Résumé
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.