the See all populations function a list of the populations is available sorted by country Two links are available View individuals which allows to display individuals contained in each populations and View individual data which allows the display of available genotyping data for a given population Austria
10. 3 Population Chudenice 116 Doubrava 117 3 Markers To view available markers in GDP the button Species robur petraea petraea Species petraea menu take to a menu where it is possible to display all available markers do an advanced search Show markers View all markers Country Austria Austria Austria Country Bosnia Herzegovina Country Croatia markers on the home page Display all available markers in GD database Advanced search Ho 0 381269 0 339454 0 317122 Ho 0 341402 Ho 0 265803 Ho 0 212072 0 255853 and in the Viewer This function allows to search for a particular markers in GD using different criteria a All markers All available markers are listed sorted by marker type ALL MARKERS Marker type gSSR Marker type Marker name CPM haplotypes 11seq gSSR chloroplastic P 7195 gSSR chloroplastic P 30249 gSSR chloroplastic P 30141 gSSR chloroplastic Compartment Measure Sequence type SSR Reference haplotypic NULL allelic allelic allelic 11 microsatellites 3655 1520 4110 8730 3025 9400 7195 2610 1100 6375 7995 1250 b Advanced search To look for a marker is possible by selecting the compartment nuclear cytoplasmic mitochondrial chloroplastic the marker type cpSSR EST_SSR RFLP Isozyme ADVANCED SEARCH FOR MARKERS WITH DATA Advanced search Compartme
11. LP haplotypes Select a csv file Parcourir The csv file format is explained below File format informations First line precise allelic fa or genotypic fg frequencies File format csv delimiter is a stand name population spes AAP AAP AAP AAP AAP AAP AGP ACP AC marker name 13 458 6 1 Meh Les Etang es Etang drea 0 006 O12 O27 005 046 OL alleles 3 Geman St Germain 2 dr 0 05 002 098 002 4 058 Oo O Portion Pomigny 3 ar D 0 M 005 022 0 08 Doo 04 Le Tempe Le Tempe 4 erage 0 073 0 05 02 002 05 5 Les Abbaye es Abbayes 5 dr 006 041 G2 0M 051 04 Bommiers dommigs 6 ale D 0 MO 005 C2 O04 0159 0 45 Chateauroux nasal air 0 0 MS O07 O21 007 0 8 02 a e d a e Population name The mentioned markers and populations in the file must exist in the database So please check their spelling The marker names in the second line and population names in the second column should be the same than those already introduced during the previous steps when the population and marker data were introduced So please check their spelling e Insert values for diversity index Diversity indices refer either to a given marker or a set of markers used in a study all used markers in a dataset To access to this insertion Add Genetic Data gt Insert Diversity Data You can insert data for one population or for many populations in GD database IMPORT DIVERSITY MEASURES Import Inse
12. X evoltr e Georeferenced database of genetic diversity GD User Manual Version 5 Date 2012 September Project Evoltree Title GD User Manual Author Fran ois Ehrenmann Validation Antoine Kremer Table of contents CODIGCUDUC s eee re ree ens eater PR REDES DES RE DD ier wr PY Pee PD e oe me ve Tere OS Ie a Do e LU ery RA 3 Orcanisation and tecnica IMIOLMaAlONS uisum ied oae En det id ent Moda deg con trie ideato do uude 3 Technical Mi Oviia Ons cou techno E rcd Sota seen oh m DM Id MCN a eee eee 3 JE SAMI SAU OM assessoria a ole locate eaten A M OLI aeolian tee 3 LOSIE PACS ou emite isa dava an fato tout orcad aa toc oen oboe alic ene eed Londen a 3 Home paze and maim parso GD uut tea ted od abite eed oque eed ad dal tem eod QM de U 5 FunctioDalitle S i ae ub ES EPA pei eer dave ub beu abes uas dada ete Gena n baleia adiado ana Diosa a oa Reddite 7 bs PT MN ec et anne ta a aaa a eet eae egw enema nae 7 Populations and sample O aap natured amet DS ia GAL SAS 7 ene esit ON Darter cere ce etch eoo nerd AEA hte od ee once ME 13 AUTE OI EE ee tem P TCR 27 EO ps 31 Eae 6 O NPR RARE rep ERR e Rs MPR Ta RR RR RR NR RN PER NR UR NR 33 Import popula on S cassia piss eite edes tassa bbs dai adia ado ada nod aca ig dd da a 35 Tipon Ind IVIQUAIS ous eit E aera nme a has 37 H DOPL T KO Socio er ee Ry OE EAT a DM Te UE MUI ee 39 Dz ETE PEE 4 Mea iie RETO TT D ETT 4 ZA GUIS UE OCIO Was erases et
