Calibrating phylogenies assuming bifurcation or budding alters inferred macroevolutionary dynamics in a densely sampled phylogeny of bivalve families

Analyses of evolutionary dynamics can be profoundly affected by age
calibrations of phylogenetic nodes under different models of lineage
branching. Most time-calibrated molecular phylogenies of extant taxa
assume a purely bifurcating model, where nodes are calibrated using the
daughter lineage with the older first occurrence in the fossil record.
Lineages can also split via budding, in which a parent lineage persists
following the origin of a daughter lineage, and nodes are calibrated using
the age of the lineage with the younger first occurrence. Here, we use the
extensive fossil record of bivalve molluscs for a large-scale empirical
test of how the choice of branching model affects macroevolutionary
analyses. We time-calibrated 91% of nodes in a phylogeny of 97 extant
bivalve families using 86 calibration points ranging in age from 2.59 to
485 Ma. Allowing budding-based calibrations minimizes conflict between the
tree topology and timing of evolutionary events in the fossil record,
reducing the summed duration of inferred “ghost lineages,” from 6.76
billion yrs (Gyr; bifurcating model) to 1.00 Gyr (budding model). Adding
31 extinct paraphyletic families – many major groups contain such extinct
taxa – shifts deep splits further back in time and raises ghost-lineage
totals to 7.86 Gyr (bifurcating) and 1.92 Gyr (budding), but more
accurately reflects the time since separation of lineages.
Lineage-through-time plots from phylogenetic data scaled under a
bifurcating model of evolution push more inferred bivalve diversification
into the Paleozoic, conflicting with other palaeontological evidence on
the magnitude of the end-Paleozoic extinction and subsequent recovery, and
strongly reduce the magnitude of the Cenozoic diversification of the
group. Consideration of the hypothesized branching model within a given
clade is essential when node-calibrating phylogenies, and for a major
clade with a robust fossil record, an evolutionary model that allows
budding and does not force bifurcations is the most appropriate one, and
likely common for many other clades as well.