Additive partitioning of multispecies distributional aggregation of local assemblages.

The distribution of species is not random in space. At the finest-resolution spatial scale, that is, field sampling locations, distributional aggregation level of different species would be determined by various factors, for example spatial autocorrelation or environmental filtering. However, few studies have quantitatively measured the importance of these factors. In this study, inspired by the statistical properties of a Markov transition model, we propose a novel additive framework to partition local multispecies distributional aggregation levels for sequential sampling-derived field biodiversity data. The framework partitions the spatial distributional aggregation of different species into two independent components: regional abundance variability and the local spatial inertia effect. Empirical studies from field amphibian surveys through line-transect sampling in southwestern China (Minya Konka) and central-southern Vietnam showed that local spatial inertia was always the dominant mechanism structuring the local occurrence and distributional aggregation of amphibians in the two regions with a latitudinal gradient from 1200 to nearly 4000 m. However, regional abundance variability is still nonnegligible in highly diverse tropical regions (i.e. Vietnam) where the altitude is not higher than 2000 m. In summary, we propose a novel framework that shows that the multispecies distributional aggregation level can be structured by two additive components. The two partitioned components could be theoretically independent. These findings are expected to deepen our understanding of the local community structure from the perspective of both spatial distribution and regional diversity patterns. The partitioning framework might have potential applications in field ecology and macroecology research.

Urban landscape-level biodiversity assessments of aquatic and terrestrial vertebrates by environmental DNA metabarcoding.

Globally, expansive urbanization profoundly alters natural habitats and the associated biota. Monitoring biodiversity in cities can provide essential information for conservation management, but the complexity of urban landscapes poses serious challenges to conventional observational and capture-based surveys. Here we assessed pan-vertebrate biodiversity, including both aquatic and terrestrial taxa, using environmental DNA (eDNA) sampled from 109 water sites across Beijing, China. Using eDNA metabarcoding with a single primer set (Tele02), we detected 126 vertebrate species, including 73 fish, 39 birds, 11 mammals, and 3 reptiles belonging to 91 genera, 46 families, and 22 orders. The probability of detection from eDNA varied substantially among species and was related to their lifestyle, as shown by the greater detectability of fish compared to that of terrestrial and arboreal (birds and mammals) groups, as well as the greater detectability of water birds compared to that of forest birds (Wilcoxon rank-sum test p = 0.007). Furthermore, the eDNA detection probabilities across all vertebrates (Wilcoxon rank-sum test p = 0.009), as well as for birds (p < 0.001), were higher at lentic sites in comparison with lotic sites. Also, the detected biodiversity was positively correlated with lentic waterbody size for fish (Spearman p = 0.012), but not for other groups. Our results demonstrate the capacity of eDNA metabarcoding to efficiently surveil diverse vertebrate communities across an extensive spatial scale in heterogenous urban landscapes. With further methodological development and optimization, the eDNA approach has great potential for non-invasive, efficient, economic, and timely assessments of biodiversity responses to urbanization, thus guiding city ecosystem conservation management.

A Bayesian-weighted approach to predicting the number of newly discovered rare species.

In natural ecological communities, most species are rare and thus susceptible to extinction. Consequently, the prediction and identification of rare species are of enormous value for conservation purposes. How many newly found species will be rare in the next field survey? We took a Bayesian viewpoint and used observed species abundance information in an ecological sample to develop an accurate way to estimate the number of new rare species (e.g., singletons, doubletons, and tripletons) in an additional unknown sample. A similar method has been developed for incidence-based data sets. Five seminumerical tests (3 abundance cases and 2 incidence cases) showed that our proposed Bayesian-weight estimator accurately predicted the number of new rare species with low relative bias and low relative root mean squared error and, accordingly, high accuracy. Finally, we applied the proposed estimator to 6 conservation-directed empirical data sets (3 abundance cases and 3 incidence cases) and found the prediction of new rare species was quite accurate; the 95% CI covered the true observed value very well in most cases. Our estimator performed similarly to or better than an unweighted estimator derived from Chao et al. and performed consistently better than the naïve unweighted estimator. We recommend our Bayesian-weight estimator for conservation applications, although the unweighted estimator of Chao et al. may be better under some circumstances. We provide an R package RSE (rare species estimation) at https://github.com/ecomol/RSE for implementation of the estimators.

