GEODIS 2 0 DOCUMENTATION 1999 2000 David Posada and Alan Templeton Contact David Posada Department of Zoology 574 WIDB Provo UT 84602 5255 USA Fax 801 378 7423 e mail dp47 email byu edu 1 INTRODUCTION GeoDis is program written in C and Java two different programs that implement the same calculations implementing the nested cladistic analysis developed by Templeton et al 1987 Its input consists in the description of a nested cladogram Templeton Sing 1993 estimated from RFLPs or DNA sequences The theory and applications are described elsewhere see recommended reading The first step is the estimation of a cladogram and the defining of a nested structure The cladogram estimation is described in Templeton et al 1992 and the nesting rules are described elsewhere and extended in Crandall 1996 We are currently working in the development of software for the cladogram estimation Meanwhile you can find some tools to help you building the cladogram at http bioag byu edu zoology crandall lab programs htm Outgroup probabilities Castelloe Templeton 1994 can also be included in the analysis Here is a typical nested cladogram 1 This cladogram consists of 21 individuals corresponding to 15 haplotype The nested cladogram is described below in the input file for GeoDis 2 INPUT FILE The first line on the file is the name of the data set being analyzed After that the population information is indicated 2 1 Populations The description of the populations can be specified by their coordinates and sample size However in the case of riparian or coastal species distances are not adequately measured simply through geographical coordinates and a matrix of pairwise distances among the different locations better describes the geographical distribution in these one dimensional habitats 2 1 1 Coordinates 2 dimensions 2 1 1 1 Degrees minutes and seconds Latitude and longitude can be specified with the standard notation degrees minutes and seconds followed by the letter N North or S South in the case of latitude and E East or W West in the case of longitude For example 23 45 00 N 34 56 78 E 2 1 1 2 Decimal degrees Latitude and longitude can be also be specified as decimal degrees In this case latitude is expressed as 0 90 degrees North and South while longitude is expressed as 0 180 degrees East and West For each population the format is Line 1 the population number and name is specified for example 1 Green Mountain Line 2 the sample size the latitude and longitude are indicated for example 7 60 22 01 N 15 20 34 E or 7 60 35 15 41 2 1 2 User defined population pairwise distances 1 dimension This information is specified as a lower triangle matrix without a diagonal the diagonal would be made by zeroes The number of populations i e the dimensions of the matrix is specified above the matrix The population number name and size are specified at each line The distance can be specified in any unit A matrix for 5 populations would look like 5 1 2 3 4 5 Pop 1 name Pop 2 name Pop 3 name Pop 4 name Pop 4 name Pop 1 size Pop 2 size Pop 3 size Pop 4 size Pop 5 size distance 2 1 distance 3 1 distance 4 1 distance 5 1 distance 3 2 distance 4 2 distance 5 2 2 distance 4 3 distance 5 3 distance 5 4 2 2 Clades The next step in the input file is the description of the nested cladogram Clades without geographical or genetic variation e g 1 8 are not included in the analysis Clades at one level are subclades at the next one e g clade 1 5 is a subclade in the nested clade 2 1 0 step clades are haplotypes The information is specified using the nesting clade as the unit For each nesting clade the composition of the clades nested within is described The clades nested within a nesting clade are denominated simply clades Hence the specification of cladogram starts at the 1 step level For each nesting clade it follows this format Line 1 name of the nesting clade for example Clade 1 1 Line 2 number of clades nested within this nesting clade Line 3 name of the clades nested within this nesting clade At the nested 1 step level the clades nested within are haplotypes We can give a name to these haplotypes for example I II III At higher nested levels 2 step 3 step 4 step Total Cladogram the name of these clades would we something like Clade 1 2 Clade 2 3 Line 4 for each clade its topological situation tip 1 interior 0 is specified Line 5 number of populations represented in the nesting clade Line 6 the populations are specified by their numbers Line 7 In this line starts the observation matrix The number of rows in this matrix corresponds to the number of clades specified in line 2 while the number of columns corresponds to the number of locations specified in line 5 For each row and starting with the first clade following the order specified in line 3 the number of individuals or copies of the clade is specified for each population Line 6 number in line 2 last line of the observation matrix This structure is repeated for each nesting clade After the last nesting clade the total cladogram in the next line the word END indicates the end of the input file 2 2 1 Outgroup weights Outgroup probabilities for each clade can be included in the analysis see Castelloe and Templeton 1994 If so they have to be specified for all the clades The outgroup weights are specified for each clade as an extra line after line 4 Line 4 For each clade the corresponding outgroup probability is specified 3 3 RUNNING GeoDis To run GeoDis the input file needs to be specified If an output file is not specified the results are echoed to the screen If the C version is used the program prompts the user for all the needed information For the Java version the appropriate checkboxes need to be specified Number of permutations A minimum number of 1000 permutations is recommend for a 5 level of statistical significance 4 GeoDis OUPUT The output of GeoDis saved to a file with the same name as the input file plus the extension out The value of the different statistics calculated is indicated for each nesting clade and its nested clades at each level Two probabilities are indicated those corresponding to significantly small P and large values P of the test statistic It is highly encouraged to use the reference key in Templeton et al 1995 for a consistent interpretation of the output 4 5 INPUT FILE EXAMPLES 1 With DMS coordinates and without outgroup weigths Hallucigenia mtDNA Name of the data set 3 Number of populations 1 Green Mountain Population number and name 7 15 41 12 N 60 21 12
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