Microeukaryote Diversity in a Marine Methanol-Fed Fluidized Denitrification System

The marine methanol-fed fluidized denitrification system operated by the Montreal Biodome includes carriers on which a denitrifying biofilm has developed. Previous observations showed a high abundance of microeukaryotes living in and around the biofilm. These eukaryotes may influence the system’s denitrification efficiency. The composition of the microeukaryote population was determined. Microscopic observations showed at least 20 different morphologies that included large numbers of ciliates. Molecular analyses of an 18S ribosomal RNA (rDNA) gene library revealed 31 different phylotypes. Alveolobiontes were the most abundant phylotypes and made up 75% of the 159 screened clones. Other eukaryotic groups, including Stramenopiles, Fungi, Amoebozoa, and nematodes, were also present. From 18S rDNA specific sequences, one of the Amoebozoa-affiliated phylotypes was visualized by fluorescence in situ hybridization. It had a rod-like irregular shape and measured less than 5 μm in length. We determined the impact of protozoans on the denitrifying activity. In a laboratory-scale batch culture assays, the denitrifying biofilm was treated with cycloheximide and nystatin that eliminated the protozoans. No difference in the denitrification rate was found. However, planktonic bacteria were more abundant in the treated culture medium.     

Microbial Symbiosis: Patterns of Diversity in the Marine Environment

SYNOPSIS. Symbiotic associations expand both the diversity ofpotential ecological niches and metabolic capabilities of thehost—symbiont combinations. Symbioses can also be consideredto have evolutionary potential in that the partnership can resultin a "new organism." Associations between chemoautotrophic bacteriaand marine invertebrates, discovered only 10 years ago, arenow found widely in nature, in habitats ranging from deep-seahydrothermal vents to coastal sediments. Here I review chemoautotroph—invertebrateassociations and discuss the benefits inferred for both partnerswith regard to the diversity of these symbioses in nature.     

Admixture and Genetic Diversity Distribution Patterns of Non-Recombining Lineages of Native American Ancestry in Colombian Populations

Genetic diversity of present American populations results from very complex demographic events involving different types and degrees of admixture. Through the analysis of lineage markers such as mtDNA and Y chromosome it is possible to recover the original Native American haplotypes, which remained identical since the admixture events due to the absence of recombination. However, the decrease in the effective population sizes and the consequent genetic drift effects suffered by these populations during the European colonization resulted in the loss or under-representation of a substantial fraction of the Native American lineages. In this study, we aim to clarify how the diversity and distribution of uniparental lineages vary with the different demographic characteristics (size, degree of isolation) and the different levels of admixture of extant Native groups in Colombia. We present new data resulting from the analyses of mtDNA whole control region, Y chromosome SNP haplogroups and STR haplotypes, and autosomal ancestry informative insertion-deletion polymorphisms in Colombian individuals from different ethnic and linguistic groups. The results demonstrate that populations presenting a high proportion of non-Native American ancestry have preserved nevertheless a substantial diversity of Native American lineages, for both mtDNA and Y chromosome. We suggest that, by maintaining the effective population sizes high, admixture allowed for a decrease in the effects of genetic drift due to Native population size reduction and thus resulting in an effective preservation of the Native American non-recombining lineages.     

Co-transmission of Related Malaria Parasite Lineages Shapes Within-Host Parasite Diversity

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Quantifying Phylogenetic Beta Diversity: Distinguishing between 'True' Turnover of Lineages and Phylogenetic Diversity Gradients

The evolutionary dissimilarity between communities (phylogenetic beta diversity PBD) has been increasingly explored by ecologists and biogeographers to assess the relative roles of ecological and evolutionary processes in structuring natural communities. Among PBD measures, the PhyloSor and UniFrac indices have been widely used to assess the level of turnover of lineages over geographical and environmental gradients. However, these indices can be considered as 'broad-sense' measures of phylogenetic turnover as they incorporate different aspects of differences in evolutionary history between communities that may be attributable to phylogenetic diversity gradients. In the present study, we extend an additive partitioning framework proposed for compositional beta diversity to PBD. Specifically, we decomposed the PhyloSor and UniFrac indices into two separate components accounting for 'true' phylogenetic turnover and phylogenetic diversity gradients, respectively. We illustrated the relevance of this framework using simple theoretical and archetypal examples, as well as an empirical study based on coral reef fish communities. Overall, our results suggest that using PhyloSor and UniFrac may greatly over-estimate the level of spatial turnover of lineages if the two compared communities show contrasting levels of phylogenetic diversity. We therefore recommend that future studies use the 'true' phylogenetic turnover component of these indices when the studied communities encompass a large phylogenetic diversity gradient.     

