Biodiversity Databases Research Articles

Using biodiversity databases to assess vascular plant diversity in Protected Areas: a case study of Parque Estadual do Forno Grande, Brazil.

The Parque Estadual do Forno Grande is a fully protected area in the southern Espírito Santo State, Brazil. It belongs to the Atlantic Forest domain, with predominantly dense, ombrophilous, seasonal semi-deciduous forests and herbaceous/shrubby vegetation on rock outcrops. The area is recognised as highly important for conservation, designated as a priority biological area for protecting the Atlantic Forest's biodiversity. Although the importance of Protected Areas in conserving the Atlantic Forest biodiversity is unquestionable, it is crucial to understand the floristic patterns within these regions to develop effective conservation strategies. We utilised national online databases to compile species lists containing relevant information about their biodiversity. The updated list of vascular plants recorded in the Parque Estadual do Forno Grande is available in the "Catálogo de Plantas das Unidades de Conservação do Brasil" and it is presented here with further information on richness, endemism and conservation status. The Parque Estadual do Forno Grande harbours 958 species of vascular plants, of which 79.2% are angiosperms, 18.4% are ferns and 2.4% are lycophytes. Amongst these species, 44% are endemic to the Atlantic Forest. There are 58 threatened species, of which six are Critically Endangered, 39 are Endangered and 13 are Vulnerable. Amongst the threatened species, 51 are endemic to the Atlantic Forest. The number of records and the species richness in this area are notably high for Atlantic Forest standards. Our findings suggest that floristic inventories of Brazilian Protected Areas are a key contribution to the general perception of how much we still do not know about our flora. It also highlights the necessity of supporting floristic surveys in poorly-known areas, especially those remaining as forest remnants.

Revision of the nomenclature status and taxonomic implications of two Lepidion species (Gadiformes: Moridae)

Lepidion lepidion and Lepidion eques are two nominal species of the genus Lepidion (Moridae) from the Mediterranean Sea and the North Atlantic Ocean, respectively. Following the publication of the latter species, several authors highlighted the morphological similarities between them, questioning their taxonomic relationship. Despite these reasonable doubts, the two species have long been considered as valid and separate species. Since the 2010s, a series of integrative studies, combining morphological and molecular analyses, have demonstrated that L. eques is a junior synonym of L. lepidion. However, the former has continued to be used inconsistently in biodiversity databases and ichthyological literature. Thus, while the “Catalog of fishes” immediately incorporated this new status, the databases “FishBase” and “WoRMS” did not, maintaining the validity of both species. Consequently, in the scientific literature, only a few authors adhere to the synonymy relationship, naming the Atlantic species as L. lepidion, while most maintain the older nomenclature of L. eques. These two nominal species represent an interesting case study on the application of taxonomic nomenclature and how the different criteria for incorporating new species affect the scientific community.

A morphological and high throughput sequencing workflow to identify Australian ants (Hymenoptera, Formicidae): a new tool for biosecurity and biodiversity

Ants are often the most ubiquitous and ecologically influential components of terrestrial systems, exhibiting an exceptionally high level of endemic diversity. Simultaneously, exotic ants can be amongst the most environmentally and economically devastating biological invaders. Distinguishing between exotic and related natives is essential for early detection and to reduce the chance of establishment, but at the species-level there remains a great deal of uncertainty among several of the most diverse, widespread and ecologically dominant genera. This taxonomic impediment negatively impacts the use of molecular techniques relying on reference databases, due to the poor state of ant DNA sequences in publicly available repositories, with many species not represented at all and others incorrectly identified. As a result, biosecurity screening for targeted exotic ants and assigning ant species-level identifications for biodiversity remain two separate areas of focus in Australia. Here we propose a workflow for the identification of ants that enables simultaneous processing of large numbers of “bulk” ant samples each containing many individuals, increasing resolution for taxonomic assignment, and generating a curated database linked to voucher specimens. We use a non-destructive DNA extraction method and compare two high throughput sequencing (HTS) metabarcoding platforms – MiSeq (Illumina) and MinION (Oxford Nanopore Technologies) – processing up to 180 bulk mixed ant samples per run. This approach allowed for the acquisition of curated DNA sequences from voucher specimens morphologically examined by expert taxonomists. This work highlights the advantages and current limitations of DNA-based identifications, the needs for standardisation, as well as the importance of a taxonomy-based curation of DNA database for both biodiversity and biosecurity.

