Metaxa2 Diversity Tools: Easing microbial community analysis with Metaxa2

DNA sequencing has become an integrated part of microbial ecology, and taxonomic marker genes such as the SSU and LSU rRNA are frequently used to assess community structure. One solution for taxonomic community analysis based on shotgun metagenomic data is the Metaxa2 software, which can extract and classify sequence fragments belonging to the rRNA genes. This paper describes the Metaxa2 Diversity Tools, a set of new open-source software programs that extends the capabilities of the Metaxa2 software. These tools allow for better handling of data from multiple samples, improved species classifications, rarefaction analysis accounting for unclassified entries, and determination of significant differences in community composition of different samples. We demonstrate the performance of the software tools on rRNA data extracted from different shotgun metagenomes, and find the tools to streamline and improve the assessments of community diversity, particularly for samples from environments for which few reference genomes are available. Finally, we establish that our resampling algorithm for determining community dissimilarity is robust to differences in coverage depth, suggesting that it forms a complement to multidimensional visualization approaches for finding differences between communities. The Metaxa2 Diversity Tools are included in recent versions (2.1 and later) of Metaxa2 (http://microbiology.se/software/metaxa2/) and facilitate implementation of Metaxa2 within software pipelines for taxonomic analysis of environmental communities.     

Habitat heterogeneity and niche structure of trees in two tropical rain forests

Dispersal-assembly theories of species coexistence posit that environmental factors play no role in explaining community diversity and structure. Dispersal-assembly theories shed light on some aspects of community structure such as species-area and species-abundance relationships. However, species environmental associations also affect these measures of community structure. Measurements of species niche breadth and overlap address this influence. Using a new continuous measure of niche and a dispersal-assembly null model that maintains species niche breadth and aggregation, we tested two hypotheses assessing the effects of habitat heterogeneity on the ability of dispersal-assembly theories to explain community niche structure. We found that in both homogenous and heterogeneous environments dispersal-assembly theories cannot fully explain observed niche structure. The performance of the dispersal-assembly null models was particularly poor in heterogeneous environments. These results indicate that non-dispersal based mechanisms are in part responsible for observed community structure and measures of community structure which include species environmental associations should be used to test theories of species diversity.     

Genetic architecture of adaptive differentiation in evolving host races of the soapberry bug,Jadera haematoloma

To explore genetic architecture and adaptive evolution, we conducted environmental and genetic experiments with two recently (ca. 100 generations) diverged, geographically adjacent races of the soapberry bug. One race occurs on a native host plant species, the other on an introduced host. We focused on three traits: length of the mouthparts, body size and development time. The first experiment was an environmental manipulation, comparing individuals of each population reared on one or the other host species (cross-rearing) and estimating three evolutionary rates for each trait. The first rate, evolutionary path compares ancestral-derived populations when both were reared on the introduced host. The second, current ecological contrast compares populations with each reared on its natal host. The third, evolved tradeoff compares the two races when reared on the native host. Differences among these rates are striking and informative. For example, development time, which appears to be relatively undifferentiated phenotypically, has actually evolved very rapidly via countergradient selection. The pattern differs for each trait, and clear developmental tradeoffs have evolved as quickly as adaptation to the new host in each. The second experiment was a two-generation line cross study. With joint-scaling analyzes, we compared purebred, hybrid and backcrossed individuals to describe genetic architecture. Additive genetic variance for mouthpart length was consistently large (ca. 60%), but the interaction of dominance, maternal effects and epistasis was important in the other traits. Rearing host strongly affected genetic architecture. There was no clear relationship between genetic architecture and rate of evolution. Selection has produced both additive and nonadditive differentiation between the host races with surprising speed, consistent with theoretical predictions about evolution in fitness-associated traits.     

Field and culture studies on the ecophysiology of the toxic dinoflagellate Alexandrium minutum (Halim) present in Greek coastal waters

In Greek coastal waters, the toxic dinoflagellate Alexandrium minutum (strain AJ879163) was detected for the first time in spring 2002. This species proliferated during spring–summer of 2002 and 2003 over a wide geographic range along the north-south Aegean Sea coastline, mostly at low concentrations (average: 10²–10³ cells L⁻¹) with one exception of higher abundance (average: 10⁵ cells L⁻¹). This study presents data on environmental (temperature, salinity, chl α, nutrients) and ecological (phytoplankton species composition, diversity, taxa dominance, community dissimilarities) parameters in the areas of A. minutum occurrence. A. minutum was isolated and grown in batch cultures used in a series of bioassay experiments for determination of its pigment composition by HPLC, half saturation constants (K_s) for nitrogen and phosphorus, and its response to different nitrogen to phosphorus (N:P) ratios.     

