Undersampling bias: the null hypothesis for singleton species in tropical arthropod surveys

Trait-based ecology of terrestrial arthropods

In focusing on how organisms' generalizable functional properties (traits) interact mechanistically with environments across spatial scales and levels of biological organization, trait-based approaches provide a powerful framework for attaining synthesis, generality and prediction. Trait-based research has considerably improved understanding of the assembly, structure and functioning of plant communities. Further advances in ecology may be achieved by exploring the trait-environment relationships of non-sessile, heterotrophic organisms such as terrestrial arthropods, which are geographically ubiquitous, ecologically diverse, and often important functional components of ecosystems. Trait-based studies and trait databases have recently been compiled for groups such as ants, bees, beetles, butterflies, spiders and many others; however, the explicit justification, conceptual framework, and primary-evidence base for the burgeoning field of 'terrestrial arthropod trait-based ecology' have not been well established. Consequently, there is some confusion over the scope and relevance of this field, as well as a tendency for studies to overlook important assumptions of the trait-based approach. Here we aim to provide a broad and accessible overview of the trait-based ecology of terrestrial arthropods. We first define and illustrate foundational concepts in trait-based ecology with respect to terrestrial arthropods, and justify the application of trait-based approaches to the study of their ecology. Next, we review studies in community ecology where trait-based approaches have been used to elucidate how assembly processes for terrestrial arthropod communities are influenced by niche filtering along environmental gradients (e.g. climatic, structural, and land-use gradients) and by abiotic and biotic disturbances (e.g. fire, floods, and biological invasions). We also review studies in ecosystem ecology where trait-based approaches have been used to investigate biodiversity-ecosystem function relationships: how the functional diversity of arthropod communities relates to a host of ecosystem functions and services that they mediate, such as decomposition, pollination and predation. We then suggest how future work can address fundamental assumptions and limitations by investigating trait functionality and the effects of intraspecific variation, assessing the potential for sampling methods to bias the traits and trait values observed, and enhancing the quality and consolidation of trait information in databases. A roadmap to guide observational trait-based studies is also presented. Lastly, we highlight new areas where trait-based studies on terrestrial arthropods are well positioned to advance ecological understanding and application. These include examining the roles of competitive, non-competitive and (multi-)trophic interactions in shaping coexistence, and macro-scaling trait-environment relationships to explain and predict patterns in biodiversity and ecosystem functions across space and time. We hope this review will spur and guide future applications of the trait-based framework to advance ecological insights from the most diverse eukaryotic organisms on Earth.

Ortuño V. The study of hidden habitats sheds light on poorly known taxa: spiders of the Mesovoid Shallow Substratum

The scarce and biased knowledge about the diversity and distribution of Araneae species in the Iberian Peninsula is accentuated in poorly known habitats such as the Mesovoid Shallow Substratum (MSS). The aim of this study was to characterize the spiders inventory of the colluvial MSS of the Sierra de Guadarrama National Park, and to assess the importance of this habitat for the conservation of the taxon. Thirty-three localities were selected across the high peaks of the Guadarrama mountain range and they were sampled for a year using subterranean traps specially designed to capture arthropods in the MSS. Species accumulation curves were built both for the observed species richness and for the non-parametric richness estimators. The literature was reviewed in order to update the distributional maps of the rarest species. Forty-two species were collected, of which four were species new to science. More than half were represented by one or two individuals which caused the accumulation curves to rise slowly and to end without reaching an asymptote. Almost half of the species showed significant increases in their Iberian distribution ranges. Two species were recorded for the first time in the Iberian Peninsula and 32 species were new additions to the spider checklist of the Sierra de Guadarrama National Park.

Characterization and comparison of poorly known moth communities through DNA barcoding in two Afrotropical environments in Gabon

Biodiversity research in tropical ecosystems—popularized as the most biodiverse habitats on Earth—often neglects invertebrates, yet invertebrates represent the bulk of local species richness. Insect communities in particular remain strongly impeded by both Linnaean and Wallacean shortfalls, and identifying species often remains a formidable challenge inhibiting the use of these organisms as indicators for ecological and conservation studies. Here we use DNA barcoding as an alternative to the traditional taxonomic approach for characterizing and comparing the diversity of moth communities in two different ecosystems in Gabon. Though sampling remains very incomplete, as evidenced by the high proportion (59%) of species represented by singletons, our results reveal an outstanding diversity. With about 3500 specimens sequenced and representing 1385 BINs (Barcode Index Numbers, used as a proxy to species) in 23 families, the diversity of moths in the two sites sampled is higher than the current number of species listed for the entire country, highlighting the huge gap in biodiversity knowledge for this country. Both seasonal and spatial turnovers are strikingly high (18.3% of BINs shared between seasons, and 13.3% between sites) and draw attention to the need to account for these when running regional surveys. Our results also highlight the richness and singularity of savannah environments and emphasize the status of Central African ecosystems as hotspots of biodiversity.

