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.

了解人口在时间上的变化对于理解物种进化和灭绝的更广泛情况至关重要。通过检查人口变化的动态，我们可以探索竞争压力和栖息地的变化导致物种分布在时间和空间中发生变化。人口可以增加或下降，或者他们的移民和移民水平有所不同。尽管从理论上讲可以直接观察这些过程，但必要观测的时间跨度几乎不切实际。幸运的是，直接观察并不是推断人群中发生变化的唯一方法，因为所有这些过程都留下了物种遗传多样性的痕迹。通过对来自人群中大量个体的物种（DNA）的遗传信息进行测序，可以阐明几千年来的物种的动力学。分析来自现代人群的数据时，数据可能不足以获取过去人口变化的全部情况 - 今天不再来自人口的任何信息将丢失。一种更强大的方法是直接采样过去人群的遗传学。这种方法使用古老的DNA：幸存在组织中的DNA，可追溯到〜120，000年。古代DNA中的研究表明，比起最初从现代数据中推断出的更复杂的人群的动力学更为复杂。至关重要的是，更新世是一个涵盖气候变化的时期，对更新世种群动态的详细检查可能会揭示物种对气候变化的影响的反应。但是，随着时间的流逝，DNA的衰减很困难，随着时间的流逝，DNA的衰减很少，而造成了相对较少的骨骼可以成功采样的骨骼，并在短片中取得了Short Pirect of Short of Short of ddna，dnna syavics complocal of de s of de s axpaig of dna，complate of dea caildics of dea是问题。其中一个结果是，迄今为止，大多数古老的DNA研究都依赖于一种称为线粒体（MT）DNA的丰富的短循环。但是，mtDNA仅通过母体线传递，无法提供有关父亲谱系的任何信息。测序大量日期的骨样品，以使MTDNA的更长序列和来自细胞核的DNA揭示男性和女性进化史，并为动物种群在过去的几十万年内变化提供了更好的了解。羊毛乳房（羊毛千摩太郎）是对环境和种类范围的范围，这是一种对环境的影响。此外，通过检查气候变化时可能受到青睐的基因，例如涉及头发生长或冷热的基因，可以研究这些基因与更多“中性”基因之间的DNA中的任何不同模式，从而帮助我们更好地理解人口统计学和适应性过程在这些人群中发生的进展。使用新的高通量技术来分析DNA，结合定位特定DNA感兴趣的DNA片段的方法，我们现在可以快速有效地分析数百种化石保留的数千个DNA代码，从而使我们能够推断出过去发生的情况。

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