Characterization of low-molecular-weight-glutenin subunit genes from the D-genome of Triticum aestivum,Aegilops crassa,Ae. cylindrica and Ae. tauschii

Twenty low-molecular-weight-glutenin subunit (LMW-GS) gene sequences from the D-genome from Aegilops crassa (2n = 4x = 28), Ae. cylindrica (2n = 4x = 28), Ae. tauschii (2n = 2x = 14) and Triticum aestivum (2n = 6x = 42) were obtained using five sets of specific allele primer pairs. Only the sequences of the first primer pair were complete coding sequences (cds) of LMW-GS, and had 305, 304, 306 and 305 LMW-m amino acid residues in Ae. crassa, Ae. cylindrica, Ae. tauschii and T. aestivum, respectively. The repetitive domain and repeat motif numbers of all LMW glutenin subunits showed eight conserved cysteine residues that lead to the same functional activity in different genome. Based on DNA and predicted protein sequences, phylogenetic trees for all sets of sequences were drawn. At the DNA level, the species closest to T. aestivum for the second, third, fourth and fifth set of sequences were Ae. cylindrica, Ae. tauschii and Ae. crassa, respectively. At the protein level, the species closest to T. aestivum based on the first, second and fifth set of sequences were Ae. cylindrica, Ae. crassa and Ae. crassa, respectively. For other sets of sequences, bread wheat proved to be a distinct species. The LMW-GS gene sequences have been recorded in the GenBank with accession numbers JQ726549–JQ726568JQ726549JQ726550JQ726551JQ726552JQ726553JQ726554JQ726555JQ726556JQ726557JQ726558JQ726559JQ726560JQ726561JQ726562JQ726563JQ726564JQ726565JQ726566JQ726567JQ726568.     

EcoIS: An image serialization library for plot-based plant flowering phenology

Image series are increasingly being used to output ecological indicators because they provide the ability to reanalyze data that has already been collected and they improve temporal as well as spatial resolution. We address both the increased utilization and the need to diversify the way they are produced by introducing an open source Python (www.python.org) library called EcoIS that creates image series from unaligned pictures of specially equipped plots. We use EcoIS to sample flowering phenology plots in a high arctic environment and create image series that later generate phenophase counts and automatically estimate phenological dates of interest. Our results exhibit one day difference between EcoIS estimations of local indicators and the ones calculated with the established field-based process. We show that EcoIS' error is similar to the one of image series generated with fixed camera setups. We see that EcoIS processes an image in 3.8 s and show how it is equipped to handle data intensive scenarios. We additionally identify in-camera automatic image formatting and image acquiring oversight as contributing factors for increasing the overall error. Our main conclusion is that EcoIS creates usable image series that maintain the spatiotemporal qualities of the original images and can successfully be utilized to generate ecological indicators. EcoIS is relevant as a replacement for traditional image series infrastructure where the cost of deploying EcoIS is smaller or less intrusive to the ecosystem.     

A phenological mid-domain effect in flowering diversity

In this paper, we test the mid-domain hypothesis as an explanation for observed patterns of flowering diversity in two sub-alpine communities of insect-pollinated plants. Observed species richness patterns showed an early-season increase in richness, a mid-season peak, and a late-season decrease. We show that a mid-domain null model can qualitatively match this pattern of flowering species richness, with R² values typically greater than 60%. We find significant or marginally significant departures from expected patterns of diversity for only 3 out of 12 year-site combinations. On the other hand, we do find a consistent pattern of departure when comparing observed versus null-model predicted flowering diversity averaged across years. Our results therefore support the hypothesis that ecological factors shape patterns of flowering phenology, but that the strength or nature of these environmental forcings may differ between years or the two habitats we studied, or may depend on species-specific characteristics of these plant communities. We conclude that mid-domain null models provide an important baseline from which to test departure of expected patterns of flowering diversity across temporal domains. Geometric constraints should be included first in the list of factors that drive seasonal patterns of flowering diversity.     

