Taxonomic Coverage Research Articles

The zoological collections of Portuguese oceanographic campaigns in former colonial territories

The Missão de Biologia Marítima (Lisboa, Portugal) and its successor institutions, were responsible for conducting oceanographic campaigns in former Portuguese colonies during the decades of 1950–1960. The primary objective was to advance the systematic study of marine resources in these territories, leading to the collection of thousands of specimens of marine fauna, particularly fishes, molluscs and crustaceans. In the late 1970s, the collection faced understaffing and was neglected, becoming largely inaccessible to the scientific community. This paper presents a comprehensive review of the collection, which is currently deposited in the Museu Nacional de História Natural e da Ciência, Universidade de Lisboa. The collection includes 7305 occurrences, for a total of over 30,000 specimens, most of which were collected in Angola, Cabo Verde and Mozambique between 1951 and 1965. The collection holds representatives of more than 1000 species and has a wide taxonomic coverage, including 19 type specimens of nine nominal taxa: the fishes Cubiceps niger Nümann in Franca, 1957, Tylosurus acus rafale Collete & Parin, 1970 and Chromis lubbocki Edwards, 1986; the cone snails Conus angolensis Paes da Franca, 1955 and Conus lucirensis Paes da Franca, 1955; the ark clam Arca geissei angolensis Paes da Franca, 1955; the squids Moroteuthis robsoni Adam, 1962 and Todarodes sagittatus angolensis Adam, 1962; and the snapping shrimp Alpheus holthuisi Ribeiro, 1964. A comprehensive description of the resulting dataset is provided, as well as a brief account of the history of these campaigns and the research conducted.

A landscape conservation perspective of state Species of Greatest Conservation Need

AbstractState Wildlife Action Plans (SWAPs), including lists of Species of Greatest Conservation Need (SGCN), outline state strategies for protecting species and habitats in the United States. In developing the current, second revision SWAPs, states are increasingly pursuing coordinated landscape conservation approaches. Analyzing SGCN lists in the first revision SWAPs, we found evidence that they already support multistate conservation. Most states address a common set of vertebrate and invertebrate groups, include most of the imperiled species from these groups, do not prioritize endemics over non‐endemics, and often include most imperiled species that are shared with neighboring states. Also, a regional SGCN coordination effort was successful. Although 65% of animals on each SGCN list were assessed as at elevated risk of extirpation by state authorities, only 43% of the combined national list were at elevated risk of global extinction. Over 40% of the combined animal SGCNs are considered globally apparently secure. Plants, snails, freshwater shrimps, and freshwater insects were poorly represented in SGCN lists. For the current SWAP revisions, we recommend improving foundational data on taxonomy, range‐wide distribution, and conservation status; expanded taxonomic coverage in SGCN lists; supporting existing and establishing new interstate initiatives; and diversifying funding mechanisms that target regional cooperation.

Assessing citizen science data quality for bird monitoring in the Iberian Peninsula

Citizen science data on biodiversity has experienced significant growth, largely driven by advancements in technology that facilitate data sharing. In recent years, mobile applications have provided a substantial boost to both the collection and sharing of this data. While this accessible information is undoubtedly valuable, we must consider the numerous biases present in this data when used for high-quality research. In this study, we analyse citizen science data for the birds of the Iberian Peninsula, comprising over 23 million unique records after filtering for duplicates (i.e., instances where the same observation was uploaded more than once). Using a 10 × 10 km square grid, we present information on well-surveyed cells (completeness) as well as temporal, taxonomic, geographical, and land use coverages. We found that the completeness of information is generally high, with better coverage around densely populated areas such as major cities and coastal regions, as well as popular birding destinations, which are frequently visited. The Mediterranean ecoregion and wetlands exhibit the highest levels of surveying. Furthermore, we observed an increase in temporal coverage since the 1980s and broad taxonomic coverage across all bird orders in the Iberian region. Our results underscore the utility of citizen science for many locations, as expressed in 10 × 10 km cells. However, they also highlight the inadequate data completeness across part of the territory, particularly in forested or sparsely inhabited areas. These findings not only identify cells suitable for bird diversity or conservation studies but also indicate areas where citizen-driven bird recording efforts should be encouraged.

