Of mammoths, microbes and molecules, paleometagenomes from the past

猛犸象、微生物和分子，来自过去的古宏基因组

• 批准号: RGPIN-2015-04184
• 负责人: Poinar, Hendrik
• 金额: $ 3.28万
• 依托单位: McMaster University
• 依托单位国家: 加拿大
• 项目类别: Discovery Grants Program - Individual
• 财政年份: 2016
• 资助国家: 加拿大
• 起止时间: 2016-01-01 至 2017-12-31
• 项目状态: 已结题
• 来源: https://www.nserc-crsng.gc.ca/ase-oro/Details-Detailles_eng.asp?id=612825
• 关键词: mammoths; microbes; molecules; paleometagenomes; past

Abundant and compelling evidence indicates that the planetary climate system is moving toward states not equalled in the last 120,000 years. The implications of these warming trends on ‘whole-ecosystem’ (i.e microbial, faunal, floral and insect) diversity remain unknown. One way to test this is to look back in time. Approximately 11,000 years ago more than 100 species of large mammals and birds went extinct in North America. While the precise causes of these losses remains unclear their underlying consequences remain exceptionally pertinent today, given our rapidly warming artic. How will biota respond given the rapidly warming north? One way to address this is to evaluate how they responded in the past, to prior climatic shits, ones that were equally or more drastic. Using genetic signatures gleaned from fossil remains, (both mammalian and microbial) we will investigate how populations responded to similar climatic shifts in the past and use this information to help prepare us for looming losses in the near future. With these data we can begin to address questions such as why was it that some went extinct (mammoth, mastodons, sloths, horses) while others persisted (bison, bears)? While many argue that climate was the direct cause of these losses, others have suggested that humans (big game hunters) played a critical role in their final demise. Perhaps effective population sizes were so small post glacial time periods that they were effectively at a ‘tipping point’, and that humans dealt the final blow. One way to disentangle these two, seemingly disparate hypotheses, is to study the genetics of the requisite fauna (mammoths) during times of extreme climate change when humans were absent, during the last glacial and interglacial, some 115-130Kyrs BP and present at the most recent one 22Kyrs BP and the Pleistocene/Holocene transition, where they ultimately went extinct some 11,000 years ago. This work is possible given our remarkable frozen heritage, i.e. the permafrost of the Canadian north, which contains the macro fossil assemblages and pollen records of deep time, but the degraded remains of their genomes. Using state-of-the-art capture (enrichment) based methods, some developed if our labs, coupled with High-Throughput Sequencing (HTS), we can now rebuild mitochondrial and entire non-repetitive nuclear genomes at reasonable costs and in record time. The following NSERC proposal seeks to build upon our research strengths and focus on methodological improvements for aDNA recovery disentangling Pleistocene-Holocene extinctions using accurate reconstructions of population sizes through time, and use novel metagenomic capture-based approaches to better understand ecosystem-level responses of microbial communities to climatic shifts through ancient environmental DNAs (aDNA). These data will be used to help predict future ecosystem responses given current estimated trajectories.

大量令人信服的证据表明，行星气候系统正朝着过去12万年来从未有过的状态发展。这些变暖趋势对“整个生态系统”（即微生物，动物，花卉和昆虫）多样性的影响仍然未知。检验这一点的一种方法是回顾过去。大约11,000年前，100多种大型哺乳动物和鸟类在北美灭绝。虽然这些损失的确切原因尚不清楚，但考虑到我们迅速变暖的北极，它们的潜在后果在今天仍然非常重要。生物群将如何应对迅速变暖的北方？解决这个问题的一种方法是评估他们在过去是如何应对之前的气候变化的，那些同样或更剧烈的变化。利用从化石遗骸中收集到的遗传特征（包括哺乳动物和微生物），我们将研究种群如何应对过去类似的气候变化，并利用这些信息帮助我们为不久的将来即将到来的损失做好准备。有了这些数据，我们就可以开始解决一些问题，比如为什么有些物种灭绝了（猛犸、乳齿象、树懒、马），而另一些物种却存活了下来（野牛、熊）？虽然许多人认为气候是这些损失的直接原因，但其他人认为人类（大型狩猎者）在他们的最终灭亡中发挥了关键作用。也许有效的人口规模是如此之小后冰川时期，他们实际上是在一个“临界点”，人类处理的最后一击。 解开这两个看似完全不同的假说的一种方法是研究人类消失时极端气候变化时期所需动物群（猛犸象）的遗传学，在最后一次冰期和间冰期，大约115- 130 Kyrs BP和最近的22 Kyrs BP和更新世/全新世过渡时期，它们最终在大约11，000年前灭绝。 这项工作是可能的，因为我们有非凡的冰冻遗产，即加拿大北部的永久冻土，其中包含了远古时代的大型化石组合和花粉记录，但它们的基因组的退化遗骸。使用最先进的基于捕获（富集）的方法，一些是我们实验室开发的，再加上高重复测序（HTS），我们现在可以以合理的成本和创纪录的时间重建线粒体和整个非重复核基因组。 以下NSERC提案旨在建立在我们的研究优势基础上，并专注于aDNA恢复的方法改进，通过准确重建种群规模来解开更新世-全新世的束缚，并使用基于宏基因组捕获的新方法来更好地了解微生物群落通过古环境DNA（aDNA）对气候变化的生态系统水平响应。这些数据将被用来帮助预测未来的生态系统响应目前的估计轨迹。