Influence of temperature and food availability on the ecological energetics of the giant scallop Placopecten magellanicus

Summary Gonad output, reproductive effort and residual reproductive value are greater in scallops (Placopecten magellanicus) from shallow water, where conditions are more favourable, than in scallops from deep water. Variation between years in these fitness correlates is also greater in shallow water scallops. High reproductive effort is associated with a greater reproductive cost, although in general reproduction in this species appears to be restrained, and only in older individuals from shallow water is there evidence of reckless reproductive behaviour. Reproductive effort increases as the animal grows older, but residual reproductive value is a maximum at age 4 years, after which it decreases with age owing to greater mortality. Localities vary in their suitability for scallop growth and reproduction, and at one Newfoundland site conditions in shallow water (10 m) are better than those in deep water (31 m). Scallops from the former have a greater fitness than those from the latter. The energy costs of reproduction have implications for life history variability in P. magellanicus, although for a considerable part of its lifetime the scallop is able to maximise gamete production in response to environmental factors (especially the food supply) without trading off reproduction against growth or maintenance.     

The myth of constant predator: prey ratios

Apparent constancy in the ratio of predator species to prey species has been offered as evidence that ecological communities are structured by interspecific interactions. If significantly different from random expectation, this effect would be one of the few sound pieces of evidence for community structure. The evidence was re-evaluated by using the data from previous studies to form species pools, and forming simulated communities by drawing species at random from these pools (with replacement). Using a correlation coefficient (number of predator species versus number of prey species), and also the statistic used by the original workers (where different), the observed predator:prey correlation was compared to that for the random communities. In five studies, the observed predator:prey ratio was not significantly different from random expectation. In the only two studies where there was significant departure from the null model, it was with more variation in the ratio than expected on a random basis. It is concluded that there is as yet no evidence for near-constant predator:prey ratios.     

loop: An R package for performing decomposition of weighted directed graphs,food web analysis and flexible network plotting

Demographic loop analysis is one of the basic methods applied in life cycle analysis in population ecology. Here, we developed an R package called “loop” to implement the algorithmic approach of loop analysis developed by a previous work. Additionally, the package can provide flexible network plotting and food web analysis as well. In this paper we illustrated the loop decomposition analysis using the life-cycle graph of a tropical tree species Vouacapoua americana; and performed food web statistics for the two real food webs for illustrating food web plotting and detecting key species in securing food web persistence. The package, including source code and binary versions, is available at the following URL: http://cran.r-project.org/web/packages/loop/.     

Anencephalus and spina bifida: An ecological approach

The ecological approach to the etiology of disease involves consideration of the complex interactions of factors related to the host, agent, and environment. Although the ecological approach was developed with regard to infectious diseases, this article suggests its application as a meaningful approach to understanding the etiology of anencephalus and spina bifida. Host, agent, and environmental factors thought to be important in the development of these malformations are discussed. Translation of this conceptual approach into a testable model is needed.Presented in part at the symposium, Anthropology and Medical Education, 44th Annual Meeting of the American Association of Physical Anthropologists, Denver, Colorado, April 9–12, 1975.     

Niche Divergence in a Brown Lemur (<Emphasis Type="Italic">Eulemur</Emphasis> spp.) Hybrid Zone: Using Ecological Niche Models to Test Models of Stability

Endogenous selection is often implicated in the maintenance of stability of natural hybrid zones. Environmental conditions often vary across these zones, suggesting that local adaptation to ecological conditions could also play a role in this process. We used niche modeling to investigate these alternatives in a hybrid zone between two species of brown lemur (Eulemur rufifrons and E. cinereiceps) in southeastern Madagascar. We produced ecological niche models (ENMs) for parental and hybrid populations and compared values of niche overlap to null expectations using identity and background tests. All three taxonomic groups had nonequivalent ENMs with limited spatial overlap, supporting a role for niche divergence and local adaptation in the maintenance of this zone. However, values of niche overlap between ENMs were not greater than null expectations controlling for background environmental differences. These results could suggest that taxa in this hybrid zone inhabit portions of their environments that are more similar to their backgrounds, i.e., niche conservatism. Nevertheless, we did find evidence of niche divergence when using background tests that examined environmental variables separately. Although we could not rule out models indicating selection against hybrids, most lines of evidence were consistent with predictions for the bounded superiority model of hybrid zone stability. This study thus provides support that exogenous, environmental selection may be responsible for maintaining the hybrid zone, and may be implicated in the evolutionary divergence of these taxa.     

