Integrative Phylogenetics: Tools for Palaeontologists to Explore the Tree of Life

SIMPLE SUMMARY: All life is derived from a single common ancestor, whose descendants coevolved with the planet, shaping the structure of biodiversity and the physical processes that operate on Earth. This complex history cannot be inferred solely by studying the genomes of living organisms, nor through analysis of the fossil remains of their extinct relatives. Only a unified approach integrating living and extinct species and drawing from both genomic and anatomical evidence can achieve this aim. In this review, we highlight recent advances, challenges, and opportunities in this endeavour. These include the development of models for analysis of anatomical data; methods for combined analysis of fossil and living species, as well as anatomical and genomic data; and the combined estimation of evolutionary relationships, geographic range, and evolutionary rates. However, the application of such methods is limited by a shortage of expertise in taxonomy and comparative anatomy, which are skills required for the compilation of anatomical datasets. Whereas there is a common concern for the incompleteness of the fossil record, knowledge with respect to the comparative anatomy of living species is equally incomplete. We anticipate that the increased demand for an integrative phylogenetic approach to reconstruct the tree of life and evolutionary patterns and processes will encourage researchers to overcome these challenges with the aim of elucidating the complexities behind organismal evolution across broad taxonomic and time scales. ABSTRACT: The modern era of analytical and quantitative palaeobiology has only just begun, integrating methods such as morphological and molecular phylogenetics and divergence time estimation, as well as phenotypic and molecular rates of evolution. Calibrating the tree of life to geological time is at the nexus of many disparate disciplines, from palaeontology to molecular systematics and from geochronology to comparative genomics. Creating an evolutionary time scale of the major events that shaped biodiversity is key to all of these fields and draws from each of them. Different methodological approaches and data employed in various disciplines have traditionally made collaborative research efforts difficult among these disciplines. However, the development of new methods is bridging the historical gap between fields, providing a holistic perspective on organismal evolutionary history, integrating all of the available evidence from living and fossil species. Because phylogenies with only extant taxa do not contain enough information to either calibrate the tree of life or fully infer macroevolutionary dynamics, phylogenies should preferably include both extant and extinct taxa, which can only be achieved through the inclusion of phenotypic data. This integrative phylogenetic approach provides ample and novel opportunities for evolutionary biologists to benefit from palaeontological data to help establish an evolutionary time scale and to test core macroevolutionary hypotheses about the drivers of biological diversification across various dimensions of organisms.