Evolutionary history of trypanosomes from South American caiman (Caiman yacare) and African crocodiles inferred by phylogenetic analyses using SSU rDNA and gGAPDH genes

In this study, using a combined data set of SSU rDNA and gGAPDH gene sequences, we provide phylogenetic evidence that supports Clustering of crocodilian trypanosomes from the Brazilian Caiman yacare (Alligatoridae) and Trypanosoma grayi, a species that Circulates between African crocodiles (Crocodilydae) and tsetse flies. In a survey of trypanosomes in Caiman yacare from the Brazilian Pantanal, the prevalence of trypanosome infection was 35% as determined by microhaematocrit and haemoculture, and 9 cultures were obtained. The morphology of trypomastigotes from caiman blood and tissue imprints was compared with those described for other crocodilian trypanosomes. Differences in morphology and growth behaviour of caiman trypanosomes were corroborated by molecular polymorphism that revealed 2 genotypes. Eight isolates were ascribed to genotype Cay01 and 1 to genotype Cay02. Phylogenetic inferences based on concatenated SSU rDNA and gGAPDII sequences showed that caiman isolates are closely related to T. grayi, constituting a well-supported monophyletic assemblage (clade T. grayi). Divergence time estimates based on clade composition, and biogeographical and geological events were used to discuss the relationships between the evolutionary histories of crocodilian trypanosomes and their hosts.

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.

The Y Chromosome of the Atelidae Family (Platyrrhini): Study by Chromosome Microdissection

In order to study the intergeneric variability of the Y chromosome, we describe the hybridization of the Y chromosome of Brachyteles arachnoides, obtained by microdissection, to metaphases of Ateles belzebuth marginatus, Lagothrix lagothricha, and Alouatta male specimens. Brachyteles arachnoides (Atelinae) has 62 chromosomes and a very small Y chromosome. Our results showed that the Brachyteles arachnoides Y chromosome probe hybridized to Lagothrix lagothricha metaphases yielding one hybridization signal on only the tiny Y chromosome, and when hybridized with Ateles belzebuth marginatus metaphases it yielded one hybridization signal on two thirds of the small acrocentric Y chromosome. However, no hybridization signal was observed in Alouatta metaphases (subfamily Alouattinae), a closely related genus in the Atelidae family. Furthermore, our data support a close phylogenetic relationship among Brachyteles, Ateles, and Lagothrix and their placement in the Atelinae subfamily, but exclude Alouatta from this group indicating its placement as basal to this group. Copyright (C) 2009 S. Karger AG, Basel

Taxonomic and Phylogenetic Relationships Between Species of the Genus Culex (Diptera: Culicidae) From Brazil Inferred From the Cytochrome c Oxidase I Mitochondrial Gene

Species of the genus Culex Linnaeus have been incriminated as the main vectors of lymphatic filariases and are important vectors of arboviruses, including West Nile virus. Sequences corresponding to a fragment of 478 bp of the cytochrome c oxidase subunit I gene, which includes part of the barcode region, of 37 individuals of 17 species of genus Culex were generated to establish relationships among five subgenera, Culex, Phenacomyia, Melanoconion, Microculex, and Carrollia, and one species of the genus Lutzia that occurs in Brazil. Bayesian methods were employed for the phylogenetic analyses. Results of sequence comparisons showed that individuals identified as Culex dolosus, Culex mollis, and Culex imitator possess high intraspecific divergence (3.1, 2.3, and 3.5%, respectively) when using the Kimura two parameters model. These differences were associated either with distinct morphological characteristics of the male genitalia or larval and pupal stages, suggesting that these may represent species complexes. The Bayesian topology suggested that the genus and subgenus Culex are paraphyletic relative to Lutzia and Phenacomyia, respectively. The cytochrome c oxidase subunit I sequences may be a useful tool to both estimate phylogenetic relationships and identify morphologically similar species of the genus Culex.

Phylogenetic relationships among species of Anopheles (Nyssorhynchus) (Diptera, Culicidae) based on nuclear and mitochondrial gene sequences

Phylogenetic relationships among 21 species of mosquitoes in subgenus Nyssorhynchus were inferred from the nuclear white and mitochondrial NADH dehydrogenase subunit 6 (ND6) genes. Bayestan phylogenetic methods found that none of the three Sections within Nyssorhynchus (Albimanus, Argyritarsis, Myzorhynchella) were supported in all analyses, although Myzorhynchella was found to be monophyletic at the combined genes Within the Albimanus Section the monophyly of the Stroder Subgroup was strongly supported and within the Myzorhynchella Section Anopheles anrunesi and An lutzu formed a strongly supported monophyletic group The epidemiologically significant Albitarsis Complex showed evidence of paraphyly (relative to An lanet-Myzorhynchella) and discordance across gene trees, and the previously synonomized species of An. dunhami and An goeldii were recovered as sister species Finally, there was evidence of complexes in several species, including An antunesi, An deaneorum, and An. strodei (c) 2010 Elsevier B.V. All rights reserved

PHYLOGENETIC AFFINITIES OF "CHANTRANSIA" STAGES IN MEMBERS OF THE BATRACHOSPERMALES AND THOREALES (RHODOPHYTA)

