The endemic sponges of Lake Baikal are vital components of one of the most unique ecosystems on the planet. To date we have yet to satisfactorily resolve their systematic relationships. Their relatively slow rates of molecular change, a short branch length to the common ancestor of extant species, and very plastic morphology in some species make robust species assignment and differentiation difficult. Using recently published genomic and transcriptomic resources, a novel Swartschewskia papyracea transcriptome and a phylogenomic approach, we have reassessed relationships within the Lubomirskiidae, a family of freshwater sponges endemic to Lake Baikal. After orthology assessment, paralog pruning and data curation, a concatenated 2710 orthogroup, 463,187 site alignment was used to infer phylogenetic interrelationships between four members of the Lubomirskiidae, several freshwater sponge species and outgroup taxa, using Bayesian and Maximum Likelihood methods. This approach conclusively answers a number of previously recalcitrant questions. It confirms the position of Swartschewskia papyracea as the sister taxon to genera Lubomirskia and Baikalospongia. It strongly supports Lubomirskia monophyly, with Baikalospongia bacillifera as the sister taxa to the two species of Lubomirskia sampled here. It also confirms the relative branching arrangement of other common freshwater taxa, including the issue of Spongillidae paraphyly. This is key for interpreting the evolution of the Spongillida as a whole, and in particular, for understanding the evolution of the still enigmatic sponges of Lake Baikal.

中文翻译：

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贝加尔湖海绵相互关系的系统发育推断

贝加尔湖特有的海绵是地球上最独特的生态系统之一的重要组成部分。迄今为止，我们还没有令人满意地解决它们的系统关系。它们的分子变化速度相对较慢，现有物种共同祖先的分支长度较短，某些物种的形态非常可塑性，这使得可靠的物种分配和分化变得困难。使用最近发表的基因组和转录组学资源、新的 Swartschewskia papyracea 转录组和系统发育方法，我们重新评估了 Lubomirskiidae（贝加尔湖特有的淡水海绵家族）之间的关系。经过直系学评估、旁系同源剪枝和数据管理后，一个串联的 2710 正交组、463、187 位点比对用于推断 Lubomirskiidae 的四个成员、几种淡水海绵物种和外群分类群之间的系统发育相互关系，使用贝叶斯和最大似然方法。这种方法最终回答了许多以前难以解决的问题。它确认了 Swartschewskia papyracea 作为 Lubomirskia 和 Baikalospongia 属的姐妹分类群的地位。它强烈支持 Lubomirskia 单系，Baikalospongia bacillifera 作为这里采样的两个 Lubomirskia 物种的姐妹分类群。它还证实了其他常见淡水类群的相对分支排列，包括 Spongillidae 并系问题。这是从整体上解释 Spongillida 进化的关键，尤其是理解贝加尔湖仍然神秘的海绵进化的关键。