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The original Introduction for my thesis

One month ago, I defended my PhD thesis and passed my viva exam, proving that basically anyone can become a Doctor these days. I got ‘minor revisions’ as a result, which was just to shorten the abstract to institutional format requirements, and cut the waffle from the Introduction. I kinda liked the waffle though, as it was written as a non-specialist introduction for my work and the field in general. So even though this didn’t make it into the final version, now published online, here it is in full below – enjoy! 🙂

“One of the central goals for palaeobiologists is to reconstruct the history and trajectory of life on Earth. Fundamental to our discipline is the use of the fossil record to capture information about historical trends in diversity, and the components of extinction and speciation. Through this, we gain insight into the patterns and processes that have shaped the architecture of life on Earth, including the birth, death and evolution of ecosystems, and the origins and future of the present day diversity. One might consider an analogy between the fossil record and the modern biota as a stop motion picture: while through observing living organisms we might get a single high definition image, it will only be part of a full motion picture brought to us by the fossil record. However, rather than being a single continuous picture, the fossil record is better thought of as highlights of a thousand different frames, all hastily edited together and then left in a dusty storeroom, to be uncovered years later devoid of all original context. The goal of palaeobiologists, then, is to revive this picture to show a single, continuous story. And what a story it is.

The core and underpinning concept for modern palaeobiology is that occurrences of fossils, and the taxa that they represent, can be grouped in space and time, and by linking consecutive groups of these and counting the taxa that they represent, we can produce diversity ‘curves’. These fossil occurrences also tell us something about the nature of extinction and speciation by providing us with apparent first- and last-appearance times for taxa. Therefore, in theory, by reading the fossil record we can identify periods of fluctuating diversity, extinction, and speciation, and apply quantitative methods to test theories applied to evolutionary laws.

Marine tetrapod diversity and its relationship to sea level during the Jurassic and Cretaceous
Marine tetrapod diversity and its relationship to sea level during the Jurassic and Cretaceous

Alas, the fossil record is not perfect, and since the first diversity curves of this nature were produced (Raup, 1972; 1975), there has been considerable debate as to the degree of faith we can place in the fossil record to produce accurate and reliable estimates of historical macroevolutionary patterns. Driving this discussion were the likes of George G. Simpson, Norman D. Newell, Jack Sepkoski, and David M. Raup. In the middle decades of the 20th Century, these authors laid the foundations for modern palaeobiology, and were among the first to quantitatively recognise mass extinctions in the fossil record – biological depletion events vastly beyond what we consider to be ‘background’ rates. Each of them had their own approaches to resolving how to read and interpret the raw fossil record. Such uncertainty is based on the simple observation that natural variation in the number of fossils we can collect through different time intervals is not an accurate reflection of the number of organisms present at that time. Instead, what the fossil record preserves is a fragmented archive, with fossils patchily clustered at different points in space and time. This is due to the architecture of the geological record, in that different environments are preserved based on principles of macrostratigraphy, and this inflicts a natural bias upon the accompanying biological record. Of this record, humans have invariably sampled in a non-uniform pattern: periods perceived to be of higher scientific interest or importance will be sampled more intensely; horizons bearing more fossils tend to be sampled more vigorously, and consequently times and places of less apparent value will be relatively under-sampled.

This brief insight into how variation in sampling might arise in fossil collections demonstrates that the fossil record is biased, both by geological and anthropogenic factors. This artefact is pervasive throughout the fossil record, but by no means intractable. If we take this principle and apply it to our understanding of how to reconstruct historical trends in diversity, then we can begin to distinguish between biological signal and sampling artefacts in the fossil record. After all, knowing your enemy is half the battle. This principle underpins the current thesis, with the theme of how uneven sampling has impacted upon our interpretation of the fossil record during key geological intervals.

Out of all major Phanerozoic interval boundaries, the Jurassic/Cretaceous (J/K) boundary, around 145 million years ago, remains plagued by this geological and biological uncertainty. Historical studies in the latter half of the 20th century recognised a distinct aberration in the biological patterns from Mesozoic background variation, and recognised the J/K boundary as a period of major faunal upheaval. While the issue of uneven sampling was commonly recognised (Raup, 1975; Sepkoski Jr et al., 1981; Sepkoski Jr, 1982; Raup and Boyajian, 1988), methods for accounting for this were relatively simple or at a coarse scale, and produced roughly the same diversity curves as those produced using raw data. Only much more recently has the recognition of the pervasive issue of uneven sampling been able to be taken into account in a more rigorous, detailed, and quantitative manner, by identification and removal of ‘sampling biases’. These advances, underpinned by our development of large, fossil occurrence databases, have led to renewed vitality in attempting to understand and compensate for the complex relationships between sampling and the fossil record. This concept of ‘sampling biases’ led to the development of a novel suite of techniques developed to counteract their influence, and each one has their own critics and advocates. Nonetheless, great leaps have been made in reconstructing long-term trends in palaeobiodiversity, and with this a more detailed understanding of major events, such as mass extinctions.

