How many species are there on Earth?

Quantification of HTLV-1 clonality and TCR diversity

Estimation of immunological and microbiological diversity is vital to our understanding of infection and the immune response. For instance, what is the diversity of the T cell repertoire? These questions are partially addressed by high-throughput sequencing techniques that enable identification of immunological and microbiological "species" in a sample. Estimators of the number of unseen species are needed to estimate population diversity from sample diversity. Here we test five widely used non-parametric estimators, and develop and validate a novel method, DivE, to estimate species richness and distribution. We used three independent datasets: (i) viral populations from subjects infected with human T-lymphotropic virus type 1; (ii) T cell antigen receptor clonotype repertoires; and (iii) microbial data from infant faecal samples. When applied to datasets with rarefaction curves that did not plateau, existing estimators systematically increased with sample size. In contrast, DivE consistently and accurately estimated diversity for all datasets. We identify conditions that limit the application of DivE. We also show that DivE can be used to accurately estimate the underlying population frequency distribution. We have developed a novel method that is significantly more accurate than commonly used biodiversity estimators in microbiological and immunological populations.

Arboreal ant colonies as 'hot-points' of cryptic diversity for myrmecophiles: the weaver ant Camponotus sp. aff. textor and its interaction network with its associates

INTRODUCTION

Systematic surveys of macrofaunal diversity within ant colonies are lacking, particularly for ants nesting in microhabitats that are difficult to sample. Species associated with ants are generally small and rarely collected organisms, which makes them more likely to be unnoticed. We assumed that this tendency is greater for arthropod communities in microhabitats with low accessibility, such as those found in the nests of arboreal ants that may constitute a source of cryptic biodiversity.

MATERIALS AND METHODS

We investigated the invertebrate diversity associated with an undescribed, but already threatened, Neotropical Camponotus weaver ant. As most of the common sampling methods used in studies of ant diversity are not suited for evaluating myrmecophile diversity within ant nests, we evaluated the macrofauna within ant nests through exhaustive colony sampling of three nests and examination of more than 80,000 individuals.

RESULTS

We identified invertebrates from three classes belonging to 18 taxa, some of which were new to science, and recorded the first instance of the co-occurrence of two brood parasitoid wasp families attacking the same ant host colony. This diversity of ant associates corresponded to a highly complex interaction network. Agonistic interactions prevailed, but the prevalence of myrmecophiles was remarkably low.

CONCLUSIONS

Our data support the hypothesis of the evolution of low virulence in a variety of symbionts associated with large insect societies. Because most myrmecophiles found in this work are rare, strictly specific, and exhibit highly specialized biology, the risk of extinction for these hitherto unknown invertebrates and their natural enemies is high. The cryptic, far unappreciated diversity within arboreal ant nests in areas at high risk of habitat loss qualifies these nests as 'hot-points' of biodiversity that urgently require special attention as a component of conservation and management programs.

The biodiversity of species and their rates of extinction, distribution, and protection

Recent studies clarify where the most vulnerable species live, where and how humanity changes the planet, and how this drives extinctions. We assess key statistics about species, their distribution, and their status. Most are undescribed. Those we know best have large geographical ranges and are often common within them. Most known species have small ranges. The numbers of small-ranged species are increasing quickly, even in well-known taxa. They are geographically concentrated and are disproportionately likely to be threatened or already extinct. Current rates of extinction are about 1000 times the likely background rate of extinction. Future rates depend on many factors and are poised to increase. Although there has been rapid progress in developing protected areas, such efforts are not ecologically representative, nor do they optimally protect biodiversity.

Influence of artifact removal on rare species recovery in natural complex communities using high-throughput sequencing

Large-scale high-throughput sequencing techniques are rapidly becoming popular methods to profile complex communities and have generated deep insights into community biodiversity. However, several technical problems, especially sequencing artifacts such as nucleotide calling errors, could artificially inflate biodiversity estimates. Sequence filtering for artifact removal is a conventional method for deleting error-prone sequences from high-throughput sequencing data. As rare species represented by low-abundance sequences in datasets may be sensitive to artifact removal process, the influence of artifact removal on rare species recovery has not been well evaluated in natural complex communities. Here we employed both internal (reliable operational taxonomic units selected from communities themselves) and external (indicator species spiked into communities) references to evaluate the influence of artifact removal on rare species recovery using 454 pyrosequencing of complex plankton communities collected from both freshwater and marine habitats. Multiple analyses revealed three clear patterns: 1) rare species were eliminated during sequence filtering process at all tested filtering stringencies, 2) more rare taxa were eliminated as filtering stringencies increased, and 3) elimination of rare species intensified as biomass of a species in a community was reduced. Our results suggest that cautions be applied when processing high-throughput sequencing data, especially for rare taxa detection for conservation of species at risk and for rapid response programs targeting non-indigenous species. Establishment of both internal and external references proposed here provides a practical strategy to evaluate artifact removal process.

