Barbara A. Whitlock

Phylogenetic Analyses of Basal Angiosperms Based on Nine Plastid, Mitochondrial, and Nuclear Genes

DNA sequences of nine genes (plastid: atpB, matK, and rbcL; mitochondrial: atp1, matR, mtSSU, and mtLSU; nuclear: 18S and 26S rDNAs) from 100 species of basal angiosperms and gymnosperms were analyzed using parsimony, Bayesian, and maximum likelihood methods. All of these analyses support the following consensus of relationships among basal angiosperms. First, Amborella, Nymphaeaceae, and Austrobaileyales are strongly supported as a basal grade in the angiosperm phylogeny, with either Amborella or Amborella and Nymphaeales as sister to all other angiosperms. An examination of nucleotide substitution patterns of all nine genes ruled out any possibility of analytical artifacts because of RNA editing and GC‐content bias in placing these taxa at the base of the angiosperm phylogeny. Second, Magnoliales are sister to Laurales and Piperales are sister to Canellales. These four orders together constitute the magnoliid clade. Finally, the relationships among Ceratophyllum, Chloranthaceae, monocots, magnoliids, and eudicots are resolved in different ways in various analyses, mostly with low support. Our study indicates caution in total evidence approaches in that some of the genes employed (e.g., mtSSU, mtLSU, and nuclear 26S rDNA) added signal that conflicted with the other genes in resolving certain parts of the phylogenetic tree.

Intraspecific Inversions Pose a Challenge for the trnH-psbA Plant DNA Barcode

Background The chloroplast trnH-psbA spacer region has been proposed as a prime candidate for use in DNA barcoding of plants because of its high substitution rate. However, frequent inversions associated with palindromic sequences within this region have been found in multiple lineages of Angiosperms and may complicate its use as a barcode, especially if they occur within species. Methodology/Principal Findings Here, we evaluate the implications of intraspecific inversions in the trnH-psbA region for DNA barcoding efforts. We report polymorphic inversions within six species of Gentianaceae, all narrowly circumscribed morphologically: Gentiana algida, Gentiana fremontii, Gentianopsis crinita, Gentianopsis thermalis, Gentianopsis macrantha and Frasera speciosa. We analyze these sequences together with those from 15 other species of Gentianaceae and show that typical simple methods of sequence alignment can lead to misassignment of conspecifics and incorrect assessment of relationships. Conclusions/Significance Frequent inversions in the trnH-psbA region, if not recognized and aligned appropriately, may lead to large overestimates of the number of substitution events separating closely related lineages and to uniting more distantly related taxa that share the same form of the inversion. Thus, alignment of the trnH-psbA spacer region will need careful attention if it is used as a marker for DNA barcoding.

The age of chocolate: a diversification history of Theobroma and Malvaceae

Dated molecular phylogenies of broadly distributed lineages can help to compare patterns of diversification in different parts of the world. An explanation for greater Neotropical diversity compared to other parts of the tropics is that it was an accident of the Andean orogeny. Using dated phylogenies, of chloroplast ndhF and nuclear DNA WRKY sequence datasets, generated using BEAST we demonstrate that the diversification of the genera Theobroma and Herrania occurred from 12.7 (11.6-14.9 [95% HPD]) million years ago (Ma) and thus coincided with Andean uplift from the mid-Miocene and that this lineage had a faster diversification rate than other major clades in Malvaceae. We also demonstrate that Theobroma cacao, the source of chocolate, diverged from its most recent common ancestor 9.9 (7.7-12.9 95% HPD) Ma, in the mid-to late-Miocene, suggesting that this economically important species has had ample time to generate significant within-species genetic diversity that is useful information for a developing chocolate industry. In addition, we address questions related to the latitudinal gradient in species diversity within Malvaceae. A faster diversification rate is an explanation for the greater species diversity at lower latitudes. Alternatively, tropical conditions may have existed for longer and occupied greater areas than temperate ones meaning that tropical lineages have had more time and space in which to diversify. Our dated molecular phylogeny of Malvaceae demonstrated that at least one temperate lineage within the family diverged from tropical ancestors then diversified at a rate comparable with many tropical lineages in the family. These results are consistent with the hypothesis that Malvaceae are more species rich in the tropics because tropical lineages within the family have existed for longer and occupied more space than temperate ones, and not because of differences in diversification rate.

