This repository contains Python and R code for the ancestry analyses of the ancient nuclear DNA from the paper The evolutionary history of dogs in the Americas.

If you reuse any of this code then please cite the paper:

Leathlobhair, M.N., Perri, A.R., Irving-Pease, E.K., Witt, K.E., Linderholm, A., Haile, J., Lebrasseur, O., Ameen, C., Blick, J., Boyko, A.R., Brace, S., Cortes, Y.N., Crockford, S.J., Devault, A., Dimopoulos, E.A., Eldridge, M., Enk, J., Gopalakrishnan, S., Gori, K., Grimes, V., Guiry, E., Hansen, A.J., Hulme-Beaman, A., Johnson, J., Kitchen, A., Kasparov, A.K., Kwon, Y.-M., Nikolskiy, P.A., Lope, C.P., Manin, A., Martin, T., Meyer, M., Myers, K.N., Omura, M., Rouillard, J.-M., Pavlova, E.Y., Sciulli, P., Sinding, M.-H.S., Strakova, A., Ivanova, V.V., Widga, C., Willerslev, E., Pitulko, V.V., Barnes, I., Gilbert, M.T.P., Dobney, K.M., Malhi, R.S., Murchison, E.P., Larson, G., Frantz, L.A.F., 2018. The evolutionary history of dogs in the Americas. Science 361, 81–85. https://doi.org/10.1126/science.aao4776

To reproduce the analyses from the paper you will need to install the following dependencies.

Python ≥ 2.7 with the following modules:

• dendropy
• graphviz
• luigi
• matplotlib
• numpy
• pathos
• psutil
• pyparsing
• scipy

pip install dendropy graphviz luigi matplotlib numpy pathos psutil pyparsing scipy 

The full list of Python modules installed in the project environment can be found in the requirements file.

R ≥ 3.4 with the following modules:

• ape
• combinat
• doParallel
• foreach
• ggplot2
• gridExtra
• RColorBrewer
• reshape2
• scales
• stringr

install.packages(c("ape", "combinat", "doParallel", "foreach", "ggplot2", "gridExtra", "RColorBrewer", "reshape2", 
                   "scales", "stringr"))

• AdmixTools
• ADMIXTURE
• graph_tool
• Plink
• TreeMix

The pipeline is broken into three luigi wrapper tasks.

• run qpDstat
• run qpF4ratio
• run qp3Pop

luigi --module pipeline_ctvt CTVTStatsPipeline

• fit qpGraph models

luigi --module pipeline_ctvt CTVTqpGraphPipeline

• run SmartPCA
• plot NJ trees
• run Treemix

luigi --module pipeline_ctvt CTVTFiguresPipeline

Evan K. Irving-Pease, PalaeoBARN, University of Oxford

This project is licensed under the MIT License - see the LICENSE.md file for details