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

在过去的几百万年里，由于气候变化、栖息地碎片化和人类影响，动物物种灭绝的数量迅速增加。我们过去了解生物多样性本质的能力有赖于将生物遗骸零碎地保存到化石记录中。一百多年来，研究化石遗骸的传统方法是通过与其他骨骼解剖学物种的形态比较来进行研究。不幸的是，大量灭绝的类群的代表性遗骸并没有提供足够的形态细节来让我们清楚地了解它们在哺乳动物进化中的地位。在生物多样性高的地区，这一点尤其困难，因为在这些地区，已灭绝的类群往往与一系列不同的现存物种具有共同的形态特征，掩盖了它们真正的进化史。因此，在热带地区，许多生物分支达到其物种多样性的最高水平，目前无法评估过去发生的生物多样性丧失的程度。近年来，通过对现代和古代DNA的分析，我们对哺乳动物进化的理解有了很大的提高，从而极大地重新绘制了生命之树。然而，有许多主要类别的分类群超出了古代DNA可接受的生存极限。这要么是因为最近有代表性的化石的地质年代，要么是因为它们的栖息地和地理位置(如温暖或潮湿的环境)，因此在气候中形成的化石迅速降解了DNA分子。其中许多区域是生物多样性最大的区域，包括前冈德瓦南超大陆的许多区域(例如非洲、马达加斯加、南美洲和澳大利亚)。蛋白质是另一类具有遗传信息的生物分子，它确实在化石中存活了一段时间，这一时间段比DNA的存活时间大一个数量级，现在可以通过最近开发的“软电离”质谱学技术进行常规分析。这项研究项目的目的是利用蛋白质序列，主要是胶原(I)的序列，可以用来解决系统发育关系。将特别关注过去发生的哺乳动物生物多样性丧失的程度(就遗传信息而言)，主要集中在以生物多样性著称的两个区域。这项研究将调查两个截然不同的全球生物多样性热点地区已灭绝的真兽目哺乳动物的代表，主要是关于南美洲上更新世生物多样性的丧失(Notounulata和Litopterna)，这反过来将使人们能够更好地了解全新世马达加斯加(Bibymalagasia)的生物多样性丧失，这些生物多样性通常被认为超出了古代DNA分析的范围。它将探索蛋白质测序在进化研究中的潜力，这将为分析其他灭绝了很久的脊椎动物物种开辟了道路。

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.