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

Abundance and diversity of host-seeking adult female mosquitoes in a coastal ecosystem in southern Mexico

Mosquito diversity influences disease risk because only certain species transmit pathogens, making the identification of species assemblages essential. To better understand mosquito diversity in the southern Gulf of Mexico, we conducted a study on Isla del Carmen, Campeche, from September 2019 to December 2020. Adult mosquitoes were collected using buccal aspirators during 24-hour cycles in mangrove and low-semideciduous forest patches across three climate seasons: norte, rainy and dry. Sampling occurred every four hours, and species were identified. Hill numbers of order q = 0, q = 1, and q = 2, non-binomial GLMs, NMDS, PERMANOVA, and generalized estimating equations were used to analyze mosquito diversity, abundance, and phenology. We collected 21,424 mosquitoes from 11 genera, 26 species, and four morphospecies. The mosquito abundance and richness peaked during the norte season (β = 1.057, z = 2.480, p = 0.013), with the season being the primary determinant of abundance (PERMANOVA, F = 7.229, R² = 0.512, p = 0.003). The vegetation type and sampling hour showed effects only when excluding the eudominant Aedes taeniorhynchus. The top five genera, Aedes, Psorophora, Mansonia, Culex and Anopheles, exhibited distinct phenological patterns, with abundance peaking between September 2019 and February 2020. Isla del Carmen is a key region for mosquito diversity in the Yucatan Peninsula, hosting species known to transmit pathogens to humans and wildlife. Our findings highlight the norte season, when cooler temperatures and moderate rainfall are present, as a critical period for mosquito activity, emphasizing the need for targeted vector surveillance and control efforts during this time in the region. This study provides valuable insights into mosquito community dynamics and their implications for public health in coastal areas of southern Mexico.

Local tree cover predicts mosquito species richness and disease vector presence in a tropical countryside landscape

Context

Land use change and deforestation drive both biodiversity loss and zoonotic disease transmission in tropical countrysides. For mosquito communities that can include disease vectors, forest loss has been linked to reduced biodiversity and increased vector presence. The spatial scales at which land use and tree cover shape mosquito communities present a knowledge gap relevant to both biodiversity and public health.

Objectives

We investigated the responses of mosquito species richness and Aedes albopictus disease vector presence to land use and to tree cover surrounding survey sites at different spatial scales. We also investigated species compositional turnover across land uses and along environmental gradients.

Methods

We paired a field survey of mosquito communities in agricultural, residential, and forested lands in rural southern Costa Rica with remotely sensed tree cover data. We compared mosquito richness and vector presence responses to tree cover measured across scales from 30 to 1000 m, and across land uses. We analyzed mosquito community compositional turnover between land uses and along environmental gradients of tree cover, temperature, elevation, and geographic distance.

Results

Tree cover was both positively correlated with mosquito species richness and negatively correlated with the presence of the common invasive dengue vector Ae. albopictus at small spatial scales of 90-250 m. Land use predicted community composition and Ae. albopictus presence.

Conclusions

The results suggest that local tree cover preservation and expansion can support mosquito species richness and reduce disease vector presence. The identified spatial range at which tree cover shapes mosquito communities can inform the development of land management practices to protect both ecosystem and public health.

Supplementary Information

The online version contains supplementary material available at 10.1007/s10980-025-02105-0.

Diversity and distribution of the caddisfly genus Atopsyche Banks, 1905 in Ecuador, with the description of seven new species (Trichoptera: Hydrobiosidae)

Atopsyche is the largest Hydrobiosidae genus on the South American continent. The genus previously included 27 species in Ecuador. In this work, we describe and illustrate seven new species of Atopsyche from the Andes of Ecuador: Atopsyche andina sp. nov., Atopsyche azuayana sp. nov., Atopsyche chocoandina sp. nov., Atopsyche jocotoco sp. nov., Atopsyche papallacta sp. nov., Atopsyche piburja sp. nov., and Atopsyche tapichalaca sp. nov. Additionally, we provide distributional information for all Ecuadorian Atopsyche, including three new country records: A. kingi, A. mayucapac, and A. neotropicalis. With these additions, there are now 37 species of Atopsyche in Ecuador, or about 75% of species in the country, according to the CHAO 2 species estimator. Finally, we provide new and more detailed illustrations for A. bolivari, A. bravoi, and A. davidsoni.

Optimal inventorying and monitoring of taxonomic, phylogenetic and functional diversity

Comparable data is essential to understand biodiversity patterns. While assemblage or community inventorying requires comprehensive sampling, monitoring focuses on as few components as possible to detect changes. Quantifying species, their evolutionary history, and the way they interact requires studying changes in taxonomic (TD), phylogenetic (PD) and functional diversity (FD). Here we propose a method for the optimization of sampling protocols for inventorying and monitoring assemblages or communities across these three diversity dimensions taking sampling costs into account. We used Iberian spiders and Amazonian bats as two case-studies. The optimal combination of methods for inventorying and monitoring required optimizing the accumulation curve of α-diversity and minimizing the difference between sampled and estimated β-diversity (bias), respectively. For Iberian spiders, the optimal combination for TD, PD and FD allowed sampling at least 50% of estimated diversity with 24 person-hours of fieldwork. The optimal combination of six person-hours allowed reaching a bias below 8% for all dimensions. For Amazonian bats, surveying all the 12 sites with mist-nets and 0 or 1 acoustic recorders was the optimal combination for almost all diversity types, resulting in >89% of the diversity and <10% bias with roughly a third of the cost. Only for phylogenetic α-diversity, the best solution was less clear and involved surveying both with mist nets and acoustic recorders. The widespread use of optimized and standardized sampling protocols and regular repetition in time will radically improve global inventory and monitoring of biodiversity. We strongly advocate for the global adoption of sampling protocols for both inventory and monitoring of taxonomic, phylogenetic and functional diversity.

