cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.82v52rd
title: Data from: A meta-analysis reveals global patterns of sediment effects on marine biodiversity

description: Sediment disturbances are important threats affecting marine biodiversity,
 but the variety of biological responses have not yet been synthesized.
 Here, we collate all available information to compare the extent of
 impacts across different taxonomic groups, habitat types, and pathways of
 impact (light attenuation, suspended sediment and sedimentation). Global
 1979-2017 Coral, fish, seagrass, sponge, macroalgae, ascidian, bryozoan,
 crustacean, echinoderm, mollusc, polychaeta We used meta-analyses to
 evaluate the effects of sediments across 842 observations found in 110
 publications. We also evaluated some of the biological and methodological
 factors that could explain the variable effects observed in different
 studies. We found a significant negative effect of sediments on
 behavioural responses, reproduction and recruitment, organism’s
 morphology, physiology, community abundance and diversity, and species
 interactions. In contrast, the overall effect on abundance of individual
 species was statistically non-significant and there was a strong positive
 effect on abundance for sponge and polychaete species. Many individual
 studies described physiological effects on coral reefs, but effects on
 diversity of soft-bottom and coral reef communities were particularly
 detrimental. Phototrophic species were generally more negatively impacted
 by sediments than heterotrophs, driven by strong physiological responses
 in crustose coralline algae and seagrass. Additionally, species with
 limited mobility were more vulnerable to sediment disturbances than highly
 mobile species. Sedimentation alone triggered more consistently negative
 effects on most biological responses than light depletion and suspended
 sediments. We found evidence for increased impacts on community diversity
 when more than one pathway of impact was present, indicating that these
 disturbances can disrupt whole ecosystems. Our meta-analysis for the first
 time provided strong quantitative support of negative effects of sediments
 on marine biodiversity. Taxonomic groups, habitat types, and life history
 characteristics were most influential in determining biological responses
 to sediment disturbances, highlighting the importance of an
 ecosystem-based approach when fully accounting for the impacts of sediment
description: Supporting Information
 for the paper "A meta-analysis reveals global patterns of sediment
 effects on marine biodiversity"List of studies included
 in the meta-analysis, including all information details, effect size,
 variability and the respective weightsSup_Table.xlsx
DOI: 10.5061/dryad.b9r9160
title: Data from: Kokanee–sockeye salmon hybridization leads to intermediate morphology and resident life history: implications for fisheries management

description: Stocking programs designed to return extirpated species to their
 historical range have become increasingly prevalent, punctuating the need
 to better understand the risks posed to recipient ecosystems. Here, we
 investigated the genetic and biological consequences of an anadromous
 sockeye salmon (Oncorhynchus nerka) stocking program in Skaha Lake,
 British Columbia, where substantial levels of hybridization/introgression
 with the native freshwater resident ecotype (kokanee) have been detected.
 We genetically-assigned 543 individuals (adult spawners, age-0 juveniles)
 to estimate stock proportions (pure-stock sockeye/kokanee or hybrid)
 between 2010 and 2017, with a subset undergoing otolith microchemistry
 analysis to determine migratory life history and maternal ancestry.
 Proportion of hybrid spawners varied from 5-20% across sampling years,
 while hybrid age-0 juveniles remained relatively constant (~11%). Hybrid
 spawners exhibited intermediate size relative to pure-stocks, with the
 vast majority being non-anadromous (92%) and of resident maternal ancestry
 (76%). Our results provide empirical support for previously hypothesized
 mechanisms of hybridization between O. nerka life-history forms, and
 underscore the importance of continued monitoring of stocking programs to
 quantify long-term fitness impacts of introgression and refine management
 strategies.
description: SNP genotypic data in
 GENALEX formatElliott_et_al_CJFAS.xlsx
DOI: 10.5061/dryad.f79j433
title: Data from: A new approach to study local adaptation in long-lived organisms: virtual transplant experiments