Composição e riqueza de espécies de uma comunidade de Coleoptera (Insecta) na Caatinga

RESUMO Os besouros apresentam grande diversidade taxonômica e funcional, no entanto, para a Região Nordeste, especialmente para a porção com vegetação de Caatinga, o conhecimento da fauna de Coleoptera é muito restrito. Por se tratar de uma região com grande diversidade de paisagens, torna-se necessário conhecer a coleopterofauna que ocorre nas diferentes fitofisionomias, buscando com isso abranger a variabilidade espacial encontrada nessa região xérica. Diante disso, o objetivo deste estudo foi realizar um levantamento das espécies de besouros no Semiárido paraibano. As coletas foram realizadas semanalmente durante quatro anos (2009-2013) utilizando uma armadilha Malaise por fitofisionomia, sendo amostrada uma área com vegetação xerófila e outra com mata ciliar. Foram coletados 6.567 indivíduos pertencentes a 383 espécies e 42 famílias de Coleoptera. Chrysomelidae (78 spp.), Curculionidae (57 spp.) e Cerambycidae (28 spp.) foram as famílias mais ricas. Em relação às mais abundantes, Chrysomelidae (30,4% dos indivíduos), Curculionidae (8,3%) e Tenebrionidae (7,7%) se destacaram. Foi verificado um elevado número de singletons e doubletons, apesar do prolongado período amostral, indicando que deve haver ainda muitas espécies a serem registradas na área de estudos. Nossos resultados demonstram uma rica fauna de besouros na região semiárida estudada e fornece uma lista de besouros de ocorrência no Semiárido paraibano, com novos registros de espécies para o estado e contribui assim com o conhecimento da diversidade de Coleoptera no Nordeste do Brasil.

Richness of Chrysomelidae (Coleoptera) depends on the area and habitat structure in semideciduous forest remnants

ABSTRACT The total area of a habitat patch can increase the local species richness both directly (through balance between immigration and extinction) and indirectly (by increasing the habitat heterogeneity and/or as an effect of sample effort). More heterogeneous environments present a wider variety of resources and conditions, allowing species to coexist through niche differentiation. This study shows that the diversity of Chrysomelidae depends on the area and habitat structure of semideciduous forest remnants. We sampled 16 remnants with Malaise traps in August 2012 to March 2013. In order to characterize the habitat, the area, structural heterogeneity of the understory, coverage and canopy height were measured. These variables were used in a path analysis to determine their direct and indirect effects on leaf beetle diversity. A total of 450 specimens from 99 species and five subfamilies were captured. The total area and the understory heterogeneity presented a positive effect on species richness, while canopy cover exerted a negative one. The canopy height only had a negative and indirect effect on leaf beetle richness. In such fragments with more area and more open spaces, plant abundance and richness tend to be higher and favor the coexistence of many Chrysomelidae species.

Mapping knowledge gaps in marine diversity reveals a latitudinal gradient of missing species richness

A reliable description of any spatial pattern in species richness requires accurate knowledge about species geographical distribution. However, sampling bias may generate artefactual absences within species range and compromise our capacity to describe biodiversity patterns. Here, we analysed the spatial distribution of 35,000 marine species (varying from copepods to sharks) to identify missing occurrences (gaps) across their latitudinal range. We find a latitudinal gradient of species absence peaking near the equator, a pattern observed in both shallow and deep waters. The tropical gap in species distribution seems a consequence of reduced sampling effort at low latitudes. Overall, our results suggest that spatial gaps in species distribution are the main cause of the bimodal pattern of marine diversity. Therefore, only increasing sampling effort at low latitudes will reveal if the absence of species in the tropics, and the consequent dip in species richness, are artefacts of sampling bias or a natural phenomenon.

Accurate understanding of species biogeographic patterns is contingent upon adequate sampling effort across space. Here, the authors analyse the distribution records for 35,000 marine species, highlighting data gaps caused by undersampling in the tropics.

Conceptual and empirical advances in Neotropical biodiversity research

The unparalleled biodiversity found in the American tropics (the Neotropics) has attracted the attention of naturalists for centuries. Despite major advances in recent years in our understanding of the origin and diversification of many Neotropical taxa and biotic regions, many questions remain to be answered. Additional biological and geological data are still needed, as well as methodological advances that are capable of bridging these research fields. In this review, aimed primarily at advanced students and early-career scientists, we introduce the concept of "trans-disciplinary biogeography," which refers to the integration of data from multiple areas of research in biology (e.g., community ecology, phylogeography, systematics, historical biogeography) and Earth and the physical sciences (e.g., geology, climatology, palaeontology), as a means to reconstruct the giant puzzle of Neotropical biodiversity and evolution in space and time. We caution against extrapolating results derived from the study of one or a few taxa to convey general scenarios of Neotropical evolution and landscape formation. We urge more coordination and integration of data and ideas among disciplines, transcending their traditional boundaries, as a basis for advancing tomorrow's ground-breaking research. Our review highlights the great opportunities for studying the Neotropical biota to understand the evolution of life.

Gamma-diversity partitioning of gobiid fishes (Teleostei: Gobiidae) ensemble along of Eastern Tropical Pacific: Biological inventory, latitudinal variation and species turnover

Gobies are the most diverse marine fish family. Here, we analysed the gamma-diversity (γ-diversity) partitioning of gobiid fishes to evaluate the additive and multiplicative components of α and β-diversity, species replacement and species loss and gain, at four spatial scales: sample units, ecoregions, provinces and realms. The richness of gobies from the realm Eastern Tropical Pacific (ETP) is represented by 87 species. Along latitudinal and longitudinal gradients, we found that the γ-diversity is explained by the β-diversity at both spatial scales, ecoregions and provinces. At the ecoregion scale, species are diverse in the north (Cortezian ecoregion) and south (Panama Bight ecoregion) and between insular and coastal ecoregions. At the province scale, we found that the species turnover between the warm temperate Northeast Pacific (WTNP), Tropical East Pacific (TEaP) and the Galapagos Islands (Gala) was high, and the species nestedness was low. At the ecoregion scale, historical factors, and phylogenetic factors have influenced the hotspots of gobiid fish biodiversity, particularly in the Cortezian, Panama Bight and Cocos Island ecoregions, where species turnover is high across both latitudinal and longitudinal gradients. At the provincial level, we found that the contributions of the β-diversity from north to south, in the WTNP, TEaP and Gala were high, as result of the high number of unique species. Species turnover was also high at this scale, with a low contribution from species nestedness that was probably due to the low species/gene flow within the provinces. These results highlight the importance and successful inclusion of a cryptobenthic fish component in ecological and biogeographical studies.