Morphology and SSU rDNA-based phylogeny of two Euplotes species from China: E. wuhanensis sp. n. and E. muscicola Kahl, 1932 (Ciliophora,Euplotida)

The living morphology, infraciliature and silverline system of two small Euplotes species, E. wuhanensis sp. n. and E. muscicola Kahl, 1932, isolated from Wuhan, central China, were investigated. Euplotes wuhanensis sp. n. is characterized by a combination of features including small size (40–50 × 25–30 μm), two conspicuously small and eight normal-sized frontoventral cirri, five transverse cirri in two groups, two marginal and two caudal cirri, seven dorsal kineties with about 12 dikinetids in the mid-dorsal row and a double-eurystomus type of dorsal silverline pattern. The Wuhan population of E. muscicola closely resembles previously described populations. The establishments of three subspecies of E. muscicola are not supported. The small subunit ribosomal RNA gene sequences were determined for both species. We propose that the two sequences under the name of E. muscicola (No. AJ305254, DQ917684 deposited in GenBank) are very likely from misidentified material. Phylogenetic analyses based on these data support the validity of both E. muscicola and E. wuhanensis as distinct species.     

Atul Butte discusses the divide between bioinformatics and the clinic

Atul Butte is an Assistant in Endocrinology and Informatics and Attending Physician at Children's Hospital, Boston, USA (http://www.chip.org), and is an Instructor in Paediatrics at Harvard Medical School (http://www.harvard.edu). He received his undergraduate degree in Computer Science from Brown University in 1991, and worked in several stints as a software engineer at Apple Computer and Microsoft Corporation. He graduated from the Brown University School of Medicine in 1995, during which he worked as a research fellow at National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK; http://www.niddk.nih.gov) through the Howard Hughes/NIH Research Scholars Program. He completed his residency in Paediatrics and Fellowship in Paediatric Endocrinology in 2001, both at Children's Hospital. During his research under Isaac Kohane (at Children's Hospital) he developed a novel methodology for analyzing large data sets of RNA expression, called Relevance Networks. His recent awards include the 2003 Emory University School of Medicine, Pathology Residents’ Choice Award, 2002 American Association for Clinical Chemistry Outstanding Speaker Award, 2002 Endocrine Society Travel Award based on presentation merit, 2001 American Association for Cancer Research Scholar-In-Training Award and the 2001 Lawson Wilkins Paediatric Endocrine Society Clinical Scholar Award.     

Automated sperm head morphology analyzer for open-source software

Sperm head morphology has been identified as a characteristic that can be used to predict a male's semen quality. In the present study, we have developed an automated sperm head morphology analysis (ASMA) plug-in for open-source ImageJ software (http://rsbweb.nih.gov/ij/). We describe the plug-in's functionality, and confirm its validity for sperm head morphology analysis using fish sperm. Sperm head morphological measurements (length and width) made with the ASMA plug-in did not differ from manual measurements. Using the plug-in to measure sperm head-shaped objects of known size, the associated plug-in error rate was < 0.5%. Brightness and contrast ratios influenced sperm head measurements, suggesting the need for standardized protocols. This plug-in was effective at measuring elliptical (i.e., Atlantic cod) as well as slightly irregular (i.e., Chinook salmon) shaped sperm heads. In conclusion, our ASMA plug-in represents a versatile alternative to costly sperm morphology software.     

