Comparative Metabolic Systems Analysis of Pathogenic Burkholderia

Burkholderia cenocepacia and Burkholderia multivorans are opportunistic drug-resistant pathogens that account for the majority of Burkholderia cepacia complex infections in cystic fibrosis patients and also infect other immunocompromised individuals. While they share similar genetic compositions, B. cenocepacia and B. multivorans exhibit important differences in pathogenesis. We have developed reconciled genome-scale metabolic network reconstructions of B. cenocepacia J2315 and B. multivorans ATCC 17616 in parallel (designated iPY1537 and iJB1411, respectively) to compare metabolic abilities and contextualize genetic differences between species. The reconstructions capture the metabolic functions of the two species and give insight into similarities and differences in their virulence and growth capabilities. The two reconstructions have 1,437 reactions in common, and iPY1537 and iJB1411 have 67 and 36 metabolic reactions unique to each, respectively. After curating the extensive reservoir of metabolic genes in Burkholderia, we identified 6 genes essential to growth that are unique to iPY1513 and 13 genes uniquely essential to iJB1411. The reconstructions were refined and validated by comparing in silico growth predictions to in vitro growth capabilities of B. cenocepacia J2315, B. cenocepacia K56-2, and B. multivorans ATCC 17616 on 104 carbon sources. Overall, we identified functional pathways that indicate B. cenocepacia can produce a wider array of virulence factors compared to B. multivorans, which supports the clinical observation that B. cenocepacia is more virulent than B. multivorans. The reconciled reconstructions provide a framework for generating and testing hypotheses on the metabolic and virulence capabilities of these two related emerging pathogens.     

Cretaceous and Paleogene Bourgueticrinina (Echinodermata,Crinoidea) of the USSR

The theca and the columnals of twenty-two lateCretaceous species of the genus Bourgueticrinus (including two new species), of one species of the genus Democrinus, of four species of the genus Conocrinus (including one new species) and of one species of the genus Paleobathycrinus known from USSR are figured and shortly described. Biometric reconstructions of stems for B. aequalis, B. bellus, B. danicus, B. fischeri and C. tauricus nov. sp. are given. A new index is used to suggest the relative flexibility of stem. Decrease in dimension and flexibility of the arms in several species take place simultaneously with an increase of stem flexibility. This fact seems to be closely related to environmental changes.     

Bipolar disjunctions in Carex: Long-distance dispersal,vicariance, or parallel evolution?

The long-standing fascination of naturalists and scientists in the evolutionary and biogeographical causes behind the pattern of distribution of bipolar plants has lead to an intense debate around the three well-known biogeographical hypotheses of vicariance, long-distance dispersal, and parallel evolution. Genus Carex, despite lacking any general long-distance dispersal devices, represents six of the 30 plant species with bipolar distribution. We aimed to evaluate the role of the three alternative mechanisms mentioned above in the origin and evolution of five bipolar Carex species. Phylogenetic and phylogeographical reconstructions using Bayesian Inference, maximum parsimony, and statistical parsimony were performed with plastid (rps16 intron) and nuclear (ITS) DNA sequences. As a result, five cases of long-distance dispersal are proposed (C. canescens, C. macloviana, C. magellanica, C. maritima, C. microglochin s.str.) with an inferred southward migration from Northern to Southern Hemisphere for three of them. On the other hand, parallel evolution seems to be the most plausible explanation to understand the particular case of the bipolar species C. microglochin s.l.     

Application of quantitative measures of gene order similarity to phylogenetic reconstructions (exemplified by bacteria of the genus <Emphasis Type="Italic">Rickettsia</Emphasis>)

Data reflecting evolutionary changes in chromosomal gene order can be used for phylogenetic reconstructions along with the results of nucleotide sequence comparison. By the example of bacteria of the genus Rickettsia, we have shown that phylogenetic reconstructions based on quantitative estimates of the similarity and cladistic analysis of gene order data, may, in some cases, amend and fill up classical phylogenetic trees. When applied, these approaches enabled us to substantiate the hypothesis that Rickettsia felis species had split before the typhus (R. typhi, R. prowazekii) and spotted fever (R. connorii) group divergence and thus R. felis does not belong to the latter group. In general, rickettsias evolved towards increasing intracellular parasitic specialization. Five Rickettsia species whose genomes have been sequenced and annotated completely actually form an evolutionary series R. bellii—R. felis—R. conorii—R. prowazekii—R. typhi. Within this series, a reduction in genome size and rapid decrease of genome rearrangement rates (genome plasticity loss) gradually occur.     

