PCOGR: phylogenetic COG ranking as an online tool to judge the specificity of COGs with respect to freely definable groups of organisms

Adaptive radiation in Lesser Antillean lizards: molecular phylogenetics and species recognition in the Lesser Antillean dwarf gecko complex, Sphaerodactylus fantasticus

The time associated with speciation varies dramatically among lower vertebrates. The nature and timing of divergence is investigated in the fantastic dwarf gecko Sphaerodactylus fantasticus complex, a nominal species that occurs on the central Lesser Antillean island of Guadeloupe and adjacent islands and islets. This is compared to the divergence in the sympatric anole clade from the Anolis bimaculatus group. A molecular phylogenetic analysis of numerous gecko populations from across these islands, based on three mitochondrial DNA genes, reveals several monophyletic groups occupying distinct geographical areas, these being Les Saintes, western Basse Terre plus Dominica, eastern Basse Terre, Grand Terre, and the northern and eastern islands (Montserrat, Marie Galante, Petite Terre, Desirade). Although part of the same nominal species, the molecular divergence within this species complex is extraordinarily high (27% patristic distance between the most divergent lineages) and is compatible with this group occupying the region long before the origin of the younger island arc. Tests show that several quantitative morphological traits are correlated with the phylogeny, but in general the lineages are not uniquely defined by these traits. The dwarf geckos show notably less nominal species-level adaptive radiation than that found in the sympatric southern clade of Anolis bimculatus, although both appear to have occupied the region for a broadly similar period of time. Nevertheless, the dwarf gecko populations on Les Saintes islets are the most morphologically distinct and are recognized as a full species (Sphaerodactylus phyzacinus), as are anoles on Les Saintes (Anolis terraealtae).

Bird hosts, blood parasites and their vectors--associations uncovered by molecular analyses of blackfly blood meals

The level of host specificity of blood-sucking invertebrates may have both ecological and evolutionary implications for the parasites they are transmitting. We used blood meals from wild-caught blackflies for molecular identification of parasites and hosts to examine patterns of host specificity and how these may affect the transmission of avian blood parasites of the genus Leucocytozoon. We found that five different species of ornithophilic blackflies preferred different species of birds when taking their blood meals. Of the blackflies that contained avian blood meals, 62% were infected with Leucocytozoon parasites, consisting of 15 different parasite lineages. For the blackfly species, there was a significant association between the host width (measured as the genetic differentiation between the used hosts) and the genetic similarity of the parasites in their blood meals. The absence of similar parasite in blood meals from blackflies with different host preferences is interpreted as a result of the vector-host associations. The observed associations between blackfly species and host species are therefore likely to hinder parasites to be transmitted between different host-groups, resulting in ecologically driven associations between certain parasite lineages and hosts species.

Comparison of HIV-1 pol and env sequences of blood, CSF, brain and spleen isolates collected ante-mortem and post-mortem

OBJECTIVES

HIV-1 infects the central nervous system (CNS) early in the course of infection. However, it is not known to what extent the virus evolves independently within the CNS and whether the HIV-RNA in cerebrospinal fluid (CSF) reflects the viral population replicating within the brain parenchyma or the systemic infection. The aim of this study was to investigate HIV-1 evolution in the CNS and the origin of HIV-1 in CSF.

MATERIALS AND METHODS

Longitudinally derived paired blood and CSF samples and post-mortem samples from CSF, brain and spleen were collected over a period of up to 63 months from three HIV-1 infected men receiving antiretroviral treatment and presenting with symptoms of AIDS dementia complex (ADC).

RESULTS

Phylogenetic analyses of HIV-1 V3, reverse transcriptase (RT) and protease sequences from patient isolates suggest compartmentalization with distinct viral strains in blood, CSF and brain. We found a different pattern of RT and accessory protease mutations in the systemic infection compared to the CNS.

CONCLUSIONS

We conclude that HIV-1 may to some extent evolve independently in the CNS and the viral population in CSF mainly reflects the infection in the brain parenchyma in patients with ADC. This is of importance in understanding HIV pathogenesis and can have implications on treatment of HIV-1 patients.

Epstein-Barr virus genotypes in multiple sclerosis

BACKGROUND

Multiple sclerosis (MS) is associated with Epstein-Barr virus (EBV) infection, but the relationship between the virus and the disease is not clear. As many different types of EBV exist, it is possible that MS is caused by one particular type of EBV. Objectives - The aim of this study was to determine whether MS is associated with a particular genotype of EBV.

MATERIALS AND METHODS

We collected blood from MS patients and controls, amplified and sequenced the latent membrane protein-1 (LMP-1) gene, and compared the groups.

RESULTS

We found a variety of LMP-1 sequences in both MS and controls, with no significant differences between the groups. Conclusion - We conclude that MS is not associated with a particular genotype of EBV.

Human parvovirus PARV4 in clotting factor VIII concentrates

BACKGROUND AND OBJECTIVES

Parvoviruses are small non-enveloped DNA viruses, relatively resistant to virus inactivation procedures. The recently identified human parvovirus PARV4, including a related genotype 2 virus (also termed PARV5), has been found to be a contaminant of pooled plasma used in the manufacture of plasma-derived products. This report describes an investigation to determine whether PARV4 is present in clotting factor concentrates.

MATERIALS AND METHODS

Factor VIII concentrates manufactured in the past 30-35 years were screened for PARV4 and human parvovirus B19 (B19V) sequences. Viral loads in products testing positive for PARV4 were quantified using a consensus TaqMan assay designed to a highly conserved region. DNA sequence analysis was performed to confirm the genotypes present.

