Rapid Biodiversity Assessment Research Articles

Do acoustic indices reflect the characteristics of bird communities in the savannas of Central Brazil?

Habitat loss and fragmentation represent two of the most significant threats to biodiversity. In some regions, like the Brazilian Cerrado, the deforestation rate can reach nearly 1 million hectares per year. Ecoacoustics and acoustic indices can be used to promote rapid assessments in threatened regions. We evaluated how two particular indices (the acoustic diversity index − ADI − and normalized difference soundscape index − NDSI) reflect bird species richness and composition in a protected area near Brasilia city. We hypothesised that ADI should reflect the characteristics of birds in the cerrado and in the gallery forest, i.e., with higher values in gallery forest than in the cerrado. Based on habitat structure, we also hypothesised that NDSI should be lower in less complex habitat, and lower in areas close to urbanized areas. We assessed 30 locations by installing automatic recorders to generate 15min wave files (48kHz, 16 bits, stereo). Manual inspection of the files revealed the presence of 107 bird species (74 in gallery forest and 47 in cerrado). Our results showed that ADI was significantly associated with species richness, being higher in gallery forest than in the cerrado. We found that NDSI values were lower in areas close to highways, an important source of impact for bird diversity. We argue that acoustic indices are a valid approach for rapid biodiversity assessment, however basic knowledge on species occurrences is essential to interpret the values provided by these indices.

A rapid biodiversity assessment of myxomycetes from a primary tropical moist forest of the Amazon basin in Ecuador

A rapid biodiversity assessment of myxomycetes from a primary tropical moist forest of the Amazon basin in Ecuador

Importance of ground refuges for the biodiversity in agricultural hedgerows

In most agro-ecosystems, hedgerows provide important habitat for many species. Unfortunately, large scale destruction of hedges has stripped this structure from many landscapes. Replanting programs have attempted to restore hedgerow habitats, but the methods employed often fail to replace the unique microhabitats (complex matrix of stones, logs and roots found along the base of the hedge) that provided key refuges to an array of animal species. We examined the influence of ground refuges on animal diversity in an agricultural landscape. We used non-lethal rapid biodiversity assessments to sample invertebrate and vertebrate taxa in 69 hedges having different levels of herbaceous cover, tree cover, and refuge availability. Co-inertia analyses compared hedge characteristics with the animal biodiversity sampled. We also used a functional index (accounting for body mass, trophic level, and metabolic mode of the species sampled) to compare hedges. In addition, large sedentary predators (e.g. snakes) were used as indicators of shelter presence/quality and as bio-indicators of food web structures. Finally we used unbiased Chao-estimates to evaluate species richness. All results were convergent and show that complexity of the base of the hedge (e.g., bank size and stone abundance) positively influenced biodiversity and predator abundance. Guidelines to restore hedgerows should integrate refuges that can be constructed by retaining the materials that are extracted during the planting of the hedges.

A rapid assessment of landscape biodiversity using diversity profiles of arthropod morphospecies

Context The assessment of land-use impacts on biodiversity is one of the central themes of landscape ecology and conservation biology. However, due to the complexity of biodiversity, it is impossible to obtain complete information about the diversity of all species even for small areas, necessitating the selection of individual species or assemblages thereof as species surrogate. In parts of the world where taxonomic expertise is lacking, species identification has hindered progress in biodiversity conservation, and the only practical, relatively-accurate option, is the use of taxonomic minimalism.

Acoustic identification of Mexican bats based on taxonomic and ecological constraints on call design

