Table 1.
Summary of sister-pair datasets for examining the relationship between substitution rates and diversification rates
| Rank | Alignment | Genes | Phylogeny | Substitutions | Number of pairs | |||
|---|---|---|---|---|---|---|---|---|
| All | Mono only (not tested) | Filtered (Mono + Welch) | Full (Welch) | |||||
| Families | Mito.All | rRNA, coI, cytB | Rabosky | Total | 54 | 41 | 41 | 50 |
| Families | Mito.Coding | coI, cytB | Rabosky | dS | 88 | 59 | 58 | 77 |
| dN | 88 | 65 | 63 | 78 | ||||
| Families | Nuc.RAG1 | rag1 | Rabosky | Total | 119 | 82 | 82 | 113 |
| dS | 119 | 44 | 44 | 65 | ||||
| dN | 119 | 45 | 43 | 62 | ||||
| Genera | Mito.All | rRNA, coI, cytB | Rabosky | Total | 183 | 71 | 48 | 64 |
| Genera | Mito.Coding | coI, cytB | Rabosky | dS | 475 | 193 | 144 | 235 |
| dN | 475 | 204 | 83 | 138 | ||||
| Genera | Nuc.RAG1 | rag1 | Rabosky | Total | 547 | 249 | 121 | 256 |
| dS | 547 | 250 | 199 | 355 | ||||
| dN | 547 | 239 | 131 | 247 | ||||
| Families | Nuc.ETOL | 19 nuclear protein-coding exons | Betancur-R | Total | 118 | 98 | 78 | – |
| dS | 118 | 98 | 75 | – | ||||
| dN | 118 | 98 | 78 | – | ||||
Rank is the taxonomic rank at which pairs are selected. Three marker sets are used for the main analysis, with the Mito. All set including non-coding sequences for additional power in estimating total substitution rates. An additional analysis uses the euteleost phylogeny of Betancur-R et al. (2013) and an associated dataset of 19 nuclear exonic sequences (Table S2 available as Supplementary Information). Datasets are further divided by the type of substitution rate estimated. Different substitution types may have different numbers of usable pairs because some PAML analyses fail due to short branch lengths or because pairs are deleted by the Welch filter, which removes shallow pairs with high variance in branch length estimates. The number of pairs remaining is shown after filtering for mutual monophyly (Mono) and after conducting the Welch filter(Welch). The monophyly filter removes pairs in which members of one or more genera are found on both sides of the pair in 80% or more of the all-taxon-assembled trees incorporating taxa without molecular data. The set of pairs filtered by both Monophyly and Welch filters formed our Filtered dataset, whereas the set of pairs filtered only by the Welch filter constituted our Full dataset