RESULTS

From a total of 175 lots of factor VIII concentrate, 28 of these contained PARV4 sequences, and in two lots both genotypes 1 and 2 were found to be present. The highest viral loads observed exceeded 10(5) copies per ml. The majority of factor VIII concentrates testing positive for PARV4 were manufactured in the 1970s and 1980s. Human B19V was also a frequent contaminant of these products.

CONCLUSIONS

PARV4 was detected in 16% of factor VIII concentrates, particularly in older batches from the 1970s and 1980s. The significance in terms of the viral safety and potential transmission to recipients of these products is not yet known.

Bread, beer and wine: Saccharomyces cerevisiae diversity reflects human history

Fermented beverages and foods have played a significant role in most societies worldwide for millennia. To better understand how the yeast species Saccharomyces cerevisiae, the main fermenting agent, evolved along this historical and expansion process, we analysed the genetic diversity among 651 strains from 56 different geographical origins, worldwide. Their genotyping at 12 microsatellite loci revealed 575 distinct genotypes organized in subgroups of yeast types, i.e. bread, beer, wine, sake. Some of these groups presented unexpected relatedness: Bread strains displayed a combination of alleles intermediate between beer and wine strains, and strains used for rice wine and sake were most closely related to beer and bread strains. However, up to 28% of genetic diversity between these technological groups was associated with geographical differences which suggests local domestications. Focusing on wine yeasts, a group of Lebanese strains were basal in an F(ST) tree, suggesting a Mesopotamia-based origin of most wine strains. In Europe, migration of wine strains occurred through the Danube Valley, and around the Mediterranean Sea. An approximate Bayesian computation approach suggested a postglacial divergence (most probable period 10,000-12,000 bp). As our results suggest intimate association between man and wine yeast across centuries, we hypothesize that yeast followed man and vine migrations as a commensal member of grapevine flora.

Isolation and partial characterization of pigment-like antibiotics produced by a new strain of Streptosporangium isolated from an Algerian soil

AIMS

Identification of a new actinomycete strain Sg3, belonging to the genus Streptosporangium and partial characterization of the produced antibacterial activities.

METHODS AND RESULTS

The strain Sg3 was isolated from an Algerian Saharan soil and identified by morphological, chemotaxonomic and phylogenetic analyses to the genus Streptosporangium. The comparison of its physiological characteristics with those of known species of Streptosporangium showed significant differences with the nearest species Streptosporangium carneum. Analysis of the 16S rDNA sequence of strain Sg3 showed a similarity level ranging between 97% and 98.8% within Streptosporangium species, with S. carneum the most closely related. Strain Sg3 showed a red coloured antibacterial activity against gram-positive bacteria on several culture media. The purification of the red pigment by chromatographic methods led to the isolation of three active products. The (1)H nuclear magnetic resonance (NMR), mass, infrared (IR) and ultraviolet-visible (UV-VIS) data of these molecules strongly suggested that they belonged to the quinone-anthracycline group with three or more rings.

CONCLUSIONS

Strain Sg3 represents a distinct phyletic line suggesting a new genomic species. It produces antibacterial activities identified as quinone-anthracycline aromatics.

SIGNIFICANCE AND IMPACT OF THE STUDY

The quinone-anthracycline antibiotics are known for their antimicrobial and antineoplastic activities and are used in chemotherapy for the treatment of many cancer diseases. The present work constitutes the first stage of a whole series of studies to be realized on these antibiotics before arriving at a possible application.

High intraspecific recombination rate in a native population of Candidatus pelagibacter ubique (SAR11)

Recombination is an important process in microbial evolution. Rates of recombination with extracellular DNA matter because models of microbial population structure are profoundly influenced by the degree to which recombination is occurring within the population. Low rates of recombination may be sufficient to ensure the lateral propagation of genes that have a high selective advantage without disrupting the clonal pattern of inheritance for other genes. High rates of recombination potentially can obscure clonal patterns, leading to linkage equilibrium, and give microbial populations a population genetic structure more akin to sexually interbreeding eukaryotic populations. We examined eight loci from nine strains of candidatus Pelagibacter ubique (SAR11), isolated from a single 2L niskin sample of natural seawater, for evidence of genetic recombination between strains. The Shimodaira-Hasegawa test revealed significant phylogenetic incongruence in seven of the genes, indicating that frequent recombination obscures phylogenetic signals from the linear inheritance of genes in this population. Statistical evidence for intragenic recombination was found for six loci. An informative sites matrix showed extensive evidence for a widespread breakdown of linkage disequilibrium. Although the mechanisms of genetic transfer in native SAR11 populations are unknown, we measured recombination rates, rho, that are much higher than point mutation rates, theta, as a source of genetic diversity in this clade. The eukaryotic model of species sharing a common pool of alleles is more apt for this SAR11 population than a strictly clonal model of inheritance in which allelic diversity is controlled by periodic selection.

Altered expression patterns of TCP and MYB genes relating to the floral developmental transition from initial zygomorphy to actinomorphy in Bournea (Gesneriaceae)

The shift from zygomorphy to actinomorphy has been intensively studied in molecular genetic model organisms. However, it is still a key challenge to explain the great morphological diversity of derived actinomorphy in angiosperms, since different underlying mechanisms may be responsible for similar external morphologies. Bournea (Gesneriaceae) is of particular interest in addressing this question, as it is a representative of primarily derived actinomorphy characteristic of a unique developmental transition from zygomorphy to actinomorphic flowers at anthesis. Using RNA in situ hybridization, the expression patterns were investigated of three different Bournea orthologues of TCP and MYB genes that have been shown to control floral symmetry in model species. Here, it is shown that the initial zygomorphic pattern in Bournea is likely a residual zygomorphy resulting from conserved expression of the adaxial (dorsal) identity gene BlCYC1. As a key novel event, the late downregulation of BlCYC1 and BlRAD and the correlative changes in the late specific expression of the abaxial (ventral) identity gene BlDIV should be responsible for the origin of the derived actinomorphy in Bournea. These results further indicate that there might be diverse pathways in the origin and evolution of derived actinomorphy through modifications of pre-existing zygomorphic developmental programs under dynamics of regulatory networks.

