Data sets for phylogenomic analyses in: Ant backbone phylogeny resolved by modelling compositional heterogeneity among sites in genomic data

Ants are the most ubiquitous and ecologically dominant arthropods on Earth, and understanding their phylogeny is crucial for deciphering their character evolution, species diversification, and biogeography. Although recent genomic data have shown promise in clarifying intrafamilial relationships across the tree of ants, inconsistencies between molecular datasets have also emerged. Here I re-examine the most comprehensive published Sanger-sequencing and genome-scale datasets of ants using model comparison methods that model among-site compositional heterogeneity to understand the sources of conflict in phylogenetic studies. My results under the best-fitting model, selected on the basis of Bayesian cross-validation and posterior predictive model checking, identify contentious nodes in ant phylogeny whose resolution is modelling-dependent. I show that the Bayesian infinite mixture CAT model outperforms empirical finite mixture models (C20, C40 and C60) and that, under the best-fitting CAT-GTR+G4 model, the enigmatic Martialis heureka is sister to all ants except Leptanillinae, rejecting the more popular hypothesis supported under worse-fitting models, that place it as sister to Leptanillinae. These analyses resolve a lasting controversy in ant phylogeny and highlight the significance of model comparison and adequate modelling of among-site compositional heterogeneity in reconstructing the deep phylogeny of insects.

蚂蚁是地球上分布最广泛、在生态上占据主导地位的节肢动物，解析其系统发育关系，对于阐明其性状演化、物种多样化进程与生物地理学格局至关重要。尽管近期的基因组数据在厘清蚁类系统树的科内亲缘关系方面展现出潜力，但不同分子数据集之间的不一致性也逐渐显现。本研究采用考虑位点间组成异质性的模型比较方法，对已发表的最全面的蚂蚁桑格测序（Sanger-sequencing）数据集与基因组规模数据集进行重新分析，旨在解析系统发育研究中冲突结果的来源。本研究基于贝叶斯交叉验证与后验预测模型检验选出最优拟合模型，其分析结果显示，蚂蚁系统发育中存在若干依赖于建模方式的争议节点。研究表明，贝叶斯无限混合CAT模型的表现优于经验有限混合模型（C20、C40与C60）；在最优拟合的CAT-GTR+G4模型下，神秘的怪蚁（Martialis heureka）是除细蚁亚科（Leptanillinae）外所有蚂蚁的姐妹群，这一结果否定了在拟合效果更差的模型下得到的主流假说——后者将怪蚁视为细蚁亚科的姐妹群。本研究解决了蚂蚁系统发育领域长期存在的争议，并凸显了模型比较与合理建模位点间组成异质性，在重建昆虫深层系统发育关系中的重要意义。