Target Taxa Research Articles

In situ and ex situ conservation gap analyses of crop wild relatives from Malawi

The study analysed the conservation gaps of the priority crop wild relatives (CWR) taxa for Malawi in order to contribute to the development of a harmonized conservation strategy that helps secure the priority CWR under in situ and ex situ. We used taxa distribution modelling, complementarity analysis and ecogeographic land characterization map to analyse spatial diversity and distribution of 123 priority taxa across different adaptive scenarios. We identified areas of observed and predicted richness, the minimum number of protected areas (PAs) that conserve the broadest ecogeographic diversity in situ and the minimum number of grid cells that capture highest diversity outside PAs to recommend the establishment of genetic reserves. We then analysed the representativeness of the conserved ecogeographic diversity of target taxa in ex situ collections to identify ex situ conservation gaps and advise for priority areas for ex situ collections. For the 123 taxa, 70.7% of the total diversity occurs in 36 PAs with 66.8% of the diversity captured in only 10 complementary PAs. Outside PAs, the broadest diversity was conserved in three grid cells of size 5 × 5 km. Fifty-three of 123 taxa have ex situ collections with only three taxa having ex situ collections at the Malawi Plant Genetic Resources Centre. The findings of this study will guide formulation of conservation actions for the priority taxa as well as lobbying for active conservation of the same under in situ and ex situ.

Caveats of fungal barcoding: a case study in Trametes s.lat. (Basidiomycota: Polyporales) in Vietnam reveals multiple issues with mislabelled reference sequences and calls for third-party annotations

DNA barcoding using the nuclear internal transcribed spacer (ITS) has become prevalent in surveys of fungal diversity. This approach is, however, associated with numerous caveats, including the desire for speed, rather than accuracy, through the use of automated analytical pipelines, and the shortcomings of reference sequence repositories. Here we use the case of a specimen of the bracket fungus Trametes s.lat. (which includes the common and widespread turkey tail, T. versicolor) to illustrate these problems. The material was collected in Vietnam as part of a biodiversity inventory including DNA barcoding approaches for arthropods, plants and fungi. The ITS barcoding sequence of the query taxon was compared against reference sequences in GenBank and the curated fungal ITS database UNITE, using BLASTn and MegaBLAST, and was subsequently analysed in a multiple alignment-based phylogenetic context through a maximum likelihood tree including related sequences. Our results initially indicated issues with BLAST searches, including the use of pairwise local alignments and sorting through Total score and E value, rather than Percentage identity, as major shortcomings of the DNA barcoding approach. However, after thorough analysis of the results, we concluded that the single most important problem of this approach was incorrect sequence labelling, calling for the implementation of third-party annotations or analogous approaches in primary sequence repositories. In addition, this particular example revealed problems of improper fungal nomenclature, which required reinstatement of the genus name Cubamyces (= Leiotrametes), with three new combinations: C. flavidus, C. lactineus and C. menziesii. The latter was revealed as the correct identification of the query taxon, although the name did not appear among the best BLAST hits. While the best BLAST hits did correspond to the target taxon in terms of sequence data, their label names were misleading or unresolved, including [Fungal endophyte], [Uncultured fungus], Basidiomycota, Trametes cf. cubensis, Lenzites elegans and Geotrichum candidum (an unrelated ascomycetous contaminant). Our study demonstrates that accurate identification of fungi through molecular barcoding is currently not a fast-track approach that can be achieved through automated pipelines.Citation: Lucking R., Truong B. V., Huong D. T. T., Le N. H., Nguyen Q. D., Nguyen V. D., Raab-Straube E. von, Bollendorff S., Govers K. & Di Vincenzo V. 2020: Caveats of fungal barcoding: a case study in Trametes s.lat. (Basidiomycota: Polyporales) in Vietnam reveals multiple issues with mislabelled reference sequences and calls for third-party annotations. – Willdenowia 50: 383–403. doi: https://doi.org/10.3372/wi.50.50302Version of record first published online on 15 September 2020 ahead of inclusion in December 2020 issue.