13. a in the GD database are organized in projects and datasets A dataset must contain data that are compatible that can be studied together It is recommanded to create a dataset for one study Users can create a project and add to this project some datasets in order to insert data When data are imported in the database only the user s laboratory can access to these data by default If he want to share his data with another partner he can grant some rights to another laboratory Data management and rights Adda new Project Add a new project to GD Add a new Dataset Add a new Dataset to GD Add or delete Rights of access on Data Give access or not to your data in GD Change password Change your password to access GD Settings Settings only for administrator 1 Adda new Project To create a new project click on the Add a new Project button A simple form allows to create a new project and to view existing projects in the database PROJECT ADMINISTRATION Create a new project Project name Existing projects Project name Creation date Evoltree 2009 03 25 15 29 40 UTC BioGeCo 2009 08 19 08 14 31 UTC ForestResearchinsitute Croatia Bosnia Herzegovina 2010 03 23 08 59 09 UTC Backto Administration menu Updated 2009 03 25 15 29 40 UTC 2009 08 19 08 14 31 UTC 2010 03 23 08 59 09 UTC 2 Adda new dataset To create a new dataset click on the Add a n
14. are the following IMPORT MARKERS Select your CSV file Parcourir Insert EST SSR nuclear chloroplastic mitochondrial gSSR nuclear chloroplastic cpSSR chloroplastic RFLP nuclear chloroplastic mitochondrial SNP nuclear Isozyme cytoplasmic RAPD nuclear File format informations rare pe makeri EST SSR make SNP makes RFLP fepe chloroplast etx pd File format csv delimiter is measure type allelic allelic Mandatory columns B Dame type s measure type compartment alle ype porpatmentiio codoninan Facultative columns sequence a allele type m biblio The allele types can be dominant or codominant For the genetic measures there are two possible options allelic or haplotypic A column titled reference can be added for isozymes The column biblio can be added providing a pdf file of the publication where the data were analysed for the first time 4 Import genetic data measures To import genetic data click on Add genetic data You can import measures by project or import diversity measures in GD database IMPORT GENETIC DATA Import Insert genotyping data Import measures by project in GD database Insert Diversity data Import diversity measures in GD database a Genotyping data The importation is made from a csv file Click on Insert genotyping data then choose a p
15. ataset Select species Dataset Isozyme geographicalStructureGeneDivll e Marker type Isozyme Diversity indices 9 Ho O He O P Oa Fis Fit Ne Diversity indices for All markers in dataset One marker in dataset Datasets geographicalStructureGeneDivil Forest_Genetic_Variation_Gomory Isozyme hetero AllRich European Beech Marker AAP Diversity indices Ho He P O A Fis Fit Ne We will obtain a map with circles that picturing the populations Their diameter is proportional to the index s value PLOT GENETIC DIVERSITY MEASURES ALL MARKERS Your selection Species robur petraea pubescens suber Marker type Isozyme Diversity indice Ho Dataset Isozyme geographicalStructureGeneDivil Latvia E Sen mes Lietuva Lithuania United Kingdom mes AT 91s T IE dE Y SIL 3roningen Mines creme ALE SZC ALETAS Ewe Nottmghi E Belarus us MEET TS a apuria AY Mispa a wre m as Kyiv re e LUDEILE rro Ukraine Bulgaria E Provdiv e Portugal dce Espana y Spain TY No rd 1 The list of the populations is available as usual with value of diversity indice selected sorted by country Click on population name in the list to visualize it on the map see below Austria Population Stamser 89 Klostermarienberg 38 Hainback 62 Bosnia Herzegovina Population Arpatdteto 135 Croatia Population Jasenovaca 8
16. ca Anie 40 11 Fagus sylvatica Anloo 81 56 Fagus sylvatica Apata 376 41 Fagus sylvatica Aralar 57 13 Fagus sylvatica Arbailles 384 12 Fagus sylvatica Arguenos 38 7 Fagus sylvatica BEREEREEREEEEREEEE BEE Aspin 288 9 Fagus sylvatica The display of genetic diversity measures is realised for a given species a given marker and a given diversity indice Available diversity indices in GD are Ho Observed heterozygosity He Expect heterozygosity P Polymorphism rate A Allelic diversity Fis Fit Inbreeding coefficients Thus select the category the genus the species check one option for the diversity indices gt Diversity indices for all markers in dataset for indices calculated on a set of markers Diversity indices for one marker in dataset for indices calculated for one marker Plot Diversity indices as Trees Genus Cedrus Cupressus Cyclobalanopsis Fagus Fraxinus Juniperus Lithocarpus Picea Pinus uercus UPUP gt P I P JSJSNJZRITRRRRMR MIMI PTPSAJS Species petraea phellos prinus pubescens pyrenaica rehderiana resinosa robur rubra E rugosa Diversity indices for All markers in dataset One marker in dataset Select species Depending the checked option it s possible to choose a type of marker first option Diversity indices for All markers in dataset One marker in d
