Estimating phylogenies for species assemblages: a complete phylogeny for the past and present native birds of New Zealand.
Estimating phylogenies for species assemblages: a complete phylogeny for the past and present native birds of New Zealand.
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估计物种组合的系统发育：新西兰过去和现在本土鸟类的完整系统发育。
DOI：
10.1016/j.ympev.2011.07.018
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发表时间：
2011
影响因子：
4.1
通讯作者：
L. Bromham
中科院分区：
文献类型：
--
作者：
R. Lanfear;L. Bromham
物种组合的系统发育对于群落生态学和宏观生态学的许多研究至关重要。然而，目前可用的组合系统发育很少，并且用于构建它们的方法有许多重要的局限性。在这里，我们估计了新西兰所有 275 种已知灭绝和现存本土鸟类的系统发育的贝叶斯后验样本。为此，我们使用了一种方法，该方法使用免费提供的数据和软件，可以合并灭绝和现存的分类群，不依赖于组合中所有物种的 DNA 序列数据，并明确解释系统发育的不确定性。这种方法产生了一组系统发育学，描述了我们对新西兰鸟类之间关系的了解和不确定性。我们还提出了一个 Python 脚本 GeneFinder，它可用于有效收集公开可用的序列数据，以便构建用于构建组合系统发育的 DNA 序列超级矩阵。我们描述的方法为估计任何物种组合的组合系统发育铺平了道路。
Phylogenies of species assemblages are vital to many studies of community ecology and macroecology. However, few assemblage phylogenies are currently available, and the approaches that have been used to construct them have had a number of important limitations. Here, we estimate a Bayesian posterior sample of phylogenies for all 275 known extinct and extant native birds of New Zealand. To do this, we use an approach that uses freely-available data and software, can incorporate both extinct and extant taxa, does not rely on having DNA sequence data available for all species in the assemblage, and explicitly accounts for phylogenetic uncertainty. This approach produces a set of phylogenies that describes our knowledge and uncertainty about the relationships among the NZ birds. We also present a python script, GeneFinder, which can be used to efficiently gather publicly available sequence data in order to construct a supermatrix of DNA sequences for constructing assemblage phylogenies. The approach we describe paves the way for estimating assemblage phylogenies for any species assemblage.