Database Of Occurrences Research Articles

The early diversification of ray-finned fishes (Actinopterygii): hypotheses, challenges and future prospects.

Actinopterygii makes up half of living vertebrate diversity, and study of fossil members during their Palaeozoic rise to dominance has a long history of descriptive work. Although research interest into Palaeozoic actinopterygians has increased in recent years, broader patterns of diversity and diversity dynamics remain critically understudied. Past studies have investigated macroevolutionary trends in Palaeozoic actinopterygians in a piecemeal fashion, variably using existing compendia of vertebrates or literature-based searches. Here, we present a comprehensive occurrence-based dataset of actinopterygians spanning the whole of the Palaeozoic. We use this to produce the first through-Palaeozoic trends in genus and species counts for Actinopterygii. Diversity through time generally tracks metrics for sampling, while major taxonomic problems pervading the Palaeozoic actinopterygian record obscure diversity trends. Many described species are concentrated in several particularly problematic 'waste-basket' genera, hiding considerable morphological and taxonomic diversity. This taxonomic confusion also feeds into a limited understanding of phylogenetic relationships. A heavy sampling bias towards Europe and North America exists in both occurrence databases and available phylogenetic matrices, with other regions underrepresented despite yielding important data. Scrutiny of the extent to which spatial biases influence the actinopterygian record is lacking, as is research on other forms of bias. Low richness in some time periods may be linked to geological biases, while the effects of taphonomic biases on Palaeozoic actinopterygians have not yet been investigated. Efforts are already underway both to redescribe poorly defined taxa and to describe taxa from underrepresented regions, helping to address taxonomic issues and accuracy of occurrence data. New methods of sampling standardisation utilising up-to-date occurrence databases will be critical in teasing apart biological changes in diversity and those resulting from bias. Lastly, continued phylogenetic work will enable the use of phylogenetic comparative methods to elucidate the origins of actinopterygian biogeography and subsequent patterns of radiation throughout their rise to dominate aquatic faunas.

Fossilbrush: An R package for automated detection and resolution of anomalies in palaeontological occurrence data

Abstract Fossil occurrence databases are indispensable resources to the palaeontological community, yet present unique data cleaning challenges. Many studies devote significant attention to cleaning fossil occurrence data prior to analysis, but such efforts are typically bespoke and difficult to reproduce. There are also no standardised methods to detect and resolve errors despite the development of an ecosystem of cleaning tools fuelled by the concurrent growth of neontological occurrence databases. As fossil occurrence databases continue to increase in size, the demand for standardised, automated and reproducible methods to improve data quality will only grow. Here, we present semi‐automated cleaning solutions to address these issues with a new R package fossilbrush. We apply our cleaning protocols to the Paleobiology Database to assess the prevalence of anomalous entries and the efficacy and impact of our methods. We find that anomalies may be effectively resolved by comparison against a published compendium of stratigraphic ranges, improving the stratigraphic quality of the data, and through methods which detect outliers in taxon‐wise occurrence stratigraphic distributions. Despite this, anomalous entries remain prevalent throughout major clades, with often more than 30% of genera in major fossil groups (e.g. bivalves, echinoderms) displaying stratigraphically suspect occurrence records. Our methods provide a way to flag and resolve anomalous taxonomic data before downstream palaeobiological analysis and may also aid in the automation and targeting of future cleaning efforts. We stress, however, that our methods are semi‐automated and are primarily for the detection of potential anomalies for further scrutiny, as full automation should not be a substitute for expert vetting. We note that some of our methods do not rely on external databases for anomaly resolution and so are also applicable to occurrences in neontological databases, expanding the utility of the fossilbrush R package.

