Data from: Comparing direct and indirect selfing rate estimates: when are population-structure estimates reliable?

The rate of self-fertilization (that is, selfing) is a key evolutionary parameter in hermaphroditic species, yet obtaining accurate estimates of selfing rates in natural populations can be technically challenging. Most published estimates are derived from population-level heterozygote deficiency (that is, FIS) or identity disequilibria (for example, the software RMES (robust multilocus estimate of selfing)). These indirect methods can be applied to population genetic survey data, whereas direct methods using progeny arrays require much larger data sets that are often difficult to collect in natural populations or even require captive breeding. Unfortunately, indirect methods rely on assumptions that can be problematic, such as negating biparental inbreeding, inbreeding disequilibrium and (for FIS) the presence of null alleles. The performance of indirect estimates against progeny-array estimates is still largely unknown. Here we used both direct progeny-array and indirect population-level methods to estimate the selfing rate in a single natural population of the simultaneously hermaphroditic freshwater snail Radix balthica throughout its reproductive lifespan using 10 highly polymorphic microsatellites. We found that even though progeny arrays (n=1034 field-collected embryos from 60 families) did not reveal a single selfed embryo, FIS-based selfing rates (n=316 adults) were significantly positive in all 6 sequential population samples. Including a locus with a high frequency of null alleles further biased FIS-based estimates. Conversely, RMES-based estimates were very similar to progeny-array estimates and proved insensitive to null alleles. The assumptions made by RMES were thus either met or irrelevant in this particular population, making RMES a valid, cost-efficient alternative to progeny arrays.

自体受精（自交）率是雌雄同体物种的关键进化参数，然而在自然种群中精准估算自交率往往存在技术层面的挑战。当前已发表的多数自交率估算结果均基于种群水平的杂合子缺失（即FIS）或同一性不平衡，其中代表性工具为软件RMES（robust multilocus estimate of selfing，稳健多位点自交率估算程序）。这类间接方法可直接应用于种群遗传调查数据，而采用子代阵列的直接估算方法则需要规模更大的数据集——这类数据在自然种群中往往难以采集，甚至需通过人工繁育才能获取。遗憾的是，间接方法依赖的诸多假设往往存在局限性，例如需排除双亲近交、近交不平衡，且针对FIS方法而言，需假定无效等位基因不存在。间接估算结果与子代阵列估算结果的对比表现，目前仍在很大程度上未被探明。本研究依托10个高度多态的微卫星标记，同时采用直接子代阵列法与间接种群水平法，对同时雌雄同体的淡水螺Radix balthica单个自然种群在其整个生殖寿命周期内的自交率进行了估算。研究结果显示，尽管子代阵列分析（样本为60个家系的1034个野外采集胚胎）未检测到任何一例自交胚胎，但基于FIS的自交率估算（样本为316个成体）在全部6个连续种群采样点中均显著为正。若纳入无效等位基因频率较高的位点，会进一步加剧基于FIS的估算结果的偏倚。与之相反，基于RMES的估算结果与子代阵列的估算结果极为相近，且不受无效等位基因的影响。因此，在该特定种群中，RMES所依赖的假设要么均得到满足，要么无关紧要，这使得RMES成为子代阵列法之外一种有效且成本高效的替代方案。