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Influence of past and current factors on the beta diversity of coastal lagoon fish communities in South America
<p><strong>Aim: </strong>We aimed to assess the relative influence of past (Quaternary paleodrainage characteristics) and current factors on the beta diversity of freshwater fishes in coastal lagoons and explore the main processes involved.</p> <p><strong>Location:</strong> Atlantic coast of South America. Taxon: Fishes (173 species)</p> <p><strong>Methods:</strong> We built a dataset of species occurrence in 129 lagoons across eight freshwater ecoregions of the world (FEOWs) located between latitudes 0° and 36° and calculated beta diversity (βjac) and its turnover (βjtu) and nestedness (βjne) components. We used a partial Mantel test and multiple regressions on distance matrices to evaluate the importance of past and current factors, and of geographical distance in determining beta diversity. Past variables were those representing the historical freshwater habitat during the last glacial maximum (LGM), and contemporary variables were those related to current habitat.</p> <p><strong>Results:</strong> We found high values of βjac within the FEOWs, with βjtu prevailing over βjne. Both past (paleodrainage) and current (drainage area, salinity, and lagoon area) factors affected species dissimilarity (βjac = 46%) and its components (βjtu = 44% and βjne =20%), although explanation was, in part, shared with geographical distance. Individually, the influence of past factors was prevalent in beta diversity and its components.</p> <p><strong>Main Conclusions:</strong> The results suggest that major changes in the availability of freshwater habitats and connectivity since the Pleistocene must have affected the colonization, extinction and recolonization processes of fishes along the eastern coast of South America. We suggest that the high beta diversity values may result from limited dispersal after extinctions in the LGM and that the dissimilar freshwater fish communities currently seen were formed mainly by heterogeneous subsets of the regional species pool that persisted in landscape refuges during past sea level increases and then recolonized coastal lagoons.</p>
Supporting code, tables and data for: Megafrugivores as fading shadows of the past: Extant frugivores and the abiotic environment as the most important determinants of the distribution of palms in Madagascar
<p>The extinction of all Madagascar's megafrugivores ca. 1000 years ago, may have left its signature on the current distribution of vertebrate-dispersed plants across the island, due to the loss of effective seed dispersal. In this study, we dissect the roles of extinct and extant frugivore distributions, abiotic variables, human impact and spatial predictors on the compositional turnover, or beta-diversity, of palm (Arecaceae) species and their fruit sizes across 40 assemblages on Madagascar. Variation partitioning showed that palm beta-diversity is mostly shaped by the distribution of extant frugivores (8 lemur, 3 bird, 2 rodent and 1 bat species) and the abiotic environment (e.g., forest cover, slope and temperature), and to a lesser extent by the distribution of extinct frugivores (5 giant lemur and 3 elephant bird<i> </i>species)<i>. </i>However, the contribution of these variables differed between dry western assemblages and wet eastern assemblages, with a more prominent role, albeit still small, of extinct megafrugivores in the west. These results suggest that palm distributions in the dry west of Madagascar, where megafrugivores were probably most abundant in the past, still show signatures of past interactions. With a fourth-corner analysis we observed that the distribution of palm species with relatively large fruits and seeds was negatively associated with home range of extant mammalian frugivores and frugivore richness of both past and extant communities, and positively associated with the hand-wing index (HWI) – a proxy for dispersal ability - of extant bird communities. This suggests that palm species with relatively large fruits tend to occur in places with fewer, small-ranged mammalian frugivores, which may indicate dysfunctional seed dispersal, although a few wide-ranging bird species may compensate this loss by dispersing the seeds of small-to medium-sized palm fruits. Our results shed new light on anachronisms in Madagascar, and how defaunation and past interactions may underlie current plant distributions.</p>
Past wet-dry climate cycles inform Central Asia's future
<p>Here we present the original dat of high-resolution pollen, sediment grain size and stable isotopes for cyclic moisture changes in Lop Nur, northwestern China, Central Asia since the Last Glacial Maximum. The pollen data includes the pollen abundance, concentration and flux of dominant types. The grain size data includes sand, silt, and clay. The stable isotope data comprises C and N. </p>
Wake vortices and dissipation in a tidally modulated flow past a three-dimensional topography