Amazonian Amphibian Diversity Is Primarily Derived from Late Miocene Andean Lineages

The Neotropics contains half of remaining rainforests and Earth's largest reservoir of amphibian biodiversity. However, determinants of Neotropical biodiversity (i.e., vicariance, dispersals, extinctions, and radiations) earlier than the Quaternary are largely unstudied. Using a novel method of ancestral area reconstruction and relaxed Bayesian clock analyses, we reconstructed the biogeography of the poison frog clade (Dendrobatidae). We rejected an Amazonian center-of-origin in favor of a complex connectivity model expanding over the Neotropics. We inferred 14 dispersals into and 18 out of Amazonia to adjacent regions; the Andes were the major source of dispersals into Amazonia. We found three episodes of lineage dispersal with two interleaved periods of vicariant events between South and Central America. During the late Miocene, Amazonian, and Central American-Chocoan lineages significantly increased their diversity compared to the Andean and Guianan-Venezuelan-Brazilian Shield counterparts. Significant percentage of dendrobatid diversity in Amazonia and Chocó resulted from repeated immigrations, with radiations at <10.0 million years ago (MYA), rather than in situ diversification. In contrast, the Andes, Venezuelan Highlands, and Guiana Shield have undergone extended in situ diversification at near constant rate since the Oligocene. The effects of Miocene paleogeographic events on Neotropical diversification dynamics provided the framework under which Quaternary patterns of endemism evolved.     

Probing Diversity in the Plankton: Using Patterns in Tintinnids (Planktonic Marine Ciliates) to Identify Mechanisms

In diversity research, the use of survey data appears to have declined in favour of experimental or modeling approaches because direct relationships are difficult to demonstrate. Here we show that use of field data can yield information concerning the mechanisms governing diversity. First, we establish that tintinnids display a global latitudinal pattern of diversity similar to other pelagic organisms; species numbers appear to peak between 20° and 30° north or south. This common large scale spatial trend has been attributed to the gradient in water column structure across the global ocean. We then examine the generality of a relationship between planktonic diversity and water column structure by considering data from the Mediterranean Sea, in which water column structure changes seasonally. Among populations of foraminifera, tintinnids, and the dinoflagellates of the genus Ceratium, we compare data from trans-Mediterranean sampling conducted at different times and monthly changes in species richness at single sites. We find that water column structure alone appears to be a poor predictor of temporal changes in diversity. Lastly, we present an example of temporal changes in tintinnid diversity based on data from an oceanographic sampling station in the N. W. Mediterranean where resources, as chlorophyll, appear distinctly unrelated to changes in water column structure. We show that short-tem temporal changes in diversity (week to week shifts) can be related to changes in chlorophyll concentration. We conclude that in tintinnids diversity can be directly linked to characteristics of food resources.     

Detection of Seven Major Evolutionary Lineages in Cyanobacteria Based on the 16S rRNA Gene Sequence Analysis with New Sequences of Five Marine Synechococcus Strains