A novel method for estimating the number of species within a region

Ecologists are often required to estimate the number of species in a region or designated area. A number of diversity indices are available for this purpose and are based on sampling the area using quadrats or other means, and estimating the total number of species from these samples. In this paper, a novel theory and method for estimating the number of species is developed. The theory involves the use of the Laplace method for approximating asymptotic integrals. The method is shown to be successful by testing random simulated datasets. In addition, several real survey datasets are tested, including forests that contain a large number (tens to hundreds) of tree species, and an aquatic system with a large number of fish species. The method is shown to give accurate results, and in almost all cases found to be superior to existing tools for estimating diversity.

DNA barcoding to map the microbial communities: current advances and future directions

During the last two decades, the DNA barcode development towards microbial community has increased dramatically. DNA barcode development is related to error-free and quick species identification which aid in understanding the microbial biodiversity, as well as the diseases related to microbial species. Here, we seek to evaluate the so-called barcoding initiatives for the microbial communities and the emerging trends in this field. In this paper, we describe the development of DNA marker-based DNA barcoding system, comparison between routine species identification and DNA barcode, and microbial biodiversity and DNA barcode for microbial communities. Two major topics, such as the molecular diversity of viruses and barcode for viruses have been discussed at the same time. We demonstrate the current status and the maker of DNA barcode for bacteria, algae, fungi, and protozoa. Furthermore, we argue about the promises, limitations, and present and future challenges of microbial barcode development.

Micromonospora polyrhachis sp. nov., an actinomycete isolated from edible Chinese black ant (Polyrhachis vicina Roger)

A novel actinomycete, designated strain NEAU-ycm2T, was isolated from edible Chinese black ants (Polyrhachis vicina Roger) and characterized using a polyphasic approach. The organism was found to have morphological and chemotaxonomic characteristics typical of the genus Micromonospora . The 16S rRNA gene sequence of strain NEAU-ycm2T showed highest similarity to those of Micromonospora sonneratiae 274745T (99.12 %), Micromonospora pattaloongensis TJ2-2T (98.85 %), Micromonospora pisi GUI 15T (98.76 %), Polymorphospora rubra TT 97-42T (98.42 %) and Micromonospora eburnea LK2-10T (98.21 %). Phylogenetic analysis based on the 16S rRNA gene and gyrB gene demonstrated that strain NEAU-ycm2T is a member of the genus Micromonospora and supported the close phylogenetic relationship to M. sonneratiae 274745T, M. pattaloongensis JCM 12833T and M. pisi GUI 15T. Furthermore, a combination of DNA–DNA hybridization and some physiological and biochemical properties indicated that the novel strain could be readily distinguished from its closest phylogenetic relatives. Therefore, it is proposed that NEAU-ycm2T represents a novel species of the genus of Micromonospora , for which the name Micromonospora polyrhachis sp. nov. is proposed. The type strain is NEAU-ycm2T ( = CGMCC 4.7100T = DSM 45886T).

Skipper Richness (Hesperiidae) Along Elevational Gradients in Brazilian Atlantic Forest

Hesperiidae are claimed to be a group of elusive butterflies that need major effort for sampling, thus being frequently omitted from tropical butterfly surveys. As no studies have associated species richness patterns of butterflies with environmental gradients of high altitudes in Brazil, we surveyed Hesperiidae ensembles in Serra do Mar along elevational transects (900-1,800 m above sea level) on three mountains. Transects were sampled 11-12 times on each mountain to evaluate how local species richness is influenced by mountain region, vegetation type, and elevational zones. Patterns were also analyzed for the subfamilies, and after disregarding species that exhibit hilltopping behavior. Species richness was evaluated by the observed richness, Jacknife2 estimator and Chao 1 estimator standardized by sample coverage. Overall, 155 species were collected, but extrapolation algorithms suggest a regional richness of about 220 species. Species richness was far higher in forest than in early successional vegetation or grassland. Richness decreased with elevation, and was higher on Anhangava mountain compared with the two others. Patterns were similar between observed and extrapolated Jacknife2 richness, but vegetation type and mountain richness became altered using sample coverage standardization. Hilltopping species were more easily detected than species that do not show this behavior; however, their inclusion did neither affect estimated richness nor modify the shape of the species accumulation curve. This is the first contribution to systematically study highland butterflies in southern Brazil where all records above 1,200 m are altitudinal extensions of the known geographical ranges of skipper species in the region.

Physical principles of fluid-mediated insect attachment - Shouldn't insects slip?

