Using Fossil Proteomics for Resolving Phylogenetics of Extinct Mammalian Orders in Ancient Biodiversity Hotspots

During the last few million years there has been a rapid increase in the numbers of faunal species becoming extinct owing to the effects of climate change, habitat fragmentation and human impact. Our ability to understand the nature of biodiversity in the past relies on the fragmentary preservation of organisms' remains into the fossil record. For over a hundred years the conventional approaches to investigating fossil remains were by morphological comparisons to other species of skeletal anatomy. Unfortunately the representative remains of a large number of extinct taxa do not provide sufficient morphological details to make our understanding of their position in mammalian evolution clear. This is particularly difficult in regions of high biodiversity, where extinct taxa often share morphological characteristics common with a range of diverse extant species, obscuring their true evolutionary history. Thus, in the tropics, where many clades of organisms reach their highest species diversity, it is currently not possible to evaluate the extent of biodiversity loss that occurred in the past. In recent years, our understanding of mammal evolution has been greatly improved by the analysis of modern and ancient DNA, and as a result, the living Tree of Life has been drastically redrawn. However, there are numerous major classes of taxa that are beyond the accepted survival limits of ancient DNA. These are either due to the geological age of the most recent representative fossils, or due to their habitation and geographical location (such as warm or wet environments) and thus fossilisation in climates that quickly degrade DNA molecules. Many of these regions are those with the greatest biodiversity, including many of the regions of the former Gondwanan supercontinent (e.g., Africa, Madagascar, South America and Australia). Proteins, another genetically-informative class of biomolecules do survive in fossils for periods of time that is orders of magnitude greater than for DNA and can now be routinely analysed by recently-developed techniques of 'soft-ionisation' mass spectrometry. The aim of this research project is to use protein sequences, predominantly those of collagen (I), can be used to resolve phylogenetic relationships. Particular interest will be placed on demonstrating the extent of mammalian biodiversity loss (in terms of genetic information) that has occurred in the past focussing primarily on two regions well-known for their biodiversity. The study will investigate representatives of extinct orders of eutherian mammals from two distinct worldwide 'biodiversity hotspots', primarily on the Plio-Pleistocene biodiversity loss in South America (Notoungulata and Litopterna), which will in turn allow for greater understanding of biodiversity loss on Holocene Madagascar (Bibymalagasia) and that are generally considered beyond the scope of ancient DNA analyses. It will explore the potential of protein sequencing for evolutionary studies, which will lead the way for the analyses of other vertebrate species that went extinct much further into the past.

The proposed research will be of direct interest to a wide range of academics and the many members of the public that have interests in palaeontology and molecular evolution. This topic is of particular interest given the cutting edge technology used to achieve the results that offer the ability to phylogenetically place extinct 'problematica' species from regions of the world where their remains are too degraded for typical ancient DNA analyses (particularly in the tropics). The greatest immediate benefit would be the Tree of Life project web project http://tolweb.org/tree/ which ultimately benefits the general public. However, the collagen-based phylogenetics could be further applied to numerous non-mammalian vertebrates worldwide and ultimately benefit a much larger group of local authorities through the identification of archaeological finds (i.e., those fragments of bone often given by members of the public to the local portable antiquities scheme officer for identification).

Furthermore, industrial scientists will also be able to use the database of collagen sequences from a wide variety of species that will be developed to help identify the species of particular samples, whether archaeological (fragmentary bone) or agricultural (meat and bone meal, fish meal, monitoring contamination in gelatine products). This would benefit academics as well as agencies such as the Department for Environment, Food and Rural Affairs. The proposed application of this collagen sequence database, that would include a consensus sequence able to be used for any mammalian sample, will provide a tool for sample identification worldwide.