Data from: Combining allele frequency and tree-based approaches improves phylogeographic inference from natural history collections

Model selection approaches in phylogeography have allowed researchers to evaluate the support for competing demographic histories, which provides a mode of inference and a measure of uncertainty in understanding climatic and spatial influences on intraspecific diversity. Here, to rank all models in the comparison set, and determine what proportion of the total support the top-ranked model garners, we conduct model selection using two analytical approaches –allele frequency-based, implemented in fastsimcoal2, and gene tree-based, implemented in PHRAPL. We then expand this model-selection framework by including an assessment of absolute fit of the models to the data. For this, we utilize DNA isolated from existing natural history collections that span the distribution of red alder (Alnus rubra) in the Pacific Northwest of North America to generate genomic data for the evaluation of 13 demographic scenarios. The quality of DNA recovered from herbarium specimen leaf tissue was assessed for its utility and effectiveness in demographic model selection, specifically in the two approaches mentioned. We present strong support for the use of herbarium tissue in the generation of genomic DNA, albeit with the inclusion of additional quality control checks prior to library preparation and analyses with multiple approaches that incorporate various data. Analyses with allele frequency spectra and gene trees predominantly support A. rubra having experienced an ancient vicariance event with intermittent and frequent gene flow between the disjunct populations. Additionally, the data consistently fit the most frequently selected model, corroborating the model selection techniques. Finally, these results suggest that the A. rubra disjunct populations do not represent separate species.

系统地理学（phylogeography）中的模型选择方法可使研究者评估竞争性种群动态历史（demographic history）的支持度，为理解气候与空间因素对种内多样性的影响提供了推断范式，同时可量化相关推断的不确定性。本研究中，为对比较集内的全部模型进行排序并确定最优模型所获得的总支持度占比，我们采用两种分析方法开展模型选择：一是基于等位基因频率的方法（已在fastsimcoal2中实现），二是基于基因树（gene tree）的方法（已在PHRAPL中实现）。随后，我们通过增加模型对数据的绝对拟合度评估拓展了该模型选择框架。为此，我们从覆盖北美太平洋西北沿岸红桤木（Alnus rubra）分布范围的现存自然历史馆藏样本中提取DNA，以此生成基因组DNA（genomic DNA），用于评估13种群动态历史场景。我们还评估了从标本馆（herbarium）叶片组织中提取的DNA的质量，以验证其在种群动态历史模型选择，尤其是前述两种分析方法中的实用性与有效性。本研究结果强烈支持使用标本馆组织样本制备基因组DNA，不过在文库构建前需增设额外的质量控制环节，并采用整合多类数据的多种分析方法开展后续分析。基于等位基因频率频谱与基因树的分析结果普遍支持红桤木曾经历过一次古老的异域分化事件（vicariance event），且间断分布种群之间存在间歇性且频繁的基因交流。此外，数据始终与最常被选中的模型相契合，验证了本研究所用模型选择方法的可靠性。最终，本研究结果表明，红桤木的间断分布种群并非独立物种。