Beetles in bamboo forests: community structure in a heterogeneous landscape of southwestern Amazonia

Amazonian bamboo forests dominated by large woody bamboo plants in the genus Guadua cover approximately 180,000 km² and represent a key resource for many organisms. In southwestern Amazonia, native bamboo forests differ in structure, biodiversity, and growth dynamics from other forest types in the region. However, with the exception of a few species in which habitat specialization or a strong habitat association has been demonstrated, little is known about how bamboo forests influence animal community structure. In an effort to understand more about the animal assemblages associated with Amazonian bamboo forests, we characterized the structure of ground-dwelling beetle assemblages living in bamboo forests and adjacent terra firme forests in a lowland rainforest site in Peru. We conducted intensive pitfall trap surveys in 13 bamboo habitat patches and 13 adjacent terra firme habitat patches to determine if there were differences in the abundance and richness of beetle species in these two habitat types. Additionally, given that southwestern Amazonia experiences distinct dry and wet seasons, we conducted our study during the dry and wet season of one year to account for differences in seasonality. We found a distinct beetle assemblage associated with each forest type, and identified a set of dominant species that significantly contributed to the distinctness in beetle community structure between bamboo and terra firme forest. The terra firme forest had a greater number of rare species than the bamboo forest. Several beetle species exhibited a strong association with the bamboo forest, including a large species of Scarabaeidae that appears to be specializing on bamboo. We also found marked differences in beetle assemblages between dry and wet seasons. Our results support the prediction that beetle community structure in bamboo forest differs from that of terra firme in terms of species richness, abundance, and composition. Bamboo-associated animal communities require more exploration and study, and must be included in regional conservation plans seeking to protect entire animal communities in southwestern Amazonia.

Variation in the diversity and richness of parasitoid wasps based on sampling effort

Parasitoid wasps are a mega-diverse, ecologically dominant, but poorly studied component of global biodiversity. In order to maximise the efficiency and reduce the cost of their collection, the application of optimal sampling techniques is necessary. Two sites in Auckland, New Zealand were sampled intensively to determine the relationship between sampling effort and observed species richness of parasitoid wasps from the family Ichneumonidae. Twenty traps were deployed at each site at three different times over the austral summer period, resulting in a total sampling effort of 840 Malaise-trap-days. Rarefaction techniques and non-parametric estimators were used to predict species richness and to evaluate the variation and completeness of sampling. Despite an intensive Malaise-trapping regime over the summer period, no asymptote of species richness was reached. At best, sampling captured two-thirds of parasitoid wasp species present. The estimated total number of species present depended on the month of sampling and the statistical estimator used. Consequently, the use of fewer traps would have caught only a small proportion of all species (one trap 7–21%; two traps 13–32%), and many traps contributed little to the overall number of individuals caught. However, variation in the catch of individual Malaise traps was not explained by seasonal turnover of species, vegetation or environmental conditions surrounding the trap, or distance of traps to one another. Overall the results demonstrate that even with an intense sampling effort the community is incompletely sampled. The use of only a few traps and/or for very short periods severely limits the estimates of richness because (i) fewer individuals are caught leading to a greater number of singletons; and (ii) the considerable variation of individual traps means some traps will contribute few or no individuals. Understanding how sampling effort affects the richness and diversity of parasitoid wasps is a useful foundation for future studies.

Only multi-taxon studies show the full range of arthropod responses to fire

Fire is a major driver in many ecosystems. Yet, little is known about how different ground-living arthropods survive fire. Using three sampling methods, and time-since-fire (last fire event: 3 months, 1 year, and 7 years), we investigate how ground-living arthropod diversity responds to fire, and how species richness, diversity, abundance, and composition of the four dominant taxa: ants, beetles, cockroaches and mites, respond. We did this in the naturally fire-prone Mediterranean-type scrubland vegetation (fynbos) of the Cape Floristic Region. Surprisingly, overall species richness and diversity was the same for all time-since-fire categories. However, when each dominant taxon was analysed separately, effect of fire on species richness and abundance varied among taxa. This emphasizes that many taxa must be investigated to really understand fire-driven events. We also highlight the importance of using different diversity measures, as fire did not influence species richness and abundance of particular taxa, while it affected others, overall greatly affecting assemblages of all taxa. Rockiness affected species richness, abundance and composition of a few taxa. We found that all time-since-fire categories supported distinctive assemblages. Some indicator species occurred across all time-since-fire categories, while others were restricted to a single time-since-fire category, showing that there is a wide range of responses to fire between taxa. Details of local landscape structure, abiotic and biotic, and frequency and intensity of fire add complexity to the fire-arthropod interaction. Overall, we show that the relationship between fire and arthropods is phylogenetically constrained, having been honed by many millennia of fire events, and highly complex. Present-day species manifest a variety of adaptations for surviving the great natural selective force of fire.

