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Biotic responses to global change include directional shifts in organismal traits. Body size, an integrative trait that determines demographic rates and ecosystem functions, is thought to be shrinking in the Anthropocene. Here, we assessed the prevalence of body size change in six taxon groups across 5025 assemblage time series spanning 1960 to 2020. Using the Price equation to partition this change into within-species body size versus compositional changes, we detected prevailing decreases in body size through time driven primarily by fish, with more variable patterns in other taxa. We found that change in assemblage composition contributes more to body size changes than within-species trends, but both components show substantial variation in magnitude and direction. The biomass of assemblages remains quite stable as decreases in body size trade off with increases in abundance.

Identifying the drivers and processes that determine globally the geographic range size of species is crucial to understanding the geographic distribution of biodiversity and further predicting the response of species to current global changes. However, these drivers and processes are still poorly understood, and no ecological explanation has emerged yet as preponderant in explaining the extent of species' geographical range. Here, we identify the main drivers of the geographic range size variation in freshwater fishes at global and biogeographic scales and determine how these drivers affect range size both directly and indirectly. We tested the main hypotheses already proposed to explain range size variation, using geographic ranges of 8,147 strictly freshwater fish species (i.e., 63% of all known species). We found that, contrary to terrestrial organisms, for which climate and topography seem preponderant in determining species' range size, the geographic range sizes of freshwater fishes are mostly explained by the species' position within the river network, and by the historical connection among river basins during Quaternary low-sea-level periods. Large-ranged fish species inhabit preferentially lowland areas of river basins, where hydrological connectivity is the highest, and also are found in river basins that were historically connected. The disproportionately high explanatory power of these two drivers suggests that connectivity is the key component of riverine fish geographic range sizes, independent of any other potential driver, and indicates that the accelerated rates in river fragmentation might strongly affect fish species distribution and freshwater biodiversity., Competing Interests: The authors declare no conflict of interest.

This study reports length-weight relationships for 38 fish species belonging to 18 families inhabiting the Magdalena River floodplain lakes of Colombia. Samples were taken during the high water season of 2008, 2010 and 2011. Two species are presented for the first time. Maximum total length records for 24 species exceed those in FishBase. [ABSTRACT FROM AUTHOR]

Ferroptosis is a newly discovered form of cell death caused by the peroxidation of fragile fatty acids in cell membranes, which combines with iron to increase reactive oxygen species and disable mitochondria. Ferroptosis has been linked to aging-related conditions, including type 2 diabetes, cardiovascular disease, and nonalcoholic fatty liver disease (NAFLD). Pentadecanoic acid (C15:0), an odd-chain saturated fat, is an essential fatty acid with the primary roles of stabilizing cell membranes and repairing mitochondrial function. By doing so, C15:0 reverses the underpinnings of ferroptosis. Under the proposed "Cellular Stability Hypothesis", evidence is provided to show that cell membranes optimally need >0.4% to 0.64% C15:0 to support long-term health and longevity. A pathophysiology of a newly identified nutritional C15:0 deficiency syndrome ("Cellular Fragility Syndrome") is provided that demonstrates how C15:0 deficiencies (≤0.2% total circulating fatty acids) can increase susceptibilities to ferroptosis, dysmetabolic iron overload syndrome, type 2 diabetes, cardiovascular disease, and NAFLD. Further, evidence is provided that C15:0 supplementation can reverse the described C15:0 deficiency syndrome, including the key components of ferroptosis. Given the declining dietary intake of C15:0, especially among younger generations, there is a need for extensive studies to understand the potential breadth of Cellular Fragility Syndrome across populations. [ABSTRACT FROM AUTHOR]

Here we present 'APCalign', an R package and accompanying browser-sourced application to align and update scientific names for Australian vascular plants to the most likely currently accepted name in the Australian Plant Census (APC) or a name in the Australian Plant Names Index (APNI). Scientific names are the label assigned to unique taxon concepts by the scientific community, but this common terminology is most useful if a taxon concept is consistently referred to by the same name. These links can be broken because of either spelling mistakes or taxonomic changes. Automated tools are required to resolve taxon lists, aligning and updating long lists of possibly erroneous scientific names to the most likely currently accepted names. It is essential that tools specific to the APC/APNI be developed, because these lists specify an endorsed national-level nomenclature used in government legislation and include the uniquely Australian concept of phrase names, absent in global taxonomic datasets. To align input names to names within the APC or APNI, 'APCalign' works progressively through a sequence of checks that combine different permutations of the input name, exact versus fuzzy matches, matches that consider the entire name input versus a subset of words, and character strings that indicate a name can be resolved only to a genus or family. The aligned names are then, when possible, updated to a currently accepted taxon concept within the APC. This package should facilitate all research outputs that require diverse scientific name lists to be merged or outdated lists to be updated. To facilitate communication, research projects, biodiversity assessments and nurseries across Australia should use the scientific names accepted by the Australian Plant Census (APC), Australia's national taxonomic standard for vascular plants. Here we present 'APCalign', an R package and browser-sourced application to efficiently align and update lists of scientific names for Australian vascular plants to the most likely currently accepted name. This package will be useful for all research outputs that require diverse scientific name lists to be updated. Image by Elizabeth Wenk. [ABSTRACT FROM AUTHOR]

Animal trait data are scattered across several datasets, making it challenging to compile and compare trait information across different groups. For plants, the TRY database has been an unwavering success for those ecologists interested in addressing how plant traits influence a wide variety of processes and patterns, but the same is not true for most animal taxonomic groups. Here, we introduce ZooTraits, a Shiny app designed to help users explore and obtain animal trait data for research in ecology and evolution. ZooTraits was developed to tackle the challenge of finding in a single site information of multiple trait datasets and facilitating access to traits by providing an easy‐to‐use, open‐source platform. This app combines datasets centralized in the Open Trait Network, raw data from the AnimalTraits database, and trait information for animals compiled by Gonçalves‐Souza et al. (2023, Ecology and Evolution 13, e10016). Importantly, the ZooTraits app can be accessed freely and provides a user‐friendly interface through three functionalities that will allow users to easily visualize, compare, download, and upload trait data across the animal tree of life—ExploreTrait, FeedTrait, and GetTrait. By using ExploreTrait and GetTrait, users can explore, compare, and extract 3954 trait records from 23,394 species centralized in the Open Traits Network, and trait data for ~2000 species from the AnimalTraits database. The app summarizes trait information for numerous taxonomic groups within the Animal Kingdom, encompassing data from diverse aquatic and terrestrial ecosystems and various geographic regions worldwide. Moreover, ZooTraits enables researchers to upload trait information, serving as a hub for a continually expanding global trait database. By promoting the centralization of trait datasets and offering a platform for data sharing, ZooTraits is facilitating advancements in trait‐based ecological and evolutionary studies. We hope that other trait databases will evolve to mirror the approach we have outlined here. [ABSTRACT FROM AUTHOR]

