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Phylogenetic analysis and identification of different serovars of Mycobacterium intracellulare at the molecular level.

Comparative 16S rRNA sequencing was used to infer the phylogenetic relationship among different serovars of the Mycobacterium avium-M. intracellulare complex as well as to define signature nucleotides characteristic for different serovars. In general, the groups defined by rRNA sequencing reflect the classification obtained with sensitin tests and pathogenicity examinations in chickens. Unique 16S rRNA sequence patterns could be defined for (1) M. avium, (2) M. intracellulare serovars 4, 5, 6, 8, 9, 10 and 11, (3) M. intracellulare serovars 12, 13, 14, 15, 17, 19 and 20, (4) M. intracellulare serovar 7 and (5) M. intracellulare serovar 18. Phylogenetically, groups 1 and 2 on one hand and groups 3, 4 and 5 on the other hand each share a common ancestor. M. paratuberculosis was indistinguishable from M. intracellulare serovars 4, 5, 6, 8, 9, 10 and 11 by this kind of analysis.

Base Sequence↗

Sequence determination and analysis of S-adenosyl-L-homocysteine hydrolase from yellow lupine (Lupinus luteus).

The coding sequences of two S-adenosyl-L-homocysteine hydrolases (SAHases) were identified in yellow lupine by screenig of a cDNA library. One of them, corresponding to the complete protein, was sequenced and compared with 52 other SAHase sequences. Phylogenetic analysis of these proteins identified three groups of the enzymes. Group A comprises only bacterial sequences. Group B is subdivided into two subgroups, one of which (B1) is formed by animal sequences. Subgroup B2 consist of two distinct clusters, B2a and B2b. Cluster B2b comprises all known plant sequences, including the yellow lupine enzyme, which are distinguished by a 50-residue insert. Group C is heterogeneous and contains SAHases from Archaea as well as a new class of animal enzymes, distinctly different from those in group B1.

Adenosylhomocysteinase↗

The Scaphopoda.

The Scaphopoda are marine infaunal carnivores that feed on foraminiferans and other microorganisms selected and manipulated by their unique feeding tentacles or captacula. Their tusk-like shell is open at both ends; the burrowing foot and captacula protrude anteriorly, while respiratory currents pass through the posterior opening. Although the scaphopods comprise one of the smallest molluskan classes in terms of species diversity, they have a worldwide distribution ranging from intertidal to depths in excess of 6000 m. Despite detailed monographic work from the late nineteenth and early twentieth centuries, however, the biology of scaphopods is today among the least understood of mollusks. To some extent, this is related to a significant departure from more typical molluscan organization inferred from studies of the larger classes. For example, the mantle cavity is elongate and restricted in space, and several associated organs are lost, including the osphradium and ctenidia; the latter is associated with the loss of auricles from the scaphopod heart. There is also little record of ontogeny in the adult shell, as the older portion is periodically decollated to maintain the posterior aperture for passage of inhalant and exhalant currents. This and other constraints on scaphopod diversification are reflected in the range limits of shell shape within the class. In contrast, the "Dentalium" egg has been a model system for experimental embryology, particularly in studies of cell lineage and early morphogenesis. Later larval development and most organogenesis is nonetheless poorly known, although recent studies have considerably enhanced our knowledge in this area. Global biogeographic patterns of scaphopod diversity have been studied only preliminarily. A general decrease in diversity with depth is broken by small diversity peaks at bathyal depths. There is also evidence for a marked latitudinal diversity gradient in the world's oceans, near equatorial in the Pacific but at approximately 20 degrees N in the Atlantic. Scaphopods have a wide diversity of ecto- and endo-symbiotic associations with other organisms, including commensal bacteria and ciliates, mutualistic anemones and corals, and parasitic algae and platyhelminths. Other documented associations include predation by naticid gastropods and ratfish, and the inhabitation of empty scaphopod shells by a variety of sipunculans and hermit crabs. Phylogeny within the class is still unresolved, although significant progress has been made recently in documenting morphological variation among families, genera, and species for application in a cladistic context. The evolutionary relationships of Scaphopoda within Mollusca are farther from resolution, with every conchiferan class a proposed sister group among modern analyses. Molecular avenues should provide significant progress in scaphopod phylogenetics, as indicated by recent comparative sequence analysis and gene expression patterns. Scaphopods comprise the most recent class of mollusks to appear in the fossil record, dating at least from the Mississippian Carboniferous (362.5 My). They appear from first-order occurrence data to have a substantially documented fossil record, with several sharp extinction and radiation events evident during their comparatively short geologic history. The unresolved position of the Scaphopoda within molluscan phylogeny, and their relatively limited range of morphological disparity but substantial derivation from other conchiferans, renders the scaphopods an enigmatic group. They represent a significant evolutionary avenue within the Mollusca, but one that is poorly examined. Nonetheless, comprehensive phylogenetic analysis and documentation of diversity within this small, monophyletic, class-level taxon, well-preserved in the fossil record, is imminently tractable, and presents a singular opportunity in the study of molluscan evolution.

