Data from: Multiple sources of character information and the phylogeny of Hawaiian drosophilids

Relationships among representatives of the five major Hawaiian Drosophila species groups were examined using data from eight different gene regions. A simultaneous analysis of these data resulted in a single most-parsimonious tree that (1) places the adiastola picture-winged subgroup as sister taxon to the other picture-winged subgroups, (2) unites the modified-tarsus species group with flies from the Antopocerus species group, and (3) places the white-tip scutellum species group as the most basal taxon. Because of the different gene sources used in this study, numerous process partitions can be erected within this data set. We examined the incongruence among these various partitions and the ramifications of these data for the taxonomic consensus, prior agreement, and simultaneous analysis approaches to phylogenetic reconstruction. Separate analyses and taxonomic consensus appear to be inadequate methods for dealing with the partitions in this study. Although detection of incongruence is possible and helps elucidate particular areas of disagreement among data sets, separation of partitions on the basis of incongruence is problematic for many reasons. First, analyzing all genes separately and then either presenting them all as possible hypotheses or taking their consensus provides virtually no information concerning the relationships among these flies. Second, despite some evidence of incongruence, there are no clear delineations among the various gene partitions that separate only heterogeneous data. Third, to the extent that problematic genes can be identified, these genes have nearly the same information content, within a combined analysis framework, as the remaining nonproblematic genes. Our data suggest that significant incongruence among data partitions may be isolated to specific relationships and the "false" signal creating this incongruence is most likely to be overcome by a simultaneous analysis. We present a new method, partitioned Bremer support, for examining the contribution of a particular data partition to the topological support of the simultaneous analysis tree.

本研究采用8个不同基因区域的数据，对夏威夷果蝇5个主要物种类群的代表物种间的亲缘关系展开探究。对上述数据开展联合分析后，得到唯一一棵最简约树（most-parsimonious tree），该树呈现出以下系统发育关系：（1）将adiastola斑翅亚群置于其余斑翅亚群的姊妹群位置；（2）将跗节特化型物种类群与安托波塞鲁斯（Antopocerus）物种类群的果蝇聚为一支；（3）将盾片白尖型物种类群定为最基部类群。由于本研究使用了不同来源的基因，该数据集可划分出多个过程分区（process partition）。本研究对这些不同分区间的数据冲突，以及上述数据在分类学共识法、预先一致性法与联合分析法这三类系统发育重建方法中的应用意义进行了探讨。单独分析与分类学共识法似乎无法妥善处理本研究中的数据分区问题。尽管检测数据冲突具备可行性，且有助于阐明不同数据集间存在分歧的具体区域，但基于数据冲突对数据分区进行划分却因诸多原因存在诸多问题。其一，将所有基因单独分析后，无论是将所有分析结果作为潜在假说呈现，还是取其共识，都几乎无法为这些果蝇的亲缘关系研究提供有效信息。其二，尽管存在一定的数据冲突证据，但仅针对异质性数据进行划分的各类基因分区之间，并无明确的分界。其三，即便能够识别存在问题的基因，在联合分析框架下，这类基因所携带的信息量与其余无问题的基因几乎并无差异。本研究数据表明，数据分区间的显著冲突可能仅局限于特定的类群关系，而造成此类冲突的"假信号"，大概率可通过联合分析得以消除。我们提出了一种全新方法——分区Bremer支持度（partitioned Bremer support），用于探究特定数据分区对联合分析树拓扑结构支持度的贡献。