DOI: 10.5061/dryad.hx3ffbgd7
title: Complex histories of gene flow and a mitochondrial capture event in a non-sister pair of bird

description: Hybridization, introgression, and reciprocal gene flow during speciation,
 specifically the generation of mitonuclear discordance, are increasingly
 observed as parts of the speciation process. Genomic approaches provide
 insight into where, when, and how adaptation operates during and after
 speciation and can measure historical and modern introgression. Whether
 adaptive or neutral in origin, hybridization can cause mitonuclear
 discordance by placing the mitochondrial genome of one species (or
 population) in the nuclear background of another species. The latter,
 introgressed species may eventually have its own mtDNA replaced or
 “captured” by other species across its entire geographical range.
 Intermediate stages in the capture process should be observable. Two
 non-sister species of Australasian monarch-flycatchers, Spectacled Monarch
 (Symposiachrus trivirgatus) mostly of Australia and Indonesia and
 Spot-winged Monarch (S. guttula) of New Guinea, present an opportunity to
 observe this process. We analysed thousands of single nucleotide
 polymorphisms (SNPs) derived from ultraconserved elements of all
 subspecies of both species. Mitochondrial DNA sequences of Australian
 populations of S. trivirgatus form two paraphyletic clades, one being
 sister to and presumably introgressed by S. guttula despite little nuclear
 signal of introgression. Population genetic analyses (e.g., tests for
 modern and historical gene flow and selection) support at least one
 historical gene flow event between S. guttula and Australian S.
 trivirgatus. We also uncovered introgression from Maluku island subspecies
 of S. trivirgatus into an island population of S. guttula, resulting in
 apparent nuclear paraphyly. We find that neutral demographic processes,
 not adaptive introgression, are the most likely cause of these complex
 population histories. We suggest that a Pleistocene extinction of S.
 guttula from mainland Australia resulted from range expansion by S.
 trivirgatus.
description: The data was collected using sequenced of ulraconserved
 element (UCE) target capture, and processed for a variety of population
 genetic and phylogenetic analyses. We also analyzed "bycatch"
 mitogenomes and previously sequenced mitochondrial genes..
description: There is a README file uploaded for the data describing each
 file, pasted below: README by: Ethan
 Gyllenhaal<br> Last updated: 4 February 2021 This
 README describes the scripts and data files used for a project assessing
 multiple aspects of gene flow in the Symposiachrus trivirgatus/guttula
 complex. The data were collected using Illumina sequencing for target
 capture of ultraconserved elements, with three main pipelines used for
 downstream processing. For phylogenetics, we roughly followed phyluce
 (https://phyluce.readthedocs.io/en/latest/). For anything involving a VCF,
 we used a pipeline based on seqcap_pop
 (https://github.com/mgharvey/seqcap_pop). For mitogenome analyses, MJA
 aligned reads to a reference mitogenome in Geneious and manually checked
 for inconsistencies.
 _______________________________<br> ------ PopGen Input
 Files -----<br> -- (sympos_popgen_input.zip) --<br>
 _______________________________ OVERALL NOTE: All of
 these input files are a 100% complete matrix with one random SNP selected
 per locus to avoid issues with LD.
 sympos_*_PCA-input.vcf - Input files for various PCAs run. The
 second "word" represents the subset of individuals used (with
 "triv" and "gutt" short for trivirgatus and guttula
 respectively. Used in sympos_PCA.R.
 sympos_*_sNMF-input.str - Input files for sNMF runs, named like
 PCA inputs (see above). Used in sympos_sNMF.R Note that all of these have
 singletons removed. sympos_ABBABABA_input.tsv.gz -
 Input file for ABBA/BABA. Used in sympos_ABBABABA.R.
 sympos_treemix-input.treemix.gz - Input file for TreeMix
 analyses, used in sympos_treemix.sh treemix_edges.zip -
 Zipped directory of files defining edges used in Supervised TreeMix
 analyses. guttula_S-trivirgatus_G-down.sfs - Site
 frequency spectrum for southern guttula and trivirgatus with guttula
 haplotypes, downsampled to 16 samples. Generated using easySFS
 (https://github.com/isaacovercast/easySFS).
 symposiachrus_mtDNA_inputs.zip - Fasta files for each
 mitochondrial region, used as input for assorted mtDNA population genetic
 analyses. Often subset or slightly altered for certain anlyses, but
 sequences should remain the same.
 ________________________________<br> ------------ Scripts
 -----------<br> -- (sympos_analysis_code.zip) --<br>
 ________________________________ sympos_PCA.R - R
 script for generating genomic PCAs using input vcf files
 (sympos_*_PCA-input.vcf). Locations of PCAs: "all-max4" in
 Figure 2B; "triv" in Figure 3C and S5; "trivGutt" in
 Figure S4C; "gutt" in Figure S7C. PCs described in Table S3.