RUbble Biodiversity Samplers: 3D‐printed coral models to standardize biodiversity censuses

Abstract To ensure standardized, quantitative and repeatable methodologies, marine ecologists have engineered a range of artificial units to survey benthic communities with varying designs depending on target taxa, life history stage and habitat. In tropical ecosystems, autonomous units have typically lacked microhabitat complexity (e.g. planar tiles), short‐term efficacy (<1 year deployment) and/or a truly standardized design to sample cryptobenthic diversity. Coral rubble is characterized by high microhabitat complexity, which is unresolved in sampling efforts. Yet, rubble can support the greatest density and diversity of metazoan taxa. We engineered RUbble Biodiversity Samplers (RUBS) as a dismantlable lightweight 3D‐printed model to standardize cryptobenthic biodiversity sampling. We demonstrate the effectiveness of RUBS with preliminary results from short‐term (1–14 days) deployments in Palau, Western Micronesia. RUbble Biodiversity Samplers uphold the microhabitat complexity inherent in coral rubble (~50% interstitial space) and provide an effective and efficient methodology to sample cryptobenthic fauna, which could be applied in comparative studies. The RUBS concept provides a platform for the broader implementation of 3D‐printed models in marine ecology to overcome issues of standardization regardless of habitat type.

A DNA mini-barcoding system for endangered unionid mussels in the Lake Biwa system in Japan

A mini-barcoding system was developed to help identify endangered unionid mussels in the Lake Biwa system in Japan. A single primer set was designed to amplify a ca. 140-bp barcode fragment based on the published mitochondrial 16S rRNA gene sequences (ca. 350 bp) of Japanese unionids. The new primers successfully amplified genomic DNA from the foot tissues of 81 specimens of 12 target taxa from the Lake Biwa region. Sequencing, BLAST-searches and phylogenetic analyses of the amplified fragments confirmed that the mini-barcode had the same identification ability as the original sequences for Lake Biwa taxa. The mini-barcoding system also obtained the short barcodes from excreted materials, indicating its usefulness in nondestructive identification of these mussels.

Leveraging public harvest to reduce invasive hybridization in Yellowstone National Park: field identification and harvest of cutthroat\xa0\xd7\xa0rainbow trout hybrids

Leveraging public harvest can be a cost-effective invasive species management tool, but target taxa must be correctly identified and removed at rates that achieve biological objectives. We explored the potential role of recreational anglers to curtail expanding hybridization between invasive rainbow trout (Oncorhynchus mykiss; RT) and native Yellowstone cutthroat trout (O. clarkii bouvieri; YCT) in the Lamar River watershed in Yellowstone National Park. We sought to (1) develop a hybrid identification key that could be used by anglers and (2) estimate angler participation, catch, and potential exploitation rates. We assessed seven morphological features of trout in the field (n = 251, 15 locations) and collected fin clips to estimate RT ancestry proportion using genetic analysis. An identification key was built using recursive partitioning to objectively distinguish YCT from RT and hybrids. A single-choice dichotomous key (white pelvic fin tip present/absent) correctly classified 93% of fish as native (YCT) or containing RT ancestry (RT or hybrid). Success increased to 97% when a second criterion was added (head spot count ≥ 6). Using angler surveys (2013–2017), we estimated that 10,000 anglers catch 50,000 trout annually. In a popular road-accessible area, most trout are probably caught and released ~ 5 times each year. The combination of high angler participation, substantial annual catch, and an accurate and easy to use identification method indicate that leveraging public harvest is a promising management tool. Invasive hybridization is a global conservation issue threatening many native taxa; this case study highlights some factors for resource managers to consider prior to implementing public harvest regulations and the benefits of standardized keys to distinguish hybrids in the field.