Summary Monitoring global biodiversity is critical for understanding responses to anthropogenic change, but biodiversity monitoring is often biased away from tropical, megadiverse areas that are experiencing more rapid environmental change. Acoustic surveys are increasingly used to monitor biodiversity change, especially for bats as they are important indicator species and most use sound to detect, localise and classify objects. However, using bat acoustic surveys for monitoring poses several challenges, particularly in megadiverse regions. Many species lack reference recordings, some species have high call similarity or differ in call detectability, and quantitative classification tools, such as machine learning algorithms, have rarely been applied to data from these areas. Here, we collate a reference call library for bat species that occur in a megadiverse country, Mexico. We use 4685 search‐phase calls from 1378 individual sequences of 59 bat species to create automatic species identification tools generated by machine learning algorithms (Random Forest). We evaluate the improvement in species‐level classification rates gained by using hierarchical classifications, reflecting either taxonomic or ecological constraints (guilds) on call design, and examine how classification rate accuracy changes at different hierarchical levels (family, genus and guild). Species‐level classification of calls had a mean accuracy of 66%, and the use of hierarchies improved mean species‐level classification accuracy by up to 6% (species within families 72%, species within genera 71·2% and species within guilds 69·1%). Classification accuracy to family, genus and guild‐level was 91·7%, 77·8% and 82·5%, respectively. The bioacoustic identification tools we have developed are accurate for rapid biodiversity assessments in a megadiverse region and can also be used effectively to classify species at broader taxonomic or ecological levels. This flexibility increases their usefulness when there are incomplete species reference recordings and also offers the opportunity to characterise and track changes in bat community structure. Our results show that bat bioacoustic surveys in megadiverse countries have more potential than previously thought to monitor biodiversity changes and can be used to direct further developments of bioacoustic monitoring programs in Mexico.

Rapid assessment of insect fauna based on local knowledge: comparing ecological and ethnobiological methods

BackgroundThe rapid assessment of biodiversity making use of surveys of local knowledge has been successful for different biological taxa. However, there are no reports on the testing of such tools for sampling insect fauna. The present study aimed to evaluate the efficiency of different ethnobiological techniques for rapid sampling of insect fauna.MethodsField research for the conventional survey of insect fauna was conducted on a private farm (9 ° 43'38.95 "S, 37 ° 45'11.97" W) , where there was intensive cultivation of okra (Abelmoschus esculentus L. (Moench)). The survey of local entomological knowledge was conducted among all the producers of okra living in the rural villages Pereira, Santa Luzia, and Nassau de Souza, within the Jacaré Curituba irrigated settlement scheme. The combined use of the techniques “free list” and projective interviews was analyzed, using two types of visual stimuli: stock photos and an entomological box.ResultsDuring the conventional survey of insect fauna, the species Bemisia tabaci biotype B, Aphis gossypii, Phenacoccus sp., Icerya purchasi and Lagria villosa were the primary pests found in the okra crop. Regarding the survey of insect pests, the results were convergent in both techniques (conventional sampling and free list). Comparing the interview with visual stimuli (pictures) and specimen witnesses (entomological box) revealed that the latter was more effective.ConclusionTechniques based on the recording and analysis of local knowledge about insects are effective for quick sampling of pest insects, but ineffective in sampling predator insects. The utilization of collected insects, infested branches, or photos of the symptoms of damage caused by pests in projective interviews is recommended.

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

BackgroundTropical mountain forests are hotspots of biodiversity hosting a huge but little known diversity of insects that is endangered by habitat destruction and climate change. Therefore, rapid assessment approaches of insect diversity are urgently needed to complement slower traditional taxonomic approaches. We empirically compare different DNA-based species delimitation approaches for a rapid biodiversity assessment of hyperdiverse leaf beetle assemblages along an elevational gradient in southern Ecuador and explore their effect on species richness estimates.Methodology/Principal FindingsBased on a COI barcode data set of 674 leaf beetle specimens (Coleoptera: Chrysomelidae) of 266 morphospecies from three sample sites in the Podocarpus National Park, we employed statistical parsimony analysis, distance-based clustering, GMYC- and PTP-modelling to delimit species-like units and compared them to morphology-based (parataxonomic) species identifications. The four different approaches for DNA-based species delimitation revealed highly similar numbers of molecular operational taxonomic units (MOTUs) (n = 284–289). Estimated total species richness was considerably higher than the sampled amount, 414 for morphospecies (Chao2) and 469–481 for the different MOTU types. Assemblages at different elevational levels (1000 vs. 2000 m) had similar species numbers but a very distinct species composition for all delimitation methods. Most species were found only at one elevation while this turnover pattern was even more pronounced for DNA-based delimitation.Conclusions/SignificanceGiven the high congruence of DNA-based delimitation results, probably due to the sampling structure, our study suggests that when applied to species communities on a regionally limited level with high amount of rare species (i.e. ~50% singletons), the choice of species delimitation method can be of minor relevance for assessing species numbers and turnover in tropical insect communities. Therefore, DNA-based species delimitation is confirmed as a valuable tool for evaluating biodiversity of hyperdiverse insect communities, especially when exact taxonomic identifications are missing.