Farmland Birds and their Importance in Agro ecosystem: A Review

Avian fauna provide a variety of functions, including predators, pollinators, scavengers, seed dispersers, pests controller, nutrient cycling, ecosystem engineers, and many others. Birds play important ecological and economic functions however they are sometimes overlooked simply because of a lack of knowledge. However, as bird populations drop globally, so do the ecological advantages given by these species. To support bird conservation, this review study focuses on the role of birds in the agro-ecosystem and their benefits to humans. Biodiversity databases and existing literature were reviewed to establish baseline information on farmland bird species and their preferences. Searches were limited to articles published between 2005 to 2024. Healthy bird populations and habitats would help to safeguard a variety of ecological functions, ultimately benefiting human health. Farmland birds are disappearing. Due to the widespread use of pesticides, lack of habitat, birds and other animals are disappearing and unnecessary harmful pest species are increasing and the agricultural environment is deteriorating. So, this review paper tries to emphasize on urgent conservation measures that are necessary for the protection of agricultural birds which are essential for the health of both natural and agricultural environments.

The Neotropical Biodiversity Mapping Initiative: Transforming Venezuelan biodiversity monitoring and capacity building

Tropical Latin America is home to an enormous share of the world's biodiversity. Despite its immense natural wealth, the region faces a significant deficit of reliable biodiversity data and lacks the local capacity necessary to collect such data. The Neotropical Biodiversity Mapping Initiative (NeoMaps or NeoMapas) is a long-term biodiversity monitoring program. NeoMaps has not only addressed these gaps in biodiversity data in one of the megadiverse tropical countries, Venezuela, but has also emerged as a model for efficiently surveying biodiversity while strengthening the local capacity needed to conduct these surveys. After three nationwide systematic surveys and international field courses in 2006, 2009, and 2010, NeoMaps assembled an invertebrate collection and biodiversity database with over 170,000 records of occurrence and abundance for birds, dung beetles, and butterflies. NeoMaps activities lead to direct outcomes by reducing biodiversity knowledge gaps for three taxonomic groups and training more than 60 conservationists from Venezuela, Colombia, Mexico, Peru, Bolivia, Brazil, Uruguay, and Spain. NeoMaps had a broader impact on national capacity building programs, and made important contributions for improving, sharing and applying national biodiversity knowledge.

The relational modeling of hierarchical data in biodiversity databases.

The unifying element of all biodiversity data is the issue of taxon hierarchy modeling. We compared 25 existing databases in terms of handling taxa hierarchy and presentation of this data. We used documentation or demo installations of databases as a source of information and next in line was the analysis of structures using R packages provided by inspected platforms. If neither of these was available, we used the public interface of individual databases. For almost half (12) of the databases analyzed, we did not find any formalized taxa hierarchy data structure, providing only biological information about taxon membership in higher ranks, which is not fully formalizable and thus not generally usable. The least effective Adjacency List model (storing parentId of a taxon) dominates among the remaining providers. This study demonstrates the lack of attention paid by current biodiversity databases to modeling taxon hierarchy, particularly to making it available to researchers in the form of a hierarchical data structure within the data provided. For biodiversity relational databases, the Closure Table type is the most suitable of the known data models, which also corresponds to the ontology concept. However, its use is rather sporadic within the biodiversity databases ecosystem.

Detailed biogeographical mapping as a useful novel tool for the conservation of endemic taxa: a case of study for Iberian orchids

Background Iberian orchids occur in plant communities designated as habitats of interest in the European Union, particularly in Mediterranean forests. Their ecological importance highlights the need for a deeper understanding of their distribution and ecological requirements in order to develop effective conservation and management policies. Methods This study focuses on the biogeographical mapping and characterisation of five Iberian and Balearic endemic orchid species at district level. Distribution data were collected from existing biodiversity databases and integrated into a Geographic Information System (GIS). In order to assign the correct biogeographical epithet to each taxon, a set of rules and criteria was developed to ensure an objective, simple and universal classification based on the species' distribution areas. Results For each orchid species, the study identified its phytosociological assignment, bioclimatic range and current conservation status. Detailed maps were produced, providing insights into the biogeographical, bioclimatic and phytosociological attributes of these taxa. Conclusions The biogeographical mapping and ecological classification presented in this study provide a basis for effective decision-making regarding the conservation and management of these orchid species. In addition, the results can be used to update their conservation status to better reflect their ecological needs and threats.

