cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.wm37pvmkj
title: Multi-species models reveal that eDNA metabarcoding is more sensitive than backpack electrofishing for conducting fish surveys in freshwater streams

description: Environmental DNA (eDNA) sampling can provide accurate, cost-effective,
 landscape-level data on species distributions. Previous studies have
 compared the sensitivity of eDNA sampling to traditional sampling methods
 for single species, but similar comparative studies on multi-species eDNA
 metabarcoding are rare. Using hierarchical species occupancy-detection
 models, we examined whether key choices associated with eDNA metabarcoding
 (primer selection, low-abundance read filtering, and the number of
 positive water samples used to classify a species as present at a site)
 affect the sensitivity of metabarcoding, relative to backpack
 electrofishing for fish in freshwater streams. Under all scenarios
 (teleostei and vertebrate primers; 0%, 0.1% and 1% read filtering
 thresholds; 1 or 2 positive samples required to classify species as
 present), we found that eDNA metabarcoding is, on average, more sensitive
 than electrofishing. Combining vertebrate and teleostei markers resulted
 in higher detection probabilities relative to the use of either marker in
 isolation. Increasing the threshold used to filter low abundance reads
 decreased species detection probabilities but did not change our overall
 finding that eDNA metabarcoding was more sensitive than electrofishing.
 Using a threshold of two positive water samples (out of 5) to classify a
 species as present typically had negligible effects on detection
 probabilities compared to using one positive water sample. Our findings
 demonstrate that eDNA metabarcoding is generally more sensitive than
 electrofishing for conducting fish surveys in freshwater streams, and that
 this outcome is not sensitive to methodological decisions associated with
 metabarcoding.
description: Raw FASTQ files generated from a MiSeq run, prior to any
 processing.
description: Sample information (metadata) for both the FISH and VERT datasets
 have been included - these are needed to perform demultiplexing of the raw
 FASTQ files.
DOI: 10.5061/dryad.6wwpzgmwm
title: Source pools and disharmony of the world’s island floras

description: Island disharmony refers to the biased representation of higher taxa on
 islands compared to their mainland source regions and represents a central
 concept in island biology. Here, we develop a generalizable framework for
 approximating these source regions and conduct the first global assessment
 of island disharmony and its underlying drivers. We compiled vascular
 plant species lists for 178 oceanic islands and 735 mainland regions.
 Using mainland data only, we modelled species turnover as a function of
 environmental and geographic distance and predicted the proportion of
 shared species between each island and mainland region. We then quantified
 the over- or under-representation of families on individual islands
 (representational disharmony) by contrasting the observed number of
 species against a null model of random colonization from the mainland
 source pool, and analysed the effects of six family-level functional
 traits on the resulting measure. Furthermore, we aggregated the values of
 representational disharmony per island to characterize overall taxonomic
 bias of a given flora (compositional disharmony), and analysed this second
 measure as a function four island biogeographical variables. Our results
 indicate considerable variation representational disharmony both within
 and among plant families. Examples of generally over-represented families
 include Urticaceae, Convolvulaceae and almost all pteridophyte families.
 Other families such as Asteraceae and Orchidaceae were generally
 under-represented, with local peaks of over-representation in known
 radiation hotspots. Abiotic pollination and a lack of dispersal
 specialization were most strongly associated with an insular
 over-representation of families, whereas other family-level traits showed
 minor effects. With respect to compositional disharmony, large,
 high-elevation islands tended to have the most disharmonic floras. Our
 results provide important insights into the taxon- and island-specific
 drivers of disharmony. The proposed framework allows overcoming the
 limitations of previous approaches and provides a quantitative basis for
 incorporating functional and phylogenetic approaches into future studies
 of island disharmony.
description: Data collection and processing is described in detail in the
 article.
DOI: 10.5061/dryad.h44j0zphg
title: Data from RACE: Resource Aware Cost-Efficient Scheduler for Cloud Fog Environment