Insects use either hairy or smooth adhesive pads to safely adhere to various kinds of surfaces. Although the two types of adhesive pads are morphologically different, they both form contact with the substrate via a thin layer of adhesive fluid. To model adhesion and friction forces generated by insect footpads often a simple "wet adhesion" model is used, in which two flat undeformable substrates are separated by a continuous layer of fluid. This review summarizes the key physical and tribological principles that determine the adhesion and friction in such a model. Interestingly, such a simple wet-adhesion model falls short in explaining several features of insect adhesion. For example, it cannot predict the observed high static friction forces of the insects, which enable them to cling to vertical smooth substrates without sliding. When taking a closer look at the "classic" attachment model, one can see that it is based on several simplifications, such as rigid surfaces or continuous layers of Newtonian fluids. Recent experiments show that these assumptions are not valid in many cases of insect adhesion. Future tribological models for insect adhesion thus need to incorporate deformable adhesive pads, non-Newtonian properties of the adhesive fluid and/or partially "dry" or solid-like contact between the pad and the substrate.

Author inflation masks global capacity for species discovery in flowering plants

Species discovery is a fundamental first step for all of biodiversity science. Recent research has claimed that the increasing number of authors associated with the description of new species represents an expanding workforce discovering the remaining new species from an ever-diminishing pool. Here, we present a comprehensive dataset from The International Plant Names Index (IPNI) of new species of flowering plant published between 1970 and 2011. We show that, on average, 1855 new species have been described annually since 1970. We show that compared to other scientific disciplines the increased number of authors on taxonomic papers is relatively small and may reflect changes in scientific practice rather than an increase in taxonomic capacity. These data, alongside published results demonstrating a lag period of 35 yr between a specimen being collected and published as a new species, strongly suggest that the global taxonomic capacity to describe new species of flowering plant is stagnant at a time of unprecedented concern for conservation and extinction.

Distribution and Conservation ofDavilla(Dilleniaceae) in Brazilian Atlantic Forest Using Ecological Niche Modeling

We have modeled the ecological niche for 12 plant species belonging to the genusDavilla(Dilleniaceae) which occur in the Atlantic Forest of Brazil. This group includes endemic species lianas threatened by extinction and is therefore a useful indicator for forest areas requiring conservation. The aims are to compare the distribution and richness of species within the protected areas, assessing the degree of protection and gap analysis of reserves for this group. We used the Maxent algorithm with environmental and occurrence data, and produced geographic distribution maps. The results show that high species richness occurs in forest and coastal forest of Espírito Santo to Bahia states. The endemic species compriseD. flexuosa, D. macrocarpa, D. flexuosa, D. grandifolia, andD. sessilifolia. In the Atlantic Forest of southeastern Brazil, the following endemic species occur:D. tintinnabulataandD. glaziovii, with this latter species being included in the “red list” due habitat loss and predatory extractivism. The indicators of species richness in the coastal region of Bahia correspond with floristic inventories that point to this area having a high biodiversity. Although this region has several protected areas, there are gaps in reserves, which, combined with anthropogenic threats and fragmentation, have caused several problems for biodiversity.

BioNames: linking taxonomy, texts, and trees

BioNames is a web database of taxonomic names for animals, linked to the primary literature and, wherever possible, to phylogenetic trees. It aims to provide a taxonomic “dashboard” where at a glance we can see a summary of the taxonomic and phylogenetic information we have for a given taxon and hence provide a quick answer to the basic question “what is this taxon?” BioNames combines classifications from the Global Biodiversity Information Facility (GBIF) and GenBank, images from the Encyclopedia of Life (EOL), animal names from the Index of Organism Names (ION), and bibliographic data from multiple sources including the Biodiversity Heritage Library (BHL) and CrossRef. The user interface includes display of full text articles, interactive timelines of taxonomic publications, and zoomable phylogenies. It is available at http://bionames.org.

Microclimatic challenges in global change biology

Despite decades of work on climate change biology, the scientific community remains uncertain about where and when most species distributions will respond to altered climates. A major barrier is the spatial mismatch between the size of organisms and the scale at which climate data are collected and modeled. Using a meta-analysis of published literature, we show that grid lengths in species distribution models are, on average, ca. 10 000-fold larger than the animals they study, and ca. 1000-fold larger than the plants they study. And the gap is even worse than these ratios indicate, as most work has focused on organisms that are significantly biased toward large size. This mismatch is problematic because organisms do not experience climate on coarse scales. Rather, they live in microclimates, which can be highly heterogeneous and strongly divergent from surrounding macroclimates. Bridging the spatial gap should be a high priority for research and will require gathering climate data at finer scales, developing better methods for downscaling environmental data to microclimates, and improving our statistical understanding of variation at finer scales. Interdisciplinary collaborations (including ecologists, engineers, climatologists, meteorologists, statisticians, and geographers) will be key to bridging the gap, and ultimately to providing scientifically grounded data and recommendations to conservation biologists and policy makers.

