MTA-MTM Research Group for Paleontology, 1476 Budapest, P, O, Box 222, Hungary.
BMC Evol Biol. 2011 Mar 10;11:66. doi: 10.1186/1471-2148-11-66.
Studies on allele length polymorphism designate several glacial refugia for Norway spruce (Picea abies) in the South Carpathian Mountains, but infer only limited expansion from these refugia after the last glaciation. To better understand the genetic dynamics of a South Carpathian spruce lineage, we compared ancient DNA from 10,700 and 11,000-year-old spruce pollen and macrofossils retrieved from Holocene lake sediment in the Retezat Mountains with DNA extracted from extant material from the same site. We used eight primer pairs that amplified short and variable regions of the spruce cpDNA. In addition, from the same lake sediment we obtained a 15,000-years-long pollen accumulation rate (PAR) record for spruce that helped us to infer changes in population size at this site.
We obtained successful amplifications for Norway spruce from 17 out of 462 pollen grains tested, while the macrofossil material provided 22 DNA sequences. Two fossil sequences were found to be unique to the ancient material. Population genetic statistics showed higher genetic diversity in the ancient individuals compared to the extant ones. Similarly, statistically significant Ks and Kst values showed a considerable level of differentiation between extant and ancient populations at the same loci.Lateglacial and Holocene PAR values suggested that population size of the ancient population was small, in the range of 1/10 or 1/5 of the extant population. PAR analysis also detected two periods of rapid population growths (from ca. 11,100 and 3900 calibrated years before present (cal yr BP)) and three bottlenecks (around 9180, 7200 and 2200 cal yr BP), likely triggered by climatic change and human impact.
Our results suggest that the paternal lineages observed today in the Retezat Mountains persisted at this site at least since the early Holocene. Combination of the results from the genetic and the PAR analyses furthermore suggests that the higher level of genetic variation found in the ancient populations and the loss of ancient allele types detected in the extant individuals were likely due to the repeated bottlenecks during the Holocene; however our limited sample size did not allow us to exclude sampling effect.This study demonstrates how past population size changes inferred from PAR records can be efficiently used in combination with ancient DNA studies. The joint application of palaeoecological and population genetics analyses proved to be a powerful tool to understand the influence of past population demographic changes on the haplotype diversity and genetic composition of forest tree species.
对等位基因长度多态性的研究为南喀尔巴阡山脉的挪威云杉（Picea abies）指定了几个冰川避难所，但推断出末次冰期后这些避难所的扩张有限。为了更好地了解南喀尔巴阡山脉云杉谱系的遗传动态，我们比较了从 Retezat 山脉全新世湖相沉积物中提取的 10700 年和 11000 年前的云杉花粉和宏观化石与同一地点现存材料中提取的 DNA。我们使用了 8 对引物，扩增了云杉 cpDNA 的短而多变的区域。此外，我们还从同一湖相沉积物中获得了长达 15000 年的云杉花粉积累率 (PAR) 记录，这有助于我们推断该地点的种群规模变化。
我们从 462 个花粉粒中成功扩增出 17 个挪威云杉，而宏观化石材料提供了 22 个 DNA 序列。两个化石序列被发现是古代材料所特有的。种群遗传统计显示，与现存个体相比，古代个体具有更高的遗传多样性。同样，在相同的基因座上，具有统计学意义的 Ks 和 Kst 值表明现存和古代种群之间存在相当程度的分化。晚冰期和全新世的 PAR 值表明，古代种群的种群规模较小，为现存种群的 1/10 或 1/5。PAR 分析还检测到两次种群快速增长期（约 11100 和 3900 年前校准年（cal yr BP））和三个瓶颈期（约 9180、7200 和 2200 cal yr BP），这可能是由气候变化和人类活动引起的。
我们的结果表明，今天在 Retezat 山脉观察到的父系谱系至少在全新世早期就存在于该地点。遗传和 PAR 分析结果的结合进一步表明，在古代种群中发现的较高遗传变异水平以及在现存个体中检测到的古代等位基因类型的丧失，可能是由于全新世期间的多次瓶颈所致；然而，我们的样本量有限，无法排除采样效应。本研究展示了如何从 PAR 记录推断过去的种群规模变化，并与古代 DNA 研究相结合。古生态学和种群遗传学分析的联合应用证明是一种强大的工具，可以帮助我们理解过去种群动态变化对森林树种的单倍型多样性和遗传组成的影响。