Community structure,social organization and ecological requirements of coral reef fish (Pomacentridae)

In the Gulf of Aqaba (Red Sea), 25 species of damselfish (Pomacentridae) which form typical interspecific communities were studied. Several species are typical for different depth zones, others are ubiquitous. Damselfish are variously specialized in feeding (herbivore, omnivore, plankton-carnivore); habitat (bottom-dwelling, midwater); home-and-shelter site (selective or unselective). Environmental factors and social structures were found to be interlinked. Species with the same social structure are similarly specialized ecologically. A hypothetical flow diagram shows the effects of abiotic and biotic factors on group size, available food, and social structure. Damselfish are extremely flexible to environmental change, showing intraspecific modification of group structure, feeding habits, reproductive strategy etc. Experimental results suggest a strong selection against redundant males. This research is considered a pilot study for future field work, aimed at a prediction of environmental influences on behaviour.Supported by the Deutsche Forschungsgemeinschaft, Bad Godesberg, and the Max-Planck-Institut für Verhaltensphysiologie, Seewiesen.     

A null model of guild proportionality,applied to stratification of a New Zealand temperate rain forest

Summary Much ecological theory assumes that the number of species that can coexist (by species packing) is limited, because competitive exclusion occurs when any pair of species within a guild is too similar — species saturation or niche limitation. If such niche limitation occurs, the proportion of species in each guild should be relatively constant — guild proportionality. This concept is applied to the guilds represented by strata in a forest. A method is produced, and used to examine a New Zealand temperate rain forest. Most strata showed no deviation from a null model of no niche limitation, i.e. no tendency to guild proportionality. The proportion of lianes was more variable than in the null model, tending to be inversely related to the proportion of epiphytes, Canopy tree proportion was significantly more constant than in the null model, but this could be interpreted as a limit caused by the size of a canopy tree individual.     

DNA sequencing of 13 cytokine gene fragments of Aotus infulatus and Saimiri sciureus,two non-human primate models for malaria

Aotus and Saimiri are non-human primate models recommended by the World Health Organization for experimental studies in malaria, especially for vaccine pre-clinical trials. However, research using these primates is hindered by the lack of specific reagents to evaluate immune responses to infection or vaccination. As a step toward developing molecular tools for cytokine expression studies in these species, primer pairs for 18 cytokine gene fragments were designed based on human DNA sequences and used to amplify the corresponding genes in Aotus infulatus and Saimiri sciureus genomic DNA samples. IFNγ, TNFα, LTA, IL2, IL3, IL4, IL5, IL6, IL10, IL12, IL13, CSF2 and TGFβ2 gene fragments were amplified and sequenced. Primer pairs for IL8, IL17, IL18, IL27 and MIF failed to generate amplification products. When compared to the available corresponding human and non-human primate sequences, most – except IL3 and IL4 – showed identity degrees above 90%. Small variations in sequence can help to explain the failure to amplify certain genes or the amplification only at lower annealing temperatures as compared to human DNA samples for several primer pairs. The sequences made available provide the basis for designing molecular tools such as primers for real time PCR specific for A. infulatus and/or S. sciureus.The nucleotide sequences reported in this paper have been submitted to the GenBank nucleotide sequence database and have been assigned accession numbers DQ985386 to DQ985389, DQ989356 to DQ989369, FJ89020 to FJ89024 and FJ89029.     

Environmental niche equivalency versus conservatism: quantitative approaches to niche evolution

Environmental niche models, which are generated by combining species occurrence data with environmental GIS data layers, are increasingly used to answer fundamental questions about niche evolution, speciation, and the accumulation of ecological diversity within clades. The question of whether environmental niches are conserved over evolutionary time scales has attracted considerable attention, but often produced conflicting conclusions. This conflict, however, may result from differences in how niche similarity is measured and the specific null hypothesis being tested. We develop new methods for quantifying niche overlap that rely on a traditional ecological measure and a metric from mathematical statistics. We reexamine a classic study of niche conservatism between sister species in several groups of Mexican animals, and, for the first time, address alternative definitions of "niche conservatism" within a single framework using consistent methods. As expected, we find that environmental niches of sister species are more similar than expected under three distinct null hypotheses, but that they are rarely identical. We demonstrate how our measures can be used in phylogenetic comparative analyses by reexamining niche divergence in an adaptive radiation of Cuban anoles. Our results show that environmental niche overlap is closely tied to geographic overlap, but not to phylogenetic distances, suggesting that niche conservatism has not constrained local communities in this group to consist of closely related species. We suggest various randomization tests that may prove useful in other areas of ecology and evolutionary biology.