Quantifying the effect of testate amoeba decomposition on peat-based water-table reconstructions

Testate amoebae are a widely-used tool for palaeohydrological reconstruction from peatlands. However, it has been observed that weak idiosomic siliceous tests (WISTs) are common in uppermost peats, but very rarely found as subfossils deeper in the peat profile. This taphonomic problem has been noted widely and it has been established that WISTs disaggregate and/or dissolve in the low pH condition of ombrotrophic peatlands. Here we investigate the effect of this taphonomic problem on water-table reconstructions from thirty European peatlands through the comparison of reconstructions based on all taxa and those with WISTs removed. In almost all cases the decomposition of WISTs does not introduce discernible bias to peatland water-table reconstructions. However, some discrepancy is apparent when large abundances of Corythion-Trinema type are present (9−12 cm deviation with 50–60% abundance of this particular taxon). We recommend that WISTs should be removed before carrying out water-table reconstructions, and that the minimum count of testate amoebae per sample should exclude WISTs to ensure the development of robust reconstructions.     

Testing whether ecological factors promote cladogenesis in a group of tiger beetles (Coleoptera: Cicindelidae)

We investigate the role of ecological differentiation in cladogenesis of a monophyletic group of North American tiger beetles, the subgenus Ellipsoptera (genus: Cicindela), by reconstructing their species-level phylogeny from mitochondrial DNA sequences. Observed reconstructions of ecological characters on the phylogeny are compared to those expected under simple null models of no association with cladogenesis. We find no evidence that ecological disparity is associated with either species coexistence, speciation or long-term persistence and/or radiation of lineages. Ecomorphological traits have evolved in response to differences in habitat occupied by species, but without detectable relationship with cladogenesis.     

Anomalous ring identification in two Australian subtropical Araucariaceae species permits annual ring dating and growth-climate relationship development

Almost all Australian tropical and subtropical regions lack annually-resolved long-term (multi-decadal to centennial scale) instrumental climate records. Reconstructing climate in these regions requires the use of sparse climate proxy records such as tree rings. Tree rings often archive annually-resolved centennial-scale climate information. However, many tropical and subtropical species have short life-spans, the timbers are poorly preserved, and there is a belief that the proxy records of these species are often compromised by ring anomalies. Additionally, for many species the relationship between climate (e.g. temperature and/or rainfall) and tree growth has not been established. These factors have led to tree-ring data being underutilized in the Australian subtropics. Trees in the Araucariaceae family, a common family in northern and eastern Australia, are both longer lived than many species in the Australian subtropics, present growth rings that are annual in nature, and their growth is known to vary with climate. In this study we examine two subtropical Araucariaceae species, Araucaria cunninghamii and Araucaria bidwillii, and quantify the relationship between their radial growth and climate variability. Ring anomalies including false, faint, locally absent, and pinching rings, are found to be present in these species, however, bomb-pulse radiocarbon dating of A. cunninghamii samples together with a whole tree approach helped to identify annual growth patterns despite such anomalous ring boundaries. Additionally, to determine which climate variables most influence growth in these species, dendrometers were installed at two locations in subtropical Southeast Queensland, Australia. We found that rainfall variability drives annual ring growth, while temperature constrains the onset and conclusion of the growth season each year. Our results demonstrate that through the use of A. cunninghamii and A. bidwillii trees which demonstrate annual growth in relation to climate variables there is potential to develop centennial scale climate reconstructions from the Australian subtropics. We provide recommendations on how to best identify ring anomalies in these species to help in the future development of long-term chronologies and climate reconstructions.     

