Glossary for TGD analysis

General terms
TGD Teleost specific whole genome duplication.
Orthogroup Clades including gene-lineages derived from TGD and their orthologs in tetrapods and basal actinopterygian (Fig. 1B in Inoue et al).

Results from gene tree analyses
1to2 Orthogroup including pairs of TGD derived genes (more precisely, gene-lineages) in more than one teleost species. Example.
1to1 Orthogroup including only one gene lineage (ignoring species-specific duplications) in all extant teleost species. Example.
1to2_DH2 _DH2: Orthogroup including human/medaka lineage specific duplicates. Example.
1to2_DH3d d: Multiply counted orthogroups (Fig. S1D; Fig. S7D). Example.

Categories for 4,809 no clear orthogroups
Table S3
(i) 818
qSeqLess100aa 818 Human query sequences of less than 100 amino acids (sequence length limitation for accurate gene tree estimation). Example.
(ii) 1,280
noBlastFish 1,280 No hits in BLAST search from teleost genomes with E-value cut-off of < 10^(-3). Example.
(iii) 1,874: No clear orthologs identified between tetrapods and teleosts in the estimated gene tree.
noOrtho/NoOrthoCand 1,425 No clear orthogroups identified. Example.
exLongDis 204 Excessively long branch lengths (tentatively ≥2.0 base substitution per site) between tetrapods and teleosts. Example.
qSeqLess4spp 152 Less than 4 sequences remained after long branch deletion process (limitation of # of sequences for phylogenetic analysis). Example.
BLASTSeqLess4spp 93 Less than 4 Blast hits. Example.
(iv) 135
UnAmbLes100 135 Limited length of unambiguously aligned sites for accurate gene tree estimation. Example.
(v) 702: Failure in BLAST search or amino acid translation due to erroneous sequence data.
noP2N 666 cDNA and amino acid sequence was not match in DB. ExampleExample.
noBlastQuery/queryLB 36 Erroneous amino acid sequence unavailable for Blast search. Example.

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