Host Specificity in Subarctic Aphids

Plants and herbivorous (or parasitic) insects form the majority of macroscopic life. The specificity of interaction between host plant and parasitic insect depends on the adaptations of both the host and the parasite. Over time, these interactions evolve and change as a result of an 'arms race' between host and parasite, and the resulting species-specific adaptations may be maintained, perpetuating these interactions across speciation events. This can lead to specialisation between species or clades. With speciation and species sorting over time, complex interactions evolve. Here, we elucidate a three-tier method to test these interactions using the aphids (Hemiptera: Aphididae) and plants of Churchill (Manitoba, Canada) as a model system. We analyzed these interactions by testing for three patterns in host specificity: monophagy, phylogenetic clustering, and cophylogeny. We defined monophagy strictly as one species feeding exclusively upon a single host plant species (an association likely driven by arms races in morphology, chemical resistance/tolerance, and visual appearance) and observed this in 7 of 22 aphid species. In all the remaining 'polyphagous' cases, there was a strong trend toward monophagy (80% of individuals were found on a single host plant species). Second, we observed two separate examples of phylogenetic clustering where groups of closely related aphid species fed upon individual plant species. Finally, we found no support for cophylogenetic relationships where both aphids and plants cospeciate to form congruent phylogenetic trees (evidence of coadaptation through an ongoing arms race). One explanation for uncovering species-specific interactions in a recently deglaciated, subarctic locality is that the species involved in the associations moved north together. Testing different levels of specificity in the most predominant species-species interactions on the planet will allow us to elucidate these patterns accurately and gives us insight into where to direct future research.

Effects of seasonality on drosophilids (Insecta, Diptera) in the northern part of the Atlantic Forest, Brazil

Seasonality is an important aspect associated with population dynamic and structure of tropical insect assemblages. This study evaluated the effects of seasonality on abundance, richness, diversity and composition of an insect group, drosophilids, including species native to the Neotropical region and exotic ones. Three preserved fragments of the northern Atlantic Forest were surveyed, where temperatures are above 20 °C throughout the year and rainfall regimes define two seasons (dry and rainy). As opposed to other studies about arthropods in tropical regions, we observed that abundance of drosophilids was significantly higher in the dry season, possibly due to biological aspects and the colonization strategy adopted by the exotic species in these environments. Contrarily to abundance, we did not observe a seasonal pattern for richness. As for other parts of the Atlantic Forest, the most representative Neotropical species (Drosophila willistoni, D. sturtevanti, D. paulistorum and D. prosaltans) were significantly more abundant in the rainy season. Among the most abundant exotic species, D. malerkotliana, Zaprionus indianus and Scaptodrosophila latifasciaeformis were more importantly represented the dry season, while D. simulans was more abundant in the rainy period. The seasonality patterns exhibited by the most abundant species were compared to findings published in other studies. Our results indicate that exotic species were significantly more abundant in the dry season, while native ones exhibited an opposite pattern.

Compositional changes in bee and wasp communities along Neotropical mountain altitudinal gradient

Climate conditions tend to differ along an altitudinal gradient, resulting in some species groups' patterns of lower species richness with increasing altitude. While this pattern is well understood for tropical mountains, studies investigating possible determinants of variation in beta-diversity at its different altitudes are scarce. We sampled bee and wasp communities (Hymenoptera: Aculeata) along an altitudinal gradient (1,000-2,000 m.a.s.l.) in a tropical mountainous region of Brazil. Trap nests and Moericke traps were established at six sampling points, with 200 m difference in altitude between each point. We obtained average climate data (1970-2000) from Worldclim v2 for altitudes at each sampling site. Nest traps captured 17 bee and wasp species from six families, and Moericke traps captured 124 morphospecies from 13 families. We found a negative correlation between altitude and species richness and abundance. Temperature, precipitation, water vapor pressure, and wind speed influenced species richness and abundance, and were correlated with altitude. β-diversity was primarily determined by species turnover as opposed to nestedness, and Aculeate community similarity was higher for more similar altitudinal ranges. Moericke traps seem to be more efficient for altitudinal surveys compared to nest traps. We found high occurrence of singleton and doubleton species at all altitudes, highlighting the need for long-term studies to efficiently assess hymenopteran diversity in these environments.

The important challenge of quantifying tropical diversity

The tropics are the repository of much of the world's biodiversity, yet are undersampled relative to temperate regions. To help fill this knowledge gap, a paper in BMC Biology explores diversity patterns in tropical African plants, as revealed by the RAINBIO database. The paper documents spatial variation in diversity and data coverage, but also highlights the challenges faced in quantifying diversity patterns using data collated from a range of sources including herbaria.See research article: http://bmcbiol.biomedcentral.com/articles/10.1186/s12915-017-0356-8 .

Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees

BACKGROUND

The plant microbiome represents one of the key determinants of plant health and productivity by providing a plethora of functional capacities such as access to low-abundance nutrients, suppression of phytopathogens, and resistance to biotic and/or abiotic stressors. However, a robust understanding of the structural composition of the bacterial microbiome present in different plant microenvironments and especially the relationship between below-ground and above-ground communities has remained elusive. In this work, we addressed hypotheses regarding microbiome niche differentiation and structural stability of the bacterial communities within different ecological plant niches.

