Wielstra Ben, Arntzen Jan W, van der Gaag Kristiaan J, Pabijan Maciej, Babik Wieslaw
Naturalis Biodiversity Center, Leiden, The Netherlands; Department of Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom.
Naturalis Biodiversity Center, Leiden, The Netherlands.
PLoS One. 2014 Oct 22;9(10):e111011. doi: 10.1371/journal.pone.0111011. eCollection 2014.
The phylogenetic relationships for rapid species radiations are difficult to disentangle. Here we study one such case, namely the genus Triturus, which is composed of the marbled and crested newts. We analyze data for 38 genetic markers, positioned in 3-prime untranslated regions of protein-coding genes, obtained with 454 sequencing. Our dataset includes twenty Triturus newts and represents all nine species. Bayesian analysis of population structure allocates all individuals to their respective species. The branching patterns obtained by data concatenation, Bayesian concordance analysis and coalescent-based estimations of the species tree differ from one another. The data concatenation based species tree shows high branch support but branching order is considerably affected by allele choice in the case of heterozygotes in the concatenation process. Bayesian concordance analysis expresses the conflict between individual gene trees for part of the Triturus species tree as low concordance factors. The coalescent-based species tree is relatively similar to a previously published species tree based upon morphology and full mtDNA and any conflicting internal branches are not highly supported. Our findings reflect high gene tree discordance due to incomplete lineage sorting (possibly aggravated by hybridization) in combination with low information content of the markers employed (as can be expected for relatively recent species radiations). This case study highlights the complexity of resolving rapid radiations and we acknowledge that to convincingly resolve the Triturus species tree even more genes will have to be consulted.
快速物种辐射的系统发育关系很难理清。在此，我们研究这样一个案例，即真螈属，它由大理石纹螈和冠螈组成。我们分析了通过454测序获得的位于蛋白质编码基因3'非翻译区的38个遗传标记的数据。我们的数据集包括20种真螈，涵盖了所有9个物种。群体结构的贝叶斯分析将所有个体分配到各自的物种。通过数据拼接、贝叶斯一致性分析和基于溯祖的物种树估计得到的分支模式彼此不同。基于数据拼接的物种树显示出较高的分支支持度，但在拼接过程中，杂合子的等位基因选择会对分支顺序产生相当大的影响。贝叶斯一致性分析将部分真螈物种树中个体基因树之间的冲突表示为低一致性因子。基于溯祖的物种树与之前基于形态学和完整线粒体DNA发表的物种树相对相似，任何冲突的内部分支都没有得到高度支持。我们的研究结果反映出，由于不完全谱系分选（可能因杂交而加剧）以及所用标记的信息含量低（对于相对近期的物种辐射来说是可以预期的），导致基因树不一致性较高。这个案例研究突出了解决快速辐射问题的复杂性，我们承认，要令人信服地解析真螈物种树，还需要参考更多的基因。