First description of underwater acoustic diversity in three temperate ponds.

The past decade has produced an increased ecological interest in sonic environments, or soundscapes. However, despite this rise in interest and technological improvements that allow for long-term acoustic surveys in various environments, some habitats’ soundscapes remain to be explored. Ponds, and more generally freshwater habitats, are one of these acoustically unexplored environments. Here we undertook the first long term acoustic monitoring of three temperate ponds in France. By aural and visual inspection of a selection of recordings, we identified 48 different sound types, and according to the rarefaction curves we calculated, more sound types are likely present in one of the three ponds. The richness of sound types varied significantly across ponds. Surprisingly, there was no pond-to-pond daily consistency of sound type richness variation; each pond had its own daily patterns of activity. We also explored the possibility of using six acoustic diversity indices to conduct rapid biodiversity assessments in temperate ponds. We found that all indices were sensitive to the background noise as estimated through correlations with the signal-to-noise ratio (SNR). However, we determined that the AR index could be a good candidate to measure acoustic diversities using partial correlations with the SNR as a control variable. Yet, research is still required to automatically compute the SNR in order to apply this index on a large data set of recordings. The results showed that these three temperate ponds host a high level of acoustic diversity in which the soundscapes were variable not only between but also within the ponds. The sources producing this diversity of sounds and the drivers of difference in daily song type richness variation both require further investigation. Such research would yield insights into the biodiversity and ecology of temperate ponds.

High-Throughput Sequencing-The Key to Rapid Biodiversity Assessment of Marine Metazoa?

The applications of traditional morphological and molecular methods for species identification are greatly restricted by processing speed and on a regional or greater scale are generally considered unfeasible. In this context, high-throughput sequencing, or metagenetics, has been proposed as an efficient tool to document biodiversity. Here we evaluated the effectiveness of 454 pyrosequencing in marine metazoan community analysis using the 18S rDNA: V1-V2 region. Multiplex pyrosequencing of the V1-V2 region was used to analyze two pooled samples of DNA, one comprising 118 and the other 37 morphologically identified species, and one natural sample taken directly from a North Sea zooplankton community. A DNA reference library comprising all species represented in the pooled samples was created by Sanger sequencing, and this was then used to determine the optimal similarity threshold for species delineation. The optimal threshold was found at 99% species similarity, with 85% identification success. Pyrosequencing was able to identify between fewer species: 67% and 78% of the species in the two pooled samples. Also, a large number of sequences for three species that were not included in the pooled samples were amplified by pyrosequencing, suggesting preferential amplification of some genotypes and the sensitivity of this approach to even low levels of contamination. Conversely, metagenetic analysis of the natural zooplankton sample identified many more species (particularly gelatinous zooplankton and meroplankton) than morphological analysis of a formalin-fixed sample from the same sampling site, suggesting an increased level of taxonomic resolution with pyrosequencing. The study demonstrated that, based on the V1-V2 region, 454 sequencing does not provide accurate species differentiation and reliable taxonomic classification, as it is required in most biodiversity monitoring. The analysis of artificially prepared samples indicated that species detection in pyrosequencing datasets is complicated by potential PCR-based biases and that the V1-V2 marker is poorly resolved for some taxa.

Evaluating a multigene environmental DNA approach for biodiversity assessment.

