AUTHOR=Barbato Mario , Orozco-terWengel Pablo , Tapio Miika , Bruford Michael W. 

TITLE=SNeP: a tool to estimate trends in recent effective population size trajectories using genome-wide SNP data

JOURNAL=Frontiers in Genetics

VOLUME=6

YEAR=2015

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2015.00109

DOI=10.3389/fgene.2015.00109

ISSN=1664-8021

ABSTRACT=<p>Effective population size (<italic>N<sub>e</sub></italic>) is a key population genetic parameter that describes the amount of genetic drift in a population. Estimating <italic>N<sub>e</sub></italic> has been subject to much research over the last 80 years. Methods to estimate <italic>N<sub>e</sub></italic> from linkage disequilibrium (LD) were developed ~40 years ago but depend on the availability of large amounts of genetic marker data that only the most recent advances in DNA technology have made available. Here we introduce <italic>SNeP</italic>, a multithreaded tool to perform the estimate of <italic>N<sub>e</sub></italic> using LD using the standard PLINK input file format (.ped and.map files) or by using LD values calculated using other software. Through <italic>SNeP</italic> the user can apply several corrections to take account of sample size, mutation, phasing, and recombination rate. Each variable involved in the computation such as the binning parameters or the chromosomes to include in the analysis can be modified. When applied to published datasets, <italic>SNeP</italic> produced results closely comparable with those obtained in the original studies. The use of <italic>SNeP</italic> to estimate <italic>N<sub>e</sub></italic> trends can improve understanding of population demography in the recent past, provided a sufficient number of SNPs and their physical position in the genome are available. Binaries for the most common operating systems are available at <ext-link ext-link-type="uri" xlink:href="https://sourceforge.net/projects/snepnetrends/" xmlns:xlink="http://www.w3.org/1999/xlink">https://sourceforge.net/projects/snepnetrends/</ext-link>.</p>