Evolutionary history and identification of conservation units in the giant otter, Pteronura brasiliensis.

The giant otter, Pteronura brasiliensis, occupies a range including the major drainage basins of South America, yet the degree of structure that exists within and among populations inhabiting these drainages is unknown. We sequenced portions of the mitochondrial DNA (mtDNA) cytochrome b (612 bp) and control region (383 bp) genes in order to determine patterns of genetic variation within the species. We found high levels of mtDNA haplotype diversity (h = 0.93 overall) and support for subdivision into four distinct groups of populations, representing important centers of genetic diversity and useful units for prioritizing conservation within the giant otter. We tested these results against the predictions of three hypotheses of Amazonian diversification (Pleistocene Refugia, Paleogeography, and Hydrogeology). While the phylogeographic pattern conformed to the predictions of the Refugia Hypothesis, molecular dating using a relaxed clock revealed the phylogroups diverged from one another between 1.69 and 0.84 Ma, ruling out the influence of Late Pleistocene glacial refugia. However, the role of Plio-Pleistocene climate change could not be rejected. While the molecular dating also makes the influence of geological arches according to the Paleogeography Hypothesis extremely unlikely, the recent Pliocene formation of the Fitzcarrald Arch and its effect of subsequently altering drainage pattern could not be rejected. The data presented here support the interactions of both climatic and hydrological changes resulting from geological activity in the Plio-Pleistocene, in shaping the phylogeographic structure of the giant otter

Isolation by distance, not rivers, control the distribution of termite species in the Amazonian rain forest

The spatial distribution of species is affected by dispersal barriers, local environmental conditions and climate. However, the effect of species dispersal and their adaptation to the environment across geographic scales is poorly understood. To investigate the distribution of species from local to broad geographic scales, we sampled termites in 198 transects distributed in 13 sampling grids in the Brazilian Amazonian forest. The sampling grids encompassed an area of 271 500 km2 and included the five major biogeographic regions delimited by Amazonian rivers. Environmental data for each transect were obtained from local measurements and remote sensing. Similar to previous studies, termite species composition at the local scale was mostly associated with measures of soil texture and chemistry. In contrast, termite species composition at broad geographic scales was associated with soil nutrients, and the geographic position of the transects. Between 17 and 30% of the variance in termite species composition could be attributed exclusively to the geographic position of the transects, but could not be attributed to measured environmental variables or the presence of major rivers. Isolation by distance may have strong effects on termite species composition due to historic processes and the spatially structured environments along distinct geological formations of Amazonia. However, in contrast to many taxa in Amazonia, there is no evidence that major rivers are important barriers to termite dispersal

Quantifying regional biodiversity in the tropics : a case study of freshwater fish in Trinidad and Tobago

Funding: European Research Council (AdG BioTIME 250189 and PoC BioCHANGE 727440) (AEM).Extinction rates are predicted to accelerate during the Anthropocene. Quantifying and mitigating these extinctions demands robust data on distributions of species and the diversity of taxa in regional biotas. However, many assemblages, particularly those in the tropics, are poorly characterized. Targeted surveys and historical museum collections are increasingly being used to meet the urgent need for accurate information, but the extent to which these contrasting data sources support meaningful inferences about biodiversity change in regional assemblages remains unclear. Here, we seek to elucidate uncertainty surrounding regional biodiversity estimates by evaluating the performance of these alternative methods in estimating the species richness and assemblage composition of the freshwater fish of Trinidad & Tobago. We compared estimates of regional species richness derived from two freshwater fish datasets: a targeted two year survey of Trinidad & Tobago rivers and historical museum collection records submitted to The University of the West Indies Zoology Museum. Richness was estimated using rarefaction and extrapolation, and assemblage composition was benchmarked against a recent literature review. Both datasets provided similar estimates of regional freshwater fish species richness (50 and 46 species, respectively), with a large overlap (85%) in species identities. Regional species richness estimates based on survey and museum data are thus comparable, and consistent in the species they include. Our results suggest that museum collection data are a viable option for setting reliable baselines in many tropical systems, thereby widening options for meaningful monitoring and evaluation of temporal trends.PostprintPeer reviewe

