Winn Jessica C, Maduna Simo N, Bester-van der Merwe Aletta E
Molecular Breeding and Biodiversity Group, Department of Genetics, Stellenbosch University, Stellenbosch, Western Cape 7602, South Africa.
Department of Ecosystems in the Barents Region, Svanhovd Research Station, Norwegian Institute of Bioeconomy Research, 9925 Svanvik, Norway.
Genomics. 2024 Jan;116(1):110771. doi: 10.1016/j.ygeno.2023.110771. Epub 2023 Dec 24.
The complex evolutionary patterns in the mitochondrial genome (mitogenome) of the most species-rich shark order, the Carcharhiniformes (ground sharks) has led to challenges in the phylogenomic reconstruction of the families and genera belonging to the order, particularly the family Triakidae (houndsharks). The current state of Triakidae phylogeny remains controversial, with arguments for both monophyly and paraphyly within the family. We hypothesize that this variability is triggered by the selection of different a priori partitioning schemes to account for site and gene heterogeneity within the mitogenome. Here we used an extensive statistical framework to select the a priori partitioning scheme for inference of the mitochondrial phylogenomic relationships within Carcharhiniformes, tested site heterogeneous CAT + GTR + G4 models and incorporated the multi-species coalescent model (MSCM) into our analyses to account for the influence of gene tree discordance on species tree inference. We included five newly assembled houndshark mitogenomes to increase resolution of Triakidae. During the assembly procedure, we uncovered a 714 bp-duplication in the mitogenome of Galeorhinus galeus. Phylogenetic reconstruction confirmed monophyly within Triakidae and the existence of two distinct clades of the expanded Mustelus genus. The latter alludes to potential evolutionary reversal of reproductive mode from placental to aplacental, suggesting that reproductive mode has played a role in the trajectory of adaptive divergence. These new sequences have the potential to contribute to population genomic investigations, species phylogeography delineation, environmental DNA metabarcoding databases and, ultimately, improved conservation strategies for these ecologically and economically important species.
软骨鱼纲中物种最为丰富的鲨目——真鲨目（真鲨）线粒体基因组（线粒体基因组）复杂的进化模式，给该目所属科和属的系统发育重建带来了挑战，尤其是皱唇鲨科（星鲨）。皱唇鲨科系统发育的当前状态仍存在争议，关于该科是单系还是并系存在不同观点。我们推测，这种变异性是由选择不同的先验划分方案以解释线粒体基因组内的位点和基因异质性所引发的。在此，我们使用了一个广泛的统计框架来选择用于推断真鲨目线粒体系发育关系的先验划分方案，测试了位点异质的CAT + GTR + G4模型，并将多物种合并模型（MSCM）纳入我们的分析，以考虑基因树不一致对物种树推断的影响。我们纳入了五个新组装的星鲨线粒体基因组，以提高皱唇鲨科的分辨率。在组装过程中，我们在短吻角鲨的线粒体基因组中发现了一个714 bp的重复序列。系统发育重建证实了皱唇鲨科内的单系性以及扩展的鼬鲨属存在两个不同的分支。后者暗示了生殖模式从胎盘生殖到非胎盘生殖的潜在进化逆转，表明生殖模式在适应性分化轨迹中发挥了作用。这些新序列有可能为种群基因组研究、物种系统地理学描绘、环境DNA宏条形码数据库做出贡献，并最终改善这些具有重要生态和经济意义物种的保护策略。