Although molecular phylogenetic studies of cyanobacteria on the basis of the 16S rRNA gene sequence have been reported, the topologies were unstable, especially in the inner branchings. Our analysis of 16S rRNA gene phylogeny by the maximum-likelihood and neighbor-joining methods combined with rate homogeneous and heterogeneous models revealed seven major evolutionary lineages of the cyanobacteria, including prochlorophycean organisms. These seven lineages are always stable on any combination of these methods and models, fundamentally corresponding to phylogenetic relationships based on other genes, e.g., psbA, rbcL, rnpB, rpoC, and tufA. Moreover, although known genotypic and phenotypic characters sometimes appear paralleled in independent lineages, many characters are not contradictory within each group. Therefore we propose seven evolutionary groups as a working hypothesis for successive taxonomic reconstruction. New 16S rRNA sequences of five unicellular cyanobacterial strains, PCC 7001, PCC 7003, PCC 73109, PCC 7117, and PCC 7335 of Synechococcus sp., were determined in this study. Although all these strains have been assigned to ``marine clusters B and C,' they were separated into three lineages. This suggests that the organisms classified in the genus Synechococcus evolved diversely and should be reclassified in several independent taxonomic units. Moreover, Synechococcus strains and filamentous cyanobacteria make a monophyletic group supported by a comparatively high statistical confidence value (80 to 100%) in each of the two independent lineages; therefore, these monophylies probably reflect the convergent evolution of a multicellular organization. Received: 3 September 1998 / Accepted: 30 November 1998     

Dating the Diversification of the Major Lineages of Ascomycota (Fungi)

Establishing the dates for the origin and main diversification events in the phylogeny of Ascomycota is among the most crucial remaining goals in understanding the evolution of Fungi. There have been several analyses of divergence times in the fungal tree of life in the last two decades, but most have yielded contrasting results for the origin of the major lineages. Moreover, very few studies have provided temporal estimates for a large set of clades within Ascomycota. We performed molecular dating to estimate the divergence times of most of the major groups of Ascomycota. To account for paleontological uncertainty, we included alternative fossil constraints as different scenarios to enable a discussion of the effect of selection of fossils. We used data from 6 molecular markers and 121 extant taxa within Ascomycota. Our various ‘relaxed clock’ scenarios suggest that the origin and diversification of the Pezizomycotina occurred in the Cambrian. The main lineages of lichen–forming Ascomycota originated at least as early as the Carboniferous, with successive radiations in the Jurassic and Cretaceous generating the diversity of the main modern groups. Our study provides new information about the timing of the main diversification events in Ascomycota, including estimates for classes, orders and families of both lichenized and non–lichenized Ascomycota, many of which had not been previously dated.     

Prokaryotic Diversity in Zostera noltii-Colonized Marine Sediments

The diversity of microorganisms present in a sediment colonized by the phanerogam Zostera noltii has been analyzed. Microbial DNA was extracted and used for constructing two 16S rDNA clone libraries for Bacteria and Archaea. Bacterial diversity was very high in these samples, since 57 different sequences were found among the 60 clones analyzed. Eight major lineages of the Domain Bacteria were represented in the library. The most frequently retrieved bacterial group (36% of the clones) was δ-Proteobacteria related to sulfate-reducing bacteria. The second most abundant group (27%) was γ-Proteobacteria, including five clones closely related to S-oxidizing endosymbionts. The archaeal clone library included members of Crenarchaeota and Euryarchaeota, with nine different sequences among the 15 analyzed clones, indicating less diversity when compared to the Bacteria organisms. None of these sequences was closely related to cultured Archaea organisms.     

Distinct Evolutionary Pressures Underlie Diversity in Simian Immunodeficiency Virus and Human Immunodeficiency Virus Lineages

Simian immunodeficiency virus (SIV) infection of rhesus macaques causes immune depletion and disease closely resembling human AIDS and is well recognized as the most relevant animal model for the human disease. Experimental investigations of viral pathogenesis and vaccine protection primarily involve a limited set of related viruses originating in sooty mangabeys (SIVsmm). The diversity of human immunodeficiency virus type 1 (HIV-1) has evolved in humans in about a century; in contrast, SIV isolates used in the macaque model evolved in sooty mangabeys over millennia. To investigate the possible consequences of such different evolutionary histories for selection pressures and observed diversity in SIVsmm and HIV-1, we isolated, sequenced, and analyzed 20 independent isolates of SIVsmm, including representatives of 7 distinct clades of viruses isolated from natural infection. We found SIVsmm diversity to be lower overall than HIV-1 M group diversity. Reduced positive selection (i.e., less diversifying evolution) was evident in extended regions of SIVsmm proteins, most notably in Gag p27 and Env gp120. In addition, the relative diversities of proteins in the two lineages were distinct: SIVsmm Env and Gag were much less diverse than their HIV-1 counterparts. This may be explained by lower SIV-directed immune activity in mangabeys relative to HIV-1-directed immunity in humans. These findings add an additional layer of complexity to the interpretation and, potentially, to the predictive utility of the SIV/macaque model, and they highlight the unique features of human and simian lentiviral evolution that inform studies of pathogenesis and strategies for AIDS vaccine design.     