description: 1. Despite the importance of local adaptation and the extended literature
 that has addressed it, there are few methods available to explore local
 adaptation across large temporal scales. However, long-term patterns are
 likely to be essential to understanding adaptation in long-lived species,
 such as trees. 2. Here, we propose a methodology named ‘virtual transplant
 experiment’ (VTE), which uses long-term climatic variability to explore
 local adaptation to climate in natural tree populations. VTEs evaluate the
 historical response of populations to their local climate and to climates
 representative of conditions in other populations. We tested our
 methodology using simulated data and applied it in two case studies on:
 (i) Pinus nigra populations at the edge of the species distribution, where
 previous research has suggested strong climate adaptation, and (ii) Fagus
 sylvatica mesic populations, where parallel experiments showed no
 adaptation to macroclimate. 3. VTE results from simulated and real-world
 data matched our expectations, suggesting that the method accurately
 identified the patterns of local adaptation to climate in tree
 populations. VTEs consistently discriminated locally adapted populations
 in synthetic data with a known degree of local adaptation. As expected, P.
 nigra populations showed adaptation to local climate in the VTE, while F.
 sylvatica populations showed no overall local advantage. 4. Our method
 provides a new way to test for local adaptation over time scales
 encompassing the complete lifespan of trees. VTEs can complement current
 methods to study local adaptation by adding the ability to explore the
 long-term response to local climate in natural populations. The advantages
 and limitations of the different approaches to studying local adaptation
 stress the importance of combining multiple approaches to test for local
 adaptation in long-lived organisms.
description: Dendro+local_dataOriginal tree ring and climate data for: (i) tree ring simulations (only precipitation data was used to generate the growth time series, folder 'Precipitation data for sinthetic'); (ii) pinus nigra growth and climate data for 5 populations in south spain, folder 'Pinus nigra data'; (iii) Fagus sylvatica growth and climate data for 3 population in Germany (total_germany_def.csv), and Romania (total_romania_def.csv).
DOI: 10.5061/dryad.kr4rf80
title: Data from: Temporal patterns of diversification in Brassicaceae demonstrate decoupling of rate shifts and mesopolyploidization events

description: Background and Aims Whole-genome duplication (WGD) events are considered
 important driving forces of diversification. At least 11 out of 52
 Brassicaceae tribes had independent mesopolyploid WGDs followed by
 diploidization processes. However, the association between mesopolyploidy
 and subsequent diversification is equivocal. Herein we show the results
 from a family-wide diversification analysis on Brassicaceae, and elaborate
 on the hypothesis that polyploidization per se is a fundamental driver in
 Brassicaceae evolution. Methods We established a time-calibrated
 chronogram based on whole plastid genomes comprising representative
 Brassicaceae taxa and published data spanning the entire Rosidae clade.
 This allowed to set multiple calibration points and anchored various
 Brassicaceae taxa for subsequent downstream analyses. All major splits
 among Brassicaceae lineages were used in BEAST analyses of individually
 analysed 48 tribes comprising 2101 taxa in total using the internal
 transcribed spacers of nuclear ribosomal DNA. Diversification patterns
 were investigated on these tribe-wide chronograms using BAMM and were
 compared with family-wide data on genome size variation and species
 richness. Key results Brassicaceae diverged 29.9 Mya during the Oligocene,
 and the majority of tribes started diversification in the Miocene with an
 average crown group age of about 12.5 Mya. This matches the cooling phase
 right after the Mid Miocene climatic optimum. Significant rate shifts were
 detected in 12 out of 52 tribes during the Mio- and Pliocene, decoupled
 from preceding mesopolyploid WGDs. Among the various factors analysed the
 combined effect of tribal crown group age and net diversification rate
 (speciation minus extinction) is likely to explain sufficiently species
 richness across Brassicaceae tribes. Conclusions The onset of the
 evolutionary splits among tribes took place under cooler and drier
 conditions. Pleistocene glacial cycles may have contributed to the
 maintenance of high diversification rates. Rate shifts are not
 consistently associated with mesopolyploid WGD. We propose, therefore,
 that WGDs in general serve as a constant "pump" for continuous
 and high species diversification.
description: Supplementary Data 2.
 ITS alignments and BEAST trees for every tribeThe zip-file contains
 all individual tribal ITS alignments, and respective output file from
 BEAST analyses.
DOI: 10.5061/dryad.t44073r
title: Data from: Reproduction and maternal care increases oxidative stress in a mouthbrooding cichlid fish