Addressing multiple facets of bias and uncertainty in continental scale biodiversity databases

The availability of biodiversity databases is expanding at unprecedented rates. Nevertheless, species occurrence data can be intrinsically biased and contain uncertainties that impact the accuracy and reliability of biodiversity estimates. In this study, we developed a reproducible framework to assess three dimensions of bias—taxonomic, spatial, and temporal—as well as temporal uncertainty associated with data collections. We utilized the vegetation plot data located in Europe, from sPlotOpen, an open-access database, as a case study. The metrics proposed for estimating bias include completeness of the species richness for taxonomic bias, Nearest Neighbor Index for spatial bias, and Pielou’s index for temporal bias. Additionally, we introduced a new method based on a negative exponential curve to model the temporal decay in biodiversity data, aiming to quantify temporal uncertainty. Finally, we assessed the sampling bias considering the influence of various spatial variables (i.e, road density, human population count, Natura 2000 network and topographic roughness). We discovered that the facets of bias and the temporal uncertainty varied throughout Europe, as did the different roles played by spatial variables in determining biases. sPlotOpen showed a clustered distribution of the vegetation plots, and an uneven distribution in sampling completeness, year of sampling and temporal uncertainty. The facets of bias were significantly explained mainly by the presence of Natura 2000 network and marginally by the human population count. These results suggest that employing an efficient procedure to examine biases and uncertainties in data collections can enhance data quality and provide more reliable biodiversity estimates.

Aspects of NCBI GenBank as a Biodiversity Information Resource

DNA sequencing of museum specimens, also known as museomics, provides new insights into the study of biodiversity, including taxonomy, phylogeny, and environmental studies. Also, sequencing specimens have led to the rediscovery of extinct species (Suzuki et al. 2016), identification of related species (Waku et al. 2016), and analysis of ancient DNA (Kanzawa-Kiriyama et al. 2016). Nucleotide sequence data have been collected for more than 30 years under the framework of the International Nucleotide Sequence Database Collaboration (INSDC) by three institutes, namely, National Center for Biotechnology Information, US (NCBI), European Bioinformatics Institute (EBI), and DNA Data Bank of Japan (DDBJ) (Arita et al. 2020). NCBI has collated a database of sequence data, GenBank, which contains approximately 494 million sequences as of April 2022 (Sayers et al. 2021). In fact, GenBank is designed with qualifiers to describe various types of biodiversity information such as "/specimen_voucher", "/lat_lon" (latitude and longitude) and "/collection_date". Also, INSDC now requires that all submissions include the sampling location and date (INSDC 2023). I surveyed the biodiversity information assigned to GenBank records to determine the potential of GenBank as a biodiversity resource. I downloaded all GenBank data as of August 2023 from the FTP site. The “/specimen_voucher” qualifier was introduced to describe specimen ID in Release 104 in December 1997. This qualifier was designed to fill the value in free text: for example, /specimen_voucher="Smith s. n. 4-IV-1995 (U. S. Natl. Herbarium)". After Release 162 in October 2007, a method of writing with a structured value of "[<institution-code>: [<collection-code>:]] <specimen_id>" was added (institution-code and collection-code are optional). There are 527,215 records (37.8%) with "/specimen_voucher" qualifier for fish, 3,096,112 records (40.3%) for insects, 1,505,556 records (39.0%) for flowering plants. But fewer than 10% of records have specimen IDs listed using this structured description. To utilize these ambiguous specimen IDs in GenBank, these IDs may need to be cleansed using databases such as NCBI BioCollections, GRSciColl (Global Registry of Scientific Collections) or AI to map them to IDs in databases rich in specimen information such as those of the Global Biodiveristy Information Facility (GBIF) and Barcode of Life System (BOLD). In GenBank, the BOLD ID is listed in the /db_xref qualifier in the “Features” field as the ID of the external database. The 70% of insect sequence data with a specimen ID in the /specimen_voucher qualifier are also assigned a BOLD ID (Nakazato and Jinbo 2022). The correspondence between specimen IDs in biodiversity information databases such as GBIF and specimen IDs in GenBank is expected to further enhance the value of museum specimens. In addition, GenBank provides the /type_material qualifier for describing the type of voucher (e.g., holotype of Asphondylia bursicola). In GenBank insect data, there were over 2,000 records for type material, and approximately 450 species were mentioned, including 269 for holotypes. We found approximately 3,000 records with type information by including “/notes” and “/specimens_voucher” qualifiers in addition to “/type_material”. Thus, GenBank has potential as a biodiversity information resource, but for more effective use, data mining and linkage with other specimen-based biodiversity databases are essential.

