Seeing genes in space & time: the evolution of neutral and functional genetic diversity using woolly mammoth

在太空中观察基因

• 批准号: NE/J010480/2
• 负责人: Ian Barnes
• 金额: $ 1.92万
• 依托单位: Natural History Museum
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2013
• 资助国家: 英国
• 起止时间: 2013 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FJ010480%2F2
• 关键词: Seeing; genes; space; time; evolution

Understanding how a population changes through time is critical to understanding the broader picture of species evolution and extinction. By examining the dynamics of population change, we can explore how, as a result of changing competitive pressures and habitats, species distributions alter through time and space. Populations can increase or decline, or differ in their levels of migration and immigration. Although it is theoretically possible to directly observe these processes, the time span across which observations would be necessary renders this all but impractical. Fortunately, direct observation is not the only way to infer changes occurring in populations, because all of these processes leave traces in the genetic diversity of a species. By sequencing pieces of genetic information of a species (DNA) from a large number of individuals within a population, it is possible to shed light on the dynamics of species going back hundreds of thousands of years. When analysing data from modern populations, data may be insufficient to acquire the full picture of past population change - any information from populations no longer around today will be lost. A far more powerful approach is to directly sample the genetics of past populations. This approach uses ancient DNA: DNA that survives trapped in tissue such as hair and bone dating back to ~120,000 years. Research in ancient DNA has shown that the dynamics of Pleistocene populations were more complicated than had been initially inferred from modern data alone. Critically, the Pleistocene is a period which covered a series of large changes in climate, and a detailed examination of Pleistocene population dynamics may shed light on how species respond to the effects of climate change.However, there are difficulties arising from the decay of DNA over time, which leaves relatively few bones that can be successfully sampled, and results in short pieces of DNA, problematic for analyses. One upshot of this is that most ancient DNA studies to date have relied on an abundant, short loop of DNA called mitochondrial (mt) DNA. However, mtDNA is only passed down through the maternal line, and cannot provide any information on the paternal lineage. Sequencing a large number of dated bone samples for longer sequences of both mtDNA, and DNA from the cell nucleus, would shed light on both male and female evolutionary history, and provide a much better insight into how animal populations have changed over the last few hundred thousand years.The woolly mammoth, an icon for both the Pleistocene and species extinction, is an ideal species in which to study how animals may be affected by climate and environmental change. Moreover, by examining genes that may be favoured during times of climate change, such as those involved in hair growth or cold adaptation, it will be possible to investigate any differing patterns in the DNA between these and more 'neutral' genes, helping us to better understand both the demographic and adaptive processes taking place in these populations.Recent progress has made such a project possible. Using new high-throughput technologies for analysing DNA, in combination with methods to locate the specific DNA fragments of interest, we can now rapidly and efficiently analyse thousands of units of DNA code from hundreds of fossil remains, allowing us to infer what happened to populations in the past.

了解种群如何随时间变化，对于理解物种进化和灭绝的更广泛图景至关重要。通过研究种群变化的动态，我们可以探索由于竞争压力和栖息地的变化，物种分布如何在时间和空间上发生变化。人口可以增加或减少，也可以在移民和移民的水平上有所不同。虽然理论上可以直接观察到这些过程，但观察所需的时间跨度使得这几乎是不切实际的。幸运的是，直接观察并不是推断种群变化的唯一方法，因为所有这些过程都在物种的遗传多样性中留下了痕迹。通过对种群中大量个体的物种遗传信息(DNA)进行排序，有可能揭示数十万年前物种的动态。在分析现代人口的数据时，数据可能不足以获得过去人口变化的全貌--今天不再存在的人口的任何信息都将丢失。一种更有效的方法是直接对过去种群的基因进行采样。这种方法使用了古老的DNA：保存在头发和骨骼等组织中的DNA，可以追溯到大约12万年前。对古代DNA的研究表明，更新世种群的动态比最初仅从现代数据推断的要复杂得多。关键的是，更新世是一段经历了一系列气候大变化的时期，对更新世种群动态的详细研究可能会揭示物种如何对气候变化的影响做出反应。但是，随着时间的推移，DNA的腐烂带来了困难，可以成功采样的骨骼相对较少，导致DNA片段较短，这对分析是有问题的。其结果之一是，到目前为止，大多数古代DNA研究都依赖于一种称为线粒体(Mt)DNA的丰富、短环的DNA。然而，线粒体DNA只通过母系遗传，不能提供任何关于父系血统的信息。对大量过时的骨骼样本进行测序，以获得更长的线粒体DNA序列，以及细胞核中的DNA，这将有助于揭示男性和女性的进化史，并提供更好的洞察过去数十万年来动物种群的变化。猛犸象是更新世和物种灭绝的象征，是研究动物如何受到气候和环境变化影响的理想物种。此外，通过研究在气候变化时期可能受到青睐的基因，例如那些与毛发生长或冷适应有关的基因，将有可能研究这些基因和更多“中性”基因之间的DNA差异模式，帮助我们更好地理解这些群体中发生的人口统计和适应过程。最近的进展使这样的项目成为可能。使用新的高通量DNA分析技术，结合定位感兴趣的特定DNA片段的方法，我们现在可以快速有效地分析数百具化石遗骸中的数千个DNA编码单位，使我们能够推断过去人口发生了什么。

项目成果

Million-year-old DNA sheds light on the genomic history of mammoths

• DOI: 10.1038/s41586-021-03224-9
• 发表时间: 2021-02-17
• 期刊: NATURE
• 影响因子: 64.8
• 作者: van der Valk, Tom;Pecnerova, Patricia;Dalen, Love
• 通讯作者: Dalen, Love