Mars J, Koster Stephanie, Babik W, France J, Kalaentzis K, Kazilas C, Martínez-Solano I, de Visser M C, Wielstra B
Institute of Biology Leiden, Leiden University, P.O. Box 9505, 2300 RA Leiden, The Netherlands; Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA Leiden, The Netherlands.
Institute of Environmental Sciences, Jagiellonian University, ul. Gronostajowa 7, 30-387 Kraków, Poland.
Mol Phylogenet Evol. 2025 Mar;204:108282. doi: 10.1016/j.ympev.2024.108282. Epub 2024 Dec 31.
The ease with which genome-wide data can nowadays be collected allows complicated phylogenetic questions to be re-evaluated. Phylogenetic relationships among newts have often proven difficult to resolve due to the prevalence of incomplete lineage sorting and introgressive hybridization. For the newt genus Lissotriton, phylogenetic relationships are not settled and there is controversy surrounding the species status of several taxa. We obtain c. 7 k nuclear DNA markers with target enrichment by sequence capture and conduct a concatenated analysis with RAxML, gene-tree summarization with ASTRAL, and species tree estimation with SNAPPER. We explore introgression between evolutionary lineages with TreeMix and Dsuite and compare how introgression events influence the different phylogenetic tools employed. We retrieve tree topologies that are discordant with previous mtDNA-based attempts, particularly concerning the phylogenetic placement of L. italicus and the L. vulgaris species complex. Yet, we also observe deviations between the phylogenetic hypotheses resulting from the different analyses. We interpret the placement of L. montandoni deep within the L. vulgaris species complex by SNAPPER, rather than as the sister taxon to the remainder of the L. vulgaris species complex according to RAxML and ASTRAL, as an artifact of introgression - well-documented in previous work and backed up by TreeMix and Dsuite analyses. Our analyses allow us to make some taxonomical recommendations: we confirm the recently proposed species status of L. kosswigi and L. graecus and propose that L. v. lantzi and L. v. schmidtleri had better be treated as subspecies. Our work also highlights areas for further taxonomic research: range-wide phylogenomic data are required to disentangle the L. boscai - L. maltzani species complex and the northern and southern lineages of L. v. vulgaris. Our study illustrates the power of target enrichment by sequence capture in tackling longstanding questions in taxa with an extensive history of hybridization and introgression.
如今，全基因组数据的收集变得轻而易举，这使得复杂的系统发育问题能够得到重新评估。由于不完全谱系分选和渐渗杂交的普遍存在，蝾螈之间的系统发育关系常常难以确定。对于滑螈属（Lissotriton）而言，系统发育关系尚未明确，几个分类单元的物种地位也存在争议。我们通过序列捕获获得了约7000个核DNA标记，并利用RAxML进行串联分析，用ASTRAL进行基因树汇总，用SNAPPER进行物种树估计。我们使用TreeMix和Dsuite探索进化谱系之间的渐渗现象，并比较渐渗事件如何影响所采用的不同系统发育工具。我们得到的树拓扑结构与之前基于线粒体DNA的研究结果不一致，特别是在意大利滑螈（L. italicus）和普通滑螈物种复合体（L. vulgaris species complex）的系统发育位置方面。然而，我们也观察到不同分析得出的系统发育假设之间存在偏差。我们将SNAPPER分析中蒙氏滑螈（L. montandoni）置于普通滑螈物种复合体深处的位置，而非像RAxML和ASTRAL分析那样将其作为普通滑螈物种复合体其余部分的姐妹分类单元，解释为渐渗的产物——这在之前的研究中有充分记录，并得到了TreeMix和Dsuite分析的支持。我们的分析使我们能够提出一些分类学建议：我们确认了最近提出的科斯维格滑螈（L. kosswigi）和希腊滑螈（L. graecus）的物种地位，并建议将兰氏滑螈（L. v. lantzi）和施氏滑螈（L. v. schmidtleri）最好视为亚种。我们的工作还突出了进一步分类学研究的领域：需要全范围的系统发育基因组数据来厘清博氏滑螈 - 马尔察尼滑螈物种复合体（L. boscai - L. maltzani species complex）以及普通滑螈（L. v. vulgaris）的南北谱系。我们的研究说明了通过序列捕获进行目标富集在解决具有广泛杂交和渐渗历史的分类单元中长期存在的问题方面的强大作用。