Deux nouveaux genres de Rhynchonellides frasniens précédemment inclus dans le genre Calviaria (Brachiopoda)

The genus CalvinariaStainbrook, 1945 is beingsubdivided by the writer into the following two new genera: Plionoptycherhynchus n. gen. based on the type species P. exformosus n. gen., n. sp., and Lateralatirostrum n. gen. based on the type species L. athabascense (Kindle, 1924).These type species are proposed as indices ofzones in the upper part of the lower Frasnian stage.The writer wishes to point out the doubtful validity of palaeogeographic reconstructions undertaken on the basis of too comprehensively, and consequently poorly, defined genera. In this connection he points out that the form occuring in the Ardennes and attributed to Eifelian species Terebratula formosaSchnur, 1851 belongs actually to a different genus and species and is of a different age.     

Phenomenological Model for Predicting the Catabolic Potential of an Arbitrary Nutrient

The ability of microbial species to consume compounds found in the environment to generate commercially-valuable products has long been exploited by humanity. The untapped, staggering diversity of microbial organisms offers a wealth of potential resources for tackling medical, environmental, and energy challenges. Understanding microbial metabolism will be crucial to many of these potential applications. Thermodynamically-feasible metabolic reconstructions can be used, under some conditions, to predict the growth rate of certain microbes using constraint-based methods. While these reconstructions are powerful, they are still cumbersome to build and, because of the complexity of metabolic networks, it is hard for researchers to gain from these reconstructions an understanding of why a certain nutrient yields a given growth rate for a given microbe. Here, we present a simple model of biomass production that accurately reproduces the predictions of thermodynamically-feasible metabolic reconstructions. Our model makes use of only: i) a nutrient''s structure and function, ii) the presence of a small number of enzymes in the organism, and iii) the carbon flow in pathways that catabolize nutrients. When applied to test organisms, our model allows us to predict whether a nutrient can be a carbon source with an accuracy of about 90% with respect to in silico experiments. In addition, our model provides excellent predictions of whether a medium will produce more or less growth than another () and good predictions of the actual value of the in silico biomass production.     

Phylogeny and infrageneric classification of Correa Andrews (Rutaceae) on the basis of nuclear and chloroplast DNA

This paper presents phylogenies of the small but ecologically and horticulturally important Australian genus Correa (Rutaceae). Consensus phylogenies generated using parsimony were congruent with their counterparts generated by Bayesian analysis, although usually less well resolved. The phylogeny generated from the second internal transcribed spacer region of the nuclear ribosomal DNA supported the monophyly of Correa and identified two well supported clades (one comprising C. lawrenceana and C. baeuerlenii and the other containing all other species of the genus). Phylogenetic reconstructions based on the combined trnL-trnF spacer and the trnK intron (including the matK gene) regions of chloroplast DNA also supported the monophyly of Correa and of the C. lawrenceana/C. baeuerlenii clade, but the topology among the other species differed markedly from that in the ITS-based phylogeny. The major clades identified in the chloroplast phylogenies seemed to follow geographic patterns rather than species boundaries, with different samples of C. glabra bearing chloroplast genotypes from different clades. These patterns are likely to be because of independent evolution of the chloroplast and nuclear genomes, and are typical of cases of introgressive hybridisation among species or incomplete lineage sorting of chloroplast genomes leading to incongruence between chloroplast and nuclear phylogenies. Thus, the phylogenies based on nuclear DNA should reflect species relations better than the chloroplast phylogeny in Correa, and we propose a new subgeneric classification of the genus on the basis of the ITS-based phylogeny and morphology. Correa subgenus Persistens Othman, Duretto and G.J. Jord., containing C. lawrenceana and C. baeuerlenii, is formally described.     