Community structures of actively growing bacteria shift along a north-south transect in the western North Pacific

Bacterial community structures and their activities in the ocean are tightly coupled with organic matter fluxes and thus control ocean biogeochemical cycles. Bromodeoxyuridine (BrdU), halogenated nucleoside and thymidine analogue, has been recently used to monitor actively growing bacteria (AGB) in natural environments. We labelled DNA of proliferating cells in seawater bacterial assemblages with BrdU and determined community structures of the bacteria that were possible key species in mediating biochemical reactions in the ocean. Surface seawater samples were collected along a north-south transect in the North Pacific in October 2003 and subjected to BrdU magnetic beads immunocapture and PCR-DGGE (BUMP-DGGE) analysis. Change of BrdU-incorporated community structures reflected the change of water masses along a north-south transect from subarctic to subtropical gyres in the North Pacific. We identified 25 bands referred to AGB as BrdU-incorporated phylotypes, belonging to Alphaproteobacteria (5 bands), Betaproteobacteria (1 band), Gammaproteobacteria (4 bands), Cytophaga-Flavobacterium-Bacteroides (CFB) group bacteria (5 bands), Gram-positive bacteria (6 bands), and Cyanobacteria (4 bands). BrdU-incorporated phylotypes belonging to Vibrionales, Alteromonadales and Gram-positive bacteria appeared only at sampling stations in a subtropical gyre, while those belonging to Roseobacter-related bacteria and CFB group bacteria appeared at the stations in both subarctic and subtropical gyres. Our result revealed phylogenetic affiliation of AGB and their dynamic change along with north-south environmental gradients in open oceans. Different species of AGB utilize different amount and kinds of substrates, which can affect the change of organic matter fluxes along transect.

Characterization of true-branching cyanobacteria from geothermal sites and hot springs of Costa Rica

Costa Rica is at the centre of the Mesoamerican biodiversity hotspot. Little is known about cyanobacteria from this region so far. Here, four isolates of the order Stigonematales (section V) were characterized in a polyphasic approach. All strains were isolated from geothermal sites and hot springs of Costa Rica. However, one of them, identified as Westiellopsis sp. Ar73, did not grow at more than 40 degrees C. Based on its identical 16S rRNA to several previously isolated Westiellopsis sp. and Fischerella muscicola strains, a ubiquitous distribution throughout tropical and subtropical regions can be implied. In contrast, the isolates MV9, MV11 and RV14 grew well up to 50-55 degrees C. Based on morphologic, ultrastructural, molecular and physiologic data, MV9, MV11 and RV14 were identified to belong to the genus Fischerella. Two distinct intergenic transcribed spacer (ITS) types, with or without tRNA genes, were detected for all Stigonematales analysed here, indicating ITS polymorphism as a characteristic feature of heterocystous cyanobacteria. In phylogenetic trees, these Fischerella spp. formed a new and distinct clade within the wider lineage of thermophilic Fischerella (Mastigocladus cf. laminosus), which might represent a geographic lineage. Thus, geographic isolation may be an underestimated aspect of microbial evolution. The strains presented here are suitable as new models to study this group of cyanobacteria.

Clonal diversity and genealogical relationships of gibel carp in four hatcheries

To conserve and utilize the genetic pool of gynogenetic gibel carp (Carassius auratus gibelio), the Fangzheng and Qihe stock hatcheries have been established in China. However, little information is available on the amount of genetic variation within and between these populations. In this study, clonal diversity in 101 fish from these two stock hatcheries and 35 fish from two other hatcheries in Wuhan and Pengze respectively was analysed for variation in serum transferrin. Thirteen clones were found in Fangzheng and Qihe, of which 12 were novel. Six clones were specific to Fangzheng and three specific to Qihe, whereas four were shared among the Fangzheng and Qihe fish. To obtain more knowledge on genetic diversity and genealogical relationships within gibel carp, the complete mitochondrial DNA (mtDNA) control region (approximately 920 bp) was sequenced in 64 individuals representing all 14 clones identified in the four hatcheries. Differences in the mtDNA sequences varied remarkably among hatcheries, with the Fangzheng and Qihe lines demonstrating high diversity and Wuhan and Pengze showing no variation. The Fangzheng and Qihe lines might represent two distinct matrilineal sources. One of the Qihe samples carried the haplotype shared by a most widely cultivated Fangzheng clone, indicating that a Fangzheng clone escaped from cultivated ponds and moved into the Qihe hatchery. Four Fangzheng samples clustered within the lineage formed mainly by Qihe samples, most likely reflecting historical gene flow from Qihe to Fangzheng. It is suggested that clones in Wuhan originated from Fangzheng, consistent with their introduction history, supporting the hypothesis that gibel carp in Pengze were domesticated from individuals in the Fangzheng hatchery.

Proteases from Bacillus: a new insight into the mechanism of action for rhizobacterial suppression of nematode populations

AIMS

The aim of this study was to investigate the role of proteases in Bacillus spp. of rhizobacteria in suppressing nematode populations and to understand their mechanism of action.