<p>LES simulation data of tidally modulated flow past an abyssal hill. Data used in the figures are available</p>
Simulated cycles of East Asian temperature and precipitation over the past 425 ka
<p>These files contain the model outputs from NorESM-L and CESM that are used to analyse and draw the main parts of Figures in our paper entitled "Simulated cycles of East Asian temperature and precipitation over past 425 ka".</p>
Molecular phylogeny reveals the past transoceanic voyages of drywood termites (Isoptera, Kalotermitidae)
<p><span>Termites are major decomposers in terrestrial ecosystems and the second most diverse lineage of social insects. The Kalotermitidae form the second-largest termite family and are distributed across tropical and subtropical ecosystems, where they typically live in small colonies confined to single wood items inhabited by individuals with no foraging abilities. How the Kalotermitidae have acquired their global distribution patterns remains unresolved. Similarly, it is unclear whether foraging is ancestral to Kalotermitidae or was secondarily acquired in a few species. These questions can be addressed in a phylogenetic framework. We inferred time-calibrated phylogenetic trees of Kalotermitidae using mitochondrial genomes of ~120 species, about 27% of kalotermitid diversity, including representatives of 21 of the 23 kalotermitid genera. Our mitochondrial genome phylogenetic trees were corroborated by phylogenies inferred from nuclear ultraconserved elements derived from a subset of 28 species. We found that extant kalotermitids shared a common ancestor 84 Mya (75–93 Mya 95% HPD), indicating that a few disjunctions among early-diverging kalotermitid lineages may predate Gondwana breakup. However, most of the ~40 disjunctions among biogeographic realms were dated at less than 50 Mya, indicating that transoceanic dispersals, and more recently human-mediated dispersals, have been the major drivers of the global distribution of Kalotermitidae. Our phylogeny also revealed that the capacity to forage is often found in early-diverging kalotermitid lineages, implying the ancestors of Kalotermitidae were able to forage among multiple wood pieces. Our phylogenetic estimates provide a platform for critical taxonomic revision and future comparative analyses of Kalotermitidae.</span></p>
Interpreting past trophic ecology of a threatened species, kea (Nestor notabilis), from museum specimens
<p>When ecosystems are under severe pressure or environments change, trophic position and intraspecific niche width may decrease or narrow, signalling that conservation action is required. In New Zealand, alpine and sub-alpine ecosystems have been extensively modified through farming since 19th century European settlement, with consequences for indigenous species such as the kea (Nestor notabilis). We investigated feather stable isotope values in the kea and predicted a lower trophic position in modern kea populations, to reflect reduced lowland habitat and a mixed diet with more plant material. We predicted that size and sex would influence trophic values in this sexually dimorphic species, with larger birds more likely to have a high protein diet. We examined potential dietary changes in 68 museum collected kea from 1880s to 2000s, first recording accession details including provenance and sex, and measuring culmen length. We used bulk carbon and nitrogen stable isotopes analyses (BSIA) of feathers and a further feather subset using compound-specific stable isotopes analyses of amino acids (CSIA-AA) to obtain isotopic values and estimate trophic position. BSIA showed δ15N values in kea feathers declined through time, and could indicate that early century kea were highly omnivorous, with δ15N values on average higher than in modern kea. Variance in δ15N values was greater after 1950, driven by a few individuals. Few differences between males and females were evident, although females in the south region had lower δ15N values. There was a tendency for large male birds to have higher trophic values, perhaps reflecting dominant male bird behaviour noted in historical records. Nonetheless, CSIA-AA performed on a subset of the data suggested that variation in BSIA is likely due to baseline changes rather than relative trophic position which may be more homogenous than these data indicate. Although there was more variability in modern kea, we suggest caution in interpretation. Stable isotope data, particularly CSIA-AA, from museum specimens can reveal potential change in ecological networks, as well as sexually dimorphic feeding patterns within species. The data can reveal temporal and regional variation in species trophic position and changes in ecosystem integrity to inform conservation decision-making.</p>
Past, present and future of chamois science
