Whole genome sequences are beginning to revolutionise our understanding of phylogenetic relationships. Yet, even whole genome sequences can fail to resolve the evolutionary history of the most rapidly radiating lineages, where incomplete lineage sorting, standing genetic variation, introgression, and other factors obscure the phylogenetic history of the group. To overcome such challenges, one emerging strategy is to integrate results across different methods. Most such approaches have been implemented on reduced representation genomic datasets, but whole genomes should provide the maximum possible evidence approach. Here, we test the ability of SNPs extracted from whole genome resequencing data, implemented in an integrative genomic approach, to resolve key nodes in the phylogeny of the mbuna, rock-dwelling cichlid fishes of Lake Malaŵi, which epitomise the phylogenetic intractability that often accompanies explosive lineage diversification. This monophyletic radiation has diversified at an unparalleled rate into several hundred species in less than two million years. Using an array of phylogenomic methods, we consistently recovered four major clades of mbuna, but a large basal polytomy among them. Although introgression between clades apparently contributed to the challenge of phylogenetic reconstruction, reduction of the dataset to non-introgressed sites still did not help to resolve the basal polytomy. On the other hand, relationships among six congeneric species pairs were resolved without ambiguity, even in one case where existing data led us to predict that resolution would be difficult. We conclude that the bursts of diversification at the earliest stages of the mbuna radiation may be phylogenetically unresolvable, but other regions of the tree are phylogenetically clearly supported. Integration of multiple phylogenomic approaches will continue to increase confidence in relationships inferred from these and other whole-genome datasets.

中文翻译：

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在岩石和坚硬的多分体之间：马拉维湖岩栖的姆布纳慈鲷的系统基因组学

全基因组序列开始彻底改变我们对系统发育关系的理解。然而，即使是全基因组序列也无法解决最快速辐射谱系的进化历史，其中不完整的谱系分类、常设遗传变异、基因渗入和其他因素掩盖了该群体的系统发育历史。为了克服这些挑战，一种新兴策略是整合不同方法的结果。大多数此类方法已在减少表示的基因组数据集上实施，但全基因组应提供最大可能的证据方法。在这里，我们测试了从全基因组重测序数据中提取的 SNP 的能力，以整合基因组方法实施，以解决 Malaŵi 湖的岩栖慈鲷鱼 mbuna 系统发育中的关键节点，这集中体现了经常伴随爆炸性谱系多样化的系统发育难处理性。在不到 200 万年的时间里，这种单系辐射以无与伦比的速度多样化为数百种。使用一系列系统基因组学方法，我们始终如一地恢复了 mbuna 的四个主要进化枝，但其中有一个大的基础多分枝。尽管进化枝之间的基因渗入显然促成了系统发育重建的挑战，但将数据集减少到非基因渗入位点仍然无助于解决基础多分法。另一方面，六个同属物种对之间的关​​系得到了明确的解决，即使在现有数据使我们预测解决困难的情况下也是如此。我们得出结论，在 mbuna 辐射的最早阶段，多样化的爆发可能在系统发育上无法解决，但树的其他区域在系统发育上得到了明确的支持。多种系统基因组方法的整合将继续增加对从这些和其他全基因组数据集推断的关系的信心。