Simulations modelling the effect of budding speciation on phylogenies

Paleobiologists have long sought to explain how alternative modes of
speciation, including budding and bifurcating cladogenesis, shape patterns
of evolution. Methods introduced over the past decade have paved the way
for a renewed enthusiasm for exploring modes of speciation in the fossil
record. However, the field does not yet have a strong intuition for how
ancestor-descendant relationships, especially those that arise from
budding speciation, might influence the shape of trees reconstructed for
fossil or living clades. We developed a simulation approach based on
classic paleobiological theory to ask what proportion of ancestral nodes
in paleontological phylogenies are expected to correspond to sampled
lineages under a range of preservational regimes. We compared our
simulated results to empirical estimates of absolute fossil record
completeness gathered from the literature and found that many fossilized
clades of marine invertebrates are likely to display upwards of 80%
sampled ancestors. Under a primarily budding model, phylogenies where 100%
of the internal nodes correspond to named species are very possible for
well-sampled clades at local and regional scales. We also leveraged our
simulation approach to ask how budding might shape extant clades. We found
that the ancestral signature of budding causes rampant hard polytomies in
extant clades. Our results highlight how budding can yield dramatic and
unrecognized effects on phylogenetic reconstruction of clades of both
living and extinct organisms.