Un Método con Ponderación Bayesiana para Predecir el Número de Especies Raras Recientemente Descubiertas Resumen En las comunidades ecológicas naturales, la mayoría de las especies son raras y por lo tanto susceptibles a la extinción. Como consecuencia, la predicción e identificación de las especies raras son de enorme valor para los propósitos de la conservación. ¿Cuántas especies recientemente descubiertas serán clasificadas como raras en el siguiente censo de campo? Tomamos un punto de vista bayesiano y utilizamos información de la abundancia observada de especies en una muestra ecológica para desarrollas una manera certera para estimar el número de nuevas especies raras (p. ej.: singleton, doubleton, y tripleton) en una muestra adicional desconocida. Un método similar se ha desarrollado para conjuntos de datos basados en la incidencia. Cinco pruebas semi-numéricas (tres casos de abundancia y dos casos de incidencia) mostraron que nuestra propuesta de estimador con ponderación bayesiana predijo con certeza el número de nuevas especies raras con un bajo sesgo relativo y un bajo error de la raíz cuadrada media relativa y, de manera acorde, una alta certeza. Finalmente, aplicamos el estimador propuesto a seis conjuntos de datos empíricos dirigidos hacia la conservación (tres casos de abundancia y tres casos de incidencia) y encontramos que la predicción de nuevas especies raras fue certera; el 95% del CI cubrió muy bien al verdadero valor observado en la mayoría de los casos. Nuestro estimador funcionó de manera similar o incluso mejor que un estimador sin ponderación derivado de Chao et al. (2015) y funcionó constantemente mejor que el simple estimador sin ponderación. Recomendamos nuestro estimador con ponderación bayesiana para ser aplicado en la conservación, aunque el estimador sin ponderación de Chao et al. (2015) puede ser mejor bajo ciertas circunstancias. Proporcionamos un paquete R para RSE (estimación de especies raras) en https://github.com/ecomol/RSE para la implementación de los estimadores.

Diet shifts by adult flightless dung beetles Circellium bacchus, revealed using DNA metabarcoding, reflect complex life histories.

Life history changes may change resource use. Such shifts are not well understood in the dung beetles, despite recognised differences in larval and adult feeding ability. We use the flightless dung beetle Circellium bacchus to explore such shifts, identifying dung sources of adults using DNA metabarcoding, and comparing these with published accounts of larval dung sources. C. bacchus is traditionally considered to specialise on the dung of large herbivores for both larval and adult feeding. We successfully extracted mammal DNA from 151 adult C. bacchus fecal samples, representing 16 mammal species (ranging from elephants to small rodents), many of which are hitherto undescribed in the diet. Adult C. bacchus showed clear dung source preferences, especially for large herbivores inhabiting dense-cover vegetation. Our approach also confirmed the presence of cryptic taxa in the study area, and we propose that this may be used for biodiversity survey and monitoring purposes. Murid rodent feces were the most commonly fed-upon dung source (77.5%) for adult C. bacchus, differing markedly from the large and megaherbivore dung sources used for larval rearing. These findings support the hypothesis of life history-specific shifts in resource use in dung beetles, and reveal a hitherto unsuspected, but ecologically important, role of these dung beetles in consuming rodent feces. The differences in feeding abilities of the larval and adult life history stages have profound consequences for their resource use and foraging strategies, and hence the ecological role of dung beetles. This principle and its ecological consequences should be explored in other scarabaeids.

First DNA Barcoding Survey in Bulgaria Unveiled Huge Diversity of Yeasts in Insects.

In this study, we conducted a comprehensive survey aimed at assessing the diversity of yeast species inhabiting the guts of various insect species collected mainly from two Bulgarian National Parks, namely, Rila, and Pirin. The insect specimens encompass a broad taxonomic spectrum, including representatives from Coleoptera, Orthoptera, Lepidoptera, Hymenoptera, Dermaptera, Isopoda, and Collembola. Yeast strains were identified with DNA barcoding using the ribosomal markers, specifically, the D1/D2 domains of the ribosomal large subunit (LSU) and the internal transcribed spacers regions ITS 1 + 2 (ITS). The analysis unveiled the presence of 89 ascomycetous and 18 basidiomycetous yeast isolates associated with the insect specimens. Furthermore, our study identified 18 hitherto unknown yeast species.

