Macroevolution with living and fossil species
Creators: name: Guillerme, Thomas
Publisher: name: figshare
Year: 2015
Subjects: subject: Molecular Biology
subject: 60102 Bioinformatics
subject: FOS: Computer and information sciences
subject: FOS: Computer and information sciences
subject: Paleontology
subject: Zoology
subject: FOS: Biological sciences
subject: FOS: Biological sciences
subject: Evolutionary Biology

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