BackgroundThere is an increasing demand for rapid biodiversity assessment tools that have a broad taxonomic coverage. Here we evaluate a suite of environmental DNA (eDNA) markers coupled with next generation sequencing (NGS) that span the tree of life, comparing them with traditional biodiversity monitoring tools within ten 20×20 meter plots along a 700 meter elevational gradient.ResultsFrom six eDNA datasets (one from each of 16S, 18S, ITS, trnL and two from COI) we identified sequences from 109 NCBI taxonomy-defined phyla or equivalent, ranging from 31 to 60 for a given eDNA marker. Estimates of alpha and gamma diversity were sensitive to the number of sequence reads, whereas beta diversity estimates were less sensitive. The average within-plot beta diversity was lower than between plots for all markers. The soil beta diversity of COI and 18S markers showed the strongest response to the elevational variation of the eDNA markers (COI: r=0.49, p<0.001; 18S: r=0.48, p<0.001). Furthermore pairwise beta diversities for these two markers were strongly correlated with those calculated from traditional vegetation and invertebrate biodiversity measures.ConclusionsUsing a soil-based eDNA approach, we demonstrate that standard phylogenetic markers are capable of recovering sequences from a broad diversity of eukaryotes, in addition to prokaryotes by 16S. The COI and 18S eDNA markers are the best proxies for aboveground biodiversity based on the high correlation between the pairwise beta diversities of these markers and those obtained using traditional methods.Electronic supplementary materialThe online version of this article (doi:10.1186/s13742-015-0086-1) contains supplementary material, which is available to authorized users.

Non-lethal rapid biodiversity assessment

For several animal taxa, non-lethal techniques that do not rely on collecting individuals are routinely used to assess biodiversity (e.g. point counts in birds). Identification often relies on the ability of the observer, are subjected to errors, but populations are not impacted. Thus, multiple counting sessions (MCS) that allow using robust analyses (e.g. unbiased Chao richness estimate) are available. However, for most species (e.g. arthropods), trap systems must be set up. Killed individuals are collected and later accurately identified in the laboratory, but unbiased MCS become unavailable. Environmental DNA bar-coding provides an alternative, yet it requires important technical support and is not designed for MCS. Lethal rapid biodiversity assessments (RBA), derived from classical trap surveys and based on less accurate identifications (morphospecies are used), have been successfully developed to relax technical constraints. In this study, we combined non-lethal and RBA approaches to address logistical, analytical and ethical issues. We tested five versions of a protocol to visually survey the macro-fauna of hedgerows. A large number of individuals were directly identified in the field, mostly arthropods but also vertebrates. Identification error varied with taxonomic level and lineage, but remained low at the morphospecies level. Importantly, estimates tended to reach asymptotes, suggesting that local richness was appropriately appraised. Like any technique, non-lethal RBA (NL-RBA) present both advantages and weaknesses, and may improve the toolbox to survey biodiversity.

DNA 염기서열에 기초한 벼과 잡초의 분자생물학적 동정

최근에 전 세계적으로 동물, 식물뿐만 아니라 균류, 해조류 등에서 활발하게 이용하는 DNA 바코드는 게놈 DNA의 단편을 이용해 종들 간의 DNA 변이를 발견하여 형태적 지식 없이 정확하게 종을 동정하고 분류하는 방법이다. 고등식물에서는 단일마커로 바코드 조건을 충족할 수 없어 엽록체 DNA의 rbcL과 matK 유전자를 표준마커로 이용하고 있다. 본 연구는 식물 표준 바코드마커와 핵 DNA의 ITS 부위를 이용하여 국내 벼과 식물 252 분류군 중 주로 농경지에서 발생하는 잡초 총 84분류군 403생태형을 바코드하여 데이터베이스를 구축하기 위하여 수행하였다. 바코드 결과 PCR 증폭과 염기서열 분석 성공률은 rbcL에서 가장 높았으며 matK에서 가장 낮았다. 그러나 바코드 갭과 종식별 해상력은 matK에서 가장 높았다. 80.9%의 염기서열 분석 성공률을 보인 ITS는 matK와의 조합에서 92.9% 까지 종 식별 해상력을 높일 수 있어 벼과 바코드에 매우 유용한 조합이었다. 벼과의 바코드데이터는 미국의 국립생물공학정보센터에 기탁하여 genbank 번호를 부여받아 공개하였다. 그러므로 형태적으로 동정이 어려운 벼과 잡초를 matK와 ITS 부위의 염기서열을 분석하여 미국의 국립생물공학정보센터에 기탁한 데이터와 비교함으로써 쉽고 간편하게 동정할 수 있게 되었다. Korean Poaceae includes approximately 80 species of the agricultural weeds. Precise species identification is the first step for more effective weed management in the agricultural fields. However, the identification of species in Poaceae is not easy without the assistance of taxonomists or identification experts although they are relatively easy to distinguish from the plants of the other family by the unique characteristics of caryopsis. Thus, DNA barcode was suggested as an alternative powerful technique for species identification by using short sections of DNA from a specific region of the genome. Two standard barcode markers of vascular plants, chloroplast rbcL and matK, and a supplementary nuclear ribosomal Internal Transcribed Spacer (ITS) region were used for barcode of major Korean Poaceae weeds, 403 individuals of 84 taxa. All the barcode markers revealed a good level of sequencing success with the lowest 73.7% for matK and the highest 88.8% for rbcL. The barcode sequences were deposited to the National Center for Biotechnology Information (NCBI) database for public use. Combined matK and ITS showed very high resolving power with 92.9%. Besides the identification of weeds for weed managment, the generated DNA barcode data could be used for many other applications such as rapid biodiversity assessment and conservation prioritization.