description: The quality of human life increases with increased usage of the Internet
 of Things (IoT). However, this massive use of IoT produces a large amount
 of data which creates a problem for data storage and analysis. Cloud
 computing is used to solve such issues like storage and processing
 requirements for data generated by IoT. However, several applications like
 traffic control, health observation, and games, etc., are time-sensitive
 and need a quick response. The delay created by sending data to the Cloud
 and then returning the Server response to the user of such programs has an
 unintended impact. To overwhelmed these limitations, the Fog computing
 concept was launched in 2012. Fog computing is an elongation of Cloud
 computing in which user services are extended to networking devices. In
 recent times the Fog computing is considered as a favorable approach to
 cope with the delay-sensitive applications. Moreover, Fog computing in
 combination with the Cloud computing model can also provide promising
 solutions to deal with compute-intensive applications. The scheduling
 challenges faced by the Fog service provider are to fulfill user requests
 with the maximum resource utilization of Fog devices while reducing the
 monetary cost of Cloud resource usage. In this research, a resource-aware
 scheduler has been proposed to distribute the incoming application modules
 to Fog devices that maximize resource utilization at the Fog layer,
 reduces the monetary cost of using Cloud resources with minimum execution
 time of applications, and minimum bandwidth usage. The proposed scheduler
 Resource Aware Cost-Efficient Scheduler (RACE) consists of two algorithms:
 ModuleScheduler: which categorizes the incoming application modules
 according to their computation and bandwidth requirements. The
 ModuleScheduler also creates a prioritized list considering the categories
 of application modules. Compare Module: Finds the suitable Fog device for
 modules execution in the prioritized list. The proposed scheduler (RACE)
 schedule the modules at the Fog layer based on their computation
 requirement and bandwidth requirement until the devices at the Fog layer
 have enough CPU capacity to accommodate the modules.
description: Since our work is related to the cloud fog environment, we have
 uploaded the relevant coding for the readers reference. The code is
 basically written in JAVA based ifog simulator. 
description: All the relevent information are expilicitly illustrated in the
 manuscript. See build.xml for examples of how to customize the build. If
 further details are required, the author would be happy to fully
 address.
DOI: 10.5061/dryad.dfn2z34zk
title: Low oxygen levels can help to prevent the detrimental effect of acute warming on mitochondrial efficiency in fish

description: Aerobic metabolism of aquatic ectotherms is highly sensitive to
 fluctuating climates. Many mitochondrial traits exhibit phenotypic
 plasticity in response to acute variations in temperature and oxygen
 availability. These responses are critical for understanding the effects
 of environmental variations on aquatic ectotherms performance. Using the
 European seabass, Dicentrarchus labrax, we determined the effects of acute
 warming and deoxygenation in vitro on mitochondrial respiratory capacities
 and mitochondrial efficiency to produce ATP (ATP/O ratio). We show that
 acute warming reduced ATP/O ratio but deoxygenation marginally raised
 ATP/O ratio, leading to compensatory effect of low oxygen availability on
 mitochondrial ATP/O ratio at high temperature. The acute effect of warming
 and deoxygenation on mitochondrial efficiency might be related to the leak
 of protons across the mitochondrial inner membrane, as the mitochondrial
 respiration required to counteract the proton leak increased with warming
 and decreased with deoxygenation. Our study underlines the importance of
 integrating the combined effects of temperature and oxygen availability on
 mitochondrial metabolism. Predictions on decline in performance of aquatic
 ectotherms due to climate change may not be accurate, since these
 predictions typically look at respiratory capacity and ignore efficiency
 of ATP production.
description: The mitochondrial respiration rates (LEAK respiration, OXPHOS
 respiration, COX activity) and the mitochondrial ATP synthesis (ATP
 production) were measured with high resolution respirometers eqquiped with
 fluorescent sensors (Oroboros Instruments, Innsbruck, Austria) and
 recorded using DatLab software. The mitochondrial efficiency to produce
 ATP (ATP/O ratio) was calculated as the ratio of ATP production to OXPHOS
 respiration.
description: The assays were performed in red muscle of seabass at 13°C and
 16°C. The animals have been fasted 24h. The mitochondria preparation was a
 homogenate. There is no missing value.
DOI: 10.5061/dryad.qz612jmcg
title: Raw data for: Plastic male mating behaviour evolves in response to the competitive environment