O (DES)CONHECIMENTO DA BIODIVERSIDADE: UMA SISTEMATIZAÇÃO SOBRE LACUNAS, LIMITAÇÕES, VIESES, DÉFICITS E RUÍDOS

With the advancements in bioinformatics and ecoinformatics tools, it has become feasible to utilize vast amounts of biodiversity information to describe biological patterns and attempt to assess the ecological and evolutionary processes underlying them, as well as to establish more effective and comprehensive conservation actions. However, existing information regarding biodiversity remains incomplete, with gaps, limitations, biases, deficits, and noise. In this regard, we acknowledge the need to discuss issues related to the use of large biodiversity databases and their quality, discussions that need to be conceptually structured. In this text, we will systematically describe the gaps, limitations, and biases in biodiversity knowledge, issues that are directly associated with the acquisition of species information in nature. Subsequently, we will outline the types of deficits and noise, which are problems associated with biodiversity databases. This is because the information present in primary records and large databases is frequently used inadequately. Additionally, we also point out perspectives on how to address these deficiencies in ecological/biogeographical work through appropriate database curation and the construction of maps of ignorance. Finally, we highlight future challenges, such as the need for new data collections, the training of new taxonomists, and the provision of financial support for the infrastructure and digitization of biological collections.

Shallow coverage in shallow waters: the incompleteness of intertidal species inventories in biodiversity database records

Shallow coverage in shallow waters: the incompleteness of intertidal species inventories in biodiversity database records

Utilizing a Dashboard for Efficient Biodiversity Data Overview and Gap-Filling Effort

Taiwan Biodiversity Information Facility has been leading the effort to integrate and mobilize biodiversity data nationally. We recently accomplished the integration of local databases and successfully developed a data portal that efficiently links to the most comprehensive biodiversity database in Taiwan: the Taiwan Biodiversity Information Alliance Data Portal. However, we identified an emerging challenge following this development. Preliminary analyses have revealed several gaps in the current dataset, impeding robust data use. For instance, land data dominates over sea data, and bird records are more abundant than those of other taxonomic groups. In our endeavour to enhance national biodiversity data coverage, we are actively exploring methodologies to address these existing data gaps. Here, we broadly define data gap as the absence of required data or information for use. Our primary objective is to empower users to identify these gaps, thereby facilitating efficient, informed survey planning and eventually filling these gaps. For this purpose, we are evaluating the effectiveness of a user-friendly dashboard, tailored for biodiversity survey planning in Taiwan. We developed and deployed a R Shiny dashboard*1 that provides users with insightful data visualizations that highlight spatial, temporal, and taxonomical data overviews. It also offers customizable filtering options, such as by major taxon groups and habitat types, for easy viewing. Additionally, the dashboard includes a download function, so users can access spatial and taxon gap information in their survey planning efforts. After deploying the dashboard, we conducted user interviews to collect feedback aimed at refining its usability and effectiveness. In addition to helping survey planning, we anticipate that this tool will also aid data users in promptly assessing data integrity within the national biodiversity data portal, thereby enabling them to identify potential data gaps and biases that may affect subsequent use. Through this presentation, we aim to share our experience in developing an interactive dashboard tailored for public use. Preliminary results had indicated that the dashboard highlighted some visible data gaps and biases, particularly in underrepresented areas such as marine habitats and less-studied taxonomic groups. Additionally, user interviews revealed a demand for a feature that provides single species data overviews, suggesting a potential area for further development to enhance the tool's utility. Some challenges remain, such as the need to enhance data granularity and user interface usability. Future work will focus on incorporating more real-time data integration and expanding the range of customizable filters. We believe these efforts will further empower users in Taiwan to conduct more informed and efficient biodiversity surveys, ultimately supporting research and policy-making to address critical biodiversity data gaps.