Accelerating and standardising IUCN Red List assessments with sRedList

The IUCN Red List of Threatened Species underpins much decision-making in conservation and plays a key role in monitoring the status and trends of biodiversity. However, the shortage of funds and assessor capacity slows the uptake of novel data and techniques, hampering its currency, applicability, consistency and long-term viability. To help address this, we developed sRedList, a user-friendly online platform that assists Red List assessors through a step-by-step process to estimate key parameters in a standardised and reproducible fashion. Through the platform, assessors can swiftly generate outputs including species' range maps, lists of countries of occurrence, lower and upper bounds of area of occupancy, habitat preferences, trends in area of habitat, and levels of fragmentation. sRedList is compliant with the IUCN Red List guidelines and outputs are interoperable with the Species Information Service (SIS; the IUCN Red List database) in support of global, regional and national assessments and reassessments. sRedList can also help assessors prioritise species for reassessment. sRedList was released in October 2023, with a complete documentation package (including text documentation, ‘cheatsheets’, and 15 video tutorials), and will soon be highlighted in the official Red List online training course. sRedList will help to bridge the gap between extinction risk research and Red List assessment practice, increase the taxonomic coverage and consistency of assessments, and ensure the IUCN Red List is up-to-date to best support conservation policy and practice across the world.

Antiviral Mx proteins have an ancient origin and widespread distribution among eukaryotes.

First identified in mammals, Mx proteins are potent antivirals against a broad swathe of viruses. Mx proteins arose within the Dynamin superfamily of proteins (DSP), mediating critical cellular processes, such as endocytosis and mitochondrial, plastid, and peroxisomal dynamics. And yet, the evolutionary origins of Mx proteins are poorly understood. Using a series of phylogenomic analyses with stepwise increments in taxonomic coverage, we show that Mx proteins predate the interferon signaling system in vertebrates. Our analyses find an ancient monophyletic DSP lineage in eukaryotes that groups vertebrate and invertebrate Mx proteins with previously undescribed fungal MxF proteins, the relatively uncharacterized plant and algal Dynamin 4A/4C proteins, and representatives from several early-branching eukaryotic lineages. Thus, Mx-like proteins date back close to the origin of Eukarya. Our phylogenetic analyses also reveal that host-encoded and NCLDV (nucleocytoplasmic large DNA viruses)-encoded DSPs are interspersed in four distinct DSP lineages, indicating recurrent viral theft of host DSPs. Our analyses thus reveal an ancient history of viral and antiviral functions encoded by the Dynamin superfamily in eukaryotes.

The Phylogenetic Relationships of Major Lizard Families Using Mitochondrial Genomes and Selection Pressure Analyses in Anguimorpha.

Anguimorpha, within the order Squamata, represents a group with distinct morphological and behavioral characteristics in different ecological niches among lizards. Within Anguimorpha, there is a group characterized by limb loss, occupying lower ecological niches, concentrated within the subfamily Anguinae. Lizards with limbs and those without exhibit distinct locomotor abilities when adapting to their habitats, which in turn necessitate varying degrees of energy expenditure. Mitochondria, known as the metabolic powerhouses of cells, play a crucial role in providing approximately 95% of an organism's energy. Functionally, mitogenomes (mitochondrial genomes) can serve as a valuable tool for investigating potential adaptive evolutionary selection behind limb loss in reptiles. Due to the variation of mitogenome structures among each species, as well as its simple genetic structure, maternal inheritance, and high evolutionary rate, the mitogenome is increasingly utilized to reconstruct phylogenetic relationships of squamate animals. In this study, we sequenced the mitogenomes of two species within Anguimorpha as well as the mitogenomes of two species in Gekkota and four species in Scincoidea. We compared these data with the mitogenome content and evolutionary history of related species. Within Anguimorpha, between the mitogenomes of limbless and limbed lizards, a branch-site model analysis supported the presence of 10 positively selected sites: Cytb protein (at sites 183 and 187), ND2 protein (at sites 90, 155, and 198), ND3 protein (at site 21), ND5 protein (at sites 12 and 267), and ND6 protein (at sites 72 and 119). These findings suggested that positive selection of mitogenome in limbless lizards may be associated with the energy requirements for their locomotion. Additionally, we acquired data from 205 mitogenomes from the NCBI database. Bayesian inference (BI) and Maximum Likelihood (ML) trees were constructed using the 13 mitochondrial protein-coding genes (PCGs) and two rRNAs (12S rRNA and 16S rRNA) from 213 mitogenomes. Our phylogenetic tree and the divergence time estimates for Squamata based on mitogenome data are consistent with results from previous studies. Gekkota was placed at the root of Squamata in both BI and ML trees. However, within the Toxicofera clade, due to long-branch attraction, Anguimorpha and (Pleurodonta + (Serpentes + Acrodonta)) were closely related groupings, which might indicate errors and also demonstrate that mitogenome-based phylogenetic trees may not effectively resolve long-branch attraction issues. Additionally, we reviewed the origin and diversification of Squamata throughout the Mesozoic era, suggesting that Squamata originated in the Late Triassic (206.05 Mya), with the diversification of various superfamilies occurring during the Cretaceous period. Future improvements in constructing squamate phylogenetic relationships using mitogenomes will rely on identifying snake and acrodont species with slower evolutionary rates, ensuring comprehensive taxonomic coverage of squamate diversity, and increasing the number of genes analyzed.