description: Male reproductive phenotypes can evolve in response to the social and
 sexual environment. The expression of many such phenotypes may also be
 plastic within an individual’s lifetime. For example, male Drosophila
 melanogaster show significantly extended mating duration following a
 period of exposure to conspecific male rivals. The costs and benefits of
 reproductive investment, and plasticity itself, can be shaped by the
 prevailing socio-sexual environment and by resource availability. We
 investigated these ideas using experimental evolution lines of D.
 melanogaster evolving under three fixed sex ratios (high, medium and low
 male-male competition) on either rich or poor adult diets. We found that
 males evolving in high-competition environments evolved longer mating
 durations overall. In addition, these males expressed a novel type of
 plastic behavioural response following exposure to rival males: they both
 significantly reduced and showed altered courtship delivery and exhibited
 significantly longer mating latencies. Plasticity in male mating duration
 in response to rivals was maintained in all of the lines, suggesting that
 the costs of plasticity were minimal. None of the evolutionary responses
 tested were consistently affected by dietary resource regimes.
 Collectively, the results show that fixed behavioural changes and new
 augmentations to the repertoire of reproductive behaviours can evolve
 rapidly.
description: Data collected as describe in read me tabs on excel file.
description: Readme files incorporated next to raw data tabs.
DOI: 10.5061/dryad.t4b8gtj0c
title: Dynamics behind disjunct distribution, hotspot-edge refugia, and discordant RADseq/mtDNA variability: insights from the Emei mustache toad

description: Background: The distribution of genetic diversity and the underlying
 processes are important for conservation planning but are unknown for most
 species and have not been well studied in many regions. In East Asia, the
 Sichuan Basin and surrounding mountains constitute an understudied region
 that exhibits a “ring” of high species richness overlapping the eastern
 edge of the global biodiversity hotspot Mountains of Southwest China. We
 examine the distributional history and genetic diversification of the Emei
 mustache toad Leptobrachium boringii , a typical “ring” element
 characterized by disjunct ranges in the mountains, by integrating
 time-calibrated gene tree, genetic variability, individual-level
 clustering, inference of population splitting and mixing from allele
 frequencies, and paleoclimatic suitability modeling. Results: The results
 reveal extensive range dynamics, including secondary contact after
 long-term isolation via westward dispersal accompanied by variability
 loss. They allow the proposal of a model that combines recurrent
 contractions caused by Quaternary climatic changes and some failed
 expansions under suitable conditions for explaining the shared disjunct
 distribution pattern. Providing exceptional low-elevation habitats in the
 hotspot area, the eastern edge harbors both long-term refugial and young
 immigrant populations. This finding and a synthesis of evidence from other
 taxa demonstrate that a certain contributor to biodiversity, one that
 preserves and receives low-elevation elements of the east in this case,
 can be significant for only a particular part of a hotspot. By clarifying
 the low variability of these refugial populations, we show that discordant
 mitochondrial estimates of diversity can be obtained for populations that
 experienced admixture, which would have unlikely left proportional
 immigrant alleles for each locus. Conclusions: Dispersal after long-term
 isolation can explain much of the spatial distribution of genetic
 diversity in this species, while secondary contact and long-term
 persistence do not guarantee a large variation. The model for the
 formation of disjunct ranges may apply to many other taxa isolated in the
 mountains surrounding the Sichuan Basin. Furthermore, this study provides
 insights into the heterogeneous nature of hotspots and discordant
 variability obtained from genome-wide and mitochondrial data.
DOI: 10.5061/dryad.t4b8gtj0d
title: Projected climate change threatens significant range contraction of Cochemiea halei (Cactaceae), an island endemic, serpentine adapted plant species at risk of extinction

