Maltseva Arina L, Varfolomeeva Marina A, Lobov Arseniy A, Tikanova Polina, Panova Marina, Mikhailova Natalia A, Granovitch Andrei I
Department of Invertebrate Zoology, St. Petersburg State University, St. Petersburg, Russia.
Laboratory of Regenerative Biomedicine, Institute of Cytology Russian Academy of Sciences, St. Petersburg, Russia.
PeerJ. 2020 Feb 13;8:e8546. doi: 10.7717/peerj.8546. eCollection 2020.
The introduction of DNA-based molecular markers made a revolution in biological systematics. However, in cases of very recent divergence events, the neutral divergence may be too slow, and the analysis of adaptive part of the genome is more informative to reconstruct the recent evolutionary history of young species. The advantage of proteomics is its ability to reflect the biochemical machinery of life. It may help both to identify rapidly evolving genes and to interpret their functions.
Here we applied a comparative gel-based proteomic analysis to several species from the gastropod family Littorinidae. Proteomes were clustered to assess differences related to species, geographic location, sex and body part, using data on presence/absence of proteins in samples and data on protein occurrence frequency in samples of different species. Cluster support was assessed using multiscale bootstrap resampling and the stability of clustering-using cluster-wise index of cluster stability. Taxon-specific protein markers were derived using IndVal method. Proteomic trees were compared to consensus phylogenetic tree (based on neutral genetic markers) using estimates of the Robinson-Foulds distance, the Fowlkes-Mallows index and cophenetic correlation.
Overall, the DNA-based phylogenetic tree and the proteomic similarity tree had consistent topologies. Further, we observed some interesting deviations of the proteomic littorinid tree from the neutral expectations. (1) There were signs of molecular parallelism in two species that phylogenetically are quite distant, but live in similar habitats. (2) Proteome divergence was unexpectedly high between very closely related and , possibly reflecting their ecology-driven divergence. (3) Conservative house-keeping proteins were usually identified as markers for cryptic species groups ("saxatilis" and "obtusata" groups in the genus) and for genera ( and species pairs), while metabolic enzymes and stress-related proteins (both potentially adaptively important) were often identified as markers supporting species branches. (4) In all five species British populations were separated from the European mainland populations, possibly reflecting their recent phylogeographic history. Altogether our study shows that proteomic data, when interpreted in the context of DNA-based phylogeny, can bring additional information on the evolutionary history of species.
基于DNA的分子标记的引入给生物系统学带来了一场革命。然而，在非常近期的分化事件中，中性分化可能过于缓慢，而对基因组适应性部分的分析对于重建年轻物种的近期进化历史更具信息价值。蛋白质组学的优势在于其能够反映生命的生化机制。它可能有助于快速识别快速进化的基因并解释其功能。
在此，我们对滨螺科的几个物种进行了基于凝胶的比较蛋白质组学分析。利用样本中蛋白质的有无数据以及不同物种样本中蛋白质出现频率的数据，对蛋白质组进行聚类，以评估与物种、地理位置、性别和身体部位相关的差异。使用多尺度自展重采样评估聚类支持，并使用聚类稳定性的聚类-wise指数评估聚类的稳定性。使用IndVal方法推导分类群特异性蛋白质标记。使用罗宾逊-福尔兹距离、福克-马洛斯指数和协表型相关性估计值，将蛋白质组树与共识系统发育树（基于中性遗传标记）进行比较。
总体而言，基于DNA的系统发育树和蛋白质组相似性树具有一致的拓扑结构。此外，我们观察到蛋白质组滨螺树与中性预期存在一些有趣的偏差。（1）在系统发育上相距甚远但生活在相似栖息地的两个物种中存在分子平行的迹象。（2）在非常密切相关的[物种名称1]和[物种名称2]之间，蛋白质组分化出人意料地高，这可能反映了它们受生态驱动的分化。（3）保守的管家蛋白通常被确定为隐秘物种组（滨螺属中的“saxatilis”和“obtusata”组）和属（[属名称1]和[属名称2]物种对）的标记，而代谢酶和应激相关蛋白（两者都可能具有重要的适应性）通常被确定为支持物种分支的标记。（4）在所有五个[物种名称]中，英国种群与欧洲大陆种群分离，这可能反映了它们近期的系统地理学历史。总之，我们的研究表明，当在基于DNA的系统发育背景下进行解释时，蛋白质组数据可以为物种的进化历史带来额外信息。
