Department of Biology, Queen's University, Kingston, Ontario, Canada.
Mol Phylogenet Evol. 2011 Feb;58(2):181-91. doi: 10.1016/j.ympev.2010.11.021. Epub 2010 Dec 7.
Gene trees will often differ from the true species history, the species tree, as a result of processes such as incomplete lineage sorting. New methods such as Bayesian Estimation of the Species Tree (BEST) use the multispecies coalescent to model lineage sorting, and directly infer the species tree from multilocus DNA sequence data. The Sulidae (Aves: Pelecaniformes) is a family of ten booby and gannet species with a global distribution. We sequenced five nuclear intron loci and one mitochondrial locus to estimate a species tree for the Sulidae using both BEST and by concatenating nuclear loci. We also used fossil calibrated strict and relaxed molecular clocks in BEAST to estimate divergence times for major nodes in the sulid phylogeny. Individual gene trees showed little phylogenetic conflict but varied in resolution. With the exception of the mitochondrial gene tree, no gene tree was completely resolved. On the other hand, both the BEST and concatenated species trees were highly resolved, strongly supported, and topologically consistent with each other. The three sulid genera (Morus, Sula, Papasula) were monophyletic and the relationships within genera were mostly consistent with both a previously estimated mtDNA gene tree and the mtDNA gene tree estimated here. However, our species trees conflicted with the mtDNA gene trees in the relationships among the three genera. Most notably, we find that the endemic and endangered Abbott's booby (Papasula abbotti) is likely basal to all other members of the Sulidae and diverged from them approximately 22 million years ago.
基因树通常会与物种历史的真实情况（种系发生树）有所不同，这是由于不完全谱系分选等过程造成的。新的方法，如贝叶斯物种树估计（BEST），利用多物种合并来模拟谱系分选，并直接从多基因座 DNA 序列数据推断物种树。鲣鸟科（鸟类：鹈形目）是一个由十种鲣鸟和塘鹅组成的家族，分布于全球各地。我们对五个核内含子基因座和一个线粒体基因座进行了测序，使用 BEST 和串联核基因座来估计鲣鸟科的物种树。我们还在 BEAST 中使用了化石校准的严格和放松的分子钟来估计鲣鸟科系统发育中主要节点的分歧时间。个体基因树显示出很少的系统发育冲突，但分辨率不同。除了线粒体基因树外，没有一个基因树是完全解决的。另一方面，无论是 BEST 还是串联的物种树，都具有高度分辨率、强烈支持，并且彼此在拓扑结构上一致。三个鲣鸟属（Morus、Sula、Papasula）是单系的，属内的关系与之前估计的 mtDNA 基因树和这里估计的 mtDNA 基因树基本一致。然而，我们的物种树与 mtDNA 基因树在三个属之间的关系上存在冲突。最值得注意的是，我们发现，特有且濒危的 Abbott's booby（Papasula abbotti）可能是鲣鸟科所有其他成员的基础，它与它们大约在 2200 万年前分化。
