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

Lead Research Organisation: University of Manchester
Department Name: Life Sciences


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.

Planned Impact

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 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.


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Description The main discovery is that bone collagen sequence information is appropriate for improving our understanding of how particular animal groups evolved in different parts of the world.
Exploitation Route The technique developed specifically as part of this project can be useful for understanding how species that went extinct beyond the limits of ancient DNA research are related to one another as well as how the relate to those that still exist today.
Sectors Environment,Culture, Heritage, Museums and Collections

Description The findings of this short-term project have been used to improve our understanding of vertebrate evolution using protein sequencing.
First Year Of Impact 2012
Sector Environment,Culture, Heritage, Museums and Collections
Impact Types Societal

Title Data from: Ancient collagen reveals evolutionary history of the endemic South American 'ungulates' 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Description Public talk about my new scientific methodologies and how they are changing our understanding of evolution in biodiversity hotspots 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact The talk sparked questions relating to our research in their local area (the Cayman Islands) and then discussions afterwards.

It became clear that a greater understanding and awareness of biodiversity in the tropics, and its decline in recent centuries due to human impact, can be used to protect the surviving species, and why this is of importance to human society.
Year(s) Of Engagement Activity 2013