Animals↗

Hox genes from the earthworm Perionyx excavatus.

The Hox genes of the oligochaete, Perionyx excavatus, were surveyed using PCR and phylogenetic analysis. We were able to identify 11 different Hox gene fragments. Comparative and phylogenetic analyses revealed that this oligochaete would have at least five Hox genes of the anterior group, including three copies of labial-type, five of the central group and one of the posterior group. This is the first report regarding sequence information and phylogenetic analysis of Hox genes in the earthworm.

Animals↗

Molecular data delineate four genera of "Thryothorus" wrens.

Wrens of the genus Thryothorus comprise over a third of the species diversity in the family Troglodytidae. In addition to this species diversity, these wrens vary in a number of behavioral characteristics, in particular in the presence and structure of vocal duets, which makes them an interesting target for comparative evolutionary ecological and behavioral study. However, no phylogenetic hypothesis for this group-which would provide a sound basis for comparative analysis-is currently available. While previous molecular phylogenetic work established conclusively that the type of this genus, Thryothorus ludovicianus (Latham), was not part of a monophyletic group with other Thryothorus, the exact limits of the genus could not be established due to limited taxon sampling. Here, we present molecular data from all but four currently recognized species of Thryothorus. These data confirm that Thryothorus is paraphyletic, and that the type T. ludovicianus does not form a monophyletic group with any other member of the genus. Based on analyses of our data, we resurrect two previously recognized wren genera, Pheugopedius and Thryophilus, and erect a new genus-Cantorchilus-to house the remaining ex-Thryothorus species. Our hypothesis of relationships will provide a firm basis for future behavioral and morphological analyses of these species.

Animals↗

Cloning and characterisation of the first drug-metabolising canine UDP-glucuronosyltransferase of the 2B subfamily.

Glucuronidation is a major route of clearance for a diverse set of both drug and endogenous substrates. The present study was undertaken to redress the lack of molecular information currently available on drug glucuronidation by the dog, a species widely used in metabolism studies by the pharmaceutical industry. A novel dog uridine diphosphate glucuronosyltransferase (UGT), designated UGT2B31 (GenBank Accession Number: AY135176), has been isolated from a dog cDNA library, expressed in V79 cells and characterised using various methods: (i) UGT2B31 sequence has been compared with mammalian UGT sequences using both sequence alignments and phylogenetic analysis; and (ii) the substrate specificity of UGT2B31 has been determined using functional analysis and compared with that obtained using UGT2B7 and dog liver microsomes. The following results were obtained: (i) sequence alignments between UGT2B31 and UGT2B15 gave the greatest degree of identity (76%); however, human UGT2B4, human UGT2B7, monkey UGT2B9 (all 75%), and rat UGT2B1 (73%) also gave a high degree of identity; (ii) phylogenetic analysis determined UGT2B31 to be most closely related to rat UGT2B1; (iii) UGT2B31 displayed a substrate specificity similar to human UGT2B7 and rat UGT2B1, catalysing the glucuronidation of phenols, opioids, and carboxylic acid-containing drugs; and (iv) UGT2B31 only formed morphine-3-glucuronide; however, kinetic analysis determined the K(m) of this reaction to be similar to that observed with UGT2B7 (both approximately 1300 microM). The results suggest that UGT2B31 plays a crucial role in drug detoxification by the dog and may be the canine equivalent of human UGT2B7.

