Todiramphus RADseq project

This repository contains a comprehensive compilation of code and expalanatory visualizations associated with the paper "Mitonuclear discordance results from incomplete lineage sorting, with no detectable evidence for gene flow, in a rapid radiation of Todiramphus kingfishers"

Reproduce analyses from this paper

• If you would like to reproduce any analyses from this paper start in the 'data' subdirectory (https://github.com/DevonDeRaad/todiramphus.radseq/tree/main/data) which will instruct you on exactly how to find the input dataset you're looking for. If you have further questions, I would be happy to hear from you at devonderaad[at]gmail.com.

Reference genome quality assessment

• Quality info for our de novo assembled reference genome including BUSCO completeness assessment is available in the subdirectory called 'reference.genome.evaluation'. A detailed report on overall contiguity from QUAST can be viewed here:

  https://devonderaad.github.io/todiramphus.radseq/reference.genome.evaluation/quast_results/results_2023_03_14_08_46_42/report.html

Distribution and sampling mapping

• The process of generating maps of the sampling and general distribution for each species can be viewed here:

  https://devonderaad.github.io/todiramphus.radseq/todi.mapping.html

Data generation

• Protocols used for DNA extraction from fresh tissue samples, and RAD library prep can be found here:

  https://github.com/DevonDeRaad/todiramphus.radseq/tree/main/lab.protocols

Sequence data to SNPs

• Code used to map raw sequence data to the reference genome and call SNPs using the Stacks pipeline can be found here:

  https://github.com/DevonDeRaad/todiramphus.radseq/tree/main/run.stacks.sh

Quality filtering raw, unfiltered SNPs

• The entire SNP filtering process, facilitated by the R packages vcfR and SNPfiltR is available to view here:

  https://devonderaad.github.io/todiramphus.radseq/todi.filt.html

Population genetic analyses

• The three descriptive pop-gen analyses performed to determine individual sample relatedness using SplitsTree, sample clustering using popVAE, and genetic diversity using Stacks 'populations' module are available for viewing here:

  https://devonderaad.github.io/todiramphus.radseq/todi.popgen.html

ADMIXTURE runs

• Information detailing our use of the program ADMIXTURE on this dataset can be found here:

  https://github.com/DevonDeRaad/todiramphus.radseq/tree/main/admixture

Pairwise divergence matrices

• All steps involved in creating pairwise divergence matrices for both mtDNA and nDNA data are available for viewing here:

  https://devonderaad.github.io/todiramphus.radseq/make.pairwise.heatmaps.html

Species tree reconstruction

• All input files and code necessary to reconstruct the mtDNA and nDNA species trees generated with IQtree2 and ASTRAL-III respectively, are available here:

  https://github.com/DevonDeRaad/todiramphus.radseq/tree/main/species.trees

• In specific, a detailed workflow showing the step-by-step process of generating gene tree alignments from filtered SNP data, generating a species tree using ASTRAL-III, and calculating gene and site condordance factors on this species tree is available here.

Compare site and gene concordance factors

• Visualize pairwise comparisons of mtDNA and nDNA site and gene concordance factors on mtDNA and nDNA species trees:

  https://devonderaad.github.io/todiramphus.radseq/vis.gCFs.sCFs.html

Species tree reconstruction using SNAPP

• The input .xml files and output tree and log files associated with running SNAPP are available here:

  https://github.com/DevonDeRaad/todiramphus.radseq/tree/main/snapp

Species network reconstruction

• The input bi-allelic SNP alignments stored as nexus files and all resulting output files for running PhyloNet are available here:

  https://github.com/DevonDeRaad/todiramphus.radseq/tree/main/phylonet

ABBA/BABA tests for gene flow

• We used Dsuite to perform ABBA/BABA tests for excess allele sharing between non-sister taxa across the phylogeny. The code, input files, and output files resulting from running Dsuite are all available here:

  https://github.com/DevonDeRaad/todiramphus.radseq/tree/main/dsuite

Species tree reconstruction with TreeMix

• All input and output files for running TreeMix are available in the directory 'treemix'. Visualizations and code for running TreeMix can be viewed at:

  https://devonderaad.github.io/todiramphus.radseq/vis.treemix.results.html