High rates of molecular evolution in hantaviruses

Hantaviruses are rodent-borne Bunyaviruses that infect the Arvicolinae, Murinae, and Sigmodontinae subfamilies of Muridae. The rate of molecular evolution in the hantaviruses has been previously estimated at approximately 10(-7) nucleotide substitutions per site, per year (substitutions/site/year), based on the assumption of codivergence and hence shared divergence times with their rodent hosts. If substantiated, this would make the hantaviruses among the slowest evolving of all RNA viruses. However, as hantaviruses replicate with an RNA-dependent RNA polymerase, with error rates in the region of one mutation per genome replication, this low rate of nucleotide substitution is anomalous. Here, we use a Bayesian coalescent approach to estimate the rate of nucleotide substitution from serially sampled gene sequence data for hantaviruses known to infect each of the 3 rodent subfamilies: Araraquara virus ( Sigmodontinae), Dobrava virus ( Murinae), Puumala virus ( Arvicolinae), and Tula virus ( Arvicolinae). Our results reveal that hantaviruses exhibit shortterm substitution rates of 10(-2) to 10(-4) substitutions/site/year and so are within the range exhibited by other RNA viruses. The disparity between this substitution rate and that estimated assuming rodent-hantavirus codivergence suggests that the codivergence hypothesis may need to be reevaluated.

Studies on Anopheles (Kerteszia) homunculus Komp (Diptera: Culicidae)

The present findings suggest that Anopheles (Kerteszia) homunculus may comprise more than one species. The rDNA ITS2 sequence data corroborate the presence of An. homunculus l.s. in Mata Atlantica, southern Brazil, and suggest that specimens from Trinidad may belong to an unnamed morphologically similar species. There is a need for additional studies to establish the geographical distribution of An. homunculus l.s. in continental South America and in Trinidad, especially in southern Mata Atlantica, Brazil.

Phylogeny of South American Pogonieae (Orchidaceae, Vanilloideae) based on sequences of nuclear ribosomal (ITS) and chloroplast (psaB, rbcL, rps16, and trnL-F) DNA, with emphasis on Cleistes and discussion of biogeographic implications

Tribe Pogonieae (Orchidaceae), as Currently known, comprises live genera distributed from South to North America and Eastern Asia. Phylogenetic inferences within Cleistes and among genera of tribe Pogonieae were made based oil nrDNA (ITS) and cpDNA (trnL-F, rps16, rbcL, and psaB) Sequence data and maximum parsimony. Eighteen species of Cleistes, members of all other genera of Pogonieae, and outgroups were sampled. Analyses based oil individual DNA regions provided similar topologies. All evidence indicates that Cleistes is paraphyletic. The North American C. divaricata and C bifaria are more closely related to the temperate genera Isotria and Pogonia than to their Central and South American congeners, the latter Constituting a monophyletic group characterized by the production of nectar as reward, tuberous roots, and their distribution in Central and South America. The Amazonian Duckeella is sister to the remainder of Pogonieae. Taxonomic and biogeographic implications are discussed, and morphological synapomorphies are given For clades obtained in the inferred molecular phylogeny. (C) 2008 Gesellschaft fur Biologische Systematik. Published by Elsevier GmbH. All rights reserved.

Molecular phylogeny of tribe Rhipsalideae (Cactaceae) and taxonomic implications for Schlumbergera and Hatiora

Tribe Rhipsalideae is composed of unusual epiphytic or lithophytic cacti that inhabit humid tropical and subtropical forests. Members of this tribe present a reduced vegetative body, a specialized adventitious root system, usually spineless areoles and flowers and fruits reduced in size. Despite the debate surrounding the classification of Rhipsalideae, no studies have ever attempted to reconstruct phylogenetic relationships among its members or to test the monophyly of its genera using DNA sequence data; all classifications formerly proposed for this tribe have only employed morphological data. In this study, we reconstruct the phylogeny of Rhipsalideae using plastid (trnQ-rps16, rpl32-trnL, psbA-trnH) and nuclear (ITS) markers to evaluate the classifications previously proposed for the group. We also examine morphological features traditionally used to delimit genera within Rhipsalideae in light of the resulting phylogenetic trees. In total new sequences for 35 species of Rhipsalideae were produced (out of 55: 63%). The molecular phylogeny obtained comprises four main clades supporting the recognition of genera Lepismium, Rhipsalis, Hatiora and Schlumbergera. The evidence gathered indicate that a broader genus Schlumbergera, including Hatiora subg. Rhipsalidopsis, should be recognized. Consistent morphological characters rather than homoplastic features are used in order to establish a more coherent and practical classification for the group. Nomenclatural changes and a key for the identification of the genera currently included in Rhipsalideae are provided. (C) 2011 Elsevier Inc. All rights reserved.

