Data from: Data set incongruence and correlated character evolution: an example of functional convergence in the hind-limbs of stifftail diving ducks

The unwitting inclusion of convergent characters in phylogenetic estimates poses a serious problem for efforts to recover phylogeny. Convergence is not inscrutable, however, particularly when one group of characters tracks phylogeny and another set tracks adaptive history. In such cases, convergent characters may be correlated with one or a few functional anatomical units and readily identifiable using comparative methods. Stifftail ducks (Oxyurinae) offer one such opportunity to study correlated character evolution and function in the context of phylogenetic reconstruction. Morphological analyses place stifftail ducks as part of a large clade of diving ducks that includes the sea ducks (Mergini), Hymenolaimus, Merganetta, and Tachyeres, and possibly the pochards (Aythyini). Molecular analyses, on the other hand, place stifftails far from other diving ducks and suggest, moreover, that stifftails are polyphyletic. Mitochondrial cytochrome b gene sequences of eight stifftail species traditionally supposed to form a clade were compared with each other and with sequences from 50 other anseriform and galliform species. Stifftail ducks are not the sister group of sea ducks, but lie outside the typical ducks (Anatinae). Of the four traditional stifftail genera, monophyly of Oxyura and its sister group relationship with Nomonyx are strongly supported. Heteronetta probably is the sister group of that clade, but support is weak. Biziura is not a true stifftail. Within Oxyura, Old World species (O. australis, O. leucocephala, O. maccoa) appear to form a clade, with New World species (O. jamaicensis, O. vittata) branching basally. Incongruence between molecules and morphology is interpreted to be the result of adaptive specialization and functional convergence in the hind limbs of Biziura and true stifftails. When morphological characters are divided into classes, only hind-limb characters are significantly in conflict with the molecular tree. Null models of synonomous and nonsynonomous substitution based on patterns of codon-degeneracy and chemical dissimilarity, likewise, indicate that the nucleotide and amino acid changes postulated by the molecular tree are more plausible than those postulated by the morphological tree. These findings teach general lessons about the utility of highly adaptive characters (in particular those related to foraging ecology) and underscore the problems that convergence can pose for attempts to recover phylogeny. They also demonstrate how the concept of natural data partitions and simple models of evolution (e.g., parsimony, likelihood, neutrality) can be used to test the accuracy of independent phylogenetic estimates and provide arguments in favor of one tree topology over another.

在系统发育推断（phylogenetic estimates）中无意纳入趋同性状（convergent characters），会对系统发育重建工作造成严重阻碍。不过，趋同现象并非不可捉摸，尤其是当一类性状追踪系统发育关系，而另一类性状对应适应性演化历史时。在此类情形下，趋同性状往往与一个或少数几个功能性解剖单元相关联，可通过比较方法轻松识别。
硬尾鸭亚科（Oxyurinae）为我们在系统发育重建框架下研究性状协同演化与功能提供了绝佳契机。形态学分析将硬尾鸭归入包含海鸭、秋沙鸭族（Mergini）、蓝鸭属（Hymenolaimus）、湍鸭属（Merganetta）以及船鸭属（Tachyeres）的大型潜水鸭支系（clade），且可能还包括潜鸭族（Aythyini）成员。而分子生物学分析则显示，硬尾鸭与其他潜水鸭类亲缘关系甚远，甚至表明硬尾鸭是多系群。
研究对8个传统上被认为构成单系支系的硬尾鸭物种的线粒体细胞色素b基因（mitochondrial cytochrome b gene）序列进行了比对，并与彼此的序列以及另外50种雁形目（anseriform）和鸡形目（galliform）物种的序列进行了比较。结果显示，硬尾鸭并非海鸭的姐妹群（sister group），而是位于典型鸭类（Anatinae，鸭亚科）之外。在传统划分的4个硬尾鸭属中，硬尾鸭属（Oxyura）的单系性（monophyly）及其与黑腹硬尾鸭属（Nomonyx）的姐妹群关系得到了强力支持。澳洲硬尾鸭属（Heteronetta）可能是该支系的姐妹群，但支持度较弱。麝鸭属（Biziura）并非真正的硬尾鸭。
在硬尾鸭属（Oxyura）内部，旧世界物种（O. australis、O. leucocephala、O. maccoa）构成一个单系支系，新世界物种（O. jamaicensis、O. vittata）则处于基部分支位置。分子与形态学结果之间的不一致，被认为是麝鸭属（Biziura）与真正硬尾鸭后肢发生适应性特化与功能趋同的结果。当将形态学性状按类别划分时，仅有后肢性状与分子系统树存在显著冲突。
基于密码子简并性（codon-degeneracy）和化学差异模式的同义替换（synonymous substitution）与非同义替换（nonsynonymous substitution）零假设模型同样显示，分子系统树所推定的核苷酸与氨基酸变化，较形态学系统树所提出的变化更具合理性。
上述研究结果不仅为我们揭示了高适应性性状（尤其是与觅食生态相关的性状）的应用价值，也凸显了趋同现象给系统发育重建工作带来的诸多难题。同时，它们也证明了自然数据分区概念与简单演化模型（如简约法（parsimony）、似然法（likelihood）、中性学说（neutrality））可用于检验独立系统发育推断的准确性，并为支持某一拓扑结构（tree topology）优于另一拓扑结构提供理论依据。