Structure and composition of a canopy-beetle community (Coleoptera) in a Neotropical lowland rainforest in southern Venezuela

Species richness, community structure and taxonomic composition are important characteristics of biodiversity. Beetle communities show distinct diversity patterns according to habitat attributes. Tropical rainforest canopies, which are well known for their richness in Coleoptera, represent such a conspicuous life zone. Here, I describe a canopy-inhabiting beetle community associated with 23 tree species in a Neotropical lowland rainforest. Adult beetles were sampled manually and in aerial traps using a large tower crane for a cumulative year. The sample revealed 6738 adult beetles, which were assigned to 862 (morpho-)species in 45 families. The most species-rich beetle families were Curculionidae (n = 246), Chrysomelidae (n = 121) and Cerambycidae (n = 89). The most abundant families were Curculionidae (n = 2746) and Chrysomelidae (n = 1409). Dominant beetle families were found in most assemblages. The beetle community consisted of 400 singletons (46.4%). A similar proportion was evident for assemblages of single tree species. I found that 74.5% of all beetle species were restricted in their occurrence on host trees to the phenological season and time of the day. This daily and seasonal migration causes patterns similar to mass effects and therefore accounts for the high proportion of singletons.

Species delimitation with limited sampling: An example from rare trapdoor spider genus Cyclocosmia (Mygalomorphae, Halonoproctidae)

The outcome of species delimitation depends on many factors, including conceptual framework, study design, data availability, methodology employed and subjective decision making. Obtaining sufficient taxon sampling in endangered or rare taxa might be difficult, particularly when non-lethal tissue collection cannot be utilized. The need to avoid overexploitation of the natural populations may thus limit methodological framework available for downstream data analyses and bias the results. We test species boundaries in rare North American trapdoor spider genus Cyclocosmia Ausserer (1871) inhabiting the Southern Coastal Plain biodiversity hotspot with the use of genomic data and two multispecies coalescent model methods. We evaluate the performance of each methodology within a limited sampling framework. To mitigate the risk of species over splitting, common in taxa with highly structured populations, we subsequently implement a species validation step via genealogical diversification index (gdi), which accounts for both genetic isolation and gene flow. We delimited eight geographically restricted lineages within sampled North American Cyclocosmia, suggesting that major river drainages in the region are likely barriers to dispersal. Our results suggest that utilizing BPP in the species discovery step might be a good option for datasets comprising hundreds of loci, but fewer individuals, which may be a common scenario for rare taxa. However, we also show that such results should be validated via gdi, in order to avoid over splitting.

Amazonian earthworm biodiversity is heavily impacted by ancient and recent human disturbance

Despite the importance of earthworms for soil formation, more is needed to know about how Pre-Columbian modifications to soils and the landscape. Gaining a deeper understanding is essential for comprehending the historical drivers of earthworm communities and the development of effective conservation strategies in the Amazon rainforest. Human disturbance can significantly impact earthworm diversity, especially in rainforest soils, and in the particular case of the Amazonian rainforest, both recent and ancient anthropic practices may be important. Amazonian Dark Earths (ADEs) are fertile soils found throughout the Amazon Basin, created by sedentary habits and intensification patterns of pre-Colombian societies primarily developed in the second part of the Holocene period. We have sampled earthworm communities in three Brazilian Amazonian (ADEs) and adjacent reference soils (REF) under old and young forests and monocultures. To better assess taxonomic richness, we used morphology and the barcode region of the COI gene to identify juveniles and cocoons and delimit Molecular Operational Taxonomic Units (MOTUs). Here we suggest using Integrated Operational Taxonomical units (IOTUs) which combine both morphological and molecular data and provide a more comprehensive assessment of diversity, while MOTUs only rely on molecular data. A total of 970 individuals were collected, resulting in 51 taxonomic units (IOTUs, MOTUs, and morphospecies combined). From this total, 24 taxonomic units were unique to REF soils, 17 to ADEs, and ten were shared between both soils. The highest richness was found in old forest sites for ADEs (12 taxonomic units) and REFs (21 taxonomic units). The beta-diversity calculations reveal a high species turnover between ADEs and REF soils, providing evidence that ADEs and REFs possess distinct soil biota. Furthermore, results suggest that ADE sites, formed by Pre-Columbian human activities, conserve a high number of native species in the landscape and maintain a high abundance, despite their long-term nature.

Global determinants of insect mitochondrial genetic diversity

Understanding global patterns of genetic diversity is essential for describing, monitoring, and preserving life on Earth. To date, efforts to map macrogenetic patterns have been restricted to vertebrates, which comprise only a small fraction of Earth's biodiversity. Here, we construct a global map of predicted insect mitochondrial genetic diversity from cytochrome c oxidase subunit 1 sequences, derived from open data. We calculate the mitochondrial genetic diversity mean and genetic diversity evenness of insect assemblages across the globe, identify their environmental correlates, and make predictions of mitochondrial genetic diversity levels in unsampled areas based on environmental data. Using a large single-locus genetic dataset of over 2 million globally distributed and georeferenced mtDNA sequences, we find that mitochondrial genetic diversity evenness follows a quadratic latitudinal gradient peaking in the subtropics. Both mitochondrial genetic diversity mean and evenness positively correlate with seasonally hot temperatures, as well as climate stability since the last glacial maximum. Our models explain 27.9% and 24.0% of the observed variation in mitochondrial genetic diversity mean and evenness in insects, respectively, making an important step towards understanding global biodiversity patterns in the most diverse animal taxon.

