The impact of death on the Tree of Life: assessing the relationship between taphonomy and phylogeny

解析生命之树，特别是了解在其最深分支中发生的事件的顺序，是目前的一个主要研究目标。这里有许多关于进化的基本问题的答案：新的群体是如何产生的，复杂的身体结构是如何组合起来的，腿和翅膀等新事物是如何产生的？化石记录在这项研究中发挥着关键作用，它产生了过渡形式，并为事件提供了时间轴，但我们评估它们提供的过滤数据的方式是否存在特别的危险？如果对化石的解释不好，它们是否会产生积极的误导？对化石的解释可能会被死亡、腐烂和保存（埋藏学）造成的偏见所扭曲，这些都是化石形成过程中不可避免的过程。可石化和不可石化的数据可能包含非常不同的“信号”，这可能会扭曲我们重建进化树和过渡的能力。此外，腐烂和分解可以使化石看起来比它们在生命中更原始。因此，埋藏过滤器对我们重建进化的能力具有非常深远的影响，但在这种背景下它们尚未得到系统的研究。因此，我将要解决的关键问题是：古生物学过滤器对我们重建进化树和从中推断出的进化事件的能力有任何影响吗？如果是，哪些生物群体受到影响，影响的方式是什么？特定化石的重要性是否是误解的结果？当埋藏学的过滤器被考虑在内时，我们对特定进化假说的理解，比如那些与主要分支起源有关的假说，是否发生了转变？为了解决这个问题，我将1）量化埋藏过滤器对我们使用经验和理论方法重建化石生物进化关系的能力的影响; 2）确定哪些类型的数据和生物群最受衰变偏差的干扰，从而在某些领域进行重点研究，并鼓励其他领域的谨慎; 3）使用埋藏过滤器的知识来重新评估生命之树。这些综合办法将使我能够检验与主要群体的起源和演变有关的具体假设。更广泛地说，它们将能够对化石记录的质量进行基本评估。通过量化这些问题的规模和分布，我们可以完善并彻底改革我们使用化石来了解生命历史的方式。

Resolving the Tree of Life, in particular understanding the sequence of events taking place in its deepest branches, is currently a major research objective. Herein lie the answers to many fundamental questions about evolution: how do new groups originate, how are complex body-plans assembled and how do novelties such as legs and wings originate? The fossil record plays a pivotal role in this research by yielding transitional forms and providing a timeline for events, but are there particular dangers in the way we evaluate the filtered data they provide? Might fossils even be positively misleading if they are poorly interpreted? Interpretation of fossils can be distorted by biases caused by death, decay and preservation (taphonomy) - inevitable processes in the formation of fossils. Fossilizable and non-fossilizable data can contain very different 'signals' which could distort our ability to reconstruct evolutionary trees and transitions (phylogeny). Furthermore, decay and decomposition can cause fossils to appear more primitive than they were in life. Taphonomic filters therefore have very profound effects upon our ability to reconstruct evolution, but they have not been systematically investigated in this context. The key question I will address is therefore: do palaeontological filters have any effect upon our ability to reconstruct evolutionary trees and the evolutionary events that are inferred from them? If so, which groups of organisms are affected and in what way? Is the supposed importance of particular fossils a result of misinterpretation? When taphonomic filters are taken into account, is our understanding of specific evolutionary hypotheses, such as those relating to the origins of major clades, transformed? In order to address this questions, I will 1) Quantify the effect of taphonomic filters upon our ability to reconstruct the evolutionary relationships of fossil organisms using empirical and theoretical approaches; 2) Identify which types of data and groups of organisms are most disrupted by decay biases, thereby enabling focused study in some areas and encouraging caution in others; 3) Use knowledge of taphonomic filters to re-evaluate the Tree of Life. These combined approaches will allow me to test specific hypotheses relating to the origin and evolution of major groups. More broadly, they will enable a fundamental assessment of the quality of the fossil record. By quantifying the scale and distribution of these problems, we can refine and radically overhaul the way in which we use fossils to inform our understanding of the history of life.