Table 3. Results from runs of STACEY with different data arrangements and different collapseHeight summary values including the Machado locality.
| Dataa | summary collapseHeight: 1x10-5 | summary collapseHeight: 1x10-4 | node depths (mut/site)e | |||||||
|---|---|---|---|---|---|---|---|---|---|---|
| retainedb | PPc | tip arrangementsd | retainedb | PPc | tip arrangementsd | mel-mir | west-west | south-west | ||
| all-mt+nuc | a | 10 | 0.25 | (OR,TR),(AR),(MC),(CN),(JR),(PU),(AG),(CU),(AC,IT),(JT),(mel),(mir) | 1 | 0.51 | (OR,TR,AR,MC,CN,JR,PU,AG,CU,AC,IT,JT),(mel,mir) | 0.000085 | 0.000062 | 0.000085 |
| all-mt+nuc | b | 10 | 0.23 | (OR,TR),(AR),(MC),(CN),(JR),(PU),(AG),(CU),(AC,IT),(JT),(mel),(mir) | 1 | 0.52 | (OR,TR,AR,MC,CN,JR,PU,AG,CU,AC,IT,JT),(mel,mir) | 0.000085 | 0.000060 | 0.000085 |
| all-nuc | a | 8 | 0.16 | (OR,TR),(AR,MC,CN),(JR),(PU),(AG),(CU),(AC,IT),(JT),(mel),(mir) | 3 | 0.13 | (OR,TR,AR,MC,CN),(JR,PU,AG,CU,AC,IT),(JT),(mel),(mir) | 0.000227 | 0.000151 | 0.000233 |
| all-nuc | b | 8 | 0.14 | (OR,TR),(AR,MC,CN),(JR),(PU),(AG),(CU),(AC,IT),(JT),(mel),(mir) | 3 | 0.14 | (OR,TR,AR,MC,CN),(JR,PU,AG,CU,AC,IT),(JT),(mel),(mir) | 0.000229 | 0.000159 | 0.000225 |
| up-mt+nuc | a | 6 | 0.51 | (OR,TR),(AR),(MC),(CN),(IT),(JT),(mel),(mir) | 2 | 0.22 | (OR,TR,AR,MC,CN,JT),(IT),(mel),(mir) | 0.000117 | 0.000115 | 0.000621 |
| up-mt+nuc | b | 6 | 0.57 | (OR,TR),(AR),(MC),(CN),(IT),(JT),(mel),(mir) | 2 | 0.20 | (OR,TR,AR,MC,CN,JT),(IT),(mel),(mir) | 0.000118 | 0.000119 | 0.000614 |
| up-nuc | a | 7 | 0.21 | (OR),(TR),(AR),(MC),(CN),(IT),(JT),(mel),(mir) | 4 | 0.45 | (OR,TR),(AR,MC,CN),(IT),(JT),(mel),(mir) | 0.000304 | 0.000287 | 0.000683 |
| up-nuc | b | 7 | 0.20 | (OR),(TR),(AR),(MC),(CN),(IT),(JT),(mel),(mir) | 4 | 0.44 | (OR,TR),(AR,MC,CN),(IT),(JT),(mel),(mir) | 0.000304 | 0.000282 | 0.000683 |
aall: all localities; up: localities upstream of the Tapajós River only; mt: sequences of mtDNA locus; nuc: sequences of nuclear loci.
bnumber of lineages retained from Cichla pinima sensu lato, excluding other species.
cPP, posterior probability of maximum a posteriori model.
dTip arrangements (those together in parentheses) depict which tips were collapsed into a single taxon for a given collapseHeight. Locality codes follow Table 1.
eFor relevant topological comparisons, the depth of the most recent common ancestor is listed. See text and S1 File for further explanation.