An approach to chemotaxonomy to the fatty acid content of some Malvaceae species

Malvales is an order of flowering plants with a controversial circumscription. The relationships between taxa, particularly Malvaceae, Bombacaceae, Sterculiaceae, and Tiliaceae, are not well delineated. Several studies have reported the fatty acid compositions of Malvaceae plants but not for taxonomic purposes. In the present study, the fatty acid composition of oilseeds from seven species belonging to the Malvaceae family was determined by capillary gas chromatography/mass spectrometry (GC/MS), and the quantitative distribution of fatty acids was analyzed by a cluster analysis With Euclidean Distance and UPGMA. The oil content in the seeds was very low (8.3-11.8%). The profile of fatty acids showed that there were two distinct groups: species rich in palmitic acid (Herissantia tiubae, Sidastrum paniculatum and Sida rhombifolia) and species rich in linoleic acid (other Sida species). The fatty acid profiles found for Sida species are consistent with other reported data. Although our data support a distinction between Sida and Sidastrum, more species should be analyzed to evaluate the real taxonomic value of differences in fatty acid content for distinguishing Malvaceae. (C) 2010 Elsevier Ltd. All rights reserved.

Placement of Kuhlmanniodendron Fiaschi & Groppo in Lindackerieae (Achariaceae, Malpighiales) confirmed by analyses of rbcL sequences, with notes on pollen morphology and wood anatomy

The phylogenetic placement of Kuhlmanniodendron Fiaschi & Groppo (Achariaceae) within Malpighiales was investigated with rbcL sequence data. This genus was recently created to accommodate Carpotroche apterocarpa Kuhlm., a poorly known species from the rainforests of Espirito Santo, Brazil. One rbcL sequence was obtained from Kuhlmanniodendron and analyzed with 73 additional sequences from Malpighiales, and 8 from two closer orders, Oxalidales and Celastrales, all of which were available at Genbank. Phylogenetic analyses were carried out with maximum parsimony and Bayesian inference; bootstrap analyses were used in maximum parsimony to evaluate branch support. The results confirmed the placement of Kuhlmanniodendron together with Camptostylus, Lindackeria, Xylotheca, and Caloncoba in a strongly supported clade (posterior probability = 0.99) that corresponds with the tribe Lindackerieae of Achariaceae (Malpighiales). Kuhlmanniodendron also does not appear to be closely related to Oncoba (Salicaceae), an African genus with similar floral and fruit morphology that has been traditionally placed among cyanogenic Flacourtiaceae (now Achariaceae). A picrosodic paper test was performed in herbarium dry leaves, and the presence of cyanogenic glycosides, a class of compounds usually found in Achariaceae, was detected. Pollen morphology and wood anatomy of Kuhlmanniodendron were also investigated, but both pollen (3-colporate and microreticulate) and wood, with solitary to multiple vessels, scalariform perforation plates and other features, do not seem to be useful to distinguish this genus from other members of the Achariaceae and are rather common among the eudicotyledons as a whole. However, perforated ray cells with scalariform plates, an uncommon wood character, present in Kuhlmanniodendron are similar to those found in Kiggelaria africana (Pangieae, Achariaceae), but the occurrence of such cells is not mapped among the angiosperms, and it is not clear how homoplastic this character could be.