Registro de la presencia de mamíferos medianos en dos zonas del municipio de Cuetzalán, en la Sierra Norte de Puebla

Introduction: Northern Puebla has a high mammal diversity due the large variety of ecosystems present. However, there is no information about their distribution or their response to fragmentation. Thus, we registered medium sized mammals in two areas with different degree of disturbance. Rancho el Paraiso which focus on cattle ranching and the Tecomateno Private Reserve which conserves habitat in the municipality of Cuetzalan, Puebla. Methods: From September 2012 to February 2013 we used transects to find tracks and scats and camera traps baited with a mix of sardine and lard. Additionally we undertook semi-structured interviews to hunters and ex-hunters with the aid of cards with images of the species potentially distributed in the area. Results: We carried out 12 field visits in each site, accumulating a total of 163 camera nights and walking 27 km in Rancho el Paraiso, while in the Tecomateno Reserve, we accumulated 145 camera nights and walked 22.5 km. Our field efforts resulted in the detection of six species for the Tecomateno Reserve and four for Rancho el Paraiso. Our semi-structured interviews documented the presence of 13 species for the Tecomateno Reserve and 11 for Rancho el Paraíso. Discussion and Conclusions: This study provides information on the mammals of Cuetzalan and their response to different levels of disturbance. It was expected to find a higher diversity in Rancho el Paraiso because it is located away from communities, however, it is used more intensively. We consider that interviews are a reliable cost effective tool to undertake rapid biodiversity assessments. These results also suggest that private nature reserves may be a good option to conserve biodiversity in fragmented areas. Key words: disturbance, mesopredators, otter, sampling, tropical montane cloud forest.

Multi-taxonomic diversity patterns in a neotropical green city: a rapid biological assessment

The growing number of urban ecology studies has raised concern about the importance of comprehending the ecological patterns and processes of urban areas in order to manage and plan them properly. In this study, we performed a rapid descriptive ecological assessment of the biodiversity patterns in a neotropical mid-sized urban area from a multi-taxonomic approach, contrasting seven taxonomic groups (i.e., vascular plants, fungi, ants, butterflies, beetles, amphibians, birds) in areas with different degree of urbanization intensity. Results of this study show that diversity patterns differ depending on the taxonomic group; thus, it was not possible to generalize specific trends in species richness, abundance, and species composition because each taxon seems to respond differently to the process or level of urbanization. Our results also highlight the relevance of using multi-taxonomic approaches to understand the relationship between biodiversity and urban environments, and underline potential benefits and limitations of using each of the studied groups when considering rapid biodiversity assessments. Based on our results, we suggest the following recommendations when performing rapid biological assessments in urban areas: evaluate as many taxa as possible, choosing the set of taxonomic groups in relation to the objectives of the study, wide the temporal and spatial survey window as much as possible, focus on several biodiversity measures, and interpreting results cautiously, as rapid assessments do not necessarily reflect ecological patterns, but just part of the history.

