Table 1.
Comparisons of topologies, branch lengths, and internal branch support values between inferred phylogenies across two replicates.
| Data set | Program | Coalescent-based ASTRAL species phylogenies (Run1 vs. Run2) | Concatenation-based ML species phylogenies (Run1 vs. Run2) | ||||
|---|---|---|---|---|---|---|---|
| Tree distance (%)a | Branch distanceb | Bipartitions with different support values (%)c | Tree distance (%)a | Branch distanceb | Bipartitions with different support values (%)c | ||
| Animal: Bees | IQ-TREE | 22.5 | NA | NA | 0.0 | 1.46138E−07 | 2.7 |
| Animal: Birds | IQ-TREE | 1.5 | NA | NA | 0.0 | 4.09E−09 | 1.5 |
| Animal: Butterflies | IQ-TREE | 4.4 | NA | NA | 0.0 | 0.000283233 | 16.7 |
| Animal: Lizards | IQ-TREE | 3.8 | NA | NA | 0.0 | 1.49E−07 | 0.0 |
| Animal: Marine fishes | IQ-TREE | 6.8 | NA | NA | 0.0 | 1.03E−08 | 0.9 |
| Animal: Rodents | IQ-TREE | 0.0 | NA | 8.8 | 0.0 | 2.83E−10 | 0.0 |
| Plant: Cardueae | IQ-TREE | 4.9 | NA | NA | 0.0 | 2.45E−10 | 0.0 |
| Plant: Caryophyllales | IQ-TREE | 0.0 | NA | 0.0 | 0.0 | 0.0 | 0.0 |
| Plant: Green plants | IQ-TREE | 1.8 | NA | NA | 0.0 | 0.0 | NA |
| Plant: Jaltomata | IQ-TREE | 0.0 | NA | 0.0 | 0.0 | 8.00E−10 | 0.0 |
| Plant: Protea | IQ-TREE | 14.5 | NA | NA | 0.0 | 3.46E−10 | 0.0 |
| Fungi: Aspergillaceae | IQ-TREE | 0.0 | NA | 0.0 | 0.0 | 1.48E−07 | 0.0 |
| Fungi: Budding yeasts | IQ-TREE | 0.0 | NA | 1.8 | 0.0 | 0.0 | 0.0 |
| Fungi: Hanseniaspora | IQ-TREE | 0.0 | NA | 0.0 | 0.0 | 0.0 | 0.0 |
| Fungi: Rhizoplaca | IQ-TREE | 10.7 | NA | NA | 0.0 | 3.32E−10 | 0.0 |
| Animal: Bees | RAxML-NG | 8.6 | NA | NA | 0.0 | 0.0 | 0.0 |
| Animal: Birds | RAxML-NG | 1.5 | NA | NA | 0.0 | 0.0 | 0.0 |
| Animal: Butterflies | RAxML-NG | 2.0 | NA | NA | 0.0 | 0.0 | 0.0 |
| Animal: Lizards | RAxML-NG | 0.0 | NA | 30.8 | 0.0 | 0.0 | 0.0 |
| Animal: Marine fishes | RAxML-NG | 4.3 | NA | NA | 0.0 | 0.0 | 0.0 |
| Animal: Rodents | RAxML-NG | 0.0 | NA | 5.9 | 0.0 | 0.0 | 0.0 |
| Plant: Cardueae | RAxML-NG | 8.5 | NA | NA | 0.0 | 0.0 | 0.0 |
| Plant: Caryophyllales | RAxML-NG | 16.3 | NA | NA | 0.0 | 0.0 | 0.0 |
| Plant: Green plants | RAxML-NG | 0.7 | NA | NA | 0.0 | 0.0 | 0.0 |
| Plant: Jaltomata | RAxML-NG | 0.0 | NA | 8.3 | 0.0 | 0.0 | 0.0 |
| Plant: Protea | RAxML-NG | 21.0 | NA | NA | 0.0 | 0.0 | 0.0 |
| Fungi: Aspergillaceae | RAxML-NG | 0.0 | NA | 0.0 | 0.0 | 0.0 | 0.0 |
| Fungi: Budding yeasts | RAxML-NG | 0.0 | NA | 0.9 | 0.0 | 0.0 | NA |
| Fungi: Hanseniaspora | RAxML-NG | 0.0 | NA | 0.0 | 0.0 | 0.0 | 0.0 |
| Fungi: Rhizoplaca | RAxML-NG | 3.6 | NA | NA | 0.0 | 0.0 | 0.0 |
For each data set, coalescent-based ASTRAL trees were reconstructed from the Run1 and Run2 sets of individual gene trees; both Run1 and Run2 used identical settings, including substitution model, random starting seed number, number of threads of execution, number of independent tree searches, and ML program; concatenation-based ML trees were inferred twice from the supermatrix using IQ-TREE and RAxML-NG with identical settings.
aPercentage of bipartitions (or internal branches) that differ between two inferred species trees was quantified the normalized Robinson–Foulds tree distance.
bBranch distance between two inferred species trees was computed by the branch score distance of Kuhner and Felsenstein with the R packages ape and phangorn.
cThe percentage of bipartitions (or internal branches) that received different bootstrap support values between two inferred species trees that were topologically identical (i.e., tree distance is 0). When topologies, branch lengths, or internal branch support values between two inferred phylogenies are identical, their estimated values are zero and are shown in bold. “NA” denotes “not applicable” due to either lack of external branch lengths in a coalescent-based ASTRAL tree, different topologies between two inferred species trees, or lack of standard bootstrap support values in the RAxML-NG analyses of the two largest data sets (plant: green plants and fungi: budding yeasts) due to computation cost.