Ecology increasingly relies on a massive volume of biodiversity occurrence records to draw insights into large‐scale biogeographical, ecological and evolutionary phenomena. This often involves defining a set of criteria that guides the collection, filtering and standardising of available records. These curation processes are often neither described in detail nor well documented. This hampers the comparability and reproducibility of studies and thus undermines the robustness of any ecological result. Yet, to date, there is no guide providing a friendly way to reason and document a complete data curation process.We reviewed the available literature on data curation, including tools such as R packages and workflows. From this assessment, we created a complete guide organised into five modules that allows users to consciously select and validate occurrence records based on these curation criteria. This is presented in the user‐friendly Shiny R OCCUR application, available at https://ecoinformatic.shinyapps.io/OCCUR/.OCCUR application provides a guide for researchers to deal with the trade‐off between data certainty and coverage generated in each data curation step. An interactive graph of these changes is provided within each module. OCCUR also produces a custom‐made final report including all steps used for data filtering. This report helps to streamline the writing of the methods section of manuscripts and technical reports, thus promoting the reproducibility of data curation processes.This Shiny application provides an interactive overview of the data curation methods and their use for handling occurrence records from public repositories. It brings together the taxonomic, temporal and spatial dimensions of data and also the identification of duplicates of the records. OCCUR can be applied for multiple purposes, such as teaching R to ecologists or enhancing reproducibility of macroecology and biogeography. [ABSTRACT FROM AUTHOR]

This paper presents a use-case conducted within the ENVRI FAIR project, examining challenges and opportunities in deploying FAIR-aligned (ensuring Findability, Accessibility, Interoperability and Reusability) scientific name-matching services across Environmental Research Infrastructures (RIs). Six services were tested using various name variations, revealing inconsistencies in match types, status reporting and handling of canonical forms and typos. These diversities pose challenges for RI data pipelines and interoperability. The paper underscores the importance of standardised tools, enhanced communication, training, collaboration and shared resources. Addressing these needs can facilitate more effective FAIR implementation within the ENVRI community and biodiversity research. This, in turn, will empower RIs to seamlessly integrate and leverage scientific names, unlocking the full potential of their data for research and policy implementation. [ABSTRACT FROM AUTHOR]

Background: The invasion success of introduced freshwater fishes is influenced by many factors, including ecological, species, and socioeconomic characteristics. Most studies that document the importance of these characteristics are conducted at local scales and/or focus on a single step of the invasion process. In this study, we aim to determine the species characteristics, ecological characteristics, and socioeconomic characteristics of non-native freshwater fish invasions. Our assessment was done at the global scale and considers all three steps of the invasion (i.e., introduction, establishment, and impact). For this purpose, we applied generalized linear models to 20 variables collected for 307 non-native species and modeled them as a function of ecological characteristics (i.e., environmental features), species traits (i.e., functional and morphological), and socioeconomic characteristics (i.e., human use and introduction pathways). We considered the number of countries in which each species was introduced, established, or had ecological impacts as a proxy of invasion step success. We also explored the specifics of species introduced through the aquaculture and the ornamental fish trade pathways. Results: We found that non-native freshwater fishes with broad diets, high parental care, and multiple introduction pathways are the most widely introduced and established worldwide. The number of countries with impacts reported was best explained by the type of introduction pathway (i.e., aquaculture or fisheries). Moreover, among non-native species introduced through aquaculture, those belonging to Cypriniformes and having broad diets were the most widely introduced and established species. In contrast, the species introduced through the ornamental fish trade pathway belonged to various taxonomic orders but were mainly native to tropical regions. Conclusions: Considering several types of factors is important when analyzing the invasion success of freshwater fish and disentangling the different invasion steps. These findings have strong implications for anticipating the profile of species with a high potential to invade many countries. [ABSTRACT FROM AUTHOR]

Habitat fragmentation due to dams is a well‐known threat to freshwater fish. Yet, the global consequences of fragmentation for the viability of freshwater fish populations are unknown. Here, we provide the first global assessment of the threats of dams to the persistence of freshwater fish species. We developed a global macroecological relationship between freshwater fish range size and body size and used this relationship to assess whether isolated range fragments are too small to support a species. Our assessment includes 7369 freshwater fish species and considers the effects of 31,780 dams globally. Furthermore, we performed a more detailed analysis of the threats of dams in Brazil, the greater Mekong region and the United States, using complementary national and regional data sets. Globally, more than half of the species analysed face extirpation in a part of their geographic range, with an average potential range loss of 3.3% (95%‐range: 0%–31.8%) across all species analysed. For 74 fish species, occurring in Brazil, China, India, the Mekong basin, the United States, South‐Africa and the East Adriatic Coast, more than 50% of their range is potentially lost. This includes 18 species threatened with extinction across their whole range. Our complementary regional analysis revealed that the potentially lost range increases by a factor of 2–4 when considering both large and small dams compared with considering only large dams (≥15 m), highlighting the need to establish more comprehensive global dam inventories. Our novel approach and global analysis identifies species at risk of extirpation as well as geographic hotspots of extirpation threat by dams, which can aid in establishing more effective strategies for global hydropower development and barrier removal efforts to optimise the trade‐offs between biodiversity conservation and the socio‐economic benefits of dams. [ABSTRACT FROM AUTHOR]

Standardizing and translating species names from different databases is key to the successful integration of data sources in biodiversity research. There are numerous taxonomic name-resolution applications that implement increasingly powerful namecleaning and matching approaches, allowing the user to resolve species relative to multiple backbones simultaneously. Yet there remains no principled approach for combining information across these underlying taxonomic backbones, complicating efforts to combine and merge species lists with inconsistent and conflicting taxonomic information. Here, we present Treemendous, an open-source software package for the R programming environment that integrates taxonomic relationships across four publicly available backbones to improve the name resolution of tree species. By mapping relationships across the backbones, this package can be used to resolve datasets with conflicting and inconsistent taxonomic origins, while ensuring the resulting species are accepted and consistent with a single reference backbone. The user can chain together different functionalities ranging from simple matching to a single backbone, to graphbased iterative matching using synonym-accepted relations across all backbones in the database. In addition, the package allows users to 'translate' one tree species list into another, streamlining the assimilation of new data into preexisting datasets or models. The package provides a flexible workflow depending on the use case, and can either be used as a stand-alone name-resolution package or in conjunction with existing packages as a final step in the name-resolution pipeline. The Treemendous package is fast and easy to use, allowing users to quickly merge different data sources by standardizing their species names according to the regularly updated database. By combining taxonomic information across multiple backbones, the package increases matching rates and minimizes data loss, allowing for more efficient translation of tree species datasets to aid research into forest biodiversity and tree ecology. [ABSTRACT FROM AUTHOR]

Aim: Climate change threatens freshwater faunal diversity. To prioritize areas for conservation, patterns in the distribution of species must be understood. We apply genetic analysis and species distribution models to identify patterns in the distribution of freshwater amphipods around Xinjiang, China, and project the impact of climate change on endemic species. Location: Xinjiang, China. Methods: A time‐calibrated tree containing 37 freshwater amphipod molecular samples from Xinjiang is built to calculate phylogenetic diversity (PD), the standardized effect sizes of PD, weighted endemism, and phylogenetic endemism, in 100 × 100 km grid cells. Niche differentiation among species in an area of high phylogenetic endemism is explored using n‐dimensional hypervolumes and principal components analyses. Present‐day and projected future suitability of habitat of endemic freshwater amphipod species is described using species distribution models. Results: Areas of high freshwater amphipod diversity occur along the western boundary of Xinjiang; Areas north of Irtysh River, Tian Shan mountains, and the eastern margin of Pamir, have high phylogenetic endemism. Seasonal temperature and average annual water temperature contribute most to niche differentiation between geographically related freshwater species, negatively affect the projected distributions of endemic amphipods, and with continued warming, reduce future range distributions or latitudinal shifts of species. Main Conclusions: High freshwater amphipod phylogenetic endemism occurs in Xinjiang. Environmental factors are responsible for niche differentiation of endemic species. Future climate change will substantially affect the geographic distributions of endemic amphipods. Conservation efforts should be prioritized in areas with highly concentrated phylogenetic endemism. [ABSTRACT FROM AUTHOR]