Multiplex polymerase chain reaction for genetically modified potato event AV43-6-G7 quantification. Proof of efficiency

One of the ways to improve the laboratory control methodology of genetically modified organisms of plant origin (GMO) is to use multiplexing - an approach that allows you to increase the number of targets and enlarge the number of simultaneously processed samples, maximizing the potential of polymerase chain reaction in real time (PCR-RT). The aim of the study is to develop a quantitative identification protocol for genetically engineered (GE) potato event AV43-6-G7 in the format of duplex PCR-RT with the use of TaqMan® PCR technology. Material and methods. The duplex system included 2 types of specific DNA-primers and fluorescence-labeled probes: the first one is for detection of transformation event AV43- 6-G7 DNA sequence, the second is for detection of Stp23 taxon-specific potato gene. PCR parameters were chosen by empirical selection of concentrations of primers and probes, Mg2+ ions, deoxyribonucleotides, stabilizing agent for polymerase, as well as primer annealing temperature and incubation duration for each stage of the cycle. Results. As a result of these studies, the composition of the reaction mixture was optimized for the detection and quantification of GE potato event AV43-6-G7 in food. Oligonucleotide primers and fluorescent probes were selected. The compositions of reaction mixtures and temperature-time parameters of PCR were tested: 2.5-fold reaction buffer for PCR-RT in the presence of ROX (carboxy-X-rhodamine), specific to the GE component primers (AV43-6-G7-f/AV43-6-G7-r) and target taxon (GRF3/ GRR3) at 300 nM/300 nM and 100 nM/100 nM, probes at 200 nM and 200 nM, respectively; bovine serum albumin - 0.04%; MgCl2 - 3.5 mM, deoxynucleoside triphosphates - 0.3 mM, as well as the temperature-time profile of the reaction (initial denaturation of 95 °C - 5 min, followed by 45 cycles: 95 °С - 20 sec, 58 °С - 20 sec, 62 °С - 40 sec). Conclusion. The validity of the developed method is confirmed by laboratory studies and testifies to its reliability.

Do Salamanders Limit the Abundance of Groundwater Invertebrates in Subterranean Habitats?

Several species of surface salamanders exploit underground environments; in Europe, one of the most common is the fire salamander (Salamandra salamandra). In this study, we investigated if fire salamander larvae occurring in groundwater habitats can affect the abundance of some cave-adapted species. We analyzed the data of abundance of three target taxa (genera Niphargus (Amphipoda; Niphargidae), Monolistra (Isopoda; Sphaeromatidae) and Dendrocoelum (Tricladida; Dedrocoelidae)) collected in 386 surveys performed on 117 sites (pools and distinct subterranean stream sectors), within 17 natural and 24 artificial subterranean habitats, between 2012 and 2019. Generalized linear mixed models were used to assess the relationship between target taxa abundance, fire salamander larvae occurrence, and environmental features. The presence of salamander larvae negatively affected the abundance of all the target taxa. Monolistra abundance was positively related with the distance from the cave entrance of the sites and by their surface. Our study revealed that surface salamanders may have a negative effect on the abundance of cave-adapted animals, and highlited the importance of further investigations on the diet and on the top-down effects of salamanders on the subterranean communities.

Morphological variations of crossed-lamellar ultrastructures of Glycymeris bimaculata (Bivalvia) serve as a marine temperature proxy

Bivalve shells are among the most promising archives for high-resolution seawater temperature reconstructions. However, despite major research advances in bivalve sclerochronology over the past decades, estimating water temperature from shells remains a challenging task. This is largely because the most frequently used and widely accepted temperature proxy in bivalves, i.e., the shell oxygen isotope (δ18Oshell) value, also requires knowledge of changes in δ18O of the water (δ18Owater) in which the bivalve lived, which is rarely available for ancient environments. According to a few recent studies, the size and shape of individual biomineral units (BMUs) of the shell ultrastructure may serve as an independent temperature proxy that is also less vulnerable to diagenetic changes than isotope chemical proxies. However, the crossed-lamellar ultrastructure, which occurs in ca. 90% of all mollusk species, has hitherto not been investigated. Here, we evaluate the potential use of morphological properties of the BMUs in Glycymeris bimaculata as a proxy for water temperature. For this purpose we introduce a suitable preparation technique (immersion for 2 m in 0.001 vol% formic acid followed by 20–30 m in 3.5 vol% H2O2) and an automated image processing technique that tremendously speed up ultrastructure analysis (5 s versus one to 2 h image processing time with automated and manual methods, respectively) and increase the robustness of BMU measurements. Glycymeris is a particularly useful target taxon, because it is a cosmopolitan genus with evolutionary roots in the Upper Cretaceous, and some species of Glycymeris can attain a lifespan of more than two hundred years, which allows for long-term, high-resolution paleoclimate reconstructions. As in other previously studied ultrastructures, larger and more elongated BMUs formed in warmer water permitting temperature estimates with an error of 2.3 °C (1 σ). Since the new temperature proxy is unaffected by other environmental variables, including salinity, it can potentially be applied to (modern and fossil) specimens from brackish environments.

