Collagen Type I: Sequence Evolution, Species Identification, and Unlocking Past Trends in Marine Biodiversity

Abstract

Our planet is currently in the midst of the sixth mass extinction crisis. In terms of our oceans, we vastly underestimate the quantity of life we exploit each year, and weigh the health of our remaining biodiversity against a backdrop of modern data. Sharpening the baseline against which the true impacts of anthropogenic activities can be accurately determined requires an interdisciplinary effort between archaeologists, historians, ecologists and conservationists, and involves a systematic assessment of ancient species abundance and biodiversity data by reaching as far and as accurately into the past as is feasible with modern technologies. Collagen type (I), the most dominant protein in vertebrate bone, combines properties of stability (of the molecule within bone), longevity (into the archaeological record) and an evolving amino acid sequence, the analysis of which facilitates its use in faunal identification of ancient bones, many of which lay beyond the reach of traditional morphological analysis. This body of work represents the most comprehensive interrogation of the collagen (I) molecule achieved to date and applies the findings to zooarchaeological deposits of marine vertebrates, focussing on fishes (Actinopterygii) and marine turtles (Chelonioidea), two groups that have been vastly understudied but represent the most diverse (fishes) and highly threatened (turtles) vertebrates on the planet. The research presented here assesses the triple-helical region of the collagen (I) molecule and investigates its chemical properties for application to conservation through archaeology. The results quantify amino acid sequence diversity and rate of evolution in fishes, with an application to phylogenetics, and examine the stabilising properties of the protein in terms of both collagen breakdown and whole bone degradation, as a function of amino acid chemistry. Using powerful mass spectrometric tools (MALDI-TOF and LC-MS/MS), this knowledge is then applied to 1,244 archaeological marine vertebrate bones from both temperate (Baltic Sea) and tropical (circum-Caribbean) regions, harnessing the potential of ancient preserved collagen to target species-level identification. The results highlight collagen (I) analysis as the cheapest, quickest and most effective tool currently available for mass taxonomic identification of archaeological non-mammalian marine vertebrate bone remains. Moreover, the proteomic toolkit has far-reaching applications, including but not limited to the detection of new archaeological understanding, exploration into the sustainability of site fisheries through time, and the enhancement of more robust fisheries baselines. The research within this thesis constitutes keystone knowledge that showcases the potential of collagen (I) in a manner that benefits archaeologists, marine biologists, conservationists and all other stakeholders, as we work towards more stringent ocean management and governance to protect what is left of our ocean biodiversity.

Date of Award	1 Jan 1824
Original language	English
Awarding Institution	The University of Manchester
Supervisor	Michael Buckley (Supervisor), Roy Wogelius (Supervisor) & Phillip Manning (Supervisor)