Although climate‐based hypotheses are widely used to explain large‐scale diversity patterns, they fall short of explaining the spatial variation among taxonomic groups. Integrating food web and metabolic theories into macroecology is a promising step forward, as they allow including explicit taxon‐specific traits that can potentially mediate the relationship between climate and diversity. Our investigation focuses on the role of body size and trophic structure in mediating the influence of contemporary climate and historical climate change on global tetrapods species richness. We used piecewise structural equation modeling to assess the direct effects of contemporary climate and climate instability of species richness and the indirect effects of climate on tetrapod richness mediated by community‐wide species traits. We found that birds and mammals are less sensitive to the direct effect of contemporary climate than amphibians and squamates. Contemporary climate and climate instability favored the species richness of mammals and amphibians. However, for birds and squamates, this link is only associated with contemporary climate. Moreover, we showed that community‐wide traits are correlated with species richness gradients. However, we highlight that this relationship is dependent upon the specific traits and taxonomic groups. Specifically, bird communities with smaller bodies and bottom‐heavy structures support higher species richness. Squamates also tend to be more diverse in communities with prevalence of smaller bodies, while mammals are correlated with top‐heavy structures. Moreover, we showed that higher contemporary climate and climate instability reduce the species richness of birds and mammals through community‐wide traits and indirectly increase squamate species richness. We also showed that body size and trophic structure are driving a global asymmetric response of tetrapod diversity to climate effects, which highlights the limitation to use the "typical" climate‐based hypotheses. Furthermore, by combining multiple theories, our research contributes to a more realistic and mechanistic understanding of diversity patterns across taxonomic groups. [ABSTRACT FROM AUTHOR]

Freshwater ecosystems are experiencing accelerating global biodiversity loss. Thus, knowing where these unique ecosystems' species richness reaches a peak can facilitate their conservation planning. By hosting more than 290 freshwater fishes, Iran is a major freshwater fish hotspot in the Middle East. Considering the accelerating rate of biodiversity loss, there is an urgent need to identify species‐rich areas and understand the mechanisms driving biodiversity distribution. In this study, we gathered distribution records of all endemic freshwater fishes of Iran (85 species) to develop their richness map and determine the most critical drivers of their richness patterns from an ecoregion approach. We performed a generalized linear model (GLM) with quasi‐Poisson distribution to identify contemporary and historical determinants of endemic freshwater fish richness. We also quantified endemic fish similarity among the 15 freshwater ecoregions of Iran. Results showed that endemic freshwater fish richness is highest in the Zagros Mountains while a moderate level of richness was observed between Zagros and Alborz Mountains. High, moderate, and low richness of endemic freshwater fish match with Upper Tigris & Euphrates, Namak, and Kavir & Lut Deserts ecoregions respectively. Kura – South Caspian Drainages and Caspian Highlands were the most similar ecoregions and Orumiyeh was the most unique ecoregion according to endemic fish presence. Precipitation and precipitation change velocity since the Last Glacial Maximum were the most important predictors of endemic freshwater fish richness. Areas identified to have the highest species richness have high priority for the conservation of freshwater fish in Iran, therefore, should be considered in future protected areas development. [ABSTRACT FROM AUTHOR]

Comparative extinction risk analysis—which predicts species extinction risk from correlation with traits or geographical characteristics—has gained research attention as a promising tool to support extinction risk assessment in the IUCN Red List of Threatened Species. However, its uptake has been very limited so far, possibly because existing models only predict a species' Red List category, without indicating which Red List criteria may be triggered. This prevents such approaches to be integrated into Red List assessments. We overcome this implementation gap by developing models that predict the probability of species meeting individual Red List criteria. Using data on the world's birds, we evaluated the predictive performance of our criterion‐specific models and compared it with the typical criterion‐blind modelling approach. We compiled data on biological traits (e.g. range size, clutch size) and external drivers (e.g. change in canopy cover) often associated with extinction risk. For each specific criterion, we modelled the relationship between extinction risk predictors and species' Red List category under that criterion using ordinal regression models. We found criterion‐specific models were better at identifying threatened species compared to a criterion‐blind model (higher sensitivity), but less good at identifying not threatened species (lower specificity). As expected, different covariates were important for predicting extinction risk under different criteria. Change in annual temperature was important for criteria related to population trends, while high forest dependency was important for criteria related to restricted area of occupancy or small population size. Our criteria‐specific method can support Red List assessors by producing outputs that identify species likely to meet specific criteria, and which are the most important predictors. These species can then be prioritised for re‐evaluation. We expect this new approach to increase the uptake of extinction risk models in Red List assessments, bridging a long‐standing research‐implementation gap. [ABSTRACT FROM AUTHOR]

Climate change affects populations over broad geographic ranges due to spatially autocorrelated abiotic conditions known as the Moran effect. However, populations do not always respond to broad‐scale environmental changes synchronously across a landscape. We combined multiple datasets for a retrospective analysis of time‐series count data (5–28 annual samples per segment) at 144 stream segments dispersed over nearly 1,000 linear kilometers of range to characterize the population structure and scale of spatial synchrony across the southern native range of a coldwater stream fish (brook trout, Salvelinus fontinalis), which is sensitive to stream temperature and flow variations. Spatial synchrony differed by life stage and geographic region: it was stronger in the juvenile life stage than in the adult life stage and in the northern sub‐region than in the southern sub‐region. Spatial synchrony of trout populations extended to 100–200 km but was much weaker than that of climate variables such as temperature, precipitation, and stream flow. Early life stage abundance changed over time due to annual variation in summer temperature and winter and spring stream flow conditions. Climate effects on abundance differed between sub‐regions and among local populations within sub‐regions, indicating multiple cross‐scale interactions where climate interacted with local habitat to generate only a modest pattern of population synchrony over space. Overall, our analysis showed higher degrees of response heterogeneity of local populations to climate variation and consequently population asynchrony than previously shown based on analysis of individual, geographically restricted datasets. This response heterogeneity indicates that certain local segments characterized by population asynchrony and resistance to climate variation could represent unique populations of this iconic native coldwater fish that warrant targeted conservation. Advancing the conservation of this species can include actions that identify such priority populations and incorporate them into landscape‐level conservation planning. Our approach is applicable to other widespread aquatic species sensitive to climate change. [ABSTRACT FROM AUTHOR]

