Phylogenetic analyses of Fringillidae (Aves : Passeriformes) using mitochondrial tRNA gene sequences and secondary structure

Fringillidae is a large and diverse family of Passeriformes. So far, however, Fringillidae relationships deduced from morphological features and by a number of molecular approaches have remained unproven. Recently, much attention has been attracted to mitochondrial tRNA genes, whose sequence and secondary structural characteristics have shown to be useful for Acrodont Lizards and deep-branch phylogenetic studies. In order to identify useful phylogenetic markers and test Fringillidae relationships, we have sequenced three major clusters of mitochondrial tRNA genes from 15 Fringillidae, taxa. A coincident tree, with coturnix as outgroup, was obtained through Maximum-likelihood method using combined dataset of 11 mitochondrial tRNA gene sequences. The result was similar to that through Neighbor-joining but different from Maximum-parsimony methods. Phylogenetic trees constructed with stem-region sequences of 11 genes had many different topologies and lower confidence than with total sequences. On the other hand, some secondary structural characteristics may provide phylogenetic information on relatively short internal branches at under-genus level. In summary, our data indicate that mitochondrial tRNA genes can achieve high confidence on Fringillidae phylogeny at subfamily level, and stem-region sequences may be suitable only at above-family level. Secondary structural characteristics may also be useful to resolve phylogenetic relationship between different genera of Fringillidae with good performance.

凤鹛属鸟类（Yuhina, Aves）的系统发育研究

本研究以凤鹛属（Yuhina）鸟类为研究对象，分别使用分子生物学性状和形 态学性状来重建凤鹛属种间的系统发育关系，为东南亚地区鹛类的起源与进化研 究提出新的见解。分子生物学研究的内群不仅包括了凤鹛属（11 种中的10 种）， 而且还包括了菲律宾特有穗鹛属（Stachyris）和绣眼鸟属（Zosterops）等近缘种。 通过测定线粒体上两个蛋白编码基因Cyt b、ND3 的全长序列和两个RNA 编码 基因 12S, 16S 的部分序列，得到长度为2379bp 的联合序列，使用最大简约法、 最大似然法和贝叶斯法进行系统发育分析的结果表明，菲律宾岛特有的穗鹛（金 冠穗鹛S. dennistouni、纹穗鹛S. striata、怀氏穗鹛S. whiteheadi）与绣眼鸟属（暗 绿绣眼Z. japonicus、红胁绣眼Z. erythropleurus、灰腹绣眼Z. palpebrosus）聚为 一支，位于凤鹛属支系内部。通过凤鹛、菲律宾穗鹛、绣眼鸟三个类群羽冠性状 演化趋势的分析，发现羽冠性状在菲律宾特有穗鹛和绣眼鸟支系中发生丢失。与 前人的研究结果相比，新发现纹喉凤鹛Y. gularis 与棕肛凤鹛Y. occipitalis 是姐妹 群，黄颈凤鹛Y. flavicollis 和白项凤鹛Y. bakeri 是姐妹群，这两个姐妹群又聚为 一大支的关系。 在分类问题上，暗绿绣眼、红胁绣眼和灰腹绣眼在本研究中与鹛类表现出近 缘关系，与前人使用绣眼鸟属其它物种进行的相关研究显示出高度一致性，说明 绣眼鸟属的系统学地位存在很大疑问，应该扩大取样进行深入研究。栗冠凤鹛 Y. everetti 与栗耳凤鹛Y. castaniceps 聚为姐妹群的关系，但是二者之间较小的遗 传距离和形态学差别显示二者之间应该为亚种关系，而不是种级关系。依据栗耳 凤鹛特有的尾羽形态提出的Staphiada 属没有得到本分子生物学研究结果的支持 （Harrison, 1986a, b）。在白腹凤鹛Y. zantholeuca 不属于凤鹛属支系这一结果的 提示下，发现白腹凤鹛独有的形态学特征，例如羽冠由冠羽形成、鼻孔半裸露、 飞羽外翈没有异色羽缘，这些独有的特征与其特殊的系统学地位相对应。因此， 我们支持前人提出的将白腹凤鹛从凤鹛属中分出去，单独成Erpornis 属的建议 （Cibois et al., 2002）。 在历史生物地理学方面，根据菲律宾特有穗鹛和绣眼鸟的近缘关系，认为菲 律宾特有穗鹛的祖先具有与现在绣眼鸟一样的跨海迁移的能力，在中新世末期（5.74Mya）由喜马拉雅地区或印度支那起源地经大巽他地区扩散到菲律宾岛屿 上，经过长期独立进化后，形成现在高度特有的穗鹛支系。更新世冰期时，大巽 他地区海平面下降，使栗冠凤鹛得以扩散至婆罗州（1.66Mya）。在上新世初期台 湾岛成陆后，由于台湾岛与中国大陆相连，褐头凤鹛Y. brunneiceps 的祖先扩散 至台湾岛屿上（5.05Mya）。高黎贡山为第四纪冰期时凤鹛属鸟类的避难场所，因 此形成了现在凤鹛属鸟类在高黎贡山地区密集分布的格局。喜马拉雅山和青藏高 原的隆起导致青藏高原上植被带的变化和喜马拉雅山南麓在第四纪冰期中避难 所的作用，是纹喉凤鹛、棕肛凤鹛、黄颈凤鹛、白项凤鹛等种类现今在喜马拉雅 山南麓密集分布的可能原因。 在凤鹛属分子系统学的研究基础上，从形态学角度探讨凤鹛属除白领凤鹛外 其它物种之间的系统发育关系。使用最先分化出来的白领凤鹛为外群以外群比较 法进行51 个形态学特征的性状极化，使用最大简约法分析后，结果不仅支持一 些分子系统学揭示的物种之间的亲缘关系，例如，栗耳凤鹛与栗冠凤鹛姐妹群的 关系，黑颏凤鹛和褐头凤鹛姐妹群的关系，三种绣眼鸟聚为一支，再与怀氏穗鹛 聚为一个大支；而且发现了新的系统关系，黄颈凤鹛与缅甸凤鹛Y. humilis 是姐 妹群，具有浅色下体的凤鹛属物种具有较近的系统关系。分子数据和形态数据对 凤鹛属系统发育树中部节点解决能力的差异，说明凤鹛属物种之间分化间隔时间 很短。 通过综述近年来核基因在鸟类分子系统发育研究中的应用情况，建议未来研 究中增加核基因的内含子序列，例如肌球素基因内含子2（ myoglobin intron Ⅱ） 或β纤维蛋白原基因内含子7（β-fibrinogen intron7, β-fibint 7）来解决本研究 中未确定的末端分枝分歧顺序。