Abundant, diverse, unknown: Extreme species richness and turnover despite drastic undersampling in two closely placed tropical Malaise traps

Arthropods account for a large proportion of animal biomass and diversity in terrestrial systems, making them crucial organisms in our environments. However, still too little is known about the highly abundant and megadiverse groups that often make up the bulk of collected samples, especially in the tropics. With molecular identification techniques ever more evolving, analysis of arthropod communities has accelerated. In our study, which was conducted within the Global Malaise trap Program (GMP) framework, we operated two closely placed Malaise traps in Padang, Sumatra, for three months. We analyzed the samples by DNA barcoding and sequenced a total of more than 70,000 insect specimens. For sequence clustering, we applied three different delimitation techniques, namely RESL, ASAP, and SpeciesIdentifier, which gave similar results. Despite our (very) limited sampling in time and space, our efforts recovered more than 10,000 BINs, of which the majority are associated with "dark taxa". Further analysis indicates a drastic undersampling of both sampling sites, meaning that the true arthropod diversity at our sampling sites is even higher. Regardless of the close proximity of both Malaise traps (< 360 m), we discovered significantly distinct communities.

How many metazoan species live in the world's largest mineral exploration region?

The global surge in demand for metals such as cobalt and nickel has created unprecedented interest in deep-sea habitats with mineral resources. The largest area of activity is a 6 million km2 region known as the Clarion-Clipperton Zone (CCZ) in the central and eastern Pacific, regulated by the International Seabed Authority (ISA). Baseline biodiversity knowledge of the region is crucial to effective management of environmental impact from potential deep-sea mining activities, but until recently this has been almost completely lacking. The rapid growth in taxonomic outputs and data availability for the region over the last decade has allowed us to conduct the first comprehensive synthesis of CCZ benthic metazoan biodiversity for all faunal size classes. Here we present the CCZ Checklist, a biodiversity inventory of benthic metazoa vital to future assessments of environmental impacts. An estimated 92% of species identified from the CCZ are new to science (436 named species from a total of 5,578 recorded). This is likely to be an overestimate owing to synonyms in the data but is supported by analysis of recent taxonomic studies suggesting that 88% of species sampled in the region are undescribed. Species richness estimators place total CCZ metazoan benthic diversity at 6,233 (+/-82 SE) species for Chao1, and 7,620 (+/-132 SE) species for Chao2, most likely representing lower bounds of diversity in the region. Although uncertainty in estimates is high, regional syntheses become increasingly possible as comparable datasets accumulate. These will be vital to understanding ecological processes and risks of biodiversity loss.

Long-term mammal herbivory on arthropod assemblages at Kruger National Park, South Africa

Protected savannas are essential reserves for biological diversity, including endangered arthropod species, however, extreme grazing by mammals has cascading impacts on the communities and disrupts the functioning of these ecosystems globally. The current study assessed the abundance, species richness and composition of arthropods at the long-term grazing exclosures of Kruger National Park, South Africa. Pitfall traps and active searches were used to sample arthropods at the ungrazed, moderately, and heavily grazed exclosures. We found that Hymenoptera, Coleoptera, Diptera and Araneae were the most abundant orders of arthropods sampled. The abundance of multi-taxon, Diptera and Hymenoptera was significantly different between exclosures. In contrast, Coleoptera had high numbers of morphospecies compared to Hymenoptera, Araneae and Diptera. Species richness for multi-taxon, Diptera and Hymenoptera was significantly high at the heavily grazed compared to moderately grazed and ungrazed exclosures. Up to 22.2%, 41.2%, and 44.4% of the morphospecies were unique to the ungrazed, moderately and heavily grazed exclosures, respectively. A high proportion of morphospecies shared between exclosures were Coleoptera (41.0%) and Hymenoptera (38.5%) compared to Diptera and Araneae with less than 5% recorded across exclosures. Thus, morphospecies within the least abundant orders, namely Diptera and Araneae, were represented by singletons that were unique to particular exclosures compared to the most abundant arthropod orders (e.g., Coleoptera and Hymenoptera). We conclude that long-term mammal grazing enhances species richness and niche composition together with sparse and unique arthropods in the protected savannas. Therefore, managed grazing regimes can serve as a tool for maintaining the integrity of the protected savannas.

First Record of the Elusive Ant Parasitoid Horismenus floridensis (Hymenoptera: Eulophidae) in Mexico and New Association with an Ant Host

Most eulophid wasps are primary parasitoids, mainly of endophytic insect larvae (Diptera, Coleoptera, Lepidoptera, Hymenoptera, Hemiptera, and Thysanoptera), but can also attack spider eggs, gall-forming mites, or nematodes. A few species are known to parasitize ants. Here we report on the occurrence of Horismenus floridensis (Schauff and Bouček) attacking Camponotus atriceps (Smith) in southern Mexico (Campeche), expanding the distribution for this eulophid species and the range of its potential hosts. We also provide an updated list of the Horismenus Walker species found in Mexico, which currently includes 21 identified species. This is the second host ant ever recorded for H. floridensis and the first reliable record of C. atriceps as a host for this eulophid wasp. The first host ant reported from Florida 35 years ago was the closely related valid species, C. floridanus (Buckley), erroneously synonymized at that time with C. atriceps (formerly, C. abdominalis (Fabricius)).

Seagrass macrobenthic biodiversity does not vary in conformity with a leaky-lagoonal confinement gradient

Coastal lagoon ecology often changes on progression from the open, well-flushed mouth region to the depositional zone furthest from the open sea. This is generally considered consequent on increasing 'confinement' and associated features, rather than on the often co-occurringly decreasing salinity. The 12 km Rainbow Channel connecting part of Moreton Bay, a microtidal leaky lagoon, to the adjacent Pacific provides a gradient of increasing confinement without any significant salinity change, i.e. a tenfold increase in water residence time for a salinity decrease of <1. Macrobenthic faunal assemblages characterising intertidal Zostera seagrass at strategic points along its length were compared to test whether their nature changed in conformity with confinement models. Results suggest that it does not; faunal abundance, species richness, evenness and composition remaining effectively unchanged along the gradient. Seagrass systems may constitute a special case because they decouple renewal times of the overlying water and local organic enrichment/decomposition; as may leaky lagoons because of their high tidal velocities.