Environmental DNA reveals temporal variation in mesophotic reefs of the Humboldt upwelling ecosystems of central Chile: Toward a baseline for biodiversity monitoring of unexplored marine habitats.

Temperate mesophotic reef ecosystems (TMREs) are among the least known marine habitats. Information on their diversity and ecology is geographically and temporally scarce, especially in highly productive large upwelling ecosystems. Lack of information remains an obstacle to understanding the importance of TMREs as habitats, biodiversity reservoirs and their connections with better-studied shallow reefs. Here, we use environmental DNA (eDNA) from water samples to characterize the community composition of TMREs on the central Chilean coast, generating the first baseline for monitoring the biodiversity of these habitats. We analyzed samples from two depths (30 and 60 m) over four seasons (spring, summer, autumn, and winter) and at two locations approximately 16 km apart. We used a panel of three metabarcodes, two that target all eukaryotes (18S rRNA and mitochondrial COI) and one specifically targeting fishes (16S rRNA). All panels combined encompassed eDNA assigned to 42 phyla, 90 classes, 237 orders, and 402 families. The highest family richness was found for the phyla Arthropoda, Bacillariophyta, and Chordata. Overall, family richness was similar between depths but decreased during summer, a pattern consistent at both locations. Our results indicate that the structure (composition) of the mesophotic communities varied predominantly with seasons. We analyzed further the better-resolved fish assemblage and compared eDNA with other visual methods at the same locations and depths. We recovered eDNA from 19 genera of fish, six of these have also been observed on towed underwater videos, while 13 were unique to eDNA. We discuss the potential drivers of seasonal differences in community composition and richness. Our results suggest that eDNA can provide valuable insights for monitoring TMRE communities but highlight the necessity of completing reference DNA databases available for this region.

Biodiversity survey and estimation for line-transect sampling.

Conducting biodiversity surveys using a fully randomised design can be difficult due to budgetary constraints (e.g., the cost of labour), site accessibility, and other constraints. To this end, ecologists usually select representative line transects or quadrats from a studied area to collect individuals of a given species and use this information to estimate the levels of biodiversity over an entire region. However, commonly used biodiversity estimators such as Rao's quadratic diversity index (and especially the Gini-Simpson index) were developed based on the assumption of independent sampling of individuals. Therefore, their performance can be compromised or even misleading when applied to species abundance datasets that are collected from non-independent sampling. In this study, we utilise a Markov chain model and derive an associated parameter estimator to account for non-independence in sequential sampling. Empirical tests on two forest plots in tropical (Barro Colorado, Island of Panama) and subtropical (Heishiding Nature Reserve of Guangdong, China) regions and the continental-scale spatial distribution of Acacia species in Australia showed that our estimators performed reasonably well. The estimated parameter measuring the degree of non-independence of subsequent sampling showed that a non-independent effect is very likely to occur when using line transects to sample organisms in subtropical regions at both local and regional spatial scales. In summary, based on a first-order Markov sampling model and using Rao's quadratic diversity index as an example, our study provides an improvement in diversity estimation while simultaneously accounting for the non-independence of sampling in field biodiversity surveys. Our study presents one possible solution for addressing the non-independent sampling of individuals in biodiversity surveys.

Elevational surveys of Sulawesi herpetofauna 1: Gunung Galang, Gunung Dako Nature Reserve.

The Indonesian island of Sulawesi has a unique geology and geography, which have produced an astoundingly diverse and endemic flora and fauna and a fascinating biogeographic history. Much biodiversity research has focused on the regional endemism in the island's Central Core and on its four peninsulas, but the biodiversity of the island's many upland regions is still poorly understood for most taxa, including amphibians and reptiles. Here, we report the first of several planned full-mountain checklists from a series of herpetological surveys of Sulawesi's mountains conducted by our team. In more than 3 weeks of work on Gunung Galang, a 2,254 m peak west of the city of Tolitoli, Sulawesi Tengah Province, on Sulawesi's Northern Peninsula, we recovered nearly fifty species of reptiles and amphibians, more than a dozen of which are either new to science or known but undescribed. The incompleteness of our sampling suggests that many more species remain to be discovered on and around this mountain.