Amino Acid Sequence↗

Immunogenetic evidence for the phylogenetic sister group relationship of dogs and bears (Mammalia, Carnivora: Canidae and Crsidae). a comparative determinant analysis of carnivoran albumin, c3 complement and immunoglobulin micro-chain.

Thirty-seven antigenic determinants were identified in the albumins, the immunoglobulin micro- and IgG(Fc) chains, and the C3 proteins of 51 carnivoran (sub)species from 31 genera, and in 12 noncarnivoran mammals. In addition to 19 determinants plesiomorphic for Carnivora as an order, 18 synapomorphic epitopes of carnivoran families revealed nine phylogenetic reaction groups: (1) canids, (2) ursids, (3) the racoon, (4) the Weddell seal, (5) the lesser panda, (6) the harbour seal, (7) mustelids, (8) viverrids and hyaenas, and (9) felids. These data identify Canoidea (Canidae, Ursidae, Phocidae, Procyonidae, Ailuridae, Mustelidae) and Feloidea (Viverridae, Hyaenidae, Felidae) as two fundamentally differentiated lineages of Carnivora, and confirm the inclusion of seals among the former. The Ursidae are the sister group of the Canidae. The antigenic determinants in the studied proteins do not subdivide the Canidae, Ursidae and Felidae into immunologically differentiated lineages.

Albumins↗

Isolation and phylogenetic analysis of bacteria with antimicrobial activities from the Mediterranean sponges Aplysina aerophoba and Aplysina cavernicola.

The aim of this study was to isolate bacteria with antimicrobial activities from the marine sponges Aplysina aerophoba and Aplysina cavernicola. The obtained 27 isolates could be subdivided into eight phylogenetically different clusters based on comparative sequence analysis of their 16S rDNA genes. The sponge isolates were affiliated with the low (Bacillus) and high G+C Gram-positive bacteria (Arthobacter, Micrococcus), as well as the alpha-Proteobacteria (unknown isolate) and gamma-Proteobacteria (Vibrio, Pseudoalteromonas). One novel Bacillus species was identified and two species were closely related to previously uncharacterized strains. Isolates with antimicrobial activity were numerically most abundant in the genera Pseudoalteromonas and the alpha-Proteobacteria. The sponge isolates show antimicrobial activities against Gram-positive and Gram-negative reference strains but not against the fungus Candida albicans. A general pattern was observed in that Gram-positive bacteria inhibited Gram-positive strains while Gram-negative bacteria inhibited Gram-negative isolates. Antimicrobial activities were also found against clinical isolates, i.e. multi-resistant Staphylococcus aureus and Staphylococcus epidermidis strains isolated from hospital patients. The high recovery of strains with antimicrobial activity suggests that marine sponges represent an ecological niche which harbors a hitherto largely uncharacterized microbial diversity and, concomitantly, a yet untapped metabolic potential.

Journal Article↗

Comparative genomic analysis of allatostatin-encoding (Ast) genes in Drosophila species and prediction of regulatory elements by phylogenetic footprinting.