Assessment of theoretical methods for the study of hydrogen abstraction kinetics of global warming gas species during their degradation and byproduct formation (IUPAC Technical Report)

Global climate change is a major concern as it leads to an increase in the average temperature of the earth’s atmosphere. The existence and persistence of some gaseous species in the atmosphere contribute to global warming. Experimental techniques are used to study the kinetics and degradation of global warming gases. However, quantum mechanical methods are also useful for the kinetic and radiative forcing study of global warming species and can precede experimental investigations. Research has also been targeted to develop more adapted procedures using ab initio and density functional theory (DFT) methods. This report provides a global perspective, in simplified manner, of the theoretical studies of the degradation of gas species in the atmosphere with an emphasis on the hydrogen abstraction kinetics of global warming gas species during their degradation and byproduct formation. En route, the results obtained from these studies are analysed and compared with experimental data where available. Our analyses indicate that the theoretical predictions are in agreement with experimental findings but the predicted parameters are dependent on the method being used. Theoretical methods are used to predict the thermodynamic parameters of reactions, and, with relevance to this report, the global warming potential (GWP) index can also be calculated. This report can be useful for future investigations involving global warming gaseous species while providing suggestions on how computations can fill in data gaps when experimental data are unavailable.

Demography and competition in Hyrax : A 17 years study

This study investigates the demography and interspecific interactions of 6 Heterohyrax brucei and 4 Procavia johnstoni populations, which inhabited 6 kopjes (rock outcrops) in the Serengeti National Park, Tanzania over a period of 17 years. On three kopjes (H1, O2 and PH2) both species lived sympatrically, while on the other three (H2, H3 and P1) either one or the other species occurred allopatrically. The rainfall pattern between 1971/1972 and 1981/1982 had undergone major changes. There was significantly less precipitation in the wet season and the dry season had become extremer and longer. The kopje vegetation, recorded as percentage crown cover of browse from bushes and trees, had changed also, decreasing between 1971/72 and 1982 on 5 kopjes. In three kopjes (H1, O2 and PH2), which were shared by both hyrax species, an increase in the number of P. johnstoni, a decrease (H1 and O2) and extinction (PH2) of H. brucei took place between the time periods 1971-1976 ("good browse years") and 1982-1984 ("poor browse years"). These changes are probably the result of indirect interspecific competition (exploitative competition) for browse material, which is the main food source for both species during the dry season. When the browsing resources are abundant coexistence on sympatric kopjes between both species is possible, but when browse is scarce the result is competitive exclusion of H. brucei by P. johnstoni. It is also argued, that P. johnstoni by being the larger species and by also being a grazer had several ecological advantages over H. brucei. In kopjes H2, H3 and P1 where H. brucei occurred allopatrically the population increased (H2, P1) or decreased (H3) during the same time period. Natural extinction was observed in kopje P1 in the allopatrically living P. johnstoni group through mange. Dispersal of 7 females and 7 males H. brucei as well as 1 female and 4 male P. johnstoni were recorded in kopjes H1, H2 and P1. One female H. brucei that immigrated successfully into kopje H2 reached an age of over 11 years. One H. brucei family group (H2) shifted its birth season from December-January to May-August. Successful natural colonization was recorded for H. brucei in kopje P1 and for P. johnstoni in H1. Two kopjes (PH2 and H3), which had no hyrax and are located far away from other hyrax populations, were experimentally colonized in 1971 and 1972 respectively. The P. Johnstoni on PH2 and the H. brucei group on H3 had been under breeding isolation for 16 years. Under such conditions P. johnstoni males can reach an age of over 8.5 years. These long-term observations have shown that the occupancy of the kopjes by both species is a dynamic process depending on the combination of several abiotic (rainfall and availability of holes and hiding places) and biotic factors (interspecific and intraspecific competition for food, interspecific cooperation, predation and parasites) as well as the degree of inbreeding dependent on the geographic isolation of the kopje.

Response to comments on "Can we name Earth's species before they go extinct?"

Mora et al. disputed that most species will be discovered before they go extinct, but not our main recommendations to accelerate species' discoveries. We show that our conclusions would be unaltered by discoveries of more microscopic species and reinforce our estimates of species description and extinction rates, that taxonomic effort has never been greater, and that there are 2 to 8 million species on Earth.

Lack of variation at phosphoglucose isomerase (pgi) in bumblebees: implications for conservation genetics studies

Assessing genetic variation underlying ecologically important traits is increasingly of interest and importance in population and conservation genetics. For some groups generally useful markers exist for examining the relative role of selection and drift in shaping genetic diversity e.g. the major histocompatibility complex in vertebrates and self-incompatibility loci in plants. For invertebrates there is no such generally useful locus. However, phosphoglucose isomerase (Pgi) has been proposed as a useful functional marker in the conservation genetics of invertebrates. Where thermal microclimate varies, balanced polymorphisms may be maintained due to trade-offs between thermally stable and kinetically advantageous allelic forms. We here report very low levels of Pgi variation in bumblebees rendering this locus to be of little use as an adaptive marker in a conservation genetics context in this group. Potential explanations for this lack of variation are considered.