17. e hic tect eal iosse telesales dante oed eevee losses taceo t OA et t fosse eo E etd Cere ure 51 Adda nem POC C oes rasa ia dada AR e ei IM MEI a EM URINE Da a 51 Od AT WE ALAS O rca da aan DD OD dO N edn ates 53 Add or delete riehts Ol ACCESS On dabas enu do Ent dE D DU EM M enue 53 ZACIG O ES a a nor a biben rarer Er boram Lom e ne ML Eme Ed aa a Tc Tee nar at 55 Delete TAS essi send TP 55 I Objectives This database contains genetic and georeferenced passport data of different genetic units that are traditionally analyzed by geneticists and ecologists Genetic data include marker data Microsatellites Single nucletotide polymorphisms PCR DNA fragments etc coming either from diploid or haploid tissue for wich genetic parameters have been calculated allelic or nucleotide frequencies diversity statistics Passport data include all other data than genetic ranging from geographic coordinates to ecological or physiographic data of the location of the genetic units Genetic units are either single individuals or populations on which the genetic and passport data are recorded Specific objectives of the applications are 1 Insert genetic and georeferenced data of natural populations 2 View geographic distribution of data 3 Export data to different format CSV GIS format population genetic software format for data analysis II Organisation and technical informations Technical informations GD is impleme
18. ercus petraea France Alberto 2010 12 295 Quercus petraea robur UK Lowe 2005 20 39 Quercus sp Europe Petit 2002 536 2454 Quercus petraea robur UK Cottrell 2004 44 216 Quercus sp CentralBalkans Slade 2008 19 75 Quercus petraea robur Poland Dering 2008 10 238 Quercus petraea robur Ireland Kelleher 2004 20 105 Quercus petraea robur Romania Curtu 2010 34 170 unlinked datasets Select dataset s m RFLP FEM1562002526 RFLP 32 334 select marker Then just select the desired alleles or haplotypes for the display Click on each allele number or click on Select all alleles button to select and display on map Change color by clicking on the colored square remove selected choice by clicking the number of the allele You can also display all populations including those not containing selected alleles Alleles data from individual data Select all alleles Click on each allele number or click on Select all alleles button to select and display on map Change color by clicking on the colored square remove selected choice by clicking the number of the allele Display all populations including those not containing selected alleles On the map frequencies are represented by pie charts The list of the populations is available as usual with the possibility to download the pie chart for each population Click on population name in the list to visualize it on the map see below RESULTS
19. ew Dataset button A simple form allows to create a new dataset and to view existing datasets by project in the database DATASET ADMINISTRATION Create a new dataset Dataset name Project Evoltree Description Create Existing datasets by project Evoltree Dataset name Description Isozyme studies CpDNA Fagus RFLP microsat Haplotypes CpDNA Fraxinus microsat haplotypes Pinus cembra genetic diversity Swiss Alps cpDNA provenance gene struct Oak Ireland Creation date 2009 07 29 12 02 17 UTC 2009 08 07 11 41 12 UTC 2009 09 10 12 05 13 UTC 2009 09 11 08 15 20 UTC 2010 04 29 07 49 00 UTC Updated 2009 07 29 12 02 17 UTC 2009 08 07 11 41 12 UTC 2009 09 10 12 05 13 UTC 2009 09 11 08 15 20 UTC 2010 04 29 07 49 00 UTC NB all tied datasets that involves all included data to the Evoltree project will be visible from the eLab Search Wizard of the official portal of the Network of Excellence Evoltree http www evoltree eu 3 Add or delete rights of access on data When a user import his data in the database only his laboratory can access to these data If he want to share his data with another partner he can grant some rights to another laboratory To access to this function Administration gt Add or delete rights of access on Data Add Modify Rights Add rights If you want to share data with another partner or laboratory
20. is modification takes effect immediately Logout and then login with your new password CHANGE PASSWORD Account informations Last name Ballian First name Dalibor E mail balliand bih net ba Account type scientist Login DBallian Laboratory Faculty of Forestry IUS Change your password 3 New password Confirm new password IV Acknowledgements For remarks or any suggestions thanks to get in touch with Audrey Jacques Gustave audrey O pierroton inra fr or Frederic Raspail Frederic Raspail pierroton inra fr
21. lable samples in the GD database can be displayed on a map Advanced search This function allows to search for a particular population in GD using different criteria Genetic data on a map Plot Allelic Haplotypic frequencies This part allows to display the allelic and the haplotypic frequencies on a map for a given species and a given marker Plot Genotypic frequencies This part allows to display the genotypic frequencies on a map using several criteria category genus species datasets markers Plot Genetic diversity measures This part allows to display the genetic diversity measures on a map using several criteria category genus species datasets markers II Functionalities 1 Viewer Main function of GD the Viewer permits to display different informations on a geographical map This function is accessible from the menu or by clicking on Population on map button or on Genetic data on map button in the home page 1 Populations and sample on a map a See all populations All available populations can be displayed on a map by clicking on See all populations button Under the map a list of these populations sorted by country is displayed with their main characteristics By clicking on population s name in the list you will focus on this population on the map Population Sample Viewer See all populations