High levels of species' extirpation in an urban environment-A case study from Berlin, Germany, covering 1700-2023.

Species loss is highly scale-dependent, following the species-area relationship. We analysed spatio-temporal patterns of species' extirpation on a multitaxonomic level using Berlin, the capital city of Germany. Berlin is one of the largest cities in Europe and has experienced a strong urbanisation trend since the late nineteenth century. We expected species' extirpation to be exceptionally high due to the long history of urbanisation. Analysing 37 regional Red Lists of Threatened Plants, Animals and Fungi of Berlin (covering 9498 species), we found that 16% of species were extirpated, a rate 5.9 times higher than at the German scale and 47.1 times higher than at the European scale. Species' extirpation in Berlin is comparable to that of another German city with a similarly broad taxonomic coverage, but much higher than in regional areas with less human impact. The documentation of species' extirpation started in the eighteenth century and is well documented for the nineteenth and twentieth centuries. We found an average annual extirpation of 3.6 species in the nineteenth century, 9.6 species in the twentieth century and the same number of extirpated species as in the nineteenth century were documented in the twenty-first century, despite the much shorter time period. Our results showed that species' extirpation is higher at small than on large spatial scales, and might be negatively influenced by urbanisation, with different effects on different taxonomic groups and habitats. Over time, we found that species' extirpation is highest during periods of high human alterations and is negatively affected by the number of people living in the city. But, there is still a lack of data to decouple the size of the area and the human impact of urbanisation. However, cities might be suitable systems for studying species' extirpation processes due to their small scale and human impact.

Breeding records of 325 bird species from Peru over 21 years based on citizen science data

AbstractBreeding is a key component of the life history of birds. Documenting diverse aspects of their breeding biology provides valuable natural history data that can be used to address questions of evolutionary, ecological, or conservation significance. Despite its importance, this information is scarce for most Neotropical species. We compiled 1180 breeding records corresponding to 325 bird species for the period 2000–2021, through an in‐depth review of photo or video records from Peru, sourced from Macaulay Library and iNaturalist platforms. We determined the geographical distribution of the breeding records, described patterns of activity and nesting behavior (i.e., host plant preference and clutch size), and explored the timing of breeding. Our study represents one of the few efforts to provide nationwide data on breeding birds in the Neotropical region. We also offer broad taxonomic coverage for further studies interested in testing hypotheses on the variation of reproductive traits and timing at both local and regional scales. The complete data set for this abstract published in the Data Article section of the journal is available in electronic format in MetaCat in JaLTER at http://db.cger.nies.go.jp/JaLTER/metacat/metacat/ERDP-2024-07.1/jalter-en.

