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migrate [2011/07/07 11:54] – heidimigrate [2011/07/14 15:02] (current) – heidi
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   * Microsatellite   * Microsatellite
   * Standard (Electrophoretic marker)   * Standard (Electrophoretic marker)
 +
 +
 +
 +
  
  
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 .... ....
 </code> </code>
-  * interleaved data: <code>+  * interleaved data (not anymore supported by MIGRATE): <code>
 <Number of populations> <number of loci> [project title 0-79] <Number of populations> <number of loci> [project title 0-79]
 <number of sites for locus1> <number of sites for locus 2> ... <number of sites for locus1> <number of sites for locus 2> ...
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 </code> </code>
  
 +**SNPs in HapMap format**: 
 +  * assumes that each SNP is biallelic 
 +  * <allele> contains the nucleotide
 +  * <number> contains the number of individuals with the specific allele 
 +  * <total> is the sum of both <code>
 +<Number of populations> <number of loci> [project title 0-79]
 +<Any Number> <title for population 0-79>
 +<Position on chromosome locus1> <TAB><allele><TAB><number><TAB><allele><TAB><number><TAB><total>
 +<Position on chromosome locus2> <TAB><allele><TAB><number><TAB><allele><TAB><number><TAB><total>
 +....
 +<Any Number> <title for population 0-79>
 +<Position on chromosome locus1> <TAB><allele><TAB><number><TAB><allele><TAB><number><TAB><total>
 +<Position on chromosome locus2> <TAB><allele><TAB><number><TAB><allele><TAB><number><TAB><total>
 +....
 +</code>
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +
 +==== Examples ====
 === Enzyme electrophoretic data (infinite allele model) === === Enzyme electrophoretic data (infinite allele model) ===
   * Genotypes   * Genotypes
   * missing data: "?"   * missing data: "?"
-  * can use multi-character coding when you use a delimiter (see the examples for microsatellites) +  * can use multi-character coding when you use a delimiter 
-**example** (2 populations and 11 loci and with 3 or 2 individuals per population: +  * 2 populations and 11 loci and with 3 or 2 individuals per population: <code>
-<code>+
  2 11 Migration rates between two Turkish frog populations  2 11 Migration rates between two Turkish frog populations
 3 Akcapinar (between Marmaris and Adana) 3 Akcapinar (between Marmaris and Adana)
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 PB16844   ee bb bb bb ab aa aa cc bb cc aa PB16844   ee bb bb bb ab aa aa cc bb cc aa
 </code> </code>
 +  * same data but with ''/'' as separator: <code>
 + 2 11 / Migration rates between two Turkish frog populations
 +3 Akcapinar (between Marmaris and Adana)
 +PB1058    e/e b/b a/b b/b b/b a/a a/a b/b ?/? c/c Rs/Rf
 +PB1059    e/e b/b a/b b/b b/b a/a a/a b/b b/b c/c Rs/Rs
 +PB1060    e/e b/b b/? b/b a/b a/a a/a b/b b/b c/c Rs/Rs
 +2 Ezine (between Selcuk and Dardanelles)
 +PB16843   e/e b/b a/b b/b a/a a/a a/a c/c b/b c/c Rf/Rf
 +PB16844   e/e b/b b/b b/b a/b a/a a/a c/c b/b c/c Rf/Rs</code>
 +
  
 === Microsatellite data === === Microsatellite data ===
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   * Genotypes   * Genotypes
   * Each individual has two alleles   * Each individual has two alleles
-  * Alleles are coded as REPEAT NUMBERS 
   * homozygote individual: needs to be coded as e.g.: 6.6 ("." is the delimiter)   * homozygote individual: needs to be coded as e.g.: 6.6 ("." is the delimiter)
   * missing data: "?’"   * missing data: "?’"
-**example:**  +  * Alleles are coded as REPEAT NUMBERS: <code>
-<code>+
  2 3 . Rana lessonae: Seeruecken versus Tal  2 3 . Rana lessonae: Seeruecken versus Tal
-2   Riedtli near G\"undelhart-H\"orhausen+2   Riedtli near Guendelhart-Hoerhausen
 0         42.45 37.31 18.18 0         42.45 37.31 18.18
 0         42.45 37.33 18.16 0         42.45 37.33 18.16
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 1         43.42 35.31 20.18 1         43.42 35.31 20.18
 </code> </code>
 +  * Alleles encoded as FRAGMENT LENGTH:
 +    * extra line with repeat number, starts with ''#M'' <code>
 + 2 3 . Rana lessonae: Seeruecken versus Tal
 +#M 2 2 2
 +2 Riedtli near Guendelhart-Hoerhausen
 +0         25.27 137.131 218.218
 +0         27.27 218.216
 +2 Tal near Steckborn
 +1         23.25 135.? 218.218
 +1         23.23 135.131 220.218
 +</code>    
  