Phylogenetic relationships and infrageneric classification of Epidendrum subgenus Amphiglottium (Laeliinae, Orchidaceae)

Epidendrum L. is the largest genus of Orchidaceae in the Neotropical region; it has an impressive morphological diversification, which imposes difficulties in delimitation of both infrageneric and interspecific boundaries. In this study, we review infrageneric boundaries within the subgenus Amphiglottium and try to contribute to the understanding of morphological diversification and taxa delimitation within this group. We tested the monophyly of the subgenus Amphiglottium sect. Amphiglottium, expanding previous phylogenetic investigations and reevaluated previous infrageneric classifications proposed. Sequence data from the trnL-trnF region were analyzed with both parsimony and maximum likelihood criteria. AFLP markers were also obtained and analyzed with phylogenetic and principal coordinate analyses. Additionally, we obtained chromosome numbers for representative species within the group. The results strengthen the monophyly of the subgenus Amphiglottium but do not support the current classification system proposed by previous authors. Only section Tuberculata comprises a well-supported monophyletic group, with sections Carinata and Integra not supported. Instead of morphology, biogeographical and ecological patterns are reflected in the phylogenetic signal in this group. This study also confirms the large variability of chromosome numbers for the subgenus Amphiglottium (numbers ranging from 2n = 24 to 2n = 240), suggesting that polyploidy and hybridization are probably important mechanisms of speciation within the group.

Phylogenetic Analyses of Eriotheca and Related Genera (Bombacoideae, Malvaceae)

Molecular and morphological data have shown that Bombacoideae and Malvoideae together form a well-supported Malvatheca clade. Phylogenetic relationships in Bombacoideae have been studied, but some genera in Bombax s. I. have not been adequately sampled for sufficiently variable molecular markers. The relationships of Eriotheca, for example, have yet to be resolved. Here, nuclear (ITS) and chloroplast (trnL-Fand matK) sequence data from 50 exemplars of Bombacoideae and seven additional taxa from other genera of Malvatheca were used to test monophyly of Eriotheca and its relationships with related genera of Bombax s. I. Parsimony and Bayesian analyses of individual and combined sequence data suggest that Eriotheca is not monophyletic as currently circumscribed but forms a paraphyletic grade containing Pachira s. 1. The newly discovered Eriotheca + Pachira clade has a probable synapomorphy of striate seeds. In addition, two other moderately supported clades emerged within the core Bombacoideae: Pseudobombax + Ceiba s. 1. and Bombax + Spirotheca + Pachira quinata. These three clades, and the African Rhodognaphalon together constitute the major clade of core Bombacoideae, whereas Adansonia appears to be more closely related to Catostemma, Scleronema, and Cavanillesia. The phylogenetic results imply three independent migrations from the New to Old World and homoplasy in staminal morphology.

Gracilariopsis mclachlanii sp nov and Gracilariopsis persica sp nov of the Gracilariaceae (Gracilariales, Rhodophyceae) from the Indian Ocean

Two new species of Gracilariopsis from the Indian Ocean are proposed-Gracilariopsis (Gp.) mclachlanii Buriyo, Bellorin et M. C. Oliveira sp. nov. from Tanzania and Gracilariopsis persica Bellorin, Sohrabipour et E. C. Oliveira sp. nov. from Iran-based on morphology and DNA sequence data (rbcL gene and SSU rDNA). Both species fit the typical features of Gracilariopsis: axes cylindrical throughout, freely and loosely ramified up to four orders, with an abrupt transition in cell size from medulla to cortex, cystocarps lacking tubular nutritive cells and superficial spermatangia. Nucleotide sequence comparisons of rbcL and SSU rDNA placed both species into the Gracilariopsis clade as distinct species from all the accepted species for this genus, forming a deeply divergent lineage together with some species from the Pacific. The new species are very difficult to distinguish on morphological grounds from other species of Gracilariopsis, stressing the importance of homologous molecular marker comparisons for the species recognition in this character-poor genus.

The genus Coleodactylus (Sphaerodactylinae, Gekkota) revisited: A molecular phylogenetic perspective

