Museum of Vertebrate Zoology, Department of Integrative Biology, University of California, Berkeley, CA 94720, USA.
Mol Phylogenet Evol. 2011 Nov;61(2):300-7. doi: 10.1016/j.ympev.2011.06.016. Epub 2011 Jul 1.
As a resource for vertebrate phylogenetics, we developed 75 new protein-coding genes using a combination of expressed sequence tags (ESTs) available in Genbank, and targeted amplification of complementary DNA (cDNA). In addition, we performed three additional analyses in order to assess the utility of our approach. First, we profiled the phylogenetic informativeness of these new markers using the online program PhyDesign. Next, we compared the utility of four different data-types used in phylogenetics: nucleotides (NUCL), amino acids (AA), 1st and 2nd codon positions only (N12), and modified sequences to account for codon degeneracy (DEGEN1; Regier et al., 2010). Lastly, we use these new markers to construct a vertebrate phylogeny and address the uncertain relationship between higher-level mammal groups: monotremes, marsupials, and placentals. Our results show that phylogenetic informativeness of the 75 new markers varies, both in the amount of phylogenetic signal and optimal timescale. When comparing the four data-types, we find that the NUCL data-type, due to the high level of phylogenetic signal, performs the best across all divergence times. The remaining three data-types (AA, N12, DEGEN1) are less subject to homoplasy, but have greatly reduced levels of phylogenetic signal relative to NUCL. Our phylogenetic inference supports the Theria hypothesis of mammalian relationships, with marsupials and placentals being sister groups.
作为脊椎动物系统发育的资源，我们使用 Genbank 中可用的表达序列标签 (EST) 组合和互补 DNA (cDNA) 的靶向扩增，开发了 75 个新的蛋白质编码基因。此外，我们进行了另外三项分析，以评估我们方法的效用。首先，我们使用在线程序 PhyDesign 分析了这些新标记的系统发育信息量。接下来，我们比较了系统发育学中使用的四种不同数据类型的效用：核苷酸 (NUCL)、氨基酸 (AA)、仅第一和第二密码子位置 (N12) 以及修改后的序列以考虑密码子简并性 (DEGEN1；Regier 等人，2010 年)。最后，我们使用这些新标记构建了一个脊椎动物系统发育树，并解决了高级哺乳动物群之间不确定的关系：单孔目动物、有袋类动物和胎盘类动物。我们的结果表明，75 个新标记的系统发育信息量不同，既有信息量的多少，也有最佳时间尺度。在比较四种数据类型时，我们发现由于高度的系统发育信号，NUCL 数据类型在所有分歧时间上表现最佳。其余三种数据类型 (AA、N12、DEGEN1) 较少受到同型性的影响，但与 NUCL 相比，它们的系统发育信号大大降低。我们的系统发育推断支持哺乳动物关系的 Theria 假说，有袋动物和胎盘动物是姐妹群。