Quantifying species diversity with a DNA barcoding-based method: Tibetan moth species (Noctuidae) on the Qinghai-Tibetan Plateau

With the ongoing loss of biodiversity, there is a great need for fast and effective ways to assess species richness and diversity: DNA barcoding provides a powerful new tool for this. We investigated this approach by focusing on the Tibetan plateau, which is one of the world's top biodiversity hotspots. There have been few studies of its invertebrates, although they constitute the vast majority of the region's diversity. Here we investigated species diversity of the lepidopteran family Noctuidae, across different environmental gradients, using measurements based on traditional morphology as well as on DNA barcoding. The COI barcode showed an average interspecific K2P distance of 9.45±2.08%, which is about four times larger than the mean intraspecific distance (1.85±3.20%). Using six diversity indices, we did not detect any significant differences in estimated species diversity between measurements based on traditional morphology and on DNA barcoding. Furthermore, we found strong positive correlations between them, indicating that barcode-based measures of species diversity can serve as a good surrogate for morphology-based measures in most situations tested. Eastern communities were found to have significantly higher diversity than Western ones. Among 22 environmental factors tested, we found that three (precipitation of driest month, precipitation of driest quarter, and precipitation of coldest quarter) were significantly correlated with species diversity. Our results indicate that these factors could be the key ecological factors influencing the species diversity of the lepidopteran family Noctuidae on the Tibetan plateau.

Algal taxonomy: a road to nowhere?

The widespread view of taxonomy as an essentially retrogressive and outmoded science unable to cope with the current biodiversity crisis stimulated us to analyze the current status of cataloguing global algal diversity. Contrary to this largely pessimistic belief, species description rates of algae through time and trends in the number of active taxonomists, as revealed by the web resource AlgaeBase, show a much more positive picture. More species than ever before are being described by a large community of algal taxonomists. The lack of any decline in the rate at which new species and genera are described, however, is indicative of the large proportion of undiscovered diversity and bears heavily on any prediction of global algal species diversity and the time needed to catalogue it. The saturation of accumulation curves of higher taxa (family, order, and classes) on the other hand suggest that at these taxonomic levels most diversity has been discovered. This reasonably positive picture does not imply that algal taxonomy does not face serious challenges in the near future. The observed levels of cryptic diversity in algae, combined with the shift in methods used to characterize them, have resulted in a rampant uncertainty about the status of many older species. As a consequence, there is a tendency in phycology to move gradually away from traditional names to a more informal system whereby clade-, specimen- or strain-based identifiers are used to communicate biological information. Whether these informal names for species-level clades represent a temporary situation stimulated by the lag between species discovery and formal description, or an incipient alternative or parallel taxonomy, will be largely determined by how well we manage to integrate historical collections into modern taxonomic research. Additionally, there is a pressing need for a consensus about the organizational framework to manage the information about algal species names. An eventual strategy should preferably come out of an international working group that includes the various databases as well as the various phycological societies. In this strategy, phycologists should link up to major international initiatives that are currently being developed, such as the compulsory registration of taxonomic and nomenclatural acts and the introduction of Life Science Identifiers.

Scaling body size fluctuations

The size of an organism matters for its metabolic, growth, mortality, and other vital rates. Scale-free community size spectra (i.e., size distributions regardless of species) are routinely observed in natural ecosystems and are the product of intra- and interspecies regulation of the relative abundance of organisms of different sizes. Intra- and interspecies distributions of body sizes are thus major determinants of ecosystems' structure and function. We show experimentally that single-species mass distributions of unicellular eukaryotes covering different phyla exhibit both characteristic sizes and universal features over more than four orders of magnitude in mass. Remarkably, we find that the mean size of a species is sufficient to characterize its size distribution fully and that the latter has a universal form across all species. We show that an analytical physiological model accounts for the observed universality, which can be synthesized in a log-normal form for the intraspecies size distributions. We also propose how ecological and physiological processes should interact to produce scale-invariant community size spectra and discuss the implications of our results on allometric scaling laws involving body mass.

Evolution of vertebrate immunity

All multicellular organisms protect themselves against pathogens using sophisticated immune defenses. Functionally interconnected humoral and cellular facilities maintain immune homeostasis in the absence of overt infection and regulate the initiation and termination of immune responses directed against pathogens. Immune responses of invertebrates, such as flies, are innate and usually stereotyped; those of vertebrates, encompassing species as diverse as jawless fish and humans, are additionally adaptive, enabling more rapid and efficient immune reactivity upon repeated encounters with a pathogen. Many of the attributes historically defining innate and adaptive immunity are in fact common to both, blurring their functional distinction and emphasizing shared ancestry and co-evolution. These findings provide indications of the evolutionary forces underlying the origin of somatic diversification of antigen receptors and contribute to our understanding of the complex phenotypes of human immune disorders. Moreover, informed by phylogenetic considerations and inspired by improved knowledge of functional networks, new avenues emerge for innovative therapeutic strategies.

