Data from: Naturally rare versus newly rare: demographic inferences on two timescales inform conservation of Galápagos giant tortoises

Long-term population history can influence the genetic effects of recent bottlenecks. Therefore, for threatened or endangered species, an understanding of the past is relevant when formulating conservation strategies. Levels of variation at neutral markers have been useful for estimating local effective population sizes (Ne) and inferring whether population sizes increased or decreased over time. Furthermore, analyses of genotypic, allelic frequency, and phylogenetic information can potentially be used to separate historical from recent demographic changes. For 15 populations of Galápagos giant tortoises (Chelonoidis sp.), we used 12 microsatellite loci and DNA sequences from the mitochondrial control region and a nuclear intron, to reconstruct demographic history on shallow (past ~100 generations, ~2500 years) and deep (pre-Holocene, >10 thousand years ago) timescales. At the deep timescale, three populations showed strong signals of growth, but with different magnitudes and timing, indicating different underlying causes. Furthermore, estimated historical Ne of populations across the archipelago showed no correlation with island age or size, underscoring the complexity of predicting demographic history a priori. At the shallow timescale, all populations carried some signature of a genetic bottleneck, and for 12 populations, point estimates of contemporary Ne were very small (i.e., < 50). On the basis of the comparison of these genetic estimates with published census size data, Ne generally represented ~0.16 of the census size. However, the variance in this ratio across populations was considerable. Overall, our data suggest that idiosyncratic and geographically localized forces shaped the demographic history of tortoise populations. Furthermore, from a conservation perspective, the separation of demographic events occurring on shallow versus deep timescales permits the identification of naturally rare versus newly rare populations; this distinction should facilitate prioritization of management action.

长期种群历史可影响近期种群瓶颈的遗传效应。因此，对于受威胁或濒危物种而言，了解其过往种群动态对制定保护策略具有重要意义。中性标记（neutral markers）的变异水平可用于估算局部有效种群大小（effective population sizes，Ne），并推断种群规模随时间的增减趋势。此外，通过对基因型、等位基因频率及系统发育信息的分析，有望区分历史种群动态与近期种群动态变化。本研究针对15个加拉帕戈斯巨龟（Chelonoidis sp.）种群，利用12个微卫星位点（microsatellite loci）、线粒体控制区（mitochondrial control region）及核内含子（nuclear intron）的DNA序列，分别在短时间尺度（约过去100代，即~2500年）与长时间尺度（全新世前，即距今超1万年）上重建其种群历史动态。在长时间尺度上，有3个种群呈现出显著的种群扩张信号，但扩张程度与发生时间均存在差异，暗示其背后的驱动机制各不相同。此外，加拉帕戈斯群岛内各种群的历史有效种群大小（Ne）估算值与岛屿年龄、面积均无相关性，这凸显了先验地预测种群历史动态的复杂性。在短时间尺度上，所有种群均表现出一定的遗传瓶颈（genetic bottleneck）信号；其中12个种群的当代有效种群大小（Ne）点估计值极低（即小于50）。将上述遗传估算值与已发表的种群普查数量（census size）数据对比后发现，有效种群大小（Ne）通常约为普查数量的0.16倍。但不同种群间的该比值存在显著差异。总体而言，本研究数据表明，独特且具有地理局限性的演化力量塑造了加拉帕戈斯巨龟种群的历史动态。此外，从保护生物学视角来看，区分发生在短时间尺度与长时间尺度的种群动态事件，可识别自然稀有种群与新近沦为稀有的种群；这一区分将有助于优化保护管理行动的优先级排序。