Putting models to a good use: a rapid assessment of Arctic seabird biodiversity indicates potential conflicts with shipping lanes and human activity

AbstractAimsTo use open access models of predicted seabird distribution data in the Arctic to create rapid assessment biodiversity maps for management purposes and for prioritization of conservation.LocationHigh Arctic, North of 60° latitude.MethodsThe predicted distributions of 27 species of Arctic seabirds were combined to create a seabird biodiversity map. The GIS layers created were based on peer‐reviewed model outputs which were calculated using the random forest algorithm and supplemented with ISO standardized metadata for quality assurance. We have overlain the species diversity and occurrence maps with known shipping lanes and areas of human activities in the Arctic to highlight areas of potential human conflict with pelagic seabirds.ResultsEntry points to the Arctic Basin for example Baffin Bay, Davis Strait, Chukchi Sea, Greenland Sea and Norwegian Sea are specific conflict zones with mean number of species occurring within 20 km of shipping zones ranging from 17 to 19 (63–70% of modelled species). We also show that these are areas of the highest intensity of human activities in the Arctic (fishing, ship traffic and accident rates).Main conclusionThese Arctic seabird biodiversity maps can be used to make decisions which take into account ecology and socio‐economy (e.g. Marxan analysis and marine protected areas MPAs) and for ecological/economic studies which can help to create a pro‐active management scheme. This is particularly important due to the future increase in human impacts in the Arctic (i.e. fishing, tourism and especially shipping). By improving upon these models and further examination into the interactions between seabirds and humans in the Arctic, we can guide important policy decisions to protect Arctic biodiversity.

Using citizen science to estimate lichen diversity

Lack of field time, access to experts, and the challenges associated with research permits make traditional approaches for determining species richness (comprehensive collection and determination of biological specimens) impractical in many situations. To accelerate local biodiversity assessments for conservation and resource management, scientists need both cost-effective survey methods and validated statistical models that link sample data to estimates of true species richness. Lichen communities are reliable indicators for the condition of many different terrestrial ecosystems because they are sensitive to environmental stress and represent a promising system in which to develop alternative approaches to biodiversity monitoring. We propose a citizen scientist-based survey methodology for macrolichen diversity in which parataxonomic units (PUs), as identified in lichen photographs, serve as species surrogates to estimate lichen diversity. We validate this method by photographically surveying lichens at five park units previously surveyed as part of the Lichen Biomonitoring Project (LBP) at George Mason University. Using the Chao2 metric to account for variation in sampling effort, we compared observed (raw PU counts) and estimated (effort-corrected) PU and species richnesses and found that, for all park units, our methodology gave similar diversity estimates to those obtained by the LBP. While PUs provide rapid assessment of diversity within a sample, they do not address the challenge of upscaling from samples to estimate total species diversity in an area. We propose a statistical method to estimate PU richness that, unlike phenomenological methods like Chao2, can exploit replication in our sampling design to explicitly model PU occupancy and detection probability. In sum, we present new methods for both surveying diversity and extrapolating sample data that can be widely applied for rapid assessment of biodiversity.

The Saproxylic Activity Index: A New Tool for the Rapid Assessment of Deadwood Species during Forest Restoration

Restoring deadwood habitat is vital in order to recreate fully functioning forest ecosystems. Letting this process occur naturally can take in excess of one hundred years, thus management practises typically try to accelerate this via the artificial addition of deadwood. Since the species which rely on deadwood often have poor dispersal abilities, restoring deadwood habitat rarely results in the full restoration of the saproxylic fauna. Furthermore, standard deadwood monitoring protocol only records the amount and type of substrate available and is not capable of determining whether saproxylic insects have been restored. Full species inventories are time-consuming, costly and require great expertise. We present a rapid biodiversity assessment tool which we believe is the first protocol for measuring saproxylic activity which is accessible to non-specialists. Utilising the exit bore holes which saproxylics create on deadwood can provide an indication of the density, richness and diversity of species present; we call this the Saproxylic Activity Index. We show that this index can detect differences in the activity of insects between substrates. As saproxylic insects provide important ecosystem functions, such as aiding in the decay of deadwood and recycling nutrients, a measure of their activity levels may indicate the rate of restoration of these ecosystem processes. We believe that further exploration of this method provides an exciting opportunity for the functional restoration of saproxylic fauna to become incorporated into mainstream forest management.