METHODS AND RESULTS

Rhizobacteria with nematicidal activity were isolated from soil samples of five root knot nematode-infested farms. Among these strains, nematotoxicities of Bacillus strains were intensively analysed. Further assays of nematicidal toxins from Bacillus sp. strain RH219 indicated an extracellular cuticle-degrading protease Apr219 was an important pathogenic factor. The Apr219 shared high similarity with previously reported cuticle-degrading proteases from Brevibacillus laterosporus strain G4 and Bacillus sp. B16 (Bacillus nematocida). The cuticle-degrading protease genes were also amplified from four other nematicidal Bacillus strains isolated from the rhizosphere. In addition to Apr219, a neutral protease Npr219 from Bacillus sp. RH219 was also investigated for activity against nematodes.

CONCLUSIONS

The wide distribution of cuticle-degrading proteases in Bacillus strains with nematicidal activity suggested that these enzymes likely play an important role in bacteria-nematode-plant-environment interactions and that they may serve as important nematicidal factors in balancing nematode populations in the soil.

SIGNIFICANCE AND IMPACT OF THE STUDY

Increased understanding of the mechanism of action of Bacillus spp. against nematodes could potentially enhance the value of these species as effective nematicidal agents and develop new biological control strategies.

Japanese case of hepatitis B virus genotypes C/D hybrid

Hepatitis B virus (HBV) is classified into eight genotypes based on complete genome sequence. Each genotype is related to geographic distribution and race. In Japan, most of the genotypes are B and C. In the present study, we report the first Japanese strain of HBV having a recombination between genotypes C and D. A 30-year-old woman was admitted to Kobe Medical Center because of liver dysfunction. She was diagnosed with spontaneous reactivation of chronic hepatitis B. She had no history of blood transfusion and her parents were negative for HBV. The phylogenetic analysis based on the complete genome sequences revealed that this strain was classified into genotype C, whereas the analysis based on Sgene sequence showed that this strain was genotype D. By using a SimPlot program, this strain was confirmed as a recombinant strain between genotypes C and D. Compared with previous recombinant strains in China, the breakpoint was the same and the difference was only 0.8% of the complete genome sequence. It was unclear whether or not this strain was transmitted from China, but the recombinant strains and intergenotypes of HBV have already existed in Japan.

Sperm motility in Mytilus edulis in relation to mitochondrial DNA polymorphisms: implications for the evolution of doubly uniparental inheritance in bivalves

Bivalves of the families Mytilidae, Unionidae, and Veneridae have an unusual mode of mitochondrial DNA (mtDNA) transmission called doubly uniparental inheritance (DUI). A characteristic feature of DUI is the presence of two gender-associated mtDNA genomes that are transmitted through males (M-type mtDNA) and females (F-type mtDNA), respectively. Female mussels are predominantly homoplasmic with only the F-type expressed in both somatic and gonadal tissue; males are heteroplasmic with the M-type expressed in the gonad and F-type in somatic tissue for the most part. An unusual evolutionary feature of this system is that an mt genome with F-coding sequences occasionally invades the male route of inheritance (i.e., a "role reversal" event), and is thereafter transmitted as a new M-type. Phylogenetic studies have demonstrated that the new or "recently masculinized" M-types may eventually replace the older or "standard" M-types over time. To investigate whether this replacement process could be due to an advantage in sperm swimming behavior, we measured differences in motility parameters and found that sperm with the recently masculinized M-type had significantly faster curvilinear velocity and average path velocity when compared to sperm with standard M-type. This increase in sperm swimming speed could explain the multiple evolutionary replacements of standard M-types by masculinized M-types that have been hypothesized for the mytilid lineage. However, our observations do not support the hypothesis that DUI originated because it permits the evolution of mitochondrial adaptations specific to sperm performance, otherwise, the evolutionarily older, standard M genome should perform better.

Heterogeneous genomic differentiation between walking-stick ecotypes: "isolation by adaptation" and multiple roles for divergent selection

Genetic differentiation can be highly variable across the genome. For example, loci under divergent selection and those tightly linked to them may exhibit elevated differentiation compared to neutral regions. These represent "outlier loci" whose differentiation exceeds neutral expectations. Adaptive divergence can also increase genome-wide differentiation by promoting general barriers to neutral gene flow, thereby facilitating genomic divergence via genetic drift. This latter process can yield a positive correlation between adaptive phenotypic divergence and neutral genetic differentiation (described here as "isolation-by-adaptation"). Here, we examine both these processes by combining an AFLP genome scan of two host plant ecotypes of Timema cristinae walking-sticks with existing data on adaptive phenotypic divergence and ecological speciation in these insects. We found that about 8% of loci are outliers in multiple population comparisons. Replicated comparisons between population-pairs using the same versus different host species revealed that 1-2% of loci are subject to host-related selection specifically. Locus-specific analyses revealed that up to 10% of putatively neutral (nonoutlier) AFLP loci exhibit significant isolation-by-adaptation. Our results suggest that selection may affect differentiation directly, via linkage, or by facilitating genetic drift. They thus illustrate the varied and sometimes nonintuitive contributions of selection to heterogeneous genomic differentiation.

Detection and molecular characterization of calf diarrhoea bovine coronaviruses circulating in South Korea during 2004-2005

Although the widespread occurrence of calf diarrhoea (CD) bovine coronavirus (BCoV) infections have been reported in most cattle producing countries, only the genetic differences in the BCoVs from American and Canadian isolates and/or strains have been identified and compared. Hence, it is unclear if the BCoVs circulating in the other countries have distinct genetic characteristics. The aim of this study was to determine the prevalence and genetic diversity of CD BCoVs based on the deduced amino acid (aa) sequences of the spike (S) and haemagglutinin/esterase (HE) proteins in South Korea. RT-PCR and nested PCR using the primer pairs specific to the nucleocapsid gene, BCoVs detected the BCoVs in 56 (15.6%) of 359 diarrhoeic faecal samples. Phylogenetic analysis of the entire S gene indicated that 10 Korean CD BCoV strains clustered with other Korean BCoV strains with different clinical forms but were different from the American and Canadian BCoV strains. Moreover, the phylogenetic data of the aa sequences of the HE gene revealed all the Korean CD strains to be distinct from the other Korean BCoV strains with different clinical forms. These results suggest that the Korean BCoVs cause endemic infections in diarrhoeic calves in Jeonnam province and have taken a different evolutionary pathway from the BCoVs in other countries. Moreover, the different BCoV strains are circulating in the different clinical forms in South Korea. These results also suggest that vaccines against the BCoVs can be developed with each Korean BCoV in different clinical forms.