Mesocyclops (Crustacea, Copepoda, Cyclopidae) in the South Pacific islands

Based mainly on recently collected material, we discuss the taxonomy and zoogeography of a (sub)tropical genus, Mesocyclops, in the South Pacific. A new species, Mesocyclops roberti sp. nov. is described from Fiji and the Wallis Islands. New data on the geographic distribution and morphology are reported for Mesocyclops medialis, Mesocyclops woutersi and Mesocyclops aspericornis. Phylogenetic reconstructions coding the intraspecifically variable characters by three different methods (unordered, unscaled and scaled coding) support close relationship of M. roberti with two Australian species (Mesocyclops brooksi and Mesocyclops notius). Both the “unordered” and “scaled” analyses show monophyly of a group composed of Australian (Mesocyclops australiensis, M. brooksi, M. notius, and Mesocyclops pubiventris) and South Pacific (M. medialis and M. roberti sp. nov.) taxa. None of the analyses supports a sister relationship of M. roberti with M. medialis (New Caledonia, Vanuatu), the only other species restricted to South Pacific, which suggests that Mesocyclops invaded the South Pacific from Australia at least twice. The sister relationship of the Australian-South Pacific clade remains unresolved, yet all reconstructions suggest a link with Asian Mesocyclops sp.     

Telomere sequence localization and karyotype evolution in higher plants

Data for chromosomal localization of theArabidopsis-type of telomeric sequence repeats (TTTAGGG)_n are compiled for 44 species belonging to 14 families of angiosperms, gymnosperms and bryophytes. For 23 species and seven families this is the first report. Species of all families, except theAlliaceae, revealed these sequences at their chromosome termini. This indicates thatArabidopsis-type telomeric repeats are highly conserved. It is inferred that they represent the basic telomere sequence of higher plant phyla. In theAlliaceae, a deviating sequence (and mechanism?) for the stabilization of chromosome termini has possibly evolved secondarily. Nine species revealed interstitial telomeric sequences in addition to the terminal ones, in three species (Vicia faba, Pinus elliottii, P. sylvestris) also at centromeric positions. Interstitial telomeric sequences may indicate karyotype reconstructions, in particular alterations of chromosome numbers by chromosome fusion — or inversions with one breakpoint within the terminal array of repeats. They may contribute to stabilization of chromosome breaks, especially centric fissions, and increase the frequency of meiotic and illegitimate recombination.     

Phylogeny and maternal donor of Kengyilia (Triticeae: Poaceae) based on chloroplast trnT–trnL sequences

The chloroplast DNA regions trnT–trnL was used to analyze to phylogenetic relationships and maternal donor of Kengyilia species and their closely related species. The Neighbor-Joining phylogenetic reconstructions partitioned the species into two reciprocally monophyletic groups. Kengyilia melanthera was related to species of Agropyron, whereas the other species were related to species of Pseudoroegneria and Roegneria. These results indicate that there have been at least two phylogenetically divergent maternal donors within Kengyilia, i.e. Agropyron (P genome) and Pseudoroegneria (St genome). In addition, the St genome of Kengyilia had several origins and diverse species of Pseudoroegneria might have taken part in the formation of polyploid species of Kengyilia.     

Coralline algae as depth indicators in the Sommières Basin (early Miocene,Southern France)

The aim of this work is to demonstrate the benefits of digital surface-quantification and species identification in the study of coralline algae. Within the well-constrained context of the Miocene Sommières Basin (Southern France), whose sedimentological and paleontological setting has been reconstructed by previous researches, the abundance of coralline algae is estimated through quantification of the area occupied by the different species, which are thoroughly described in order to make future taxonomic-revisions as easy as possible. Coralline distribution patterns are studied along a bathymetric gradient to assess the response of the major groups and of the different species to variations in water depth. Surface quantification highlights clear trends both at the species level and higher taxonomic ranks, showing that coralline algae can be a quite accurate instrument in paleoenvironmental reconstructions. Among the clearly identified species, Lithophyllum sp. A, Sporolithon sp. A, and Spongites fruticulosus prefer shallow-water; Mesophyllum roveretoi dominates at intermediate depth together with Lithothamnion ponzonense, while Phymatolithon sp. A occurs at the lower limit of the photic zone. The approach presented here can be applied to a variety of different contexts, providing a powerful instrument for the interpretation of coralline-algal associations.     

