empirical data(psmcfa files)

The zip file contains the input files for PSMC from the empirical data of threespine sticklebacks in the study. Seventeen of them are from RAD data, and one of them is from whole genome sequencing data

Plot PSMC results

The file contains functions written in R. The functions are used to visualize the results from PSMC

Generating PSMC input files from empirical RAD data

The files contains a script written in R. The script creates input files for PSMC from empirical RAD data using tag files and allele files. Tag files and allele files are generated through pstacks in Stacks v1.13

Generating PSMC input files from simulated data

The file contains a function written in R. This function randomly samples RAD loci from chromosomes simulated by ms (Hudson 2002), and transforms the RAD data into a ".psmcfa" file for PSMC analysis

mtDNA_alignments

The zip file contains the three mtDNA alignments used in this study. "mitogenomes.fas" is the alignment of the mitogenomes of the 81 individuals included in this study together with an outgroup. Control Region was removed from the alignment. Based on it, two other alignments, "alignment_with_1994-cytb.fas" and "alignment_with_2008-cytb.fas", were created by incorporating the data from Orti et al. (1994) and Makinen & Merila (2008), respectively

SNPs_subset

A VCF file containing a random subset (1%) of all SNPs discovered in this study. This file was used for conducting PCA and calculating nucleotide diversity

Hansen et al 2010 MEC.xlsx

Brown trout microsatellite data (61 loci). The data set consists of samples from three wild brown trout populations in Western Jutland, Denmark, along with samples from two hatchery strains used for stocking. The samples of wild trout populations consist of contemporary samples (2000-2006). Moreover, two of the populations are also represented by historical samples from 1943-1956. See Hansen et al. (2010) for further details. The data file is in MSA format [Dieringer D, Schlotterer C (2003) Microsatellite Analyser (msa): a platform independent analysis tool for large microsatellite data sets. Molecular Ecology Notes, 3, 167–169]

Brown trout microsatellite data

The file contains microsatellite data (21 loci) from six wild brown trout populations in Western Jutland, Denmark, along with samples from two hatchery strains used for stocking the rivers. The samples from the wild populations consist of contemporary samples (2000-2006) and historical pre-stocking samples (1927-1956), the latter obtained by analyzing DNA from archived scale samples. See Hansen et al. (2009) for further details on the data and study. The file format is MSA [Dieringer D, Schlotterer C (2003) Microsatellite Analyser (msa): a platform independent analysis tool for large microsatellite data sets. Molecular Ecology Notes, 3, 167–169]

752309 – Supplemental material for Examining Spillover Effects From Teach For America Corps Members in Miami-Dade County Public Schools

<p>Supplemental material, 752309 for Examining Spillover Effects From Teach For America Corps Members in Miami-Dade County Public Schools by Ben Backes, Michael Hansen, Zeyu Xu, and Victoria Brady in Journal of Teacher Education</p

Additional file 5: of Genetic and phenotypic variation along an ecological gradient in lake trout Salvelinus namaycush

First and second principal coordinate (PC) scores (PC1 and PC2) of an individual-based PC analysis on ecotype genotype. Populations were grouped by approximate confidence ellipses for each ecotype (lean = black circles; humper = light grey circles; siscowet = dark grey circles; redfin = red circles). (DOCX 67 kb