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repository for Miller and Lavertsky ddRAD of Melanerpes
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SNP_datasets
iq_ml_analysis
LICENSE.txt
Melanerpes_samples.csv
PCA.RESULTS.png
README.md
Structure_Figure.pdf
lookup.pl
structure.sh
structure_harvest_allmelanerpes.tar.gz

README.md

melanerpes_ddrad

Repository (data and associated code) for:

Miller and Lavretsky (in prep) Speciation without gene flow: rapid development of post-zygotic isolation in a New World woodpecker clade

File 1: melanerpes_ddrad_autosome_allsnps.nex

This file is all SNPs from the autosome dataset for all 105 samples sequenced. This includes outgroup species (which increases the number of SNPs). We score heterozygous sites with the IUAPAC ambiguity code for the consensus basecall (i.e. G/C -> Y).

This file is used to generate the SplitsTree network and the IQ-TREE maximum likelihood tree.

File 2: Melanerpes_samples.csv

This file lists the all 105 museum samples, with museum voucher number, sex, collecting locality for all 105 samples included in the study.

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