Meyer Britta S, Matschiner Michael, Salzburger Walter
Zoological Institute, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland; Evolutionary Ecology of Marine Fishes, GEOMAR Helmholtz Centre for Ocean Research Kiel, Düsternbrooker Weg 20, 24105 Kiel, Germany.
Zoological Institute, University of Basel, Vesalgasse 1, 4051 Basel, Switzerland; Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, Oslo, Norway.
Mol Phylogenet Evol. 2015 Feb;83:56-71. doi: 10.1016/j.ympev.2014.10.009. Epub 2014 Nov 26.
The species-flocks of cichlid fishes in the East African Great Lakes Victoria, Malawi and Tanganyika constitute the most diverse extant adaptive radiations in vertebrates. Lake Tanganyika, the oldest of the lakes, harbors the morphologically and genetically most diverse assemblage of cichlids and contains the highest number of endemic cichlid genera of all African lakes. Based on morphological grounds, the Tanganyikan cichlid species have been grouped into 12-16 distinct lineages, so-called tribes. While the monophyly of most of the tribes is well established, the phylogenetic relationships among the tribes remain largely elusive. Here, we present a new tribal level phylogenetic hypothesis for the cichlid fishes of Lake Tanganyika that is based on the so far largest set of nuclear markers and a total alignment length of close to 18kb. Using next-generation amplicon sequencing with the 454 pyrosequencing technology, we compiled a dataset consisting of 42 nuclear loci in 45 East African cichlid species, which we subjected to maximum likelihood and Bayesian inference phylogenetic analyses. We analyzed the entire concatenated dataset and each marker individually, and performed a Bayesian concordance analysis and gene tree discordance tests. Overall, we find strong support for a position of the Oreochromini, Boulengerochromini, Bathybatini and Trematocarini outside of a clade combining the substrate spawning Lamprologini and the mouthbrooding tribes of the 'H-lineage', which are both strongly supported to be monophyletic. The Eretmodini are firmly placed within the 'H-lineage', as sister-group to the most species-rich tribe of cichlids, the Haplochromini. The phylogenetic relationships at the base of the 'H-lineage' received less support, which is likely due to high speciation rates in the early phase of the radiation. Discordance among gene trees and marker sets further suggests the occurrence of past hybridization and/or incomplete lineage sorting in the cichlid fishes of Lake Tanganyika.
东非大湖维多利亚湖、马拉维湖和坦噶尼喀湖中的丽鱼科鱼类物种群是脊椎动物中现存最多样化的适应性辐射类群。坦噶尼喀湖是这些湖泊中最古老的，拥有形态和遗传上最多样化的丽鱼科鱼类组合，并且是所有非洲湖泊中特有丽鱼属数量最多的。基于形态学依据，坦噶尼喀湖丽鱼科物种已被归为12 - 16个不同的谱系，即所谓的族。虽然大多数族的单系性已得到充分确立，但各族之间的系统发育关系在很大程度上仍然难以捉摸。在此，我们基于迄今为止最大的核标记集和接近18kb的总比对长度，提出了一个关于坦噶尼喀湖丽鱼科鱼类的新的族级系统发育假说。利用454焦磷酸测序技术进行新一代扩增子测序，我们编制了一个数据集，该数据集由45种东非丽鱼科物种中的42个核基因座组成，并对其进行了最大似然法和贝叶斯推断系统发育分析。我们分析了整个串联数据集以及每个标记，并进行了贝叶斯一致性分析和基因树不一致性检验。总体而言，我们发现有力支持将 Oreochromini族、Boulengerochromini族、Bathybatini族和Trematocarini族置于一个包含基质产卵的 Lamprologini族和“H - 谱系”口育族的分支之外，而这两个族都被有力支持为单系的。Eretmodini族被稳固地置于“H - 谱系”内，作为丽鱼科中物种最丰富的族——Haplochromini族的姐妹群。“H - 谱系”基部的系统发育关系得到的支持较少，这可能是由于辐射早期的高物种形成率所致。基因树和标记集之间的不一致进一步表明坦噶尼喀湖丽鱼科鱼类中发生了过去的杂交和/或不完全谱系分选。
