Phylogenomics has the power to uncover complex phylogenetic scenarios across the genome. In most cases, no single topology is reflected across the entire genome as the phylogenetic signal differs among genomic regions due to processes, such as introgression and incomplete lineage sorting. Baleen whales are among the largest vertebrates on Earth with a high dispersal potential in a relatively unrestricted habitat, the oceans. The fin whale (Balaenoptera physalus) is one of the most enigmatic baleen whale species, currently divided into four subspecies. It has been a matter of debate whether phylogeographic patterns explain taxonomic variation in fin whales. Here we present a chromosome-level whole genome analysis of the phylogenetic relationships among fin whales from multiple ocean basins. First, we estimated concatenated and consensus phylogenies for both the mitochondrial and nuclear genomes. The consensus phylogenies based upon the autosomal genome uncovered monophyletic clades associated with each ocean basin, aligning with the current understanding of subspecies division. Nevertheless, discordances were detected in the phylogenies based on the Y chromosome, mitochondrial genome, autosomal genome and X chromosome. Furthermore, we detected signs of introgression and pervasive phylogenetic discordance across the autosomal genome. This complex phylogenetic scenario could be explained by a puzzle of introgressive events, not yet documented in fin whales. Similarly, incomplete lineage sorting and low phylogenetic signal could lead to such phylogenetic discordances. Our study reinforces the pitfalls of relying on concatenated or single locus phylogenies to determine taxonomic relationships below the species level by illustrating the underlying nuances which some phylogenetic approaches may fail to capture. We emphasize the significance of accurate taxonomic delineation in fin whales by exploring crucial information revealed through genome-wide assessments.

中文翻译：

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长须鲸（Balaenoptera physalus）的系统基因组学和普遍的全基因组系统发育不一致


系统基因组学有能力揭示整个基因组中复杂的系统发育场景。在大多数情况下，整个基因组中没有反映单一拓扑，因为基因组区域之间的系统发育信号由于基因渗入和不完整谱系排序等过程而不同。须鲸是地球上最大的脊椎动物之一，在相对不受限制的栖息地——海洋中具有很高的扩散潜力。长须鲸（Balaenoptera physalus）是最神秘的须鲸物种之一，目前分为四个亚种。系统发育地理学模式是否可以解释长须鲸的分类变异一直是一个争论的问题。在这里，我们对来自多个洋盆的长须鲸之间的系统发育关系进行了染色体水平的全基因组分析。首先，我们估计了线粒体和核基因组的串联和共有系统发育。基于常染色体基因组的共识系统发育发现了与每个海洋盆地相关的单系进化枝，这与目前对亚种划分的理解是一致的。然而，基于 Y 染色体、线粒体基因组、常染色体基因组和 X 染色体的系统发育发现了不一致。此外，我们在常染色体基因组中检测到基因渗入和普遍的系统发育不一致的迹象。这种复杂的系统发育情景可以用一系列渐渗事件来解释，但长须鲸尚未有记录。同样，不完整的谱系排序和低系统发育信号也可能导致这种系统发育不一致。 我们的研究通过说明某些系统发育方法可能无法捕获的潜在细微差别，强化了依赖串联或单基因座系统发育来确定物种水平以下的分类关系的陷阱。我们通过探索全基因组评估揭示的关键信息来强调长须鲸准确分类学划分的重要性。