Characterization of HMW-PBPs from the rod-shaped actinomycete Corynebacterium glutamicum: peptidoglycan synthesis in cells lacking actin-like cytoskeletal structures

Analysis of the complete genome sequence of Corynebacterium glutamicum indicated that, in addition to ftsI, there are eight proteins with sequence motifs that are strongly conserved in penicillin binding proteins (PBPs): four genes that code for high-molecular-weight (HMW)-PBPs (PBP1a, PBP1b, PBP2a and PBP2b), two genes encoding low-molecular-weight PBPs (PBP4 and PBP4b) and two probable beta-lactamases (PBP5 and PBP6). Here, the function of the four HMW-PBPs in C. glutamicum was investigated using a combination of genetic knockouts, enhanced green fluorescent protein 2 (EGFP2) fusions and penicillin staining of membrane preparations. The four HMW-PBPs were expressed in a growing culture of C. glutamicum, but none of four pbp genes was individually essential for the growth of the bacterium, and only the simultaneous disruption of both pbp1b and pbp2b was lethal. The fused EGFP2-PBP proteins were functional in vivo, which allowed correct determination of their cellular localization. EGFP2 fusions to PBP1a, PBP1b and PBP2b localized at the poles and at the septum, whereas EGFP2-PBP2a was predominantly found at the septum. Cefsulodin treatment specifically delocalized PBP1a and PBP1b (class A HMW-PBPs), whereas mecillinam caused the specific delocalization of PBP2b and PBP2a (class B HMW-PBPs). The results provide new insight into the mechanisms involved in the synthesis of the cell wall in this bacterial species, which lacks a known actin-like cytoskeletal structure.

The role of tropical dry forest as a long-term barrier to dispersal: a comparative phylogeographical analysis of dry forest tolerant and intolerant frogs

We used a comparative phylogeographical approach to investigate the origins of the disjunct wet forest biota of the Golfo Dulce region along the Pacific slope of Costa Rica. This region is isolated by Pacific dry forests north and south and isolated from Caribbean wet forests by mountains. We studied three sympatric lowland frog species in the Craugastor fitzingeri species group that prefer wet forest but differ in their response to dry habitats. In dry forest, C. fitzingeri can survive along streams while C. crassidigitus and C. talamancae are entirely absent. We collected samples from across the ranges of all three species, and obtained mitochondrial DNA sequence data from the COI and cytochrome b genes. We observed significant phylogeographical structure in C. crassidigitus and C. talamancae, but much less in C. fitzingeri, demonstrating that mountain barriers and dry forest habitat have reduced mitochondrial gene flow in the strictly wet-forest species. Additionally, we discovered that the Golfo Dulce and Central Panama populations of C. crassidigitus appear to have diverged in the Pliocene or earlier, suggesting that the dry forest separating these populations is old. Our phylogenetic analysis of 12 of approximately 16 species of the C. fitzingeri species group suggests that the three lowland species are each other's closest relatives. Because of this shared phylogenetic history, we attribute the striking differences in phylogeographical structure to the different ecologies of the frogs. In summary, we find that what appear to be minor differences in the natural history of these three closely related species may profoundly impact the potential for dispersal, range size, and cladogenesis.

Partial sequencing of sodA gene and its application to identification of Streptococcus dysgalactiae subsp. dysgalactiae isolated from farmed fish

AIMS

To investigate the difference between Lancefield group C Streptococcus dysgalactiae (GCSD) strains isolated from diseased fish and animals by sequencing and phylogenetic analysis of the sodA gene.

METHODS AND RESULTS

The sodA gene of Strep. dysgalactiae strains isolated from fish and animals were amplified and its nucleotide sequences were determined. Although 100% sequence identity was observed among fish GCSD strains, the determined sequences from animal isolates showed variations against fish isolate sequences. Thus, all fish GCSD strains were clearly separated from the GCSD strains of other origin by using phylogenetic tree analysis. In addition, the original primer set was designed based on the determined sequences for specifically amplify the sodA gene of fish GCSD strains. The primer set yield amplification products from only fish GCSD strains.

CONCLUSIONS

By sequencing analysis of the sodA gene, the genetic divergence between Strep. dysgalactiae strains isolated from fish and mammals was demonstrated. Moreover, an original oligonucletide primer set, which could simply detect the genotype of fish GCSD strains was designed.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study shows that Strep. dysgalactiae isolated from diseased fish could be distinguished from conventional GCSD strains by the difference in the sequence of the sodA gene.

