Fabián A. Michelangeli

A Phylogeny of the Monocots, as Inferred from rbcL and atpA Sequence Variation, and a Comparison of Methods for Calculating Jackknife and Bootstrap Values

Abstract A phylogenetic analysis of the monocots was conducted on the basis of nucleotide sequence variation in two genes (atpA, encoded in the mitochondrial genome, and rbcL, encoded in the plastid genome). The taxon sample of 218 angiosperm terminals included 177 monocots and 41 dicots. Among the major results of the analysis are the resolution of a clade comprising four magnoliid lineages (Canellales, Piperales, Magnoliales, and Laurales) as sister of the monocots, with the deepest branch within the monocots between a clade consisting of Araceae, Tofieldiaceae, Acorus, and Alismatales, and a clade that includes all other monocots. Nartheciaceae are placed as the sister of Pandanales, and Corsiaceae as the sister of Liliales. The Triuridaceae, represented by three genera, including Lacandonia, are resolved as monophyletic and placed in a range of positions, generally within Pandanales. Dasypogonaceae and Arecaceae diverge sequentially from a clade that includes all other commelinid taxa, and within the latter group Poales s. lat. are sister of a clade in which Zingiberales and Commelinales are sisters. Within Poales s. lat., Trithuria (Hydatellaceae) and Mayaca appear to be closely related to some or all elements of Xyridaceae. A comparison was conducted of jackknife and bootstrap values, as computed using strict-consensus (SC) and frequency-within-replicates (FWR) approaches. Jackknife values tend to be higher than bootstrap values, and for each of these methods support values obtained with the FWR approach tend to exceed those obtained with the SC approach.

A Cladistic Analysis of the Genus Tococa (Melastomataceae) Based on Morphological Data

Abstract Phylogenetic relationships in the myrmecophytic genus Tococa (Melastomataceae) were investigated using morphological data. The data matrix comprised 42 ingroup taxa, two of them previously described as Microphysca, the monotypic genus Myrmidone, and 11 species of the genus Miconia as outgroups. Vegetative and floral characters were used, in addition to characters drawn from seeds using both light and electron microscopy. A cladistic analysis of the morphological matrix, containing 58 informative characters, resulted in 224 most parsimonious trees. This analysis shows that Tococa is not monophyletic, both because there are some species of Tococa more closely related to Miconia than to the remaining species of Tococa, and because Myrmidone and Microphysca are nested within Tococa. However, it is possible to recognize a large, well-supported clade that includes Myrmidone and most species of Tococa. This clade is here defined as Tococa sensu stricto. The tooth in the dorsal side of the anther connective that has been informally proposed in the past as a synapomorphy for Tococa, although present in most species of Tococa sensu stricto, is not a synapomorphy for the genus. Synapomorphies for Tococa sensu stricto include the presence of emarginate petals, truncate ovaries and straight anticlinal walls in the cells of the seed testa. Within Tococa sensu stricto, ant domatia have evolved at least twice, and have been secondarily lost at least once. Communicating Editor: Kathleen A. Kron

Phylogeny of Miconia (Melastomataceae): Patterns of Stamen Diversification in a Megadiverse Neotropical Genus

Phylogenetic relationships within Miconia and other genera in the Neotropical tribe Miconieae were investigated using a maximum parsimony analysis of nuclear internal transcribed spacer and ndhF nucleotide sequences. Included were all sections in Miconia (212 species, ∼20% of the genus) and 12 of the 15 remaining genera assigned to the tribe (an additional 239 species). Given the tribe’s reputation for problematic generic distinctions, it was not surprising that most traditionally recognized taxonomic groups—both genera and sections—were shown to be polyphyletic or paraphyletic. Nevertheless, Miconia is composed of several distinct monophyletic groups, with a large majority of the species belonging to only four clades. Some of these groups represent parts of sections proposed in the last revision of the genus, but most of the diversification seems to have occurred in geographical areas that are more restricted than would have been predicted by the distribution of these sections. Moreover, parallel evolutionary trends are seen in anther form, i.e., shifts from elongate to shorter anthers and from minute‐pored to large‐pored or slitlike dehiscent anthers. These changes may relate to pollinator shifts, especially from buzz pollination to nonvibrational pollination. Thus, the major evolutionary diversifications within the tribe have been obscured by convergence in stamen morphology, leading to many arbitrary generic and sectional circumscriptions.

