Linda M. Prince

Unraveling the Evolutionary Radiation of the Families of the Zingiberales Using Morphological and Molecular Evidence

The Zingiberales are a tropical group of monocotyledons that includes bananas, gingers, and their relatives. The phylogenetic relationships among the eight families currently recognized are investigated here by using parsimony and maximum likelihood analyses of four character sets: morphological features (1), and sequence data of the (2) chloroplast rbcL gene, (3) chloroplast atpB gene, and (4) nuclear 18S rDNA gene. Outgroups for the analyses include the closely related Commelinaceae + Philydraceae + Haemodoraceae + Pontederiaceae + Hanguanaceae as well as seven more distantly related monocots and paleoherbs. Only slightly different estimates of evolutionary relationships result from the analysis of each character set. The morphological data yield a single fully resolved most-parsimonious tree. None of the molecular datasets alone completely resolves interfamilial relationships. The analyses of the combined molecular dataset provide more resolution than do those of individual genes, and the addition of the morphological data provides a well-supported estimate of phylogenetic relationships: (Musaceae ((Strelitziaceae, Lowiaceae) (Heliconiaceae ((Zingiberaceae, Costaceae) (Cannaceae, Marantaceae))))). Evidence from branch lengths in the parsimony analyses and from the fossil record suggests that the Zingiberales originated in the Early Cretaceous and underwent a rapid radiation in the mid-Cretaceous, by which time most extant family lineages had diverged.

Repeated evolution of net venation and fleshy fruits among monocots in shaded habitats confirms a priori predictions: evidence from an ndhF phylogeny

We present a well-resolved, highly inclusive phylogeny for monocots, based on ndhF sequence variation, and use it to test a priori hypotheses that net venation and vertebrate-dispersed fleshy fruits should undergo concerted convergence, representing independent but often concurrent adaptations to shaded conditions. Our data demonstrate that net venation arose at least 26 times and was lost eight times over the past 90 million years; fleshy fruits arose at least 21 times and disappeared 11 times. Both traits show a highly significant pattern of concerted convergence (p<10−9), arising 16 times and disappearing four times in tandem. This phenomenon appears driven by even stronger tendencies for both traits to evolve in shade and be lost in open habitats (p<10−13–10−29). These patterns are among the strongest ever demonstrated for evolutionary convergence in individual traits and the predictability of evolution, and the strongest evidence yet uncovered for concerted convergence. The rate of adaptive shifts per taxon has declined exponentially over the past 90 million years, as expected when large-scale radiations fill adaptive zones.

Phylogenetic Analyses of Amomum (Alpinioideae: Zingiberaceae) Using ITS and matK DNA Sequence Data

Abstract Comparative sequencing of the nuclear ribosomal Internal Transcribed Spacer (ITS) and the chloroplast matK coding and non-coding regions was used to examine the evolutionary relationships among 53 accessions representing 13 genera of the Zingiberaceae, including 31 accessions of Amomum (Alpinioideae). Phylogenetic analyses of the ITS and matK sequences alone and in combination using maximum parsimony methods produced a moderately supported topology within Alpinioideae. Our results indicated that Amomum as currently defined is polyphyletic with three major groups of species that do not correspond with any previously recognized sectional classification of the genus. Our analyses also identified Paramomum as sister to Elettariopsis, which are both embedded within one group of Amomum. The other two groups of Amomum share common ancestors with additional genera of the Alpinioideae. ITS and matK sequences provide new data for inferring relationships within Amomum and allow fresh interpretations of morphological characters (such as anther appendage and fruit type) that may be of value in future classifications.

Molecular Phylogeny and Redefined Generic Limits of Calathea (Marantaceae)

Abstract Calathea, with an estimated 285 species, is the largest genus of Marantaceae and an important component of Neotropical herbaceous diversity. The genus is also of high importance for horticulture as species are cultivated for their showy, patterned leaves. Previous molecular phylogenetic studies indicated that the genus is polyphyletic, but have not provided a basis for redefining generic limits due to incomplete taxon sampling. To address this problem we analyzed DNA sequence data from three plastid markers (matK with flanking 3′ trnK intron, trnL intron and trnL-trnF intergenic spacer) and one nuclear marker (ITS) under a maximum parsimony criterion for a large and representative taxon sample covering all previously proposed infrageneric entities, and representing the full range of morphological variation known in the genus. Our results confirm that Calathea is polyphyletic. One clade, including subgenus Calathea, the C. lanicaulis group, and the genus Sanblasia, is sister to a clade formed by Ischnosiphon and Pleiostachya. The genus Monotagma is placed as sister to this clade. The remaining species form a second strongly supported clade as sister to a clade containing these other genera. Based on these findings Calathea is recircumscribed in a narrow sense and Sanblasia is placed in synonymy. The genus Goeppertia is resurrected and redefined to include all members of the second Calathea clade. Morphological characters defining each genus are provided. A total of 246 new combinations are made.