A systematic review of ground-based shooting to control overabundant mammal populations

Abstract Context Ground-based shooting is widely used in management programs aiming to alleviate the impacts of invasive or overabundant wildlife populations. However, evaluations of individual shooting operations have shown variable results, and the effectiveness of ground-shooting as a population-management intervention has not been systematically examined. Aims Our review aimed to (1) assess the efficacy of shooting as a population management tool, and (2) identify commonalities among studies that will help managers identify situations where ground-shooting is most likely to be effective. Methods We systematically reviewed the literature to identify studies involving ground-shooting. From each study, we collated information about operational objectives, target taxa, geographic context, type of shooter used, effort, effectiveness, and use of additional control tools. Key results Most studies had no a priori quantifiable objectives. However, 60% of the 64 case studies produced a detectable reduction in population density and/or damage. The most common type of operation used unpaid or commercial harvest-oriented shooters to reduce herbivore density or damage. Only 30% of the operations that used volunteer shooters or recreational hunters achieved their objectives. Target taxa, geographic area or integration of shooting with other population-control methods had no detectable effect on the effectiveness of shooting operations. Common factors that hindered the effectiveness of shooting operations included immigration of target species from adjacent areas (n=13), decreasing effort from shooters as the target population declined (n=7) and selective harvesting (n=7). Conclusions Ground-based shooting can be an effective management tool for overabundant wildlife populations, but many shooting operations did not achieve a notable decrease in animal abundance or damage. The source of failure could often be attributed to an inability to remove a sufficient proportion of the population to cause a population decline. Implications Managers contemplating using ground-based shooting to reduce the impacts or density of wildlife populations should (1) carefully consider whether this is a suitable management tool to achieve the desired outcomes, (2) establish clear objectives that aim to meet defined outcomes and allow for continuous improvement, and (3) ensure that operations are sufficiently resourced to achieve and maintain those objectives.

Online Monitoring of Global Attitudes Towards Wildlife

Human factors are increasingly recognised as central to conservation of biodiversity. Despite this, there are no existing systematic efforts to monitor global trends in perceptions of wildlife. With traditional news reporting now largely online, the internet presents a powerful means to monitor global attitudes towards species. In this work we develop a method using the Global Database of Events, Language, and Tone (GDELT) to scan global news media, allowing us to identify and download conservation-related articles. Applying supervised machine learning techniques, we filter irrelevant articles to create a continually updated global dataset of news coverage for seven target taxa: lion, tiger, saiga, rhinoceros, pangolins, elephants, and orchids, and observe that over two-thirds of articles matching a simple keyword search were irrelevant. We examine coverage of each taxa in different regions, and find that elephants, rhinos, tigers, and lions receive the most coverage, with daily peaks of around 200 articles. Mean sentiment was positive for all taxa, except saiga for which it was neutral. Coverage was broadly distributed, with articles from 73 countries across all continents. Elephants and tigers received coverage in the most countries overall, whilst orchids and saiga were mentioned in the smallest number of countries. We further find that sentiment towards charismatic megafauna is most positive in non-range countries, with the opposite being true for pangolins and orchids. Despite promising results, there remain substantial obstacles to achieving globally representative results. Disparities in internet access between low and high income countries and users is a major source of bias, with the need to focus on a diversity of data sources and languages, presenting sizable technical challenges. Tackling these will depend on the development of more advanced natural language tools in a wildlife conservation context, as well as the development of systems to access more, and more diverse, data sources.