description: Threats faced by narrowly distributed endemic plant species in the face of
 the Earth’s sixth mass extinction and climate change exposure are
 especially severe for taxa on islands. We investigated the current and
 projected distribution and range changes of Cochemiea halei, an island
 endemic cactus. This taxon is of conservation concern, currently listed as
 vulnerable on the International Union for the Conservation of Nature Red
 List and as a species of special concern under Mexican federal law. The
 goals of this study are to 1). identify the correlations between climate
 variables and current suitable habitat for C. halei; 2). determine if the
 species is a serpentine endemic or has a facultative relationship with
 ultramafic soils; 3). predict range changes of the species based on
 climate change scenarios. Location: The island archipelago in Bahía
 Magdalena on the Pacific coast, Baja California Sur, Mexico. Main
 conclusions: The occurrence of the species is found to be strongly
 correlated with ultramafic soils. The most important climate predictor for
 habitat suitability is annual temperature range. The species is predicted
 to undergo range contractions from 21% to 53%, depending on the severity
 and duration of exposure to climate change. The broader implications for a
 wide range of narrowly adapted, threatened and endemic plant species
 indicate an urgent need for threat assessment based on habitat suitability
 and climate change modeling.
description: We used temperature and precipitation variables at 30 arcsecond
 resolution and soil type, employing multiple species distribution modeling
 methods, to identify important climate and soil conditions driving current
 habitat suitability. The best model of current suitability is used to
 predict possible effects of four climate change scenarios based on best
 case to worst case representative concentration pathways, with projected
 climate data from two general circulation models, over two time
 periods.
DOI: 10.4232/1.14683
title: ARD-DeutschlandTrend 2024
title: ARD-DeutschlandTrend 2024
DOI: 10.5061/dryad.gqnk98sk4
title: Social competition stimulates cognitive performance in a sex-specific manner

description: Social interactions are thought to be a critical driver in the evolution
 of cognitive ability. Cooperative interactions, such as pair bonding,
 rather than competitive interactions have been largely implicated in the
 evolution of increased cognition. This is despite competition
 traditionally being a very strong driver of trait evolution. Males of many
 species track changes in their social environment and alter their
 reproductive strategies in response to anticipated levels of competition.
 We predict this to be cognitively challenging. Using a Drosophila
 melanogaster model we are able to distinguish between the effects of a
 competitive environment versus generic social contact by exposing flies to
 same-sex same-species competition vs different species partners, shown to
 pose non-competitive contacts. Males increase olfactory learning/memory
 and visual memory after exposure to conspecific males only, a pattern
 echoed by increased expression of synaptic genes and an increased need for
 sleep. For females, largely not affected by mating competition, the
 opposite pattern was seen. The results indicate that specific social
 contacts dependent on sex, not simply generic social stimulation, may be
 an important evolutionary driver for cognitive ability in fruit flies.
DOI: 10.5061/dryad.pzgmsbcj4
title: Data from: Temperature does not influence functional response of amphipods consuming different trematode prey

