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.在系统发育估计中无意纳入趋同性状（convergent characters），会为系统发育重建工作带来严重阻碍。不过趋同现象并非难以捉摸，尤其是当一类性状追踪系统发育关系，而另一类性状追踪适应性演化历史时。在此类情形下，趋同性状往往与一个或少数几个功能解剖单元相关联，可通过比较分析方法轻松识别。 硬尾鸭亚科（Oxyurinae）为我们在系统发育重建框架下研究相关联的性状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族（Mergini）、Hymenolaimus、Merganetta以及Tachyeres的大型潜水鸭支系（clade），且可能还包括潜鸭族（Aythyini）。而分子分析则将硬尾鸭置于远离其他潜水鸭类的位置，且进一步表明硬尾鸭为多系群。 我们对8个传统上被认为构成单一支系的硬尾鸭物种的线粒体细胞色素b基因（mitochondrial cytochrome b gene）序列进行了相互比对，并与另外50种雁形目（Anseriformes）和鸡形目（Galliformes）物种的序列进行了比对。研究结果显示，硬尾鸭并非海鸭的姊妹群（sister group），而是位于典型鸭类（Anatinae）之外。 在4个传统硬尾鸭属中，Oxyura的单系性（monophyly）及其与Nomonyx的姊妹群关系得到了强烈支持。Heteronetta大概率是该支系的姊妹群，但支持度较弱。Biziura并非真正的硬尾鸭。 在Oxyura属内，旧世界物种（O. australis、O. leucocephala、O. maccoa）似乎构成一个单系支系，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性被认为是Biziura与真正硬尾鸭后肢适应性特化和功能趋同导致的结果。当将形态学性状划分为不同类别时，仅后肢性状与分子树存在显著冲突。 基于密码子简并性（codon-degeneracy）和化学差异性模式构建的同义替换（synonymous substitution）与非同义替换（nonsynonymous substitution）零模型同样表明，分子树所推定的核苷酸与氨基酸变化相较于形态学树所推定的更为合理可信。 这些发现为我们提供了关于高度适应性性状（尤其是与觅食生态相关的性状）实用性的一般性经验教训，并凸显了趋同现象给系统发育重建工作带来的挑战。同时，它们也展示了如何利用自然数据分区概念和简单的演化模型（如简约法（parsimony）、似然法（likelihood）、中性模型（neutrality））来检验独立系统发育估计的准确性，并为支持某一树拓扑结构（tree topology）而非另一拓扑结构提供依据。