Genetic structure at range edge: Low diversity and high inbreeding in Southeast Asian mangrove (Avicennia marina) populations

Understanding the genetic composition and mating systems of edge populations provides important insights into the environmental and demographic factors shaping species’ distribution ranges. We analysed samples of the mangrove Avicennia marina from Vietnam, northern Philippines and Australia, with microsatellite markers. We compared genetic diversity and structure in edge (Southeast Asia, and Southern Australia) and core (North and Eastern Australia) populations, and also compared our results with previously published data from core and southern edge populations. Comparisons highlighted significantly reduced gene diversity and higher genetic structure in both margins compared to core populations, which can be attributed to very low effective population size, pollinator scarcity and high environmental pressure at distribution margins. The estimated level of inbreeding was significantly higher in northeastern populations compared to core and southern populations. This suggests that despite the high genetic load usually associated with inbreeding, inbreeding or even selfing may be advantageous in margin habitats due to the possible advantages of reproductive assurance, or local adaptation. The very high level of genetic structure and inbreeding show that populations of A. marina are functioning as independent evolutionary units more than as components of a metapopulation system connected by gene flow. The combinations of those characteristics make these peripheral populations likely to develop local adaptations and therefore to be of particular interest for conservation strategies as well as for adaptation to possible future environmental changes.

Long-term effectiveness of sowing high and low diversity seed mixtures to enhance plant community development on ex-arable fields

Questions: How is succession on ex-arable land affected by sowing high and low diversity mixtures of grassland species as compared to natural succession? How long do effects persist? Location: Experimental plots installed in the Czech Republic, The Netherlands, Spain, Sweden and the United Kingdom. Methods: The experiment was established on ex-arable land, with five blocks, each containing three 10 m x 10 m experiment tal plots: natural colonization, a low- (four species) and high-diversity (15 species) seed mixture. Species composition and biomass was followed for eight years. Results: The sown plants considerably affected the whole successional pathway and the effects persisted during the whole eight year period. Whilst the proportion of sown species (characterized by their cover) increased during the study period, the number of sown species started to decrease from the third season onwards. Sowing caused suppression of natural colonizing species, and the sown plots had more biomass. These effects were on average larger in the high diversity mixtures. However, the low diversity replicate sown with the mixture that produced the largest biomass or largest suppression of natural colonizers fell within the range recorded at the five replicates of the high diversity plots. The natural colonization plots usually had the highest total species richness and lowest productivity at the end of the observation period. Conclusions: The effect of sowing demonstrated dispersal limitation as a factor controlling the rate of early secondary succession. Diversity was important primarily for its 'insurance effect': the high diversity mixtures were always able to compensate for the failure of some species.

Dietary iron depletion at weaning imprints low microbiome diversity and this is not recovered with oral nano Fe(III)

Alterations in the gut microbiota have been recently linked to oral iron. We conducted two feeding studies including an initial diet-induced iron-depletion period followed by supplementation with nanoparticulate tartrate-modified ferrihydrite (Nano Fe(III): considered bioavailable to host but not bacteria) or soluble ferrous sulfate (FeSO4: considered bioavailable to both host and bacteria). We applied denaturing gradient gel electrophoresis and fluorescence in situ hybridization for study-1 and 454-pyrosequencing of fecal 16S rRNA in study-2. In study-1, the within-community microbial diversity increased with FeSO4 (P = 0.0009) but not with Nano Fe(III) supplementation. This was confirmed in study-2, where we also showed that iron depletion at weaning imprinted significantly lower within- and between-community microbial diversity compared to mice weaned onto the iron-sufficient reference diet (P < 0.0001). Subsequent supplementation with FeSO4 partially restored the within-community diversity (P = 0.006 in relation to the continuously iron-depleted group) but not the between-community diversity, whereas Nano Fe(III) had no effect. We conclude that (1) dietary iron depletion at weaning imprints low diversity in the microbiota that is not, subsequently, easily recovered; (2) in the absence of gastrointestinal disease iron supplementation does not negatively impact the microbiota; and (3) Nano Fe(III) is less available to the gut microbiota.