Aim: Contemporary environmental, historical and evolutionary factors are increasingly used to decipher the drivers of spatial patterns of species richness. Evidence of such correlations for Chinese reptiles is scarce and poorly understood. We therefore explored the validity of the environmental capacity, historical climatic stability and diversification rates hypotheses on Chinese lizard richness. Location: Mainland China. Taxon: Squamata: Sauria. Methods: We mapped the distribution ranges of all 237 lizards in mainland China using a combination of different datasets. We used current environmental conditions (ambient energy, environmental productivity, and habitat heterogeneity), historical climate stability indices (long term: since ~3.3 Ma and short term: since the last glacial maximum) and mean tip diversification rates, to test whether current environmental conditions, historical climate change and diversification rates drive contemporary richness patterns of lizards in China. We applied piecewise structural equation models (pSEM) to jointly evaluate our hypotheses, considering direct and indirect effects. Results: Chinese lizards showed strong latitudinal diversity gradients. We found consistent support for contemporary climatic and environmental factors relationships with richness. Richness was also positively correlated with short‐term climatic stability, but less so with long‐term stability. Diversification rates were seldom found to be positively correlated with lizard richness. Main Conclusions: Our results support the environmental capacity and historical climate hypotheses, which link high richness to highly productive warm and stable regions (and low richness to cold and unstable regions). We conclude that post‐speciation dispersal and short‐term climatic oscillations quickly swamp the long‐term signal of diversification rates and climatic fluctuations, creating strong current climate–richness associations. [ABSTRACT FROM AUTHOR]

Cyprinidae (Teleostei: Cypriniformes) is the predominate family among Bhutan's freshwater fishes, yet significant gaps exist in the knowledge of their diversity and assemblage. Cyprinids were sampled from 54 plots across four river basins (Aiechhu, Jaldakachhu, Mangdechhu, and Punatsangchhu) using systematic sampling at an interval of 5 km. A total of 850 individuals belonging to 22 species and 13 genera were recorded. Aiechhu had the highest diversity and evenness (H'= 1.66±0.28, J'= 0.95±0.03), followed by Punatsangchhu (H'= 1.58±0.34, J'= 0.94±0.04). Meanwhile, Jaldakachhu and Mangdechhu exhibited the lowest diversity and evenness (H'= 0.90±0.66, J'= 0.84±0.54 and H'= 0.54±0.70, J'= 0.38±0.49, respectively). There was a significant difference in diversity among river basins (χ2 (3)= 20.98, p < 0.001) with specific variation between Mangdechhu and Punatsangchhu (Z= 3.80, p= 0.00), Mangdechhu and Aiechhu (Z= 3.35, p= 0.01), and Jaldakachhu and Punatsangchhu (Z= 2.83, p= 0.03). Canonical correspondence analysis indicated that cyprinid assemblage was significantly correlated with environmental variables (r= 0.94, p= 0.001 in axis 1 and r= 0.82, p= 0.001 in axis 2) explaining 77% of variance. Axis 1 was positively correlated with temperature (r= 0.92), total dissolved solids (r= 0.53), conductivity (r= 0.51), and salinity (r= 0.39) and negatively correlated with elevation (r= --0.69). Axis 2 was negatively correlated with total hardness (r= --0.82) and dissolved oxygen (r= --0.65). Cluster analysis identified three clusters based on dominant species. Further studies exploring other river basins of Bhutan are needed to better understand the ecological dynamics of cyprinids in Bhutan. [ABSTRACT FROM AUTHOR]

Background. Taxonomic identification through DNA barcodes gained considerable traction through the invention of next-generation sequencing and DNA metabarcoding. Metabarcoding allows for the simultaneous identification of thousands of organisms from bulk samples with high taxonomic resolution. However, reliable identifications can only be achieved with comprehensive and curated reference databases. Therefore, custom reference databases are often created to meet the needs of specific research questions. Due to taxonomic inconsistencies, formatting issues, and technical difficulties, building a custom reference database requires tremendous effort. Here, we present taxalogue, an easy-to-use software for creating comprehensive and customized reference databases that provide clean and taxonomically harmonized records. In combination with extensive geographical filtering options, taxalogue opens up new possibilities for generating and testing evolutionary hypotheses. Methods. taxalogue collects DNA sequences from several online sources and combines them into a reference database. Taxonomic incongruencies between the different data sources can be harmonized according to available taxonomies. Dereplication and various filtering options are available regarding sequence quality or metadata information. taxalogue is implemented in the open-source Ruby programming language, and the source code is available at https://github.com/nwnoll/taxalogue. We benchmark four reference databases by sequence identity against eight queries from different localities and trapping devices. Subsamples from each reference database were used to compare how well another one is covered. Results. taxalogue produces reference databases with the best coverage at high identities for most tested queries, enabling more accurate, reliable predictions with higher certainty than the other benchmarked reference databases. Additionally, the performance of taxalogue is more consistent while providing good coverage for a variety of habitats, regions, and sampling methods. taxalogue simplifies the creation of reference databases and makes the process reproducible and transparent. Multiple available output formats for commonly used downstream applications facilitate the easy adoption of taxalogue in many different software pipelines. The resulting reference databases improve the taxonomic classification accuracy through high coverage of the query sequences at high identities. [ABSTRACT FROM AUTHOR]

In an epoch of rapid environmental change, understanding and predicting how biodiversity will respond to a changing climate is an urgent challenge. Since we seldom have sufficient long‐term biological data to use the past to anticipate the future, spatial climate–biotic relationships are often used as a proxy for predicting biotic responses to climate change over time. These 'space‐for‐time substitutions' (SFTS) have become near ubiquitous in global change biology, but with different subfields largely developing methods in isolation. We review how climate‐focussed SFTS are used in four subfields of ecology and evolution, each focussed on a different type of biotic variable – population phenotypes, population genotypes, species' distributions, and ecological communities. We then examine the similarities and differences between subfields in terms of methods, limitations and opportunities. While SFTS are used for a wide range of applications, two main approaches are applied across the four subfields: spatial in situ gradient methods and transplant experiments. We find that SFTS methods share common limitations relating to (i) the causality of identified spatial climate–biotic relationships and (ii) the transferability of these relationships, i.e. whether climate–biotic relationships observed over space are equivalent to those occurring over time. Moreover, despite widespread application of SFTS in climate change research, key assumptions remain largely untested. We highlight opportunities to enhance the robustness of SFTS by addressing key assumptions and limitations, with a particular emphasis on where approaches could be shared between the four subfields. [ABSTRACT FROM AUTHOR]

Biodiversity data records contain inaccuracies and biases. To overcome this limitation and establish robust geographic patterns, ecologists often curate records keeping those that are most suitable for their analyses. Yet, this choice is not straightforward and the outcome of the analysis may vary due to a trade‐off between data quality and volume. This problem is particularly recurrent for less‐studied groups with patchy sampling effort. The latitudinal pattern of mosses richness remains inconsistent across studies and these may emerge purely from sampling artefacts. Our main objective here is to assess the effect of different curation criteria on this spatial pattern in the Temperate Northern Hemisphere (above 20° latitude). We contrasted the geographical distribution of moss species records and the latitude‐species richness relation obtained under different data curation scenarios. These scenarios comprehend five sources of taxonomical standardisations and eight data cleaning filters. The analyses are based on the selection of well‐surveyed cells at 100 km cell resolution. The application of some 'data curation scenarios' severely affects the number of records selected for analysis and substantially changes the proportion of richness per cell. The sensitivity to data curation becomes detectable at regional and at the cell scales showing a large shift in the latitudinal richness peak in Europe, from 60° N to 45° N latitude, when only preserved specimens are selected and duplicates based on date of collection and coordinates are excluded. Our results stress the importance of justifying the criteria used for filtering biodiversity data retrieved from biodiversity databases to avoid detecting misleading patterns. Curating records under particular criteria compromises the information in some areas displaying different spatial information of mosses. This problem can be ameliorated if data filtering is combined with identifying well‐surveyed cells, render relatively constant results under different combinations of filtering even for less well‐known groups such as mosses. [ABSTRACT FROM AUTHOR]