This study evaluated the phylogenetic relationship among samples of ""Chantransia"" stage of the Batrachospermales and Thoreales from several regions of the world based on sequences of two genes-the plastid-encoded RUBISCO LSU gene (rbcL) and the nuclear SSU ribosomal DNA gene (SSU rDNA). All sequences of ""Chantransia macrospora"" were shown to belong to Batrachospermum macrosporum based on both molecular markers, confirming evidence from previous studies. In contrast, nine species are now associated with ""Chantransia pygmaea,"" including seven species of the Batrachospermales and two of the Thoreales. Therefore, the presence of ""C. macrospora"" in a stream can be considered reliable evidence that it belongs to B. macrosporum, whereas the occurrence of ""C. pygmaea"" does not allow the recognition of any particular species, since it is associated with at least nine species. Affinities of ""Chantransia"" stages to particular taxa were congruent for 70.5% of the samples comparing the rbcL and SSU analyses, which were associated with the same or closely related species for both markers. Sequence divergences have been reported in the ""Chantransia"" stage in comparison to the respective gametophyte, and this matter deserves further attention.

Phylogenetic analysis of the Brazilian microendemic Paepalanthus subgenus Xeractis (Eriocaulaceae) inferred from morphology

Paepalanthus subgenus Xeractis (Eriocaulaceae) comprises 28 recognized species endemic to the Espinhaco Range, in Minas Gerais state, Brazil. Most species of the subgenus are restricted to small localities and critically endangered, but still in need of systematic study. The monophyly of the subgenus has already been tested, but only with a few species. Our study presents the first phylogenetic hypothesis within the group, based on morphology. A maximum parsimony analysis was conducted on a matrix of 30 characters for 30 terminal taxa, including all species of the subgenus and two outgroups. The biogeographical hypotheses for the subgenus were inferred based on dispersal-vicariance analysis (DIVA). The analysis provided one most-parsimonious hypothesis that supports most of the latest published subdivisions (sections and series). However, some conflicts remain concerning the position of a few species and the relationships between sections. The distribution and origin(s) of microendemism are also discussed, providing the ground for conservation strategies to be developed in the region. (C) 2011 The Linnean Society of London, Botanical Journal of the Linnean Society, 2011, 167, 137-152.

Contrasting phylogenetic signals and evolutionary rates in floral traits of Neotropical lianas

The diversity of floral forms has long been considered a prime example of radiation through natural selection. However, little is still known about the evolution of floral traits, a critical piece of evidence for the understanding of the processes that may have driven flower evolution. We studied the pattern of evolution of quantitative floral traits in a group of Neotropical lianas (Bignonieae, Bignoniaceae) and used a time-calibrated phylogeny as basis to: (1) test for phylogenetic signal in 16 continuous floral traits; (2) evaluate the rate of evolution in those traits; and (3) reconstruct the ancestral state of the individual traits. Variation in floral traits among extant species of Bignonieae was highly explained by their phylogenetic history. However, opposite signals were found in floral traits associated with the attraction of pollinators (calyx and corolla) and pollen transfer (androecium and gynoecium), suggesting a differential role of selection in different floral whorls. Phylogenetic independent contrasts indicate that traits evolved at different rates, whereas ancestral character state reconstructions indicate that the ancestral size of most flower traits was larger than the mean observed sizes of the same traits in extant species. The implications of these patterns for the reproductive biology of Bignonieae are discussed. (C) 2011 The Linnean Society of London, Biological Journal of the Linnean Society, 2011, 102, 378-390.

Phylogenetic relationships in Kumanoa (Batrachospermales, Rhodophyta) species in Brazil with the proposal of Kumanoa amazonensis sp nov.

This Study evaluated the species-level taxonomy and phylogenetic relationship among Kumanoa species from Brazil with other regions of the world based on the plastid-encoded RUBISCO large Subunit gene (rhcL). Partial rbcL sequences were obtained for 11 Kulnanoa specimens. Eight species are recognised from Brazil on the basis of molecular and morphological data: seven previously described (K abilii, K ambignia, K. breviarticulata, K. cipoensis, K. equisetoidea, K. globospora and K procarpa) and a new species here proposed (K. amazonensis sp. nov. Necchi & Vis). The new species has reduced and dense whorls but differs from the two closest related species in lacking secondary fascicles. Previously proposed infrageneric categories were not supported by the molecular data. Species described and endemic (K. breviarticulata, K. cipoensis, K equiseloidea and K. procarpa) to Brazil are not grouped together but are variously related to other species from North America, Europe and Australasia. With the species recognised in this study using molecular and morphological data and those previously distinguished by morphology, 13 species of Kumanoa are Currently documented from Brazil.

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.