A test of metabarcoding for Early Detection and Rapid Response monitoring for non-native forest pest beetles (Coleoptera)

In response to the threat of introductions of non-native forest insects, the Early Detection and Rapid Response (EDRR) program in Alaska monitors for arrivals of non-native insects, an effort that is limited by the time required to process samples using morphological methods. We compared conventional methods of processing EDRR traps with metabarcoding methods for processing the same samples. We deployed Lindgren funnel traps at three points of entry in Alaska using standard EDRR methods and trap samples were later processed using routine sorting and identification based on morphology. Samples were then processed using High Throughput Sequencing (HTS) metabarcoding methods. In three samples bycatch was included and in three samples non-native species were added. Morophological and HTS methods yielded generally similar results for scolytine and cerambycid beetle assemblages, but HTS provided more species-resolution identifications (46 species) than morphological methods (4 species plus the 3 non-native species known a priori). None of the non-native species were detected by HTS. Including bycatch did not appear to hinder identifications of scolytine and cerambycid beetles by HTS. From among the bycatch, two Palearctic species adventive to North America, Placusa incompleta Sjöberg, 1934 and Hydrophoria lancifer (Harris, 1780), are newly reported from Alaska. We do not recommend replacing our current morphological monitoring methods with HTS methods because we believe that we would be more likely to detect known non-native pest species using morphology. However, we would use HTS to increase our sample size without greatly increasing time required to process samples. We would also recommend HTS methods for surveillance monitoring where the set of target taxa is not limited to known pest species.

A fecal sequel: Testing the limits of a genetic assay for bat species identification.

DNA metabarcoding assays are powerful tools for delving into the DNA in wildlife feces, giving unprecedented ability to detect species, understand natural history, and identify pathogens for a range of applications in management, conservation, and research. Next-generation sequencing technology is developing rapidly, which makes it especially important that predictability and reproducibility of DNA metabarcoding assays are explored together with the post-depositional ecology of the target taxon’s fecal DNA. Here, we defined the constraints of an assay called ‘Species from Feces’ used by government agencies, research groups, and non-governmental organizations to identify bat species from guano. We tested assay sensitivity by examining how time and humidity affect the ability to recover and successfully sequence DNA in guano, assessing whether a fecal pellet from a rare bat species could be detected in a background of feces from other bat species, and evaluating the efficacy of Species from Feces as a survey tool for bat roosts in temperate and tropical areas. We found that the assay performs well with feces over two years old in dry, cool environments, and fails by 12 months at 100% relative humidity. We also found that it reliably identifies rare DNA, has great utility for surveying roosts in temperate and tropical regions, and detects more bat species than do visual surveys. We attribute the success of Species from Feces to characteristics of the assay paired with application in taxa that are particularly well-suited for fecal DNA survival. In a time of rapid evolution of DNA metabarcoding approaches and their use with feces, this study illustrates the strengths and limitations of applied assays.

Applicability of the vital dyes neutral red and fluorescein diacetate to differentiate between alive and dead non-copepod zooplankton

It is a common practice for planktonologists to use neutral red (NR) staining to identify viable copepods in marine zooplankton. A new fluorescent dye, fluorescein diacetate (FDA), has also been successfully applied to Copepoda. Meanwhile, almost nothing is known about if NR- and FDA-based viability assays are applicable to many other zooplankton taxa. In this study, efficiencies of NR and FDA staining were evaluated and compared for different taxa and developmental stages of the Black Sea non-copepod zooplankton. Both the dyes were shown to stain well larvae of polychaetes, gastropods and bivalves, rotifers, fish eggs, barnacle nauplii, decapod zoeae, and the heterotrophic dinoflagellate Noctiluca sсintillans. Dominant species of Cladocera (Pleopis polyphemoides, Evadne spinifera, Pseudevadne tergestina) were stained efficiently with FDA only. Some taxa had sufficient statistics of positive staining only with one of the dyes, NR (e.g. appendicularians and chaetognaths) or FDA (e.g. barnacle cyprids). Correspondingly, more data are demanded to fill the gaps in the target taxa. The dyes proved to be taxa-specific and hence, their reliable application should be based on their target groups.