METHODS

We sampled the rhizosphere soil, root, stem, and leaf endosphere of field-grown poplar trees (Populus tremula × Populus alba) and applied 16S rRNA amplicon pyrosequencing to unravel the bacterial communities associated with the different plant habitats.

RESULTS

We found that the structural variability of rhizosphere microbiomes in field-grown poplar trees (P. tremula × P. alba) is much lower than that of the endosphere microbiomes. Furthermore, our data not only confirm microbiome niche differentiation reports at the rhizosphere soil-root interface but also clearly show additional fine-tuning and adaptation of the endosphere microbiome in the stem and leaf compartment. Each plant compartment represents an unique ecological niche for the bacterial communities. Finally, we identified the core bacterial microbiome associated with the different ecological niches of Populus.

CONCLUSIONS

Understanding the complex host-microbe interactions of Populus could provide the basis for the exploitation of the eukaryote-prokaryote associations in phytoremediation applications, sustainable crop production (bio-energy efficiency), and/or the production of secondary metabolites.

Gauging megadiversity with optimized and standardized sampling protocols: A case for tropical forest spiders

Characterizing and monitoring biodiversity and assessing its drivers require accurate and comparable data on species assemblages, which, in turn, should rely on efficient and standardized field collection. Unfortunately, protocols that follow such criteria remain scarce and it is unclear whether they can be applied to megadiverse communities, whose study can be particularly challenging. Here, we develop and evaluate the first optimized and standardized sampling protocol for megadiverse communities, using tropical forest spiders as a model taxon. We designed the protocol COBRA-TF (Conservation Oriented Biodiversity Rapid Assessment for Tropical Forests) using a large dataset of semiquantitative field data from different continents. This protocol combines samples of different collecting methods to obtain as many species as possible with minimum effort (optimized) and widest applicability and comparability (standardized). We ran sampling simulations to assess the efficiency of COBRA-TF (optimized, non-site-specific) and its reliability for estimating taxonomic, phylogenetic, and functional diversity, and community structure by comparing it with (1) commonly used expert-based ad hoc protocols (nonoptimized, site-specific) and (2) optimal protocols (optimized, site-specific). We then tested the performance and feasibility of COBRA-TF in the field. COBRA-TF yielded similar results as ad hoc protocols for species (observed and estimated) and family richness, phylogenetic and functional diversity, and species abundance distribution. Optimal protocols detected more species than COBRA-TF. Data from the field test showed high sampling completeness and yielded low numbers of singletons and doubletons. Optimized and standardized protocols can be as effective in sampling and studying megadiverse communities as traditional sampling, while allowing data comparison. Although our target taxa are spiders, COBRA-TF can be modified to apply to any highly diverse taxon and habitat as long as multiple collecting techniques exist and the unit effort per sample is comparable. Protocols such as COBRA-TF facilitate studying megadiverse communities and therefore may become essential tools for monitoring community changes in space and time, assessing the effects of disturbances and selecting conservation areas.

Hill number as a bacterial diversity measure framework with high-throughput sequence data

Bacterial diversity is an important parameter for measuring bacterial contributions to the global ecosystem. However, even the task of describing bacterial diversity is challenging due to biological and technological difficulties. One of the challenges in bacterial diversity estimation is the appropriate measure of rare taxa, but the uncertainty of the size of rare biosphere is yet to be experimentally determined. One approach is using the generalized diversity, Hill number (N_a), to control the variability associated with rare taxa by differentially weighing them. Here, we investigated Hill number as a framework for microbial diversity measure using a taxa-accmulation curve (TAC) with soil bacterial community data from two distinct studies by 454 pyrosequencing. The reliable biodiversity estimation was obtained when an increase in Hill number arose as the coverage became stable in TACs for a ≥ 1. In silico analysis also indicated that a certain level of sampling depth was desirable for reliable biodiversity estimation. Thus, in order to attain bacterial diversity from second generation sequencing, Hill number can be a good diversity framework with given sequencing depth, that is, until technology is further advanced and able to overcome the under- and random-sampling issues of the current sequencing approaches.

Designing Standardized and Optimized Surveys to Assess Invertebrate Biodiversity in Tropical Irrigated Rice Using Structured Inventory and Species Richness Models

Insect pest management depends on simple, rapid, and reliable sampling methods that should also be standardized and optimized. We tested structured inventory, community characterization, and sampling optimization approaches on the invertebrate fauna of Philippine irrigated rice, undisrupted by pesticides, using seven field methods and species richness models. Canopy and floodwater invertebrates were intensively and repetitively sampled from 600 quadrats (∼0.1-m(2) planar area) over dry and wet cropping seasons in one field at the International Rice Research Institute in the Philippines. In the canopy, pooled counts from D-Vac and plant dissections (PD) on the same rice hills ("absolute methodology") were compared with three other methods (i.e., FARMCOP, Blower-Vac, sweep-net), while, in the floodwater, the area collector ("absolute methodology") was compared with three other methods (i.e., FARMCOP, Blower-Vac, strainer-net). Overall, 25 and 50% of the observed richness of canopy and floodwater taxa, respectively, were caught by all four methods. Estimated inventory completeness for the canopy and floodwater averaged 82 and 98%, respectively, after all methods were pooled. To maximize observed richness, optimization results for the canopy recommended allocating the highest sampling effort to D-Vac and PD, followed by the Blower-Vac, whereas the area collector should be assigned the highest sampling effort in the floodwater, followed by the strainer-net or Blower-Vac. Our results suggest that structured inventory and species richness models are useful tools for setting optimization criteria and stopping rules for sampling crop-invertebrate assemblages based on inventory completeness and for enabling more informative biodiversity comparisons.

