6 research outputs found
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
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
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
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)
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 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