A preliminary phylogeny of the tribe Miconieae (Melastomataceae) based on nrITS sequence data and its implications on inflorescence position

Miconieae is the most diverse tribe of Melastomataceae, with 30 genera and over 2200 species. The tribe is characterized by fleshy fruits and partially to totally inferior ovaries. To test monophyly of the tribe and assess phylogenetic relationships within it, sequence data from nrITS were gathered and analyzed for 110 taxa in Miconieae and 32 putative outgroups. The tribe Miconieae is not resolved as monophyletic, but rather composed of two distinct clades: one composed of the cauliflorous genera Henriettea, Henriettella, Loreya and Bellucia, and a second clade with all other taxa in Miconieae, sister to a polytomy that includes representatives from tribes Merianieae and Blakeeae. Terminal inflorescences are optimized as basal within Miconieae, with lateral inflorescences evolving in at least four different instances. Cauliflory does not appear to be derived from truly axillary inflorescences; instead it seems to have evolved independently. The terminal-flowered genera Tococa, Conostegia, Tetrazygia, Anaectocalyx, Charianthus, Calycogonium, and Leandra pro parte seem to be derived from within the large genus Miconia, as is Clidemia, a genus with both axillary inflorescences and terminal inflorescences that are deflexed to a lateral position by an axillary branch. Maieta and Necranium, both with axillary inflorescences, are resolved as derived from within Clidemia.

A phylogenetic evaluation of Leandra (Miconieae, Melastomataceae): a polyphyletic genus where the seeds tell the story, not the petals

Melastomataceae is a tropical family of 4500–5000 species divided into nine tribes. The largest tribe, Miconieae, is composed of approximately 2200 species in 30 genera and is found exclusively in the Neotropics. Previous phylogenetic analyses of the Miconieae have suggested that many of the genera are derived from a paraphyletic Miconia. However, these analyses only included six species of the large genus Leandra, so its phylogenetic affinities remained unclear. As currently defined Leandra is characterized by acute petals and terminal inflorescences, but some species of Miconia, Clidemia and Ossaea also have these characters. In this study, we present an analysis of nrITS sequence data for a sample of 63 species of Leandra. The genus is clearly resolved as polyphyletic, but some distinct and well‐supported clades exist. Some of these partially correspond to sections recognized in the nineteenth century by Cogniaux, or to geographic distribution. The distribution of seed structure characters is better correlated with the phylogeny than traditional characters, such as petal morphology. Seed appendages in Leandra have evolved independently at least four times.

Multiple Events of Dispersal and Radiation of the Tribe Miconieae (Melastomataceae) in the Caribbean