Differences in the response sensitivity of stomatal index to atmospheric CO2 among four genera of Cupressaceae conifers

Background and Aims

The inverse relationship between stomatal density (SD: number of stomata per mm² leaf area) and atmospheric concentration of CO₂ ([CO₂]) permits the use of plants as proxies of palaeo-atmospheric CO₂. Many stomatal reconstructions of palaeo-[CO₂] are based upon multiple fossil species. However, it is unclear how plants respond to [CO₂] across genus, family or ecotype in terms of SD or stomatal index (SI: ratio of stomata to epidermal cells). This study analysed the stomatal numbers of conifers from the ancient family Cupressaceae, in order to examine the nature of the SI–[CO₂] relationship, and potential implications for stomatal reconstructions of palaeo-[CO₂].

Methods

Stomatal frequency measurements were taken from historical herbarium specimens of Athrotaxis cupressoides, Tetraclinis articulata and four Callitris species, and live A. cupressoides grown under CO₂-enrichment (370, 470, 570 and 670 p.p.m. CO₂).

Key Results

T. articulata, C. columnaris and C. rhomboidea displayed significant reductions in SI with rising [CO₂]; by contrast, A. cupressoides, C. preissii and C. oblonga show no response in SI. However, A. cupressoides does reduce SI to increases in [CO₂] above current ambient (approx. 380 p.p.m. CO₂). This dataset suggests that a shared consistent SI–[CO₂] relationship is not apparent across the genus Callitris.

Conclusions

The present findings suggest that it is not possible to generalize how conifer species respond to fluctuations in [CO₂] based upon taxonomic relatedness or habitat. This apparent lack of a consistent response, in conjunction with high variability in SI, indicates that reconstructions of absolute palaeo-[CO₂] based at the genus level, or upon multiple species for discrete intervals of time are not as reliable as those based on a single or multiple temporally overlapping species.     

Molecular systematics and global phylogeography of angel sharks (genus Squatina)

Angel sharks of the genus Squatina represent a group comprising 22 extant benthic species inhabiting continental shelves and upper slopes. In the present study, a comprehensive phylogenetic reconstruction of 17 Squatina species based on two mitochondrial markers (COI and 16S rRNA) is provided. The phylogenetic reconstructions are used to test biogeographic patterns. In addition, a molecular clock analysis is conducted to estimate divergence times of the emerged clades. All analyses show Squatina to be monophyletic. Four geographic clades are recognized, of which the Europe–North Africa–Asia clade is probably a result of the Tethys Sea closure. A second sister group relationship emerged in the analyses, including S. californica (eastern North Pacific) and S. dumeril (western North Atlantic), probably related to the rise of the Panamanian isthmus. The molecular clock analysis show that both lineage divergences coincide with the estimated time of these two geological events.     

Molecular phylogeny of the harvestmen genus Sabacon (Arachnida: Opiliones: Dyspnoi) reveals multiple Eocene–Oligocene intercontinental dispersal events in the Holarctic

We investigated the phylogeny and biogeographic history of the Holarctic harvestmen genus Sabacon, which shows an intercontinental disjunct distribution and is presumed to be a relatively old taxon. Molecular phylogenetic relationships of Sabacon were estimated using multiple gene regions and Bayesian inference for a comprehensive Sabacon sample. Molecular clock analyses, using relaxed clock models implemented in BEAST, are applied to date divergence events. Biogeographic scenarios utilizing S-DIVA and Lagrange C++ are reconstructed over sets of Bayesian trees, allowing for the incorporation of phylogenetic uncertainty and quantification of alternative reconstructions over time. Four primary well-supported subclades are recovered within Sabacon: (1) restricted to western North America; (2) eastern North American S. mitchelli and sampled Japanese taxa; (3) a second western North American group and taxa from Nepal and China; and (4) eastern North American S. cavicolens with sampled European Sabacon species. Three of four regional faunas (wNA, eNA, East Asia) are thereby non-monophyletic, and three clades include intercontinental disjuncts. Molecular clock analyses and biogeographic reconstructions support nearly simultaneous intercontinental dispersal coincident with the Eocene–Oligocene transition. We hypothesize that biogeographic exchange in the mid-Tertiary is likely correlated with the onset of global cooling, allowing cryophilic Sabacon taxa to disperse within and among continents. Morphological variation supports the divergent genetic clades observed in Sabacon, and suggests that a taxonomic revision (e.g., splitting Sabacon into multiple genera) may be warranted.     