Lizards (Reptilia: Squamata) from the Caatinga, northeastern Brazil: Detailed and updated overview

AbstractThe Caatinga is the largest seasonal dry tropical forest in South America and it has been historically neglected in terms of its biodiversity. Regarding lizards, different studies led to the current knowledge of diversity and endemism in Caatinga, but detailed syntheses are scarce in the literature. We present the most detailed and up-to-date synthesis of knowledge about Caatinga lizards by providing a detailed (i) list of species; (ii) taxonomic richness patterns; (iii) knowledge gaps and spatial biases; and (iv) detailed distribution maps of all species that contain at least one occurrence record within Caatinga limits. We created a distribution database using occurrences of lizards in Caatinga based on scientific collections, field collection, and literature. We produce up-to-date distribution maps, calculate the Extent of Occurrence and provide the environmental and bioclimatic profile for each species recorded. We draw taxonomic richness and sampling gap maps. Our database has 20,538 records of occurrence of lizards of the Caatinga. We recorded 93 lizard species (13 families), 52.7% of which are endemic. Forthy-four percent of the species present restricted distributions. We identified that 53% of the Caatinga area (or 70% of the municipalities) has no record of occurrence of lizards. The data presented are an important step towards synthesizing in detail the accumulated knowledge about Caatinga lizards and is crucial for accurate strategies for the conservation planning. It directs actions to advance our knowledge on Caatinga lizards: to concentrate inventories in sample void areas; continuous update of the species occurrence database, advance in the generation of autoecology data for species.

Spatial patterns of evolutionary diversity in Cactaceae show low ecological representation within protected areas

Mapping biodiversity patterns across taxa and environments is crucial to address the evolutionary and ecological dimensions of species distribution, suggesting areas of particular importance for conservation purposes. Within Cactaceae, spatial diversity patterns are poorly explored, as are the abiotic factors that may predict these patterns. We gathered geographic and genetic data from 921 cactus species by exploring both the occurrence and genetic databases, which are tightly associated with drylands, to evaluate diversity patterns, such as phylogenetic diversity and endemism, paleo-, neo-, and superendemism, and the environmental predictor variables of such patterns in a global analysis. Hotspot areas of cacti diversity are scattered along the Neotropical and Nearctic regions, mainly in the desertic portion of Mesoamerica, Caribbean Island, and the dry diagonal of South America. The geomorphological features of these regions may create a complexity of areas that work as locally buffered zones over time, which triggers local events of diversification and speciation. Desert and dryland/dry forest areas comprise paleo- and superendemism and may act as both museums and cradles of species, displaying great importance for conservation. Past climates, topography, soil features, and solar irradiance seem to be the main predictors of distinct endemism types. The hotspot areas that encompass a major part of the endemism cells are outside or poorly covered by formal protection units. The current legally protected areas are not able to conserve the evolutionary diversity of cacti. Given the rapid anthropogenic disturbance, efforts must be reinforced to monitor biodiversity and the environment and to define/plan current and new protected areas.

Dispersals from the West Tethys as the source of the Indo-West Pacific diversity hotspot in comatulid crinoids

AbstractConspicuous centers of biodiversity are frequently attributed to local conditions that promote speciation or resistance to extinction, but recent diversification studies indicate this mode of explanation might not be very general, so it may be fruitful to revisit the role of dispersal in concentrating biodiversity. Here we consider the processes underlying the marine diversity hotspot in the Indo-West Pacific among comatulid crinoids, suspension-feeding echinoderms conspicuous on modern tropical reefs. We used ancestral-range reconstruction on a phylogeny of extant crinoids, assembled a new occurrence database of fossil comatulids and interrogated it with probabilistic preservational models, and developed a morphological character matrix to estimate the relationships among living and fossil comatulids. Ancestral-range reconstruction on a phylogeny of extant comatulids recovers an origin outside the Indo-Pacific and elevated dispersal into it. A new occurrence database records the comatulid clade spreading out gradually from origin in the Early Jurassic of the West Tethys. Comatulids do not appear in their modern hotspot until the Oligocene, and taphonomic analyses show these results cannot be explained solely as a result of inadequate sampling in Asia and Oceania. Finally, phylogenetic analyses demonstrate that deeply nested crown-group comatulids had originated before the clade became well established in the East Tethys, implying many independent dispersals into the modern hotspot. These consilient results suggest a biodiversity hotspot that owes its existence to dispersals out of the ancient West Tethys rather than to elevated in situ diversification.