The role of the YXFGLa family of allatostatin (AST) peptides in dipterans is not well-established. The recent completion of sequencing of genomes for multiple Drosophila species provides an opportunity to study the evolutionary variation of the allatostatins and to examine regulatory elements that control gene expression. We performed comparative analyses of Ast genes from seven Drosophila species (Drosophila melanogaster, Drosophila simulans, Drosophila ananassae, Drosophila yakuba, Drosophila pseudoobscura, Drosophila mojavensis, and Drosophila grimshawi) and used phylogenetic footprinting methods to identify conserved noncoding motifs, which are candidates for regulatory regions. The peptides encoded by the Ast precursor are nearly identical across species with the exception of AST-1, in which the leading residue may be either methionine or valine. Phylogenetic footprinting predicts as few as 3, to as many as 17 potential regulatory sites depending on the parameters used during analysis. These include a Hunchback motif approximately 1.2 kb upstream of the open reading frame (ORF), overlapping motifs for two Broad-complex isoforms in the first intron, and a CF2-II motif located in the 3'-UTR. Understanding the regulatory elements involved in Ast expression may provide insight into the function of this neuropeptide family.

Amino Acid Sequence↗

High guanine-cytosine content is not an adaptation to high temperature: a comparative analysis amongst prokaryotes.

The causes of the variation between genomes in their guanine (G) and cytosine (C) content is one of the central issues in evolutionary genomics. The thermal adaptation hypothesis conjectures that, as G:C pairs in DNA are more thermally stable than adenonine:thymine pairs, high GC content may he a selective response to high temperature. A compilation of data on genomic GC content and optimal growth temperature for numerous prokaryotes failed to demonstrate the predicted correlation. By contrast, the GC content of Structural RNAs is higher at high temperatures. The issue that we address here is whether more freely evolving sites in exons (i.e. codonic third positions) evolve in the same manner as genomic DNA as a whole, Showing no correlated response, or like structural RNAs showing a strong correlation. The latter pattern would provide strong support for the thermal adaptation hypothesis, as the variation in GC content between orthologous genes is typically most profoundly seen at codon third sites (GC3). Simple analysis of completely sequenced prokaryotic genomes shows that GC3, but not genomic GC, is higher on average in thermophilic species. This demonstrates, if nothing else, that the results from the two measures cannot be presumed to be the same. A proper analysis, however, requires phylogenetic control. Here, therefore, we report the results of a comparative analysis of GC composition and optimal growth temperature for over 100 prokaryotes. Comparative analysis fails to show, in either Archea or Eubacteria, any hint of connection between optimal growth temperature and GC content in the genome as a whole, in protein-coding regions or, more crucially at GC. Conversely, comparable analysis confirms that GC content of structural RNA is strongly correlated with optimal temperature. Against the expectations of the thermal adaptation hypothesis, within prokaryotes GC content in protein-coding genies, even at relatively freely evolving sites, cannot be considered an adaptation to the thermal environment.

Adaptation, Physiological↗

On the systematic status of the late Neogene hominoids from Yunnan Province, China.

Late Miocene and Pliocene hominoids from Yunnan Province in southern China have been recovered from four sites or site complexes: Xiaolongtan, Yangyi, Shihuiba and Yuanmou. Of these, Shihuiba and Yuanmou are among the most prolific fossil hominoid sites in Eurasia, and they have yielded important evidence that is critical for documenting the evolutionary history, biogeography and paleobiology of later Neogene hominids. The aim of this paper is to clarify their taxonomy and nomenclature, and to present a preliminary synthesis of their phylogenetic relationships and biogeography. The morphological pattern and degree of variation observed in the fossil samples is consistent with there being a single, sexually dimorphic species represented at each site. Provisionally, we consider the Shihuiba, Xiaolongtan and Yuanmou samples to belong to two separate species within a single genus. The valid names for these species are Lufengpithecus lufengensis (from Shihuiba) and L. keiyuanensis (from Xiaolongtan and Yuanmou). From a phylogenetic perspective, the currently available evidence suggests that Lufengpithecus is either a primitive hominid that represents the sister taxon of the Ponginae+Homininae or a primitive sister taxon to the Ponginae. We tend to favor the second alternative, but acknowledge that a more comprehensive comparative analysis is needed to substantiate the phylogenetic and taxonomic affinities of Lufengpithecus. Importantly, the Yunnan fossil apes provide a unique temporal perspective on the evolutionary history of hominoids. Their continued occurrence during the late Miocene and Pliocene (approximately 8-2Ma), when hominoids became extinct throughout the rest of Eurasia, suggests that southern China (and presumably southeast Asia in general) was an important refugium for hominoids, including the ancestors of the orang-utans and gibbons. The uplift of the Tibetan plateau and its impact on regional climatic conditions may have been an important contributing factor in isolating the hominoids geographically and ecologically. We speculate that changed climatic condition in the mid-Pliocene, and possibly the arrival of Homo soon after, may have precipitated the regional extinction of large hominoids in southern China and in mainland southeast Asia.