Cymbella stomachsis sp. nov. (Bacillariophyta; Cymbellaceae), a new species from Guangdong Province, China

A new diatom species from the genus Cymbella C. Agardh is described from samples collected during a survey of freshwater diatoms from Modaomen Channel, Guangdong Province, China. With the aid of light microscopy (LM) and scanning electron microscopy (SEM), we give a detailed morphological description of Cymbella stomachsis sp. nov., which is placed in the genus Cymbella according to the shared features of asymmetry about the apical axis, deflection of the external terminal raphe fissures towards the dorsal margin, and the presence of apical pore fields and stigmata. Although it shares some similar structural features with C. tumida, C. stuxbergii, C. stuxbergioides, C. pesudostuxbergii, C. mexicana and C. australica, C. stomachsis sp. nov. is easily distinguished by the valve outline, the shape and density of areola, and the appearance of a lack of an intermissio at the central nodule. Especially, the structure of the intermissio is absent in similar taxa. This work is important for its enrichment of our understanding of the genus Cymbella and improvement of the database of diatom biodiversity and distribution in China.

Herpetofauna of Laguna Blanca National Park, Argentinean Patagonia: species list and conservation status

Laguna Blanca National Park (LBNP) is located in the mid-west of Neuquén Province, Argentina. It was created in 1940 with the aim of conserving the nesting and breeding habitats of an important diversity of birds. Until now, there have been no exclusive works that address the herpetofauna present. The aim of this article is to provide an updated inventory of reptile and amphibian species in LBNP. We used four sources of information to create the species list: 1) data coming from field observations; 2) specimens deposited in herpetological collections; 3) scientific literature review; 4) online biodiversity databases. We confirm the occurrence of 18 species of herpetofauna in LBNP, including 13 reptiles and 5 amphibians. We also included six species with probable presence according to the range of distribution and habitat similarity. We added the conservation status of the national and international lists for each species. Five species are in some threat category at the national (Vulnerable, Endangered) or international level (Endangered, Critically Endangered). Seven taxa are listed as “Species of Vertebrates of Special Value” by the Administración de Parques Nacionales. Despite being protected within a national park, the herpetofauna present face threats such as prolonged drought events, habitat modification due to the presence of livestock, introduced exotic species, and emerging diseases. Conservation efforts are imperative to protect these species and mitigate their threats.

PhyloNext: a pipeline for phylogenetic diversity analysis of GBIF-mediated data

BackgroundUnderstanding biodiversity patterns is a central topic in biogeography and ecology, and it is essential for conservation planning and policy development. Diversity estimates that consider the evolutionary relationships among species, such as phylogenetic diversity and phylogenetic endemicity indices, provide valuable insights into the functional diversity and evolutionary uniqueness of biological communities. These estimates are crucial for informed decision-making and effective global biodiversity management. However, the current methodologies used to generate these metrics encounter challenges in terms of efficiency, accuracy, and data integration.ResultsWe introduce PhyloNext, a flexible and data-intensive computational pipeline designed for phylogenetic diversity and endemicity analysis. The pipeline integrates GBIF occurrence data and OpenTree phylogenies with the Biodiverse software. PhyloNext is free, open-source, and provided as Docker and Singularity containers for effortless setup. To enhance user accessibility, a user-friendly, web-based graphical user interface has been developed, facilitating easy and efficient navigation for exploring and executing the pipeline. PhyloNext streamlines the process of conducting phylogenetic diversity analyses, improving efficiency, accuracy, and reproducibility. The automated workflow allows for periodic reanalysis using updated input data, ensuring that conservation strategies remain relevant and informed by the latest available data.ConclusionsPhyloNext provides researchers, conservationists, and policymakers with a powerful tool to facilitate a broader understanding of biodiversity patterns, supporting more effective conservation planning and policy development. This new pipeline simplifies the creation of reproducible and easily updatable phylogenetic diversity analyses. Additionally, it promotes increased interoperability and integration with other biodiversity databases and analytical tools.

