Justus Liebig University Giessen, Giessen, Germany.
University of Basel, Basel, Switzerland.
BMC Ecol Evol. 2024 Apr 8;24(1):42. doi: 10.1186/s12862-024-02235-0.
Species flocks in ancient lakes, and particularly those arising from adaptive radiation, make up the bulk of overall taxonomic and morphological diversity in these insular ecosystems. For these mostly young species assemblages, classical mitochondrial barcoding markers have so far been key to disentangle interspecific relationships. However, with the rise and further development of next-generation sequencing (NGS) methods and mapping tools, genome-wide data have become an increasingly important source of information even for non-model groups.
Here, we provide, for the first time, a comprehensive mitogenome dataset of freshwater gastropods endemic to Sulawesi and thus of an ancient lake invertebrate species flock in general. We applied low-coverage whole-genome sequencing for a total of 78 individuals including 27 out of the 28 Tylomelania morphospecies from the Malili lake system as well as selected representatives from Lake Poso and adjacent catchments. Our aim was to assess whether mitogenomes considerably contribute to the phylogenetic resolution within this young species flock. Interestingly, we identified a high number of variable and parsimony-informative sites across the other 'non-traditional' mitochondrial loci. However, although the overall support was very high, the topology obtained was largely congruent with previously published single-locus phylogenies. Several clades remained unresolved and a large number of species was recovered polyphyletic, indicative of both rapid diversification and mitochondrial introgression.
This once again illustrates that, despite the higher number of characters available, mitogenomes behave like a single locus and thus can only make a limited contribution to resolving species boundaries, particularly when introgression events are involved.
古老湖泊中的物种群体，尤其是那些由适应性辐射产生的物种群体，构成了这些岛屿生态系统中总体分类和形态多样性的大部分。对于这些主要的年轻物种组合，经典的线粒体条形码标记一直是解开种间关系的关键。然而，随着下一代测序（NGS）方法和图谱工具的兴起和进一步发展，即使对于非模式群体，全基因组数据也成为越来越重要的信息来源。
在这里，我们首次提供了苏拉威西特有淡水腹足动物的综合线粒体基因组数据集，因此也是古老湖泊无脊椎动物物种群体的综合数据集。我们应用低覆盖率全基因组测序对总共 78 个个体进行了测序，包括来自马利利湖系统的 28 个 Tylomelania 形态种中的 27 个以及来自波索湖和相邻集水区的选定代表。我们的目的是评估线粒体基因组是否能极大地提高这个年轻物种群体的系统发育分辨率。有趣的是，我们在其他“非传统”线粒体基因座中鉴定出了大量可变和简约信息丰富的位点。然而，尽管整体支持率非常高，但得到的拓扑结构与以前发表的单基因座系统发育关系基本一致。几个分支仍然没有解决，许多物种呈多系发生，表明快速多样化和线粒体渗入的同时发生。
这再次表明，尽管可用的特征数量较多，但线粒体基因组的行为与单个基因座相似，因此在解决物种边界问题时，特别是在涉及渗入事件时，只能做出有限的贡献。
