PDF(Pubmed)
Abstract：
Small populations with limited range are often threatened by inbreeding and reduced genetic diversity, which can reduce fitness and exacerbate population decline. One of the most extreme natural examples is the Devils Hole pupfish (Cyprinodon diabolis), an iconic and critically endangered species with the smallest known range of any vertebrate. This species has experienced severe declines in population size over the last 30 years and suffered major bottlenecks in 2007 and 2013, when the population shrunk to 38 and 35 individuals, respectively. Here, we analysed 30 resequenced genomes of desert pupfishes from Death Valley, Ash Meadows and surrounding areas to examine the genomic consequences of small population size. We found extremely high levels of inbreeding (FROH = 0.34-0.81) and an increased amount of potentially deleterious genetic variation in the Devils Hole pupfish as compared to other species, including unique, fixed loss-of-function alleles and deletions in genes associated with sperm motility and hypoxia. Additionally, we successfully resequenced a formalin-fixed museum specimen from 1980 and found that the population was already highly inbred prior to recent known bottlenecks. We thus document severe inbreeding and increased mutation load in the Devils Hole pupfish and identify candidate deleterious variants to inform management of this conservation icon.
摘要：
范围有限的小种群往往受到近亲繁殖和遗传多样性降低的威胁,这会降低健身水平，加剧人口减少。最极端的自然例子之一是魔鬼洞p（Cyprinodondiabolis），一种标志性和极度濒危的物种，在任何脊椎动物中已知范围最小。该物种在过去30年中经历了种群规模的严重下降，并在2007年和2013年遭受了主要瓶颈，当时种群减少到38和35个个体，分别。这里,我们分析了30个来自死亡谷的沙漠p鱼的重新测序基因组，灰草甸和周边地区，以检查小种群规模的基因组后果。我们发现，与其他物种相比，魔鬼洞p的近亲繁殖水平极高（FROH=0.34-0.81），并且潜在的有害遗传变异量增加，包括独特的，与精子运动和缺氧相关的固定功能缺失等位基因和基因缺失。此外,我们成功地对1980年的福尔马林固定博物馆标本进行了重新测序，发现该种群在最近已知的瓶颈之前已经是高度近交的。因此，我们记录了魔鬼洞p鱼的严重近亲繁殖和突变负荷的增加，并确定了候选的有害变体，以告知该保护图标的管理。