In the light of all of this progress, however, the J/K boundary remains relatively untouched. For other Mesozoic period boundaries, such as the Triassic/Jurassic, and the end-Cretaceous, we have a much deeper understanding and appreciation of the abiotic and biotic processes that drove major biological changes, and on an order of magnitude greater than that for the J/K boundary. Our current understanding of the J/K interval instead is relatively piecemeal, with events often referred to in passing within broader-scale studies, but with the common note that the interval is somewhat interesting, or worthy of additional investigation. This field of uncertainty prompted the development of this thesis. Originally, I set out with a simple task: to provide insight into the biological patterns that define the Jurassic/Cretaceous boundary, and unlock the processes that might be driving such patterns. In the wake of this comes the question that places this work in historical context: does a more nuanced reading of the Jurassic/Cretaceous boundary indicate that it represented a mass extinction as originally perceived (Raup and Sepkoski Jr, 1982; Raup and Boyajian, 1988), a minor extinction as more recent studies suggest, or something entirely different?

Research overview

Given that I started this thesis with a quote about the value of precision and asking the right questions, it would seem appropriate that I finish this initial overview with a precise set of questions to address. Originally when setting out on this research project, I wanted to answer the question: was there a mass extinction in tetrapods at the Jurassic/Cretaceous boundary? However, as the project developed, it transformed into several nested sub-questions that ask much more precise questions about the nature of changes through this interval.

  • What was the scale of any extinction across the Jurassic/Cretaceous boundary?
  • How did the timing, magnitude, and tempo of this vary between different groups?
  • What was the ecological response of different tetrapod groups to any such extinction?
  • To what extent do environmental factors correlate with biological changes through the Jurassic/Cretaceous boundary?

By asking questions about the scale, timing, and impact of events, the need for a rigorous analytical approach is invoked, and goes beyond the simple initial question of whether or not there was a mass extinction. More importantly, these questions highlight the scope of this thesis, and place it into the context of significant and topical discussions about the current state of life on this planet. Often palaeobiologists are asked about the relevance of their research in a global scientific context. The standard response often is along the lines of ‘the past is the key to the present and future’. However, the question we should perhaps be asking is ‘To what extent can the fossil record be used to understand the present and predict the future, and what are its limitations?’ By asking questions in a more precise manner, we are able to understand the limits of our knowledge, and recognise the broader role our research can play, as well as factor in uncertainty in reconstructed trends. That is not to say that the sole purpose of palaeobiological research of this manner is in future-casting; rather, this is perhaps the most relevant and impactful region upon which our field can play a part in a research climate that is moving progressively towards measurably economic or societal outcomes. There is substantial merit alone in attempting to unravel the complex web of the co-evolution of life on this planet, but the same principle exists here too in that by working within a strong quantitative framework, we are able to infer the limits of our understanding of major macroevolutionary patterns and processes.

The individual chapters of this thesis reflect attempts to provide insight into the above questions at three different scales. Firstly, these questions are asked of all major tetrapod groups that were around in the Jurassic/Cretaceous interval, ranging from the largest sauropod dinosaurs to the smallest of amphibians. Working on this large scale allows in depth exploration of clade interactions and aspects of ecological replacement, the potential synchronicity of any J/K boundary event, the impact of broad-scale sampling issues, and the differential drivers of recovered patterns of diversity and extinction. Secondly, a medium-scale case study involving Crocodyliformes – the group that includes modern crocodylians and their ancestors – as an attempt to place stronger constraints on what we can say about the scale and mode of extinction, and how this variation influences our understanding of the external drivers of resulting patterns. Finally, macroevolution is put largely aside to explore the taxonomy and systematics of a particularly unusual group within Crocodyliformes known as atoposaurids. By exploring the components of this group, the fine-level dynamics of one specific J/K boundary-crossing clade are illuminated, and a richer understanding of the patterns of Crocodyliformes as a whole is developed. As such, this thesis is structured in a cascade style, with each successive chapter representing a more detailed investigation into the former, and each providing reciprocal insight to the other. To begin with, a detailed review of our current understanding of the biotic and abiotic patterns across the Jurassic/Cretaceous boundary is presented.”

Tada! So yeah, waffley, but I like it, and hope you did too 🙂