Phylogenetic Tree Construction from Ultraconserved Elements

The phylogeny was built based on two sets of UCEs: 5,472 baits for 5,060 UCEs in tetrapods^{57 (link)} and 2,628 baits for 1,314 UCEs in acanthomorphs^{69 (link)}. We used the Phyluce software^{70 (link)} to locate the probes in the reference genomes of our 68 species with 6 additional species contained in our original dataset. We extracted a flanking region of ±1,000 bp for each probe and aligned them with Mafft aligner version 7.470 (ref. ^{71 (link)}). We then created a 75% completion matrix, that is, each alignment contains at least 75% of the taxa (55 species), resulting in 63 alignments from the acanthomorph set and 2,742 probes from the tetrapod set (all alignments are available on Figshare). A phylogenetic tree was built using IQ-TREE version 2.0.3 (ref. ^{72 (link)}), with the appropriate substitution model inferred for each of the 2,805 alignments, a maximum likelihood tree search and 1,000 bootstrap replicates. To validate our tree, we also estimated a second tree based on a MultiZ alignment to the human genome and obtained similar results (Extended Data Fig. 9). The phylogenetic tree was calibrated to absolute time using the chronos function of the ‘ape’ package in R, with a smoothing parameter lambda of 0 and a ‘relaxed’ model^{73 (link),74 (link)}. Fourteen nodes were calibrated following previously published calibrations. The robustness of the tree was assessed by removing each node independently (see Extended Data Fig. 3).

Actinopterygii/Sarcopterygii: divergence time 416 million years ago (Ma), upper bound 425.4 Ma^{75 (link)}

The first node in the Actinopterygii group: divergence time 378.2 Ma^{76 (link)}

Sauropsida (birds and reptiles)/Synapsida (mammals): divergence time 313.4 Ma^{77 (link)}

Archosauria (birds)/Testudines: divergence time 260 Ma^{78 (link)}

The basal nodes of the Lepidosauria: divergence time 222.8 Ma^{79 (link)}

First mammalian node, Eutheria/Metatheria: divergence time 160.7 Ma^{75 (link)}

Galloanserae/Neoaves: divergence time 66 Ma^{77 (link)}

Glire/Primates: divergence time 61.7 Ma^{77 (link)}

Basal gekkotan node: divergence time 54 Ma^{80 (link)}

Passeriformes/Psittaciformes: divergence time 51.81 Ma^{81 (link)}

Cynoglossidae/Paralichthyidae: divergence time 50 Ma^{76 (link)}

Sus scrofa/other Cetartiodactyla: divergence time 48.5 Ma^{77 (link)}

Canidae/Arctoidea: divergence time 37.1 Ma^{75 (link)}

Hominoidea/Cercopithecoidea: divergence time 23.5 Ma^{77 (link)}