Department of Biology, University of British Columbia Okanagan, Kelowna, BC, Canada.
Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT.
J Hered. 2018 Aug 24;109(6):631-640. doi: 10.1093/jhered/esy016.
Empirical population genetic studies generally rely on sampling subsets of the population(s) of interest and of the nuclear or organellar genome targeted, assuming each is representative of the whole. Violations of these assumptions may impact population-level parameter estimation and lead to spurious inferences. Here, we used targeted capture to sequence the full mitochondrial genome from 123 individuals of the Galapagos giant tortoise endemic to Pinzón Island (Chelonoidis duncanensis) sampled at 2 time points pre- and postbottleneck (circa 1906 and 2014) to explicitly assess differences in diversity estimates and demographic reconstructions based on subsets of the mitochondrial genome versus the full sequences and to evaluate potential biases associated with diversity estimates and demographic reconstructions from postbottlenecked samples alone. Haplotypic diversities were equal between the temporal samples based on the full mitochondrial genome, but single gene estimates suggested either decreases or increases in diversity depending upon the region. Demographic reconstructions based on the full sequence were more similar between the temporal samples than those based on the control region alone, or a subset of 3 regions, where the trends in population size changes shifted in magnitude and direction between the temporal samples. In all cases, the estimated coalescent point was more distant for the historical than contemporary sample. In summary, our results empirically demonstrate the influence of sampling bias when interpreting population genetic patterns and punctuate the need for careful consideration of potentially conflicting evolutionary signal across the mitochondrial genome.
经验种群遗传学研究通常依赖于对感兴趣的群体（s）和核或细胞器基因组的子集进行采样，假设每个子集都代表整个群体。违反这些假设可能会影响群体水平的参数估计，并导致虚假推断。在这里，我们使用靶向捕获技术对 123 个平塔岛加拉帕戈斯象龟（Chelonoidis duncanensis）的个体的完整线粒体基因组进行测序，这些个体在瓶颈期（约 1906 年和 2014 年）之前和之后的两个时间点进行采样，以明确评估基于线粒体基因组子集与全序列的多样性估计和种群重建的差异，并评估仅来自瓶颈后样本的多样性估计和种群重建的潜在偏差。基于完整线粒体基因组的时间样本的单倍型多样性相等，但单基因估计表明多样性要么减少，要么增加，这取决于区域。基于完整序列的种群重建比基于控制区或 3 个区域子集的重建更相似，其中种群大小变化的趋势在时间样本之间在幅度和方向上发生了变化。在所有情况下，历史样本的估计聚结点都比当代样本更远。总之，我们的结果从经验上证明了在解释种群遗传模式时采样偏差的影响，并强调需要仔细考虑线粒体基因组中潜在的冲突进化信号。
