This repository contains the code, some datasets and results for the manuscript "Ancient divergence of Indian and Tibetan wolves revealed by recombination-aware phylogenomics" in Molecular Ecology.
The Aligning_and_Filtering folder contains scripts for the following categories: Trimming, alignment, calling SNPs using freebayes, additional filtering steps, and attaching the Y chromosome onto the Dog reference genome.
The Genomewide_Summary_Analysis folder contains scripts and results for running Admixture, Principle Component Analysis, and inferring the pairwise Fst.
The GeneFlow_Analyses folder contains the scripts and results for the D statistic, F3 statistic analyses, and qpGraph.
The Phylogenomics folder contains the scripts and results for inferring the autosomal, mitogenome, and X chromosome phylogeny.
The TopologyweightAnalysis folder contains the scripts and results for inferring Topology weights using Twisst and inferring the distributions of topology weights.
The Recombination_Analysis folder contains scripts and results for inferring the recombination rates based from the domestic dog genome and inferring the autosomal and X chromosome phylogeny from low recombination regions.
The newly sequenced whole genome reads of 1 Asian golden jackal, 4 Indian wolves, and 2 Tibetan wolves used in this paper are available at the NCBI Sequence Read Archive (SRA) under the BioProject PRJNA736617 with Genbank Accession Nos SRR14777842- SRR14777848. The mitogenomes of 13 newly sequenced canids are available on NCBI under accession numbers MZ433367-MZ433379.