The bark and ambrosia beetles (Coleoptera: Curculionidae: Scolytinae and Platypodinae) of American Samoa.

A survey of five of the islands of American Samoa was conducted from 2016-2018 utilizing multi-funnel traps baited with ethanol and quercivorol (attractants for xyleborine ambrosia beetles). Specimens of Scolytinae and Platypodinae from this survey, as well as specimens in the American Samoa Community College Collection were identified. A total of 53 species of Scolytinae and two species of Platypodinae are reported. Fourteen species of Scolytinae and one species of Platypodinae are reported as new to American Samoa. The following new synonymy and new combinations are proposed: Xyleborinus artelineatus (Beeson, 1929) (=Xyleborinus cinctipennis (Schedl, 1980) syn. nov.; Ambrosiophilus wilderi (Beeson, 1929) comb. nov. from Ambrosiodmus; Beaverium swezeyi (Beeson, 1929) comb. nov. from Xyleborus; and Debus fallaxoides (Schedl, 1955) comb. nov. from Xyleborus. The distribution on the islands of American Samoa and taxonomic history of each species is provided.

Rainforest and cloud forest Scolytodes (Curculionidae, Scolytinae, Hexacolini) from the Arthropods of La Selva inventory in Costa Rica: new species, new synonymy, new records.

Quantitative collecting efforts over the last several decades in Costa Rica have resulted in many new species of insects. The Arthropods of La Selva projects included collecting from a typical lowland Neotropical forest and up an altitudinal transect, and has provided many valuable samples of insects, spiders and mites potentially new to science. We describe 18 new species in the bark beetle genus Scolytodes Ferrari, 1867, 14 of which were collected during this project: S.angulus Jordal & Kirkendall, sp. nov., S.sufflatus Jordal & Kirkendall, sp. nov., S.squamatifrons Jordal & Kirkendall, sp. nov., S.comosus Jordal & Kirkendall, sp. nov., S.spatulatus Jordal & Kirkendall, sp. nov., S.seriatus Jordal & Kirkendall, sp. nov., S.profundus Jordal & Kirkendall, sp. nov., S.catinus Jordal & Kirkendall, sp. nov., S.fimbriatus Jordal & Kirkendall, sp. nov., S.sulcifrons Jordal & Kirkendall, sp. nov., S.planifrons Jordal & Kirkendall, sp. nov., S.porosus Jordal & Kirkendall, sp. nov., S.mundus Jordal & Kirkendall, sp. nov., S.callosus Jordal & Kirkendall, sp. nov., S.parvipilus Jordal & Kirkendall, sp. nov., S.plenus Jordal & Kirkendall, sp. nov., S.niger Jordal & Kirkendall, sp. nov., and S.simplex Jordal & Kirkendall, sp. nov. One species, Scolytodesminutissimus Schedl, 1952, is redescribed to match the holotype. We give new Costa Rica records for S.costabilis Wood, 1974, which is the correct name for S.obesus Wood, 1975 (syn. nov.). We report Costa Rica as a new country record for six species: Scolytodesclusiacolens Wood, 1967, S.crinalis Wood, 1978, S.culcitatus (Blandford, 1897), S.libidus Wood, 1978, S.reticulatus (Wood, 1961), and S.spadix (Blackman, 1943). From a closely related genus, we provide the first record for Central America (and only the second collection) of Pycnarthrumfulgidum Wood, 1977.

Dolichopodidae of riverbeds and springs in Croatia with an updated checklist of Croatia (Diptera).

Several invertebrate surveys in Croatia conducted between 2005 and 2014 and including; e.g., Plitvice Lakes, produced 123 bycatch samples of Dolichopodidae (Diptera) from 68 sampling sites collected at 36 localities in seven counties. Seventy-seven were retrieved from emergence traps, six from pan traps and 40 were collected with sweep net and/or aspirator. They contained 420 dolichopodid flies that belonged to 64 species in 22 genera. Four species, Campsicnemus umbripennis, Hercostomus chetifer, Liancalus virens and Syntormon pallipes, accounted for over half of the yields. Contrary to most species that were found in largest numbers in rivers, and their beds in particular, S. pallipes and Hercostomus gracilis were considerably more abundant at springs. Fifty-five species could be added to the national checklist which raises the total number to 94 species. All species records are given, the habitat of each species is described, if possible, and taxonomic notes are provided for some dubious species. Finally, elements are presented to support the assumption that the extant dolichopodid species richness of Croatia is at least three- to fourfold of the current number.