Phylogenetic group distribution among Escherichia coli isolated from rivers in Sao Paulo State, Brazil

The phylogenetic group distribution of Escherichia coli strains isolated from the Sorocaba and Jaguari Rivers located in the State of Sao Paulo, Brazil, is described. E. coli strains from group D were found in both rivers while one strain from group B2 was isolated from the Sorocaba river. These two groups often include strains that can cause extraintestinal diseases. Most of the strains analyzed were allocated into the phylogenetic groups A and B1, supporting the hypothesis that strains from these phylogenetic groups are more abundant in tropical areas. Though both rivers are located in urbanized and industrialized areas where the main source of water pollution is considered to derive from domestic sewage, our results suggest that the major sources of contamination in the sampling sites of both rivers might have originated from animals and not humans.

The timing of Neotropical speciation dynamics: A reconstruction of Myiopagis flycatcher diversification using phylogenetic and paleogeographic data

Neotropical forests have brought forth a large proportion of the world`s terrestrial biodiversity, but the underlying evolutionary mechanisms and their timing require further elucidation. Despite insights gained from phylogenetic studies, uncertainties about molecular clock rates have hindered efforts to determine the timing of diversification processes. Moreover, most molecular research has been detached from the extensive body of data on Neotropical geology and paleogeography. We here examine phylogenetic relationships and the timing of speciation events in a Neotropical flycatcher genus (Myiopagis) by using calibrations from modern geologic data in conjunction with a number of recently developed DNA sequence dating algorithms and by comparing these estimates with those based on a range of previously proposed molecular clock rates. We present a well-supported hypothesis of systematic relationships within the genus. Our age estimates of Myiopagis speciation events based on paleogeographic data are in close agreement with nodal ages derived from a ""traditional"" avian mitochondrial 2%/My clock, while contradicting other clock rates. Our comparative approach corroborates the consistency of the traditional avian mitochondrial clock rate of 2%/My for tyrant-flycatchers. Nevertheless, our results argue against the indiscriminate use of molecular clock rates in evolutionary research and advocate the verification of the appropriateness of the traditional clock rate by means of independent calibrations in individual studies. (C) 2009 Elsevier Inc. All rights reserved.

Phylogenetic relationships, diversification and biogeography in Neotropical Brotogeris parakeets

Aim We present a molecular phylogenetic analysis of Brotogeris (Psittacidae) using several distinct and complementary approaches: we test the monophyly of the genus, delineate the basal taxa within it, uncover their phylogenetic relationships, and finally, based on these results, we perform temporal and spatial comparative analyses to help elucidate the historical biogeography of the Neotropical region. Location Neotropical lowlands, including dry and humid forests. Methods Phylogenetic relationships within Brotogeris were investigated using the complete sequences of the mitochondrial genes cyt b and ND2, and partial sequences of the nuclear intron 7 of the gene for Beta Fibrinogen for all eight species and 12 of the 17 taxa recognized within the genus (total of 63 individuals). In order to delinetae the basal taxa within the genus we used both molecular and plumage variation, the latter being based on the examination of 597 skin specimens. Dates of divergence and confidence intervals were estimated using penalized likelihood. Spatial and temporal comparative analyses were performed including several closely related parrot genera. Results Brotogeris was found to be a monophyletic genus, sister to Myiopsitta. The phylogenetic analyses recovered eight well-supported clades representing the recognized biological species. Although some described subspecies are diagnosably distinct based on morphology, there was generally little intraspecific mtDNA variation. The Amazonian species had different phylogenetic affinities and did not group in a monophyletic clade. Brotogeris diversification took place during the last 6 Myr, the same time-frame as previously found for Pionus and Pyrilia. Main conclusions The biogeographical history of Brotogeris implies a dynamic history for South American biomes since the Pliocene. It corroborates the idea that the geological evolution of Amazonia has been important in shaping its biodiversity, argues against the idea that the region has been environmentally stable during the Quaternary, and suggests dynamic interactions between wet and dry forest habitats in South America, with representatives of the Amazonian biota having several independent close relationships with taxa endemic to other biomes.

Cladistic analysis of continuous modularized traits provides phylogenetic signals in Homo evolution

Evolutionary novelties in the skeleton are usually expressed as changes in the timing of growth of features intrinsically integrated at different hierarchical levels of development(1). As a consequence, most of the shape- traits observed across species do vary quantitatively rather than qualitatively(2), in a multivariate space(3) and in a modularized way(4,5). Because most phylogenetic analyses normally use discrete, hypothetically independent characters(6), previous attempts have disregarded the phylogenetic signals potentially enclosed in the shape of morphological structures. When analysing low taxonomic levels, where most variation is quantitative in nature, solving basic requirements like the choice of characters and the capacity of using continuous, integrated traits is of crucial importance in recovering wider phylogenetic information. This is particularly relevant when analysing extinct lineages, where available data are limited to fossilized structures. Here we show that when continuous, multivariant and modularized characters are treated as such, cladistic analysis successfully solves relationships among main Homo taxa. Our attempt is based on a combination of cladistics, evolutionary- development- derived selection of characters, and geometric morphometrics methods. In contrast with previous cladistic analyses of hominid phylogeny, our method accounts for the quantitative nature of the traits, and respects their morphological integration patterns. Because complex phenotypes are observable across different taxonomic groups and are potentially informative about phylogenetic relationships, future analyses should point strongly to the incorporation of these types of trait.