Traditionally, evolutionary trees were calibrated to geological based on the ages of the oldest fossils of living lineages. Unfortunately, fossils are always younger than their evolutionary lineages because of the delay between genome divergence and its anatomical manifestation, as well as the problems with the patchy rock record. The only way to establish an accurate evolutionary timescale is using molecular clock methodology which uses these same fossils to establish minimum constraints on the ages of clades, calibrating the genetic distance between living lineages to geological time.
Molecular clock methods are diverse and they often yield equally disparate results (Donoghue and Yang 2016). In our research we have explored the relative efficacy of molecular clock methods, in particular, exploring how palaeontological and stratigraphic data are interpreted to calibrate the molecular clock. This work has encompassed theory (e.g. O’Reilly et al. 2015), empirical (e.g. dos Reis et al. 2015) and simulation-based analyses (e.g. Warnock et al. 2017), with the aim of establishing how fossil and biogeographic calibrations should be formulated and which approach yields the most accurate, if not precise, results.
Early vertebrate evolution
The origin of vertebrates represents one of the most fundamental events in animal evolution. This occurs not only because this episode represents the establishment of our own evolutionary lineage, but because it coincides with one a singularly dramatic episode in genetic and developmental evolution. Hence, it is the focus of interest of researchers from a great variety of disciplines, including palaeontologists, comparative anatomists, embryologists, as well as developmental geneticists and molecular phylogeneticists.
Our aim is to provide an integrated framework for understanding the sequence of events in which the body plan of vertebrates and jawed vertebrates was established. This is achieved through comparative analysis of living and fossil vertebrates, and their immediate relatives among the invertebrates. This is used as a basis for the development of schemes of their evolutionary relationships (e.g. Gabbott et al. 2016), and the resulting patterns of character evolution (e.g. Donoghue and Keating 2014), used subsequently to constrain hypotheses of developmental and genomic evolution (e.g. Donoghue and Purnell 2005).
In particular, we have focussed on the evolution of development of the vertebrate skeleton, uncovering the sequence and nature of appearance of each of the component embryological systems that comprise the skeleton (e.g. Keating et al. 2018). This has revealed that what is taken to be a single coherent ‘vertebrate skeleton’ is actually an evolutionary and embryological chimaera that is characteristic of the group of living jawed vertebrates alone (e.g. Donoghue and Sansom 2002).
Early animal evolution
Comparisons of the patterns of embryology exhibited by animals has been the major resource in attempts to reconstruct their evolutionary history, ever since the first phylogeny was constructed by the comparative embryologist Ernst Haeckel in the 1870s. The attempt has always been to infer the nature of deep ancestors by identifying common embryological features among living relatives, but these inferences invariably rely upon incomplete information, and conclusions are often fine balanced. If only there were a fossil record of embryology, to provide direct insight into the embryology of animals from the time at which the major groups of animals first emerged.
Although embryos have the preservation potential of snot, amazingly, over the past decade fossilised embryos have been discovered from sites in China, Siberia, Australia and the USA, providing unforseen insights embryology before, during and after the Cambrian evolutionary explosion of animal diversity (e.g. Dong et al. 2017; Yin et al. 2017). Together with a worldwide team of collaborators, our group is working to elucidate the embryology, affinity and phylogenetic significance of the embryo fossil record using Synchrotron Radiation X-ray Tomographic Microscopy (SRXTM) at the Swiss Light Source to fully characterise these fossils.
Early plant evolution
The origin and early diversification of land plants was a transformative episode in the evolution of our planet, doubling the oxygen yield from photosynthesis and increasing weathering rates, ultimately shaping modern biogeochemical cycles. However, our understanding of this episode is confused because of systematic biases in the rock record, insufficient anatomical understanding of the earliest land plants, and a lack of resolution on the evolutionary relationships among primitive living plants.
In collaboration with colleagues in the UK, Europe, and China, we are seeking to resolve the relationships between living land plants (e.g. Puttick et al. 2018). In this framework, we aim to establish the sequence in which land plant bodyplan characters evolution (complemented by SRXTM analysis of charcoalified fossil remains), their relation to developmental and genomic evolution, as well as the timescale over which these characters evolution (e.g. Morris et al. 2018). Ultimately, we aim to establish an integrative biological and geological timescale from which to elucidate the co-evolution of land plants and the Earth System.