Cynthia M. Morton

Inferring Complex Phylogenies Using Parsimony: An Empirical Approach Using Three Large DNA Data Sets for Angiosperms

To explore the feasibility of parsimony analysis for large data sets, we conducted heuristic parsimony searches and bootstrap analyses on separate and combined DNA data sets for 190 angiosperms and three outgroups. Separate data sets of 18S rDNA (1,855 bp), rbcL (1,428 bp), and atpB (1,450 bp) sequences were combined into a single matrix 4,733 bp in length. Analyses of the combined data set show great improvements in computer run times compared to those of the separate data sets and of the data sets combined in pairs. Six searches of the 18S rDNA + rbcL + atpB data set were conducted; in all cases TBR branch swapping was completed, generally within a few days. In contrast, TBR branch swapping was not completed for any of the three separate data sets, or for the pairwise combined data sets. These results illustrate that it is possible to conduct a thorough search of tree space with large data sets, given sufficient signal. In this case, and probably most others, sufficient signal for a large number of taxa can only be obtained by combining data sets. The combined data sets also have higher internal support for clades than the separate data sets, and more clades receive bootstrap support of > or = 50% in the combined analysis than in analyses of the separate data sets. These data suggest that one solution to the computational and analytical dilemmas posed by large data sets is the addition of nucleotides, as well as taxa.

Phylogenetic relationships of Rutaceae: a cladistic analysis of the subfamilies using evidence from RBC and ATP sequence variation.

Sequence data for plastid rbcL and atpB from members of Anacardiaceae, Burseraceae, Cneoraceae, Meliaceae, Ptaeroxylaceae, Rutaceae, and Simaroubaceae were analyzed cladistically to evaluate the familial and subfamilial circumscriptions of Rutaceae. Taxa representing all subfamilies and tribes were sampled. The analysis shows that Rutaceae are paraphyletic, with Spathelia and Dictyoloma (Rutaceae), Harrisonia (Simaroubaceae), Cneorum (Cneoraceae), and Ptaeroxylon (Ptaeroxylaceae) forming a clade sister to all other Rutaceae. Circumscription of Rutaceae to include all of these taxa is recommended. This analysis indicates that Simaroubaceae and Meliaceae are the outgroups closest to Rutaceae. Correlation of the molecular phylogenies with biochemical data indicates that chemotaxonomic information is more reliable than fruit type as an indicator of familial and subfamilial circumscriptions. The subfamilial classification needs revision; none of the subfamilies of more than one genus is monophyletic.

Biogeographic patterns in Mediterranean and Macaronesian species of Saxifraga (Saxifragaceae) inferred from phylogenetic analyses of ITS sequences

A biogeographic study of Saxifraga section Saxifraga was performed based on phylogenetic analyses of ITS (internal transcribed spacer) sequences of nuclear ribosomal DNA. ITS sequences from 21 species and 31 populations were examined to identify colonization patterns for the two species of Saxifraga occurring in Macaronesia and for S. globulifera in the west Mediterranean basin. Phylogenetic analysis of the sequence data yield a single most parsimonious tree with many of the major clades well supported by bootstrap and decay values. The ITS tree provided resolution at specific and populational levels that points to two biogeographic patterns within the genus. In contrast to the molecular evidence provided by other authors for a Mediterranean origin of several Macaronesian genera of angiosperms, our results indicate that the Madeiran archipelago was colonized a single time by a species of Saxifraga originating from the Eurosiberian region. On the other hand, the molecular evidence also suggests that populations of S. globulifera from North Africa have been isolated for a long time from populations occurring in the Iberian Peninsula, and that the endemic S. reuteriana has evolved from the Iberian populations of S. globulifera. The Mediterranean Sea has probably been an effective isolating barrier for some plant groups that occur in Europe and North Africa.

Polyploid speciation inHedera (Araliaceae): Phylogenetic and biogeographic insights based on chromosome counts and ITS sequences

Variation in chromosome number and internal transcribed sequences (ITS) of nrDNA is used to infer phylogenetic relationships of a wide range ofHedera species. Polyploidy was found to be frequent inHedera, with diploid, tetraploid, hexaploid and octoploid populations being detected. Nucleotide additivity occurs in the ITS sequences of one tetraploid (H. hibernica) and two hexaploid species (H. maderensis, H. pastuchovii), suggesting that all three species originated by allopolyploidisation. ITS sequence polymorphism and nucleotide characters may indicate the presence of an ancient genome persistent only in some allopolyploid species. Phylogenetic analyses of ITS sequence data reveal two lineages ofHedera: one containing all sequences belonging to extant diploids plus the tetraploidH. algeriensis, and a second that includes this ancient ITS type and others exclusive to several polyploid species. The origin of the polyploids is evaluated on the basis of morphology, chromosome counts, ITS sequence polymorphism, and phylogenetic analyses. Reconstruction of reticulate evolution inHedera agrees with two allopolyploid areas on both sides of the Mediterranean basin. Morphological, molecular and cytological evidence also suggests an active dispersal ofHedera populations that may account for three independent introductions in Macaronesia.

Phylogenetic relationships of Lecythidaceae: a cladistic analysis using rbcL sequence and morphological data.