Investigation on the ecological impact of constructing and activities of petrochemical industries of petrochemical special economic zone of Mahshahr on the abundance and diversity of macrobenthic fauna in Jafari Creek, north-west of the Persian Gulf

The impact of Petrochemical Special Economic Zone (PETZONE) activities on the health status of Jafari Creek was studied by assessing the changes in macroinvertebrate assemblages in nine sites during September 2006- January 2008. Furthermore to evaluate the ecological status of the Jafari Creek the WFD indices (i.e. AMBI, M-AMBI) were used. The relationship between spatial pattern of macro invertebrate assemblages and ambient factors (i.e. water temperature, salinity, pH, dissolved oxygen, turbidity, electrical conductivity, total dissolved solid, total hardness, total nitrogen, ammonia, total phosphorous, chemical oxygen demand, biological oxygen demand, sediment grain size distribution, sediment organic content, heavy metals contents) was measured. Background Enrichment indices, Contamination factor and Contamination degree, were used to assess the health status in the study area based on Nickel, Lead, Cadmium and Mercury contents of the sediments. The macrobenthic communities had a low diversity and were dominated by opportunistic taxa, and the AMBI and M-AMBI indices need to be calibrated before using in Persian Gulf and its coastal waters. The BIO-ENV analysis identified pH, dissolved oxygen, TDS, and the total organic content of sediments as the major environmental variables influencing the infaunal pattern. This suggests that management should attempt to ensure minimal disturbance to environmental variables underlying the spatial variation in macroinvertebrate assemblages. Background Enrichment indices showed that the health of Jafari Creek has declined over time due to the constant discharge of heavy metals to the Creek system. Furthermore WQS index shows that the quality condition of the water column in Jafari Creek, regard to the calculated number (3) is week. These indices also identified a significant degree of pollution in the study area. The decrease in the ecological potential of Jafari Creek was best highlighted by the alteration in macrobenthic assemblages.

Structure and diversity of intertidal benthic diatom assemblages in contrasting shores: a case study from the Tagus estuary1

The structure of intertidal benthic diatoms assemblages in the Tagus estuary was investigated during a 2-year survey, carried out in six stations with different sediment texture. Nonparametric multivariate analyses were used to characterize spatial and temporal patterns of the assemblages and to link them to the measured environmental variables. In addition, diversity and other features related to community physiognomy, such as size-class or life-form distributions, were used to describe the diatom assemblages. A total of 183 diatom taxa were identified during cell counts and their biovolume was determined. Differences between stations (analysis of similarity (ANOSIM), R=0.932) were more evident than temporal patterns (R=0.308) and mud content alone was the environmental variable most correlated to the biotic data (BEST, rho=0.863). Mudflat stations were typically colonized by low diversity diatom assemblages (H' similar to 1.9), mainly composed of medium-sized motile epipelic species (250-1,000 mu m(3)), that showed species-specific seasonal blooms (e.g., Navicula gregaria Donkin). Sandy stations had more complex and diverse diatom assemblages (H' similar to 3.2). They were mostly composed by a large set of minute epipsammic species (<250 mu m(3)) that, generally, did not show temporal patterns. The structure of intertidal diatom assemblages was largely defined by the interplay between epipelon and epipsammon, and its diversity was explained within the framework of the Intermediate Disturbance Hypothesis. However, the spatial distribution of epipelic and epipsammic life-forms showed that the definition of both functional groups should not be over-simplified.

Bird diversity and environmental gradients in Britain:a test of the species-energy hypothesis

1. We tested the species diversity-energy hypothesis using the British bird fauna. This predicts that temperature patterns should match diversity patterns. We also tested the hypothesis that the mechanism operates directly through effects of temperature on thermoregulatory loads; this further predicts that seasonal changes in temperature cause matching changes in patterns of diversity, and that species' body mass is influential.

2. We defined four assemblages using migration status (residents or visitors) and season (summer or winter distribution). Records of species' presence/absence in a total of 2362, 10 x 10-km, quadrats covering most of Britain were used, together with a wide selection of habitat, topographic and seasonal climatic data.

3. We fitted a logistic regression model to each species' distribution using the environmental data. We then combined these individual species models mathematically to form a diversity model. Analysis of this composite model revealed that summer temperature was the factor most strongly associated with diversity.

4. Although the species-energy hypothesis was supported, the direct mechanism, predicting an important role for body mass and matching seasonal patterns of change between diversity and temperature, was not supported.

5. However, summer temperature is the best overall explanation for bird diversity patterns in Britain. It is a better predictor of winter diversity than winter temperature. Winter diversity is predicted more precisely from environmental factors than summer diversity.

6. Climate change is likely to influence the diversity of different areas to different extents; for resident species, low diversity areas may respond more strongly as climate change progresses. For winter visitors, higher diversity areas may respond more strongly, while summer visitors are approximately neutral.

