Kalaentzis Konstantinos, Koster Stephanie, Arntzen Jan W, Bogaerts Sergé, France James, Franzen Michael, Kazilas Christos, Litvinchuk Spartak N, Olgun Kurtuluş, de Visser Manon, Wielstra Ben
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; Hydrobiological Station of Rhodes (HCMR), 85131 Rhodes, Greece.
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.
Mol Phylogenet Evol. 2025 Feb;203:108237. doi: 10.1016/j.ympev.2024.108237. Epub 2024 Nov 17.
Resolving the order of speciation events that occurred in rapid succession is inherently hard and typically requires a phylogenomic approach. A case in point concerns the previously unresolved phylogeny of the three species of banded newt (genus Ommatotriton). We obtain c. 7k nuclear DNA markers using target enrichment by sequence capture and analyze the dataset using maximum likelihood inference of concatenated data with RAxML, summary multi-species coalescent analysis with ASTRAL and Bayesian species tree inference using a diffusion model with SNAPPER, and use TreeMix and PhyloNet to test for interspecific gene flow. All analyses recover three distinct species with no evidence of interspecific gene flow. All analyses retrieved the topology (O. nesterovi, (O. ophryticus, O. vittatus)), with high support. SNAPPER did show the tendency to get stuck in a local optimum, resulting in a different but still highly supported topology. Furthermore, we notice that fewer SNAPPER runs get stuck in a local optimum when we include an outgroup. Therefore, we recommend the exploration of multiple independent runs and the use of an outgroup with this approach. The banded newt radiation illustrates the use of genome-wide data to tackle formerly unresolved phylogenies.
解决快速连续发生的物种形成事件的顺序本质上是困难的，通常需要系统发育基因组学方法。一个恰当的例子是关于带状蝾螈（Ommatotriton属）三个物种之前未解决的系统发育问题。我们通过序列捕获的目标富集获得了约7000个核DNA标记，并使用RAxML对串联数据进行最大似然推断、使用ASTRAL进行总结多物种合并分析以及使用带有SNAPPER的扩散模型进行贝叶斯物种树推断来分析数据集，还使用TreeMix和PhyloNet来测试种间基因流。所有分析都恢复出三个不同的物种，没有种间基因流的证据。所有分析都检索到了拓扑结构（内斯特罗夫带状蝾螈，（奥弗里蒂克带状蝾螈，带纹带状蝾螈）），且支持度很高。SNAPPER确实显示出陷入局部最优的趋势，导致了一个不同但仍然得到高度支持的拓扑结构。此外，我们注意到当我们纳入一个外类群时，较少的SNAPPER运行会陷入局部最优。因此，我们建议使用这种方法时探索多个独立运行并使用外类群。带状蝾螈的辐射说明了利用全基因组数据来解决以前未解决的系统发育问题。