A mitogenomic perspective on the ancient, rapid radiation in the Galliformes with an emphasis on the Phasianidae

Background: The Galliformes is a well-known and widely distributed Order in Aves. The phylogenetic relationships of galliform birds, especially the turkeys, grouse, chickens, quails, and pheasants, have been studied intensively, likely because of their close association with humans. Despite extensive studies, convergent morphological evolution and rapid radiation have resulted in conflicting hypotheses of phylogenetic relationships. Many internal nodes have remained ambiguous. Results: We analyzed the complete mitochondrial (mt) genomes from 34 galliform species, including 14 new mt genomes and 20 published mt genomes, and obtained a single, robust tree. Most of the internal branches were relatively short and the terminal branches long suggesting an ancient, rapid radiation. The Megapodiidae formed the sister group to all other galliforms, followed in sequence by the Cracidae, Odontophoridae and Numididae. The remaining clade included the Phasianidae, Tetraonidae and Meleagrididae. The genus Arborophila was the sister group of the remaining taxa followed by Polyplectron. This was followed by two major clades: ((((Gallus, Bambusicola) Francolinus) (Coturnix, Alectoris)) Pavo) and (((((((Chrysolophus, Phasianus) Lophura) Syrmaticus) Perdix) Pucrasia) (Meleagris, Bonasa)) ((Lophophorus, Tetraophasis) Tragopan))). Conclusions: The traditional hypothesis of monophyletic lineages of pheasants, partridges, peafowls and tragopans was not supported in this study. Mitogenomic analyses recovered robust phylogenetic relationships and suggested that the Galliformes formed a model group for the study of morphological and behavioral evolution.