Study on the Diversity and Distribution of Spider Fauna at Sree Krishna College Campus of Thrissur District, Kerala, India

Field survey was conducted to record the diversity of spiders at different sites in the Sree Krishna College Campus of Thrissur district during September 2022 to February 2023. Around 51 species of spiders belonging to 36 genera under 14 families were recorded. Salticidae family was represented with twelve species followed by Araneidae (10 sps.), Oxyopidae (5 sps.), Theridiidae (4 sps.), Lycosidae, (3 sps.), Tetragnathidae (3 sps.) and Sparassidae (3 sps.), Thomisidae (2 sps.), Pholcidae (2 sps.). But, Hersilidae, Linyphiidae, Uloboridae, Cheiracanthiidae and Sicariidae family members were very less. Spider population in different sites exhibited variation in species abundance and richness. Shannon index, Simpson index, Margalef Richness index, Berger-Parker index and Menhinick’s Index evaluated were 3.423, 0.9580, 9.540, 0.9101and 3.709 respectively. The abundance and percent occurrence of different spider species revealed variation in their distribution. For the study the entire campus has been surveyed, by dividing the area into four sites, Site A, Site B, Site C and Site D. Species composition and diversity indices studies revealed that more diversity in the site C followed by Site D, Site B and Site A. These types of surveys are important for the study of the prevalence of the spider population in given habitats and to create a biodiversity database of spider.

RARE SPECIES OF FIRE FLIES (LEPIDOPTERA, PYRALOIDEA) OF THE HETMANSKYI NATIONAL NATURE PARK

Hetmanskyi National Nature Park is one of two national parks created in Sumy region. The Park, located in Okhtyrka district of the south-eastern part of Sumy region, reaches a total area of 23 360,1 ha, including 11 673,2 ha of land provided for permanent use. The article presents the results of research on the species composition of fire flies in the Hetmanskyi National Nature Park, conducted from 2016 to 2023. As a result, 120 species of fire flies from 10 subfamilies were identified, making this area one of the most studied in the north-east of Ukraine. Most of these species are widespread in the region. Among them, 13 species had not been recorded in Sumy region before this study: Synaphe punctalis (Fabricius, 1775), Elegia fallax (Staudinger, 1881), Pempelia palumbella (Denis & Schiffermüller, 1775), Acrobasis glaucella Staudinger, 1859, Phycitodes saxicola Vaughan, 1870, Elegia similella Zincken, 1818, Homoeosoma inustella Ragonot, 1884, Cadra furcatella (Herrich-Schäffer, 1849), Chrysocrambus craterella (Scopoli, 1763), Catoptria mytilella (Hubner, 1805), Atralata albofascialis (Treitschke, 1829), Pyrausta rectefascialis Toll, 1936, Pyrausta aerealis (Hübner, 1793). The article provides information on these species, including their distribution in Europe and Ukraine (representation in the GBIF and UkrBIN global biodiversity databases) and our findings in the Park, as well as some biological and ecological features. The article notes that insect species from the steppe zone and the Black Sea region are increasingly being registered in Sumy region. Species from more southern regions of Ukraine may be expanding their range due to climate change and vegetation succession in the Park, in particular due to the invasion of alien plants. In general, the species composition of fire flies on the territory of the Park has been studied unevenly so these results do not reflect the full picture of fire flies fauna of the Park and require further research.

The Biodiversity of Blackflies (Diptera: Simuliidae) in Brazil: New Distribution Records and Updated Checklist.