<p><span>The chamois <em>Rupicapra</em> spp. is the most abundant mountain ungulate of Europe and the Near East, where it occurs as two species, the Northern chamois <em>R. rupicapra</em> and the Southern chamois <em>R. pyrenaica</em>. Here, we provide a state-of-the-art overview of research trends and the most challenging issues in chamois research and conservation, focusing on taxonomy and systematics, genetics, life history, ecology and behavior, physiology and disease, management, and conservation. Research on <em>Rupicapra</em> has a longstanding history and has contributed substantially to the biological and ecological knowledge of mountain ungulates. Although the number of publications on this genus has markedly increased over the past two decades, major differences persist with respect to knowledge of species and subspecies, with research mostly focusing on the Alpine chamois <em>R. r. rupicapra</em> and, to a lesser extent, the Pyrenean chamois <em>R. p. pyrenaica</em>. In addition, a scarcity of replicate studies of populations of different subspecies and/or geographic areas limits the advancement of chamois science. Since environmental heterogeneity impacts behavioral, physiological and life history traits, understanding the underlying processes would be of great value from both an evolutionary and conservation/management standpoint, especially in the light of ongoing climatic change. Substantial contributions to this challenge may derive from a quantitative assessment of reproductive success, investigation of fine-scale foraging patterns, and a mechanistic understanding of disease outbreak and resilience. Improving conservation status, resolving taxonomic disputes, identifying subspecies hybridization, assessing the impact of hunting and establishing reliable methods of abundance estimation are of primary concern. Despite being one of the most well-known mountain ungulates, substantial field efforts to collect paleontological, behavioral, ecological, morphological, physiological and genetic data on different populations and subspecies are still needed to ensure a successful future for chamois conservation and research.</span></p>
Predicting past and future SARS-CoV-2-related sick leave using discrete time Markov modelling
<p><strong>Background: </strong>Prediction of SARS-CoV-2-induced sick leave among healthcare workers (HCWs) is essential for being able to plan the healthcare response to the epidemic.</p> <p><strong>Methods: </strong>During first wave of the SARS-Cov-2 epidemic (April 23<sup>rd </sup>to June 24<sup>th</sup>, 2020), the HCWs in the greater Stockholm region in Sweden were invited to a study of past or present SARS-CoV-2 infection. We develop a discrete time Markov model using a cohort of 9449 healthcare workers (HCWs) who had complete data on SARS-CoV-2 RNA and antibodies as well as sick leave data for the calendar year 2020. The one-week and standardized longer term transition probabilities of sick leave and the ratios of the standardized probabilities for the baseline covariate distribution were compared with the referent period (an independent period when there were no SARS-CoV-2 infections) in relation to PCR results, serology results and gender.</p> <p><strong>Results:</strong> The one-week probabilities of transitioning from healthy to partial sick leave or full sick leave during the outbreak as compared to after the outbreak were highest for healthy HCWs testing positive for large amounts of virus (ratio: 3.69, (95% confidence interval, CI: 2.44-5.59) and 6.67 (95% CI: 1.58-28.13), respectively). The proportion of all sick leaves attributed to COVID-19 during outbreak was at most 55% (95% CI: 50%-59%).</p> <p><strong>Conclusions: </strong>A robust Markov model enabled use of simple SARS-CoV-2 testing data for quantifying past and future COVID-related sick leave among HCWs, which can serve as a basis for planning of healthcare during outbreaks.</p>
Genome-wide DNA methylation patterns harbor signatures of hatchling sex and past incubation temperature in a species with environmental sex determination
<p>Conservation of thermally sensitive species depends on monitoring organismal and population-level responses to environmental change in real time. Epigenetic processes are increasingly recognized as key integrators of environmental conditions into developmentally plastic responses, and attendant epigenomic datasets hold potential for revealing cryptic phenotypes relevant to conservation efforts. Here, we demonstrate the utility of genome-wide DNA methylation (DNAm) patterns in the face of climate change for a group of especially vulnerable species, those with temperature-dependent sex determination (TSD). Due to their reliance on thermal cues during development to determine sexual fate, contemporary shifts in temperature are predicted to skew offspring sex ratios and ultimately destabilize sensitive populations. Using reduced-representation bisulfite sequencing, we profiled the DNA methylome in blood cells of hatchling American alligator (<em>Alligator mississippiensis</em>), a TSD species lacking reliable markers of sexual dimorphism in early life-stages. We identified 120 sex-associated differentially methylated cytosines (DMCs; FDR < 0.1) in hatchlings incubated under a range of temperatures, as well as 707 unique temperature-associated DMCs. We further developed DNAm-based models capable of predicting hatchling sex with 100% accuracy (in 20 training samples and 4 test samples) and past incubation temperature with a mean absolute error of 1.2˚C (in 4 test samples) based on the methylation status of 20 and 24 loci, respectively. Though largely independent of epigenomic patterning occurring in the embryonic gonad during TSD, DNAm patterns in blood cells may serve as non-lethal markers of hatchling sex and past incubation conditions in conservation applications. These findings also raise intriguing questions regarding tissue-specific epigenomic patterning in the context of developmental plasticity. </p>