Assessing the Influence of Saline and Alkaline Environments in the Preservation of Pampean Diatoms: An Experimental Approach

Diatom dissolution is controlled by environmental conditions prevailing during fossilization. In Pampean shallow lakes, diatom dissolution showed important correlations with gradients of salinity, pH, carbonate, and bicarbonate, being these the most probable causes of the observed shifts in Holocene assemblages preservation. In the present contribution, a series of experiments were conducted in order to demonstrate the effect that physical-chemical lake characteristics exert on Pampean diatom assemblages preservation. Three experimental assemblages were subjected to the effect of three concentrations of two salts, NaCl (0.6, 1.2 and 3M) and NaHCo3 (0.6, 0.9, and 1.2M), and two pH values (7 and 10). Aliquots of the experimental solutions were removed once each five days for 20 days, and analyzed for changes in dissolved silica concentration (SiDi), relative and absolute abundances of diatoms, and dissolution indices (DDI) based on the target taxon Cyclotella meneghiniana. All the experimental solutions increased the SiDi significantly, particularly since day 10. These increased SiDi values were accompanied by significant changes in the DDI, which reached maximum values at pH 10, and by evidence of dissolution observed in SEM images, whereas no significant changes in relative or absolute abundances of diatoms were registered. These experimental results demonstrated the impact that water chemistry can exert on diatom dissolution in Pampean shallow lakes, even during short-term exposures. Given the naturally high pH, NaCl and NaHCo3 concentrations characteristic of many of these lakes, these experimental findings can be confidently extrapolated to the interpretation of the dissolution trends found in modern and fossil sedimentary assemblages.

Gomphonella olivacea (Bacillariophyceae) – a new phylogenetic position for a well-known taxon, its typification, new species and combinations

Background and aims – Within the project “German Barcode of Life – Diatoms” common diatoms of German waters were routinely isolated and cultivated. In order to understand the taxonomy and phylogeny of the genus Gomphonema, one of the most common taxa of Central Europe, known currently either under the name Gomphonema olivaceum in Europe or Gomphoneis olivacea in America, was studied.
 Methods – Twenty unialgal strains were established from five different water bodies in Germany and one from Lake Balaton, Hungary, which supplied molecular data (18S V4 and rbcL) besides morphometric and ultrastructural data. In addition, on eight populations from different water bodies including the type from Denmark, morphometric and micromorphological studies by light and scanning electron microscopy were performed.
 Key results – Molecular and micromorphological data show that the target taxon neither belongs to Gomphonema Ehrenb. nor to Gomphoneis Cleve. By reinstating the genus name Gomphonella Rabenh., the nomenclatural and taxonomic enigma of this taxon is solved, and with the presentation of the type by Hornemann the authorship of the epithet is clarified. Molecular data for the unialgal strains and several environmental clones show that there is more diversity in the Gomphonella olivacea clade than can be identified morphologically. In addition, the establishment of the new species Gomphonella coxiae and Gomphonella acsiae is supported. The molecular data classified Gomphonella species as belonging to the Cymbellales but not to the Gomphonemataceae. In addition, molecular data put Gomphoneis tegelensis R.Jahn & N.Abarca also into Gomphonella. In order to make the genera Gomphoneis and Gomphonema monophyletic, their astigmate members are transferred to Gomphonella.
 Conclusions – The results clarify that the gomphonemoid outline is not restricted to the family Gomphonemataceae but seem to be distributed across the entire order Cymbellales. This is shown in this paper for the revived genus Gomphonella, which contains the astigmate group of Gomphoneis and Gomphonema besides the longly disputed G. olivacea. Only a polyphasic approach, combining molecular and micromorphological data for taxonomy, nomenclatural evaluation, and observations from clonal cultures can reveal the full intricacies of evolutionary relations.

Improved detection of rare, endangered and invasive trout in using a new large‐volume sampling method for eDNA capture

AbstractEnvironmental DNA (eDNA) detection probability increases with volume of water sampled. Common approaches for collecting eDNA samples often require many samples since these approaches usually use fine filters, which restrict the volume of water that can be sampled. An alternative to collecting many, small volume water samples using fine filters may be to collect fewer, large volume water samples using coarse filters that do not clog as rapidly. We used mesocosm experiments and field evaluations to compare coarse filter‐large water volume samples (hereafter large volume filter samples) versus fine filter‐small water volume samples (hereafter small volume filter samples) for detection and quantification of rainbow trout (Oncorhynchus mykiss) and bull trout (Salvelinus confluentus) DNA. We found that large volume filter sampling can be an effective approach for detecting DNA of low‐density target taxa. In mesocosm experiments, large‐volume and small‐volume water samples detected similar quantities of rainbow trout DNA. In the field, large volume samples more frequently detected bull trout DNA, had higher bull trout DNA copy number, and higher total DNA concentrations than small volume samples. However, sampling higher water volumes increased the potential for PCR inhibition so the DNA workflow had to be altered for large volume samples. Combining larger water volume samples with other strategies, like increasing PCR sensitivity and the number of PCR replicates, will improve detection of rare species, which is crucial for advancing conservation and ecological understanding.