Seed Coat Morphology in Gentianopsis (Gentianaceae)

Abstract Seed coat morphology is examined in 16 taxa of Gentianopsis, Pterygocalyx, and Gentianella, including representatives from 14 taxa of Gentianopsis, to resolve inconsistencies in previous reports and make new observations using a low vacuum mode of SEM. Four characters are proposed to describe variation in seed coat morphology of this group: (1) the outer periclinal walls of testa; (2) sculpting of inner periclinal walls; (3) seed shape; and (4) seed length. The distinctive papillate seeds of many species of Gentianopsis are the result of inflated outer periclinal walls of testa cells. In some species, the outer periclinal walls of the testa are collapsed inwards, revealing previously unreported sculpting on the inner periclinal walls. Seeds are irregularly angular-ovate or fusiform in Gentianopsis and discoid in Pterygocalyx. Seed length varies from 0.22 to 1.0 mm. These data provide another line of evidence for phylogenetic relationships of Gentianopsis and Pterygocalyx to other members of Swertiinae, and illuminate the affinities of fossil seeds from New England that have been assigned to Gentianopsis.

Polyphyly of Rulingia and Commersonia (Lasiopetaleae, Malvaceae s.l.)

The primarily Australian genera Rulingia R.Br. and Commersonia J.R. & G.Forst., as currently circumscribed, are distinguished from each other by the number of antisepalous staminodes. Although most taxonomic treatments recognise Rulingia and Commersonia as separate genera, recent phylogenetic analyses and morphological observations have suggested that neither is monophyletic. In the present study, we test the monophyly of both genera with a phylogenetic analysis of 80 individuals of Rulingia and Commersonia, representing 46 species, using three chloroplast markers. Our analyses recovered the following two well supported clades: Clade 1 includes three species referable to Commersonia and 17 to Rulingia and Clade 2 includes 20 species referable to Commersonia and six to Rulingia. Type species of both Commersonia and Rulingia are in Clade 1, although Commersonia has priority. These results are used to identify lineages that will be formally recognised in accompanying taxonomic treatments. The extensive polyphyly of both Commersonia and Rulingia suggests that the staminode character previously used to separate these two genera is highly homoplastic. We discuss alternative androecial characters that may prove to be synapomorphies for Clades 1 and 2.

A revision of Commersonia including Rulingia (Malvaceae s.l. or Byttneriaceae)

A taxonomic revision and DNA sequence analysis of all species previously attributed to Rulingia R.Br. and Commersonia J.R.Forst. & G.Forst. resulted in two major groupings, referred to a redefined Commersonia and a new genus (Androcalva C.F.Wilkins & Whitlock 2011). In total, 25 species are now recognised within Commersonia, including the type species of Rulingia, and 14 species previously included in Rulingia and 10 in Commersonia. Three of these are described as new (C. apella C.F.Wilkins, C. erythrogyna C.F.Wilkins and C. gilva C.F.Wilkins). A new subspecies, C. magniflora subsp. oblongifolia C.F.Wilkins, is recognised and C. bartramia (L.) Merr. var. tahitensis Dorr is raised to species level as C. tahitensis (Dorr) C.F.Wilkins & Whitlock. Two new combinations are made, Rulingia platycalyx Benth. and R. parviflora Endl. as C. parviflora (Endl.) C.F.Wilkins & Whitlock; and R. cistifolia Steetz and R. rugosa Steetz as C. rugosa (Steetz) F.Muell. The redefined Commersonia is monophyletic and characterised by anthers with sublatrorse dehiscence and mainly hairy staminodes, compared with extrorse dehiscence and glabrous staminodes as seen in Androcalva.

