Of mammoths, microbes and molecules, paleometagenomes from the past

大量令人信服的证据表明，地球气候系统正朝着过去12万年未曾达到的状态发展。这些变暖趋势对“整个生态系统”（即微生物、动物、植物和昆虫）多样性的影响仍然未知。检验这一点的一个方法是回顾过去。大约11000年前，北美有100多种大型哺乳动物和鸟类灭绝。虽然这些损失的确切原因尚不清楚，但鉴于我们的北极迅速变暖，它们的潜在后果在今天仍然非常重要。在北方迅速变暖的情况下，生物群将如何应对？解决这个问题的一种方法是评估它们过去是如何应对之前的气候变化的，那些同样剧烈或更剧烈的气候变化。利用从化石遗骸（包括哺乳动物和微生物）中收集到的遗传特征，我们将调查过去人类是如何应对类似的气候变化的，并利用这些信息帮助我们为不久的将来迫在眉睫的损失做好准备。有了这些数据，我们可以开始解决这样的问题：为什么有些物种灭绝了（猛犸象、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（大型猎物猎人）在它们的最终消亡中发挥了关键作用。也许冰河时期后的有效种群规模非常小，以至于它们实际上处于一个“临界点”，人类造成了最后的打击。***解开这两个看似不相干的假设的一种方法是，在人类消失的极端气候变化时期研究必要的动物群（猛犸象）的遗传学，在最后一次冰川期和间冰期，大约115-130千万年，最近的一个22千万年，以及更新世/全新世过渡时期，它们最终在大约11000年前灭绝。***这项工作是可能的，因为我们有非凡的冷冻遗产，即加拿大北部的永久冻土，它包含了宏观化石组合和深时间的花粉记录，但它们的基因组的退化遗骸。利用我们实验室开发的最先进的捕获（富集）方法，加上高通量测序（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提案旨在建立我们的研究优势，并专注于改进方法，利用精确的种群大小随时间的重建来解开更新世-全新世灭绝的aDNA恢复，并使用新的基于宏基因组捕获的方法来更好地理解微生物群落对气候变化的生态系统水平的响应。这些数据将用于根据目前估计的轨迹来帮助预测未来生态系统的反应。

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.