Methodological Aspects of Molecular Phylogeny of Fishes

魚類分子親緣關係之方法論

Guillaume Lecointre

《Zoological Studies》 35卷3期 (1996/07) Pp. 161-177

摘要

過去三十年以來，在探討魚類親緣關係的方法上發生二個重大的改變。首先，在60年代的末期將支序分類學的觀念引入魚類學，使魚類的系統分類有長足的進展。其次是分子的方法特別是DNA的資料的累積，提供了探討親緣關係上一個有用的特徵，尤其是那些用形態的方法尚未解決的問題。但是時至今日，這些對於整體魚類系統分類的衝擊卻十分有限。無論其研究的目的為何，為了避免為實驗所遮蔽（experimental screens），在不同的分子方法中應該要選擇可以確認的分子結構的方式，例如求其序列（sequencing）。在基因、物種、甚至系統樹的建構上，都要避免可能的陷阱。如此才能考慮正確的親緣關係。分子學家（遺傳學家）與形態學家對於親緣樹的概念有許多的差異。前者最常運用距離矩陣，並且很自然的認為這是在序列排列與系統樹的建構上的一種必然方法。支序學者則大部份都是形態學家。多數的分子學家還無法完成整體的親緣關係。只有最大簡約法（parsimony）能夠鑑定同緣的特徵，也就是真正的親緣關係。親緣關係是一部生命的歷史的總結，必須用假說演繹法來得到。最大簡約法在這方面應該優於距離矩陣法。

關鍵字

魚類之分子親緣關係 ； 親緣關係之重構 ； 穩定性 ； 系統分類 ； 系統樹

並列摘要

Fish phylogeny has seen 2 major methodological changes during the last 30 years. First, the introduction of cladistics in Ichthyology in the late 1960s led to dramatic progress in fish classification and phylogeny. Second, molecular methods and especially DNA sequence data offered new collections of discrete characters useful for phylogenetic investigations, especially for phylogenetic problems left unresolved by morphological characters. But until now, their impact on fish phylogeny has remained limited. Whatever the aim of a study, fundamental or applied, different kinds of molecular methods exist, among which those allowing identification of molecular structures (such as sequencing) should be preferred, in order to avoid ”experimental screens” which are described herein. The choice of genes, species, and tree-construction methods presents pitfalls that one should avoid. Robustness of phylogenetic trees should be considered. Differences exist between molecularists (geneticists) and morphologists as to their respective conceptions of phylogenetic trees. Distance-matrix methods are widely used in the 1st group, and a naive essentialist way to consider sequence alignment and trees is often encountered. Cladistics was born in the world of morphologists. Most molecularists have not yet reached the corresponding ”phylogenetic maturity”. Only parsimony methods allow researchers to identify in fine homologuous characters, and are, therefore, really phylogenetic. A phylogeny, as an inference on the history of life, must be performed with hypotheticodeductive methods. Parsimony methods should therefore be preferred over distance-matrix methods.

並列關鍵字

Fish molecular phylogeny ； Phylogenetic reconstruction ； Robustness ； Systematics ； Trees