BACKGROUND Baleen whales (Mysticeti) are the largest animals on earth and their evolutionary history has been studied in detail, but some relationships still remain contentious. In particular, reconstructing the phylogenetic position of the gray whales (Eschrichtiidae) has been complicated by evolutionary processes such as gene flow and incomplete lineage sorting (ILS). Here, whole-genome sequencing data of the extant baleen whale radiation allowed us to identify transposable element (TE) insertions in order to perform phylogenomic analyses and measure germline insertion rates of TEs. Baleen whales exhibit the slowest nucleotide substitution rate among mammals, hence we additionally examined the evolutionary insertion rates of TE insertions across the genomes. RESULTS In eleven whole-genome sequences representing the extant radiation of baleen whales, we identified 91,859 CHR-SINE insertions that were used to reconstruct the phylogeny with different approaches as well as perform evolutionary network analyses and a quantification of conflicting phylogenetic signals. Our results indicate that the radiation of rorquals and gray whales might not be bifurcating. The morphologically derived gray whales are placed inside the rorqual group, as the sister-species to humpback and fin whales. Detailed investigation of TE insertion rates confirm that a mutational slow down in the whale lineage is present but less pronounced for TEs than for nucleotide substitutions. CONCLUSIONS Whole genome sequencing based detection of TE insertions showed that the speciation processes in baleen whales represent a rapid radiation. Large genome-scale TE data sets in addition allow to understand retrotransposition rates in non-model organisms and show the potential for TE calling methods to study the evolutionary history of species.

中文翻译：

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rorquals 的后系统基因组学表明祖先种群规模大且辐射速度快。

背景须鲸（Mysticeti）是地球上最大的动物，它们的进化历史已经被详细研究过，但一些关系仍然存在争议。特别是，重建灰鲸（Eschrichtiidae）的系统发育位置已因基因流和不完全谱系分类（ILS）等进化过程而变得复杂。在这里，现存须鲸辐射的全基因组测序数据使我们能够识别转座因子 (TE) 插入，以便进行系统基因组分析和测量 TE 的种系插入率。须鲸在哺乳动物中表现出最慢的核苷酸替代率，因此我们另外检查了基因组中 TE 插入的进化插入率。结果 在代表须鲸现存辐射的 11 个全基因组序列中，我们确定了 91,859 个 CHR-SINE 插入，这些插入用于用不同的方法重建系统发育，并进行进化网络分析和相互冲突的系统发育信号的量化。我们的结果表明，rorquals 和灰鲸的辐射可能没有分叉。形态学上衍生的灰鲸被置于 rorqual 组内，作为座头鲸和长须鲸的姐妹物种。对 TE 插入率的详细调查证实，鲸鱼谱系中存在突变减慢，但 TE 的突变速度不如核苷酸取代明显。结论 基于全基因组测序的 TE 插入检测表明，须鲸的物种形成过程代表了一种快速辐射。大型基因组规模的 TE 数据集还允许了解非模式生物中的逆转录转座率，并显示 TE 调用方法研究物种进化历史的潜力。