Spider Diversity in the Fragmented Forest-Steppe Landscape of Northeastern Ukraine: Temporal Changes under the Impact of Human Activity

Semi-natural forests and dry grasslands are highly fragmented and influenced by human activity. Despite the small area, they serve as the refuge for habitat-specific species and enhance agrolandscape biodiversity. We studied spiders in Velykoburlutskyi Steppe Regional Landscape Park (northeastern Ukraine) for 10 years and found 224 species of 26 families; of these, 27 are rare and require protection. The araneofauna of small forests in gullies is poorer than that of the large oakeries and hosts fewer sylvatic species; the dry grassland fauna is rich, has typical steppe traits, and varies depending on topography and grazing history. The ungrazed gully hosted 125 spider species. The richest assemblages (97 species) were at the bottom, and they were similar to those of meadows and forest edges. The most typical steppe assemblages were formed on the ungrazed slope (77 species). The human-induced disturbance had a negative effect on spiders: we found only 63 species at the grazed bottom and 62 on the slope. After abrupt grazing cessation, four spider species appeared and occurred constantly at the bottom, while no species left this habitat. Grazing on the slopes declined gradually, and spider assemblages did not change significantly after the final cessation; moreover, they enriched on the abandoned slope (75 species). The presence of rare species and a variety of spider assemblages confirm the conservation value of the study site and the need to maintain its mosaic pattern.

Deep mtDNA Sequence Divergences and Possible Species Radiation of Whip Spiders (Arachnida, Amblypygi, Phrynidae, Phrynus/Paraphrynus) among Caribbean Oceanic and Cave Islands

Islands—whether classic oceanic islands or habitat islands such as isolated thermal vents, mountain tops, or caves—often promote the diversification of lineages that colonize them. We examined CO1 mtDNA sequence divergences within the tailless whip spider genus Phrynus Lamarck, 1809 (Amblypygi: Phrynidae) among oceanic islands and among cave ’islands´ distributed across the Caribbean archipelago and on the continental mainland. The significance of this study lies in the extensive taxon sampling of a supposedly depauperate lineage (considering its age), over a large proportion of its geographical range, and the discovery of deep mtDNA sequence divergences. We sampled thousands of specimens—and sequenced 544, including six outgroup species—across 173 localities on 17 islands (135 localities) and five countries on the North to South American mainland (38 localities), including a total of 63 caves. Classical taxonomy identified ten named Phrynus and two Paraphrynus Moreno, 1940 species. Paraphrynus seems to be paraphyletic and nested in Phrynus. Uncorrected genetic distances within named species and among morphological species ranged up to 15% and 19%, respectively. Geographic distances explained a significant portion of genetic distances on islands (19%, among both subterranean and epigean specimens), and for epigean specimens on the mainland (27%). Species delimitation analyses indicated that the 12 named species harbored from 66 to well over 100 putative species. The highest number of species was indicated by the GMYC method (114 species) while the Bayesian Poisson tree processes (bPTP) and the BP&P relaying on the Markov chain Monte Carlo Bayesian Phylogenetic model estimated an upper level of 110 species. On the other hand, the recently recommended and relatively conservative distance-based (phylogeny free) ASAP model has the greatest support for 73 species. In either case, nearly all putative species are tightly limited to a single locality, often a small cave system, and sometimes to the surrounding epigean area. Caribbean Phrynus diversity has likely been vastly underestimated, likely due to both morphological crypsis and the ignorance of Caribbean cave fauna. Although mtDNA sequences can suggest species limits, nuclear DNA sequencing and detailed morphological research are necessary to corroborate them and explore whether this phenomenon constitutes species radiation or perhaps just mtDNA divergences as a consequence of, for example, stationary females and actively dispersing males.

Seasonal changes in the diversity, host preferences and infectivity of mosquitoes in two arbovirus-endemic regions of Costa Rica

BACKGROUND

Mosquitoes are vectors of various arboviruses belonging to the genera Alphavirus and Flavivirus, and Costa Rica is endemic to several of them. The aim of this study was to describe and analyze the community structure of such vectors in Costa Rica.

METHODS

Sampling was performed in two different coastal locations of Costa Rica with evidence of arboviral activity during rainy and dry seasons. Encephalitis vector surveillance traps, CDC female gravid traps and ovitraps were used. Detection of several arboviruses by Pan-Alpha and Pan-Flavi PCR was attempted. Blood meals were also identified. The Normalized Difference Vegetation Index (NDVI) was estimated for each area during the rainy and dry seasons. The Chao2 values for abundance and Shannon index for species diversity were also estimated.

RESULTS

A total of 1802 adult mosquitoes belonging to 55 species were captured, among which Culex quinquefasciatus was the most caught species. The differences in NDVI were higher between seasons and between regions, yielding lower Chao-Sørensen similarity index values. Venezuelan equine encephalitis virus, West Nile virus and Madariaga virus were not detected at all, and dengue virus and Zika virus were detected in two separate Cx. quinquefasciatus specimens. The primary blood-meal sources were chickens (60%) and humans (27.5%). Both sampled areas were found to have different seasonal dynamics and population turnover, as reflected in the Chao2 species richness estimation values and Shannon diversity index.

CONCLUSION

Seasonal patterns in mosquito community dynamics in coastal areas of Costa Rica have strong differences despite a geographical proximity. The NDVI influences mosquito diversity at the regional scale more than at the local scale. However, year-long continuous sampling is required to better understand local dynamics.