A new Australian genus, Androcalva, separated from Commersonia (Malvaceae s.l. or Byttneriaceae)

A new genus, Androcalva C.F.Wilkins & Whitlock, is here described and includes 22 species previously described as Commersonia, four species formerly described as Rulingia and seven new species, including A. aphrix C.F.Wilkins, A. perlaria C.F.Wilkins, A. bivillosa C.F.Wilkins, A. adenothalia C.F.Wilkins, A. fragifolia C.F.Wilkins, A. incilis C.F.Wilkins and A. lachna C.F.Wilkins. Rulingia pauciflora Turcz. is here placed in synonymy with C. gaudichaudii J.Gay as A. gaudichaudii. Recognition of Androcalva is supported by the results of a previous molecular phylogenetic analysis demonstrating that neither Rulingia nor Commersonia as previously circumscribed is monophyletic. Species of Androcalva share characters of extrorse anther dehiscence and glabrous central staminodes. In contrast, species in the redefined Commersonia have anthers with sublatrorse dehiscence and hairy central staminodes. Taxonomic descriptions, a key, distribution maps, conservation status and illustrations are presented.

Seed coat micromorphology of Gordonia sensu lato (including Polyspora and Laplacea; Theaceae)

Species of Gordonia s.l. are characterized by having seeds with prominent flattened apical wings. However, recent molecular phylogenetic studies show that this concept of Gordonia is not monophyletic, with species occurring in two tribes of Theaceae. We examine seed coat micromophology of 14 species of Gordonia s.l., including representatives from all proposed lineages, and ten species from six genera from all three tribes of Theaceae. We observed that seeds from Gordonieae, including two species of Gordonia s.l., have irregularly protruding groups of cells on the seed coat that appear to be unique in the family. Seeds of Theeae, including all remaining species of Gordonia s.l., lack protruding cells and include testa cells that are isodiametric to elongate. Seeds of Stewartieae lack protrusions and elongate testa cells, and often have sculpting visible below the seed coat. Seeds of Gordonia s.l. from Gordonieae appear significantly smaller than species placed in Theeae. These results may help to infer relationships of fossilized seeds previously identified as Gordonia.

Seringia revised to include Keraudrenia (Lasiopetaleae: Malvaceae s.l.)

Abstract. Seringia J.Gay and Keraudrenia J.Gay are widely spread in Australia, and one species occurs in Madagascar. Revision of these closely related genera suggested that neither genus is monophyletic on the basis of morphological or preliminary molecular data. As a result, Keraudrenia is subsumed into Seringia. There are now 20 species of Seringia, including the currently accepted type species Seringia platyphylla J.Gay (=Seringia arborescens (W.T.Aiton) Druce). Five new species S. adenogyna C.F.Wilkins, S. cacaobrunnea C.F.Wilkins, S. elliptica C.F.Wilkins, S. undulata C.F.Wilkins and S. saxatilis C.F.Wilkins are described. Four species of Keraudrenia initially described as Seringia and recognised as the latter by F. J. H. von Mueller are reinstated (S. adenolasia F.Muell., S. corollata Steetz, S. lanceolata Steetz, S. nephrosperma F.Muell.). Five previous combinations of Keraudrenia and Seringia as Seringia are recognised (S. hermanniifolia (J.Gay) F.Muell., S. hillii (Benth.) F.Muell., S. hookeriana (Walp.) F.Muell., S. integrifolia (Steud.) F.Muell., S. velutina (Steetz) F.Muell.) and five new combinations are made (S. collina (Domin) C.F.Wilkins & Whitlock, S. denticulata (C.T.White) C.F.Wilkins & Whitlock, S. exastia (C.F.Wilkins) C.F.Wilkins & Whitlock, S. katatona (C.F.Wilkins) C.F.Wilkins & Whitlock, S. macrantha (Baill.) C.F.Wilkins & Whitlock. Keraudrenia collina var. multiflora Domin is placed in synonymy under S. nephrosperma F.Muell. Keraudrenia corollata var. denticulata C.T.White is recognised as a distinct species, S. denticulata (C.T.White) C.F.Wilkins & Whitlock. Anatomical studies, taxonomic descriptions, distribution maps, illustrations and identification keys are presented for Seringia, and an identification key to genera of the tribe Lasiopetaleae is provided.