Extracting Data from Legacy Taxonomic Literature: Applications for planning field work

Traditional taxonomic publications have served as a biological data repository accumulating vast amounts of data on species diversity, geographical and temporal distributions, ecological interactions, taxonomic relations, among many other types of information. However, the fragmented nature of taxonomic literature has made this data difficult to access and use to its full potential. Current anthropogenic impact on biodiversity demands faster knowledge generation, but also making better use of what we already have. This could help us make better-informed decisions about conservation and resources management. In past years, several efforts have been made to make taxonomic literature more mobilized and accessible. These include online publications, open access journals, the digitization of old paper literature and improved availability through online specialized repositories such as the Biodiversity Heritage Library (BHL) and the World Spider Catalog (WSC), among others. Although easy to share, PDF publications still have most of their biodiversity data embedded in strings of text making them less dynamic and more difficult or impossible to read and analyze without a human interpreter. Recently developed tools as GoldenGATE-Imagine (GGI) allow transforming PDFs in XML files that extract and categorize taxonomically relevant data. These data can then be aggregated in databases such as Plazi TreatmentBank, where it can be re-explored, queried and analyzed. Here we combined several of these cybertaxonomic tools to test the data extraction process for one potential application: the design and planning of an expedition to collect fresh material in the field. We targeted the ground spider Teutamus politus and other related species from the Teutamus group (TG) (Araneae; Liocranidae). These spiders are known from South East Asia and have been cataloged in the family Liocranidae; however, their relations, biology and evolution are still poorly understood. We marked-up 56 publications that contained taxonomic treatments with specimen records for the Liocranidae. Of these publications, 20 contained information on members of the TG. Geographical distributions and occurrences of 90 TG species were analyzed based on 1,309 specimen records. These data were used to design our field collection in a way that allowed us to optimize the collection of adult specimens of our target taxa. The TG genera were most common in Indonesia, Thailand and Malaysia. From these, Thailand was the second richest but had the most records of T. politus. Seasonal distribution of TG specimens in Thailand suggested June and July as the best time for collecting adults. Based on these analyses, we decided to sample from mid-July to mid-August 2018 in the three Thai provinces that combined most records of TG species and T. politus. Relying on the results of our literature analyses and using standard collection methods for ground spiders, we captured at least one specimen of every TG genus reported for Thailand. Our one-month expedition captured 231 TG spiders; from these, T. politus was the most abundant species with 188 specimens (95 adults). By comparison, a total of 196 specimens of the TG and 66 of T. politus had been reported for the same provinces in the last 40 years. Our sampling greatly increased the number of available specimens, especially for the genera Teutamus and Oedignatha. Also, we extended the known distribution of Oedignatha and Sesieutes within Thailand. These results illustrate the relevance of making biodiversity data contained within taxonomic treatments accessible and reusable. It also exemplifies one potential use of taxonomic legacy data: to more efficiently use existing biodiversity data to fill knowledge gaps. A similar approach can be used to study neglected or interesting taxa and geographic areas, generating a better biodiversity documentation that could aid in decision making, management and conservation.

