描述原核生物核心基因组SNP GC含量随时间演化的简单随机模型
A simple stochastic model to describe the evolution over time of core genome SNP GC content in prokaryotes
摘要：
生物体中的基因组由核苷酸腺嘌呤（A）、鸟嘌呤（G）、胞嘧啶（C）和胸腺嘧啶（T）组成。所有原核生物的基因组都由双链DNA组成，其中一条链的A和G（嘌呤）分别与另一条链的T和C（嘧啶）结合。因此，一条链上A的数量几乎等于另一条链上T的数量，一条链的G和另一条链的C也是如此。在全球范围内，这种关系被形式化为Chargaff的第一奇偶性规则;其strandwise等价物是Chargaff的第二奇偶性规则。因此，任何双链DNA基因组的GC含量可以表示为%GC=100%-%AT。原核生物GC含量的变化在分类群之间可以是实质性的，但在微生物基因组内通常是小的。已发现这种变化与生育和环境因素有关。由于基因组内的新单核苷酸多态性（SNP）至少部分与环境有关，SNP GC含量可以被认为是生物体环境影响，生活方式和生育力的复合测量。我们提出了一个数学模型，该模型描述了在高斯白噪声干扰下，微生物基因组中SNP GC含量如何随时间演变为AT->GC和GC->AT突变率的函数。该模型表明，在非重组细菌中，突变首先会在不知不觉中积累，然后突然波动失控。因此，突变率的微小变化可能突然变得不可持续，如果没有足够早地抵消，最终会导致物种灭绝。这个模型，这是特别适合于共生原核生物，符合穆勒的棘轮预测的情况下，并可能表明，这并不总是一个渐进的，退化的过程。
英文摘要：
Genomes in living organisms consist of the nucleotides adenine (A), guanine (G), cytosine (C) and thymine (T). All prokaryotes have genomes consisting of double-stranded DNA, where the A's and G's (purines) of one strand bind respectively to the T's and C's (pyrimidines) of the other. As such, the number of A's on one strand nearly equals the number of T's on the other, and the same is true of one strand's G's and the other's C's. Globally, this relationship is formalized as Chargaff's first parity rule; its strandwise equivalent is Chargaff's second parity rule. Therefore, the GC content of any double-stranded DNA genome can be expressed as %GC=100%-%AT. Variation in prokaryotic GC content can be substantial between taxa but is generally small within microbial genomes. This variation has been found to correlate with both phylogeny and environmental factors. Since novel single-nucleotide polymorphisms (SNPs) within genomes are at least partially linked to the environment, SNP GC content can be considered a compound measure of an organism's environmental influences, lifestyle and phylogeny. We present a mathematical model that describes how SNP GC content in microbial genomes evolves over time as a function of the AT->GC and GC->AT mutation rates with Gaussian white noise disturbances. The model suggests that, in non-recombining bacteria, mutations can first accumulate unnoticeably and then abruptly fluctuate out of control. Thus, minuscule variations in mutation rates can suddenly become unsustainable, ultimately driving a species to extinction if not counteracted early enough. This model, which is suited specifically to symbiotic prokaryotes, conforms to scenarios predicted by Muller's ratchet and may suggest that this is not always a gradual, degrading process.
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