Sand Flies (Diptera: Psychodidae) From the Brazilian Atlantic Forest Domain Collected With Malaise Traps.

Here, we present the results of a 2-yr sampling using malaise traps along the Atlantic Forest domain from the northeast to the south of Brazil. In total, 217 sand flies were collected, of which the most abundant species was Bichromomyia flaviscutellata (Mangabeira, 1942) (60.4%), followed by Psychodopygus ayrozai (Barretto & Coutinho, 1940) (11%) and Micropygomyia schreiberi (Martins, Falcão & Silva, 1975) (4.1%), and the remaining less abundant species comprised 10.1% of the total of sand flies collected. We report the occurrence for the first time of: 1) B. flaviscutellata, Pintomyia fischeri (Pinto, 1926), Ps. ayrozai, and Psychodopygus carreirai (Barretto, 1946) in the state of Alagoas; 2) Psychodopygus claustrei (Abonnenc, Lèger & Fauran,1979), Psychodopygus amazonensis (Root, 1934), and Sciopemyia sordellii (Shannon & del ponte, 1927) in the state of Bahia; 3) Nyssomyia anduzei (Rozeboom, 1942) in the state of Pernambuco; and 4) B. flaviscutellata, M. schreiberi, Ps. ayrozai, and Psychodopygus davisi (Root, 1934) in the state of Sergipe. Our results present novel records of sand flies collected with malaise traps in the Atlantic Forest domain demonstrating that different collecting methods such as malaise traps can provide new interesting data about these insects that are natural vectors of many pathogens.

Improving biodiversity assessment of anuran amphibians using DNA barcoding of tadpoles. Case studies from Southeast Asia.

Amphibian populations are dramatically declining, while their inventory is far from being achieved. Tadpoles are usually overlooked from biodiversity survey, whereas their consideration will optimize species counts and knowledge of their ecological and developmental requirements is essential in conservation planning. Two mitochondrial markers, 16S (397 new sequences obtained) and COI (343 new sequences obtained), are used to test DNA barcoding on a set of larval and adult Asian amphibians represented by 83 recognized species from 65 sites. The advantages and drawbacks of each marker are assessed, COI barcoding being advocated for global DNA barcoding, whereas 16S suits for taxonomically or geographically restricted DNA barcoding. About half of the collected tadpoles were badly identified or incompletely named in the field. All tadpole sequences (except one case of probable introgressive hybridization) were correctly assigned to their respective species. Finally six clusters of tadpole sequences without conspecific adults were revealed, stressing the importance of collecting and taking into account tadpoles in biodiversity survey and conservation planning.

Challenges to barcoding an entire flora.

DNA barcodes are species-specific genetic markers that allow taxonomic identification of biological samples. The promise of DNA barcoding as a rapid molecular tool for conducting biodiversity inventories has catalysed renewed efforts to document and catalogue the diversity of life, parallel to the large-scale sampling conducted by Victorian naturalists. The unique contribution of DNA barcode data is in its ability to identify biotic material that would be impossible to classify using traditional taxonomic keys. However, the utility of DNA barcoding relies upon the construction of accurate barcode libraries that provide a reference database to match to unidentified samples. Whilst there has been much debate in the literature over the choice and efficacy of barcode markers, there has been little consideration of the practicalities of generating comprehensive barcode reference libraries for species-rich floras. Here, we discuss several challenges to the generation of such libraries and present a case study from a regional biodiversity hotspot in southern Quebec. We suggest that the key challenges include (i) collection of specimens for rare or ephemeral species, (ii) limited access to taxonomic expertise necessary for reliable identification of reference specimens and (iii) molecular challenges in amplifying and matching barcode data. To be most effective, we recommend that sampling must be both flexible and opportunistic and conducted across the entire growing season by expert taxonomists. We emphasize that the success of the global barcoding initiative will depend upon the close collaboration of taxonomists, plant collectors, and molecular biologists.