Potato late blight (Phytophthora infestans) disease forecasting using an auto-encoded long short-term memory recurrent neural networks in North-Western Algeria

Potato late blight, caused by Phytophthora infestans (Mont.) de Bary, is the most destructive disease that threatens potato producers in North-Western Algeria. In these areas, it is not rare that potato growers miss crucial treatments or apply unnecessary ones during growing seasons. To address this situation, the introduction of a scientific-based decision support system should improve the disease management strategy and reduce growing costs to farmers, consumers, and protect the environment. For this purpose, we set up a supervised deep-learning classification process (long-short-term-memory/autoencoder) that classify and predict early late blight outbreak 30 days ahead of its occurrence based on a set of determinant climatic factors. The classification results of the long short term memory-autoencoders (LSTM’s-AE) regarding our multi-annual potato late blight disease occurrence database confirms that the unimodal BlightT_LSTM-AE model that accounts for temperature is the overall best model and temperature is the key parameter to a valid prediction of early late blight disease outbreak, in all targeted regions.

Ecological niche models and point distribution data reveal a differential coverage of the cacao relatives (Malvaceae) in South American protected areas

For many regions, such as in South America, it is unclear how well the existent protected areas network (PAs) covers different taxonomic groups and if there is a coverage bias of PAs towards certain biomes or species. Publicly available occurrence data along with ecological niche models might help to overcome this gap and to quantify the coverage of taxa by PAs ensuring an unbiased distribution of conservation effort. Here, we use a published occurrence database of 271 species from the cacao family (Malvaceae) to explore how South American PAs cover species with different distribution, abundance, and threat status. Furthermore, we compared the performance of online databases, expert knowledge, and modelled species distributions in estimating species coverage in PAs. We found 79 species from our survey (29% of the total) lack any record inside South American PAs and that 20 out of 23 species potentially threatened with extinction are not covered by PAs. The area covered by South American PAs was low across biomes, except for Amazonia, which had a relative high PA coverage, but little information on species distribution within PA available. Also, raw georeferenced occurrence data were underestimating the number of species in PAs, and projections from ecological niche models were more prone to overestimating the number of species represented within PAs. We discuss that the protection of South American flora in heterogeneous environments demand for specific strategies tailored to particular biomes, including collecting specimens inside PAs in less collected areas, and the delimitation of areas for protection in more known areas.

Assessing Climate Change Impacts on Island Bees: The Aegean Archipelago.

Simple SummaryIn this study, we conducted, for the first time, an extensive climate change impact assessment of bee pollinators in the Aegean Islands, Greece, a regional bee hotspot in the Mediterranean. We located the current biodiversity and future extinction hotspots in the region and identified areas in urgent need for conservation prioritization, by undertaking an overlap analysis with the established protected areas network in Greece. Most bee species occurring in the archipelago are expected to face severe range contractions and there is evidence of an underlying extinction debt in the study area. Our work could serve as the baseline for the integration of a rather neglected, yet extremely economically and ecologically important taxonomic group, the bees, in the systematic conservation planning in the archipelago.Pollinators’ climate change impact assessments focus mainly on mainland regions. Thus, we are unaware how island species might fare in a rapidly changing world. This is even more pressing in the Mediterranean Basin, a global biodiversity hotspot. In Greece, a regional pollinator hotspot, climate change research is in its infancy and the insect Wallacean shortfall still remains unaddressed. In a species distribution modelling framework, we used the most comprehensive occurrence database for bees in Greece to locate the bee species richness hotspots in the Aegean, and investigated whether these might shift in the future due to climate change and assessed the Natura 2000 protected areas network effectiveness. Range contractions are anticipated for most taxa, becoming more prominent over time. Species richness hotspots are currently located in the NE Aegean and in highly disturbed sites. They will shift both altitudinally and latitudinally in the future. A small proportion of these hotspots are currently included in the Natura 2000 protected areas network and this proportion is projected to decrease in the coming decades. There is likely an extinction debt present in the Aegean bee communities that could result to pollination network collapse. There is a substantial conservation gap in Greece regarding bees and a critical re-assessment of the established Greek protected areas network is needed, focusing on areas identified as bee diversity hotspots over time.