 Also includes a section for assessing the significance of association
 between nuclear clusters and mtDNA haplogroup.
 sympos_sNMF.R - R script for running sNMF for four tests in paper
 using input structure-like files (sympos_*_sNMF-input.str). Locations of
 sNMF plots: "all-max4" in Figure 2A; "triv" in Figure
 3B; "trivGutt" in Figure S4B; "gutt" in Figure S7B.
 PCs described in Table S3. sympos_ABBABABA.R - Script
 for running ABBA/BABA analyses. This takes in a gzipped, tab delimited
 format of derived allele freqs made using a script from
 https://github.com/simonhmartin/genomics_general. Does all combinations in
 paper, using bootstrap_functions.R to actually run the calculations.
 Separates ones in Figure 4 from Table S2.
 bootstrap_functions.R - Script for running ABBA/BABA bootstraps.
 This contains f and D statistics, but only D is used here. It generates
 the value of the statistics, a range of bootstrapped values, bootstrapped
 p-value, Z value, and a density graph of the values of the
 bootstraps. sympos_treemix.sh - Shell script for
 running TreeMix, assumes you are in directory all the input files, some of
 which are in treemix_edges.zip. Runs up to three migration edges for the
 unsupervised and all four supervised analyses.
 sympos_treemixPlot.R - R script for plotting all the
 afformentioned TreeMix functions. Most aren't included, but Figure S3
 includes "base0", "base1", and "GagDia2".
 The others resulted in no major changes in topology.
 snapp_input_maker.sh - Driver script for converting a VCF to
 diploid SNAPP input (i.e. Nexus input for processing in Beauti). Converts
 from VCF to haploid SNAPP using
 https://github.com/BEAST2-Dev/SNAPP/tree/master/script, then to diploid
 SNAPP using a custom python script (SNAPP_haploid_to_diploid.py), and
 finally adding lines for a new nexus file using sed commands. Requires a
 lot of manual file/value entering by user, but you should get the idea of
 it! SNAPP_haploid_to_diploid.py - Script for converting
 a tab-delimited set of haploid nexus SNP data to diploid data. Takes and
 outputs "middle" lines, header and footer done by
 "snapp_input_maker.sh". Note that it's "dumb" and
 needs the input to be named "snapp_dip.txt" and outputs
 "snapp_out.txt". sympos_dadi_models.py - File
 specifying dadi models, based on the twoPop model set included in dadi.
 Notable additions are the admixture event models.
 sympos_dadi_run.py - Script made for running dadi models. Process
 is described in the file, essentially loads SFS, specifies parameters, and
 uses a function and driver for loop to conduct each run and output a messy
 file of parameters for each model and each run.
 process_dadi_output.py - Script made for turning the messy output
 from "sympos_dadi_run.py" into more concise output files
 (*.out). Then uses those files to output the best run for each model based
 on log likelihoods calculated by dadi.
 __________________________________<br> ---- Phylogenetics
 Input Files ---<br> ---- (sympos_phylo_input.zip) ----<br>
 __________________________________
 sympos_snapp-input.vcf - VCF files used for making the SNAPP
 input nexus. sympos_SNAPP.nex - Nexus file used for
 SNAPP analysis. Resulting tree in Figure 2D.
 sympos_mtDNA-BEAST_input.nex - Input nexus file for mtDNA BEAST
 phylogeny, output is sympos_BEAST_mtDNA.tre.
 sympos_UCE-RAxML_input.phylip - Input phyilip file for UCE RAxML
 phylogeny, output is sympos_RAxML_UCE.tre.
 sympos_UCE-RAxML_chars.charsets - Charsets file used for
 partitioning afformentioned phylip, output is
 sympos_RAxML_UCE.tre. sympos_UCE-SVDQ_input.nex - Nexus
 file used for UCE SVDQuartets tree, output is
 sympos_SVDQ_UCE.tre.
 ______________________________<br> --------- Tree Files
 ---------<br> -- (sympos_phylo_trees.zip) --<br>
 ______________________________ sympos_BEAST_mtDNA.tre -
 Mitochondrial phylogeny made in BEAST for all of our samples, with some
 genbank samples added. A supermatrix of our mitogenomes and assorted
 additions from genbank additions. Used in Figure 1B. Input was
 sympos_BEAST_input.nex. sympos_RAxML_UCE.tre -
 Phylogenetic tree for all samples in this study plus an outgroup (Myiagra
 ruficollis), made using a concatenated matrix of ultraconserved elements
 in RAxML. Used in Figure 1A. Input was sympos_UCE-RAxML_input.phylip and
 charset used for partitioning was
 sympos_UCE-RAxML_chars.charsets. sympos_SVDQ_UCE.tre -
 Phylogenetic tree for major populations in this study, made using the
 species tree approach SVDQuartets. Used in Figure 2c. Input was
 sympos_UCE-SVDQ_input.nex. Loci identified using
 sympos_UCE-RAxML_chars.charsets.