The Effect of Sampling Bias on Evaluating the Diversity and Distribution Patterns of Iranian Spiders (Arachnida: Araneae)

Although spiders constitute a highly diversified group of animals, the knowledge regarding their geographic distribution (i.e., the so-called Wallacean shortfall) and diversity patterns is incipient on a global scale; while attempts to explore such patterns have been made for the highly diversified Neotropical fauna, several Old World regions are historically neglected. Aiming to close this gap, the present study provides the most comprehensive review of spatial variation in the diversity patterns of the spider fauna of Iran. We also examined the effects of sampling biases on the results. We gathered a database with 4434 non-duplicate records of 935 species of spiders from Iran, 215 of which are currently considered endemic to the country. We showed that, despite a significant improvement in state-of-the-art taxonomic research regarding this fauna in the past 20 years, the Iranian spider fauna suffers from a highly uneven distribution of records throughout the country and its ecoregions. Additionally, highly sampled areas are typically near large cities. We also found a high correlation between the number of records and species of spiders and the number of records of plants and other animals in Iran, suggesting that the biodiversity shortfalls herein described for spiders are corroborated by other taxa. The biases reported herein are likely to be observed for other countries, as the area alone explained only 33.24% of the spider species richness among 171 compared countries. We hope that the present study stimulates further sampling and research aiming to explore this fauna and the underlying biological processes related to its patterns of diversity and distribution.

Species conservation profiles of the endemic spiders Troglohyphantes (Araneae, Linyphiidae) from the Alps and the north-western Dinarides

Background

The genus Troglohyphantes Joseph, 1882 (Araneae, Linyphiidae) includes 131 species, mainly distributed across the main European mountain ranges. The Alps and the north-western Dinarides account for 66 species, most of them showing narrow or even point-like distributions. The majority of Troglohyphantes spiders dwell in subterranean habitats including caves, mines, soil litter, rocky debris and other moist and shaded retreats. Despite being intensively studied from taxonomic, ecological and biogeographic standpoints, knowledge on the status of conservation and on the potential risk of extinction of these spiders is lagging. To date, only three species have been included in the global IUCN Red List, but their status has not been updated ever since their last assessment in 1996. The aim of this contribution is to assess the Alpine and north-western Dinaric species of the genus Troglohyphantes and to re-assess the species previously evaluated, according to the last version of the IUCN Red List Categories and Criteria.

New information

Amongst the 66 species here considered, 62 had sufficient data to allow the quantification of their Extent Of Occurrence (EOO) and Area Of Occupancy (AOO). Most of the species have a narrow distribution range, with an estimated EOO < 20,000 km² and AOO < 2,000 km², meeting the thresholds for the inclusion in the threatened categories. Five species have a more widespread distribution (EOO > 20,000 km²), extending across multiple countries. The quality of the data on distribution of four species was not sufficient to provide a reliable estimation of the distribution range.A continuing decline in EOO, AOO and habitat quality was inferred for 30 species. The majority of them were subterranean specialised species, with a reduced thermal tolerance and a low dispersal ability. Accordingly, changes in subterranean microclimatic conditions due to climate change represent a major threat for these species. Land-use change and habitat alteration were identified as additional relevant threats for several species.A considerable proportion of the species here assessed was found in protected areas and in sites of the Natura 2000 network. In addition, 14 species are formally protected by national and sub-national legislation. At present, 25 species are listed in the regional Red Lists.Long-term monitoring programmes, management plans for both the species and their habitats, expansion of the extant protected areas and designation of new ones, should be considered as the most effective approaches to species conservation.

A Distribution-Free Model for Longitudinal Metagenomic Count Data

Longitudinal metagenomics has been widely studied in the recent decade to provide valuable insight for understanding microbial dynamics. The correlation within each subject can be observed across repeated measurements. However, previous methods that assume independent correlation may suffer from incorrect inferences. In addition, methods that do account for intra-sample correlation may not be applicable for count data. We proposed a distribution-free approach, namely CorrZIDF, which extends the current method to model correlated zero-inflated metagenomic count data, offering a powerful and accurate solution for detecting significance features. This method can handle different working correlation structures without specifying each margin distribution of the count data. Through simulation studies, we have shown the robustness of CorrZIDF when selecting a working correlation structure for repeated measures studies to enhance the efficiency of estimation. We also compared four methods using two real datasets, and the new proposed method identified more unique features that were reported previously on the relevant research.

Mammals of Cajuru State Forest and surroundings: a neglected but important Protected Area for the Cerrado conservation in the São Paulo state, Brazil

Abstract: The Cerrado has been severely impacted by anthropogenic disturbances, with a tiny proportion of its original extent remaining in its southern portions. In the state of São Paulo, only 7% of this vegetation remains and relatively little is known about the biodiversity of these fragments. To fill this knowledge gap, we inventoried medium and large-sized terrestrial mammals of a neglected region, including a sustainable use protected area, Cajuru State Forest (CSF), adjacent native vegetation remnants protected by the Native Vegetation Protection Law and owned by a paper and cellulose company (Dois Córregos Farm; DCF), and their surroundings. We recorded 20 native mammal species, five of which are endangered with extinction, including the giant anteater, puma, and maned wolf. We found no significant differences in species richness between CSF and DCF but we found higher estimated species richness for the surrounding areas. Besides encompassing a larger and more heterogeneous area, the surrounding area still has a relatively high proportion (>30%) of native vegetation, providing habitat and resources for many species. The estimated mammal species richness for the entire study area was similar to that found in the largest protected area of the Cerrado in São Paulo State, the Jataí Ecological Station and its surroundings. We conclude that our study area still harbors a relatively rich community of large mammals and is important for the conservation of endangered species. This finding is particularly timing since the current State administration is considering to transfer the economic exploitation of CSF to the private sector. We therefore endorse an existing proposal to uplist this protected area, which still lacks a management plan, to a more restricted management category. Besides actions regarding this governmental PA, we argue that it is also important to involve the private sector in a conservation plan for the region.

Improving Taxonomic Practices and Enhancing Its Extensibility—An Example from Araneology

Planetary extinction of biodiversity underscores the need for taxonomy. Here, we scrutinize spider taxonomy over the last decade (2008–2018), compiling 2083 published accounts of newly described species. We evaluated what type of data were used to delineate species, whether data were made freely available, whether an explicit species hypothesis was stated, what types of media were used, the sample sizes, and the degree to which species constructs were integrative. The findings we report reveal that taxonomy remains largely descriptive, not integrative, and provides no explicit conceptual framework. Less than 4% of accounts explicitly stated a species concept and over one-third of all new species described were based on 1–2 specimens or only one sex. Only ~5% of studies made data freely available, and only ~14% of all newly described species employed more than one line of evidence, with molecular data used in ~6% of the studies. These same trends have been discovered in other animal groups, and therefore we find it logical that taxonomists face an uphill challenge when justifying the scientific rigor of their field and securing the needed resources. To move taxonomy forward, we make recommendations that, if implemented, will enhance its rigor, repeatability, and scientific standards.