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.

Speedy speciation in a bacterial microcosm: new species can arise as frequently as adaptations within a species

Microbiologists are challenged to explain the origins of enormous numbers of bacterial species worldwide. Contributing to this extreme diversity may be a simpler process of speciation in bacteria than in animals and plants, requiring neither sexual nor geographical isolation between nascent species. Here, we propose and test a novel hypothesis for the extreme diversity of bacterial species-that splitting of one population into multiple ecologically distinct populations (cladogenesis) may be as frequent as adaptive improvements within a single population's lineage (anagenesis). We employed a set of experimental microcosms to address the relative rates of adaptive cladogenesis and anagenesis among the descendants of a Bacillus subtilis clone, in the absence of competing species. Analysis of the evolutionary trajectories of genetic markers indicated that in at least 7 of 10 replicate microcosm communities, the original population founded one or more new, ecologically distinct populations (ecotypes) before a single anagenetic event occurred within the original population. We were able to support this inference by identifying putative ecotypes formed in these communities through differences in genetic marker association, colony morphology and microhabitat association; we then confirmed the ecological distinctness of these putative ecotypes in competition experiments. Adaptive mutations leading to new ecotypes appeared to be about as common as those improving fitness within an existing ecotype. These results suggest near parity of anagenesis and cladogenesis rates in natural populations that are depauperate of bacterial diversity.

DNA barcoding of Northern Nearctic Muscidae (Diptera) reveals high correspondence between morphological and molecular species limits

BACKGROUND

Various methods have been proposed to assign unknown specimens to known species using their DNA barcodes, while others have focused on using genetic divergence thresholds to estimate "species" diversity for a taxon, without a well-developed taxonomy and/or an extensive reference library of DNA barcodes. The major goals of the present work were to: a) conduct the largest species-level barcoding study of the Muscidae to date and characterize the range of genetic divergence values in the northern Nearctic fauna; b) evaluate the correspondence between morphospecies and barcode groupings defined using both clustering-based and threshold-based approaches; and c) use the reference library produced to address taxonomic issues.

RESULTS

Our data set included 1114 individuals and their COI sequences (951 from Churchill, Manitoba), representing 160 morphologically-determined species from 25 genera, covering 89% of the known fauna of Churchill and 23% of the Nearctic fauna. Following an iterative process through which all specimens belonging to taxa with anomalous divergence values and/or monophyly issues were re-examined, identity was modified for 9 taxa, including the reinstatement of Phaonia luteva (Walker) stat. nov. as a species distinct from Phaonia errans (Meigen). In the post-reassessment data set, no distinct gap was found between maximum pairwise intraspecific distances (range 0.00-3.01%) and minimum interspecific distances (range: 0.77-11.33%). Nevertheless, using a clustering-based approach, all individuals within 98% of species grouped with their conspecifics with high (>95%) bootstrap support; in contrast, a maximum species discrimination rate of 90% was obtained at the optimal threshold of 1.2%. DNA barcoding enabled the determination of females from 5 ambiguous species pairs and confirmed that 16 morphospecies were genetically distinct from named taxa. There were morphological differences among all distinct genetic clusters; thus, no cases of cryptic species were detected.

CONCLUSIONS

Our findings reveal the great utility of building a well-populated, species-level reference barcode database against which to compare unknowns. When such a library is unavailable, it is still possible to obtain a fairly accurate (within ~10%) rapid assessment of species richness based upon a barcode divergence threshold alone, but this approach is most accurate when the threshold is tuned to a particular taxon.

Surveying the microbiome of ants: comparing 454 pyrosequencing with traditional methods to uncover bacterial diversity

We are only beginning to understand the depth and breadth of microbial associations across the eukaryotic tree of life. Reliably assessing bacterial diversity is a key challenge, and next-generation sequencing approaches are facilitating this endeavor. In this study, we used 16S rRNA amplicon pyrosequencing to survey microbial diversity in ants. We compared 454 libraries with Sanger-sequenced clone libraries as well as cultivation of live bacteria. Pyrosequencing yielded 95,656 bacterial 16S rRNA reads from 19 samples derived from four colonies of one ant species. The most dominant bacterial orders in the microbiome of the turtle ant Cephalotes varians were Rhizobiales, Burkholderiales, Opitutales, Xanthomonadales, and Campylobacterales, as revealed through both 454 sequencing and cloning. Even after stringent quality filtering, pyrosequencing recovered 445 microbe operational taxonomic units (OTUs) not detected with traditional techniques. In comparing bacterial communities associated with specific tissues, we found that gut tissues had significantly higher diversity than nongut tissues, and many of the OTUs identified from these groups clustered within ant-specific lineages, indicating a deep coevolutionary history of Cephalotes ants and their associated microbes. These lineages likely function as nutritional symbionts. One of four ant colonies investigated was infected with a Spiroplasma sp. (order Entomoplasmatales), a potential ant pathogen. Our work shows that the microbiome associated with Cephalotes varians is dominated by a few dozen bacterial lineages and that 454 sequencing is a cost-efficient tool to screen ant symbiont diversity.

