Data from: Meta-analysis reveals lower genetic diversity in overfished populations

Pinsky ML, Palumbi SR

Date Published: September 10, 2013

DOI: http://dx.doi.org/10.5061/dryad.jt683

 

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Title Modified BOTTLESIM source code
Downloaded 26 times
Description Source code from BOTTLESIM program, modified slightly to report A50 (allelic richness from 50 individuals), to work for population sizes >1000, and to compile under Mac OS X 10.8.4 with XCode. The code only allows use of the "Diploid singlelocus, constant population size" simulation module. For original source code, see Kuo, C.-H. & Janzen, F.J. (2003). BOTTLESIM: a Bottleneck Simulation Program for Long-Lived Species With Overlapping Generations. Molecular Ecology Notes, 3, 669–673, available from http://chkuo.name/software/BottleSim.html.
Download BottleSimA50.cpp (214.0 Kb)
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Title R code for bottlenecks in stepping-stone populations
Downloaded 18 times
Description Script written for R to simulate a bottleneck in a set of populations connected by stepping-stone migration. Assumes diploid individuals and calculates the number of immigrants from each population as a Poisson random number with mean m*Ne2 (for a total of 2*m*Ne2 alleles). We use Ne2 from the focal population (the one receiving the immigrants). Returns a list with two vectors: 1) meanA (allelic richness for each generation, where the first entry is the pre-bottleneck value); and 2) meanHe (expected heterozygosity for each generation, where the first entry is the pre-bottleneck value).
Download bottle_step 2013-04-14.r (3.998 Kb)
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Title Genetic diversity database
Downloaded 81 times
Description This CSV (comma-separated) file contains microsatellite diversity data from marine fishes that was compiled from published papers, theses, and white papers. See our published paper for the criteria we used to select data. The readme file explains the columns.
Download divloci_2013-07-06.csv (2.914 Mb)
Download README.txt (1.632 Kb)
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When using this data, please cite the original publication:

Pinsky ML, Palumbi SR (2014) Meta-analysis reveals lower genetic diversity in overfished populations. Molecular Ecology 23(1): 29-39. http://dx.doi.org/10.1111/mec.12509

Additionally, please cite the Dryad data package:

Pinsky ML, Palumbi SR (2013) Data from: Meta-analysis reveals lower genetic diversity in overfished populations. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.jt683
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