An analysis of the floristic composition and diversity of Amazonian forests including those of the Guiana Shield

A large number of newly published and unpublished hectare plots in Amazonia and the Guiana Shield area allow an analysis of family composition and testing of hypotheses concerning alpha-diversity in the south American rain forest. Using data from 94 plots the family-level floristic patterns in wet tropical South America are described. To test diversity patterns, 268 plots are used in this large area. Contrary to a widely held belief, western Amazonian plots are not necessarily the most diverse. Several central Amazonian plots have equal or even higher tree diversity. Annual rainfall is not a good estimator for tree diversity in the Amazonia area and Guiana shield. Plots in the Guiana Shield area (and eastern Amazonia) usually have lower diversity than those in central or western Amazonia. It is argued that this is not because of low rainfall or low nutrient status of the soil but because of the small area of the relatively isolated rain forest area in eastern Amazonia and the Guiana Shield. The low diversity on nutrient-poor white sand soils in the Amazon basin is not necessarily due to their Low nutrient status but is, at least partly, caused by their small extent and fragmented nature.

Diversity of the ichthyofauna in the Serra do Mar State Park- Núcleo Santa Virgínia, Sáo Paulo State, Brazil

The aim of this work was to assess and compare the diversity of the ichthyofauna in three headwater rivers of Paraíba-do-Sul basin in the Serra do Mar State Park, Núcleo Santa Virgínia. A total of 1,774 specimens of 16 species of fishes belonging to 6 families were caught. Characiforms were the most abundant fish at all three sites, followed by Cyprinodontiformes, Siluriformes, and Perciformes. The Shannon index (H′), evenness (E), and the Jaccard and Morisita-Horn similarity indexes were low, indicating both low diversity and low similarity of species among the three streams. The values of these indexes should be evaluated according to the biotic and abiotic conditions in each environment. It is clear that in mountain streams of the Atlantic Forest, these low values occur because of the presence of a few abundant and many rare species.

Diversity and three-dimensional structures of the alpha Mcr of the methanogenic Archaea from the anoxic region of Tucuruí Lake, in Eastern Brazilian Amazonia

ABSTRACT: Methanogenic archaeans are organisms of considerable ecological and biotechnological interest that produce methane through a restricted metabolic pathway, which culminates in the reaction catalyzed by the Methyl-coenzyme M reductase (Mcr) enzyme, and results in the release of methane. Using a metagenomic approach, the gene of the a subunit of mcr (mcrα) was isolated from sediment sample from an anoxic zone, rich in decomposing organic material, obtained from the Tucuruí hydroelectric dam reservoir in eastern Brazilian Amazonia. The partial nucleotide sequences obtained were 83 to 95% similar to those available in databases, indicating a low diversity of archaeans in the reservoir. Two orders were identified -the Methanomicrobiales, and a unique Operational Taxonomic Unit (OTU) forming a clade with the Methanosarcinales according to low bootstrap values. Homology modeling was used to determine the three-dimensional (3D) structures, for this the partial nucleotide sequence of the mcrα were isolated and translated on their partial amino acid sequences. The 3D structures of the archaean mcrα observed in the present study varied little, and presented approximately 70% identity in comparison with the mcrα of Methanopyrus klanderi. The results demonstrated that the community of methanogenic archaeans of the anoxic C1 region of the Tucurui reservoir is relatively homogeneous.

Spatial patterns of species richness and phylogenetic diversity of woody plants in the neotropical savannas of Brazil

Savanna woody plant communities are widespread in Brazil, where this vegetation type can be divided into core-central and marginal areas within its range of distribution. The study of diversity patterns of plant communities can provide insights into the distribution, biogeography, and diversity of plant species in widespread biomes. The objectives of this study were to measure standard and phylogenetic indices of diversity in woody plant communities of the savanna vegetation of Brazil (Cerrado) throughout its extensive range. Based on a metaanalysis, the diversity indexes were compared using traditional statistical methods, a phylogenetic approach, and by mapping. Similar patterns were found for phylogenetic and traditional indexes of diversity in core and marginal areas, suggesting that both lower and higher diversity sites can occur within the Cerrado geographical area. The only difference was found in low diversity, disjunct savanna sites within the Amazon basin, which are isolated by the Amazon River from the more continuous central-southern Cerrado area.

The impact of plant diversity and fertilization on fitness of a generalist grasshopper

In many environments land use intensification is likely to result in a decrease in species richness and in an increase in eutrophication. Although the importance of both factors for higher trophic levels such as insect herbivores is well documented, their impact has rarely been studied in combination. Herbivorous insects have a strong impact on the functioning of ecosystems and it is therefore important to understand how they are affected by eutrophication in high or low diversity environments. We used a grassland biodiversity experiment to investigate the combined effect of fertilization and plant diversity loss on the fitness of the generalist grasshopper Chorthippus parallelus by rearing grasshopper nymphs for four weeks in cages on unfertilized or fertilized (NPK) subplots across a species richness gradient from 1 to 60 plant species. Survival, the number of oothecae, body mass and the number of hatchlings were measured separately for each cage. Plant diversity had no effect on any of the grasshopper fitness measures, neither in unfertilized nor in fertilized plots. NPK-fertilization reduced grasshopper survival but increased body mass of males and reproductive success of the surviving females. Fertilization effects were not mediated by plant community structure, productivity or composition, suggesting that higher food plant quality was one of the main drivers. There was no interaction between plant diversity and fertilization on any of the measures. In conclusion, an increase in eutrophication, in both species-rich and species-poor grasslands, could lead to higher reproductive success and therefore higher abundances of herbivorous insects including insect pests, with fertilization effects dominating plant diversity effects.

