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

利用化石蛋白质组学解决古代生物多样性热点地区已灭绝哺乳动物目的系统发育学问题

• 批准号: NE/K000799/1
• 负责人: Michael Buckley
• 金额: $ 10.05万
• 依托单位: University of Manchester
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2012
• 资助国家: 英国
• 起止时间: 2012 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FK000799%2F1
• 关键词: Using; Fossil; Proteomics; Resolving; Phylogenetics

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.

在过去的几百万年里，由于气候变化、生境破碎化和人类的影响，动物物种灭绝的数量迅速增加。我们过去理解生物多样性本质的能力依赖于生物体遗骸的碎片保存到化石记录中。一百多年来，研究化石遗骸的传统方法是通过与其他物种的骨骼解剖学进行形态学比较。不幸的是，大量灭绝分类群的代表性遗骸没有提供足够的形态学细节，使我们清楚地了解它们在哺乳动物进化中的地位。这在生物多样性高的地区尤其困难，在那里，灭绝的分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历史。因此，在热带地区，许多生物分支的物种多样性达到最高水平，目前无法评估过去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得到了极大的提高，因此，生命之树被彻底重新绘制。然而，有许多主要类别的分类群超出了公认的古代DNA的生存极限。这可能是由于最新代表性化石的地质年龄，或者是由于它们的居住地和地理位置（如温暖或潮湿的环境），从而在快速降解DNA分子的气候中发生了生物降解。其中许多地区是生物多样性最丰富的地区，包括前冈瓦纳超大陆的许多地区（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的时间比DNA长几个数量级，现在可以通过最近开发的“软电离”质谱技术进行常规分析。本研究项目的目的是使用蛋白质序列，主要是胶原蛋白（I）的序列，可用于解决系统发育关系。特别感兴趣的将是展示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），主要集中在两个以生物多样性闻名的地区。该研究将调查来自两个不同的全球“生物多样性热点”的真兽目哺乳动物灭绝的代表，主要是南美洲上新世-更新世生物多样性丧失（Notoungulata和Litopterna），这反过来又可以更好地了解全新世马达加斯加（Bibymalagasia）的生物多样性丧失，并且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，这将为分析过去灭绝得更早的其他脊椎动物物种开辟道路。

项目成果

Collagen Fingerprinting: A New Screening Technique for Radiocarbon Dating Ancient Bone.

• DOI: 10.1371/journal.pone.0150650
• 发表时间: 2016
• 期刊: PloS one
• 影响因子: 3.7
• 作者: Harvey VL;Egerton VM;Chamberlain AT;Manning PL;Buckley M
• 通讯作者: Buckley M

Species Identification of Bovine, Ovine and Porcine Type 1 Collagen; Comparing Peptide Mass Fingerprinting and LC-Based Proteomics Methods.

• DOI: 10.3390/ijms17040445
• 发表时间: 2016-03-24
• 期刊: International journal of molecular sciences
• 影响因子: 5.6
• 作者: Buckley M

A molecular phylogeny of Plesiorycteropus reassigns the extinct mammalian order 'Bibymalagasia'.

• DOI: 10.1371/journal.pone.0059614
• 发表时间: 2013
• 期刊: PloS one
• 影响因子: 3.7
• 作者: Buckley M

High-throughput collagen fingerprinting of intact microfaunal remains; a low-cost method for distinguishing between murine rodent bones.

• DOI: 10.1002/rcm.7483
• 发表时间: 2016-04-15
• 期刊: Rapid communications in mass spectrometry : RCM
• 作者: Buckley M;Gu M;Shameer S;Patel S;Chamberlain AT
• 通讯作者: Chamberlain AT

Ancient collagen reveals evolutionary history of the endemic South American 'ungulates'.

古老的胶原蛋白揭示了南美地方性“无凝结”的进化史。

• DOI: 10.1098/rspb.2014.2671
• 发表时间: 2015-05-07
• 期刊: Proceedings. Biological sciences
• 作者: Buckley M