Tree image located on main page.
|# single-copy orthologs||150|
|Fossil calibrations||Node 75 (ROOT) at 514-636.1myaNode 74 at 432.6-636.1myaNode 72 at 98.17-514myaNode 67 at 514-636.1myaNode 64 at 487-636.1myaNode 62 at 322.83-521myaNode 1 at 319.9-521myaNode 61 at 319.9-411myaNode 2 at 130.3-411myaNode 60 at 319.9-411myaNode 58 at 306.9-411myaNode 57 at 306.9-411myaNode 51 at 313.7-411myaNode 25 at 226.4-411myaNode 50 at 313.7-411myaNode 30 at 208.5-411myaNode 49 at 271.8-411myaNode 35 at 195.31-411myaNode 34 at 129.41-411myaNode 48 at 129.41-411myaNode HY25 at 89.9-93.9myaNode HY13 at 23-28.4mya|
|Contentious nodes||HY3 cladeLLONG65 (Crustaceans)|
|Gene families for Dupliphy||38195|
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.