Multinational coordination required for conservation of over 90% of marine species

Marine species are declining at an unprecedented rate, catalyzing many nations to adopt conservation and management targets within their jurisdictions. However, marine species and the biophysical processes that sustain them are naive to international borders. An understanding of the prevalence of cross-border species distributions is important for informing high-level conservation strategies, such as bilateral or regional agreements. Here, we examined 28,252 distribution maps to determine the number and locations of transboundary marine plants and animals. More than 90% of species have ranges spanning at least two jurisdictions, with 58% covering more than 10 jurisdictions. All jurisdictions have at least one transboundary species, with the highest concentrations of transboundary species in the USA, Australia, Indonesia, and the Areas Beyond National Jurisdiction. Distributions of mapped biodiversity indicate that overcoming the challenges of multinational governance is critical for a much wider suite of species than migratory megavertebrates and commercially exploited fish stocks-the groups that have received the vast majority of multinational management attention. To effectively protect marine biodiversity, international governance mechanisms (particularly those related to the Convention on Biological Diversity, the Convention on Migratory Species, and Regional Seas Organizations) must be expanded to promote multinational conservation planning, and complimented by a holistic governance framework for biodiversity beyond national jurisdiction.

Every Single Specimen Counts: A New Docosia Winnertz (Diptera: Mycetophilidae) Species Described from a Singleton

Simple Summary

A new fungus gnat species has been described from a single specimen collected from Georgia (Sakartvelo). The new species, named after its occurrence in Caucasia as Docosia caucasica sp. n., is distinguished from congeners by the characters in male terminalia and a unique COI sequence. As a substantial proportion of species in ecological communities tend to be rare, about 20–30% of new insect taxa have been described from a singleton so far. Therefore, following high-quality standards when describing new species, particularly when dealing with minimalistic material, is crucial. As much as possible, using multiple sets of characters, like morphology and DNA sequencing, is encouraged.

Abstract

A new species—Docosia caucasica sp. n.—has been described from material collected from the Lesser Caucasus Mountains in Georgia (Sakartvelo). The new species belongs to a group of Palaearctic species characterized by distinct posterolateral processes of gonocoxites and apically modified setae at the posteroventral margin of the gonocoxites medially. Within the group, D. caucasica sp. n. is most similar to D. landrocki Laštovka and Ševčík, 2006 in having a similar outline of the medial process of posteroventral margin of the gonocoxites and the gonostylus. There is also a marked difference within the partial cytochrome c oxidase subunit 1 gene (COI) sequence of D. caucasica sp. n. and other Docosia spp. available in public databases. As the new species is described from a single male specimen only, the adequacy and code compliance of that are discussed.

Mangroves are an overlooked hotspot of insect diversity despite low plant diversity

BACKGROUND

The world's fast disappearing mangrove forests have low plant diversity and are often assumed to also have a species-poor insect fauna. We here compare the tropical arthropod fauna across a freshwater swamp and six different forest types (rain-, swamp, dry-coastal, urban, freshwater swamp, mangroves) based on 140,000 barcoded specimens belonging to ca. 8500 species.

RESULTS

We find that the globally imperiled habitat "mangroves" is an overlooked hotspot for insect diversity. Our study reveals a species-rich mangrove insect fauna (>3000 species in Singapore alone) that is distinct (>50% of species are mangrove-specific) and has high species turnover across Southeast and East Asia. For most habitats, plant diversity is a good predictor of insect diversity, but mangroves are an exception and compensate for a comparatively low number of phytophagous and fungivorous insect species by supporting an unusually rich community of predators whose larvae feed in the productive mudflats. For the remaining tropical habitats, the insect communities have diversity patterns that are largely congruent across guilds.

CONCLUSIONS

The discovery of such a sizeable and distinct insect fauna in a globally threatened habitat underlines how little is known about global insect biodiversity. We here show how such knowledge gaps can be closed quickly with new cost-effective NGS barcoding techniques.

Image-based Automated Species Identification: Can Virtual Data Augmentation Overcome Problems of Insufficient Sampling?

Automated species identification and delimitation is challenging, particularly in rare and thus often scarcely sampled species, which do not allow sufficient discrimination of infraspecific versus interspecific variation. Typical problems arising from either low or exaggerated interspecific morphological differentiation are best met by automated methods of machine learning that learn efficient and effective species identification from training samples. However, limited infraspecific sampling remains a key challenge also in machine learning. In this study, we assessed whether a data augmentation approach may help to overcome the problem of scarce training data in automated visual species identification. The stepwise augmentation of data comprised image rotation as well as visual and virtual augmentation. The visual data augmentation applies classic approaches of data augmentation and generation of artificial images using a Generative Adversarial Networks (GAN) approach. Descriptive feature vectors are derived from bottleneck features of a VGG-16 convolutional neural network (CNN) that are then stepwise reduced in dimensionality using Global Average Pooling and PCA to prevent overfitting. Finally, data augmentation employs synthetic additional sampling in feature space by an oversampling algorithm in vector space (SMOTE). Applied on four different image datasets, which include scarab beetle genitalia (Pleophylla, Schizonycha) as well as wing patterns of bees (Osmia) and cattleheart butterflies (Parides), our augmentation approach outperformed a deep learning baseline approach by means of resulting identification accuracy with non-augmented data as well as a traditional 2D morphometric approach (Procrustes analysis of scarab beetle genitalia).

