Efrain De Luna

Ordinal Phylogeny within the Hypnobryalean Pleurocarpous Mosses Inferred from Cladistic Analyses of Three Chloroplast DNA Sequence Data Sets: trnL-F, rps4, and rbcL

Abstract Classification of families of hypnobryalean mosses into the Hypnales, Leucodontales, and Hookeriales has been taxonomically difficult. Several researchers have sequenced different genes for independent phylogenetic studies of these three pleurocarp groups. Our goal is to summarize available molecular data and compile the largest data set to infer phylogenetic relationships among families as basis for classification at ordinal level. Sequences of rbcL, trnL-F, and rps4 loci for 38 exemplars of most families of Hypnales, Leucodontales, and Hookeriales were analyzed to evaluate whether or not each of the three orders is monophyletic. Cladistic analyses of combined sequences, using five taxa in the Bryales as outgroups, reveal a robust clade (decay > 5) including all hypnobryalean pleurocarps. Within this group, one clade (decay = 2) includes only taxa of the Hookeriales, and is sister to a large monophyletic group (Hypnales sensu lato) containing all other taxa (decay = 2) previously in the Leucodontales and Hypnales. These relationships suggest that the ordinal level taxonomy needs to be reconsidered since major lineages detected do not correspond to the traditional Leucodontales or Hypnales. These two orders are not supported by any molecular evidence from rbcL, trnL-F, or rps4, either analyzed singly or in different combinations. Additionally, present results indicate the need for changes to the current system of three suborders of Hypnales and four of the Leucodontales. Phylogenetic reconstructions based on molecular data emphasize the need for a re-examination of the taxonomic relevance of morphological characters and corroborate previous interpretations of sporophytic morphological similarities as multiple transitions to similar solutions to epiphytism among the pleurocarps.

The Transition to Pleurocarpy: A Phylogenetic Analysis of the Main Diplolepidous Lineages Based on rbcL Sequences and Morphology

Hypotheses of character evolution require a phylogeny for polarization of transformations and optimization of state changes. Our goal is to provide a phylogenetic hypothesis for diplolepidous mosses to investigate the evolution of morphological features associated with the transition to pleurocarpy. We performed cladistic analyses of morphological and molecular data sets for exemplars of the main diplolepidous lineages. These analyses were designed to sample families commonly included in the Leucodontales, Hookeriales, and Hypnales with some exemplars also from the Bryales. Diplolepidous taxa (Bryaceae, Splachnaceae, Orthotrichaceae, Macromitriaceae, and Hedwigiaceae) were included as close outgroups, and Dicranum scoparium, Grimmia apocarpa, and Funaria hygrometrica were included as distant outgroups. We constructed a molecular data set derived from sequences of the chloroplast rbcL gene for 36 species, 22 of which were pleurocarp exemplars. In the molecular analysis, the bryalean pleurocarps were the sister group of acrocarp exemplars from the Bryales. However, in the analyses of combined morphological and rbcL data, the bryalean pleurocarps were the sister group of a clade that includes the 11 exemplars from the Leucodontales, Hypnales, and Hookeriales, thus pleurocarpy appeared monophyletic. Decay analyses suggested that the grouping of bryalean and hypnobryalean pleurocarps together was weak, whereas both the hypnobryalean and bryalean pleurocarp clades were individually robust. Present cladistic analyses provide an inferential basis for structural investigations of branching systems and the evolution of pleurocarpy in a phylogenetic

TAXONOMIC STATUS OF ARTIBEUS JAMAICENSIS TRIOMYLUS INFERRED FROM MOLECULAR AND MORPHOMETRIC DATA

Abstract The taxonomic status of Artibeus jamaicensis triomylus was evaluated by mitochondrial cytochrome-b sequences, as well as cranial morphometric comparisons with 4 other subspecies of the A. jamaicensis complex and 5 species of large Artibeus. Phylogenetic analyses showed that 2 monophyletic groups exist within A. jamaicensis complex, separated by a sequence divergence of 3.6%. One clade grouped samples of A. j. triomylus from western Mexico, and the other contained samples of A. j. yucatanicus, A. j. richardsoni, A. j. paulus, and A. j. jamaicensis from the Gulf of Mexico, Central America, and the Caribbean. Additionally, multivariate analyses revealed a significant divergence in quantitative cranial characters between A. j. triomylus and non-triomylus specimens. These results, in conjunction with morphological data previously reported, suggest that A. j. triomylus represents a distinct and monophyletic lineage, consequently deserving recognition at the species rank.