This study examined in detail the rbcL sequence and morphological support for subfamilial relationships and monophyly of Lecythidaceae. Initially we needed to establish relationships of Lecythidaceae among other dicot families. To complete this we examined 47 rbcL sequences of 25 families along with molecular observations from several large analyses of rbcL data. All analyses strongly support the monophyly of the asterid III grouping. This analysis revealed Lecythidaceae to be paraphyletic and indicated potential outgroup relationships with Sapotaceae. Once relationships had been evaluated using molecular data we then concentrated on analyzing separate and combined morphological and molecular databases. The topology of the morphological data set was similar to the rbcL sequence and combined data sets except for the positioning of Napoleonaeoideae, Grias, Gustavia, and Oubanguia. According to the combined results, Planchonioideae, Lecythidoideae. and Foetidioideae are monophyletic, whereas the subfamily Napoleonaeoideae are paraphyletic. Nested within Napolconaeoideae, we found Asteronthos forms a strongly supported clade with Oubanguia (Scytopetalaceae). Foetidia, the only genus of Foetidioideae, is sister to Planchonioideae, and this clade is sister to Lecythidoideae. The [(Planchonioideae, Foetidioideae) Lecythidoideae are sister to Asteranthos/Oubanguia. Napoleonaeoideae are sister to the rest of Lecythidaceae.

Newly Sequenced Nuclear Gene (Xdh) for Inferring Angiosperm Phylogeny1

Abstract The nuclear gene xanthine dehydrogenase (Xdh) was sequenced for 247 genera representing all major lineages of angiosperms and “gymnosperms,” and the results were analyzed using likelihood and parsimony methods. The overall topology is mostly congruent with previously published trees based on chloroplast rbcL, atpB, and matK sequences. A total of 190 of the 253 nodes (71%) of the Xdh tree received bootstrap support greater than 50%. The likelihood tree was comparable in robustness to the matK topology, which exhibited 79% of the nodes with bootstrap support greater than 50%, and to the reported 7%–24% support observed for individual analyses of rbcL, atpB, and 18S ribosomal DNA clades. The number of parsimony-informative sites (1068, 69%) was similar to that of the matK (1083, 62%) study. The likelihood tree depicts angiosperms as monophyletic, with Ceratophyllum L. (Ceratophyllaceae) as sister to the rest of the flowering plants, followed successively by Amborellaceae, Nymphaeaceae, and Austrobaileyales clades as sisters to the remaining angiosperms. Acorus L. plus the remaining monocots, magnoliids, and Chloranthaceae diverge after the Austrobaileyales. Eudicots are supported and include a basal grade of Ranunculales–Proteaceae, Sabiaceae, Trochodendraceae, Buxaceae, Gunneraceae, and Dilleniaceae–Santalaceae, which are subsequent sister to the remaining eudicots. The remaining eudicots are split into two clades. The first clade consists of the Ericales, Cornales, and euasterids I and II (lamids–campanulids). The second clade consists of the following orders: Saxifragales, Myrtales–Caryophyllales–Cucurbitales, Crossosomatales, Geraniales, Rosales–Fabales–Fagales, Celastrales, Malpighiales, Brassicales–Malvales, Oxalidales, and Sapindales. Xdh data provided good support in the Caryophyllales, Ericales and Cornales, euasterids I (lamids), Magnoliales and Laurales, Malvales, Rutaceae, Oxalidales, Brassicales, and Sapindales. A future combined analysis of Xdh and other DNA data sets will have a strong potential to enhance resolution and internal support for angiosperm phylogenetics and provide insights into angiosperm evolution using biparental information.

New Subfamily Classification for the Rutaceae

Abstract Thirty-four species representing all subfamilies and tribes of the Rutaceae Juss. were included in phylogenetic analyses that utilize six molecular data sets from five chloroplast markers, three from the noncoding region (the rps16 gene intron, the trnL–trnF intergenic spacer, and the atpB–rbcL spacer) and two from coding genic regions (rbcL, atpB), with the sixth marker from the Xdh nuclear gene. Based on the large number of nucleotide characters from the chloroplast and nuclear regions as well as the high levels of resolution and support from both parsimony and Bayesian analyses, the results are sufficiently robust to justify reclassification of the Rutaceae, with four subfamilies recognized in contrast to the traditional seven. This subfamily classification includes major rearrangements: (1) taxa within the subfamily Aurantioideae Horan. remain the same; (2) subfamily Cneoroideae Webb encompass the subfamilies Spathelioideae Engl. and Dictyolomatoideae Engl., Harrisonia R. Br. ex A. Juss. of the Simaroubaceae DC., Cneorum L. of the Cneoraceae Vest, and Ptaeroxylon Eckl. & Zeyh. of the Ptaeroxylaceae J.-F. Leroy; (3) subfamily Rutoideae Arn. include Ruta L. and Chloroxylon DC. of subfamily Flindersioideae Luerss.; and (4) subfamily Amyridoideae Link unite Flindersia R. Br. of subfamily Flindersioideae with subfamily Toddalioideae K. Koch and taxa previously included in subfamily Rutoideae.

Phylogenetic Relationships of the Chrysobalanaceae Inferred from Chloroplast, Nuclear, and Morphological Data1

Abstract The Chrysobalanaceae, a pantropical family containing about 525 species, has often been nested within the Rosaceae despite evidence for recognizing it as a separate family. In 1963, Prance clearly placed Chrysobalanaceae as a distinct family containing 17 genera. However, the family has been linked with various other families and orders and recently has been placed within the order Malpighiales. Because of these discrepancies, a phylogenetic analysis for the family was launched to examine its monophyly and to investigate the relationships within the Chrysobalanaceae as well as its relationships to other groups. Comparative phylogenetic analyses were performed using morphological, rbcL, and ITS sequences. The data sets were analyzed independently and in combination. After exploration for hard incongruencies among the independent data sets, a simultaneous analysis of all the data was completed. The combined analysis resulted in a resolved, supported topology with several unambiguous morphological synapomorphies. The resulting topology indicated that the family is a well-defined monophyletic group that is sister to Euphronia Mart. & Zucc. (Euphroniaceae). The present tribal groupings, however, are paraphyletic.