Currently, according to the most recent Simuliidae World Inventory, there are 97 valid species of blackflies recorded in Brazil, some of which act as vectors for zoonoses such as human onchocerciasis and mansonellosis in the northern and central-western regions of the country. Meanwhile, other species can cause serious socioeconomic problems due to the nuisance of female bites. Therefore, accurate knowledge of their distribution is crucial for the development and implementation of successful preventive strategies. With this aim, this study reviewed and updated the geographical distribution of the blackfly fauna throughout the Brazilian states. The data were compiled from three main sources: geographic information of material deposited at the Simuliidae Collection of the Instituto Oswaldo Cruz (CSIOC-IOC), a comprehensive review of scientific literature, and online biodiversity databases. We present a total of 71 new distribution records of 38 different Simuliidae species for 24 Brazilian states. Neither of these sets of records has been included in the Simuliidae World Inventory. Consequently, an updated Brazilian Simuliidae checklist, comprising a total of 98 valid species, is presented, highlighting these new distribution records. We also discuss six dubious records for the country and the implications of this updated data for the Simuliidae species richness of Brazil, its states, and biomes. This information is essential for future studies in the taxonomy, systematics, and biogeography of this family in Brazil.

Beta diversity and regionalization of the western Atlantic marine biota

AbstractAimUnderstanding the factors determining marine community variations is important for biogeography and conservation. Beta diversity is a metric for mapping species composition variations between communities and regionalizing biota. Ecoregions are commonly used for regionalization, but their empirical testing has been limited. Our aim is to map marine species composition variations in the Western Atlantic, identify variables related to these variations, and regionalize areas based on community distribution. Additionally, we test whether currently proposed ecoregions represent unique biota units and specific environmental conditions.LocationWestern Atlantic Ocean.TaxonVertebrates, invertebrates and algae.MethodsWe constructed a large marine biodiversity database, including vertebrates, invertebrates, and algae, totalling over 4 million records. We used the generalized dissimilarity model (GDM) to identify variables most related to species composition variations and map beta‐diversity variations. We employed an unsupervised classifier for community regionalization. To test if the ecoregion regionalization boundaries are corroborated by species distribution data, we used the Sørensen index. To assess if ecoregions correspond to environmental units, we checked if areas had distinct environmental conditions using a PCA of 134 marine environmental variables.ResultsThe GDM explained a high variation in species composition, 61% in the complete database. Analysing vertebrates, invertebrates and algae separately also yielded relatively high results: 46%, 54%, and 33%, respectively. Coastal areas differed from open sea areas in composition. Environmental variables combined better explained beta diversity than isolated variables. The regionalization based on GDM was not congruent with ecoregion boundaries. Moreover, ecoregions showed no distinction in species composition or environmental conditions.Main ConclusionsThis study's regionalization is crucial for marine biodiversity conservation, focusing on understanding species composition patterns between coastal and open sea areas to develop tailored conservation strategies. Despite sampling limitations, the study advances marine biogeography knowledge by analysing over 4 million species records and 134 environmental variables. This comprehensive approach enhances understanding marine species distribution and diversity and aiding the development of effective conservation measures.

How taxonomic change influences forecasts of the Linnean shortfall (and what we can do about it)?

AbstractThe gap between the number of described species and the number of species that actually exist is known as the Linnean shortfall and is of fundamental importance for biogeography and conservation. Unsurprisingly, there have been many attempts to quantify its extent for different taxa and regions. In this Perspective, we argue that such forecasts remain highly problematic because the extent of the shortfall does depend not only on the rates of exploration (sampling undescribed taxa) on which estimates have been commonly based but also on the rates of taxonomic change (lumping and splitting). These changes highly depend on the species concepts adopted and the information and methods used to delimit species. Commonly used methods of estimating the number of unknown species (e.g. discovery curves, taxon ratios) can underestimate or overestimate the Linnean shortfall if they do not effectively account for trends and rates of taxonomic change. A further complication is that the history of taxonomic change is not well documented for most taxa and is not typically available in biodiversity databases. Moreover, wide geographic and taxonomic variation in the adoption of species concepts and delimitation methods mean that comparison of estimates of the Linnean shortfall between taxa and even for the same taxon between regions may be unreliable. Given the high likelihood of future taxonomic changes for most major taxa, we propose two main strategies to consider the influence of taxonomic change on estimates of unknown species: (i) a highly conservative approach to estimating the Linnean shortfall, restricting analysis to groups and regions where taxonomies are relatively stable and (ii) explicitly incorporating metrics of taxonomic change into biodiversity models and estimates. In short, relevant estimates of the number of known and unknown species will only be achieved by accounting for the dynamic nature of the taxonomic process itself.