Variation in inhibitor effects on qPCR assays and implications for eDNA surveys

Aquatic environmental DNA (eDNA) surveys are sometimes impacted by polymerase chain reaction (PCR) inhibitors. We tested varying concentrations of different inhibitors (humic, phytic, and tannic acids; crude leaf extracts) for impacts on quantitative PCR (qPCR) assays designed for eDNA surveys of bighead and silver carp (Hypophthalmichthys nobilis and Hypophthalmichthys molitrix). We also tested for inhibition by high concentrations of exogenous DNA, hypothesizing that DNA from increasingly closely related species would be increasingly inhibitory. All tested inhibitors impacted qPCR, though only at very high concentrations — likely a function, in part, of having used an inhibitor-resistant qPCR solution. Closer phylogenetic relatedness resulted in inhibition at lower exogenous DNA concentrations, but not at relatively close phylogenetic scales. Inhibition was also influenced by the qPCR reporter dye used. Importantly, different qPCR assays responded differently to the same inhibitor concentrations. Implications of these results are that the inclusion of more than one assay for the same target taxa in an eDNA survey may be an important countermeasure against false negatives and that internal positive controls may not, in the absence of efforts to maximize inhibition compatibility, provide useful information about the inhibition of an eDNA assay.

Ruminal Microbial Populations and Fermentation Characteristics in Beef Cattle Grazing Tropical Forage in Dry Season and Supplemented with Different Protein Levels.

We tested the hypothesis that supplementation with protein improves fermentation parameters without damaging the rumen microbial populations of beef cattle grazing Urochloa brizantha cv. Marandu during the dry season. Four rumen-cannulated Nellore bulls (571 ± 31kg of body weight) were used in a 4 × 4 Latin square design. The treatments were not supplemented with concentrate (only free-choice mineral salt ad libitum) and supplemented (supplements with low-LPSU, medium-MPS, and high protein supplement-HPS), supplying 155, 515, and 875g/animal/day of crude protein (CP), respectively. The abundance of each target taxon was calculated as a fraction of the total 16S rRNA gene copies in the samples, using taxon-specific and domain bacteria primers. There was no difference (P > 0.05) across treatments for intakes of dry matter (DM), forage and neutral detergent fiber (NDF), digestibility of DM and NDF, and ruminal pH. Animals supplemented with concentrate had greater (P < 0.05) intakes and digestibility of CP, ether extract and non-fibrous carbohydrate contents of the substrates (EE + NFC), and ruminal ammonia nitrogen (RAN) compared to control. Bulls that received only mineral salt had lower proportions of Butyrivibrio fibrisolvens and had greater (P < 0.05) proportions of Fibrobacter succinogenes, Ruminococcus albus, Ruminococcus flavefaciens, Methanogen archaea than bulls supplemented with concentrate. The MPS animals had greater (P < 0.05) intake and digestibility of CP, RAN concentration, and had lower (P < 0.05) proportions of Fibrobacter succinogenes, Ruminococcus flavefaciens, and Selenomonas ruminantium than LPSU animals. The HPS provided higher (P < 0.05) intake of CP, RAN and proportion of Ruminococcus albus when compared with MPS. In conclusion, supply of 515g/animal/day of protein via supplement provides better ruminal conditions for the growth of cellulolytic bacteria of bulls on pasture during dry season.

Overlooked and undervalued: the neglected role of fauna and a global bias in ecological restoration assessments

Globally increasing rates of mine site discontinuations are resulting in the need for immediate implementation of effective conservation and management strategies. Surveying vegetation structure is a common method of assessing restoration success; however, responses of fauna to mine site restoration remain largely overlooked and understudied despite their importance within ecosystems as ecological engineers, pollinators, and restoration facilitators. Here we review the current state of the use of fauna in assessments of mine site restoration success globally, and address biases or shortcomings that indicate the assessment approach may undershoot closure and restoration success. We identified just 101 peer-reviewed publications or book chapters over a 49-year period that assess responses of fauna to mine site restoration globally. Most studies originate in Australia, with an emphasis on just one company. Assessments favour general species diversity and richness, with a particular focus on invertebrate responses to mine site restoration. Noteworthy issues included biases towards origin of study, study type, and target taxa. Further searches of the grey literature relating to fauna monitoring in mine site restoration, which was far more difficult to access, yielded six monitoring/guidance documents, three conference proceedings, two book chapters without empirical data, and a bulletin. As with peer-reviewed publications, grey literature focussed on invertebrate responses to restoration, or mentioned fauna only at the most basic level. We emphasise the need for global re-evaluation of regulatory standards to address these major limitations in assessing the capacity of the mining industry to comprehensively and representatively restore faunal communities after mining.