Turning Up the Heat on a Hotspot: DNA Barcodes Reveal 80% More Species of Geometrid Moths along an Andean Elevational Gradient

We sampled 14,603 geometrid moths along a forested elevational gradient from 1020-3021 m in the southern Ecuadorian Andes, and then employed DNA barcoding to refine decisions on species boundaries initially made by morphology. We compared the results with those from an earlier study on the same but slightly shorter gradient that relied solely on morphological criteria to discriminate species. The present analysis revealed 1857 putative species, an 80% increase in species richness from the earlier study that detected only 1010 species. Measures of species richness and diversity that are less dependent on sample size were more than twice as high as in the earlier study, even when analysis was restricted to an identical elevational range. The estimated total number of geometrid species (new dataset) in the sampled area is 2350. Species richness at single sites was 32-43% higher, and the beta diversity component rose by 43-51%. These impacts of DNA barcoding on measures of richness reflect its capacity to reveal cryptic species that were overlooked in the first study. The overall results confirmed unique diversity patterns reported in the first investigation. Species diversity was uniformly high along the gradient, declining only slightly above 2800 m. Species turnover also showed little variation along the gradient, reinforcing the lack of evidence for discrete faunal zones. By confirming these major biodiversity patterns, the present study establishes that incomplete species delineation does not necessarily conceal trends of biodiversity along ecological gradients, but it impedes determination of the true magnitude of diversity and species turnover.

Exploring the Leaf Beetle Fauna (Coleoptera: Chrysomelidae) of an Ecuadorian Mountain Forest Using DNA Barcoding

Background

Tropical mountain forests are hotspots of biodiversity hosting a huge but little known diversity of insects that is endangered by habitat destruction and climate change. Therefore, rapid assessment approaches of insect diversity are urgently needed to complement slower traditional taxonomic approaches. We empirically compare different DNA-based species delimitation approaches for a rapid biodiversity assessment of hyperdiverse leaf beetle assemblages along an elevational gradient in southern Ecuador and explore their effect on species richness estimates.

Methodology/Principal Findings

Based on a COI barcode data set of 674 leaf beetle specimens (Coleoptera: Chrysomelidae) of 266 morphospecies from three sample sites in the Podocarpus National Park, we employed statistical parsimony analysis, distance-based clustering, GMYC- and PTP-modelling to delimit species-like units and compared them to morphology-based (parataxonomic) species identifications. The four different approaches for DNA-based species delimitation revealed highly similar numbers of molecular operational taxonomic units (MOTUs) (n = 284–289). Estimated total species richness was considerably higher than the sampled amount, 414 for morphospecies (Chao2) and 469–481 for the different MOTU types. Assemblages at different elevational levels (1000 vs. 2000 m) had similar species numbers but a very distinct species composition for all delimitation methods. Most species were found only at one elevation while this turnover pattern was even more pronounced for DNA-based delimitation.

Conclusions/Significance

Given the high congruence of DNA-based delimitation results, probably due to the sampling structure, our study suggests that when applied to species communities on a regionally limited level with high amount of rare species (i.e. ~50% singletons), the choice of species delimitation method can be of minor relevance for assessing species numbers and turnover in tropical insect communities. Therefore, DNA-based species delimitation is confirmed as a valuable tool for evaluating biodiversity of hyperdiverse insect communities, especially when exact taxonomic identifications are missing.

Spintharus flavidus in the Caribbean-a 30 million year biogeographical history and radiation of a 'widespread species'

The Caribbean island biota is characterized by high levels of endemism, the result of an interplay between colonization opportunities on islands and effective oceanic barriers among them. A relatively small percentage of the biota is represented by ‘widespread species,’ presumably taxa for which oceanic barriers are ineffective. Few studies have explored in detail the genetic structure of widespread Caribbean taxa. The cobweb spider Spintharus flavidus Hentz, 1850 (Theridiidae) is one of two described Spintharus species and is unique in being widely distributed from northern N. America to Brazil and throughout the Caribbean. As a taxonomic hypothesis, Spintharus “flavidus” predicts maintenance of gene flow among Caribbean islands, a prediction that seems contradicted by known S. flavidus biology, which suggests limited dispersal ability. As part of an extensive survey of Caribbean arachnids (project CarBio), we conducted the first molecular phylogenetic analysis of S. flavidus with the primary goal of testing the ‘widespread species’ hypothesis. Our results, while limited to three molecular loci, reject the hypothesis of a single widespread species. Instead this lineage seems to represent a radiation with at least 16 species in the Caribbean region. Nearly all are short range endemics with several distinct mainland groups and others are single island endemics. While limited taxon sampling, with a single specimen from S. America, constrains what we can infer about the biogeographical history of the lineage, clear patterns still emerge. Consistent with limited overwater dispersal, we find evidence for a single colonization of the Caribbean about 30 million years ago, coinciding with the timing of the GAARLandia landbridge hypothesis. In sum, S. “flavidus” is not a single species capable of frequent overwater dispersal, but rather a 30 my old radiation of single island endemics that provides preliminary support for a complex and contested geological hypothesis.

