Orsinietal_SNP_genotyping

SNP genotyping results. Nineteen populations distributed at regional scale in Belgium were used for this analysis. Individual ID and sample location are show

Genotypes Natterjack Toad

The data file contains two spread sheets. The first shows the total dataset, with in the first column the sample codes, in the second the spawn string code when individuals were sampled from the same spawn string, in the third the name of the subpopulation, in the fourth the site number, and in the fith and sixth column the X and Y coordinates, respectively (Lambert-72 coordinates). The next 11 columns represent the different microsatellite markers. Alleles are separated by a forward slash. Missing genotypes are indicated with 'NA'. The second spread sheet contains the dataset without full siblings except one per family, that was used for the landscape genetic analyses

Orsinietal_mtDNA_alignment

fasta file showing the alignment of the partial sequence of the COI mtDNA gene. Individual ID and correspondent NCBI accession number are show

Orsinietal_micros_genotyping

Microsatellite genotyping results. Nineteen populations distributed at regional scale in Belgium were used for this analysis. Individual ID and sample location are show

Appendix B. Output summary of the Colonize randomization procedure using population N1998 as sink, repeated for LN1880, Barin, Mogot, NbNP2, O1Bol, OB23, and the pooled regional samples (excluding the ancient N1880 and N1550 samples).

Output summary of the Colonize randomization procedure using population N1998 as sink, repeated for LN1880, Barin, Mogot, NbNP2, O1Bol, OB23, and the pooled regional samples (excluding the ancient N1880 and N1550 samples)

Supplement 1. Colonize: a tool to estimate the number of individuals colonizing a new habitat.

<h2>File List</h2><blockquote> <h3><i>All files at once</i></h3> <blockquote> <p><a href="colonize_linux.zip">colonize_linux.zip</a> -- all files for Linux at once <br> <a href="colonize_windows.zip">colonize_windows.zip</a> -- all files for Windows at once </p> </blockquote> <h3><i>Source code</i></h3> <blockquote> <p><a href="colonize.cpp">colonize.cpp</a> -- C++ source code </p> </blockquote> <h3><i>Manual</i></h3> <blockquote> <p><a href="colonize_manual.pdf">colonize_manual.pdf</a> -- manual in portable document format </p> </blockquote> <h3><i>Example files</i></h3> <blockquote> <p><a href="example.dat">example.dat</a> -- example file </p> </blockquote> <h3><i>Executables</i></h3> <blockquote> <p><a href="colonize">colonize</a> -- executable for Linux operating systems <br> <a href="colonize.exe">colonize.exe</a> -- executable for Windows operating systems </p> </blockquote> <h3><i>Readme files</i></h3> <blockquote> <p><a href="readme_linux.txt">readme_linux.txt</a> -- installation instructions for Linux <br> <a href="readme_windows.txt">readme_windows.txt</a> -- installation instructions for Windows </p> </blockquote> </blockquote><h2>Description</h2><blockquote> <p>We provide the source code and executables for Windows and Linux operating systems, and a short description of the program.</p> <p>The software program Colonize was developed to estimate the range of colonizers allowed to account for the observed allele frequencies in a sampled focal population given the observed allele frequencies in a sampled source population. This is done by creating random samples based on source and target population samples and given a number of colonists, and comparing the observed differences in allelic composition with the difference between the original samples. In this way probabilities are calculated for the minimum and maximum number of individuals colonizing the focal population. These probabilities can then be combined in a joint probability for each number of colonizers. There are a few assumptions to be met: there is no gametic linkage disequilibrium among the analyzed loci, and there has been no substantial genetic drift in source nor target population between the time of colonization and the moment of sampling. The program is available in a Windows and Linux version from <a href="mailto:[email protected]">[email protected]</a> and from the website <a href="http://bio.kuleuven.be/eco/colonize">http://bio.kuleuven.be/eco/colonize</a>, as well as in the <i>Ecological Archives</i> Supplements.</p> </blockquote

Appendix A. A table showing sample sizes and allele frequencies of the eight studied Kenyan populations of Daphnia barbata at microsatellite loci Dp291, Dp339, and Dma35R.

A table showing sample sizes and allele frequencies of the eight studied Kenyan populations of Daphnia barbata at microsatellite loci Dp291, Dp339, and Dma35R

Dryad Data Vangestel et al

Dryad Data Vangestel et a

Daphnia sinensis microsatellite genotypes

Microsatellite genotypes of Daphnia sinensis (6 loci), from 12 reservoirs and natural water bodies, including missing genotype values. Clonal richness and diversity in the paper were calculated on the basis of complete multilocus genotypes only. Genotypes are coded per locus as two consecutive three digit alleles

SNP sequences and GENALEX file

Sequences of the 250 SNPs (together with their functional annotations) are available in tab 1 of the file. In tab 2, the original GENALEX file on the 183 successfully genotyped SNPs is provided