Assessing the performance of short 18S rDNA markers for environmental DNA metabarcoding of marine protists

AbstractMarine protists are globally distributed and sensitive to environmental conditions, which makes them a focal group when studying the effects of climate change on biodiversity and ocean health. However, they are a highly diverse group with varying evolutionary histories and morphologies and widely variable preservation potential in the fossil record. Thus, their past diversity and composition are poorly known. Paleogenetics, which relies, among other approaches, on DNA metabarcoding of sedimentary ancient DNA (sedaDNA), provides a promising avenue to explore the past history and responses of marine protists to global change. Choosing the right marker for sedaDNA studies is critical, striking a balance between marker length and taxonomic resolution. While marker guides exist for modern environmental DNA surveys, a thorough assessment of existing short markers for sedaDNA studies targeting protists is lacking. In this study, we report on a comparison of in silico PCR for eight short 18S rDNA markers, including one from the Tara Oceans initiative and a longer marker commonly used in modern marine eDNA studies. We analyze their taxonomic coverage and resolution, taxonomic overlap and uniqueness between markers, co‐amplification of non‐protist taxa, and amplicon size differences across taxonomic groups. Additionally, we provide a detailed analysis of diatoms, dinoflagellates, haptophytes, and chlorophytes. Our study is aimed at supporting project‐specific marker choices for characterizing protist composition and diversity. While we focus on marine protists, our results are applicable to other aquatic and terrestrial environments.

Authentication of seafood species on the ASFIS list (FAO) by in-silico evaluation of primers for metabarcoding

Given the remarkable biodiversity among the seafood species entering the food supply chain, authentication is a crucial component in ensuring transparent trade. DNA metabarcoding stands out as the leading methodology for determining species composition within complex food matrices. Nevertheless, the selection of primer pairs is critical, as it may introduce biases into species identification. In this investigation, we evaluated previously described primers for their in-silico efficacy in identifying both edible marine species on the ASFIS (FAO) list and the main terrestrial animal species frequently incorporated as ingredients in processed seafood products. Selected primers covered the Cytochrome c Oxidase subunit I (COI), the Cytochrome b (cytb), the 16S rRNA (16S) and the 12S rRNA (12S) mitochondrial regions. Results showed that, out of 53 pairs analysed, one primer pair targeting the COI region obtained the best performance in terms of taxonomic coverage for both ASFIS and terrestrial species. Notably, each primer pair showed a unique taxonomic profile, suggesting their potential for addressing various seafood authentication issues as the detection of novel food ingredients (e.g., jellyfish, red algae, insects) or endangered species. Overall, these outcomes deliver valuable insights for selecting metabarcoding primers to improve the traceability of seafood products and contribute to the development of an innovative Food Safety Management System.

The implications of estimating rarity in Brazilian reptiles from GBIF data based on contributions from citizen science versus research institutions

AbstractUnderstanding the distribution of rare species is important for conservation prioritisation. Traditionally, museums and other research institutions have served as depositories for specimens and biodiversity information. However, estimating abundance from these sources is challenging due to spatiotemporally biased collection methods. For instance, large‐bodied reptiles that are found near research institutions or in popular, easily accessible sites tend to be overrepresented in collections compared to smaller species found in remote areas. Recently, a substantial number of observations have been amassed through citizen (or community) science initiatives, which are invaluable for monitoring purposes. Given the unstructured nature of this sampling, these datasets are often affected by biases, such as taxonomic, spatial and temporal preferences. Therefore, analysing data from these two sources can lead to different abundance estimates. This study compiled data on Brazilian reptile species from the Global Information Biodiversity Facility (GBIF). It employed a community‐ecology approach to analyse data from research institutions and citizen science initiatives, separately and collectively, to assess taxonomic and spatial species coverage and predict species rarity. Using a 1‐degree hexagonal grid, we analysed the spatial distribution of reptile communities and calculated rarity indices for 754 reptile species. Our findings reveal that 87 species were exclusively recorded in the citizen science subset, while 212 were recorded only by research institutions. The number of observations per species in the citizen science data followed a Gambin distribution, which aligns with the expected pattern of abundance in natural communities, unlike the data from research institutions. This suggests that citizen science data may be a more accurate source for estimating species abundance and rarity. The discrepancies in rarity classifications between the datasets were likely due to differences in sample size and potentially other sampling parameters. Nevertheless, combining data collected by both research institutions and citizen science initiatives can help to fill knowledge gaps in reptile species occurrence, thus enhancing the foundation for conservation efforts on a national scale.