Density-related changes in selection pattern for major histocompatibility complex genes in fluctuating populations of voles

Host-pathogen interactions are of particular interest in studies of the interplay between population dynamics and natural selection. The major histocompatibility complex (MHC) genes of demographically fluctuating species are highly suitable markers for such studies, because they are involved in initiating the immune response against pathogens and display a high level of adaptive genetic variation. We investigated whether two MHC class II genes (DQA1, DRB) were subjected to contemporary selection during increases in the density of fossorial water vole (Arvicola terrestris) populations, by comparing the neutral genetic structure of seven populations with that estimated from MHC genes. Tests for heterozygosity excess indicated that DQA1 was subject to intense balancing selection. No such selection operated on neutral markers. This pattern of selection became more marked with increasing abundance. In the low-abundance phase, when populations were geographically isolated, both overall differentiation and isolation-by-distance were more marked for MHC genes than for neutral markers. Model-based simulations identified DQA1 as an outlier (i.e. under selection) in a single population, suggesting the action of local selection in fragmented populations. The differences between MHC and neutral markers gradually disappeared with increasing effective migration between sites. In the high-abundance year, DQA1 displayed significantly lower levels of overall differentiation than the neutral markers. This gene therefore displayed stronger homogenization than observed under drift and migration alone. The observed signs of selection were much weaker for DRB. Spatial and temporal fluctuations in parasite pressure and locus-specific selection are probably the most plausible mechanisms underlying the observed changes in selection pattern during the demographic cycle.

Quantitative analyses of the abundance and composition of ammonia-oxidizing bacteria and ammonia-oxidizing archaea of a Chinese upland red soil under long-term fertilization practices

The abundance and composition of soil ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) were investigated by using quantitative real-time polymerase chain reaction, cloning and sequencing approaches based on amoA genes. The soil, classified as agri-udic ferrosols with pH (H(2)O) ranging from 3.7 to 6.0, was sampled in summer and winter from long-term field experimental plots which had received 16 years continuous fertilization treatments, including fallow (CK0), control without fertilizers (CK) and those with combinations of fertilizer nitrogen (N), phosphorus (P) and potassium (K): N, NP, NK, PK, NPK and NPK plus organic manure (OM). Population sizes of AOB and AOA changed greatly in response to the different fertilization treatments. The NPK + OM treatment had the highest copy numbers of AOB and AOA amoA genes among the treatments that received mineral fertilizers, whereas the lowest copy numbers were recorded in the N treatment. Ammonia-oxidizing archaea were more abundant than AOB in all the corresponding treatments, with AOA to AOB ratios ranging from 1.02 to 12.36. Significant positive correlations were observed among the population sizes of AOB and AOA, soil pH and potential nitrification rates, indicating that both AOB and AOA played an important role in ammonia oxidation in the soil. Phylogenetic analyses of the amoA gene fragments showed that all AOB sequences from different treatments were affiliated with Nitrosospira or Nitrosospira-like species and grouped into cluster 3, and little difference in AOB community composition was recorded among different treatments. All AOA sequences fell within cluster S (soil origin) and cluster M (marine and sediment origin). Cluster M dominated exclusively in the N, NP, NK and PK treatments, indicating a pronounced difference in the community composition of AOA in response to the long-term fertilization treatments. These findings could be fundamental to improve our understanding of the importance of both AOB and AOA in the cycling of nitrogen and other nutrients in terrestrial ecosystems.

Pseudomonas community structure and antagonistic potential in the rhizosphere: insights gained by combining phylogenetic and functional gene-based analyses

The Pseudomonas community structure and antagonistic potential in the rhizospheres of strawberry and oilseed rape (host plants of the fungal phytopathogen Verticillium dahliae) were assessed. The use of a new PCR-DGGE system, designed to target Pseudomonas-specific gacA gene fragments in environmental DNA, circumvented common biases of 16S rRNA gene-based DGGE analyses and proved to be a reliable tool to unravel the diversity of uncultured Pseudomonas in bulk and rhizosphere soils. Pseudomonas-specific gacA fingerprints of total-community (TC) rhizosphere DNA were surprisingly diverse, plant-specific and differed markedly from those of the corresponding bulk soils. By combining multiple culture-dependent and independent surveys, a group of Pseudomonas isolates antagonistic towards V. dahliae was shown to be genotypically conserved, to carry the phlD biosynthetic locus (involved in the biosynthesis of 2,4-diacetylphloroglucinol - 2,4-DAPG), and to correspond to a dominant and highly frequent Pseudomonas population in the rhizosphere of field-grown strawberries planted at three sites in Germany which have different land use histories. This population belongs to the Pseudomonas fluorescens phylogenetic lineage and showed closest relatedness to P. fluorescens strain F113 (97% gacA gene sequence identity in 492-bp sequences), a biocontrol agent and 2,4-DAPG producer. Partial gacA gene sequences derived from isolates, clones of the strawberry rhizosphere and DGGE bands retrieved in this study represent previously undescribed Pseudomonas gacA gene clusters as revealed by phylogenetic analysis.

Genetic diversity and population structure of Escherichia coli isolated from freshwater beaches

Escherichia coli is an important member of the gastrointestinal tract of humans and warm-blooded animals (primary habitat). In the external environment outside the host (secondary habitat), it is often considered to be only a transient member of the microbiota found in water and soil, although recent evidence suggests that some strains can persist in temperate soils and freshwater beaches. Here we quantified the population genetic structure of E. coli from a longitudinal collection of environmental strains isolated from six freshwater beaches along Lake Huron and the St. Clair River in Michigan. Multilocus enzyme electrophoresis (MLEE) and multilocus sequence typing (MLST) revealed extensive genetic diversity among 185 E. coli isolates with an average of 40 alleles per locus. Despite evidence for extensive recombination generating new alleles and genotypic diversity, several genotypes marked by distinct MLEE and MLST profiles were repeatedly recovered from separate sites at different times. A PCR-based phylogrouping technique showed that the persistent, naturalized E. coli belonged to the B1 group. These results support the hypothesis that persistent genotypes have an adaptive advantage in the secondary habitat outside the host.