description: Investment in reproduction and post-zygotic parental care is an
 energetically costly, yet fundamental aspect of the life history
 strategies in many species. Recently, oxidative stress has received
 attention as a potential mediator in the trade-off between reproduction,
 growth and survival. During activities that increase metabolic activity,
 such as providing offspring care, an overproduction of reactive oxygen
 species can occur that cannot be counteracted by antioxidants, leading to
 oxidative stress and tissue damage. Here, we investigated the oxidative
 costs of reproduction and maternal care over the course of the
 reproductive cycle in a mouthbrooding cichlid fish within socially stable
 and unstable environments. We manipulated social stability by disrupting
 the habitat in socially unstable tanks. We expected to see an increase in
 the burden of maternal care within unstable environments due to increased
 male harassment of females as a byproduct of increased male-male
 aggression. We found that brooding females have higher levels of oxidative
 stress than non-brooding females and oxidative stress fluctuates
 throughout the reproductive cycle. These fluctuations were driven by a
 spike in reactive oxygen metabolites at the beginning of brood care
 followed by an increase in antioxidant defense. Surprisingly, the link
 between reproduction and oxidative stress was not different between
 females from stable or unstable environments. Our study illustrates a more
 complete picture of the physiological costs of reproduction and parental
 care throughout different stages of care rather than a simplistic
 end-point observation of how reproduction and parental care affect an
 individual.
description: SAWECKI-2019-Reproduction-and-Oxidative-Stress-in-a-Mouthbrooding-Cichlid-FishThis zip file contains two excel documents. One document used for analysis of female oxidative stress and the other for analysis of the male status shifts in stable and unstable environments. There are also 4 R scripts that were used for running linear mixed models and generalized linear mixed models.
DOI: 10.5061/dryad.r9r0vj7
title: Data from: Carbon dynamics and environmental controls of a hilly tea plantation in Southeast China

description: Tea plantations are widely distributed and continuously expanding across
 subtropical China in recent years. However, carbon flux exchanges from tea
 plantation ecosystems are poorly understood at the ecosystem level. In
 this study, we use the eddy covariance technique to quantify the magnitude
 and temporal variations of the net ecosystem exchange (NEE) in tea
 plantation in Southeast China over four years (2014-2017). The result
 showed that the tea plantation was a net carbon sink, with an annual NEE
 that ranged from -182.40 g C m-2 to -301.51 g C m-2, which was a much
 lower carbon sequestration potential than other ecosystems in subtropical
 China. Photosynthetic photon flux density (PPFD) explained the highest
 proportion of the variation in NEE and gross primary productivity (GPP)
 (for NEE: F=389.89, P &lt; 0.01; for GPP: F=1018.04, P &lt; 0.01),
 and air temperature (Ta) explained the highest proportion of the variation
 in ecosystem respiration (RE) (F=13141.81, P &lt; 0.01). The strong
 pruning activity in April not only reduced the carbon absorption capacity
 but also provided many plant residues for respiration, which switched the
 tea plantation to a carbon source from April to June. Suppression of NEE
 at higher air temperatures was due to the decrease in GPP more than the
 decrease in RE, which indicated that future global warming may transform
 this subtropical tea plantation from a carbon sink to carbon source.
description: energy
 balancedaily flux and
 meteorological datamonthly flux and
 meteorological data
DOI: 10.5061/dryad.1gh5376
title: Data from: Functional morphology of a lobopod: case study of an onychophoran leg

description: Segmental, paired locomotory appendages are a characteristic feature of
 Panarthropoda — a diversified clade of moulting animals that includes
 onychophorans (velvet worms), tardigrades (water bears), and arthropods.
 While arthropods acquired a sclerotised exoskeleton and articulated limbs,
 onychophorans and tardigrades possess a soft body and unjointed limbs
 called lobopods, which they inherited from Cambrian lobopodians. To date,
 the origin and ancestral structure of the lobopods and their
 transformation into the jointed appendages are all poorly understood. We
 therefore combined high-resolution computed tomography with high-speed
 camera recordings to characterise the functional anatomy of a trunk
 lobopod from the onychophoran Euperipatoides rowelli. Three-dimensional
 reconstruction of the complete set of muscles and muscle fibres as well as
 non-muscular structures revealed the spatial relationship and relative
 volumes of the muscular, excretory, circulatory, and nervous systems
 within the leg. Locomotory movements of individual lobopods of E. rowelli
 proved far more diverse than previously thought and might be governed by a
 complex interplay of fifteen muscles, including one promotor, one remotor,
 one levator, one retractor, two depressors, two rotators, one flexor and
 two constrictors as well as muscles for stabilisation and haemolymph
 control. We discuss the implications of our findings for understanding the
 evolution of locomotion in panarthropods.
description: Suppl_movie_1Supplementary Movie 1. External and internal anatomy of the lobopod in E. rowelli.Suppl_movie_2Supplementary Movie 2. Haemal space inside the lobopod of E. rowelli.Suppl_movie_3Supplementary Movie 3. Muscles involved in hydrostatic pressure control, stabilisation and claw movements in E. rowelli.Suppl_movie_4Supplementary Movie 4. Individual muscles composing the lobopod of E. rowelli.Suppl_movie_5Supplementary Movie 5. High-speed footage of a walking specimen of E. rowelli.
DOI: 10.15468/dl.5d4v48
title: Occurrence Download