Nucleotide sequence data from a mitochondrial gene (16S) and two nuclear genes (c-mos, RAG-1) were used to evaluate the monophyly of the genus Coleodactylus, to provide the first phylogenetic hypothesis of relationships among its species in a cladistic framework, and to estimate the relative timing, of species divergences. Maximum Parsimony, Maximum Likelihood and Bayesian analyses of the combined data sets retrieved Coleodactylus as a monophyletic genus, although weakly Supported. Species were recovered as two genetically and morphological distinct clades, with C. amazonicus populations forming the sister taxon to the meridionalis group (C. brachystoma, C. meridionalis, C. natalensis, and C. septentrionalis). Within this group, C. septentrionalis was placed as the sister taxon to a clade comprising the rest of the species, C. meridionalis was recovered as the sister species to C. brachystoma, and C natalensis was found nested within C. meridionalis. Divergence time estimates based on penalized likelihood and Bayesian dating methods do not Support the previous hypothesis based on the Quaternary rain forest fragmentation model proposed to explain the diversification of the genus. The basal cladogenic event between major lineages of Coleodactylus was estimated to have occurred in the late Cretaceous (72.6 +/- 1.77 Mya), approximately at the same point in time than the other genera of Sphaerodactylinae diverged from each other. Within the meridionalis group, the split between C. septentrionalis and C. brachystoma + C. meridionalis was placed in the Eocene (46.4 +/- 4.22 Mya), and the divergence between C. brachystoma and C. meridionalis was estimated to have occurred in the Oligocene (29.3 +/- 4.33 Mya). Most intraspecific cladogenesis occurred through Miocene to Pliocene, and only for two conspecific samples and for C. natalensis could a Quaternary differentiation be assumed (1.9 +/- 1.3 Mya). (C) 2008 Elsevier Inc. All rights reserved.

Five vicarious genera from Gondwana: the Velloziaceae as shown by molecules and morphology

Background and Aims The amount of data collected previously for Velloziaceae neither clarified relationships within the family nor helped determine an appropriate classification, which has led to huge discordance among treatment by different authors. To achieve an acceptable phylogenetic result and understand the evolution and roles of characters in supporting groups, a total evidence analysis was developed which included approx. 20 % of the species and all recognized genera and sections of Velloziaceae, plus outgroups representatives of related families within Pandanales. Methods Analyses were undertaken with 48 species of Velloziaceae, representing all ten genera, with DNA sequences from the atpB-rbcL spacer, trnL-trnF spacer, trnL intron, trnH-psbA spacer, ITS ribosomal DNA spacers and morphology. Key Results Four groups consistently emerge from the analyses. Persistent leaves, two phloem strands, stem cortex divided in three regions and violet tepals support Acanthochlamys as sister to Velloziaceae s. s., which are supported mainly by leaves with marginal bundles, transfusion tracheids and inflorescence without axis. Within Velloziaceae s. s., an African Xerophyta + Talbotia clade is uniquely supported by basal loculicidal capsules; an American clade, Barbacenia s. l. + Barbaceniopsis + Nanuza + Vellozia, is supported by only homoplastic characters. Barbacenia s. l. (Aylthonia + Barbacenia + Burlemarxia + Pleurostima) is supported by a double sheath in leaf vascular bundles and a corona; Barbaceniopsis + Nanuza + Vellozia is not supported by an unambiguous character, but Barbaceniopsis is supported by five characters, including diclinous flowers, Nanuza + Vellozia is supported mainly by horizontal stigma lobes and stem inner cortex cells with secondary walls, and Vellozia alone is supported mainly by pollen in tetrads. Conclusions The results imply recognition of five genera (Acanthochlamys (Xerophyta (Barbacenia (Barbaceniopsis, Vellozia)))), solving the long-standing controversies among recent classifications of the family. They also suggest a Gondwanan origin for Velloziaceae, with a vicariant pattern of distribution.

Croton laceratoglandulosus (Euphorbiaceae s.s.), a new glandular-stipulate species from Brazil and Bolivia, and its systematic position based on molecular analysis

Croton laceratoglandulosus, a new species from the dry forests of the Brazilian states of Piaui, Ceara, Bahia and Minas Gerais, and the Bolivian department of Santa Cruz, is described and illustrated here. Molecular sequence data demonstrate that it is most closely related to the taxa of Croton section Cascarilla, and not to sections Medea or Barhamia, which also have glandular calyces and laciniate stipules. (C) 2008 The Linnean Society of London, Botanical Journal of the Linnean Society, 2008, 158, 493-498.