A molecular phylogenetic investigation of Opisthonecta and related genera (Ciliophora, Peritrichia, Sessilida)

The gene encoding 18S small subunit ribosomal RNA (ssu rRNA) was sequenced in the sessiline peritrichs Opisthonecta minima and Opisthonecta matiensis, whose free-swimming, paedomorphic trophonts resemble telotrochs. Using these new sequences, phylogenetic trees were constructed with four different methods to test a previously published association between Opisthonecta henneguyi and members of the families Vorticellidae and Astylozoidae. All trees had similar topologies, with O. minima, O. henneguyi, Vorticella microstoma, and Astylozoon enriquesi forming a well-supported, certainly monophyletic clade. On the basis of genetic evidence, genera of the families Opisthonectidae and Astylozoidae are assigned to the family Vorticellidae, which already includes some species with free-swimming morphotypes. The ssu rRNA sequence of O. matiensis places it in the family Epistylididae; its taxonomic revision will be left to another group of authors. A close association of Ophrydium versatile with members of the family Vorticellidae was confirmed, casting doubt on the validity of the family Ophrydiidae. Epistylis galea, Campanella umbellaria, and Opercularia microdiscum are confirmed as comprising an extremely distinct, monophyletic, but morphologically heterogeneous clade that is basal to other clades of sessiline peritrichs.

Population genetics of Plasmodium resistance genes in Anopheles gambiae: no evidence for strong selection

Anopheles mosquitoes are the primary vectors for malaria in Africa, transmitting the disease to more than 100 million people annually. Recent functional studies have revealed mosquito genes that are crucial for Plasmodium development, but there is presently little understanding of which genes mediate vector competence in the wild, or evolve in response to parasite-mediated selection. Here, we use population genetic approaches to study the strength and mode of natural selection on a suite of mosquito immune system genes, CTL4, CTLMA2, LRIM1, and APL2 (LRRD7), which have been shown to affect Plasmodium development in functional studies. We sampled these genes from two African populations of An. gambiae s.s., along with several closely related species, and conclude that there is no evidence for either strong directional or balancing selection on these genes. We highlight a number of challenges that need to be met in order to apply population genetic tests for selection in Anopheles mosquitoes; in particular the dearth of suitable outgroup species and the potential difficulties that arise when working within a closely-related species complex.

In situ lateral transfer of symbiosis islands results in rapid evolution of diverse competitive strains of mesorhizobia suboptimal in symbiotic nitrogen fixation on the pasture legume Biserrula pelecinus L

The multi-billion dollar asset attributed to symbiotic nitrogen fixation is often threatened by the nodulation of legumes by rhizobia that are ineffective or poorly effective in N(2) fixation. This study investigated the development of rhizobial diversity for the pasture legume Biserrula pelecinus L., 6 years after its introduction, and inoculation with Mesorhizobium ciceri bv. biserrulae strain WSM1271, to Western Australia. Molecular fingerprinting of 88 nodule isolates indicated seven were distinctive. Two of these were ineffective while five were poorly effective in N(2) fixation on B. pelecinus. Three novel isolates had wider host ranges for nodulation than WSM1271, and four had distinct carbon utilization patterns. Novel isolates were identified as Mesorhizobium sp. using 16S rRNA, dnaK and GSII phylogenies. In a second study, a large number of nodules were collected from commercially grown B. pelecinus from a broader geographical area. These plants were originally inoculated with M. c bv. biserrulae WSM1497 5-6 years prior to isolation of strains for this study. Nearly 50% of isolates from these nodules had distinct molecular fingerprints. At two sites diverse strains dominated nodule occupancy indicating recently evolved strains are highly competitive. All isolates tested were less effective and six were ineffective in N(2) fixation. Twelve randomly selected diverse isolates clustered together, based on dnaK sequences, within Mesorhizobium and distantly to M. c bv. biserrulae. All 12 had identical sequences for the symbiosis island insertion region with WSM1497. This study shows the rapid evolution of competitive, yet suboptimal strains for N(2) fixation on B. pelecinus following the lateral transfer of a symbiosis island from inoculants to other soil bacteria.

A novel cadherin-like gene from western corn rootworm, Diabrotica virgifera virgifera (Coleoptera: Chrysomelidae), larval midgut tissue

A cadherin-like gene associated with larval midgut tissues was cloned from western corn rootworm (Diabrotica virgifera virgifera: Coleoptera), an economically important agricultural pest in North America and Europe and the primary target pest species for corn hybrids expressing Cry3 toxins from Bacillus thuringiensis (Bt). The full-length cDNA (5371 bp in length) encodes an open reading frame for a 1688 amino acid polypeptide. The putative protein has similar architecture to cadherin-like proteins isolated from lepidopteran midguts that have been shown to bind to Cry1 Bt toxins and have been implicated in Bt resistance. The D. v. virgifera cadherin-like gene is expressed primarily in the larval midgut and regulated during development, with high levels of expression observed in all instars and adults but not pupae. The corresponding genomic sequence spans more than 90 kb and is interspersed with 30 large introns. The genomic organization of the cadherin-like gene for this coleopteran species bears strong resemblance to lepidopteran cadherins suggesting a common molecular basis for susceptibility to Cry3 toxins in Coleoptera.

Characterization and expression of mouse Cdc50c during spermatogenesis

Cdc50p is a transmembrane protein required for polarized growth in Saccharomyces cerevisiae. The knowledge on physiological functions of its mammalian homologs, however, is limited. Using database analysis, we identified one mouse testis expressed sequence tag, named Cdc50c, encoding a previously uncharacterized homolog of Cdc50p. Similar to yeast Cdc50p, the putative Cdc50c protein contains three transmembrane spanning regions. Its orthologs are present in many species such as fish, avian and human, suggesting its evolutionary conservation. In multitissue reverse transcription-polymerase chain reaction analyses the mRNA for Cdc50c was predominately detected in testis. The onset of the gene expression coincides with the first appearance of spermatocytes during testicular development. In situ hybridization analyses revealed that Cdc50c mRNA localized in pachytene spermatocytes and round and elongated spermatids. Our data suggest that Cdc50c might play important roles during spermatogenesis.