Congruence between comparative morphology and molecular phylogenies: Evolution of the male genital skeletal/muscular system in the subtribe Polyommatina (Lepidoptera,Lycaenidae)

The skeleton and musculature of male genitalia were studied in species of a model butterfly group (subtribe Polyommatina, Lycaenidae). In total, we analyzed 45 species of the tribe Polyommatini most of which were previously used in the molecular phylogenetic study (Talavera et al., 2013). The studied morphological characters were mapped on the molecular trees, which allowed us to reveal trends of morphological changes and to estimate the age of their origin. As a result, chronology of evolution of skeleton and musculature traits was established. It was shown that periods of slow morphological evolution alternated in the subtribe Polyommatina with those of a high rate of origin of new traits. For example, topography of the intravalvar muscles has not changed for 26 MY preserving their initial fan-shaped attachment. The evolution of intravalvar muscles started 10 MYA, proceeded slowly during the first 5 MY, and then accelerated during the last 5 MY resulting in the extensive splitting of the musculature in most monophyletic lineages. Mapping the morphological characters on the phylogeny demonstrated that the rates of skeleton and muscle evolution within the skeleton/musculature apparatus were different. In most cases the intravalvar musculature evolved much faster than the skeleton. The cladistic interpretation of states of morphological traits was found to be consistent with phylogenetic reconstructions based on analysis of multiple molecular markers. Moreover, morphological synapomorphies were found for the lineages Alpherakya + Glabroculus and Aricia + (Alpherakya + Glabroculus), which had low statistical support in molecular phylogenetic analysis. Additionally, in some cases molecular studies helped to reveal trends in the evolution of morphological traits. For example, the unpaired uncus and the compact juxta are not plesiomorphic for Cupidina as previously thought; instead, they were shown to have evolved secondarily within this subtribe.     

Molecular Evidence for Multiple Origins of the European Spined Loaches (Teleostei,Cobitidae)

We present a phylogenetic investigation of the Northern Clade, the major monophyletic clade within the freshwater fish family Cobitidae, one of the most prominent families of freshwater fishes found in Asian and European waters. Phylogenetic reconstructions based on the cytochrome b and RAG-1 genes show the genera Microcobitis, Sabanejewia, Koreocobitis and Kichulchoia as monophyletic groups. These reconstructions also show a Cobitis sensu lato and a Misgurnus sensu lato group. The Cobitis sensu lato group includes all species of Cobitis, Iksookimia, Niwaella and Kichulchoia, while the Misgurnus sensu lato group includes Misgurnus, Paramisgurnus and Koreocobitis. Although the monophyly of both the Cobitis sensu lato and Misgurnus sensu lato groups is supported, relationships within the groups are incongruent with current generic definitions. The absence of monophyly of most genera included in the Cobitis sensu lato group (Cobitis, Iksookimia and Niwaella) or their low genetic differentiation (Kichuchoia) supports their consideration as synonyms of Cobitis. Molecular phylogenies indicate that the Asian species of Misgurnus experienced a mitochondrial introgression from a lineage of Cobitis. We also find two nuclear haplotypes in the same Cobitis species from the Adriatic area that, in the absence of morphological differentiation, may indicate molecular introgression. Most lineages within the Northern Clade consist of species found in East Asia. However, some lineages also contain species from Europe and Asia Minor. The phylogenetic relationships presented here are consistent with previous studies suggesting an East Asian origin of the Northern Clade. According to the current distributions and phylogenetic relationships of the Misgurnus sensu lato and Cobitis clade lineages, particularly of M. fossilis and C. melanoleuca, the range expansion of East Asian species into Europe was most likely via Siberia into Northern and Central Europe. Phylogenetic analyses also show that the Cobitis sensu lato group consists of two clear subgroups (I and II), each presenting geographical differences. Subgroup I is distributed exclusively in East Asian drainages with an Eastern European offshoot (C. melanoleuca), whereas Subgroup II includes species widespread throughout Europe (including the Mediterranean), Asia Minor, the Black Sea and the Caucasus, with some lineages related to species restricted to East Asia.