Animal body size distributions: patterns, mechanisms and implications

Documenting the shape of the frequency distribution of species body sizes for an animal taxon appears at first sight a straightforward task. However, a variety of patterns has been reported, and a consensus is only now being reached through an understanding of how potential biases may affect observed shapes of distributions. A new body of evidence suggests that, at large scales, size distributions are right-skewed, even on logarithmic axes. If body size distributions can be described with certainty, this will allow assessment of the mechanisms proposed to generate them, and will be an important step towards understanding the structure and dynamics of animal assemblages.

The neutral-niche debate: a philosophical perspective

Ecological communities around the world are under threat while a consensus theory of community structure remains elusive. In the last decade ecologists have struggled with two seemingly opposing theories: niche-based theory that explains diversity with species’ differences and the neutral theory of biodiversity that claims that much of the diversity we observe can be explained without explicitly invoking species’ differences. Although ecologists are increasingly attempting to reconcile these two theories, there is still much resistance against the neutral theory of biodiversity. Here we argue that the dispute between the two theories is a classic example of the dichotomy between philosophical perspectives, realism and instrumentalism. Realism is associated with specific, small-scale and detailed explanations, whereas instrumentalism is linked to general, large-scale, but less precise accounts. Recognizing this will help ecologists get both niche-based and neutral theories in perspective as useful tools for understanding biodiversity patterns.

Functional characterizations of chemosensory proteins of the alfalfa plant bug Adelphocoris lineolatus indicate their involvement in host recognition

Insect chemosensory proteins (CSPs) have been proposed to capture and transport hydrophobic chemicals from air to olfactory receptors in the lymph of antennal chemosensilla. They may represent a new class of soluble carrier protein involved in insect chemoreception. However, their specific functional roles in insect chemoreception have not been fully elucidated. In this study, we report for the first time three novel CSP genes (AlinCSP1-3) of the alfalfa plant bug Adelphocoris lineolatus (Goeze) by screening the antennal cDNA library. The qRT-PCR examinations of the transcript levels revealed that all three genes (AlinCSP1-3) are mainly expressed in the antennae. Interestingly, these CSP genes AlinCSP1-3 are also highly expressed in the 5^th instar nymphs, suggesting a proposed function of these CSP proteins (AlinCSP1-3) in the olfactory reception and in maintaining particular life activities into the adult stage. Using bacterial expression system, the three CSP proteins were expressed and purified. For the first time we characterized the types of sensilla in the antennae of the plant bug using scanning electron microscopy (SEM). Immunocytochemistry analysis indicated that the CSP proteins were expressed in the pheromone-sensitive sensilla trichodea and general odorant-sensitive sensilla basiconica, providing further evidence of their involvement in chemoreception. The antennal activity of 55 host-related semiochemicals and sex pheromone compounds in the host location and mate selection behavior of A. lineolatus was investigated using electroantennogram (EAG), and the binding affinities of these chemicals to the three CSPs (AlinCSP1-3) were measured using fluorescent binding assays. The results showed several host-related semiochemicals, (Z)-3-hexen-1-ol, (E)-2-hexen-1-al and valeraldehyde, have a high binding affinity with AlinCSP1-3 and can elicit significant high EAG responses of A. lineolatus antennae. Our studies indicate the three antennae-biased CSPs may mediate host recognition in the alfalfa plant bug A. lineolatus.

Brachymeria pandora (Crawford) (Hymenoptera: Chalcididae) as a new parasitoid of Thyrinteina leucocerae (Rindge) (Lepidoptera: Geometridae) in Brazil

This is the first report of Brachymeria pandora (Crawford) (Hymenoptera: Chalcididae)-parasitizing pupae of the eucalyptus defoliator Thyrinteina leucocerae (Rindge) (Lepidoptera: Geometridae) in Brazil.

Evolution of the immune system in the lower vertebrates

The evolutionary emergence of vertebrates was accompanied by the invention of adaptive immunity. This is characterized by extraordinarily diverse repertoires of somatically assembled antigen receptors and the facility of antigen-specific memory, leading to more rapid and efficient secondary immune responses. Adaptive immunity emerged twice during early vertebrate evolution, once in the lineage leading to jawless fishes (such as lamprey and hagfish) and, independently, in the lineage leading to jawed vertebrates (comprising the overwhelming majority of extant vertebrates, from cartilaginous fishes to mammals). Recent findings on the immune systems of jawless and jawed fishes (here referred to as lower vertebrates) impact on the identification of general principles governing the structure and function of adaptive immunity and its coevolution with innate defenses. The discovery of conserved features of adaptive immunity will guide attempts to generate synthetic immunological functionalities and thus provide new avenues for intervening with faulty immune functions in humans.