Animals↗

A phylogenetic analysis of the correlates of sleep in birds.

Quantitative comparative studies of sleep have focused exclusively on mammals. Such studies have repeatedly found strong relationships between the time spent in various sleep states and constitutive variables related to morphology, physiology, and life history. These studies influenced the development of several prominent hypotheses for the functions of sleep, but the applicability of these patterns and hypotheses to non-mammalian taxa is unclear. Here, we present the first quantitative analysis of sleep in a non-mammalian taxon (birds), focusing on the daily amount of time spent in slow-wave sleep (SWS) and rapid-eye movement (REM) sleep as determined by electrophysiological methods. We examined the relationships between constitutive and sleep variables in 23 avian species following earlier studies in mammals, but also considered an index of exposure to predators while asleep and controlled for shared evolutionary history among taxa. Overall, our results were very different from those obtained for mammals. Most remarkably, the relationships between both SWS time and REM sleep time and all constitutive variables were very weak and markedly non-significant, even though we had adequate power to detect correlations typical of the mammalian data. Only an index of exposure to predation during sleep was significantly related to sleep time, which is the only result common to both birds and mammals. Our results suggest that further insight into the function(s) of sleep across the animal kingdom may require an expansion of sleep research beyond the current mammalian paradigm.

Animals↗

Gene family evolution and homology: genomics meets phylogenetics.

With the advent of high-throughput DNA sequencing and whole-genome analysis, it has become clear that the coding portions of the genome are organized hierarchically in gene families and superfamilies. Because the hierarchy of genes, like that of living organisms, reflects an ancient and continuing process of gene duplication and divergence, many of the conceptual and analytical tools used in phylogenetic systematics can and should be used in comparative genomics. Phylogenetic principles and techniques for assessing homology, inferring relationships among genes, and reconstructing evolutionary events provide a powerful way to interpret the ever increasing body of sequence data. In this review, we outline the application of phylogenetic approaches to comparative genomics, beginning with the inference of phylogeny and the assessment of gene orthology and paralogy. We also show how the phylogenetic approach makes possible novel kinds of comparative analysis, including detection of domain shuffling and lateral gene transfer, reconstruction of the evolutionary diversification of gene families, tracing of evolutionary change in protein function at the amino acid level, and prediction of structure-function relationships. A marriage of the principles of phylogenetic systematics with the copious data generated by genomics promises unprecedented insights into the nature of biological organization and the historical processes that created it.

Animals↗

Evaluation of using a short region of the recA gene for rapid and sensitive speciation of dominant bifidobacteria in the human large intestine.

The feasibility of intragenerically characterizing bifidobacteria by a comparison of a short region within the recA gene was tested. An approximately 300 bp fragment of the recA gene was PCR-amplified from six species from the genus Bifidobacterium using primers directed to two universally conserved regions of the recA gene. A phylogenetic analysis of the sequenced recA products compared favorably to classification based on the 16S rRNA sequences of the species tested. To apply this rapid methodology to unknown human intestinal bifidobacteria, 46 isolates were randomly chosen from the feces of four subjects and initially characterized by RFLP analysis of a PCR-amplified region of their 16S RNA genes. From a representative of the dominant RFLP family in each of the subjects, the recA segment was PCR-amplified, sequenced and phylogenetically analyzed. All four isolates were found to be related to one another and to B. longum and B. infantis. These results illustrate that the recA gene may be useful for intrageneric phylogenetic analysis as well as for the identification of unknown fecal bifidobacteria.

