Faculty of Biosciences and Aquaculture, Nord University, Universitetsalléen 11, 8026, Bodø, Norway.
Centre for Environmental Sciences, Research Group Zoology: Biodiversity and Toxicology, Hasselt University, Agoralaan Gebouw D, 3590, Diepenbeek, Belgium.
BMC Ecol Evol. 2022 Nov 3;22(1):127. doi: 10.1186/s12862-022-02085-8.
The hydrogeological history of Lake Tanganyika paints a complex image of several colonization and adaptive radiation events. The initial basin was formed around 9-12 million years ago (MYA) from the predecessor of the Malagarasi-Congo River and only 5-6 MYA, its sub-basins fused to produce the clear, deep waters of today. Next to the well-known radiations of cichlid fishes, the lake also harbours a modest clade of only two clupeid species, Stolothrissa tanganicae and Limnothrissa miodon. They are members of Pellonulini, a tribe of clupeid fishes that mostly occur in freshwater and that colonized West and Central-Africa during a period of high sea levels during the Cenozoic. There is no consensus on the phylogenetic relationships between members of Pellonulini and the timing of the colonization of Lake Tanganyika by clupeids.
We use short-read next generation sequencing of 10X Chromium libraries to sequence and assemble the full mitochondrial genomes of S. tanganicae and L. miodon. We then use Maximum likelihood and Bayesian inference to place them into the phylogeny of Pellonulini and other clupeiforms, taking advantage of all available full mitochondrial clupeiform genomes. We identify Potamothrissa obtusirostris as the closest living relative of the Tanganyika sardines and confirm paraphyly for Microthrissa. We estimate the divergence of the Tanganyika sardines around 3.64 MYA [95% CI: 0.99, 6.29], and from P. obtusirostris around 10.92 MYA [95% CI: 6.37-15.48].
These estimates imply that the ancestor of the Tanganyika sardines diverged from a riverine ancestor and entered the proto-lake Tanganyika around the time of its formation from the Malagarasi-Congo River, and diverged into the two extant species at the onset of deep clearwater conditions. Our results prompt a more thorough examination of the relationships within Pellonulini, and the new mitochondrial genomes provide an important resource for the future study of this tribe, e.g. as a reference for species identification, genetic diversity, and macroevolutionary studies.
坦噶尼喀湖的水文地质历史描绘了多次殖民和适应辐射事件的复杂图景。该湖最初的盆地形成于 9-1200 万年前（MYA），由马拉加拉西-刚果河的前身形成，仅在 5-600 万年前，其次盆地融合形成了今天清澈深邃的湖水。除了著名的丽鱼科鱼类辐射，该湖还拥有一个适度的仅由两种鲱鱼组成的小分支，即坦噶尼喀沙丁鱼和小口马鲛。它们是鲱科鱼类的佩隆努利尼族的成员，这个鲱科鱼类的部落主要生活在淡水中，在新生代海平面上升期间殖民到西非和中非。关于佩隆努利尼族成员的系统发育关系以及鲱鱼殖民坦噶尼喀湖的时间，目前还没有共识。
我们使用 10X Chromium 文库的短读长下一代测序对 S. tanganicae 和 L. miodon 的完整线粒体基因组进行测序和组装。然后，我们利用所有可用的完整鲱形目线粒体基因组，采用最大似然法和贝叶斯推断法将它们置于佩隆努利尼族和其他鲱形目鱼类的系统发育中。我们确定钝吻鲱为坦噶尼喀沙丁鱼的最接近的现存亲缘种，并确认微鲱的并系性。我们估计坦噶尼喀沙丁鱼的分化时间约为 3.6400 万年前[95%置信区间：0.99，6.29]，与 P. obtusirostris 的分化时间约为 10.9200 万年前[95%置信区间：6.37-15.48]。
这些估计表明，坦噶尼喀沙丁鱼的祖先与河流祖先分化，并在马拉加拉西-刚果河形成时进入原坦噶尼喀湖，在深清水条件开始时分化为两个现存物种。我们的结果促使人们更深入地研究佩隆努利尼族内部的关系，新的线粒体基因组为该部落的未来研究提供了重要资源，例如作为物种鉴定、遗传多样性和宏观进化研究的参考。
