Ancient proteins resolve the evolutionary history of Darwin's South American ungulates

The project aimed to characterize the collagen type I (COL1) sequences from Pleistocene Macrauchenia sp. and Toxodon sp. bone samples, and by comparison with existing COL1 sequences available from genomic sources establish the phylogenetic position of both extinct species. In order to resolve their phylogenetic position, COL1 was extracted from two Toxodon (samples MLP201204, MACN201212, York12, York13) and two Macrauchenia (samples MLP201212, MACN201202, York14, York15). In addition, modern and Pleistocene COL1 was extracted from additional species currently not present in available databases (Mylodon darwinii, Cyclopes didactylus, Hippopotamus amphibius, Tapirus terrestris) or from species for which COL1 sequences are available (Equus sp., Oryceropus afer). All extractions were performed at BioArCh, University of York (UK). Analyses took place on Bruker maXis HD (Macrauchenia sp., Toxodon sp., Equus sp.) and Thermo Scientific Hybrid Quadruopole-Orbitrap (Macrauchenia sp., Toxodon sp., Mylodon darwinii, Cyclopes didactylus, Hippopotamus amphibius, Tapirus terrestris, Oryceropus afer) platforms.

本项目旨在对更新世（Pleistocene）后弓兽属（Macrauchenia sp.）与箭齿兽属（Toxodon sp.）骨样本中的I型胶原蛋白（COL1）序列进行特征解析，并通过与现有基因组来源的COL1序列比对，明确这两种已灭绝物种的系统发育位置。为解析二者的系统发育位置，研究人员分别从4件箭齿兽样本（MLP201204、MACN201212、York12、York13）与4件后弓兽样本（MLP201212、MACN201202、York14、York15）中提取了COL1序列。此外，研究人员还从两类物种中提取了COL1序列：一类为现有数据库未收录其COL1序列的物种，包括达尔文大地懒（Mylodon darwinii）、二趾树懒（Cyclopes didactylus）、河马（Hippopotamus amphibius）与低地貘（Tapirus terrestris）；另一类为已有COL1序列公开的物种，包括马属（Equus sp.）与土豚（Orycteropus afer）。所有胶原提取实验均在英国约克大学BioArCh实验室完成。质谱分析分别采用布鲁克（Bruker）maXis HD质谱仪（用于后弓兽属、箭齿兽属及马属样本）与赛默飞世尔（Thermo Scientific）四极杆-轨道阱混合质谱仪（用于后弓兽属、箭齿兽属、达尔文大地懒、二趾树懒、河马、低地貘及土豚样本）进行。