Geographical-Historical Analysis of the Herbarium Specimens Representing the Economically Important Family Amaranthaceae (Chenopodiaceae-Amaranthaceae Clade) Collected in 1821-2022 and Preserved in the Herbarium of the Jagiellonian University in Krakow.

Herbaria constitute a form of documentation, store and secure comparative material, as well as constitute an extra original gene bank. They are an invaluable database among others for the biological, ethnobotanical and agricultural sciences. The digitization of herbarium collections significantly facilitates access to archival materials; however, searching them is still time-consuming. Therefore, our work aims to analyze the herbarium collection of 8801 sheets for specimens representing the economically important family Amaranthaceae (Chenopodiaceae-Amaranthaceae clade) deposited the oldest herbarium in Poland, the herbarium of the Jagiellonian University (KRA). These specimens have been collected from almost all the continents in dozens of countries for over 200 years. The analyses conducted, including the taxonomic coverage, geographical characteristics and origin, temporal coverage and utility importance of representative species, present the discussed resources in a more accessible way and may become a more attractive form for scientists potentially interested in more advanced research work.

Utilizing profile hidden Markov model databases for discovering viruses from metagenomic data: a comprehensive review.

Profile hidden Markov models (pHMMs) are able to achieve high sensitivity in remote homology search, making them popular choices for detecting novel or highly diverged viruses in metagenomic data. However, many existing pHMM databases have different design focuses, making it difficult for users to decide the proper one to use. In this review, we provide a thorough evaluation and comparison for multiple commonly used profile HMM databases for viral sequence discovery in metagenomic data. We characterized the databases by comparing their sizes, their taxonomic coverage, and the properties of their models using quantitative metrics. Subsequently, we assessed their performance in virus identification across multiple application scenarios, utilizing both simulated and real metagenomic data. We aim to offer researchers a thorough and critical assessment of the strengths and limitations of different databases. Furthermore, based on the experimental results obtained from the simulated and real metagenomic data, we provided practical suggestions for users to optimize their use of pHMM databases, thus enhancing the quality and reliability of their findings in the field of viral metagenomics.

A set of nematode rRNA cistron databases and a primer assessment tool to enable more flexible and comprehensive metabarcoding.

The ITS-2-rRNA has been particularly useful for nematode metabarcoding but does not resolve all phylogenetic relationships, and reference sequences are not available for many nematode species. This is a particular issue when metabarcoding complex communities such as wildlife parasites or terrestrial and aquatic free-living nematode communities. We have used markerDB to produce four databases of distinct regions of the rRNA cistron: the 18S rRNA gene, the 28S rRNA gene, the ITS-1 intergenic spacer and the region spanning ITS-1_5.8S_ITS-2. These databases comprise 2645, 254, 13,461 and 10,107 unique full-length sequences representing 1391, 204, 1837 and 1322 nematode species, respectively. The comparative analysis illustrates the complementary value but also reveals a better representation of Clade III, IV and V than Clade I and Clade II nematodes in each case. Although the ITS-1 database includes the largest number of unique full-length sequences, the 18S rRNA database provides the widest taxonomic coverage. We also developed PrimerTC, a tool to assess primer sequence conservation across any reference sequence database, and have applied it to evaluate a large number of previously published rRNA cistron primers. We identified sets of primers that currently provide the broadest taxonomic coverage for each rRNA marker across the nematode phylum. These new resources will facilitate more comprehensive metabarcoding of nematode communities using either short-read or long-read sequencing platforms. Further, PrimerTC is available as a simple WebApp to guide or assess PCR primer design for any genetic marker and/or taxonomic group beyond the nematode phylum.

The potential of acoustic monitoring of aquatic insects for freshwater assessment.

