Are combined analyses better than single gene phylogenies? A case study using SSU rDNA and rbcL sequence comparisons in the Zygnematophyceae (Streptophyta)

Although the combination of different genes in phylogenetic analyses is a promising approach, the methodology is not well established and analyses often suffer from inadequate, noncongruent taxon sampling, long-branch attraction, or conflicting evolutionary models of the genes analyzed. Conflicts or congruence between multigene and single-gene phylogenies, as well as the assumed superiority of the multigene approach, are often difficult to assess solely because of incongruent taxon sampling. In the present study, a data set of 43 nuclear-encoded SSU rDNA and plastid-encoded rbcL gene sequences was generated from the same strains of conjugating green algae (Zygnematophyceae, Streptophyta). Phylogenetic analyses used the genes individually and in combination, either as concatenated sequences or with the log-likelihood summation method. Single-gene analyses, although mostly congruent, revealed some conflicting nodes and showed different patterns of statistical support. Combined analyses confidently resolved the conflicts between the single-gene analyses, enhanced phylogenetic resolution, and were better supported by morphological information. Long-branch taxa were not the same for the two genes analyzed, and, thus, their effect on phylogenetic resolution was minimized in the combined analyses.     

Regeneration of Enteromorpha

Young plants of E. intestinalis have been grown in culture. Cutting off the thalli of attached plants just above the basal rhizoids leads to the regeneration of new branches. After a short time the point of wounding is indistinguishable. The process can be repeated many times; each regeneration resulting in a more branched thallus. Segments of unattached plants kept in culture may give rise to rhizoids from the basal cut ends and to papillae from the upper ends. They may also produce “bottle brush” forms similar to those found amongst ship-fouling algae. Such forms seem to arise when “swarmers” are retained in the parent cell and germinate in situ to give aggregations of juvenile plants. Their formation can be stimulated by a temperature shock.     

基于核内核糖体小亚基序列的蝗总科系统发育关系分析

用核糖体SSURdna全序列对蝗总科（Acridoidea）进行了分子系统学研究。依据测定的8种蝗虫的SSU Rdna全序列 (平均 1.844 bp),并从GenBank中选取了6种内群种类和2种外群种类的SSU Rdna同源序列,进行序列分析。利用Clustal、MEGA 和 PHYLIP 软件构建分子系统树（距离邻接法Neighbor-Joining,NJ;最小进化法 Minimum Evolution）。结果显示： (1) 蝗总科是一个单系类群;(2) 锥头蝗科（Chrotogonidae）和瘤锥蝗科（Pyrgomorphidea）亲缘关系较近,为蝗总科最原始的类群;(3) 网翅蝗科（Arcypteridae）和槌角蝗科（Gomphoceridae）有较近的亲缘关系; (4) 斑翅蝗科 （Oedipodidae）为最进化的类群; (5) SSU Rdna序列保守性强,转换transition）取代的速率大于或接近颠换（transversion）取代的速率;(6) 在系统树中,总科首先分离,大多数同科不同属的类群以高置信度聚合在一起,说明SSU Rdna序列适合用于蝗总科的系统发育关系分析。