Leafhopper food plants in a Neotropical forest in Panama (Hemiptera: Cicadellidae)

The leafhoppers (Cicadellidae) are a group of insects that suck sap from vascular plants. The host plants of most species of Cicadellidae are unknown, but some species are known to have a wide range of food plants, while others are host plant specific. The aim of this study was to record the food and host plants for leafhoppers in a Neotropical rainforest. The study area was located in the lowland forests of Panama Province (Central Panama) in two National Parks. Sampling was done in the undergrowth, canopy and emergent strata to collect the cicadellids feeding on the trees, shrubs, seedlings, and vines there. We collected 118 cicadellid adult representing 24 species, 21 genera, and six subfamilies, which fed on 49 species of plants, belonging to 31 families. The subfamily with the largest number of species was the Cicadellinae with 11, while the plant family with the most species was the Fabaceae with five species, and the favorite plant was Anacardium excelsum, which hosted six cicadellid species and 10 individuals. According to estimates by Shannon Weiner, leafhopper communities are more diverse on trees than on shrubs, vines, or grasses.

Tourist species bias estimates of extrapolated species density in dispersive taxa: a case study from a litter beetle assemblage in temperate woodland

Extrapolative nonparametric estimators of species density are commonly used in community ecology. However, they are dependent on either (1) their use on non-dispersive taxa, or (2) the ability to separate tourists from residents in dispersive taxa. We undertook ten years of leaf litter sampling in an ancient woodland in the New Forest, Southern England. We identified all the beetles from those samples and assigned them a residency status (residents, stratum tourists, and habitat tourists). Extrapolations, using the Chao 2, first- and second-order jackknife, and bootstrap approaches, of all sampled beetles all showed large overestimates of species richness when compared with extrapolations based on just residents. We recommend that the estimators should be used with caution as estimates of actual species density for dispersive taxa unless the natural history of most species in a community is well known. This applies especially to tropical ecosystems where many species have not been described. This reinforces the need for more descriptive natural history.

Spider (Arachnida-Araneae) diversity in an amazonian altitudinal gradient: are the patterns congruent with mid-domain and rapoport effect predictions?

Abstract: The Mid-Domain Effect (MDE) and the Rapoport (RE) effect are two biogeographical theories that make predictions about biogeogaphic patterns. MDE predicts higher richness in the central portions of a gradient if it is within a bounded domain. RE predicts a positive relation between altitude and species range size along an altitudinal gradient. Our aim was to document the distribution of spider species richness along an altitudinal gradient in the Brazilian Amazon, and to test the influence of MDE and RE on the diversity patterns. Our study was conducted at the Pico da Neblina (Amazonas state, Brazil), and we sampled spiders at six different altitudes using two methods: nocturnal hand sampling and a beating tray. We obtained 3,140 adult spiders from 39 families, sorted to 529 species/morphospecies. Richness declined continuously with an altitude increase, but the fit with the MDE richness estimates was very weak and was not significant. Range size was not related to altitude, i. e., no RE. Finally, the abundance distribution within each species range varied more specifically, which prevented the occurrence of a RE at the community level. The influence of MDE was extremely low, a consequence of our community characteristics, formed mostly by small range size species. Short and medium range species were located at all altitudes, preventing a significant relation between range size and altitude. The distribution of abundance within a species range varied specifically and do not support a RE hypothesis.

Comparative patterns in taxonomic and functional spider diversities between tropical vs. temperate forests

High diversity in tropical compared to temperate regions has long intrigued ecologists, especially for highly speciose taxa like terrestrial arthropods in tropical rainforests. Previous studies showed that arthropod herbivores account for much tropical diversity, yet differences in the diversity of predatory arthropods between tropical and temperate systems have not been properly quantified. Here, we present the first standardized tropical-temperate forest quantification of spider diversities, a dominant and mega-diverse taxon of generalist predators. Spider assemblages were collected using a spatially replicated protocol including two standardized sampling methods (vegetation sweep netting and beating). Fieldwork took place between 2010 and 2015 in metropolitan (Brittany) and overseas (French Guiana) French territories. We found no significant difference in functional diversity based on hunting guilds between temperate and tropical forests, while species richness was 13-82 times higher in tropical versus temperate forests. Evenness was also higher, with tropical assemblages up to 55 times more even than assemblages in temperate forests. These differences in diversity far surpass previous estimates and exceed tropical-temperate ratios for herbivorous taxa.

Diversity and seasonal variation of ground and understory spiders from a tropical mountain cloud forest

We made intensive samplings to study the seasonal response of spiders across different forest strata (ground and understory) in a tropical mountain cloud forest from Mexico. We sampled spiders from ten plots in six sampling events during the dry and rainy season, to analyze their abundance, structure (distribution of abundance among species), diversity and the response of the five dominant species at each stratum. Results demonstrated that seasonal patterns of spider communities differed among strata, revealing a complex spatiotemporal dynamic. Abundance, structure, diversity of ground spiders, as well as the responses of four dominant species at this stratum, showed low seasonal variations. In contrast, a strong seasonal variation was observed for the understory assemblage, with lowest abundance and highest diversity in the rainy season, and different assemblage structures for each season. Seasonal patterns of each assemblage seem linked to the responses of their dominant species. We found high co-occurrence among most of the ground dominant species with similar habitat use and with multivoltine patterns, contrasting with low co-occurrence among most of the understory dominant species with similar habitat use and univoltine patterns. Our results showed that the spiders' assemblages of tropical mountain cloud forest (opposed to what is found in temperate and boreal forests) increase their species richness with the height, and that their responses to seasonal change differ between strata. Management programs of these habitats should consider the spatial and temporal variations found here, as a better understanding of their ecological dynamics is required to support their sustainable management.

