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/J009490/1
• 负责人: Adrian Lister
• 金额: $ 3.61万
• 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: 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%2FJ009490%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.

了解种群随时间的变化对于了解物种进化和灭绝的更广泛的图景至关重要。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，物种分布如何随时间和空间而变化。人口可能会增加或减少，或者迁徙和移民水平有所不同。尽管理论上可以直接观察这些过程，但观察所需的时间跨度使得这几乎不切实际。幸运的是，直接观察并不是推断种群发生变化的唯一方法，因为所有这些过程都会在物种的遗传多样性中留下痕迹。通过对种群内大量个体的物种遗传信息 (DNA) 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，数据可能不足以全面了解过去人口变化的情况——来自当今已不复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人群的遗传学进行采样。这种方法使用古老的 DNA：被困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根据现代数据推断的更为复杂。重要的是，更新世是一个涵盖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 的衰变会带来困难，导致能够成功取样的骨骼相对较少，并导致 DNA 片段较短，给分析带来问题。其结果之一是，迄今为止，大多数古代 DNA 研究都依赖于一种丰富的、短的 DNA 环，称为线粒体 (mt) DNA。然而，线粒体DNA仅通过母系传承，并不能提供任何有关父系的信息。对大量已年代久远的骨骼样本进行测序，以获得更长的线粒体 DNA 和细胞核 DNA 序列，将揭示雄性和雌性的进化史，并更好地了解动物种群在过去数十万年中的变化。猛犸象是更新世和物种灭绝的标志，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，通过检查在气候变化时期可能受到青睐的基因，例如那些涉及毛发生长或寒冷适应的基因，将有可能研究这些基因与更“中性”基因之间的DNA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。利用新的高通量 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个化石遗骸中的数千个 DNA 代码单元，使我们能够推断过去人群发生了什么。

项目成果

Genetic Insight into an Extinct Population of Asian Elephants (Elephas maximus) in the Near East

对近东亚洲象（Elephas maximus）灭绝种群的遗传洞察

• DOI: 10.5334/oq.36
• 发表时间: 2018
• 期刊: Open Quaternary
• 作者: Girdland-Flink L

Mammoth and musk ox ESR-dated to the Early Midlandian at Aghnadarragh, County Antrim, Northern Ireland, and the age of the Fermanagh Stadial

猛犸象和麝牛 ESR——可追溯到北爱尔兰安特里姆郡阿格纳达拉赫的早期米德兰时代，以及弗马纳体育场的时代

• DOI: 10.1002/gj.2668
• 发表时间: 2015
• 期刊: Geological Journal
• 影响因子: 1.8
• 作者: Lister A

Mammoth evolution in the late Middle Pleistocene: The Mammuthus trogontherii-primigenius transition in Europe

中更新世晚期猛犸象的演化：欧洲猛犸象-原始猛犸象的转变

• DOI: 10.1016/j.quascirev.2022.107693
• 发表时间: 2022
• 期刊: Quaternary Science Reviews
• 影响因子: 4
• 作者: Lister A

Dental remains of fossil elephants from Turkey

来自土耳其的化石大象的牙齿遗骸

• DOI: 10.1016/j.quaint.2011.05.042
• 发表时间: 2012
• 期刊: Quaternary International
• 影响因子: 2.2
• 作者: Albayrak E

The evolutionary and phylogeographic history of woolly mammoths: a comprehensive mitogenomic analysis.

• DOI: 10.1038/srep44585
• 发表时间: 2017-03-22
• 期刊: Scientific reports
• 影响因子: 4.6
• 作者: Chang D;Knapp M;Enk J;Lippold S;Kircher M;Lister A;MacPhee RD;Widga C;Czechowski P;Sommer R;Hodges E;Stümpel N;Barnes I;Dalén L;Derevianko A;Germonpré M;Hillebrand-Voiculescu A;Constantin S;Kuznetsova T;Mol D;Rathgeber T;Rosendahl W;Tikhonov AN;Willerslev E;Hannon G;Lalueza-Fox C;Joger U;Poinar H;Hofreiter M;Shapiro B
• 通讯作者: Shapiro B