There is a variety of taxonomic and nomenclatural databases, curated at different intervals and using different criteria to decide which species names are listed as accepted and which are considered synonyms. Botanical collections, such as herbaria or botanical gardens, maintain data that link names to plant material. The choice of the used database affects the naming of the plant specimens. If data from different institutions are to be matched, inconsistencies may arise. A solution that allows the use of different databases side by side would be beneficial in our opinion. The linking of botanical taxonomic and nomenclatural datasets by utilizing standardized Semantic Web technologies allows the coexistence of several lists. In this study, we conducted a mapping of The Plant List, World Flora Online, and the Integrated Taxonomic Information System provided in Darwin Core Archive files to the Simple Knowledge Organization System and created an interlinked version of these datasets. The developed graphical user interface visualized the contents of the included taxonomic databases. The usefulness and usability of the GUI were positively evaluated in interviews with five scientific employees and curators of four different botanical gardens. Citation: Schrumpf A., Killinger M., Schiessle P. & Scherp A. 2024: On the coexistence of taxonomic botanical databases – a user study. – Willdenowia 53: 309–316. https://doi.org/10.3372/wi.53.53308 Version of record first published online on 01 February 2024. [ABSTRACT FROM AUTHOR]

Taylor's power law (TPL) describes the expected range of parameters of the mean-variance scaling relationship and has been extensively used in studies examining temporal variations in abundance. Few studies though have focused on biological and ecological covariates of TPL, while its statistical inherences have been extensively debated. In the present study, we focused on species-specific features (i.e. functional traits) that could be influential to temporal TPL. We combined field surveys of 180 fish species from 972 sites varying from small streams to large rivers with data on 31 ecological traits describing species-specific characteristics related to three main niche dimensions (trophic ecology, life history, and habitat use). For each species, the parameters of temporal TPL (intercept and slope) were estimated from the log-log mean-variance relationships while controlling for spatial dependencies and biological covariates (species richness and evenness). Then, we investigated whether functional traits explained variations in TPL parameters. Differences in TPL parameters among species were explained mostly by life history and environmental determinants, especially TPL slope. Life history was the main determinant of differences in TPL parameters and thereby aggregation patterns, with traits related to body size being the most influential, thus showing a high contrast between small-sized species with short lifespans and large-bodied migratory fishes, even after controlling for phylogenetic resemblances. We found that life history traits, especially those related to body size, mostly affect TPL and, as such, can be determinants of temporal variability of fish populations. We also found that statistical effects and phylogenetic resemblances are embedded in mean-variance relationships for fish, and that environmental drivers can interact with ecological characteristics of species in determining temporal fluctuations in abundance., (© 2024 The Author(s). Journal of Animal Ecology © 2024 British Ecological Society.)

Summary: Taxonomic checklists used to verify published plant names and identify synonyms are a cornerstone of biological research. Four global authoritative checklists for vascular plants exist: Leipzig Catalogue of Vascular Plants, World Checklist of Vascular Plants, World Flora Online (successor of The Plant List, TPL), and WorldPlants. We compared these four checklists in terms of size and differences across taxa.We matched taxon names of these checklists and TPL against each other, identified differences across checklists, and evaluated the consistency of accepted names linked to individual taxon names. We assessed geographic and phylogenetic patterns of variance.All checklists differed strongly compared with TPL and provided identical information on c. 60% of plant names. Geographically, differences in checklists increased from low to high latitudes. Phylogenetically, we detected strong variability across families. A comparison of name‐matching performance on taxon names submitted to the functional trait database TRY, and a check of completeness of accepted names evaluated against an independent, expert‐curated checklist of the family Meliaceae, showed a similar performance across checklists.This study raises awareness on the differences in data and approach across these checklists potentially impacting analyses. We propose ideas on the way forward exploring synergies and harmonizing the four global checklists. This article is part of the Special Collection 'Global plant diversity and distribution'. See https://www.newphytologist.org/global-plant-diversity for more details. [ABSTRACT FROM AUTHOR]

Identifying hydropower dam operations that lessen detrimental effects on downstream fauna could inform conservation strategies for native fishes. We compared occurrence of native fishes in 20 shoal habitats downstream from two differently operated hydropower dams in the Coosa River system, Georgia, USA. Species richness averaged 7 and 11, respectively, in surveys downstream from (1) a hydropeaking dam and (2) a dam with a re-regulation structure that stabilized downstream flows. In contrast, surveys in two nearby reference communities averaged 19 and 24 species. Species persisting downstream from the dams tended toward water-column orientation, larger body size, longer life span, and greater prevalence in tributary stream collections, compared with missing or rarely captured species. We observed no evidence of recovery toward reference conditions when operations were paused for 28 months at the hydropeaking dam. Our observations suggest that (1) strongly contrasting dam operations can result in similar alterations to native fish assemblages, potentially reflecting effects of thermal alteration by hypolimnetic water release, and (2) periodic dispersal from tributary streams may enhance fish persistence in flow-altered rivers. [ABSTRACT FROM AUTHOR]

Linking records for the same taxa between different databases is an essential step when working with biodiversity data. However, name-matching alone is error-prone, because of issues such as homonyms (unrelated taxa with the same name) and synonyms (same taxon under different names). Therefore, most projects will require some curation to ensure that taxon identifiers are correctly linked. Unfortunately, formal guidance on such curation is uncommon and these steps are often ad hoc and poorly documented, which hinders transparency and reproducibility, yet the task requires specialist knowledge and cannot be easily automated without careful validation. Here, we present a case study on linking identifiers between the GBIF and NCBI taxonomies for a species checklist. This represents a common scenario: finding published sequence data (from NCBI) for species chosen by occurrence or geographical distribution (from GBIF). Wikidata, a publicly editable knowledge base of structured data, can serve as an additional information source for identifier linking. We suggest a software toolkit for taxon name-matching and datacleaning, describe common issues encountered during curation and propose concrete steps to address them. For example, about 2.8% of the taxa in our dataset had wrong identifiers linked on Wikidata because of errors in name-matching caused by homonyms. By correcting such errors during data-cleaning, either directly (through editing Wikidata) or indirectly (by reporting errors in GBIF or NCBI), we crowdsource the curation and contribute to community resources, thereby improving the quality of downstream analyses. [ABSTRACT FROM AUTHOR]