The emergence of a cryptic lineage and cytonuclear discordance through past hybridization in the Japanese fire-bellied newt, Cynops pyrrhogaster (Amphibia: Urodela)
<p> Discrepancies in geographic variation patterns between nuclear DNA and mitochondrial DNA (mtDNA) are the result of the complicated differentiation processes in organisms and the key to understanding their true evolutionary process. The genetic differentiation of the northern and southern Izu lineages of the Japanese newt <em>Cynops pyrrhogaster</em> was investigated <span>through their single nucleotide polymorphism</span> variations by multiplexed ISSR genotyping by sequencing (MIG-seq). We found three genetic groups (Tohoku, N-Kanto, and S-Kanto) those not detected by mtDNA in the northern lineage. N-Kanto has intermediate genetic characteristics between Tohoku and S-Kanto. The western populations of N-Kanto are close to S-Kanto, whereas the eastern populations of N-Kanto are close to Tohoku. Tohoku, N-Kanto, and S-Kanto are now moderately isolated from each other and have unique genetic characteristics. An estimation of the evolutionary history by t<span>he </span><span>Approximate Bayesian Computation </span>approach suggested that Tohoku diverged from the common ancestor of S-Kanto and S-Izu. Then, S-Kanto and S-Izu split and the recent hybridization between Tohoku and S-Kanto gave rise to N-Kanto. The origin of N-Kanto through the hybridization is relatively young and seems to be related to changes in the distributions of Tohoku and S-Kanto as a result of the climatic oscillation in the Pleistocene. We concluded that the mitochondrial genome of S-Kanto was captured into Tohoku and the past original mitochondrial genome of Tohoku was entirely swept out from Tohoku through the hybridization. </p>
Fig. 2 in PAST DISTRIBUTION OF TILIA-FEEDING PHYLLONORYCTER MICROMOTH (LEPIDOPTERA: GRACILLARIIDAE) IN THE RUSSIAN FAR EAST BASED ON SURVEY OF HISTORICAL HERBARIUM
Fig. 2. Herbarium specimens of Tilia amurensis with Phyllonorycter mines, originating
Range-wide intraspecific variation reflects past adaptation to climate in a gypsophile Mediterranean shrub
<p>Phenotypic differences among populations stem from the interaction between neutral and adaptive processes, and phenotypic plasticity. Although clinal trait variation along climatic gradients often evolves in widely-distributed species, it is unknown whether substrate specialization, such as that of Mediterranean gypsum plants, has constrained adaptation to climate. Using a common garden experiment with two contrasting watering treatments, we quantified phenotypic plasticity, assessed evidence for footprints of selection using FST - QST comparisons, and identified the ecological factors driving genetically-based phenotypic differentiation of 11 populations encompassing the full environmental range of the gypsum shrub Lepidium subulatum. We found evidence for genetic differentiation among populations related to climatic differences, with populations from warmer and drier sites showing lower specific leaf area (SLA) and leaf N, earlier phenology, greater water use efficiency (WUE) and greater fitness. Multiple lines of evidence suggest that this differentiation was driven by past divergent selection rather than neutral processes. All populations showed high phenotypic plasticity, indicating that plasticity has not been selected against, even in populations from sites with harsher climatic conditions.<br>Synthesis. Our results indicate that, despite strong substrate specialization, adaptive differentiation related to climatic gradients occurs in this species. However, we also found that populations from mesic sites may be particularly vulnerable to future climate change given their relatively lower fitness under both wet and dry conditions.</p>
Immersive Audio Remixing of Mono Recordings of the 1950s and 1960s: Rediscovering Musical Treasures from the Past