Integrating historical observations alters projections of eastern North American spruce–fir habitat under climate change

AbstractSpruce–fir (Picea–Abies) forests of the North American Acadian Forest Region are at risk of disappearing from the northeastern United States and Canada due to climate change. Species distribution models (SDMs) have been used to predict changes in this critical transitional ecosystem in the past, but none have addressed how seasonal patterns of temperature and precipitation interact to influence tree species abundance. Inferences have also been limited by contemporary inventory data that could not fully characterize species ranges because they either, (1) only sampled species occurrence after large‐scale human disturbance and settlement, or (2) did not span critical geopolitical boundaries (e.g., the US–Canadian border) that intersect the focal species' range(s). Here, we built new SDM models to better assess the bioclimatic distribution of four spruce–fir species and to test the importance of seasonal climate interactions. We compiled an extensive database of tree occurrence and abundance from recent (~1955–2012) and historical time periods (1623–1869) to model current species distributions and to predict how these might change under future climate. We found that including historical tree data in our SDMs revealed previously unrecognized suitable habitat along the southern edge of species' contemporary ranges. Random forest models predicted occurrence with high accuracy (area under receiver operator curve >0.98), and the seasonal climate variables that emerged as most important for these cold‐adapted species all included interactions that reflected sensitivity to colder temperatures, and preferences for wet weather concentrated in the winter months. Under moderate climate warming (representative concentration pathway 6.0), the northeastern United States retained additional suitable habitat when historical data were included through 2060 for three of the four species: red spruce (Picea rubens), black spruce (Picea mariana), and balsam fir (Abies balsamea), while white spruce (Picea glauca) habitat contracted into Canada. In contrast, future predictions from models that used contemporary data alone forecast extirpation for all four species from the northeastern United States. Overall, these findings highlight that prediction of species ranges in transitional ecosystems that span geopolitical boundaries and gradients of intense land use are improved when historical data and seasonal climate interactions of both temperature and precipitation variables are incorporated.

Global geographical and latitudinal variation in butterfly species richness captured through a comprehensive country‐level occurrence database

AbstractMotivationInsects provide vital ecological functions and account for over half of all described species. An at least basic understanding of their geographical distributions is key for addressing a range of central ecological and evolutionary questions and to inform conservation. However, even for popular groups, such as butterflies, the knowledge of species’ distributions at global scale remains highly incomplete. To address this information gap, we present a data product of comprehensive country‐level occurrences for the 19,327 accepted species of extant butterflies. This compilation is based on a quality‐controlled combination of 165 literature sources and publicly available occurrence records from Global Biodiversity Information Facility (GBIF), harmonized to a global master taxonomy, and constitutes 159,659 (87,506 unique) species–country combinations. We developed a protocol for the integration of country‐level information from literature into the process of cleaning/validating species point occurrence records that facilitates dynamic updates of these country‐level checklist data. Such occurrence records are available for less than 54% of the species, with an apparent bias towards temperate regions and taxa. We use this combined database for a global assessment of the geographical variation in the diversity of butterflies, including an analysis of latitudinal gradients in the species richness—the first undertaken at this higher resolution. Country‐level richness decreases from the equator to the poles, both with and without control for country sizes. The presented data and analyses highlight the potential of leveraging multiple types of distribution information, particularly for taxa with limited data and their incorporation in ecological and conservation analysis. Our database and associated workflows provide a basis for an improved biogeographical understanding and conservation of insect biodiversity.Main types of variables containedCountry‐level occurrences and their sources.Spatial location and grainGlobal, 256 countries.Time period and grain1861 to 2021.Major taxa and level of measurement19,191 accepted species of extant butterflies.Software format.csv, .shp.