Genomic Analysis of Wild Tomato Introgressions Determining Metabolism- and Yield-Associated Traits

With the aim of determining the genetic basis of metabolic regulation in tomato fruit, we constructed a detailed physical map of genomic regions spanning previously described metabolic quantitative trait loci of a Solanum pennellii introgression line population. Two genomic libraries from S. pennellii were screened with 104 colocated markers from five selected genomic regions, and a total of 614 bacterial artificial chromosome (BAC)/cosmids were identified as seed clones. Integration of sequence data with the genetic and physical maps of Solanum lycopersicum facilitated the anchoring of 374 of these BAC/cosmid clones. The analysis of this information resulted in a genome-wide map of a nondomesticated plant species and covers 10% of the physical distance of the selected regions corresponding to approximately 1% of the wild tomato genome. Comparative analyses revealed that S. pennellii and domesticated tomato genomes can be considered as largely colinear. A total of 1,238,705 bp from both BAC/cosmid ends and nine large insert clones were sequenced, annotated, and functionally categorized. The sequence data allowed the evaluation of the level of polymorphism between the wild and cultivated tomato species. An exhaustive microsynteny analysis allowed us to estimate the divergence date of S. pennellii and S. lycopersicum at 2.7 million years ago. The combined results serve as a reference for comparative studies both at the macrosyntenic and microsyntenic levels. They also provide a valuable tool for fine-mapping of quantitative trait loci in tomato. Furthermore, they will contribute to a deeper understanding of the regulatory factors underpinning metabolism and hence defining crop chemical composition.

Evolutionary history of Ramphastos toucans: Molecular phylogenetics, temporal diversification, and biogeography

The toucan genus Ramphastos (Piciformes: Ramphastidae) has been a model in the formulation of Neotropical paleobiogeographic hypotheses. Weckstein (2005) reported on the phylogenetic history of this genus based on three mitochondrial genes, but some relationships were weakly supported and one of the subspecies of R. vitellinus (citreolaemus) was unsampled. This study expands on Weckstein (2005) by adding more DNA sequence data (including a nuclear marker) and more samples, including R v. citreolaemus. Maximum parsimony, maximum likelihood, and Bayesian methods recovered similar trees, with nodes showing high support. A monophyletic R. vitellinus complex was strongly supported as the sister-group to R. brevis. The results also confirmed that the southeastern and northern populations of R. vitellinus ariel are paraphyletic. X v. citreolaemus is sister to the Amazonian subspecies of the vitellinus complex. Using three protein-coding genes (COI, cytochrome-b and ND2) and interval-calibrated nodes under a Bayesian relaxed-clock framework, we infer that ramphastid genera originated in the middle Miocene to early Pliocene, Ramphastos species originated between late Miocene and early Pleistocene, and intra-specific divergences took place throughout the Pleistocene. Parsimony-based reconstruction of ancestral areas indicated that evolution of the four trans-Andean Ramphastos taxa (R. v. citreolaemus, R. a. swainsonii, R. brevis and R. sulfuratus) was associated with four independent dispersals from the cis-Andean region. The last pulse of Andean uplift may have been important for the evolution of R. sulfuratus, whereas the origin of the other trans-Andean Ramphastos taxa is consistent with vicariance due to drying events in the lowland forests north of the Andes. Estimated rates of molecular evolution were higher than the ""standard"" bird rate of 2% substitutions/site/million years for two of the three genes analyzed (cytochrome-b and ND2). (C) 2009 Elsevier Inc. All rights reserved.

Cathepsin L-like genes of Trypanosoma vivax from Africa and South America - characterization, relationships and diagnostic implications

We characterized sequences from genes encoding cathepsin L-like (CatL-like) cysteine proteases from African and South American isolates of Trypanosoma vivax and T. vivax-like organisms, and evaluated their suitability as genetic markers for population structure analysis and diagnosis. Phylogenetic analysis of sequences corresponding to CatL-like catalytic domains revealed substantial polymorphism, and clades of sequences (TviCatL1-9) were separated by large genetic distances. TviCatL1-4 sequences were from cattle isolates from West Africa (Nigeria and Burkina Faso) and South America (Brazil and Venezuela), which belonged to the same T. vivax genotype. T. vivax-like genotypes from East Africa showed divergent sequences, including TviCatL5-7 for isolates from Mozambique and TviCatL8-9 for an isolate from Kenya. Phylogenetic analysis of CatL-like gene data supported the relationships among trypanosome species reflected in the phylogenies based on the analysis of small subunit (SSU) of ribosomal RNA gene sequence data. The discovery of different CatL-like sequences for each genotype, defined previously by ribosomal DNA data, indicate that these sequences provide useful targets for epidemiological and population genetic studies. Regions in CatL-like sequences shared by all T. vivax genotypes but not by other trypanosomes allowed the establishment of a specific and sensitive diagnostic PCR for epidemiological studies in South America and Africa. (C) 2008 Elsevier Ltd. All rights reserved.