 === Sequence data === === Sequence data ===
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 **examples:** **examples:**
 +  * two populations with a single DNA-locus: <code>
 +2 1 Make believe data set using simulated data (1 locus)
 +50
 +3 Tallahassee (Mars)
 +Peter     ACACCCAACACGGCCCGCGGACAGGGGCTCGAGGGATCACTGACTGGCAC
 +Donald    ACACAAAACACGGCCCGCGGACAGGGGCTCGAGGGGTCACTGAGTGGCAC
 +Christian ATACCCAGCACGGCCGGCGGACAGGGGCTCGAGGGAGCACTGAGTGGAAC
 +3 St. Marks
 +Lucrezia  ACACCCAACACGGCCCGCGGACAGGGGCTCGAGGGATCACTGACTGGCAC
 +Isabel    ACACAAAACACGGCCCGCGGACAGGGGCTCGAGGGGTCACTGAGTGGCAC
 +Yasmine   ATACCCAGCACGGCCGGCGGACAGGGGCTCGAGGGAGCACTGAGTGGAAC
 +</code>
   * not interleaved (2 population with 2 loci): <code>   * not interleaved (2 population with 2 loci): <code>
    2 2 Make believe data set using simulated data (2 loci)    2 2 Make believe data set using simulated data (2 loci)
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 fuefLoc2  TCGACTAGATATGCAGCAAATACGAGGGGCATGCGTCCCAGATGTG fuefLoc2  TCGACTAGATATGCAGCAAATACGAGGGGCATGCGTCCCAGATGTG
 </code> </code>
-  * interleaved (2 populations with 2 loci): <code>+  * interleaved (2 populations with 2 loci) (not anymore supported by MIGRATE): <code>
    2 2 Make believe data set using simulated data (2 loci, interleaved)    2 2 Make believe data set using simulated data (2 loci, interleaved)
 50 46 50 46
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   GAGGGTCATGCGTCCCAGATGTG   GAGGGTCATGCGTCCCAGATGTG
   GAGGGGCATGCGTCCCAGATGTG   GAGGGGCATGCGTCCCAGATGTG
 +</code>
 +
 +=== SNP data ===
 +  * uses the same nucleotide nomenclature as the sequence data
 +  * same format as sequence data
 +  * linked SNP: more than one site on one line
 +  * unlinked SNP: one site per line
 +  * two formats:
 +    * ''N'': nucleotide format <code>
 +N 2 2 Make believe data set using simulated data (2 population and 2 loci)
 +1 4
 +3 3 pop1
 +ind1      A
 +ind2      A
 +ind3      A
 +ind1      ACAC
 +ind2      ACAC
 +ind3      ACGC
 +2 pop2
 +ind4      C
 +ind5      C
 +ind4      TGGA
 +ind5      TCGA
 +</code>
 +    * ''H'': HapMap format <code>
 +# using the HapMap data format, but does produce the same result (yet) as the dataset above
 +H 2 2 Make believe data set using simulated data (2 population and 2 loci)
 +3 pop1
 +1    A 3 C 0 3
 +1000 A 3 T 0 3
 +1010 C 3 G 0 3
 +1011 A 2 G 1 3
 +1015 C 3 A 0 3
 +2 pop2
 +1    A 0 C 2 2
 +1000 A 0 T 2 2
 +1010 C 1 G 1 2
 +1011 A 0 G 2 2
 +1015 C 0 A 2 2
 </code> </code>
  
 ===== How to cite ===== ===== How to cite =====
-Please cite the 1999 and the 2001 papers and one of the others:\\ +Beerli, P. (2009) How to use migrate or why are markov chain monte carlo programs dicult to use? In G. Bertorelle, M. W. Bruford, H. C. Hau e, A. Rizzoli, and C. Vernesi, editors, Population Genetics for Animal Conservation, volume 17 of Conservation Biology, pages 42-79. Cambridge University Press, Cambridge UK, 2009.
-  * Beerli, P. 1997-2004. Migrate: documentation and program, part of LAMARC. Version 2.0. Revised December 23, 2004. Distributed over the Internet, http://evolution.gs.washington.edu/lamarc.html [Downloaded: ...date....] +
-  * Beerli, P., and J. Felsenstein. 2001. PNAS. +
-  * Beerli, P., and J. Felsenstein. 1999. Maximum likelihood estimation of migration rates and population numbers of two populations using a coalescent approach. Genetics 152(2): 763-773. +
-  * Beerli, P. 1998. Estimation of migration rates and population sizes in geographically structured populations. In: Advances in molecular ecology (Ed. G. Carvalho). NATO-ASI workshop series. IOS Press, Amsterdam. Pp. 39-53.+
migrate.1310032445.txt.gz · Last modified: 2011/07/07 11:54 by heidi