Classification of the biological diversity on Earth is foundational to all areas of research within the natural sciences. Reliable biological nomenclatural and taxonomic systems facilitate efficient access to information about organisms and their names over time. However, broadly sharing, accessing, delivering, and updating these resources remains a persistent problem. This barrier has been acknowledged by the biodiversity data sharing community, yet concrete efforts to standardize and continually update taxonomic names in a sustainable way remain limited. High diversity groups such as arthropods are especially challenging as available specimen data per number of species is substantially lower than vertebrate or plant groups. The Terrestrial Parasite Tracker Thematic Collections Network project developed a workflow for gathering expert-verified taxonomic names across all available sources, aligning those sources, and publishing a single resource that provides a model for future endeavors to standardize digital specimen identification data. The process involved gathering expert-verified nomenclature lists representing the full taxonomic scope of terrestrial arthropod parasites, documenting issues experienced, and finding potential solutions for reconciliation of taxonomic resources against large data publishers. Although discordance between our expert resources and the Global Biodiversity Information Facility are relatively low, the impact across all taxa affects thousands of names that correspond to hundreds of thousands of specimen records. Here, we demonstrate a mechanism for the delivery and continued maintenance of these taxonomic resources, while highlighting the current state of taxon name curation for biodiversity data sharing. [ABSTRACT FROM AUTHOR]

Advancing knowledge of biodiversity requires global open‐access databases. Having large‐scale information on plant distributions, functional traits and evolutionary history will enable the scientific community to improve its understanding of the patterns and drivers of plant diversity on a global scale.The Global Inventory of Floras and Traits (GIFT) is a global database of regional plant checklists that has proven successful in documenting biogeographical patterns of plants. Since the release of the first version of GIFT, the database kept on expanding. We introduce GIFT version 3.0, which contains 5169 plant checklists referring to 3400 regions worldwide. These checklists include a total of 371,148 land plant species, mostly vascular plants, of which 354,848 have accepted species names, and species‐level data for 109 functional traits. This new version of GIFT relies on new resources for taxonomic name standardization, is matched to a new plant phylogeny, comes with a new trait aggregation workflow and includes additional environmental variables.We also present the GIFTR‐package, which contains all necessary functions to retrieve distributional, functional, phylogenetic, and environmental data from the GIFT database. The package comes with a dedicated website, https://biogeomacro.github.io/GIFT/, which includes three vignettes to guide users in retrieving data from GIFT.The recent development of GIFT and its associated R‐package provide ecologists with access to one of the largest plant databases. This will foster research into regional to global patterns of plant diversity and their underlying mechanisms. The ability to retrieve and cite data from any previous and current instance of the GIFT database will ensure the reproducibility of studies that utilise it. [ABSTRACT FROM AUTHOR]

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Research over the past decade has shown that quantifying spatial variation in ecosystem properties is an effective approach to investigating the effects of environmental change on ecosystems. Yet, current consensus among scientists is that we need a better understanding of short‐ and long‐term (temporal) variation in ecosystem properties to plan effective ecosystem management and predict future ecologies.Trait‐based approaches can be used to reconstruct ecosystem properties from long‐term ecological records and contribute significantly to developing understandings of ecosystem change over decadal to millennial time‐scales.Here, we synthesise current trait‐based approaches and explore how organisms' functional traits (FTs) can be scaled across time and space. We propose a framework for reconstructing long‐term variation in ecosystems by means of analysing FTs derived from palaeoecological datasets. We then summarise challenges that must be overcome to reconcile trait‐based approaches with palaeo‐datasets. Finally, we discuss the benefits and limitations of trait‐based reconstructions of ecosystem temporal dynamics and suggest future directions for research.Reconstructing environmental properties through time vis‐à‐vis FTs can be separated into two parts. The first is to record trait data for organisms present in modern ecosystems, and the second is to reconstruct temporal variability in FTs from palaeoecological datasets, capturing changes in trait composition over time. Translating palaeoecological datasets into FTs is challenging due to taphonomic, taxonomic and chronological uncertainties, as well as uniformitarian assumptions. Explicitly identifying and addressing these challenges is important to effectively calculate changes in FT through time.Palaeo‐trait research offers insights into questions related to short‐ and long‐term ecosystem functioning, environmental change and extinction and community assembly rules across time. As work in this area matures, we expect that trait‐based approaches integrating palaeoecology and neo‐ecology will improve understanding of past ecologies and provide a deeper insight of their implications for present‐day and future ecosystem management and conservation. Read the free Plain Language Summary for this article on the Journal blog. [ABSTRACT FROM AUTHOR]

The coastal basins of eastern Brazil are influenced by geomorphologic and climatic changes that caused river captures and temporary paleo‐connections due to sea‐level oscillations. These two events can lead to isolation and connection among coastal rivers and have a strong influence on the distribution of freshwater fishes in this region. Characidium bahiense is a small fish species with a wide distribution, ranging from the coastal basins of the North Group of the Northeastern Mata Atlântica ecoregion to São Francisco and Parnaíba ecoregions. The allopatric distribution of C. bahiense associated with the possible morphological and molecular variations among geographically isolated populations stimulated this study.Here, we use an integrative approach, encompassing morphological and mitonuclear data, and paleodrainage reconstruction to better understand the evolutionary history of C. bahiense and to test the putative effects of the current configuration of basins and historical drainage rearrangements on the genetic structuring of the species.Our mitochondrial data show that C. bahiense is not a monophyletic species since the specimens from one locality are more closely related to Characidium cf. lagosantense than to other populations of C. bahiense. Multilocus analyses, however, recovered the monophyly of this species, although the molecular delimitation method considers each mitochondrial DNA lineages as a separated species. Overall, the morphological data revealed some intraspecific overlapping variation, suggesting that all specimens of C. bahiense are conspecific.Molecular analyses combined with geomorphological information suggest that the current distribution of C. bahiense is the result of climate change that directly affected river flow dynamics and recent riverine captures during the Pleistocene.The use of multiple data sources not only provides a more reliable interpretation of the evolutionary history of a species, but can also avoid arbitrary taxonomic decisions. Future phylogeographic studies involving other freshwater fish species with a similar distribution to C. bahiense are necessary to assist in understanding the scenarios presented here. [ABSTRACT FROM AUTHOR]

Tropical lands harbour the highest number of species, resulting in the ubiquitous latitudinal diversity gradient (LDG). However, exceptions to this pattern have been observed in some taxa, explained by the interaction between the evolutionary histories and environmental factors that constrain species' physiological and ecological requirements. Here, we applied a deconstruction approach to map the detailed species richness patterns of Actinopterygian freshwater fishes at the class and order levels and to disentangle their drivers using geographical ranges and a phylogeny, comprising 77% (12 557) of all described species. We jointly evaluated seven evolutionary and ecological hypotheses posited to explain the LDG: diversification rate, time for speciation, species–area relationship, environmental heterogeneity, energy, temperature seasonality and past temperature stability. We found distinct diversity gradients across orders, including expected, bimodal and inverse LDGs. Despite these differences, the positive effect of evolutionary time explained patterns for all orders, where species-rich regions are inhabited by older species compared to species-poor regions. Overall, the LDG of each order has been shaped by a unique combination of factors, highlighting the importance of performing a joint evaluation of evolutionary, historical and ecological factors at different taxonomic levels to reach a comprehensive understanding on the causes driving global species richness patterns. [ABSTRACT FROM AUTHOR]