The Ordovician diversification of sea urchins: systematics of the Bothriocidaroida (Echinodermata: Echinoidea)

The echinoids of the order Bothriocidaroida represent the initial burst of sea urchin diversification. They were the first echinoids to achieve widespread biogeographical dispersal and achieved high levels of species richness compared to other clades of stem group echinoids. Following long-standing controversy regarding their phylogenetic affinities within the phylum Echinodermata, bothriocidaroids are now regarded as echinoids. The species- and genus-level phylogenetic relationships of the bothriocidaroids, are, however, less clearly known. We herein compile a database of bothriocidaroid occurrences, undertake detailed phylogenetic analyses of all named species within the Bothriocidaroida, and provide updated diagnoses for all species. Our phylogenetic analysis includes species belonging to three genera: Bothriocidaris, Unibothriocidaris and Neobothriocidaris. Furthermore, we describe a new species, Neobothriocidaris pentlandensis sp. nov., from the Silurian of Scotland and Sweden, using micro-computed tomography and scanning electron microscopy. This species has implications for understanding the diversity dynamics of bothriocidaroids before and after the Late Ordovician mass extinction and the palaeobiogeographical distribution of bothriocidaroids in the Silurian. Using Bayesian and parsimony-based phylogenetics, we demonstrate that Neobothriocidaris is a distinct clade, and depending upon the analytical technique, Unibothrioidaris and Bothriocidaris are also resolved as monophyletic. Unibothriocidaris appears to have become extinct in the Sandbian, while Neobothriocidaris and Bothriocidaris survived the Late Ordovician extinction events and lasted at least until the Ludlow. Furthermore, we performed statistical time-calibration of our phylogenetic trees and show that bothriocidaroids originated in the Dapingian or Darriwilian, diversifying in the Darriwilian to Sandbian and reaching peak diversity in the Sandbian and Katian. This Sandbian and Katian peak is similar to that observed in other echinoderm clades, as well as other animal groups during the Ordovician radiation, and may be linked to heightened sea level and expansive tropical shelves present in the Upper Ordovician, and to new inhabitable environments linked with Ordovician oxygenation.

Abstract TP91: Incidence Of Long-term Acute Medical Events In Treated Patients With Acute Ischemic Stroke From A United States Administrative Database

There is limited information on long-term risk of acute medical events after acute ischemic stroke (AIS) treatment with tissue plasminogen activator (tPA) or mechanical thrombectomy (MT). We sought to determine the incidence of seven acute medical events at 1 and 5 years after AIS treatment using an administrative database. The Optum Clinformatics Data Mart database was used to construct the cohort of patients aged 30+ years with AIS diagnosis (ICD-10 I63 or ICD-9 433.x1, 434.x1, 436 or DRG 061-063) during the period: 01/01/2015-06/30/2020 with at least 1-year observation prior to cohort entry. Using procedure coding (CPT or ICD-9/10), patients were grouped as tPA only, MT only, tPA+MT, or untreated. Excluded were patients with an acute event in year preceding first AIS treatment, or first AIS diagnosis for untreated patients. Acute medical events were assessed at 1 and 5 years. The denominator was calculated as the person-years (PY) (per 100) from AIS diagnosis date or treatment, until event occurrence date or database end. The Charlson-comorbidity score (CCS) was used to measure concomitant illness severity.The 313,756-patient AIS cohort was mostly male, had a mean age of 72 years, with 8% receiving intervention. In the first year, cardiovascular event rates were highest in the tPA+MT group for recurrent AIS (10.9/100 PY), myocardial infarction (4.8/100 PY), and venous thromboembolism (4.3/100 PY). All-cause mortality (35.2/100 PY) and urinary tract infections (31.4/100 PY) were highest in the tPA+MT group. The tPA group had the highest rate for pneumonia (18.6/100 PY). The untreated group had the lowest rate for all events. All event rates decreased at 5 years, with the largest decline (-34%) in recurrent AIS.Stroke patients remain at significant risk of morbidity in the first year after stroke, in spite of treatment, but rates of acute medical events decrease over time possibly related to prevention strategies.

