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，可帮助研究者评估相互竞争的种群历史假说的支持度，为解析气候与空间因素对种内多样性的影响提供了标准化推断范式与不确定性量化手段。本研究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，采用两种分析方法开展模型选择：其一为基于等位基因频率的方法（已在fastsimcoal2软件中实现），其二为基于基因树的方法（已在PHRAPL软件中实现）。随后，我们通过评估模型对数据的绝对拟合优度，拓展了该模型选择框架。为此，我们利用覆盖北美太平洋西北地区红桤木（Alnus rubra）分布范围的现有自然历史标本馆藏中提取的DNA，生成基因组数据，以评估13种种群历史情景。我们针对从标本馆标本叶片组织中回收的DNA开展质量评估，以验证其在种群模型选择（尤其是上述两种分析方法中）的实用性与有效性。研究结果证实，使用标本馆组织可成功制备基因组DNA，尽管需在文库构建前增设质量控制步骤，并结合多种整合不同数据类型的分析方法。基于等位基因频率频谱与基因树的分析结果，均主要支持红桤木曾经历一次古代隔离分化事件，且其隔离种群间存在间歇性且频繁的基因交流。此外，观测数据与最常被选中的模型高度拟合，进一步验证了本研究采用的模型选择技术的可靠性。综上，本研究结果表明，红桤木的隔离种群并非独立物种。