Ancient DNA from lake sediments: Bridging the gap between paleoecology and genetics
Ancient DNA from lake sediments: Bridging the gap between paleoecology and genetics
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DOI：
10.1186/1471-2148-11-30
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发表时间：
2011-01-27
影响因子：
3.4
通讯作者：
Poinar, Hendrik N.
中科院分区：
文献类型：
--
作者：
Anderson-Carpenter, Lynn L.;McLachlan, Jason S.;Poinar, Hendrik N.
背景：世界上许多地区的第四纪植物生态学历来依赖于对小型淡水湖沉积物中宏观和微观化石的形态识别。在这里，我们报告了从全新世植物大型化石和大量湖泊沉积物中可靠地产生DNA序列数据的新方案，用于推断生态变化。这将使根据化石和相关沉积物估计的人口普查人口的变化与种群基因变化直接相关。结果：我们成功地对样本进行了DNA测序，样本包括从北美西部五大湖地区全新世湖泊沉积物中提取的大量沉积物和种子、叶片碎片、鳞茎和Samaras。总体而言，DNA产量很低。然而，我们能够可靠地扩增出只有10个拷贝的短cpDNA片段的样本，几乎没有可检测到的PCR抑制。我们对2000年前的沉积物的成功率最高，但我们能够成功地从4600年前的样本中扩增出DNA。DNA序列在79%的时间里与提取它们的大型化石的分类身份相匹配。例外情况表明，附近沉积物中的DNA分子可能渗透或附着在沉积物中的大型化石中。结论：从全新世沉积物中提取古代DNA的能力可能会让人们对长期环境变化的遗传后果有新的令人兴奋的见解。我们在化石材料中发现的DNA拷贝数很低，而且从单个宏化石提取中发现了多个序列变体，这突出表明需要仔细的实验和实验室协议。这些议定书的进一步应用应有助于更好地理解环境变化的生态和进化后果。
Background: Quaternary plant ecology in much of the world has historically relied on morphological identification of macro- and microfossils from sediments of small freshwater lakes. Here, we report new protocols that reliably yield DNA sequence data from Holocene plant macrofossils and bulk lake sediment used to infer ecological change. This will allow changes in census populations, estimated from fossils and associated sediment, to be directly associated with population genetic changes.Results: We successfully sequenced DNA from 64 samples (out of 126) comprised of bulk sediment and seeds, leaf fragments, budscales, and samaras extracted from Holocene lake sediments in the western Great Lakes region of North America. Overall, DNA yields were low. However, we were able to reliably amplify samples with as few as 10 copies of a short cpDNA fragment with little detectable PCR inhibition. Our success rate was highest for sediments < 2000 years old, but we were able to successfully amplify DNA from samples up to 4600 years old. DNA sequences matched the taxonomic identity of the macrofossil from which they were extracted 79% of the time. Exceptions suggest that DNA molecules from surrounding nearby sediments may permeate or adhere to macrofossils in sediments.Conclusions: An ability to extract ancient DNA from Holocene sediments potentially allows exciting new insights into the genetic consequences of long-term environmental change. The low DNA copy numbers we found in fossil material and the discovery of multiple sequence variants from single macrofossil extractions highlight the need for careful experimental and laboratory protocols. Further application of these protocols should lead to better understanding of the ecological and evolutionary consequences of environmental change.