20 years since the introduction of DNA barcoding: from theory to application

Traditionally, taxonomic identification has relied upon morphological characters. In the last two decades, molecular tools based on DNA sequences of short standardised gene fragments, termed DNA barcodes, have been developed for species discrimination. The most common DNA barcode used in animals is a fragment of the cytochrome c oxidase (COI) mitochondrial gene, while for plants, two chloroplast gene fragments from the RuBisCo large subunit (rbcL) and maturase K (matK) genes are widely used. Information gathered from DNA barcodes can be used beyond taxonomic studies and will have far-reaching implications across many fields of biology, including ecology (rapid biodiversity assessment and food chain analysis), conservation biology (monitoring of protected species), biosecurity (early identification of invasive pest species), medicine (identification of medically important pathogens and their vectors) and pharmacology (identification of active compounds). However, it is important that the limitations of DNA barcoding are understood and techniques continually adapted and improved as this young science matures.

Assessing the cross platform performance of marine mammal indicators between two collocated acoustic recorders

Equipment and deployment strategies for remote passive acoustic sensing of marine environments must balance memory capacity, power requirements, sampling rate, duty-cycle, deployment duration, instrument size, and environmental concerns. The impact of different parameters on the data and applicability of the data to the specific questions being asked should be considered before deployment. Here we explore the effect of recording and detection parameters on marine mammal acoustic data across two platforms. Daily classifications of marine mammal vocalizations from two passive acoustic monitors with different subsampling parameters, an AURAL and a Passive Aquatic Listener (PAL), collocated in the Bering Sea were compared. The AURAL subsampled on a pre-set schedule, whereas the PAL sampled via an adaptive protocol. Detected signals of interest were manually classified in each dataset independently. The daily classification rates of vocalizations were similar. Detections from the higher duty-cycle but lower sample rate AURAL were limited to species and vocalizations with energy below 4kHz precluding detection of echolocation signals. Temporal coverage from the PAL audio files was limited by the adaptive sub-sampling protocol. A method for classifying ribbon (Histriophoca fasciata) and bearded seal (Erignathus barbatus) vocalizations from the sparse spectral time histories of the PAL was developed. Although application of the acoustic entropy as a rapid assessment of biodiversity was not reflective of the number of species detected, acoustic entropy was robust to changes in sample rate and window length.

Biodiversity Sampling Using a Global Acoustic Approach: Contrasting Sites with Microendemics in New Caledonia

New Caledonia is a Pacific island with a unique biodiversity showing an extreme microendemism. Many species distributions observed on this island are extremely restricted, localized to mountains or rivers making biodiversity evaluation and conservation a difficult task. A rapid biodiversity assessment method based on acoustics was recently proposed. This method could help to document the unique spatial structure observed in New Caledonia. Here, this method was applied in an attempt to reveal differences among three mountain sites (Mandjélia, Koghis and Aoupinié) with similar ecological features and species richness level, but with high beta diversity according to different microendemic assemblages. In each site, several local acoustic communities were sampled with audio recorders. An automatic acoustic sampling was run on these three sites for a period of 82 successive days. Acoustic properties of animal communities were analysed without any species identification. A frequency spectral complexity index (NP) was used as an estimate of the level of acoustic activity and a frequency spectral dissimilarity index (Df) assessed acoustic differences between pairs of recordings. As expected, the index NP did not reveal significant differences in the acoustic activity level between the three sites. However, the acoustic variability estimated by the index Df, could first be explained by changes in the acoustic communities along the 24-hour cycle and second by acoustic dissimilarities between the three sites. The results support the hypothesis that global acoustic analyses can detect acoustic differences between sites with similar species richness and similar ecological context, but with different species assemblages. This study also demonstrates that global acoustic methods applied at broad spatial and temporal scales could help to assess local biodiversity in the challenging context of microendemism. The method could be deployed over large areas, and could help to compare different sites and determine conservation priorities.