22. lat latitude alt altitude country laboratory Evoltree code origin stand Population or sample name Facultative columns stand name forest name region collect date collector name collect method source stand long stand lat remarks Respect the title of the columns case and spelling Latitudes and longitudes are in decimal degrees Try to have as much as possible different names for your populations 2 Import individuals By clicking on Add individuals we access to a simple form just select the csv file and click on insert to upload individuals IMPORT INDIVIDUALS Select your CSV file Parcourir Insert Individuals are inserted in the database AFTER their population The csv file format is described below It is important that the population name in this file are the same that in the previous file in other words check that the file for populations and the file for individuals contains the same population names File format informations First line precise population or sample File format csv delimiter is pido Mandatory columns name population or sample m Species 3 Import markers Facultative columns m lat latitude long longitude By clicking on Add markers we access to a simple form just select the csv file and click on insert to upload markers Marker s types available in GD
23. nt chloroplastic Select compartment Marker type EST SSR RFLP Select marker type the result is displayed in a list and for each line a link View data allows to localize all populations having data for the marker MARKERS Your selection Compartment chloroplastic Marker type gSSR Species with Marker Measure Mark Co rtment t latio arker name t mpa popu n Fraxinus excelsior Molecular View Fraxinus Ecology 2004 13 3437 3452 data angustifolia CCPM2 3 4 6 7 10 chloroplastic haplotypic Pinus pinaster CPM1520 chloroplastic allelic CPM2610 chloroplastic allelic CPM3025 chloroplastic allelic Pinus Pinaster Pinus pinaster CPM3655 chloroplastic allelic CPM6375 chloroplastic allelic TOC MENT Picea abies CPM7195 chloroplastic allelic Pinus pinaster CPM8730 chloroplastic allelic Pinus pinaster 2 Exportation Exportation is actually available for individual data on allelic and or haplotypic frequencies Exportation is accessible from the Viewer when the geographical map is displayed with the frequencies distribution Export data button is located under the continue button Populations in Dataset s Population name Species Download the graphic Dragov lug Quercus robur Load Dubica Quercus robur Load Krizancija Quercus robur Load Okucani Quercus robur Load Samobor Quercus robur Load Vogosca robur Quercus robur Load Export data
24. nted in Ruby On Rails 2 and is optimized for Mozilla Firefox Database is managed by PostgreSQL version 8 4 and PostGIS Maps are provided by Google MapsTM 2 Organisation 1 Login page a eg cs DATABASE m Home page Viewer Import data Administration My files T BHO LS avril mercredi 11 2012 WELCOME TO GD DATABASE Please authenticate you default login evoltree password EvolElab Username jevoltree Password required fields Log in J Authentication is necessary to access to GD Login and password are provided by the administrator and are defined as follow first letter of the first name in upper case followed by the name with the first letter in upper case too an example for Mr John Doe it s JDoe 2 Home page and main parts of GD The home page allows access to the two main parts of the software The menu on the top provides access to viewer importation functionalities data administration and to saved files Import data Administration MAU XU RU ovni mercredi 11 2012 Logged as Evoltree evoltree WELCOME TO GD DATABASE The GD database Georeferenced Database of Genetic Diversity contains genetic and georeferenced passport data of different genetic units populations single trees that are traditionally analyzed in genetic surveys conducted in natural populations The main objective is to view data either allelic haplotypic frequencies or