WEEVILS AND PLANTS: PHYLOGENETIC VERSUS ECOLOGICAL MEDIATION OF EVOLUTION OF HOST PLANT ASSOCIATIONS IN CURCULIONINAE (COLEOPTERA: CURCULIONIDAE)

A great proportion of biodiversity is accounted for by organisms, particularly insects, intimately associated with plants. Knowing whether ecological or phylogenetic factors chiefly influence the evolution of host plant associations is essential to understanding speciation in, and therefore factors influencing diversity of, phytophagous insects. Through examination of known host plant associations in Curculioninae and comparison with available reconstructed phylogenetic relationships of certain taxa of Curculioninae, little, if any, evidence for cospeciation (parallel cladogenesis) is found. In curculionine taxa where sufficient host plant and/or phylogenetic data are available, weevil species are narrowly to broadly oligophagous; a number of related weevil species are associated with a single host plant species; many weevil genera have host plant ranges spanning distantly related plant taxa; and available weevil reconstructed phylogenies are not concordant with plant relationships. Rather, for at least some weevil taxa, evolution appears to be mediated by one or more of a variety of strictly ecological factors, particularly habitat associations. General applications of these results include biological control, pollination biology, conservation and restoration biology, and use of patterns in insect – host plant associations to resolve problems in plant classification.

PATTERNS OF DIVERSITY IN THE CANADIAN INSECT FAUNA

The diversity of the Canadian insect fauna decreases and its composition (at all taxonomic levels) changes as climates become progressively more harsh toward the north. This climatic trend dominates patterns of diversity, but many other factors interact to produce the observed patterns. In the arctic, species richness is greatest in the west. Farther south, overall species richness is greatest in the west (especially British Columbia), associated with coastal and cordilleran habitats, and to a somewhat smaller degree in the southeast (especially Ontario), associated with deciduous forests and particularly with transitional forests which occupy a large area of southeastern Canada. However, certain taxa are better represented in the west or in the east, depending on present-day habitats and on historical factors. These conclusions, based chiefly on a sample of taxa of different types, are possible only because basic systematic work has been carried out to distinguish and map the species. Preliminary data on numerical patterns, such as the numbers of species relative to different potential resources such as host plants in different zones, tend to suggest that the occurrence of species in the north may depend so heavily on climatic factors that potential resources are not fully exploited and the effects of interspecific interactions on diversity are reduced.

DIVERSITY OF SOIL ARTHROPODS IN CANADA: SYSTEMATIC AND ECOLOGICAL PROBLEMS

Data on diversity are fundamental to our understanding of both natural and disturbed ecosystems. Yet, despite their real and potential importance, knowledge of the diversity of non-pterygote soil arthropods in Canada still is very incomplete. This is illustrated with information on diversity from nine non-pterygote arthropod taxa: Tardigrada, Chilopoda, Diplopoda, Symphyla, Pauropoda, Protura, Collembola, Pseudoscorpionida, and Oribatida, and faunal lists are given for six of these taxa. Although valuable family and generic keys have been published recently, few monographic works or user-friendly keys to species are available. Autecological information essential to explaining the functional role of soil arthropods remains inadequate. Fortunately, the needs of other disciplines and issues are causing a change. For example, current ecological research recognizes that the roles of soil arthropods in decomposition, nutrient cycling, and soil formation are more complex than previously supposed, palaeoecologists require new or corroborating data to interpret their fossil assemblages, and issues such as agroecosystem management, environmental indicators, and global change require a more thorough knowledge of soil communities. Researchers in these areas face poor data on diversity based on inadequate systematics, which limit their understanding of the composition and organisation of soil arthropod communities. This inadequacy presents both a challenge and an opportunity to soil arthropod systematists and ecologists.

Evolution of lymphoid tissues

Lymphoid organs are integral parts of all vertebrate adaptive immune systems. Primary lymphoid tissues exhibit a remarkable functional dichotomy: T cells develop in specialized thymopoietic tissues located in the pharynx, whereas B cells develop in distinct areas of general hematopoietic areas, such as the kidney or bone marrow. Among secondary lymphoid tissues, the spleen is present in all vertebrates, whereas lymph nodes represent an innovation particular to mammals and some birds. A comparative analysis of anatomical, functional and genomic features thus reveals the core components of adaptive immune systems. Such information has guided recent attempts at reconstructing lymphopoietic functions in vivo and in the future might inspire the development of new strategies for medical interventions restoring and modulating immune functions.