Data from: Detecting selection on temporal and spatial scales: a genomic time-series assessment of selective responses to devil facial tumor disease

Detecting loci under selection is an important task in evolutionary biology. In conservation genetics detecting selection is key to investigating adaptation to the spread of infectious disease. Loci under selection can be detected on a spatial scale, accounting for differences in demographic history among populations, or on a temporal scale, tracing changes in allele frequencies over time. Here we use these two approaches to investigate selective responses to the spread of an infectious cancer—devil facial tumor disease (DFTD)—that since 1996 has ravaged the Tasmanian devil (Sarcophilus harrisii). Using time-series ‘restriction site associated DNA’ (RAD) markers from populations pre- and post DFTD arrival, and DFTD free populations, we infer loci under selection due to DFTD and investigate signatures of selection that are incongruent among methods, populations, and times. The lack of congruence among populations influenced by DFTD with respect to inferred loci under selection, and the direction of that selection, fail to implicate a consistent selective role for DFTD. Instead genetic drift is more likely driving the observed allele frequency changes over time. Our study illustrates the importance of applying methods with different performance optima e.g. accounting for population structure and background selection, and assessing congruence of the results.

检测受选择位点（loci under selection）是进化生物学（evolutionary biology）中的一项重要研究任务。在保护遗传学（conservation genetics）领域，检测选择压力是探究种群对传染病传播适应性的核心环节。受选择位点可通过两种方式检测：其一为空间尺度（spatial scale）法，需兼顾种群间的种群历史动态差异；其二为时间尺度（temporal scale）法，通过追踪等位基因频率（allele frequencies）随时间的变化实现。本研究采用这两种方法，探究传染性癌症——袋獾面部肿瘤病（devil facial tumor disease, DFTD）——传播所引发的选择响应；该疾病自1996年起便大肆肆虐袋獾（Sarcophilus harrisii）种群。本研究利用来自DFTD入侵前、入侵后种群以及未感染DFTD的种群的时间序列‘限制性酶切位点相关DNA（restriction site associated DNA, RAD）’标记，推断由DFTD驱动的受选择位点，并探究不同方法、种群及时间点下选择信号不一致的情况。受DFTD影响的种群之间，在所推断的受选择位点及其选择方向上均缺乏一致性，这表明DFTD并未对种群产生一致的选择作用。反之，遗传漂变（genetic drift）更可能是观测到的等位基因频率随时间变化的驱动因素。本研究阐明了采用不同性能最优条件的方法（例如兼顾种群结构（population structure）与背景选择（background selection））以及评估研究结果一致性的重要性。