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/J009342/1
• 负责人: Peter Young
• 金额: $ 41.6万
• 依托单位: University of York
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2012
• 资助国家: 英国
• 起止时间: 2012 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=NE%2FJ009342%2F1
• 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.

了解种群如何随着时间的推移而变化，对于了解物种进化和灭绝的更广泛情况至关重要。通过研究种群变化的动态，我们可以探索如何，由于不断变化的竞争压力和栖息地，物种分布改变通过时间和空间。人口可能增加或减少，或在移徙和移民水平上有所不同。虽然理论上可以直接观察这些过程，但观察所需的时间跨度使这几乎不切实际。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会在物种的遗传多样性中留下痕迹。通过对一个种群中大量个体的物种遗传信息（DNA）片段进行测序，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遗传学进行采样。这种方法使用了古老的DNA：可以追溯到12万年前的头发和骨骼等组织中的DNA。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更为复杂。重要的是，更新世是一个气候发生一系列重大变化的时期，对更新世种群动态的详细研究可能有助于了解物种如何应对气候变化的影响。然而，随着时间的推移，DNA的衰变带来了困难，这使得可以成功取样的骨骼相对较少，导致DNA片段较短，难以分析。结果之一是，迄今为止，大多数古代DNA研究都依赖于一种称为线粒体（mt）DNA的丰富的短环DNA。然而，线粒体DNA仅通过母系传递，不能提供父系血统的任何信息。对大量年代久远的骨骼样本进行线粒体DNA和细胞核DNA的测序，将有助于了解男性和女性的进化史，并更好地了解动物种群在过去几十万年中的变化。长毛猛犸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，例如那些与头发生长或寒冷适应有关的基因，将有可能研究这些基因与更“中性”基因之间DNA的任何不同模式，帮助我们更好地了解这些人群中发生的人口统计和适应过程。最近的进展使这样一个项目成为可能。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来自数百个化石遗骸的数千个DNA代码单元，使我们能够推断过去种群发生了什么。

项目成果

Resurrecting phenotypes from ancient DNA sequences: promises and perspectives

从古代 DNA 序列中复活表型：承诺和前景

• DOI: 10.1139/cjz-2014-0337
• 发表时间: 2015
• 期刊: Canadian Journal of Zoology
• 影响因子: 1.4
• 作者: Campbell K

Holarctic genetic structure and range dynamics in the woolly mammoth.

• DOI: 10.1098/rspb.2013.1910
• 发表时间: 2013-11-07
• 期刊: Proceedings. Biological sciences
• 作者: Palkopoulou E;Dalén L;Lister AM;Vartanyan S;Sablin M;Sher A;Edmark VN;Brandström MD;Germonpré M;Barnes I;Thomas JA
• 通讯作者: Thomas JA

Interordinal gene capture, the phylogenetic position of Steller's sea cow based on molecular and morphological data, and the macroevolutionary history of Sirenia.

序间基因捕获、基于分子和形态学数据的虎头海牛的系统发育位置，以及海牛的宏观进化历史。

• DOI: 10.1016/j.ympev.2015.05.022
• 发表时间: 2015
• 期刊: Molecular phylogenetics and evolution
• 影响因子: 4.1
• 作者: Springer MS