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Internal nodes are labeled as: <Node ID>_Bootstrap_Concordance
# species76
# single-copy orthologs150
Fossil calibrationsNode 75 (ROOT) at 514-636.1mya
Node 74 at 432.6-636.1mya
Node 72 at 98.17-514mya
Node 67 at 514-636.1mya
Node 64 at 487-636.1mya
Node 62 at 322.83-521mya
Node 1 at 319.9-521mya
Node 61 at 319.9-411mya
Node 2 at 130.3-411mya
Node 60 at 319.9-411mya
Node 58 at 306.9-411mya
Node 57 at 306.9-411mya
Node 51 at 313.7-411mya
Node 25 at 226.4-411mya
Node 50 at 313.7-411mya
Node 30 at 208.5-411mya
Node 49 at 271.8-411mya
Node 35 at 195.31-411mya
Node 34 at 129.41-411mya
Node 48 at 129.41-411mya
Node HY25 at 89.9-93.9mya
Node HY13 at 23-28.4mya
Contentious nodesHY3 clade
65 (Crustaceans)
Gene families for Dupliphy38195
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Methods (brief)

Orthogroups were obtained from OrthoDBv8. Single copy sequences were aligned with PASTA and RAxML was used to make gene trees. ASTRAL was used to estimate the species tree topology from gene trees while RAxML on a concatenated alignment was used to estimate branch lengths in terms of relative substitutions. r8s was used with the fossil calibrations to get branch lengths in terms of millions of years. This species tree was then used with CAFE and Dupliphy to reconstruct ancestral gene counts and gains and losses were assessed.