Divergence times were estimated in RHINO for both tree topologies and all datasets.
RHINO is a modified version of QDATE (Rambaut and Bromham 1998; Cooper et al.
2001) which allows for rate heterogeneity in different parts of the ML tree during branch
length estimation. In this case rates were allowed to vary between deuterostome taxa and
the other metazoans. Trees were constrained to a mammal-bird divergence time of either
288 Ma (Lee 1999) or 310 Ma for comparative purposes, although estimated divergence
margins were very similar for both dates and so only the 310 Ma results are shown as ranges
in Figure 3.2. Parameter values are shown in Table 3.1. Although these results are based
on a very small sample, they fall in the middle of the range of previous estimates
(Figure 3.3), with an estimated divergence for these genes falling between 687 and 914 Ma,
at least 100 myr prior to the Cambrian ‘explosion’. It is expected that larger studies
incorporating more genes, taxa, and fossil constraints will greatly improve on these
estimates.
Table 3.1 Parameter values
a Number of nucleotide sites.
b Fraction of those sites that are invariant.
c alpha value for the discrete gamma distribution. Both b and c were estimated from the data.
d Tree topologies as shown in Figure 3.2A and B.
e Likelihood score for each of the two topologies.
f Results of an SH test (Shimodaira and Hasegawa 1999) which compares the likelihood score with
that of the ML tree for each dataset. High values denote likelihoods close to the ML value and vice
versa. ‘Best’ indicates an ML tree. No tree was found to be significantly worse than the ML tree at
10 per cent.
60 RICHARD A.FORTEY ET AL.