These files describe the exact data used in the paper "Sequence differences at
orthologous microsatellites inflate estimates of human-chimpanzee differentiation" 
by M Kwong & TJ Pemberton (BMC Genomics 15:990 [2014]). These data are a calibrated
subset of the combined human-chimpanzee dataset reported in the paper "Population
Structure in a Comprehensive Genomic Data Set on Human Microsatellite Variation" by
TJ Pemberton, M DeGiorgio, NA Rosenberg (G3:Genes|Genomes|Genetics 3:903-919 [2013]),
restricted to only the 138 microsatellites with the same STR structure in both humans
and chimpanzees, and with PCR fragment length genotypes converted to repeat numbers
as described in the article.

*Version 1.0 of the package of files - created by TJP, May 30, 2014

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1. kwongEtAl2014.MS5879.numRpts.stru

This file includes the exact microsatellite data used by Kwong & Pemberton (2014) in
their human-chimpanzee and population-genetic analyses. The format is that used by
the STRUCTURE program. The first line gives the list of microsatellites. After the
first line, each individual is listed on two consecutive lines. The first five columns
include the following information:

(1) Individual code number as reported in Pemberton et al. (2013).
(2) Population code number as reported in Pemberton et al. (2013).
(3) Population name.
(4) Location.
(5) Pre-defined geographic region affiliation as reported in Pemberton et al. (2013).

The next columns contain genotypes (measured in numbers of repeats). The left-to-right
order of the genotypes corresponds to the left-to-right order of the microsatellite
names on the first line of the file. The placement of genotypes on the first versus
second line for an individual is arbitrary. Missing data is denoted by "-9".

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2. kwongEtAl2014.MS5879.numRpts.loci

This file contains information on the 138 microsatellite markers included in the
calibrated human-chimpanzee dataset in file #1.

The first five columns include the following information:

(1) Marshfield screening set
(2) Microsatellite name (as given in row 1 of file #1)
(3) Size of repeat unit.
(4) Chimpanzee chromosome.
(5) Chimpanzee physical map position (bp; UCSC release panTro4)
(6) Human chromosome.
(7) Human physical map position (bp; NCBI Build 36)

Human physical map positions were taken from "Sequence determinants of human 
microsatellite variability" by TJ Pemberton, CI Sandefur, M Jakobsson, NA Rosenberg
(BMC Genomics 10:612 [2009]).

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3. kwongEtAl2014.subsets.txt

This file includes the source data set and subset membership information for 
the individuals included in file #1 as reported in "Population Structure in a
Comprehensive Genomic Data Set on Human Microsatellite Variation" by TJ Pemberton,
M DeGiorgio, NA Rosenberg (G3:Genes|Genomes|Genetics 3:903-919 [2013]). The first
five columns are as described in #1 above. In the next columns "1" indicates the
inclusion of an individual in that set and "0" indicates exclusion.

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4. kwongEtAl2014.codes.txt

This file contains code numbers that have been used to represent populations in files
associated with the Kwong et al. (2014) paper. The columns include the following
information:

(1) Population code number as reported in Pemberton et al. (2013).
(2) Population name as reported in Pemberton et al. (2013).
(3) Location.
(4) Pre-defined geographic region affiliation as reported in Pemberton et al. (2013).
(5) Species [Human or Chimpanzee].

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