Copyright of Functional Ecology is the property of Wiley-Blackwell and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Crustaceana is the property of Brill Academic Publishers and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Aim: Palaeoecological data are crucial for comprehending large‐scale biodiversity patterns and the natural and anthropogenic drivers that influence them over time. Over the last decade, the availability of open‐access research databases of palaeoecological proxies has substantially increased. These databases open the door to research questions needing advanced numerical analyses and modelling based on big‐data compilations. However, compiling and analysing palaeoecological data pose unique challenges that require a guide for producing standardized and reproducible compilations. Innovation: We present a step‐by‐step guide of how to process fossil pollen data into a standardized dataset compilation ready for macroecological and palaeoecological analyses. We describe successive criteria that will enhance the quality of the compilations. Though these criteria are project and research question‐dependent, we discuss the most important assumptions that should be considered and adjusted accordingly. Our guide is accompanied by an R‐workflow—called FOSSILPOL—and corresponding R‐package—called R‐Fossilpol—that provide a detailed protocol ready for interdisciplinary users. We illustrate the workflow by sourcing and processing Scandinavian fossil pollen datasets and show the reproducibility of continental‐scale data processing. Main Conclusions: The study of biodiversity and macroecological patterns through time and space requires large‐scale syntheses of palaeoecological datasets. The data preparation for such syntheses must be transparent and reproducible. With our FOSSILPOL workflow and R‐package, we provide a protocol for optimal handling of large compilations of fossil pollen datasets and workflow reproducibility. Our workflow is also relevant for the compilation and synthesis of other palaeoecological proxies and as such offers a guide for synthetic and cross‐disciplinary analyses with macroecological, biogeographical and palaeoecological perspectives. However, we emphasize that expertise and informed decisions based on palaeoecological knowledge remain crucial for high‐quality data syntheses and should be strongly embedded in studies that rely on the increasing amount of open‐access palaeoecological data. [ABSTRACT FROM AUTHOR]

Climate and land‐use/land‐cover change ("global change") are restructuring biodiversity, globally. Broadly, environmental conditions are expected to become warmer, potentially drier (particularly in arid regions), and more anthropogenically developed in the future, with spatiotemporally complex effects on ecological communities. We used functional traits to inform Chesapeake Bay Watershed fish responses to future climate and land‐use scenarios (2030, 2060, and 2090). We modeled the future habitat suitability of focal species representative of key trait axes (substrate, flow, temperature, reproduction, and trophic) and used functional and phylogenetic metrics to assess variable assemblage responses across physiographic regions and habitat sizes (headwaters through large rivers). Our focal species analysis projected future habitat suitability gains for carnivorous species with preferences for warm water, pool habitats, and fine or vegetated substrates. At the assemblage level, models projected decreasing habitat suitability for cold‐water, rheophilic, and lithophilic individuals but increasing suitability for carnivores in the future across all regions. Projected responses of functional and phylogenetic diversity and redundancy differed among regions. Lowland regions were projected to become less functionally and phylogenetically diverse and more redundant while upland regions (and smaller habitat sizes) were projected to become more diverse and less redundant. Next, we assessed how these model‐projected assemblage changes 2005–2030 related to observed time‐series trends (1999–2016). Halfway through the initial projecting period (2005–2030), we found observed trends broadly followed modeled patterns of increasing proportions of carnivorous and lithophilic individuals in lowland regions but showed opposing patterns for functional and phylogenetic metrics. Leveraging observed and predicted analyses simultaneously helps elucidate the instances and causes of discrepancies between model predictions and ongoing observed changes. Collectively, results highlight the complexity of global change impacts across broad landscapes that likely relate to differences in assemblages' intrinsic sensitivities and external exposure to stressors. [ABSTRACT FROM AUTHOR]

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Copyright of Actualidades Biológicas is the property of Universidad de Antioquia and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Copyright of Boletín Científico Centro de Museos de Historia Natural is the property of Universidad de Caldas and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Freshwater ecosystems have experienced a great loss of biodiversity in the recent century due to eutrophication and loss of habitats, particularly in agricultural lowlands. Some of these ecosystems have recently been re‐established, or entirely new lakes have been created to improve nutrient removal, biodiversity, and recreation.Fish have an important structuring role in lake ecosystems, but little is known about the temporal development of fish species richness or composition in new or re‐established lakes, especially in comparison with natural lakes. We investigated the influence of environmental variables and landscape features on fish species richness and fish assemblage in drainage basins and in 34 new (between 0 and 99 years) and 193 natural lakes in Denmark, using structural equation modelling.Fish species richness in drainage basins is influenced primarily by basin elevation, lake area, and salinity at the basin outlet; low‐salinity coastal regions are important migration pathways for many freshwater fish species, not just for anadromous or catadromous species. Land use does not appear to influence richness at the drainage basin scale, indicating that the influence of anthropogenic activities is minor or that significant effects thereof occurred a long time ago (decades to centuries).The drainage basin richness defines the apparent pool of species that may colonise lakes within the basin, but the actual number of species is particularly influenced by stream network connectivity. Disconnected lakes have fewer species, a deficit that is sustained over long time scales.In addition to the influence of stream connectivity, lake characteristics such as elevation, surface area, and water chemistry (alkalinity and pH) are also important predictors of fish species richness, whereas we did not find any effect of lake nutrient concentrations. The direct effect of land use was not evaluated. Ordination analysis shows that fish assemblage depends on both lake type (new/natural) and stream connectivity (connected/disconnected). Furthermore, species‐specific occurrences reveal some differences between new and natural lakes and indicate that stocking plays a role in new lakes.While new and natural lakes may initially differ in terms of both how many and which species they contain, they converge over time in a process that can be enhanced by improving stream connectivity. [ABSTRACT FROM AUTHOR]

Range size is one of the most important criteria for determining species conservation status. It is an outcome of multiple factors, including a species' ecological tolerance and propensity to disperse, availability and temporal stability of suitable habitat patches, and between‐patch connectivity. Understanding the determinants of range size could help identify the main threats, which may differ among species.Subterranean species typically have smaller ranges than their surface counterparts. However, the determinants of their ranges are poorly known. The aim of this study was to test three potential determinants of species range size (habitat type, body size, and species age) using the species of the amphipod genus Niphargus. The study was performed within the Dinarides (south‐east Europe), a global subterranean hotspot.The only significant determinant of range size was the habitat in which the species lived. The species with the smallest ranges inhabit fissure systems in the upper layers of the carbonate massifs with predominantly vertical water flow. The species with the largest ranges live in the deepest zone – the permanently flooded phreatic with lateral water flow. These results imply that differences in connectivity among habitats determine the range sizes of aquatic subterranean species.The vertical gradient in habitat connectivity indicates the vulnerability of the species to climate change. Desertification and longer periods of drought will probably have a greater effect on fauna in fissures than in the phreatic zone. In addition, lowering the groundwater table might exacerbate the fragmentation of intermediate habitats, possibly enhancing local extinction.The habitat ecology of subterranean species should be considered in International Union for Conservation of Nature assessments. Given that the most narrowly distributed aquatic subterranean species live in habitats subjected to climatic drying, the protection of subterranean fauna depends on the management of surface habitats such as forests. [ABSTRACT FROM AUTHOR]