Stable Patterns of CENH3 Occupancy Through Maize Lineages Containing Genetically Similar Centromeres

While the approximate chromosomal position of centromeres has been identified in many species, little is known about the dynamics and diversity of centromere positions within species. Multiple lines of evidence indicate that DNA sequence has little or no impact in specifying centromeres in maize and in most multicellular organisms. Given that epigenetically defined boundaries are expected to be dynamic, we hypothesized that centromere positions would change rapidly over time, which would result in a diversity of centromere positions in isolated populations. To test this hypothesis, we used CENP-A/cenH3 (CENH3 in maize) chromatin immunoprecipitation to define centromeres in breeding pedigrees that included the B73 inbred as a common parent. While we found a diversity of CENH3 profiles for centromeres with divergent sequences that were not inherited from B73, the CENH3 profiles from centromeres that were inherited from B73 were indistinguishable from each other. We propose that specific genetic elements in centromeric regions favor or inhibit CENH3 accumulation, leading to reproducible patterns of CENH3 occupancy. These data also indicate that dramatic shifts in centromere position normally originate from accumulated or large-scale genetic changes rather than from epigenetic positional drift.     

Phylogeny in Aid of the Present and Novel Microbial Lineages: Diversity in Bacillus

Bacillus represents microbes of high economic, medical and biodefense importance. Bacillus strain identification based on 16S rRNA sequence analyses is invariably limited to species level. Secondly, certain discrepancies exist in the segregation of Bacillus subtilis strains. In the RDP/NCBI databases, out of a total of 2611 individual 16S rDNA sequences belonging to the 175 different species of the genus Bacillus, only 1586 have been identified up to species level. 16S rRNA sequences of Bacillus anthracis (153 strains), B. cereus (211 strains), B. thuringiensis (108 strains), B. subtilis (271 strains), B. licheniformis (131 strains), B. pumilus (83 strains), B. megaterium (47 strains), B. sphaericus (42 strains), B. clausii (39 strains) and B. halodurans (36 strains) were considered for generating species-specific framework and probes as tools for their rapid identification. Phylogenetic segregation of 1121, 16S rDNA sequences of 10 different Bacillus species in to 89 clusters enabled us to develop a phylogenetic frame work of 34 representative sequences. Using this phylogenetic framework, 305 out of 1025, 16S rDNA sequences presently classified as Bacillus sp. could be identified up to species level. This identification was supported by 20 to 30 nucleotides long signature sequences and in silico restriction enzyme analysis specific to the 10 Bacillus species. This integrated approach resulted in identifying around 30% of Bacillus sp. up to species level and revealed that B. subtilis strains can be segregated into two phylogenetically distinct groups, such that one of them may be renamed.     

Intra-Host Diversity and Emergence of Unique GBV-C Viral Lineages in HIV Infected Subjects in Central China

GB virus C (GBV-C), which is highly prevalent among HIV/AIDS, seemed to slow the HIV disease progression. The HIV/GBV-C co-infected individuals may represent an interesting model for the investigation of the role played by HIV infection and/or the immune system in driving the evolution of the GBV-C viral populations. The present study investigated the prevalence and population dynamics of GB virus C in HIV infected individuals representing 13 geographic regions of Hubei Province of China. Approximately 37% of HIV-1 infected individuals were infected with GBV-C and genotype 3 is appeared to be predominant. Utilizing the 196 complete E2 nucleotide sequence data from 10 HIV/GBV-C infected individuals and employing coalescence based phylogenetic approaches; the present study has investigated the intra-host dynamics of GBV-C. The results revealed patient-specific unique GBV-C viral lineages and each viral lineage showed the evidence of rapid population expansion in respective HIV-1 infected patients, thus suggesting HIV-1 was unlikely to have been inhibiting effect on the GBV-C viral replication. GBV-C in all patients has experienced intense purifying selection, suggesting the GBV-C viral invasion and subsequent expansion within the HIV-1 infected hosts without any modification of the functional epitopes at their membrane protein. The finding of within host GBV-C recombinant sequences indicated recombination was one of the significant forces in the evolution and divergence of GBV-C.     

