Readme file for "Cichla_microsatellite_data.txt"
04/2012

Data presented in "Simultaneous delimitation of species and quantification of interspecific hybridization in Amazonian peacock cichlids (genus Cichla) using multi-locus data" by Stuart C. Willis, Jason Macrander, Izeni P. Farias, & Guillermo Orti in revision for BMC Evolutionary Biology (2012)

For questions about the file, contact swillis4@gmail.com.

The aforementioned file contains genotypes of 12 di-nucleotide simple tandem repeat (microsatellite) loci from species in the South American cichlid genus Cichla (Teleostei: Cichlidae). The values given are all fragment lengths, NOT the number of repeats, as several of the loci exhibit imperfect repeat patterns (i.e. a mixture of odd and even allele lengths). The data were collected in 2010 using fluorescently labeled PCR primers and the LIZ500 size standard on an Applied Biosystems (ABI) 3730XL and scored using custom bins and panels with Genemapper (ABI). Other details about these loci can be found in the manuscript referenced above, and "Polymoprhic microsatellite loci for the Amazonian Peacock Basses, Cichla orinocensis and C. temensis, and cross-species amplification in other Cichla species" by Jason Macrander, Stuart Willis, Shane Gibson, Guillermo Orti, and Tomas Hrbek in Molecular Ecology
Resources (2012).

The format of the tab-delimited text file is as follows:
The first row contains column headings.
The second and remaining rows contain data for individuals, two (2) rows per individual. The data are formatted for easy use in the program STRUCTURE, with some modifications required.
The first column identifies each individual to species.
The second column identifies from which locality the individual was collected (see manuscript for exact details).
The third column specifies the individual's unique identifier.
The fourth and remaining columns include the microsatellite genotypes, with the data for each locus in a separate column. As mentioned before, the two allele lengths for an individual are placed sequentially on two rows in each column.

Each microsatellite data cell contains an allele (fragment) length in base pairs, with missing data specified by the value "-9" as recommended by the STRUCTURE documentation.