Molecular Paleoecology of Permafrost Mammals

北极是众所周知的独特的生物科学资源，因为它包含了过去气候波动和生物群与极端环境之间相互作用的特殊记录。初步研究表明，来自永久冻土的动物骨骼包含另一项关于全球变化的重要记录--遗传记录，详细描述了晚更新世以来的动物群演化。初步研究表明，古代DNA技术和聚合酶链式反应(PCR)可以用来从靠近道森、育空地区和阿拉斯加费尔班克斯的大量永久冻土样本中恢复、扩增长达600个碱基对的线粒体DNA(MtDNA)，并对其进行测序。这些永久冻土沉积物可以追溯到20000到50000年前，其中包含来自该地区以前居民的数千块骨骼，使这一资源成为国宝，包括世界上最大的更新世遗传信息集合。除了测试长期存在的系统性问题外，从这些骨骼中提取的DNA还可以用于研究过去环境变化的后果，如白令大陆桥的开放，以及气候和人类活动对种群遗传的影响。永冻层DNA将用于研究几个问题，这些问题涉及晚更新世生态对现代种群遗传学的影响，以及当前环境变化和生物引入的影响与最近相比如何。对狼(Canis Lupus)、驼鹿(Alcesgias)和麋鹿(Cervus Elaffus)各约20个标本的线粒体控制区和细胞色素b DNA序列进行了大约200-300bp的测序，以研究晚更新世以来遗传多样性的变化。这三个分类群在北美都有几千多年的化石记录，但现代北美种群的遗传多样性足够有限，最近似乎出现了瓶颈。这些结果将与北美驯鹿(Rangifer Tarandus)和棕熊(Ursus Arctos)的分析结果进行对比，这两种动物在北美也有很长的记录，但在现代种群中具有适度的遗传多样性，这可能是因为整个晚更新世的种群规模很大。除了检查遗传多样性随时间的变化外，永久冻土DNA将被用来评估晚更新世种群与现代种群的关系。我们将区分四种可能的选择：1)现存种群的DNA序列在系统发育上与旧大陆的那些不同，并与北美晚更新世的前身直接相关。这一结果意味着整个更新世的遗传连续性和大陆隔离，现代种群在相对孤立的情况下幸存于最近的冰川条件和大型动物群灭绝事件中；2)现代种群的DNA序列与永久冻土中的那些没有共同的祖先，这意味着北美的血统在过去18,000年的某个时候灭绝了，并被存在于Beringia的旧世界祖先的DNA单倍型所取代；3)现代种群具有与北美和旧世界晚更新世的DNA单倍型相关的混合DNA单倍型，暗示着新旧世界种群之间的最近混杂；4)现代和永久冻土种群都混合了新旧大陆祖先的DNA单倍型，这意味着晚更新世大陆混合的历史。古代DNA研究承诺可以通过实时观察进化变化，但受到样本数量和可能分析的时间框架的限制。这个项目将实现这一潜力，因为它允许在数万年的时间框架内记录两个大的、采样充分的自然种群(费尔班克斯和道森)的基因变化。它还将有助于更好地了解在永久冻土条件下进行分子保存所涉及的因素，以及对当前采矿作业发现的标本实行适当的储存和处理制度。对于这一宝贵的资源，目前还没有有组织的收集计划，每年数百个来自这个基因博物馆的标本被简单地冲走下游

The Arctic is well known as a unique scientific resource for biologybecause it contains exceptional records of past climatic fluctuations andthe concomitant interactions between biota and an extreme environment.Preliminary research has shown that the bones from animals from thepermafrost contain a further important record of global change - a geneticrecord, detailing faunal evolution through the Late Pleistocene.Preliminary studies reveal that ancient DNA techniques and the polymerasechain reaction (PCR) can be used to recover, amplify, and sequencemitochondrial DNA (mtDNA) of up to 600 base pairs (bp) in length from avariety of permafrost specimens from extensive deposits near Dawson, YukonTerritories and Fairbanks, Alaska. These permafrost deposits date from 20to 50 thousand years ago and contain thousands of bones from previousinhabitants of the area, making this resource a national treasure,comprising the largest collection of Pleistocene genetic information in theworld. In addition to testing long-standing systematic issues, DNA fromthese bones can be used to examine the consequences of past environmentalchanges, such as the opening of the Bering land bridge, and climate andanthropogenic effects on population genetics.Permafrost DNA will be used to examine several questions concerning theeffects of Late Pleistocene ecology on the genetics of modern populations,and how the effects of current environmental change and biologicalintroductions compare with that of the recent past. Mitochondrial controlregion and cytochrome b DNA sequences of approximately 200-300 bp will besequenced from about 20 specimens each of wolf (Canis lupus), moose (Alcesgigas) and elk (Cervus elaphus) to examine how genetic diversity haschanged since the Late Pleistocene. All three taxa have fossil records ofmore than several thousand years in North America, yet the geneticdiversity of modern North American populations is sufficiently limited thatrecent bottlenecks appear to have occurred. These results will becontrasted with those from analyses of the caribou (Rangifer tarandus) andthe brown bear (Ursus arctos), which also have a long record in NorthAmerica but have moderate amounts of genetic diversity in modernpopulations, perhaps due to large population sizes throughout the LatePleistocene.As well as examining changes in genetic diversity through time, thepermafrost DNA will be used to assess the relationship of Late Pleistocenepopulations to their modern counterparts. We will distinguish among fourpossible alternatives: 1) extant populations have DNA sequences that arephylogenetically distinct from those in the Old World and are directlyrelated to those from Late Pleistocene North American predecessors. Thisresult implies genetic continuity and continental isolation throughout theLate Pleistocene and that modern populations survived recent glacialconditions and megafaunal extinction events in relative isolation; 2) DNAsequences of modern populations do not share a common ancestry with thosein the permafrost implying that North American lineages went extinctsometime in the past 18,000 years and were replaced by those of an OldWorld ancestry existing in Beringia; 3) modern populations have a mixtureof DNA haplotypes that are related to those from the Late Pleistocene ofNorth America and the Old World implying recent admixture between Old andNew World populations; and 4) both modern and permafrost populations have amixture of DNA haplotypes of Old and New World ancestry implying a historyof continental mixing over the Late Pleistocene.Ancient DNA research has promised to allow evolutionary change tobe observed through real time but has been constrained by the number ofsamples and time frame that it has been possible to analyse. This projectwill fulfil that potential since it permits genetic change to be recordedin two large, well sampled natural populations (Fairbanks and Dawson) overa time frame of tens of thousands of years. It will also lead to a betterunderstanding of the factors involved in molecular preservation underpermafrost conditions, and suitable storage and handling regimes forspecimens uncovered by current mining operations. No organized collectingprogram currently exists for this valuable resource, and each year hundredsof specimens from this genetic museum are simply washed away downstream