Molecular phylogenetics of Ruscaceae sensu lato and related families (Asparagales) based on plastid and nuclear DNA sequences

Abstract

Background: Previous phylogenetics studies of Asparagales, although extensive and generally well supported, have left several sets of taxa unclearly placed and have not addressed all relationships within certain clades thoroughly (some clades were relatively sparsely sampled). One of the most important of these is sampling within and placement of Nolinoideae (Ruscaceae s.l.) of Asparagaceae sensu Angiosperm Phylogeny Group (APG) III, which subfamily includes taxa previously referred to Convallariaceae, Dracaenaaceae, Eriospermaceae, Nolinaceae and Ruscaceae.

Methods: A phylogenetic analysis of a combined data set for 126 taxa of Ruscaceae s.l. and related groups in Asparagales based on three nuclear and plastid DNA coding genes, 18S rDNA (1796 bp), rbcL (1338 bp) and matK (1668 bp), representing a total of approx. 4·8 kb is presented. Parsimony and Bayesian inference analyses were conducted to elucidate relationships of Ruscaceae s.l. and related groups, and parsimony bootstrap analysis was performed to assess support of clades.

Key results: The combination of the three genes results in the most highly resolved and strongly supported topology yet obtained for Asparagales including Ruscaceae s.l. Asparagales relationships are nearly congruent with previous combined gene analyses, which were reflected in the APG III classification. Parsimony and Bayesian analyses yield identical relationships except for some slight variation among the core asparagoid families, which nevertheless form a strongly supported group in both types of analyses. In core asparagoids, five major clades are identified: (1) Alliaceae s.l. (sensu APG III, Amarylidaceae-Agapanthaceae-Alliaceae); (2) Asparagaceae-Laxmanniaceae-Ruscaceae s.l.; (3) Themidaceae; (4) Hyacinthaceae; (5) Anemarrhenaceae-Behniaceae-Herreriaceae-Agavaceae (clades 2-5 collectively Asparagaceae s.l. sensu APG III). The position of Aphyllanthes is labile, but it is sister to Themidaceae in the combined maximum-parsimony tree and sister to Anemarrhenaceae in the Bayesian analysis. The highly supported clade of Xanthorrhoeaceae s.l. (sensu APG III, including Asphodelaceae and Hemerocallidaceae) is sister to the core asparagoids. Ruscaceae s.l. are a well-supported group. Asparagaceae s.s. are sister to Ruscaceae s.l., even though the clade of the two families is weakly supported; Laxmanniaceae are strongly supported as sister to Ruscaceae s.l. and Asparagaceae. Ruscaceae s.l. include six principal clades that often reflect previously named groups: (1) tribe Polygonateae (excluding Disporopsis); (2) tribe Ophiopogoneae; (3) tribe Convallarieae (excluding Theropogon); (4) Ruscaceae s.s. + Dracaenaceae + Theropogon + Disporopsis + Comospermum; (5) Nolinaceae, (6) Eriospermum.

Conclusions: The analyses here were largely conducted with new data collected for the same loci as in previous studies, but in this case from different species/DNA accessions and greater sampling in many cases than in previously published analyses; nonetheless, the results largely mirror those of previously conducted studies. This demonstrates the robustness of these results and answers questions often raised about reproducibility of DNA results, given the often sparse sampling of taxa in some studies, particularly the earliest ones. The results also provide a clear set of patterns on which to base a new classification of the subfamilies of Asparagaceae s.l., particularly Ruscaceae s.l. (= Nolinoideae of Asparagaceae s.l.), and examine other putatively important characters of Asparagales.

Fig. 1.

The single shortest tree from successive weighting of plastid rbcL and matK (analysis A) for Ruscaceae s.l. and related groups of Asparagales. Numbers of substitutions are indicated below each branch (DELTRAN optimization), and bootstrap percentages >50 % are given above each branch. Triangles indicate branches not present in the strict consensus tree of 5760 equally MP trees by Fitch analysis (equal weight). Tree length is 5435 steps with CI = 0·70 and RI = 0·85. The dashed line in the lower left-hand corner marks the point where the non-core asparagoids are attached to this part of the tree (non-core taxa are not shown; this part of the tree is identical to that show in Fig. 2).

Fig. 2.

One MP tree from combined DNA data (analysis B) for 121 taxa of Asparagales. Numbers of substitutions are indicated below each branch, and bootstrap percentages >50 % are given above each branch. Triangles indicate groups not present in the strict consensus tree of the Fitch analysis. Bars show points at which changes in microsporogenesis have taken place. Tree length is 6442 steps with CI = 0·71 and RI = 0·85. A, Asparagaceae; B, Laxmanniaceae; C, Alliaceae s.l.; D, Agavaceae s.l.; E, Hyacinthaceae; F, Aphyllanthaceae; G, Themidaceae; H, Xanthorrhoeaceae s.l.

Fig. 3.

Bayesian tree from combined DNA analysis (analysis C) for 121 taxa of Asparagales. The numbers above branches are posterior probabilities from 5 × 10⁶ generations with the GTR + I + G model. A, Asparagaceae; B, Laxmanniaceae.