Environmental proteomics reveals taxonomic and functional changes in an enriched aquatic ecosystem

Aquatic ecosystem enrichment can lead to distinct and irreversible changes to undesirable states. Understanding changes in active microbial community function and composition following organic matter loading in enriched ecosystems can help identify biomarkers of such state changes. In a field experiment, we enriched replicate aquatic ecosystems in the pitchers of the northern pitcher plant, Sarracenia purpurea. Shotgun metaproteomics using a custom metagenomic database identified proteins, molecular pathways, and contributing microbial taxa that differentiated control ecosystems from those that were enriched. The number of microbial taxa contributing to protein expression was comparable between treatments; however, taxonomic evenness was higher in controls. Functionally active bacterial composition differed significantly among treatments and was more divergent in control pitchers than in enriched pitchers. Aerobic and facultative anaerobic bacteria contributed most to identified proteins in control and enriched ecosystems, respectively. The molecular pathways and contributing taxa in enriched pitcher ecosystems were similar to those found in larger enriched aquatic ecosystems and are consistent with microbial processes occurring at the base of detrital food webs. Detectable differences between protein profiles of enriched and control ecosystems suggest that a time series of environmental proteomics data may identify protein biomarkers of impending state changes to enriched states

Co-assortment in integron-associated gene cassette assemblages in environmental DNA samples

<p>Abstract</p> <p>Background</p> <p>It has been shown that integron-associated gene cassettes exist largely in tandem arrays of variable size, ranging from antibiotic resistance arrays of three to five cassettes up to arrays of more than 100 cassettes associated with the vibrios. Further, the ecology of the integron/gene cassette system has been investigated by showing that very many different cassettes are present in even small environmental samples. In this study, we seek to extend the ecological perspective on the integron/gene cassette system by investigating the way in which this diverse cassette metagenome is apportioned amongst prokaryote lineages in a natural environment.</p> <p>Results</p> <p>We used a combination of PCR-based techniques applied to environmental DNA samples and ecological analytical techniques to establish co-assortment within cassette populations, then establishing the relationship between this co-assortment and genomic structures. We then assessed the distribution of gene cassettes within the environment and found that the majority of gene cassettes existed in large co-assorting groups.</p> <p>Conclusions</p> <p>Our results suggested that the gene cassette diversity of a relatively pristine sampling environment was structured into co-assorting groups, predominantly containing large numbers of cassettes per group. These co-assorting groups consisted of different gene cassettes in stoichiometric relationship. Conservatively, we then attributed co-assorting cassettes to the gene cassette complements of single prokaryote lineages and by implication, to large integron-associated arrays. The prevalence of large arrays in the environment raises new questions about the assembly, maintenance and utility of large cassette arrays in prokaryote populations.</p

Persistence Through Collaboration at Sea for Off-Shore and Coastal Operations

Collaboration (Bruzzone et al. 2013a, b, c, d, e, f) is often mentioned as an opportunity to develop new capabilities for autonomous systems; indeed this paper proposes a practical application where use this approach to enhance the autonomy of the systems during operations in coastal areas or around offshore platforms. The proposed case deals with developing a collaborative approach (Bruzzone et al. 2013a, b, c, d, e, f) among an USV (Unmanned Surface Vehicle) with several AUV (Autonomous Underwater Vehicles) to guarantee persistent surveillance over a marine area (Shkurti et al. 2012). Obviously, the proposed solution could be adopted also for defense and homeland security (Bruzzone et al. 2011a, b, 2010) as well as for archeological site protection in consistence with related cost analysis. The authors propose a technological solution as well as a simulation framework to validate and demonstrate the capabilities of this new approach as well as to quantify expected improvements

Temporal overlap and co-occurrence in a guild of sub-tropical tephritid fruit flies

