Telling the Evolutionary Time: Molecular Clocks and the Fossil Record

Discussion

Crown-groups versus stem-groups

Understanding the difference between crown-groups, stem-groups, and how fossils
provide minimum age estimates for these is of crucial importance when comparing our
molecular estimates with fossil-based ones. The two terms were initially introduced by
Jefferies (1979) but his stem-group definition only referred to the stem representatives
(Figure 8.2), implying the existence of paraphyletic groups (Doyle and Donoghue 1993;
Smith 1994). We have therefore adopted the usage of Magallón and Sanderson (2001)
including both stem representatives and the crown-group in the stem-group definition,
and our usage of stem-group corresponds with the total-group concept of Jefferies
(1979). Following the definitions of Magallón and Sanderson (2001), a crown-group is the
least inclusive monophyletic group that includes all the extant members of a clade
(Figure 8.2). The crown-group may include extinct representatives, but only those that
diverged after the origin of the most recent common ancestor of all extant
representatives. The stem-group is the most inclusive monophyletic group containing the
extant members of a clade, but no other extant taxa, plus all the extinct lineages that
diverge from the lineage leading to the crown-group (Figure 8.2). The crown-group age
corresponds to the first phylogenetic split within the crown-group, and only fossils
demonstrated to be nested within the crown-group can provide a minimum age estimate
for the crown-group. The stem-group age may be considerably older and corresponds to
the split between the crown-group in question and its extant sister group (Magallón and
Sanderson 2001), and any representative, though preferably a stem-taxon, may provide a
minimum age estimate for the stem-group (Figure 8.2). Also note that an age estimate for
the origin of the sister clade may provide the best available estimate for the stem-group
age, and this is what the implied age column in Table 8.1 indicates.

Interpreting incongruence

We need to consider what different types of incongruence might represent while
comparing our molecular-based estimates with those based on fossils. The most easily
interpreted type is the case where the fossil evidence indicates an older age than our
corresponding molecular estimate. In this case, either the assignment of the fossil taxon to
the group in question is wrong, or else the molecular estimate fails to infer the taxon age
correctly. There are examples for both these cases. The fossil Amaranthaceae from the
Santonian-Campanian (Collinson et al. 1993), for example, has been confirmed to be
something other than Amaranthaceae (Friis, personal communication), and one might
suspect that some other assignments such as the Maastrichtian Bombacaceae (Muller
1981) also fall into this category. There are, however, several examples in which solid
fossil evidence indicates that our molecular estimates are underestimating the taxon age,
and in particular, this pattern is seen among some of the more derived groups (see below
for a more detailed account of sources of error in the molecular estimates).
The reverse pattern, where molecular estimates indicate older ages than the available
fossil evidence, is less easily interpreted. In some cases there may be good reasons to

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