DOI: 10.5061/dryad.ff18q9d
title: Data from: Whole genome shotgun phylogenomics resolves the pattern and timing of swallowtail butterfly evolution

description: Evolutionary relationships have remained unresolved in many well-studied
 groups, even though advances in next-generation sequencing and analysis,
 using approaches such as transcriptomics, anchored hybrid enrichment, or
 ultraconserved elements, have brought systematics to the brink of whole
 genome phylogenomics. Recently, it has become possible to sequence the
 entire genomes of numerous non-biological models in parallel at reasonable
 cost, particularly with shotgun sequencing. Here we identify orthologous
 coding sequences from whole-genome shotgun sequences, which we then use to
 investigate the relevance and power of phylogenomic relationship inference
 and time-calibrated tree estimation. We study an iconic group of
 butterflies - swallowtails of the family Papilionidae - that has remained
 phylogenetically unresolved, with continued debate about the timing of
 their diversification. Low-coverage whole genomes were obtained using
 Illumina shotgun sequencing for all genera. Genome assembly coupled to
 BLAST-based orthology searches allowed extraction of 6,621 orthologous
 protein-coding genes for 45 Papilionidae species and 16 outgroup species
 (with 32% missing data after cleaning phases). Supermatrix phylogenomic
 analyses were performed with both maximum-likelihood (IQ-TREE) and
 Bayesian mixture models (PhyloBayes) for amino acid sequences, which
 produced a fully resolved phylogeny providing new insights into
 controversial relationships. Species tree reconstruction from gene trees
 was performed with ASTRAL and SuperTriplets and recovered the same
 phylogeny. We estimated gene site concordant factors to complement
 traditional node-support measures, which strengthens the robustness of
 inferred phylogenies. Bayesian estimates of divergence times based on a
 reduced dataset (760 orthologs and 12% missing data) indicate a
 mid-Cretaceous origin of Papilionoidea around 99.2 million years ago (Ma)
 (95% credibility interval: 68.6-142.7 Ma) and Papilionidae around 71.4 Ma
 (49.8-103.6 Ma), with subsequent diversification of modern lineages well
 after the Cretaceous-Paleogene event. These results show that shotgun
 sequencing of whole genomes, even when highly fragmented, represents a
 powerful approach to phylogenomics and molecular dating in a group that
 has previously been refractory to resolution.
description: Appendix S1 - Pipeline
 from raw reads to phylogenomics and dating analysisScripts used to perform
 the analyses presented in this study.Appendix S2 - Dataset 1
 with 760 genes (amino acids format)Phylogenomic dataset of
 Papilionoidea including 760 orthologous genes in amino acid format
 (Dataset 1).Appendix S3 - Dataset 2
 with 6621 genes (amino acids format)Phylogenomic dataset of
 Papilionoidea including 6,621 orthologous genes in amino acid format
 (Dataset 2).Appendix S4 - Dataset 3
 with 760 genes (nucleotides format with gene partitions)Phylogenomic dataset of
 Papilionoidea including 760 orthologous genes in nucleotide format
 (Dataset 3).Appendix S5 - Dataset 4
 with 6407 genes (nucleotides format with gene
 partitions)Phylogenomic dataset of
 Papilionoidea including 6,621 orthologous genes in nucleotide format
 (Dataset 4).Appendix S6 -
 Phylogenomic treesPhylogenomic trees of
 Papilionoidea inferred with both maximum-likelihood and Bayesian inference
 using 760 orthologous genes (Dataset 1) and 6,621 orthologous genes
 (Dataset 2).Appendix S7 - tree
 filesTree files of the
 molecular phylogenomic analyses of Papilionoidea as inferred with IQ-TREE
 and PhyloBayes.Appendix S8 - Gene- and
 site-concordance and discordance factorsAppendix S8. Gene- and
 site-concordance and discordance factors estimated with the Datasets 1 and
 3 (760-gene) and Dataset 2 (6621-gene).Appendix S9 - Dated
 trees with GTSAppendix S9. Bayesian
 dated trees of Papilionoidea inferred with the 760-gene dataset and the
 mixture model CAT-GTR (PhyloBayes).Appendix S10 -
 Chronogram filesAppendix S10. Tree files
 of molecular divergence-time estimation of Papilionoidea as inferred with
 the PhyloBayes CAT-GTR model following four different analyses of the
 760-gene dataset.Appendix S11 - Prior and
 posterior distributionsAppendix S11. Comparison
 of prior and posterior distributions for nodes with set fossil
 calibrations. Bayesian posterior distributions are not driven by the
 uniform prior distributions used to calibrate the five nodes with fossil
 calibrations.Appendix S12 -
 Phylogenomic tree with cross-contamAppendix S12.
 Phylogenomic tree of Papilionoidea inferred with the Bayesian mixture
 model using an amino-acid dataset comprised of 2,993 orthologous genes
 selected without the cross-contamination check.Appendix S13 -
 Correlation cross-conta vs. no cross-contaAppendix S13.
 Correlations of branch lengths as inferred with the 2,993-gene (without
 CroCo) versus the 6,621-gene (with CroCo) datasets (a), and as inferred
 with the 760-gene versus the 6,621-gene datasets (both with CroCo) (b).
 Units are the number of substitutions per site per branch. Note the higher
 correlation (R2) obtained when comparing branch lengths between the
 760-gene and 6,621-gene datasets with cross-contamination
 excluded.