Phylogenetic Relationships of the Pseudobulbous Tillandsia species (Bromeliaceae) Inferred from Cladistic Analyses of ITS 2, 5.8S Ribosomal RNA Gene, and ETS Sequences

Abstract Tillandsia subgenus Tillandsia as defined by Gardner includes 269 species in five groups. Within Group I, species in the Tillandsia bulbosa complex share a remarkable synapomorphy: a pseudobulb. We sampled the 13 species of pseudobulbous Tillandsia (including T. intermedia) in addition to 18 species from the five groups of subgenus Tillandsia and four species as outgroups to perform phylogenetic analyses of sequences from two nuclear ribosomal DNA markers (ITS 2 + 5.8S and ETS). Three combined parsimony analyses explored the effects of indels treated as missing data, fifth character states, and with the simple indel coding method. Results show that all 13 species of pseudobulbous Tillandsia are placed within a group that also includes five non-pseudobulbous species. The pseudobulb habit is optimized as a synapomorphy for this group although with three reversals. Our analyses also show that sequence variation at ITS 2 + 5.8S and ETS provided resolution and indels are an important source of phylogenetic information. All previously used chloroplast markers have been shown to be almost invariant even among distantly related species in Tillandsia. Therefore, both nuclear markers assayed here are promising sources of sequence variation for reconstruction of phylogenetic relationships among species of Tillandsia and other Bromeliaceae.

Molecular Phylogeny of the Suborder Leucodontineae (Musci; Leucodontales) Inferred from rbcL Sequence Data

rbcL sequence data (1324 bp on average). Our analyses indicate (1) that Antitrichia is distantly related to the other members of Leucodontaceae and should be excluded from the family, (2) that Cryphaeaceae form a monophyletic clade, not with Anomodontaceae and Leptodontaceae, but with Leucodontaceae, refuting the placement of Leucodontaceae and Cryphaeaceae in different superfamilies, (3) that Forsstroemia, variously classified in Leucodontaceae, Cryphaeaceae or Leptodontaceae, forms a monophyletic clade with Neckera (Neckeraceae), and (4) that the presumed monophyly of Anomodon and that of Anomodontaceae are not supported.

The Circumscription and Phylogenetic Relationships of the Hedwigiaceae (Musci)

The Hedwigiaceae are a group of plagiotropic mosses of uncertain relationships either with the Orthotrichales or the Isobryales. A total of 41 morphological characters was studied in nine species of six genera in the Hedwigiaceae, 12 species of five families in the Orthotrichales, and 12 species of five families in the Leucodontineae (Isobryales). Two aditional species represented the Hypnales, and Funaria hygrometrica (Funariales) was used as the outgroup. Based on cladistic analyses, Rhacocarpus and Bryowijkia are excluded from the family. The Hedwigiaceae are here circumscribed to include only the genera Braunia, Hedwigia, Hedwigidium, and Pseudobraunia. This monophyletic group is supported by two unique synapomorphies: papillose pseudo-paraphyllia and a globular protonemal development. Other synapomorphies for the Hedwigiaceae are: sinuous leaf cell walls, flagelliform branches, ecostate leaves, yellow paraphyses, and eperistomate capsules. The sister group of the Hedwigiaceae is a large clade that includes the cladocarpous representatives of the Orthotrichales, plus the Leucodontineae, and the Hypnales. This relationship is supported by three synapomorphies: plagiotropic shoots, presence of pseudoparaphyllia, and differentiated perichaetial leaves. The Orthotrichales appear to be paraphyletic: cladocarpous taxa (such as Erpodium and Groutiella) are more related to the Leucodontineae than to the acrocarpous taxa (such as Orthotrichum). The formulation of hypotheses about monophyletic groups and their relationships involves a search for putative synapomorphies. Fundamental in this search is the use of outgroups for hypotheses of character polarization (Watrous and Wheeler 1981; Farris 1982; Donoghue and Cantino 1984; Maddison et al. 1984; Clark and Curran 1986). The present study of the taxonomic problems in the Hedwigiaceae Schimper illustrates some of the common problems and necessary assumptions in outgroup analysis. These include, for example, unknown outgroups and higher level relationships, uncertain monophyly of outgroups, and unclear character homologies and polarity due to widely divergent outgroups (Kraus 1988; Wheeler

