Macroevolution with living and fossil species

Although many biodiversity studies focus on living species, the vast majority of species that
ever lived are long extinct. It is therefore crucial to combine data from both living and fossil
species to fully understand macroevolutionary patterns and processes. This thesis focuses
on ways to combine both living and fossil taxa into phylogenies and investigates how the
resulting phylogenies can be used to investigate macroevolutionary questions.
In the first part of the thesis, I ran extensive simulation analyses to test the effect of
missing data on phylogenetic topologies when using the Total Evidence method. This
method builds phylogenies using both molecular data for living taxa and morphological
data for living and fossil taxa. I tested how various proportions of missing morphological
data among living taxa, fossil taxa, and the two combined, affected my ability to recover
the correct tree topology. I found that the amount of missing morphological data among
living taxa was the most crucial aspect for accurately placing living and fossil taxa in the
same phylogeny. Following these conclusions, I performed a systematic review of the
coded morphological data available for living mammal species. I recorded the amount of
morphological data available for each mammalian order and tested whether this data was
randomly distributed across the phylogeny or biased towards certain clades. The results of
this analysis showed that although morphological data is scarce for living mammals, it is at
least generally randomly distributed across the phylogeny and therefore should not bias the
placement of fossil taxa towards particular clades.
For the second part of the thesis, I used Total Evidence phylogenies containing both living
and fossil taxa to investigate whether mammals radiated during the Cenozoic in response
to the infamous Cretaceous-Palaeogene (K-Pg) mass extinction event, 66 million years
ago. Previous studies show support for an effect of the K-Pg extinction event on mammalian
diversification when using palaeontological data but no support using neontological
data. I used a novel time-slicing method for quantifying changes in morphological diversity
(disparity) through time to describe the patterns of mammalian diversification across the
K-Pg boundary. I found no significant difference in disparity before and after the K-Pg
boundary. This suggests that, even though many terrestrial vertebrates (including the nonavian
dinosaurs) went extinct during the K-Pg extinction event, it had no significant effect
on mammalian morphological diversification. These results refute the popular belief that mammals only began diversifying after the extinction of the non-avian dinosaurs, and shows
the advantage of using living and fossil species to answer macroevolutionary questions.
Finally, I discuss future avenues of research for improving analyses that include living
and fossil species as well as the advantages of using both living and fossil taxa when
investigating macroevolutionary questions. I argue that all macroevolutionary studies should
include both types of data to advance our understanding of biodiversity.