Studies of community assembly have emphasized snapshot comparisons of spatially replicated samples from natural assemblages. Agro-ecosystems are characterized by relatively little habitat heterogeneity and no dispersal barriers for actively flying insects. Therefore, dynamic patterns of species segregation and aggregation are more likely to reflect the direct or indirect effects of species interactions. We studied the temporal organization of a guild of 21 congeneric species of Anastrepha that colonized fruit orchards in Monte Alegre do Sul, São Paulo, Brazil. This assemblage also included the introduced Mediterranean fruit fly Ceratitis capitata. One hundred six consecutive weekly censuses (11 Jan 2002-16 Jan 2004) of flies in guava, loquat, and peach orchards revealed a pattern of minimum abundance during the coldest months of each year (June and July) and a maximum abundance during periods of flowering and fruit ripening. Overall, phenological overlap was greater than expected by chance. However, conditioned on the pattern of seasonal abundances, temporal occurrence and abundance matrices exhibited patterns of significant species segregation and anti-nestedness. In each year, the 3 orchards contained a small number of species pairs that exhibited statistically significant temporal segregation or aggregation. Most aggregated and segregated pairs reflected seasonal shifts in species presences that were not related to variation in air temperature. Most of the significant pairwise associations involved C. capitata: 8 of the 11 segregated pairs and 2 of the 7 aggregated pairs. These results suggest that species interactions between introduced and native species can be an important determinant of species associations in agro-ecosystems

The Influence of Fire on a Rare Serpentine Plant Assemblage: A Five Year Study of Darlingtonia Fens

Premise of the study: Serpentine soils have attracted the attention of evolutionary biologists for decades due to their high number of rare and endemic taxa, though less is known about the ecological factors that govern the diversity and composition of serpentine communities. Theory suggests that vegetation on these low-productivity soils will be relatively resilient to fire, the most common natural disturbance in serpentine systems. Methods: We studied the recovery of vegetation in Darlingtonia fens, a unique habitat dominated by herbaceous perennials, from a major fire that burned ~202,000 hectares in California and Oregon’s Klamath Mountains in 2002. We established permanent plots in 8 unburned and 8 burned fens in 2003 and recorded percent cover of vascular plant species. We re-sampled plots each year through 2007. Key results: Burned fens had less plant cover than unburned fens for two years after the fire. Average species density was ~10% lower in burned fens one year after the fire but ~4-8% higher for the next four years. Burned fens exhibited greater evenness, but not until four years after the fire. Differences in community composition were detected between the two fen types, but species ranks were similar, and species neither were added to, nor removed from, the burned assemblages. Conclusions: Burning of Darlingtonia fens has detectable, albeit modest effects on serpentine communities. Because fens have little or no canopy cover, fire has little influence on light availability in this system. This relatively small resource change, combined with high soil moisture and well-developed underground organs of fen plants, produces a highly resilient assemblage.Organismic and Evolutionary BiologyOther Research Uni

Robust estimation of microbial diversity in theory and in practice

Quantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of microbial diversity has received renewed attention with the advent of large-scale metagenomic studies. Here, we consider what the diversity observed in a sample tells us about the diversity of the community being sampled. First, we argue that one cannot reliably estimate the absolute and relative number of microbial species present in a community without making unsupported assumptions about species abundance distributions. The reason for this is that sample data do not contain information about the number of rare species in the tail of species abundance distributions. We illustrate the difficulty in comparing species richness estimates by applying Chao's estimator of species richness to a set of in silico communities: they are ranked incorrectly in the presence of large numbers of rare species. Next, we extend our analysis to a general family of diversity metrics ("Hill diversities"), and construct lower and upper estimates of diversity values consistent with the sample data. The theory generalizes Chao's estimator, which we retrieve as the lower estimate of species richness. We show that Shannon and Simpson diversity can be robustly estimated for the in silico communities. We analyze nine metagenomic data sets from a wide range of environments, and show that our findings are relevant for empirically-sampled communities. Hence, we recommend the use of Shannon and Simpson diversity rather than species richness in efforts to quantify and compare microbial diversity.Comment: To be published in The ISME Journal. Main text: 16 pages, 5 figures. Supplement: 16 pages, 4 figure