Aquatic insects are a major indicator used to assess ecological condition in freshwater environments. However, current methods to collect and identify aquatic insects require advanced taxonomic expertise and rely on invasive techniques that lack spatio-temporal replication. Passive acoustic monitoring (PAM) is emerging as a non-invasive complementary sampling method allowing broad spatio-temporal and taxonomic coverage. The application of PAM in freshwater ecosystems has already proved useful, revealing unexpected acoustic diversity produced by fishes, amphibians, submerged aquatic plants, and aquatic insects. However, the identity of species producing sounds remains largely unknown. Among them, aquatic insects appear to be the major contributor to freshwater soundscapes. Here, we estimate the potential number of soniferous aquatic insects worldwide using data from the Global Biodiversity Information Facility. We found that four aquatic insect orders produce sounds totalling over 7000 species. This number is probably underestimated owing to poor knowledge of aquatic insects bioacoustics. We then assess the value of sound producing aquatic insects to evaluate ecological condition and find that they might be useful despite having similar responses in pristine and degraded environments in some cases. Both expert and automated identifications will be necessary to build international reference libraries and to conduct acoustic bioassessment in freshwaters. This article is part of the theme issue 'Towards a toolkit for global insect biodiversity monitoring'.

Detecting the invisible through DNA metabarcoding: The role of gelatinous taxa in the diet of two demersal Antarctic key stone fish species (Notothenioidei)

AbstractGelatinous zooplankton (GZP), i.e., ctenophores, cnidarian medusae, chaetognaths, appendicularians and salps, are considered climate change winners. This becomes particularly obvious in the Southern Ocean, which has undergone a significant shift from a krill‐based to a salp‐based ecosystem over the last decades. A better knowledge on the role of gelatinous invertebrates as prey is needed to predict the impact of such a gelatinous shift. Until recently, GZP was considered as a “trophic dead end”. However, their true importance in diets has remained unresolved due to the rapid digestion of their watery and soft tissues in predators' stomachs. In this study, we want to validate the paradigm shift from GZP being considered as “survival food” to be considered a “regular” prey item for two demersal fish species (Notothenia rossii and N. coriiceps) of Potter Cove, South Shetland Islands, using a multimarker (COI and 18S) metabarcoding approach. We found that GZP taxa commonly occurred in the diets of both species, represented by pelagic tunicates (appendicularians, salps), cnidarians, chaetognaths and ctenophores. Salps were the most abundant prey group, preyed upon by each individual of both species, reaching 98.7% relative read abundance for 18S. We recovered a wide range of different taxa in their diets, from primary producers to highly abundant invertebrates, thus the two nototheniid species can be regarded as “natural samplers” of the ecosystem in study. Finally, we want to point out the importance of multimarker metabarcoding approaches for broad ecological assessments, given the differential amplification and sequencing success of different markers for specific groups and the unequal taxonomic coverage of the reference databases. The output of each marker was highly complementary, since an important prey item such as salps, was only detected with 18S, while other taxa (e.g., Arthropoda) were represented with a higher taxonomic resolution with COI.

In silico assessment of 18S rDNA metabarcoding markers for the characterization of nematode communities.

Nematodes are keystone actors of soil, freshwater and marine ecosystems, but the complexity of morphological identification has limited broad-scale monitoring of nematode biodiversity. DNA metabarcoding is increasingly used to assess nematode diversity but requires universal primers with high taxonomic coverage and high taxonomic resolution. Several primers have been proposed for the metabarcoding of nematode diversity, many of which target the 18S rRNA gene. In silico analyses have a great potential to assess key parameters of primers, including taxonomic coverage, resolution and specificity. Based on a recently-available reference database, we tested in silico the performance of fourteen commonly used and one newly optimized primer for nematode metabarcoding. Most primers showed very good coverage, amplifying most of the sequences in the reference database, while four markers showed limited coverage. All primers showed good taxonomic resolution. Resolution was particularly good if the aim was the identification of higher-level taxa, such as genera or families. Overall, species-level resolution was higher for primers amplifying long fragments. None of the primers was highly specific for nematodes as, despite some variation, they all amplified a large number of other eukaryotes. Differences in performance across primers highlight the complexity of the choice of markers appropriate for the metabarcoding of nematodes, which depends on a trade-off between taxonomic resolution and the length of amplified fragments. Our in silico analyses provide new insights for the identification of the most appropriate primers, depending on the study goals and the origin of DNA samples. This represents an essential step to design and optimize metabarcoding studies assessing nematode diversity.