description: Direct consumption on free-living cercariae stages of trematodes by
 non-host organisms interferes with trematode transmission and leads to
 reduced infections in the next suitable hosts. Consumer functional
 responses provide a useful tool to examine relationships between
 consumption rates and ecologically relevant prey densities, whilst also
 accounting for abiotic factors that likely influence consumption rates. We
 investigated how temperature influences the consumer functional response
 of the amphipod Gammarus lacustris towards the cercariae of three
 freshwater trematodes (Diplostomum, Apatemon and Trichobilharzia).
 Amphipods displayed different functional responses towards the parasites,
 with Type II responses for Diplostomum and Type I responses for Apatemon
 prey. Temperature did not alter the consumption rate of the amphipod
 predator. Trichobilharzia was likely consumed at similar proportions as
 Diplostomum, however this could not be fully evaluated due to low
 replication. Whilst Type II responses of invertebrate predators are common
 to various invertebrate prey types, this is the first time a non-filter
 feeding predator has been shown to exhibit Type I response towards
 cercarial prey. The prey-specific consumption patterns of amphipods were
 related to cercarial distribution in the water column rather than to the
 size of cercariae or temperature influence. The substantial energy flow
 into food webs by non-host consumer organisms highlights the importance of
 understanding the mechanisms that modulate functional responses and direct
 predation in the context of parasitic organisms.
DOI: 10.5061/dryad.5qfttdz30
title: Environmental DNA effectively captures functional diversity of coastal fish communities

description: Robust assessments of taxonomic and functional diversity are essential
 components of research programs aimed at understanding current
 biodiversity patterns and forecasting trajectories of ecological changes.
 Yet, evaluating marine biodiversity along its dimensions is challenging
 and dependent on the power and accuracy of the available data collection
 methods. Here we combine three traditional survey methodologies
 [Underwater Visual Census strip transects (UVCt), Baited Underwater Videos
 (BUVs) and Small Scale Fishery catches (SSFc)], and one novel molecular
 technique [eDNA metabarcoding (eDNA) – 12S rRNA and Cytochrome Oxidase
 Subunit 1 (COI)] to investigate their efficiency and complementarity in
 assessing fish diversity. We analysed 1,716 multi-method replicates at a
 basin scale to measure taxonomic and functional diversity of Mediterranean
 fish assemblages. Taxonomic identities were investigated at species, genus
 and family level. Functional identities were assessed using combinations
 of morphological, behavioral and trophic traits. We show that: i) SSFc
 provided the higher taxonomic diversity estimates followed by eDNA, and
 then UVCt and BUV; ii) eDNA was the only method able to gather the whole
 spectrum of considered functional traits, showing the most functionally
 diversified and least redundant fish assemblages; iii) the eDNA
 effectiveness in describing functional structure reflected its lack of
 selectivity toward any considered functional trait. Our findings suggest
 that the reach of environmental DNA analysis stretches beyond taxon
 detection efficiency and provides new insights about the potential of
 metabarcoding in ecological studies.
DOI: 10.5061/dryad.3xsj3txdm
title: Ocean acidification induces distinct transcriptomic responses across life history stages of the sea urchin Heliocidaris erythrogramma

description: Ocean acidification (OA) from seawater uptake of rising carbon dioxide
 emissions impairs development in marine invertebrates, particularly in
 calcifying species. Plasticity in gene expression is thought to mediate
 many of these physiological effects, but how these responses change across
 life history stages remains unclear. The abbreviated lecithotrophic
 development of the sea urchin Heliocidaris erythrogramma provides a
 valuable opportunity to analyze gene expression responses across a wide
 range of life history stages, including the benthic, post-metamorphic
 juvenile. We measured the transcriptional response to OA in H.
 erythrogramma at three stages of the life cycle (embryo, larva, and
 juvenile) in a controlled breeding design. The results reveal a broad
 range of strikingly stage-specific impacts of OA on transcription,
 including changes in the number and identity of affected genes; the
 magnitude, sign, and variance of their expression response; and the
 developmental trajectory of expression. The impact of OA on transcription
 was notably modest in relation to gene expression changes during
 unperturbed development and dwarfed by genetic contributions from
 parentage. The latter result suggests that natural populations may provide
 an extensive genetic reservoir of resilience to OA. Taken together, these
 results highlight the complexity of the molecular response to OA, its
 substantial life history stage specificity, and the importance of
 contextualizing the transcriptional response to pH stress in light of
 normal development and standing genetic variation to better understand the
 capacity for marine invertebrates to adapt to OA.