Upstream range shifts of freshwater fishes have been documented in recent years due to ongoing climate change. River fragmentation by dams, presenting physical barriers, can limit the climatically induced spatial redistribution of fishes. Andean freshwater ecosystems in the Neotropical region are expected to be highly affected by these future disturbances. However, proper evaluations are still missing. Combining species distribution models and functional traits of Andean Amazon fishes, coupled with dam locations and climatic projections (2070s), we (a) evaluated the potential impacts of future climate on species ranges, (b) investigated the combined impact of river fragmentation and climate change and (c) tested the relationships between these impacts and species functional traits. Results show that climate change will induce range contraction for most of the Andean Amazon fish species, particularly those inhabiting highlands. Dams are not predicted to greatly limit future range shifts for most species (i.e., the Barrier effect). However, some of these barriers should prevent upstream shifts for a considerable number of species, reducing future potential diversity in some basins. River fragmentation is predicted to act jointly with climate change in promoting a considerable decrease in the probability of species to persist in the long-term because of splitting species ranges in smaller fragments (i.e., the Isolation effect). Benthic and fast-flowing water adapted species with hydrodynamic bodies are significantly associated with severe range contractions from climate change., (© 2020 John Wiley & Sons Ltd.)

The Yarlung Zangbo River is a river with abundant hydropower resources but fragile biodiversity in China. As an important benchmark for both research and ecological management, there is still a lack of knowledge about the swimming ability of fishes in the Yarlung Zangbo River. The induced flow velocity (U ind ), critical swimming speed (U crit ), and burst swimming speed (U burst ) of five Schizothoracinae species were tested in this study. Relative swimming ability related to body length and body shape was calculated. The results indicated that the average absolute swimming speeds (U ind-a , U crit-a , and U burst-a ) of all the experimental fish were 10.20 ± 0.01, 57.58 ± 3.28, and 69.54 ± 2.94 cm/s, respectively, and the corresponding relative U ind , U crit , and U burst related to body length (U ind-l , U crit-l , U burst-l ) were 1.15 ± 0.07, 5.04 ± 0.26, and 7.23 ± 0.28 BL/s, respectively. Moreover, relative U ind , U crit , and U burst related to body shape (U ind-s , U crit-s , and U burst-s ) were 0.80 ± 0.13, 2.49 ± 0.51, and 4.32 ± 0.57 cm -2 /s, respectively. No significantly differences in relative swimming speeds existed among five species. Only Oxygymnocypris stewartii was significantly weaker in U burst-s than Schizothorax o'connori. The body shape showed a stronger relationship with swimming speed than the body length did. Schizothoracinae fish in the Yarlung Zangbo River basin are less sensitive to the water flow and performed weaker U crit and U burst compared to those in the Yangtze River basin, indicating that Schizothoracinae fish in the Yarlung Zangbo River may be more susceptible to threats from environmental changes. The paper enriched the research on the swimming ability of Schizothoracinae fishes and provided efficient data for the fish conservation in the Yarlung Zangbo River., (© 2024 Fisheries Society of the British Isles.)

Current knowledge about the impacts of urbanisation on bird assemblages is based on evidence from studies partly or wholly undertaken in the breeding season. In comparison, the non-breeding season remains little studied, despite the fact that winter conditions at higher latitudes are changing more rapidly than other seasons. During the non-breeding season, cities may attract or retain bird species because they offer milder conditions or better feeding opportunities than surrounding habitats. However, the range of climatic, ecological and anthropogenic mechanisms shaping different facets of urban bird diversity in the non-breeding season are poorly understood. We explored these mechanisms using structural equation modelling to assess how urbanisation affects the taxonomic, phylogenetic and functional diversity of avian assemblages sampled worldwide in the non-breeding season. We found that minimum temperature, elevation, urban area and city age played a critical role in determining taxonomic diversity while a range of factors-including productivity, precipitation, elevation, distance to coasts and rivers, socio-economic (as a proxy of human facilitation) and road density-each contributed to patterns of phylogenetic and functional diversity. The structure and function of urban bird assemblages appear to be predominantly shaped by temperature, productivity and city age, with effects of these factors differing across seasons. Our results underline the importance of considering multiple hypotheses, including seasonal effects, when evaluating the impacts of urbanisation on biodiversity., (© 2024 The Author(s). Global Change Biology published by John Wiley & Sons Ltd.)

Aim: Understanding the determinants of species distribution and richness is key to explaining global ecological patterns. We examined the current knowledge about terrestrial mammals in tidal marshes and evaluated whether species richness increased with the marsh surface area and/or with their proximity to the equator and whether species distribution ranges decreased with latitude. Location: Global. Methods: We reviewed the existing literature on terrestrial mammals in tidal marshes. We examined their ecological characteristics (e.g. habitat specialists, native or alien), predicted their variation in species richness and range size along latitude, and explored factors, such as surface area, underlying the global patterns found. Results: We found 962 records, describing 125 mammalian species using tidal marshes worldwide, also including several alien species. Most species (95%) were not marsh specialized, and some (18%) were of conservation concern. There were information gaps in South America, Africa, Australia and Asia, and a lack of information about mammalian ecological roles worldwide. We found that species richness increased with surface area, and showed a bimodal pattern peaked between 40° and 50° latitude in each hemisphere. We found no relationship between latitude and species range size. Main conclusions: Our worldwide findings revealed a broader range of tidal marshes inhabited by terrestrial mammals, and higher values of species richness than previously reported. The bimodal pattern of species richness was consistent with the species–area hypothesis, but it also suggested that further studies of species distribution in relation to historical and environmental factors will yield significant insights about variables driving richness in tidal marshes. Despite terrestrial mammal ubiquitous distribution in these ecosystems, there are considerable geographic gaps as regards knowledge about their functional importance and the impact of alien species on tidal marsh functioning. Consequently, extending our research efforts is key to planning the conservation of these coastal ecosystems. [ABSTRACT FROM AUTHOR]

Assessment of biodiversity using metabarcoding data, such as from bulk or environmental DNA sampling, is becoming increasingly relevant in ecology, biodiversity sciences and monitoring. Thereby, the taxonomic identification of species from their DNA sequences relies strongly on reference databases that link genetic sequences to taxonomic names. These databases vary in completeness and availability, depending on the taxonomic group studied and the genetic region targeted. The incompleteness of reference databases is an important argument to explain the nondetection by metabarcoding of species supposedly present. However, there exist further and generally overlooked problems with reference databases that can lead to false or inaccurate inferences of taxonomic assignment. Here, we synthesize all possible problems inherent to reference databases. In particular, we identify a complete, mutually nonexclusive list of seven classes of challenges when it comes to selecting, developing and using a reference database for taxonomic assignment. These are: (i) mislabelling, (ii) sequencing errors, (iii) sequence conflict, (iv) taxonomic conflict, (v) low taxonomic resolution, (vi) missing taxa and (vii) missing intraspecific variants. For each problem identified, we provide a description of possible consequences on the taxonomic assignment process. We illustrate the respective problem with examples taken from the literature or obtained by quantitative analyses of public databases, such as GenBank or BOLD. Finally, we discuss possible solutions to the identified problems and how to navigate them. Only by raising users' awareness of the limitations of metabarcoding data and DNA reference databases will adequate interpretations of these data be achieved. [ABSTRACT FROM AUTHOR]