Primate malarias as a model for cross-species parasite transmission.

Parasites regularly switch into new host species, representing a disease burden and conservation risk to the hosts. The distribution of these parasites also gives insight into characteristics of ecological networks and genetic mechanisms of host-parasite interactions. Some parasites are shared across many species, whereas others tend to be restricted to hosts from a single species. Understanding the mechanisms producing this distribution of host specificity can enable more effective interventions and potentially identify genetic targets for vaccines or therapies. As ecological connections between human and local animal populations increase, the risk to human and wildlife health from novel parasites also increases. Which of these parasites will fizzle out and which have the potential to become widespread in humans? We consider the case of primate malarias, caused by Plasmodium parasites, to investigate the interacting ecological and evolutionary mechanisms that put human and nonhuman primates at risk for infection. Plasmodium host switching from nonhuman primates to humans led to ancient introductions of the most common malaria-causing agents in humans today, and new parasite switching is a growing threat, especially in Asia and South America. Based on a wild host-Plasmodium occurrence database, we highlight geographic areas of concern and potential areas to target further sampling. We also discuss methodological developments that will facilitate clinical and field-based interventions to improve human and wildlife health based on this eco-evolutionary perspective.

The Amazon River plume, a barrier to animal dispersal in the Western Tropical Atlantic

The dispersal of marine organisms can be restricted by a set of isolation mechanisms including hard barriers or hydrological features. In the Western Atlantic Ocean, the Amazon River discharge has been shown to act as a biogeographical barrier responsible for the differences in reef fish communities between Caribbean Sea and Northeast Brazil continental shelves. Here, we compare the diversity of all Animalia phyla from biogeographic ecoregions along the Tropical Western Atlantic continental shelf to test the hypothesis that the Amazon River plume spatially structures species diversity. For that, we used beta diversity estimators and multivariate ecological analysis on a database of species occurrence of the whole animal kingdom including 175,477 occurrences of 8,375 species from six ecoregions along the Western Tropical Atlantic. Results of the whole animal kingdom and the richest phyla showed that the Caribbean Sea and Tropical Brazil ecoregions are isolated by the Amazon River Plume, broadening and confirming the hypothesis that it acts as a soft barrier to animal dispersal in the Western Tropical Atlantic. Species sharing is larger northwestwards, in direction of the Caribbean than the opposite direction. Beyond species isolation due to local characteristics such as low salinity and high turbidity, our results suggest the dominant northwestward currents probably play a major role in animal dispersion: it enhances the flux of larvae and other planktonic organisms with reduced mobility from Brazil to Caribbean and hinders their contrary movement. Thus, the Amazon area is a strong barrier for taxa with reduced dispersal capacity, while species of pelagic taxa with active swimming may transpose it more easily.

New technologies can support data collection on endangered shark species in the Mediterranean Sea

In the last 50 yr, shark populations showed steep declines in the Mediterranean Sea. The IUCN lists most Mediterranean species as threatened (55%), while considering 27.5% of them Data Deficient. Here, sharks are currently one of the rarest and more elusive groups of animals, and data from fisheries and scientific monitoring still insufficiently support robust abundance and distribution assessments. New technologies can fill this data gap by linking people and scientists through new monitoring strategies. SharkPulse, an international collaborative project, aims at creating a large world database of shark occurrence records by mining images on the web, social networks, and private archives. Here we analyzed 1186 sharkPulse records from the Mediterranean Sea. We collected records to characterize spatio-temporal patterns on 37 species, highlighting distribution changes for 5, and, by using generalized linear models, estimating trends in sighting for the most abundant species. With 273 records, Hexanchus griseus had the most sighting records since the beginning of the series. We identified pupping areas and aggregation sites for immature Prionace glauca and Isurus oxyrinchus; pinpointed strongholds of the Critically Endangered Squatina squatina to focus conservation efforts; and identified broader than previously reported regional distribution ranges for Alopias superciliosus, Dalatias licha, Heptranchias perlo, H. griseus, Oxynotus centrina, and P. glauca. We confirmed that fishing is still the major threat for Mediterranean sharks and call for a greater effort in controlling the emerging patterns with efficient conservation effort indexes. If properly standardized, opportunistic data can efficiently and cost-effectively advance our understanding of shark abundance, distribution, and conservation status.