In the Caribbean region, the Melastomataceae are represented by about 450 species (from 28 genera), close to 400 of them endemic. The majority of these endemic species (approximately 330) belong to the tribe Miconieae, a monophyletic group characterized by flowers with inferior or partly inferior ovaries that develop into baccate fruits, stamens with no or only poorly developed connective appendages, and the absence of megastyloids and imbricate bracts at the base of the flowers. A phylogenetic analysis of 460 accessions from 450 species of the tribe Miconieae, including 139 present in the Antilles (103 of these endemic), was performed based on nuclear (nrITS) and plastid (ndhF) DNA sequence data. This analysis shows that most of the Caribbean endemics are the product of five radiation events: (1) a clade containing the Caribbean endemic (or near-endemic) genera Pachyanthus, Calycogonium, Tetrazygia and Charianthus, as well as a few representatives of Miconia and Leandra. (2) The genus Mecranium. (3) The Caribbean species of Miconia section Chaenopleura (which are probably not the sister group of Andean Chaenopleura). (4) The Greater Antillean species of Clidemia and Ossaea (including Sagraea). (5) The Lesser Antillean representatives of Clidemia. Caribbean endemics that are more closely related to mainland species, rather than other Caribbean species are rare, and these often are segregates of widespread continental species. Because of a lack of resolution at the base of several clades, it is currently not possible to determine which mainland groups are the closest relatives of these Caribbean endemics, thus preventing us from establishing unequivocally the geographical origins of these species.ResumenEn la región del Caribe la familia Melastomataceae está representada por cerca de 450 especies (de 28°géneros), 400 de ellas endémicas. La mayoría de estas especies (approximately 330) pertenecen a la tribu Miconieae, un grupo monofilético caracterizado por flores con ovario parcial o totalmente ínfero que se desarrollan en frutos bayados, estambres con apéndices ausentes o poco desarrollados, ausencia de mega estiloides, y la ausencia de brácteas imbricadas en la base del as flores. Se realizó un análisis filogenético basado en secuencias nucleares (nrITS) de cloroplasto (ndhF) para la tribu Miconieae. El análisis incluyó 460 individuos, representando 450 especies de la tribu, de las cuales 139 están presentes en el Caribe (103 de estas endémicas). El análisis muestra que la mayoría de las especies endémicas del Caribe son producto de cinco eventos de radiación: (1) Un clado que contiene los géneros endémicos (o casi endémicos) Pachyanthus, Calycogonium, Tetrazygia y Charianthus, así como representantes de Miconia y Leandra. (2) El género Mecranium. (3) las especies Antillanas de Miconia sección Chaenopleura. (4) Las especies de las Antillas mayores de Clidemia y Ossaea (incluyendo Sagraea). (5) Las especies de las Antillas menores de Clidemia. Especies endémicas del Caribe que son hermanas o que están cercanamente relacionadas con especies del continente, y no con especies de la región son raras, y generalmente son segregadas de especies de amplia distribución. Debido a la falta de resolución en la base de muchos de estos clados en este estudio, en este momento no es posible determinar con precisión que grupos presentes en el continente son hermanos a los grupos del Caribe, por lo que no es posible establecer los orígenes geográficos de la mayoría de grupos endémicos.

Requirement for Vacuolar H+-ATPase Activity and Ca2+ Gradient during Entry of Rotavirus into MA104 Cells

ABSTRACT The mechanism by which rotavirus and other nonenveloped viruses enter the cell is still not clear. We have proposed an endocytosis model where the critical step for virus uncoating and membrane permeabilization is the decrease in Ca2+ concentration in the endosome. In this paper, we monitored rotavirus entry by measuring α-sarcin-rotavirus coentry and infectivity in MA104 cells. The participation of endocytosis, acidification, and endosomal Ca2+ concentration on virus entry was studied by inhibiting the endosomal H+-ATPase with bafilomycin A1 and/or increasing the extracellular calcium reservoir by addition of 10 mM CaEGTA. Rotavirus-α-sarcin coentry was inhibited by bafilomycin A1 and by addition of 10 mM CaEGTA. These effects were additive. These substances induced a significant inhibition of infectivity without affecting virus binding and postentry steps. These results are compatible with the interpretation that bafilomycin A1 and CaEGTA block rotavirus penetration from the endosome into the cytoplasm and support our hypothesis of a Ca2+-dependent endocytosis model.