Hybrid Origin and Genomic Mosaicism of Dubautia scabra (Hawaiian Silversword Alliance; Asteraceae, Madiinae)

Abstract Incongruence among different estimates of species relationships in plants, from different molecules, cytogenetic data, biogeographic data, morphological/anatomical data or other sources, has been used frequently as an indication of introgression, hybrid species origin, or chloroplast (cp) capture. In plants, these incongruences are most often seen between data derived from the nuclear vs. the cp genomes and the nuclear markers used for comparison usually have been from the nuclear ribosomal (nr) internal transcribed spacer region (ITS). The amount of genomic material shared between introgressing species can be highly variable. In some of these cases, other nuclear genomic regions have moved between species without leaving a signature on the nrITS. An example of well-supported phylogenetic incongruence is the placement of Dubautia scabra (DC.) D. D. Keck in the Hawaiian silversword alliance (HSA); evolutionary hypotheses for D. scabra based on molecular as opposed to cytogenetic data are strongly discordant. In this paper, we test these two conflicting phylogenetic hypotheses regarding the evolutionary relationships of Dubautia scabra using evidence from six low-copy nuclear genes, as well as multiple chloroplast noncoding regions and nrITS. The nrITS region is also examined for the presence of multiple copy types. Incongruence between inferred relationships based on nuclear chromosomal arrangements and molecular phylogenetic data from chloroplast DNA and nrITS is resolved in favor of a hypothesis of ancient hybridization rather than cytogenetic homoplasy involving dysploidy. Most single-copy nuclear genes track histories of D. scabra compatible with cytogenetic data whereas chloroplast and nrITS data track a common, different history that appears to reflect hybridization with a chromosomally distinct lineage that also occurs on Maui Nui and Hawai‘i (the Big Island).

Larsenianthus, a new Asian genus of Gingers (Zingiberaceae) with four species

Abstract Larsenianthus W. J. Kress & Mood, gen. nov. is described with one new combination and three new species. Larsenianthus careyanus (Benth.) W. J. Kress & Mood, comb. nov., is widespread in India and present-day Bangladesh; Larsenianthus wardianus W. J. Kress, Thet Htun & Bordelon, sp. nov., is from upper Myanmar in Kachin State; Larsenianthus assamensis S. Dey, Mood, & S. Choudhury, sp. nov., is restricted to Assam, India; and Larsenianthus arunachalensis M. Sabu, Sanoj & T.Rajesh Kumar, sp. nov., has only been found in Arunachal Pradesh, India. A phylogenetic analysis using the plastid trnK intron and nuclear ITS DNA sequence data indicates that the four species of Larsenianthus form a monophyletic lineage that is sister to Hedychium, a geographically widespread genus of about 50 species in tribe Zingibereae of subfamily Zingiberoideae. A dichotomous key and three-locus DNA barcodes are provided as aids for the identification of the four species of Larsenianthus.

Species Status of Sclerocactus brevispinus, S. wetlandicus, and S. glaucus: Inferences from Morphology, Chloroplast DNA Sequences, and AFLP Markers

We examine patterns of variation in 12 continuous morphological traits, chloroplast DNA sequences from 10 intergenic spacer regions (petA-psbJ, psbk-trnS, psbM-trnD, rpob-trnC, trnC-trnD, trnGCUtrnG2S, trnFM-trnUGA, atpF-atpH, trnT-trnD, trnQ-psbk), atpF, and rpl16, and Amplified Fragment Length Polymorphism (AFLP) genetic markers in Sclerocactus glaucus sensu lato (5S. brevispinus, S. glaucus, and S. wetlandicus), a complex that historically has been considered conspecific and afforded protection under the Endangered Species Act. This complex is considered to represent three different species by some authors. We describe the expected patterns of morphological, DNA, and AFLP variation under the conditions that (a) the complex is a single species, and (b) that there are three antonymous species. We show that morphological evidence is consistent with the presence of three significantly different morphological species. Chloroplast DNA sequences provide evidence that the populations of S. glaucus (restricted to Colorado) are a lineage distinct from the populations of S. brevispinus and S. wetlandicus (restricted to Utah). AFLP genetic markers reveal significant genetic divergence among S. brevispinus, S. glaucus, and S. wetlandicus. Equally important, there is greater divergence among species than among populations within the species. The three sources of evidence all support the presence of three species and not a single species. These results indicate that protection of S. glaucus as a threatened species under the Endangered Species Act, as historically prescribed, includes populations of three species, two in Utah (S. brevispinus and S. wetlandicus) and one in Colorado (S. glaucus).