Adolescent↗

The marsupial placenta: a phylogenetic analysis.

The structure, physiology, and endocrinology of the yolk sac placenta of different marsupial groups is compared and phylogenetically analyzed to provide information on placental characters in the marsupial stem species. We conclude that the marsupial stem species possessed a functional yolk sac placenta. Histotrophic nutrition by uterine secretion decreased during late pregnancy and at least half of the yolk sac was vascularized at the time of shell coat rupture. Due to yolk sac fusion, the larger part of the avascular, bilaminar yolk sac could not serve as a placenta at late gestation in the polyovular marsupial stem species. The bilaminar yolk sac gained a relatively greater importance for nutrition in monovular australidelphians. In macropodids a greater proportion of the yolk sac remained bilaminar at the time of shell coat rupture than in the stem species. Another derived feature of macropodids is the sustained plasma progesterone synthesis that is in turn responsible for an extended secretory phase of the uterus and a lengthened gestation. The placenta of the marsupial stem species was probably capable of metabolising histo- and hemotrophes. Recognition of pregnancy during early stages of development is a derived character of macropodids that we suggest did not occur in the marsupial stem species. However, birth and birth behaviour were apparently induced by prostaglandins in the marsupial stem species. Although the yolk sac formed the definitive placenta, it is likely that the allantois provided a supplementary placental function in the marsupial stem species, but that the role of the allantois became progressively less important during the evolution of marsupial placentation.

Animals↗

Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research.

Frequent outbreaks of highly pathogenic avian influenza and the increasing data available for comparative analysis require a central database specialized in influenza viruses (IVs). We have established the Influenza Virus Database (IVDB) to integrate information and create an analysis platform for genetic, genomic, and phylogenetic studies of the virus. IVDB hosts complete genome sequences of influenza A virus generated by Beijing Institute of Genomics (BIG) and curates all other published IV sequences after expert annotation. Our Q-Filter system classifies and ranks all nucleotide sequences into seven categories according to sequence content and integrity. IVDB provides a series of tools and viewers for comparative analysis of the viral genomes, genes, genetic polymorphisms and phylogenetic relationships. A search system has been developed for users to retrieve a combination of different data types by setting search options. To facilitate analysis of global viral transmission and evolution, the IV Sequence Distribution Tool (IVDT) has been developed to display the worldwide geographic distribution of chosen viral genotypes and to couple genomic data with epidemiological data. The BLAST, multiple sequence alignment and phylogenetic analysis tools were integrated for online data analysis. Furthermore, IVDB offers instant access to pre-computed alignments and polymorphisms of IV genes and proteins, and presents the results as SNP distribution plots and minor allele distributions. IVDB is publicly available at http://influenza.genomics.org.cn.

Databases, Genetic↗

[Anatomo-histologic findings clarifying the phylogenetic relationships between salmonoid fish (Salmonoidei)].

The comparative anatomo-histological analysis of the medial gut of Osmeridae and Plecoglossidae after Iwai (1962) has revealed a great similarity in the structure of this entosomatic organ suggesting their phylogenetically close nature. On the contrary, the fine structure of the medial gut in these two families substantially differs from the structure of this organ in Salmonoidee. Pronounced distinctions were found between the structure of the medial gut of smelts and that of the pike (Esox lucius Linné). The complicatedly differentiated medial gut of the pike is so different from the primitive gut of modern smelts that the hypothesis (Starks, 1930; Berg, 1940) on the origin of Ecosoidei from ancient Osmeridae does not seem probable. The data obtained by the anatomo-histological analysis in combination with data of other sciences should be taken into consideration when creating the natural system of Salmonoidei, since they contribute to more exact character of their phylogenetic relations.

Animals↗