Expression of Nonstructural Rotavirus Protein NSP4 Mimics Ca2+ Homeostasis Changes Induced by Rotavirus Infection in Cultured Cells

ABSTRACT Rotavirus infection modifies Ca2+ homeostasis, provoking an increase in Ca2+ permeation, the cytoplasmic Ca2+ concentration ([Ca2+]cyto), and total Ca2+ pools and a decrease in Ca2+ response to agonists. A glycosylated viral protein(s), NSP4 and/or VP7, may be responsible for these effects. HT29 or Cos-7 cells were infected by the SA11 clone 28 strain, in which VP7 is not glycosylated, or transiently transfected with plasmids coding for NSP4-enhanced green fluorescent protein (EGFP) or NSP4. The permeability of the plasma membrane to Ca2+ and the amount of Ca2+ sequestered in the endoplasmic reticulum released by carbachol or ATP were measured in fura-2-loaded cells at the single-cell level under a fluorescence microscope or in cell suspensions in a fluorimeter. Total cell Ca2+ pools were evaluated as 45Ca2+ uptake. Infection with SA11 clone 28 induced an increase in Ca2+ permeability and 45Ca2+ uptake similar to that found with the normally glycosylated SA11 strain. These effects were inhibited by tunicamycin, indicating that inhibition of glycosylation of a viral protein other than VP7 affects the changes of Ca2+ homeostasis induced by infection. Expression of NSP4-EGFP or NSP4 in transfected cells induced the same changes observed with rotavirus infection, whereas the expression of EGFP or EGFP-VP4 showed the behavior of uninfected and untransfected cells. Increased 45Ca2+ uptake was also observed in cells expressing NSP4-EGFP or NSP4, as evidenced in rotavirus infection. These results indicate that glycosylated NSP4 is primarily responsible for altering the Ca2+ homeostasis of infected cells through an initial increase of cell membrane permeability to Ca2+.

Are mitochondrial genes useful for the analysis of monocot relationships

A phylogenetic analysis of monocots and related dicots was conducted, using a four-gene matrix consisting of two genes from the plastid genome (matK and rbcL) and two from the mitochondrial genome (atpA/atp1 and cob). The taxon sample includes 101 monocots and 36 dicots, and all four genes were sampled for all 137 taxa. Jackknife support was assessed for clades resolved by the four-gene analysis, and compared to support for the same clades by each of the four three-gene subset matrices, in order to quantify the degree to which each gene contributed to or detracted from support for each clade. Instances of positively and negatively correlated support for clades by genes of the same and different genomes were observed. In particular, the placement of Acorus within a clade that also includes Tofieldiaceae, Araceae, and Alismatales s.s., as opposed to its frequent placement as sister of all other monocots, is supported by atpA and matK. The results indicate that genes from the mitochondrial genome provide a unique test of relationships that have been inferred with plastid-encoded genes.

Developmental microbial ecology of the crop of the folivorous hoatzin

The hoatzin (Opisthocomus hoazin) is a South American strict folivorous bird, with a crop microbial ecosystem that ferments dietary plants. Chicks progressively become independent from the adult-fed regurgitated crop liquids, and we hypothesized that the crop bacterial ecosystem develops through ecological succession mechanisms, as they grow into adults. The aim of this work was to compare the crop bacterial community in hoatzins from three age groups: newly hatched chicks, juveniles and adults by sequencing 16S rRNA genes and using the G2 PhyloChip. Cloning yielded a total of 2123 nearly full-length sequences binned into 294 operational taxonomic units (OTUs) (with <97% homology) belonging to 7 phyla, with 91% of novel OTUs. The microarray identified a diverse bacterial community dominated by Firmicutes and Bacteroidetes, with ∼1400 taxa grouped in 40 phyla that included those detected by cloning. In comparison with the adult, the hoatzin chick crop had a greater abundance of Flavobacteriaceae, Clostridiaceae and Lachnospiraceae but lacked phyla DSS1, Deferribacteres and Termite group 1, which were mostly present in adults. The overall community structure of the crop of the hoatzin changes with age in a complex manner, probably responding to new niches made available through dietary changes related to the transition from dependent to independent feeding.