<p><strong>IMPORTANT NOTE</strong></p> <p>The song <em>B-A-B-Y</em> was written by Isaac Hayes and David Porter, then also arranged by Booker T. Jones and Steve Cropper, and performed by Carla Thomas in 1966.</p> <p>The following binaural sound remixes of <em>B-A-B-Y</em> have been performed in a research context, with four various HRTF profiles coming from the Listen HRTF Database by Ircam, for the AES research paper “Immersive Audio Remixing of Mono Recordings of the 1950s and 1960s: Rediscovering Musical Treasures from the Past”, presented at the 156th AES Convention on June 15-17, 2024, in Madrid, Spain. </p> <p>I, the undersigned Jean Viardot, the first author of this paper, testify that nothing about the composition, the arrangement, or any element of the musical content of the song, has been manipulated to obtain this remix. Only the sound rendering of a digitalized version of the original master has been manipulated and modified to address the research questions being stated in the abovementioned paper.</p> <p>To date (5/11/2024), I have not made any profit with this remix, and I forbid anyone to publish it without my permission. For any intention to publish, broadcast, or market this remix, please contact me beforehand.</p>
Sedimentary DNA of a human‐impacted lake in Western Canada (Cultus Lake) reveals changes in micro‐eukaryotic diversity over the past ~200 years
<p>Although the use of genetic analyses of sedimentary DNA to track changes in biodiversity has increased over the last decade, questions remain as to how well DNA captures past ecological conditions. Even less is known about how extracellular and intracellular DNA are archived in lake sediments and whether the two fractions yield similar information. Here we characterized the changes of micro‐eukaryotic communities over the past ~200 years in Cultus Lake (British Columbia, Canada), for which a rich body of limnological data and a pre‐existing multi‐proxy paleolimnological study exist. We generated and analyzed 18S rRNA gene amplicons and found that extracellular and intracellular DNA provided different insights, with the preservation of extracellular DNA compromised in sediments older than ~30 years. Principal Coordinates and indicator species analyses based on intracellular DNA showed that changes in micro‐eukaryotic diversity occurred at similar time periods as those identified with the classical paleolimnological study. For instance, decreases of Opisthokonta amplicons occurred during years with elevated numbers of sockeye salmon spawners, which might be associated with an increase of herbivory by juvenile sockeye salmon. Furthermore, two diatom species identified morphologically exhibited similar temporal dynamics to two diatom taxa identified genetically, suggesting that sedimentary DNA can track past diatom species changes as well as micro‐eukaryotic community changes. Overall, our study provides insights into the use of extracellular and intracellular DNA in sedimentary records and showed that sedimentary DNA enriches our understanding of micro‐eukaryotic community changes over centennial time scales.</p>
Data from: Data for habitat quality or quantity? Niche marginality across 21 plants and animals suggests differential responses between highland and lowland species to past climatic changes
<p>Climatic changes can affect species distributions, population abundance, and evolution. Such organismal responses could be determined by the amount and quality of available habitats, which can vary independently. In this study, we assessed changes in habitat quantity and quality independently to generate explicit predictions of the species' responses to climatic changes between Last Glacial Maximum (LGM) and present day. We built ecological niche models and distribution models for 21 reptile, mammal, and plant taxa from the Baja California peninsula inhabiting lowland or highland environments. Geological data suggests the CCSM global circulation model is a better representation of LGM climate for the Baja California peninsula. Significant niche divergence was detected for all clades within species, along with significant differences in the niche breadth and area of distribution between northern and southern clades. Most clades showed a reduction in distribution area towards LGM. Further, niche marginality (used as a measure of habitat quality) was higher during LGM for most clades, except for northern highland species. Our results suggest that changes in habitat quantity and quality can affect organismal response independently. This allows the prediction of genomic signatures associated with changes in effective population size and selection pressure that could be explicitly tested to support our models.</p>
Replication Package: The Past, Present, and Future of Research on the Continuous Development of AI
<p>Replication package for the publication regarding the <strong>The Past, Present, and Future of Research on the Continuous Development of AI.</strong></p> <p> </p> <p> </p>
Fig. 2 in Echoes from the past¦ rediscovering Isoscelipteron fulvum Costa, 1863 (Neuroptera¦ Berothidae) in Italy.
Fig. 2.- Sampling trap and micro-habitat in which the female specimen was collected in 2017.
Figure 4 in Past ecosystems drive the evolution of the early diverged Symphyta (Hymenoptera: Xyelidae) since the earliest Eocene
Figure 4. Photograph of Proxyelia pankowskii gen. et sp. nov. Holotype FOBU14313. Scale bar: 1 mm.
Fig. 1 in Past, present and future of host‾parasite co-extinctions
Fig. 1. Cumulative number of documented species extinctions according to IUCN (2014).
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.