Song Shuli, Zhao Jinliang, Li Chenhong
Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, China.
Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai 201306, China.
Mol Phylogenet Evol. 2017 Jun;111:44-55. doi: 10.1016/j.ympev.2017.03.014. Epub 2017 Mar 18.
The sinipercids are freshwater fishes endemic to East Asia, mainly in China. Phylogenetic studies on the sinipercids have made great progress in the last decades, but interspecific relationships and evolutionary history of the sinipercids remain unresolved. Lack of distinctive morphological characters leads to problems in validating of some species, such as Siniperca loona. Moreover, genetic data are needed to delimitate species pairs with explicit hypothesis testing, such as in S. chuatsi vs. S. kneri and Coreoperca whiteheadi vs. C. liui. Here we reconstructed phylogeny of the sinipercids with an unprecedented scale of data, 16,943 loci of single-copy coding sequence data from nine sinipercid species, eight putative sister taxa and two outgroups. Targeted sequences were collected using gene enrichment and Illumina sequencing, yielding thousands of protein coding sequences and single nucleotide polymorphisms (SNPs) data. Maximum likelihood and coalescent species tree analyses resulted in identical and highly supported trees. We confirmed that the centrarchids are sister to the sinipercids. A monophyletic Sinipercidae with two genera, Siniperca and Coreoperca was also supported. Different from most previous studies, S. scherzeri was found as the most basal taxon to other species of Siniperca, which consists of two clades: a clade having S. roulei sister to S. chuatsi and S. kneri, and a clade consisting S. loona sister to S. obscura and S. undulata. We found that both S. loona and C. liui are valid species using Bayes factor delimitation (BFD) based on SNPs data. Species delimitation also provided decisive support for S. chuatsi and S. kneri being two distinct species. We calibrated a chronogram of the sinipercids based on 100 loci and three fossil calibration points using BEAST, and reconstructed ancestral ranges of the sinipercids using Lagrange Analysis (DEC model) and Statistical Dispersal-Vicariance Analysis (S-DIVA) implemented in RASP. Divergence time estimates and ancestral habitat reconstruction suggested a wide-ranging distribution of the common ancestor of the sinipercids in southern China at 53.1 million years ago (CI: 30.4-85.8Ma). The calibrated time tree is consistent with historical climate changes and geological events that might have shaped the current distribution of the sinipercids.
鳜科鱼类是东亚特有的淡水鱼，主要分布在中国。在过去几十年里，对鳜科鱼类的系统发育研究取得了很大进展，但鳜科鱼类的种间关系和进化历史仍未得到解决。缺乏明显的形态特征导致一些物种的鉴定出现问题，如大眼鳜。此外，需要遗传数据来通过明确的假设检验来界定物种对，如翘嘴鳜与斑鳜以及伍氏鲈鲤与抚仙湖鲈鲤。在这里，我们用前所未有的数据规模重建了鳜科鱼类的系统发育，这些数据来自9种鳜科鱼类、8个假定的姐妹类群和2个外类群的16943个单拷贝编码序列位点。使用基因富集和Illumina测序收集目标序列，产生了数千个蛋白质编码序列和单核苷酸多态性（SNP）数据。最大似然法和溯祖物种树分析得到了相同且支持度很高的树。我们证实太阳鱼科是鳜科的姐妹类群。还支持了一个包含鳜属和鲈鲤属两个属的单系鳜科。与大多数以前的研究不同，发现谢氏鳜是鳜属其他物种的最基部类群，鳜属由两个分支组成：一个分支中，长体鳜是翘嘴鳜和斑鳜的姐妹种；另一个分支中，大眼鳜是暗色鳜和波纹鳜的姐妹种。我们基于SNP数据使用贝叶斯因子界定法（BFD）发现大眼鳜和抚仙湖鲈鲤都是有效物种。物种界定也为翘嘴鳜和斑鳜是两个不同物种提供了决定性支持。我们使用BEAST基于100个位点和三个化石校准点校准了鳜科鱼类的时间树，并使用RASP中实现的拉格朗日分析（DEC模型）和统计扩散 - 隔离分析（S - DIVA）重建了鳜科鱼类的祖先分布范围。分歧时间估计和祖先栖息地重建表明，鳜科鱼类的共同祖先在5310万年前（置信区间：3040 - 8580万年前）在中国南方广泛分布。校准后的时间树与可能塑造了鳜科鱼类当前分布的历史气候变化和地质事件一致。