A revised and dated phylogeny of cobweb spiders (Araneae, Araneoidea, Theridiidae): A predatory Cretaceous lineage diversifying in the era of the ants (Hymenoptera, Formicidae)

Cobweb spiders (Theridiidae) are highly diverse from the perspective of species richness, morphological diversity, variety of web architecture, and behavioral repertoires. The family includes over 50% of social spiders, a behavioral rarity among the order, and members of the family are furthermore the subject of research on venom, silk biomechanics, kleptoparasitism and web building, among other traits. Theridiidae is one of the most abundant groups of spiders, and thus key insect predators in many different ecosystems and is among relatively few spider families that show high degree of myrmecophagy. Modern comparative studies on all these fronts are best buttressed on a phylogenetic foundation. Our goal here is to offer a revised, dated, phylogenetic hypothesis for the family by summarizing previously published data from multiple molecular and morphological studies through data-mining, and adding novel data from several genera. We also test the hypothesis that the origin and diversification of cobweb spiders coincides with that of ants on which many species specialize as prey. The new phylogeny is largely congruent with prior studies and current taxonomy and should provide a useful tool for theridiid classification and for comparative analyses. Nevertheless, we also highlight the limitations of currently available data-the state of the art in Theridiidae phylogenetics-offering weak support for most of the deeper nodes in the phylogeny. Thus the need is clear for modern phylogenomic approaches to obtain a more solid understanding, especially of relationships among subfamilies. We recover the monophyly of currently recognized theridiid subfamilies with the exception of some enigmatic 'pholcommatines' (Styposis, Phoroncidia) and putative 'hadrotarsines' (Audifia, Tekellina) whose placement is uncertain in our analyses. Theridiidae dates back some 100 mya to the Cretaceous, a period of diversification in flowering plants and many groups of insects, including ants. The origin of cobweb spiders, and hence the cobweb-a speciallized trap for pedestrian prey-coincides with a major diversification shift in ants. The family becomes abundant in fossil record 50-40 mya as ants also diversify and reach dominance and contemporary patterns of abundances of theridiids and ants show the same trends, with increasing relative abundance towards the equator and at lower altitudes. We find that among orbiculariae, lineages that specialize on ant prey are non-randomly clustered within Theridiidae. Given these findings we hypothesize that the origin of the gumfoot web was a stepping stone that facilitated the capture of ants and resulted in specialized myrmecophagy in a number of 'basal' theridiids. We also document a subsequent loss in myrmecophagy, and associated increase in speciation rates, as 'recent' theridiid groups evolve diverse web forms and many return to the capture of aerial prey.

Sampling a biodiversity hotspot: the orchid-bee fauna (Hymenoptera: Apidae) of Tarapoto, northeastern Peru, the richest and most diverse site of the Neotropics

The orchid-bee fauna of the region of Tarapoto, northeastern Peru, was surveyed using seventeen different scents as baits to attract orchid-bee males. Six hundred and fifty-nine males belonging to 41 species were actively collected with insect nets during 120 hours in late July and early August, 2012. Euglossa dressleri Moure, 1968, Euglossa laurensi Bembé, 2008, and Euglossa maculilabris Moure, 1968, three species belonging to the Euglossa cybelia species-group, are here reported for Peru for the first time. Previous sporadic and unpublished samplings in the area recorded eleven additional species. With 53 species, the region of Tarapoto can be considered the richest single site in the Neotropics for orchid bees. Diversity, estimated with the Shannon-Wiener diversity index (H' = 3.02), was also the highest ever recorded for orchid bees.

Integrating and visualizing primary data from prospective and legacy taxonomic literature

Specimen data in taxonomic literature are among the highest quality primary biodiversity data. Innovative cybertaxonomic journals are using workflows that maintain data structure and disseminate electronic content to aggregators and other users; such structure is lost in traditional taxonomic publishing. Legacy taxonomic literature is a vast repository of knowledge about biodiversity. Currently, access to that resource is cumbersome, especially for non-specialist data consumers. Markup is a mechanism that makes this content more accessible, and is especially suited to machine analysis. Fine-grained XML (Extensible Markup Language) markup was applied to all (37) open-access articles published in the journal Zootaxa containing treatments on spiders (Order: Araneae). The markup approach was optimized to extract primary specimen data from legacy publications. These data were combined with data from articles containing treatments on spiders published in Biodiversity Data Journal where XML structure is part of the routine publication process. A series of charts was developed to visualize the content of specimen data in XML-tagged taxonomic treatments, either singly or in aggregate. The data can be filtered by several fields (including journal, taxon, institutional collection, collecting country, collector, author, article and treatment) to query particular aspects of the data. We demonstrate here that XML markup using GoldenGATE can address the challenge presented by unstructured legacy data, can extract structured primary biodiversity data which can be aggregated with and jointly queried with data from other Darwin Core-compatible sources, and show how visualization of these data can communicate key information contained in biodiversity literature. We complement recent studies on aspects of biodiversity knowledge using XML structured data to explore 1) the time lag between species discovry and description, and 2) the prevelence of rarity in species descriptions.

