Atmosphere and Ocean Research Institute, The University of Tokyo, 5-1-5Kashiwanoha, Kashiwa-shi, Chiba 277-8564, Japan.
BMC Evol Biol. 2011 Jun 22;11:177. doi: 10.1186/1471-2148-11-177.
Freshwater harbors approximately 12,000 fish species accounting for 43% of the diversity of all modern fish. A single ancestral lineage evolved into about two-thirds of this enormous biodiversity (≈ 7900 spp.) and is currently distributed throughout the world's continents except Antarctica. Despite such remarkable species diversity and ubiquity, the evolutionary history of this major freshwater fish clade, Otophysi, remains largely unexplored. To gain insight into the history of otophysan diversification, we constructed a timetree based on whole mitogenome sequences across 110 species representing 55 of the 64 families.
Partitioned maximum likelihood analysis based on unambiguously aligned sequences (9923 bp) confidently recovered the monophyly of Otophysi and the two constituent subgroups (Cypriniformes and Characiphysi). The latter clade comprised three orders (Gymnotiformes, Characiformes, Siluriformes), and Gymnotiformes was sister to the latter two groups. One of the two suborders in Characiformes (Characoidei) was more closely related to Siluriformes than to its own suborder (Citharinoidei), rendering the characiforms paraphyletic. Although this novel relationship did not receive strong statistical support, it was supported by analyzing independent nuclear markers. A relaxed molecular clock Bayesian analysis of the divergence times and reconstruction of ancestral habitats on the timetree suggest a Pangaean origin and Mesozoic radiation of otophysans.
The present timetree demonstrates that survival of the ancestral lineages through the two consecutive mass extinctions on Pangaea, and subsequent radiations during the Jurassic through early Cretaceous shaped the modern familial diversity of otophysans. This evolutionary scenario is consistent with recent arguments based on biogeographic inferences and molecular divergence time estimates. No fossil otophysan, however, has been recorded before the Albian, the early Cretaceous 100-112 Ma, creating an over 100 million year time span without fossil evidence. This formidable ghost range partially reflects a genuine difference between the estimated ages of stem group origin (molecular divergence time) and crown group morphological diversification (fossil divergence time); the ghost range, however, would be filled with discoveries of older fossils that can be used as more reasonable time constraints as well as with developments of more realistic models that capture the rates of molecular sequences accurately.
淡水拥有约 12000 种鱼类，占现代鱼类多样性的 43%。单一的祖先谱系进化成了大约三分之二的这种巨大的生物多样性（≈7900 种），目前分布在除南极洲以外的世界各大洲。尽管这种鱼类具有显著的物种多样性和普遍性，但这个主要的淡水鱼类类群，骨鳔总目（Otophysi）的进化历史在很大程度上仍未被探索。为了深入了解骨鳔总目的多样化历史，我们构建了一个基于 110 种鱼类的全线粒体基因组序列的时间树，这些鱼类代表了 64 个科中的 55 个科。
基于明确对齐序列（9923bp）的分区最大似然分析，自信地恢复了骨鳔总目的单系性，以及两个组成亚群（鲤形目和脂鲤形目）。后者包括三个目（电鳗目、脂鲤目、鲶形目），电鳗目与后两个目关系最密切。脂鲤形目的两个亚目之一（脂鲤亚目）与鲶形目比与自己的亚目（锯脂鲤亚目）更密切相关，使得脂鲤形目是并系的。尽管这种新的关系没有得到强有力的统计支持，但它得到了分析独立核标记的支持。对时间树上的分歧时间进行放松分子钟贝叶斯分析，并重建祖先栖息地表明，骨鳔总目的起源于泛大陆，并在中生代辐射进化。
本时间树表明，通过两次连续的泛大陆大灭绝，祖先谱系的存活，以及随后在侏罗纪到早白垩世的辐射，塑造了现代骨鳔总目的家族多样性。这种进化情景与基于生物地理推断和分子分歧时间估计的最近论点是一致的。然而，在白垩纪早期的阿尔布期（100-112Ma）之前，没有发现任何骨鳔总目的化石，这使得没有化石证据的时间跨度超过了 1 亿年。这个巨大的幽灵范围部分反映了在茎群起源的估计年龄（分子分歧时间）和冠群形态多样化的估计年龄（化石分歧时间）之间的真实差异；然而，幽灵范围将随着更古老的化石的发现而得到填补，这些化石可以作为更合理的时间限制，以及更现实的模型的发展，这些模型可以准确地捕捉分子序列的速度。
