Molecular phylogeny of the Arctoidea (Carnivora): Effect of missing data on supertree and supermatrix analyses of multiple gene data sets
Molecular phylogeny of the Arctoidea (Carnivora): Effect of missing data on supertree and supermatrix analyses of multiple gene data sets
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DOI：
10.1016/j.ympev.2006.05.025
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发表时间：
2006-10-01
影响因子：
4.1
通讯作者：
Strobeck, Curtis
中科院分区：
文献类型：
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作者：
Fulton, Tara L.;Strobeck, Curtis
利用超树和超矩阵分析方法，基于4个核序列标签位点（STS）和1个核外显子（IRBP），对79种犬科食肉动物的系统发育关系进行了研究。我们恢复了三个主要的arctoid谱系，熊科，鳍足类，和鼬，作为单系，熊科（熊）强烈支持作为基础arctoid谱系。在鳍足目中，海豹亚科（Phoenae）是Otaroidea的姐妹[Otariidae（海狮和海狮）和Odobenidae（海象）。Phocid亚科和部落的命名得到了支持，但海狮和海狮之间的otariid亚科分裂没有得到支持。鼬总科的所有科的名称都得到了有力的支持：鼬科（臭鼬）、小熊猫科（单型小熊猫）、鼬科（黄鼠狼、獾、水獭）和浣熊科（浣熊）。一个新的假设，小熊猫的位置被恢复，把它作为分支后，Mephitidae和鼬科+ Procyonidae之前。在鼬科，亚科分类的变化被认为是。这项研究代表了迄今为止在分子研究中对犬形目动物进行的最全面的采样，并包含了最完整的南猿科分子系统发育学。我们的数据集也被用于缺失数据对超树和超矩阵分析的影响的实证研究。无法获得所有分类群中所有基因的序列，因此检查了具有不同量的缺失数据的数据集的两个变体。缺失数据的量没有很强的影响，相反，系统发育分辨率更依赖于存在足够的信息字符。超树和超矩阵的方法进行等价与不完整的数据和高度一致的冲突只出现在弱支持的领域，这表明需要更多的信息字符，自信地解决密切的物种关系。(c)2006年爱思唯尔公司All rights reserved.
Phylogenetic relationships of 79 caniform carnivores were addressed based on four nuclear sequence-tagged sites (STS) and one nuclear exon, IRBP, using both supertree and supermatrix analyses. We recovered the three major arctoid lineages, Ursidae, Pinnipedia, and Musteloidea, as monophyletic, with Ursidae (bears) strongly supported as the basal arctoid lineage. Within Pinnipedia, Phocidae (true seals) were sister to the Otaroidea [Otariidae (fur seals and sea lions) and Odobenidae (walrus)]. Phocid subfamily and tribal designations were supported, but the otariid subfamily split between fur seals and sea lions was not. All family designations within Musteloidea were strongly supported: Mephitidae (skunks), Ailuridae (monotypic red panda), Mustelidae (weasels, badgers, otters), and Procyonidae (raccoons). A novel hypothesis for the position of the red panda was recovered, placing it as branching after Mephitidae and before Mustelidae + Procyonidae. Within Mustelidae, subfamily taxonomic changes are considered. This study represents the most comprehensive sampling to date of the Caniformia in a molecular study and contains the most complete molecular phylogeny for the Procyonidae. Our data set was also used in an empirical examination of the effect of missing data on both supertree and supermatrix analyses. Sequence for all genes in all taxa could not be obtained, so two variants of the data set with differing amounts of missing data were examined. The amount of missing data did not have a strong effect; instead, phylogenetic resolution was more dependent on the presence of sufficient informative characters. Supertree and supermatrix methods performed equivalently with incomplete data and were highly congruent; conflicts arose only in weakly supported areas, indicating that more informative characters are required to confidently resolve close species relationships. (c) 2006 Elsevier Inc. All rights reserved.