Data-driven determination of zooplankton bioregions and robustness analysis

Identifying biogeographic regions through cluster analysis of species distribution data is a common method for partitioning ecosystems. Selecting the appropriate cluster analysis method requires a comparison of multiple algorithms. In this study, we demonstrate a data-driven process to select a method for bioregionalization based on community data and test its robustness to data variability following these steps:•We aggregated and curated zooplankton community observations from expeditions in the Northeast Pacific.•We determined the best bioregionalization approach by comparing nine cluster analysis methods using ten goodness of clustering indices.•We evaluated the robustness of the bioregionalization to different sources of sampling and taxonomic variability by comparing the bioregionalization of the overall dataset with bioregionalizations of subsets of the data.The K-means clustering of the log-chord transformed abundance was selected as the optimal method for bioregionalization of the zooplankton dataset. This clustering resulted in the emergence of four bioregions along the cross-shelf gradient: the Offshore, Deep Shelf, Nearshore, and Deep Fjord bioregions. The robustness analyses demonstrated that the bioregionalization was consistent despite variability in the spatial and temporal frequency of sampling, sampling methodology, and taxonomic coverage.

Low coverage of species constrains the use of DNA barcoding to assess mosquito biodiversity

Mosquitoes (Culicidae) represent the main vector insects globally, and they also inhabit many of the terrestrial and aquatic habitats of the world. DNA barcoding and metabarcoding are now widely used in both research and routine practices involving mosquitoes. However, these methodologies rely on information available in databases consisting of barcode sequences representing taxonomically identified voucher specimens. In this study, we assess the availability of public data for mosquitoes in the main online databases, focusing specifically on the two most widely used DNA barcoding markers in Culicidae: COI and ITS2. In addition, we test hypotheses on possible factors affecting species coverage (i.e., the percentage of species covered in the online databases) for COI in different countries and the occurrence of the DNA barcode gap for COI. Our findings showed differences in the data publicly available in the repositories, with a taxonomic or species coverage of 28.4–30.11% for COI in BOLD + GenBank, and 12.32% for ITS2 in GenBank. Afrotropical, Australian and Oriental biogeographic regions had the lowest coverages, while Nearctic, Palearctic and Oceanian had the highest. The Neotropical region had an intermediate coverage. In general, countries with a higher diversity of mosquitoes and higher numbers of medically important species had lower coverage. Moreover, countries with a higher number of endemic species tended to have a higher coverage. Although our DNA barcode gap analyses suggested that the species boundaries need to be revised in half of the mosquito species available in the databases, additional data must be gathered to confirm these results and to allow explaining the occurrence of the DNA barcode gap. We hope this study can help guide regional species inventories of mosquitoes and the completion of a publicly available reference library of DNA barcodes for all mosquito species.

Broadening applications of stochastic patch occupancy models over three decades

AbstractAimStochastic patch occupancy models (SPOMs) are a type of spatial population simulation. They are arguably well‐suited to guide conservation in human‐altered landscapes, but their appropriateness for a wide range of species and landscape types has often been questioned. Here, we provide an overview of how SPOM research has expanded over the last three decades and discuss the untapped potential for these models to inform current conservation strategies.LocationWorldwide.MethodsWe carried out a systematic review of studies that have fitted SPOMs to real species and landscapes. We assessed temporal trends in SPOMs' use in conservation and management studies, their taxonomic and geographic coverage, and the attributes of studied landscapes. We quantitatively and qualitatively evaluated whether the authors' modelling choices reflected the perceived advantages and disadvantages of SPOMs.ResultsThe proportion of SPOMs used to answer conservation questions has increased over time. Questions of where, when and how to conserve have all been addressed, sometimes considering additional aspects such as cost‐effectiveness and climate change. Taxonomic diversity coverage has increased over time, and SPOMs have been used in landscapes with a higher proportion of suitable habitat. They have, however, been predominantly applied in temperate biomes. Few studies have explored parameter extrapolation in taxonomically and ecologically related species with mixed results.Main ConclusionsOver the past three decades, authors have exploited the simplicity and flexibility of SPOMs to answer a broad range of questions with practical implications. The use of SPOMs in less fragmented landscapes, and for an increasing range of taxa, suggests that the strictest definitions of their applicability can be challenged. Stochastic patch occupancy models have untapped potential for informing conservation under climate change. Given the urgent need to plan for large numbers of species with limited data for fitting, SPOMs could better fulfil their potential to guide conservation if parameters could be extrapolated to data‐deficient landscapes and species.