Table 1.
Summary of 45 comparative MCMC divergence time runs, including justification and parameter settings.
| MCMC run | #loci | #outgroups | #constraints | Comment |
|---|---|---|---|---|
| 1 | 7 | 8 | 0 | Testing joint prior |
| 2 | 4 | 10 | 0 | Testing joint prior |
| 3 | 7 | 8 | 6 | Reference run nDNA |
| 4 | 8 | 8 | 6 | See 3,+mtDNA |
| 5 | 1 | 8 | 6 | mtDNA only |
| 6 | 7 | 8 | 6 | See 3, 4 of 6 flamingo species excluded |
| 7 | 4 | 10 | 6 | See 3, 4 loci only1 |
| 8 | 4 | 10 | 7 | See 7, anhinga constraint added |
| 9 | 5 | 9 | 6 | See 3, 5 loci only |
| 10 | 5 | 9 | 7 | See 9, anhinga constraint added |
| 11 | 6 | 8 | 6 | See 3, 6 loci only |
| 12 | 4 | 10 | 2 | See 7, youngest constraints only |
| 13 | 5 | 9 | 2 | See 9, youngest constraints only |
| 14 | 6 | 8 | 2 | See 11, youngest constraints only |
| 15 | 7 | 8 | 2 | See 3, youngest constraints only |
| 16 | 4 | 3 | 2 | See 12, reduced outgroup sampling2 |
| 17 | 5 | 3 | 2 | See 13, reduced outgroup sampling2 |
| 18 | 6 | 3 | 2 | See 14, reduced outgroup sampling2 |
| 19 | 7 | 3 | 2 | See 15, reduced outgroup sampling2 |
| 20 | 6 | 8 | 6 | See 3, 1 locus excluded |
| 21 | 6 | 8 | 6 | See 3, 1 locus excluded |
| 22 | 6 | 8 | 6 | See 3, 1 locus excluded |
| 23 | 6 | 8 | 6 | See 3, 1 locus excluded |
| 24 | 6 | 8 | 6 | See 3, 1 locus excluded |
| 25 | 6 | 8 | 6 | See 3, 1 locus excluded |
| 26 | 7 | 8 | 6 | See 3, constraint maxima increased to 65 or 303 |
| 27 | 7 | 8 | 6 | See 26, uniform prior distribution |
| 28 | 7 | 8 | 6 | See 26, 95% prior range at 65 or 303 |
| 29 | 7 | 8 | 6 | See 3, loci unpartitioned |
| 30 | 7 | 8 | 7 | See 3, + minPhoenicopteridae = 5.33 constraint4 |
| 31 | 7 | 8 | 3 | See 15, + minPhoenicopteridae = 5.33 constraint4 |
| 32 | 7 | 8 | 4 | See 3, sistergroup (grebe) taxa excluded |
| 33 | 7 | 8 | 5 | See 3, stem penguin constraint excluded |
| 34 | 7 | 8 | 5 | See 3, stem fregatebird constraint excluded |
| 35 | 7 | 8 | 5 | See 3, stem gannet constraint excluded |
| 36 | 7 | 8 | 5 | See 3, stem pelican constraint excluded |
| 37 | 7 | 8 | 4 | See 3, oldest constraints only |
| 38 | 7 | 8 | 3 | See 15, stem penguin constraint added |
| 39 | 7 | 8 | 3 | See 15, stem fregatebird constraint added |
| 40 | 7 | 8 | 3 | See 15, stem gannet constraint added |
| 41 | 7 | 8 | 3 | See 15, stem pelican constraint added |
| 42 | 7 | 8 | 1 | See 3, stem penguin constraint only |
| 43 | 7 | 8 | 1 | See 3,stem fregatebird constraint only |
| 44 | 7 | 8 | 1 | See 3,stem gannet constraint only |
| 45 | 7 | 8 | 1 | See 3,stem pelican constraint only |
1Several combinations of loci were tested; analyses were limited to 4–7 loci (<4 loci failed to yield a robust phylogeny).
2Reduced outgroup sampling follows Torres et al. (2014).
3Prior range extended to 65 MY (K–T boundary) for all constraints, except youngest, Podicipedidae (30 MY; early Oligocene), constraint. Default lognormal prior distribution lognormal, SD = 1.
4Additional constraint is not based on fossil evidence, rather investigated to test consistency of Miocene/Pliocene divergence of crown Phoenicopteridae with overall aquatic bird.