PDF(Pubmed)
Abstract：
BACKGROUND: To unravel the evolutionary history of a complex group, a comprehensive reconstruction of its phylogenetic relationships is crucial. This requires meticulous taxon sampling and careful consideration of multiple characters to ensure a complete and accurate reconstruction. The phylogenetic position of the Orestias genus has been estimated partly on unavailable or incomplete information. As a consequence, it was assigned to the family Cyprindontidae, relating this Andean fish to other geographically distant genera distributed in the Mediterranean, Middle East and North and Central America. In this study, using complete genome sequencing, we aim to clarify the phylogenetic position of Orestias within the Cyprinodontiformes order.
RESULTS: We sequenced the genome of three Orestias species from the Andean Altiplano. Our analysis revealed that the small genome size in this genus (~ 0.7 Gb) was caused by a contraction in transposable element (TE) content, particularly in DNA elements and short interspersed nuclear elements (SINEs). Using predicted gene sequences, we generated a phylogenetic tree of Cyprinodontiformes using 902 orthologs extracted from all 32 available genomes as well as three outgroup species. We complemented this analysis with a phylogenetic reconstruction and time calibration considering 12 molecular markers (eight nuclear and four mitochondrial genes) and a stratified taxon sampling to consider 198 species of nearly all families and genera of this order. Overall, our results show that phylogenetic closeness is directly related to geographical distance. Importantly, we found that Orestias is not part of the Cyprinodontidae family, and that it is more closely related to the South American fish fauna, being the Fluviphylacidae the closest sister group.
CONCLUSIONS: The evolutionary history of the Orestias genus is linked to the South American ichthyofauna and it should no longer be considered a member of the Cyprinodontidae family. Instead, we submit that Orestias belongs to the Orestiidae family, as suggested by Freyhof et al. (2017), and that it is the sister group of the Fluviphylacidae family, distributed in the Amazonian and Orinoco basins. These two groups likely diverged during the Late Eocene concomitant with hydrogeological changes in the South American landscape.
RESULTS: We sequenced the genome of three Orestias species from the Andean Altiplano. Our analysis revealed that the small genome size in this genus (~ 0.7 Gb) was caused by a contraction in transposable element (TE) content, particularly in DNA elements and short interspersed nuclear elements (SINEs). Using predicted gene sequences, we generated a phylogenetic tree of Cyprinodontiformes using 902 orthologs extracted from all 32 available genomes as well as three outgroup species. We complemented this analysis with a phylogenetic reconstruction and time calibration considering 12 molecular markers (eight nuclear and four mitochondrial genes) and a stratified taxon sampling to consider 198 species of nearly all families and genera of this order. Overall, our results show that phylogenetic closeness is directly related to geographical distance. Importantly, we found that Orestias is not part of the Cyprinodontidae family, and that it is more closely related to the South American fish fauna, being the Fluviphylacidae the closest sister group.
CONCLUSIONS: The evolutionary history of the Orestias genus is linked to the South American ichthyofauna and it should no longer be considered a member of the Cyprinodontidae family. Instead, we submit that Orestias belongs to the Orestiidae family, as suggested by Freyhof et al. (2017), and that it is the sister group of the Fluviphylacidae family, distributed in the Amazonian and Orinoco basins. These two groups likely diverged during the Late Eocene concomitant with hydrogeological changes in the South American landscape.
摘要：
背景：为了解开复杂群体的进化史，全面重建其系统发育关系至关重要。这需要细致的分类单元采样和对多个字符的仔细考虑，以确保完整和准确的重建。Orestias属的系统发育位置已部分根据不可用或不完整的信息进行了估计。因此,它被分配给鲤科，将这种安第斯鱼与分布在地中海的其他地理上遥远的属联系起来，中东、北美和中美洲。在这项研究中,使用完整的基因组测序，我们的目的是阐明Orestias在Cyprinodontiformes顺序中的系统发育位置。
结果：我们对来自安第斯高原的三种Orestias物种的基因组进行了测序。我们的分析表明，该属中的小基因组大小（〜0.7Gb）是由转座因子（TE）含量的收缩引起的，特别是在DNA元件和短散布核元件（SINE）中。使用预测的基因序列，我们使用从所有32个可用基因组以及3个外群物种中提取的902个直系同源物，生成了Cyprinodontiformes的系统发育树。我们通过考虑12个分子标记（8个核基因和4个线粒体基因）的系统发育重建和时间校准以及分层分类采样来补充此分析，以考虑该顺序几乎所有科和属的198个物种。总的来说,我们的结果表明，系统发育接近度与地理距离直接相关。重要的是,我们发现Orestias不是鲤科的一部分，它与南美鱼类动物更密切相关，是Fluviphylacidae最亲密的姐妹组。
结论：Orestias属的进化史与南美鱼鳞科有关，不应再将其视为Cyprinodonetidae家族的成员。相反，我们认为Orestias属于Orestiidae家族，正如Freyhof等人所建议的那样。(2017),它是螺旋藻科的姐妹组，分布在亚马逊和奥里诺科盆地。在始新世晚期，伴随着南美景观的水文地质变化，这两组可能发生了分歧。
结果：我们对来自安第斯高原的三种Orestias物种的基因组进行了测序。我们的分析表明，该属中的小基因组大小（〜0.7Gb）是由转座因子（TE）含量的收缩引起的，特别是在DNA元件和短散布核元件（SINE）中。使用预测的基因序列，我们使用从所有32个可用基因组以及3个外群物种中提取的902个直系同源物，生成了Cyprinodontiformes的系统发育树。我们通过考虑12个分子标记（8个核基因和4个线粒体基因）的系统发育重建和时间校准以及分层分类采样来补充此分析，以考虑该顺序几乎所有科和属的198个物种。总的来说,我们的结果表明，系统发育接近度与地理距离直接相关。重要的是,我们发现Orestias不是鲤科的一部分，它与南美鱼类动物更密切相关，是Fluviphylacidae最亲密的姐妹组。
结论：Orestias属的进化史与南美鱼鳞科有关，不应再将其视为Cyprinodonetidae家族的成员。相反，我们认为Orestias属于Orestiidae家族，正如Freyhof等人所建议的那样。(2017),它是螺旋藻科的姐妹组，分布在亚马逊和奥里诺科盆地。在始新世晚期，伴随着南美景观的水文地质变化，这两组可能发生了分歧。