Diversity and phylogeny of Baltic Sea picocyanobacteria inferred from their ITS and phycobiliprotein operons

Picocyanobacteria of the genus Synechococcus span a range of different colours, from red strains rich in phycoerythrin (PE) to green strains rich in phycocyanin (PC). Here, we show that coexistence of red and green picocyanobacteria in the Baltic Sea is widespread. The diversity and phylogeny of red and green picocyanobacteria was analysed using three different genes: 16S rRNA-ITS, the cpeBA operon of the red PE pigment and the cpcBA operon of the green PC pigment. Sequencing of 209 clones showed that Baltic Sea picocyanobacteria exhibit high levels of microdiversity. The partial nucleotide sequences of the cpcBA and cpeBA operons from the clone libraries of the Baltic Sea revealed two distinct phylogenetic clades: one clade containing mainly sequences from cultured PC-rich picocyanobacteria, while the other contains only sequences from cultivated PE-rich strains. A third clade of phycourobilin (PUB) containing strains of PE-rich Synechococcus spp. did not contain sequences from the Baltic Sea clone libraries. These findings differ from previously published phylogenies based on 16S rRNA gene analysis. Our data suggest that, in terms of their pigmentation, Synechococcus spp. represent three different lineages occupying different ecological niches in the underwater light spectrum. Strains from different lineages can coexist in light environments that overlap with their light absorption spectra.

Phylogeography and historical demography of the Italian treefrog, Hyla intermedia, reveals multiple refugia, population expansions and secondary contacts within peninsular Italy

We investigated the geographical patterns of genetic diversity in the Italian treefrog through sequence analysis of a mitochondrial cytochrome b gene fragment. Three main mitochondrial lineages were identified, distributed in northern, central and southern Italy, respectively. Their divergence appears indicative of a split time largely predating Late Pleistocene climatic oscillations, and syntopy between them was only observed in the geographically intermediate populations. The historical demographic reconstructions suggest that in both northern and central Italy, an expansion occurred during the last major glacial phase, when a vast widening of the lowland habitats followed the glaciation-induced fall of the sea level. Instead, in southern Italy an expansion event likely followed the end of the last glaciation, although the inference of expansion appears less reliable for the southern clade than for the others. Within this geographical area, a sharp phylogeographic discontinuity separated peninsular from Sicilian populations, and the overall pattern of diversity suggests that the latter derived from a recent colonization of the island, probably through a Late Pleistocene land bridge. Phylogenetic, phylogeographic and historical demographic analyses thus concur in delineating a scenario of multiple refugia, with four groups of populations which survived the last glacial-interglacial cycles in at least three distinct refugia arranged along peninsular Italy, and have recently come into contact following range expansions. Therefore, these results support the hypothesis that a plethora of microevolutionary processes, rather than the prolonged stability of populations, were mainly responsible for shaping the patterns of diversity within this major biodiversity hotspot.

Characterization of black band disease in Red Sea stony corals

Microbial communities associated with black band disease (BBD) in massive stony corals from the Northern Red Sea (Eilat) were examined for the first time using molecular tools and microscopy. A high microbial diversity was revealed in the affected tissue in comparison with the healthy area of the same colony. Microscopy revealed the penetration of cyanobacteria into the coral mesoglea and adjacent tissues. Cyanobacterial sequences from Red Sea BBD-affected corals formed a cluster with sequences previously identified from black band and red band diseased corals from the Indo-Pacific and Caribbean. In addition, 11 sequences belonging to the genus Vibrio were retrieved. This group was previously documented as pathogenic to corals. Sulfate-reducing bacteria, a group known to be associated with BBD and produce toxic sulfide, were studied using specific primers for the amplification of the dissimilatory sulfite reductase gene (dsrA). This technique facilitated and improved the resolution of the study of diversity of this group. All the sequences obtained were closely related to sequences of the genus Desulfovibrio and 46% showed high homology to Desulfovibrio desulfuricans. The complex nature of BBD and the lack of success in isolating a single causative agent suggest that BBD may be considered a polymicrobial disease.

Comparative genomics provides evidence for the 3-hydroxypropionate autotrophic pathway in filamentous anoxygenic phototrophic bacteria and in hot spring microbial mats

Stable carbon isotope signatures of diagnostic lipid biomarkers have suggested that Roseiflexus spp., the dominant filamentous anoxygenic phototrophic bacteria inhabiting microbial mats of alkaline siliceous hot springs, may be capable of fixing bicarbonate via the 3-hydroxypropionate pathway, which has been characterized in their distant relative, Chloroflexus aurantiacus. The genomes of three filamentous anoxygenic phototrophic Chloroflexi isolates (Roseiflexus sp. RS-1, Roseiflexus castenholzii and Chloroflexus aggregans), but not that of a non-photosynthetic Chloroflexi isolate (Herpetosiphon aurantiacus), were found to contain open reading frames that show a high degree of sequence similarity to genes encoding enzymes in the C. aurantiacus pathway. Metagenomic DNA sequences from the microbial mats of alkaline siliceous hot springs also contain homologues of these genes that are highly similar to genes in both Roseiflexus spp. and Chloroflexus spp. Thus, Roseiflexus spp. appear to have the genetic capacity for carbon dioxide reduction via the 3-hydroxypropionate pathway. This may contribute to heavier carbon isotopic signatures of the cell components of native Roseiflexus populations in mats compared with the signatures of cyanobacterial cell components, as a similar isotopic signature would be expected if Roseiflexus spp. were participating in photoheterotrophic uptake of cyanobacterial photosynthate produced by the reductive pentose phosphate cycle.