Socio-Economic Impacts of Occurrences on Railways

The paper presents partial outputs of an applied research project aimed at evaluating the socio-economic impacts of occurrences emerging on the railway and their reflection into the economic evaluation of railway construction projects. The article builds on the research results presented within previous scientific articles where the unit impacts of sub-categories of occurrences on the Czech railways were determined using a detailed Database of Occurrences for the 2011-2018 period. These impacts were related both to one railway station and one kilometre of the wide line for the occurrence sub-categories. The values obtained were subsequently verified on case studies of specific railway infrastructure projects implemented in the Czech Republic. The results of the case studies raised the need to create an alternative methodology for the evaluation of socio-economic impacts, which would more accurately reflect the real situation on the railway. The aim of the paper is to modify the originally designed methodology for evaluating the socio-economic impacts of occurrences into a new methodology, which would relate the impacts of occurrences only to a standard kilometre of wide line, i.e. without taking account of separate impacts of occurrences on one railway station. The proposed methodology was verified on a case study, which compares the real values of socio-economic impacts emerging on the railway in the period under research, the values determined using the original methodology and the values determined according to the newly modified methodology.

Data on Holocene Fossil Benthic Foraminifera from Sunda Shelf, Offshore Southeastern Peninsular Malaysia

This paper documents a database of fossil foraminiferal occurrences from a core sample (2 m) retrieved from offshore southeastern Peninsular Malaysia, in 1993, with additional data on their modern distribution from published source. Five sub-samples were analysed for foraminiferal studies (0.1 m, 0.4 m, 0.6 m, 1.2 m, and 2.0 m), alongside with their diversity indices values. In addition, we also present the lithological description of the core sediment, together with the radiocarbon age of our sample. These data are potentially be reused in other paleoceanography related research, such as reconstructing paleo environments, and for future research on the Late-Quaternary/Holocene sedimentary and sea-level history of Sunda Shelf.

Drivers of phylogenetic structure in Amazon freshwater fish assemblages

AbstractAimPhylogenetic relatedness among species can provide useful information on the diversification history and past dispersal events that may have shaped contemporary assemblages. Here, using of the most comprehensive fish occurrence database currently available and a global molecular phylogeny of ray‐finned fishes, we evaluate the respective roles of historical and contemporary processes in generating and maintaining fish assemblage phylodiversity patterns among 97 sub‐drainages covering the Amazon River basin.LocationAmazon River basin.TaxonFreshwater fishes.MethodsUsing a large comprehensive database of freshwater fish species distributions, and a global molecular phylogeny of ray‐finned (actinopterygian) fishes, we estimated historical and contemporary environmental effects on sub‐drainage fish phylodiversity patterns using three phylogenetic metrics standardized for richness effect: Phylogenetic Diversity (ses.PD), Mean pairwise Phylogenetic Distance between species capturing patterns at older evolutionary timescales (ses.MPD), and Mean Nearest Taxon Distance capturing patterns at younger evolutionary timescales (ses.MNTD).ResultsWe found significant effects of elevation gradients, contemporary climate, and water types on assemblage phylodiversity patterns. Furthermore, we found significant relationships among the three phylogenetic metrics used, and between these metrics and the distance of sub‐drainages to the Amazon River mouth, representing the Amazon basin West‐East longitudinal gradient.Main conclusionsPhylogenetic diversity showed a highly non‐random spatial distribution across the Amazon basin. Beyond significant regional effects of several contemporary and historical drivers, there was a significant West‐East decline in sub‐drainage assemblages phylogenetic clustering, along with an increase in phylogenetic diversity. These latter patterns suggest deeper evolutionary divergences among taxa located to the East, and more recent radiations in the Western sub‐drainages. Based on these findings and given that assemblages are, on average more species‐rich in sub‐basins of the Western part of the basin than in their Eastern relatives, we conclude that Western Amazon can be seen as an evolutionary “cradle” of biodiversity for freshwater fishes.