Diversity Patterns of Bornean Butterfly Assemblages

Borneo contains a diverse rainforest butterfly community, but its forests are under threat from logging and ENSO- (El Niño Southern Oscillation) induced fires. Contrasts in butterfly assemblage structure were examined in nine 450 ha landscapes in logged forest, primary unburned continuous and isolated forest, and forest affected by surface fires during the 1997/98 ENSO event. Temporally the effect of the 1997/98 ENSO event was followed in a single burned landscape from 1997 to 2004. In total, 517 species were present in 190 sampling sites. There was a five-fold difference in species richness among landscapes, with highest richness in continuous landscapes and lowest richness in burned landscapes. Richness was also higher in logged forest than proximate unlogged forest. Temporally, species richness dropped dramatically from 1997 to 1998, but afterwards increased remaining, however, substantially lower than pre-ENSO (1997) sampling. Sites in burned landscapes were distinct from other sites in terms of vegetation structure with the slash-and-burn area the most dissimilar to other landscapes. There was much less structure among unburned landscapes. The pattern of butterfly community composition was similar to that of vegetation structure with the community from the slash-and-burn area the most distinct. However, there was much less overlap among sites from different landscapes. Temporally, 1998 possessed the most distinct assemblage when compared to assemblages from other years. The community composition was, however, slowly returning to a pre-disturbance composition. Variance in community composition explained by environmental and spatial factors differed substantially among landscapes. The spatial fraction was the only explanatory component in recently burned landscapes and a proximate small unburned isolate, but explained no variation in logged landscapes. The environmental fraction explained substantial amounts of variation in logged landscapes and the slash-and-burn area. When all landscapes were pooled high proportions of variation in butterfly community composition were explained by both geographic distance between sites and environmental variables. In contrast when only unburned landscapes were considered, most variation was explained by the geographic distance among them. Despite differences among landscapes there was a general pattern of relatively sharp decline in similarity at short distances that levels out over greater distances, a result that agrees with previous studies on other tropical species assemblages.     

Patterns of Vertebrate Diversity and Protection in Brazil

Most conservation decisions take place at national or finer spatial scales. Providing useful information at such decision-making scales is essential for guiding the practice of conservation. Brazil is one of the world’s megadiverse countries, and consequently decisions about conservation in the country have a disproportionate impact on the survival of global biodiversity. For three groups of terrestrial vertebrates (birds, mammals, and amphibians), we examined geographic patterns of diversity and protection in Brazil, including that of endemic, small-ranged, and threatened species. To understand potential limitations of the data, we also explored how spatial bias in collection localities may influence the perceived patterns of diversity. The highest overall species richness is in the Amazon and Atlantic Forests, while the Atlantic Forest dominates in terms of country endemics and small-ranged species. Globally threatened species do not present a consistent pattern. Patterns for birds were similar to overall species richness, with higher concentrations of threatened species in the Atlantic Forest, while mammals show a more generalized pattern across the country and a high concentration in the Amazon. Few amphibians are listed as threatened, mostly in the Atlantic Forest. Data deficient mammals occur across the country, concentrating in the Amazon and southeast Atlantic Forest, and there are no data deficient birds in Brazil. In contrast, nearly a third of amphibians are data deficient, widespread across the country, but with a high concentration in the far southeast. Spatial biases in species locality data, however, possibly influence the perceived patterns of biodiversity. Regions with low sampling density need more biological studies, as do the many data deficient species. All biomes except the Amazon have less than 3% of their area under full protection. Reassuringly though, rates of protection do correlate with higher biodiversity, including higher levels of threatened and small-ranged species. Our results indicate a need for expanded formal protection in Brazil, especially in the Atlantic forest, and with an emphasis on fully protected areas.