Phylogenetic Analysis of Cestrum Section Habrothamnus (Solanaceae) Based on Plastid and Nuclear DNA Sequences

Abstract Phylogenetic analysis of DNA sequences from chloroplast regions and nuclear ribosomal ITS was conducted to test the monophyly of Cestrum sect. Habrothamnus and investigate its relationships with other sections of Cestrum. Molecular divergence was very low among the sampled species, suggesting a rapid diversification in Cestrum. Individual and combined analyses of these molecular data sets using maximum parsimony and Bayesian inference reject the monophyly of the traditionally recognized sections of Cestrum, including sect. Habrothamnus. Infrageneric classifications will require significant revision. Nevertheless, the resolved monophyletic clades in this molecular analysis are geographically structured.

Morphometrics and the Identification of Braunia andrieuxii and B. secunda (Hedwigiaceae, Bryopsida)

Abstract Although previous cladistic analyses revealed Braunia secunda and B. andrieuxii as two lineages and valid species, they have been considered synonyms due to morphological similarities and sympatric distribution. This study was undertaken to evaluate which morphological characters best distinguish these two species. A total of 180 specimens of B. andrieuxii and 112 of B. secunda from the U.S. and Mexico were examined for morphometric analyses. Digital images of capsules, leaves, and groups of leaf cells were used to extract 31 linear measurements. Specimens were subdivided into seven geographic groups to compare levels of variation within and between species with univariate and multivariate analyses. Most characters are similar among groups within species, except the length of the revolute leaf margin and apical and upper leaf cells, which are significantly different between species (ANOVA and MRT). Partitioned Canonical Variates Analyses on eight variables of leaf cells and seven variables of vegetative leaves identified significant Mahalanobis distances between the two species. These methods also revealed that the revolute leaf margin and upper leaf cells contribute most to the distinction between species.

Phylogenetic relationships of the Thuidiaceae and the non-monophyly of the Thuidiaceae and the Leskeaceae based on rbcL, rps4 and the rps4-trnS intergenic spacer

Abstract We explored molecular data in order to establish the phylogenetic relationships of the Thuidiaceae. We sampled nine genera and 13 species of Thuidiaceae, and included representatives of 15 families that have been considered related to Thuidiaceae at some point. We used two chloroplast codifier genes (rbcL and rps4) and the rps4-trnS intergenic spacer. Our combined parsimony analyses retrieved a clade containing 12 exemplars of Thuidiaceae representing eight genera (Thuidium, Thuidiopsis, Pelekium, Aequatoriella, Abietinella, Rauiella, Haplocladium and Actinothuidium) but with the inclusion of Leskea polycarpa and exclusion of Hylocomiopsis making the Thuidiaceae non-monophyletic as currently defined, and the Leskeaceae polyphyletic. The name Thuidiaceae is retained for the informal “thuidioid” group of taxa. The Rhytidiaceae (Rhytidium rugosum) was found sister to the clade of Thuidiaceae s.lat and Leskea polycarpa. The rps4-trnS spacer added characters that improved resolution and may be of value for similar studies at family level in other pleurocarpous mosses.

New Moss Records for Mexico from the Lacandona Tropical Rain Forest, Chiapas

Abstract This paper reports nine new moss records for Mexico from the Lacandona Forest: Calymperes rubiginosum, Fissidens guianensis var. guianensis, Mniomalia viridis, Orthostichella hexasticha, Orthostichopsis praetermisa, Phyllodrepanium falcifolium, Syrrhopodon flexifolius, Syrrhopodon africanus subsp. graminicola, and Syrrhopodon hornschuchii. Findings reported here demonstrate that there is still incomplete knowledge of the moss diversity in the Lacandona tropical rain forest region. Future research in tropical forests of southeastern Mexico and Central America will help to corroborate the continuity of distributional patterns from South America to North America through the Central American bridge.