Of mammoths, microbes and molecules, paleometagenomes from the past

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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.