The fungal literature-based occurrence database for southern West Siberia (Russia).

BackgroundThe paper presents the initiative on literature-based occurrence data mobilisation of fungi and fungi-related organisms (literature-based occurrences, Darwin Core MaterialCitation) to develop the Fungal literature-based occurrence database for the southern West Siberia (FuSWS). The initiative on mobilisation of literature-based occurrence data started in the northern part of West Siberia in 2016. The present project extends the initiative to the southern regions and includes ten administrative territories (Tyumen Region, Sverdlovsk Region, Chelyabinsk Region, Omsk Region, Kurgan Region, Tomsk Region, Novosibirsk Region, Kemerovo Region, Altai Territory and Republic of Altai). The area occupies the central to southern part of the West Siberian Plain and extends for about 1.5 K km from the west to the east from the eastern slopes of the Ural Mountains to Yenisey River and from north to south—about 1.3 K km. The total area equals about 1.4 million km2.The initiative is actively growing in spatial, collaboration and data accumulation terms. The working group of about 30 mycologists from eight organisations dedicated to the data mobilisation was created as part of the Siberian Mycological Society (informal organisation since 2019). They have compiled the almost complete bibliographic list of mycology-related papers for the southern West Siberia, including over 900 publications for the last two centuries (the earliest dated 1800). All literature sources were digitised and an online library was created to integrate bibliography metadata and digitised papers using Zotero bibliography manager. The analysis of published sources showed that about two-thirds of works contain occurrences of fungi for the scope of mobilisation.At the time of the paper submission, the database had been populated with a total of about 8 K records from 93 sources. The dataset is uploaded to GBIF, where it is available for online search of species occurrences and/or download. The project's page with the introduction, templates, bibliography list, video-presentations and written instructions is available (in Russian) at the web site of the Siberian Mycological Society. The initiative will be continued in the following years to extract the records from all published sources.New informationThe paper presents the first project with the aim of literature-based occurrence data mobilisation of fungi and fungi-related organisms in the southern West Siberia. The full bibliography and a digital library of all regional mycological publications created for the first time includes about 900 published works. By the time of paper submission, nearly 8 K occurrence records were extracted from about 90 literature sources and integrated into the FuSWS database published in GBIF.

Continental‐scale shifts in termite diversity and nesting and feeding strategies

Typically, termites are treated as a single guild, which ignores important internal diversity, including diverse feeding and nesting traits. These termite traits are crucial for both ecosystem‐level fluxes and trophic webs, with implications for vertebrate species. Despite their ecological importance, the large‐scale distribution of termite feeding and nesting traits and the relationship with termite diversity is largely unknown. We investigated whether functional diversity, species richness and feeding (wood, litter, grass and dung) and nesting trait (aboveground mound, belowground nest, inside tree or outside tree nest) distributions of termites were climatically controlled. To address this gap, we assembled a continental‐scale database of termite traits and occurrence in Australia and modelled termite nesting and feeding traits in response to macroclimate. Functional richness and evenness increased primarily with temperature. Australia showed multiple hotspots of termite diversity with each hotspot showing a distinct guild composition. The large‐scale distribution of nesting traits showed that aboveground nesting species were the most common nesting guild in the dry and wet tropics, while belowground nesting dominated in seasonally cold arid environments, demonstrating a strong climatic control on nesting strategy. Given their large biomass and many interactions with other species, the macroecology of termite traits may be especially important in predicting shifts in other species' distributions at continental and global scales.