Non-native spiders change assemblages of Hawaiian forest fragment kipuka over space and time

We assessed how assemblages of spiders were structured in small Hawaiian tropical forest fragments (Hawaiian, kipuka) within a matrix of previous lava flows, over both space (sampling kipuka of different sizes) and time (comparison with a similar study from 1998). Standardized hand-collection by night was carried out in May 2016. In total, 702 spiders were collected, representing 6 families and 25 (morpho-)species. We found that the number of individuals, but not species richness, was highly correlated with the area of sampled forest fragments, suggesting that kipuka act as separate habitat islands for these predatory arthropods. Species richness was significantly lower in the lava matrix outside the kipuka compared to the kipuka habitats, although there was no statistical difference in species composition between the two habitats, largely because of similarity of non-native species in both habitats. Over the last 20 years, the abundance of non-native spider species substantially increased in both kipuka and lava habitats, in marked contrast to the vegetation that has remained more intact. With endemicity of terrestrial arthropods reaching over 95% in native forests, non-native predatory species present a critical challenge to the endemic fauna.

Relative Efficiency of Pitfall Trapping vs. Nocturnal Hand Collecting in Assessing Soil-Dwelling Spider Diversity along A Structural Gradient of Neotropical Habitats

Assessing spider diversity remains a great challenge, especially in tropical habitats where dozens of species can locally co-occur. Pitfall trapping is one of the most widely used techniques to collect spiders, but it suffers from several biases, and its accuracy likely varies with habitat complexity. In this study, we compared the efficiency of passive pitfall trapping versus active nocturnal hand collecting (NHC) to capture low understory-dwelling spider taxonomical (morpho-species) and functional (hunting guilds) diversity along a structural gradient of habitats in French Guiana. We focused on four habitats describing a structural gradient: garden to the orchard to the forest edge to the undisturbed forest. Overall, estimated morpho-species richness and composition did not vary consistently between habitats, but abundances of ground-hunting spiders decreased significantly with increasing habitat complexity. We found habitat-dependence differences in taxonomic diversity between sampling strategies: NHC revealed higher diversity in the orchard, whereas pitfalls resulted in higher diversity in the forest. Species turnover resulted in high dissimilarity in species composition between habitats using either method. This study shows how pitfall trapping is influenced by habitat structure, rendering this sampling method incomplete for complex, tropical environments. However, pitfall traps remain a valuable component of inventories because they sample distinct assemblage of spiders.

Faunistic analysis of Ichneumonidae (Hymenoptera) in Guarana (Paullinia cupana) crop, with new records of genera for the Brazilian Amazon

ABSTRACT: Ichneumonidae are solitary parasitoids that mainly attack larvae and pupae of Lepidoptera, Coleoptera and Hymenoptera, which constitute important agricultural pests. The objective of the present paper was to characterize the assemblage of Ichneumonidae associated to the conventional and organic cultivation of Guarana (Paullinia cupana) crop in Manaus City (Amazonas State, Brazil) with faunistic analysis. The samples were collected at Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA), using Malaise and Moericke traps, between September 2012 and February 2013. We collected 296 specimens of Ichneumonidae, represented by 14 subfamilies, 41 genera and 63 morphospecies. The faunistic analysis revealed the predominance of rare and less frequent genera (54.2% in conventional and 47.1% in organic crop management). Venturia Schrottky was highlighted as superabundant, super frequent and constant (46.4% of the specimens) in conventional cultivation. In organic cultivation, Eiphosoma Cresson (15.6% of the specimens), Venturia (15.1%), Polycyrtidea Viereck (7%), Stethantyx Townes (6%), Enicospilus Stephens and Diapetimorpha Viereck (both 5.5%), Polycyrtus Spinola and Podogaster Brullé (both 5%) were more abundant, more frequent and constant. The observed differences reflect the type of crop management. Considering that organic crop management do not use agrochemicals, there is a greater diversification of the landscape. On the other hand, a reduction in richness and abundance has been observed in conventional crop management, due to its greater alteration and uniformity of the landscape. This study evidences a high number of rare, less frequent and accidental genera, and reveals the predominant groups in each crop cultivation system.

Ground spiders (Arachnida, Araneae) associated with urban forest fragments in southern Amazon

Abstract: Forest fragments in urban areas comprise important habitats for a wide variety of species, however, conservationist policies for their maintenance and conservation are still incipient. This study examined the richness and abundance of the ground-spider assemblage in five forest fragments, with areas ranging between 18.5 and 103.98 ha, in the urban perimeter of Sinop, northern Mato Grosso State, southern Amazon region of Brazil. Sampling was carried out using the mini-Winkler extractor and pitfall traps in the dry (July) and rainy (November) seasons of 2017. All fragments were characterized in relation to the area and the Index of Biotic Integrity (IBI), to assess the effect of these variables on richness and abundance of soil spider assemblage. A total of 653 spiders were sampled, corresponding to 25 families and 52 species. Salticidae, Theridiidae, Lycosidae, Linyphiidae, Oonopidae and Symphytognathidae were the most abundant families (63.3% of the total sample). The assemblage was characterized by the dominance of hunting spiders (393 ind.; 60.2%) over web-building spiders (260 ind.; 39.8%). Greater spider abundance and richness was obtained during the rainy season (517 ind.; 79.2%; 41 spp.) as compared with the dry season (136 ind.; 20.8%; 24 spp.). Only 13 species occurred in dry and rainy season. Two species were recorded for the first time in the Amazon region, namely, Anapistula aquytabueraRheims & Brescovit, 2003 (Symphytognathidae) and Opopaea concolor (Blackwall, 1859) (Oonopidae). Species richness was not affected by IBI and area of fragment. Although the statistical model is not significant, species richness increases slightly with IBI and area of fragment. Similarly, abundance of spiders was not affected by IBI and area of fragment. Regardless of the area size, all evaluated forest fragments showed a low and regular IBI, demonstrating that these habitats have suffered with the pressures inherent from the urban perimeter, including the constant expansion of human occupation as well as misuse by the population. Nonetheless, these same fragments revealed considerable richness of species of ground spiders and can thus be categorized as important habitats for the maintenance of regional biodiversity. Therefore, action strategies must be set out to ensure their conservation.