25. on map This function allows to display the allelic frequencies the haplotypic frequencies the genotypic frequencies or the different diversity indices on a geographical map a Plot Allelic Haplotypic frequencies The display of allelic or haplotypic frequencies is realised for a given species and a given marker So must be selected acategory one or more genus one or more species Allelic Haplotypic frequencies Category Trees Quercus 3408 20696 Fagus 1055 1833 Pinus 564 11718 Picea 130 3165 Fraxinus 279 4564 Cupressus 145 0 Cedrus 61 0 Abies 134 534 Juniperus 38 0 Nothofagus 12 60 Select genus Numbers between brackets indicates respectfully numbers of the populations and individuals currently stored in the database Species macranthera 2 5 mongolica 33 501 petraea 806 3958 pubescens 343 1463 pyrenaica 44 163 robur 1388 6551 rubra 124 585 semiserrata 10 390 serrata 22 58 sp 385 2050 From this selection then must be selected one or more dataset datasets are organized into two sections corresponding to the different compartment chloroplastic and nuclear Datasets in these two sections can be linked or unlinked two datasets are linked when the study uses the same names and descriptions of markers the marker Select dataset s chloropla stic linked datasets Quercus petraea robur NorthEastFrance GuichouxONF 2 Qu
26. pic frequencies Category Genus engleriana longipetiolata moesiaea orientalis orientalis From this selection then must be selected one dataset a marker Then just select the desired genotype s for the display Dataset Isozyme hetero AllRich European Beech Marker ACP Isozyme Genotype s On the map frequencies are represented by pie charts The list of the populations is available as usual with the possibility to download the pie chart for each population Click on population name in the list to visualize it on the map see below RESULTS FOR GENOTYPIC FREQUENCIES Marker name ACP Fullscreen United rd Kingdom Ireland as da benapyce o Ay Eire Belarus Yepaina Ukraine a Moldova qd V j r 2 Georgia a TM 2 A x c Ti FETE New 7 Portugal Espana y Spain LET ow s Google c Dataset documentation Isozyme hetero AllRich European Beec c Plot genetic diversity measures Populations in Dataset s Population name Species Abetone 1 210 34 Fagus sylvatica Abetone 2 211 34 Fagus sylvatica Abetone 3 212 34 Fagus sylvatica Abruzzes 205 32 Fagus sylvatica Achenkirch 335 53 Fagus sylvatica Aigoual 31 16 Fagus sylvatica Akulla 272 29 Fagus sylvatica Alba lula 301 40 Fagus sylvatica Alberes 61 5 Fagus sylvatica Fagus sylvatica Altengsbach 248 49 Fagus sylvatica Altube 60 13 Fagus sylvatica Amorbach 324 55 Fagus sylvati
27. roject and a dataset to insert the data Import genotyping data Project Evoltree Select a dataset Isozyme studies Select a csv file Parcourir Insertdata NB The data inserted in a dataset belonging to the project Evoltree will be visible from the eLab Wizard Evoltree portal The csv file format 1s described below File format informations File format csv delimiter is LL Sample species egend colormaeri markeri FDMonTravalljobur 58 pse FOMonTmvai obu q pe FDMonTravail obur 158 64 2 columns one for each allele Haplotypic data population individual population species legend color RFLP FEM122 fc 1 Ficuzza pyrenaica green haplo22 You can specify a color fc 2 Ficuzza pyrenaica green haplo22 for haplotypic data For the haplotypes it s possible to define the color that will be used for the pie charts for the display of haplotypic frequencies in the column legend color b Diversity data It involves data collected on the population level comprise frequencies and diversity statistics diversity indices allelic and haplotypic frequencies e Insert Allelic Genotypic frequencies To access to it Add Genetic Data gt Insert Diversity data gt Insert Allelic Genotypic Frequencies Then select a project and a dataset Import allelic genotypic frequencies Project Evoltree Select a dataset FairOak CpDNA RF
28. rt data for one population Import diversity measures for one population in GD database Insert data for many populations Import diversity measures for many populations in GD database Insert data for one population This menu allows to import diversity measures for one population in GD database Click on your project choose a dataset a population a marker and seize values for indices He Ho P A Fis Fit IMPORT DATA FOR ONE POPULATION New diversity measures Project Evoltree Dataset FairOak CpDNA RFLP haplotypes Population El Anasser Marker AAP Insert data for many populations This menu allows to import diversity measures for many populations in GD database Click on your project choose a dataset and select your csv file containing data IMPORT DATA FOR MANY POPULATIONS New diversity measures Project Evoltree Select a dataset FairOak_CpDNA_RFLP_haplotypes O Daremnrir Select a csv file Parcourir Available indices in GD are the following Ho observed heterozygosity He expected heterozygosity P polymorphism rate A allelic diversity Ft Fis inbreeding coefficients Ne efficiency number of alleles The csv file format is explained below File format informations One marker First line precise remarks File format csv delimiter is RN Columns with diversity index name for title Set of markers
Download Pdf Manuals
Related Search