description: A dataset containing 496446 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Africa",
 "DatasetKey is one of (Naturalis Biodiversity Center (NL) - Botany, Tropicos MO Specimen Data, The System-wide Information Network for Genetic Resources (SINGER), A global database for the distributions of crop wild relatives, Svalbard Global Seed Vault Collection, Botanical Database of Southern Africa (BODATSA): Botanical Collections, Royal Botanic Gardens, Kew - Herbarium Specimens, FLOTROP, a massive contribution to plant diversity data for open ecosystems in Tropical Africa., Meise Botanic Garden Herbarium (BR), Tropicos Specimens Non-MO, Bioversity Collecting Mission Database)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Poaceae"
 ]
}

 The dataset includes 496446 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001797-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bwnfju
title: Occurrence Download

description: A dataset containing 1944 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Pteronura brasiliensis"
 ]
}

 The dataset includes 1944 records from 106 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001827-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.qv3811j
title: Data from: More is less: net gain in species richness, but biotic homogenization over 140 years

description: While biodiversity loss continues globally, assessments of regional and
 local change over time have been equivocal. Here, we assess changes in
 plant species richness and beta diversity over 140 years at the level of
 regions within a country. Using 19th‐century flora censuses for 14 Danish
 regions as a baseline, we overcome previous criticisms concerning short
 time series and neglect of completely altered habitats. We find that
 species composition has changed dramatically and directionally across all
 regions. Substantial species losses were more than offset by large gains,
 resulting in a net increase in species richness in all regions. The
 occupancy of initially widespread species increased, while initially rare
 species lost terrain. These changes were accompanied by strong biotic
 homogenization; i.e. regions are more similar now than they were 140 years
 ago. Species declining in Denmark were found to be in similar decline all
 over Northern Europe.
description: Data - More is Less -
 Nielsen et al - Ecol Lett 2019Data on 1958 plant
 species from Denmark. Historical data (1857 to 1883) and present data
 (2012) from the same regions. Data contains two data-files, one with
 presence-absence data from 14 Danish regions and one with regional
 abundance data from 10 Danish regions (for calculations and precausions
 relating to abundance, please see App. 2 of publication). The presence
 absence data file also includes data on whether species are native or
 exotic to Denmark.Nielsenetal_2019.xlsx
DOI: 10.5061/dryad.pp6g8v3
title: Data from: The effect of a multi-target protocol on cetacean detection and abundance estimation in aerial surveys

description: A double-platform protocol was implemented in the Bay of Biscay and
 English Channel during SCANS-III survey (2016). Two observation platforms
 using different protocols were operating on-board a single aircraft: the
 reference platform ("Scans"), targeting cetaceans, and the
 "Megafauna" platform, recording all the marine fauna visible at
 the sea surface (jellyfishes to seabirds). We tested for a potential bias
 in small cetacean detection and density estimation when recording all
 marine fauna. At a small temporal scale (30 seconds, roughly 1.5 km), our
 results provided overall similar perception probabilities for both
 platforms. Small cetacean perception was higher following the detection of
 another cetacean within the previous 30 seconds in both platforms. The
 only prior target that decreased small cetacean perception during the
 subsequent 30 seconds was seabirds, in the Megafauna platform. However, at
 a larger scale (study area), this small-scale perception bias had no
 effect on the density estimates, which were similar for the two protocols.
 As a result, there was no evidence of lower performance regarding small
 cetacean population monitoring for the multitarget protocol in our study
 area. Because our study area was characterised by moderate cetacean
 densities and small spatial overlap of cetaceans and seabirds, any
 extrapolation to other areas or time requires caution. Nonetheless, by
 permitting the collection of cost-effective quantitative data for marine
 fauna, anthropogenic activities and marine litter at the sea surface, the
 multi-target protocol is valuable for optimizing logistical and financial
 resources to efficiently monitor biodiversity and study community ecology.
description: Data_for_Lambert_et_al_2019_RSOSData and codes used to conduct analyses presented in the paper Lambert et al 2019 "The effect of a multi-target protocol on cetacean detection and abundance estimation in aerial surveys".
DOI: 10.15468/dl.j3taru
title: Occurrence Download

description: A dataset containing 2356 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Electrona carlsbergi",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 2356 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001821-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.