MDS, Rodrigues PES, Ott R. Diversity, composition and phenology of araneid orb-weavers (Araneae, Araneidae) associated with riparian forests in southern Brazil

The Araneidae is a speciose family including web-spinning spiders that are very abundant in various terrestrial ecosystems. Several studies demonstrate that changes in vegetation surrounding rivers, streams and brooks affect the associated araneofauna. The aim of this research was to compare differences found in diversity (abundance and richness), composition and phenology of Araneidae spiders sampled in different habitats in four riparian forest catchments in southern Brazil. Samples were taken from riparian forests in four rivers of Rio Grande do Sul State: Piratini, Camaquã, Sinos and Maquiné rivers, each in a different hydrographic basin. Samples were taken twice seasonally on each basin during two years, sampling the araneofauna of the tree-shrub strata with beating tray. Six transects were employed on each basin, two per habitat: edge with grassland, forest interior and river edge. Araneids totalled 20 genera and 65 species. Comparing riparian forests significant differences are found. Spider abundance differed among riparian forests as well as species richness. Overall, Piratini river riparian forest had the higher abundance and richness for Araneidae; the lower values were in Sinos river forest. The stronger degradation and fragmentation of the riparian forests of Sinos river probably influenced the results, with human disturbance gradients associated negatively to web building. We present data on the diversity of these spiders, which were very abundant in the riparian forest interior and very rich in species in the grassland/riparian forest edge. Species composition also differs among the studied habitats (the above plus river/riparian forest edge). For the most abundant species the phenological pattern across the seasons was also analysed.

The orchid-bee fauna (Hymenoptera: Apidae) of a forest remnant in the southern portion of the Brazilian Amazon

The orchid-bee fauna of the region of Porto Velho, in the state of Rondônia, Brazil, close to the southernmost limits of the Amazon Basin, was surveyed for the first time using five different scents as baits to attract orchid-bee males. Five hundred and twenty-one males belonging to five genera and 29 species were collected with bait traps during 26 non-consecutive days from November, 2011 to January, 2012. Eulaema nigrita Lepeletier, 1841 and Eulaema meriana (Olivier, 1789) were the most common species in the region and, together, represented almost 50% of all collected bees. Although the observed richness conforms to similar inventories in the region, the diversity (H'= 2.43) found in the present study is one of the highest ever recorded for orchid bees in the Amazon Basin.

Cyberdiversity: improving the informatic value of diverse tropical arthropod inventories

In an era of biodiversity crisis, arthropods have great potential to inform conservation assessment and test hypotheses about community assembly. This is because their relatively narrow geographic distributions and high diversity offer high-resolution data on landscape-scale patterns of biodiversity. However, a major impediment to the more widespread application of arthropod data to a range of scientific and policy questions is the poor state of modern arthropod taxonomy, especially in the tropics. Inventories of spiders and other megadiverse arthropods from tropical forests are dominated by undescribed species. Such studies typically organize their data using morphospecies codes, which make it difficult for data from independent inventories to be compared and combined. To combat this shortcoming, we offer cyberdiversity, an online community-based approach for reconciling results of independent inventory studies where current taxonomic knowledge is incomplete. Participating scientists can upload images and DNA barcode sequences to dedicated databases and submit occurrence data and links to a web site (www.digitalSpiders.org). Taxonomic determinations can be shared with a crowdsourcing comments feature, and researchers can discover specimens of interest available for loan and request aliquots of genomic DNA extract. To demonstrate the value of the cyberdiversity framework, we reconcile data from three rapid structured inventories of spiders conducted in Vietnam with an independent inventory (Doi Inthanon, Thailand) using online image libraries. Species richness and inventory completeness were assessed using non-parametric estimators. Community similarity was evaluated using a novel index based on the Jaccard replacing observed with estimated values to correct for unobserved species. We use a distance-decay framework to demonstrate a rudimentary model of landscape-scale changes in community composition that will become increasingly informative as additional inventories participate. With broader adoption of the cyberdiversity approach, networks of information-sharing taxonomists can more efficiently and effectively address taxonomic impediments while elucidating landscape scale patterns of biodiversity.

Diversity and population characteristics of terrestrial isopods (Crustacea, Oniscidea) across three forest environments in southern Brazil

Terrestrial isopods are important and dominant component of meso and macrodecomposer soil communities. The present study investigates the diversity and species composition of terrestrial isopods on three forests on the Serra Geral of the state of Rio Grande do Sul, Brazil. The area has two natural formations (Primary Woodland and Secondary Woodland) and one plantation of introduced Pinus. The pitfall traps operated from March 2001 to May 2002, with two summer periods and one winter. There were 14 sampling dates overall. Of the five species found: Alboscia silveirensis Araujo, 1999, Atlantoscia floridana (van Name, 1940), Benthana araucariana Araujo & Lopes, 2003 (Philoscidae), Balloniscus glaber Araujo & Zardo, 1995 (Balloniscidae) and Styloniscus otakensis (Chilton, 1901) (Styloniscidae); only A. floridana is abundant on all environments and B. glaber is nearly exclusive for the native forests. The obtained data made it possible to infer about population characteristics of this species. The Similarity Analysis showed a quantitative difference among the Secondary forest and Pinus plantation, but not a qualitative one. The operational sex ratio (OSR) analysis for A. floridana does not reveal significant differences in male and female proportions among environments. The reproductive period identified in the present study for A. floridana was from spring to autumn in the primary forest and Pinus plantation and during all year for the secondary forest. The OSR analysis for B. glaber reveals no significant differences in abundance between males and females for secondary forest, but the primary forest was a significant difference. The reproductive period for B. glaber extended from summer to autumn (for primary and secondary forest). This is the first record for Brazil of an established terrestrial isopod population in a Pinus sp. plantation area, evidenced by the presence of young, adults and ovigerous females, balanced sex ratio, expected fecundity and reproduction pattern, as compared to populations from native vegetation areas.