Intestinal Microbial Diversity during Early-Life Colonization Shapes Long-Term IgE Levels

Microbial exposure following birth profoundly impacts mammalian immune system development. Microbiota alterations are associated with increased incidence of allergic and autoimmune disorders with elevated serum IgE as a hallmark. The previously reported abnormally high serum IgE levels in germ-free mice suggests that immunoregulatory signals from microbiota are required to control basal IgE levels. We report that germ-free mice and those with low-diversity microbiota develop elevated serum IgE levels in early life. B cells in neonatal germ-free mice undergo isotype switching to IgE at mucosal sites in a CD4 T-cell- and IL-4-dependent manner. A critical level of microbial diversity following birth is required in order to inhibit IgE induction. Elevated IgE levels in germ-free mice lead to increased mast-cell-surface-bound IgE and exaggerated oral-induced systemic anaphylaxis. Thus, appropriate intestinal microbial stimuli during early life are critical for inducing an immunoregulatory network that protects from induction of IgE at mucosal sites.

Collection of data on plant height along the plant diversity gradient in the Jena Experiment (Main Experiment, time series since 2002)

This data set contains a time series of plant height measurements (vegetative and reproductive) from the main experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In addition, data on species specific plant heights for the main experiment are available from 2002. In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. 1. Plant height was recorded, generally, twice a year just before biomass harvest (during peak standing biomass in late May and in late August). Methodologies of measuring height have varied somewhat over the years. In earlier year the streched plant height was measured, while in later years the standing height without streching the plant was measured. Vegetative height was measured either as the height of the highest leaf or as the length of the main axis of non-flowering plants. Regenerating height was measured either as the height of the highest flower on a plant or as the height of the main axis of flowering. Sampled plants were either randomly selected in the core area of plots or along transects in defined distances. For details refer to the description of individual years. Starting in 2006, also the plots of the management experiment, that altered mowing frequency and fertilized subplots (see further details in the general description of the Jena Experiment) were sampled. 2. Species specific plant height was recorded two times in 2002: in late July (vegetative height) and just before biomass harvest during peak standing biomass in late August (vegetative and regenerative height). For each plot and each sown species in the species pool, 3 plant individuals (if present) from the central area of the plots were randomly selected and used to measure vegetative height (non-flowering indviduals) and regenerative height (flowering individuals) as stretched height. Provided are the means over the three measuremnts per plant species per plot.

Plant height along the plant diversity gradient in the Jena Experiment (Main Experiment, year 2007)

This data set contains measurements of plant height: vegetative height (heighest leaf) and regenerative height (heighest flower) in 2007 from the Main Experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the Main Experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. In 2007, plant height was recorded twice a year just before biomass harvest (during peak standing biomass in late May and in late August). For target plant individuals at 10 points separated by 1 m each along a transect in the central area in the plots, vegetative height (heighest leaf) and regenerative height (heighest flower) were measured as standing height (without stretching the plant). In 2007, also the plots of the management experiment, that altered mowing frequency and fertilized subplots (see further details below) were sampled by measuring vegatation height five times, every 0.5m on a 3m transekt along the side of the management plots. Provided are the individual measurements and the mean over the measured plants.

Plant height along the plant diversity gradient in the Jena Experiment (Main Experiment, year 2008)

This data set contains measurements of plant height: vegetative height (heighest leaf) and regenerative height (heighest flower) in 2008 from the Main Experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the Main Experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. In 2008, plant height was recorded twice a year just before biomass harvest (during peak standing biomass in late May and in late August). For target plant individuals at 10 points separated by 1 m each along a transect in the central area in the plots, vegetative height (heighest leaf) and regenerative height (heighest flower) were measured as standing height (without stretching the plant). In 2008, also the plots of the management experiment, that altered mowing frequency and fertilized subplots (see further details below) were sampled by measuring vegatation height five times, every 1m on a 5m transekt along the side of the management plots. Provided are the individual measurements and the mean over the measured plants.