cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v41ns1rsf
title: Swimming and defense - competing needs across ontogeny in armored fishes (Agonidae)

description: Biological armors are potent model systems for understanding the complex
 series of competing demands on protective exoskeletons; after all, armored
 organisms are the product of millions of years of refined engineering
 under the harshest conditions. Fishes are no strangers to armor, with
 various types of armor plating common to the 400 million years of
 evolution in both jawed and jawless fishes. Here we focus on the poachers
 (Agonidae), a family of armored fishes native to temperate waters of the
 Pacific rim. We examined armor morphology, body stiffness, and swimming
 performance in the Northern Spearnose Poacher (Agonopsis vulsa) over
 ontogeny.  As juveniles, these fishes make frequent nocturnal
 forays into the water column in search of food, while heavily armored
 adults are bound to the benthos. Most armor dimensions and density
 increase with body length, as does body stiffness. Juvenile poachers have
 enlarged spines on their armor whereas adults invest more mineral in armor
 plate bases. Adults are stiffer and accelerate faster than juveniles with
 an anguilliform swimming mode. Subadults more closely approximate adults
 more than smaller juveniles, with regards to both swimming and armor
 mechanics. Poacher armor serves multiple functions over ontogeny, from
 facilitating locomotion, slowing sinking, and providing defense.
description: Armor morphometrics were measured from micro-CT data (Bruker
 Skyscan 1173)  Swimming behaviors were captured using a
 GoPro Hero4 Swimming kinematics were analyzed using a
 custom MatLab script github.com/CDonatelli/PoacherArmorMechanics (Donatelli et al., 2017) All data were statistically analyzed using the R programming language
description: Scaling morphometrics & armor mineral density - use
 PoacherScalingCode.R w/ ArmorMorphometrics.csv or
 PoacherBMD_R.csv   For swimming
 kinematics - use PoacherNotebook.Rmd with PoacherKinematics.csv and
 PoacherMTSMerge.csv. Former are kinematics data, latter are stress/strain
 data from MTS.  
 ProcessedMTSData.zip are MTS stress-displacement data in the
 raw.
DOI: 10.5061/dryad.1c59zw3sc
title: Data from: Insights in the diagnosis of a retinal arteriovenous malformation

description: Objective: To describe a patient with vitreous hemorrhage due to
 peripheral retinal ischemia and neovascularization, who was diagnosed with
 an underlying retinal arteriovenous malformation. Methods: A 15-year old
 girl presented with sudden-onset painless visual loss in the right eye.
 She underwent a full ophthalmologic work-up. Results: BCVA was less than
 20/400 in the right eye, 20/20 in the left eye. Intraocular pressure and
 anterior segment examination were unremarkable. Fundoscopy revealed an
 impenetrable vitreous hemorrhage in the right eye. The left eye was
 completely unremarkable. Examination during a 23-gauge pars plana
 vitrectomy showed dilated, tortuous arteriovenous vessels extending from
 the optic disc and peripheral neovascularization. A clinical diagnosis of
 retinal arteriovenous malformation was made. During surgery, a peripheral
 retinal photocoagulation was completed to avoid rebleeding. During the
 post-operative period, a fluorescein angiography demonstrated additional
 macular microangiopathy and diffuse retinal nonperfusion in the periphery.
 MRI brain revealed no cerebral or orbital vascular anomaly, confirming a
 retinal arteriovenous malformation group 1. Conclusion: Retinal
 arteriovenous malformations are thought of to be stable over time. However
 complications such as ischemia, neovascularization and vitreous hemorrhage
 might occur. Observation is warranted.  As such, timely treatment
 can be offered to avoid complications.
description: Data was collected by full ophthalmologic work-up using
 ultrasonography, fluoangiography and OCT of the macula
DOI: 10.5061/dryad.rxwdbrv5d
title: Climate manipulations differentially affect plant population dynamics within versus beyond northern range limits

description: Predicting species’ range shifts under future climate is a central goal of
 conservation ecology. Studying populations within and beyond multiple
 species’ current ranges can help identify whether demographic responses to
 climate change exhibit directionality, indicative of range shifts, and
 whether responses are uniform across a suite of species. We quantified the
 demographic responses of six native perennial prairie species planted
 within and, for two species, beyond their northern range limits to a
 three-year experimental manipulation of temperature and precipitation at
 three sites spanning a latitudinal climate gradient in the Pacific
 Northwest, USA. We estimated population growth rates (λ) using integral
 projection models and tested for opposing responses to climate in
 different demographic vital rates (demographic compensation). Where
 species successfully established reproductive populations, warming
 negatively affected λ at sites within species’ current ranges. Contrarily,
 warming and drought positively affected λ for the two species planted
 beyond their northern range limits. Most species failed to establish a
 reproductive population at one or more sites within their current ranges,
 due to extremely low germination and seedling survival. We found little
 evidence of demographic compensation buffering populations to the climate
 treatments. Synthesis: These results support predictions across a suite of
 species that ranges will need to shift with climate change as populations
 within current ranges become increasingly vulnerable to decline. Species
 capable of dispersing beyond their leading edges may be more likely to
 persist, as our evidence suggests that projected changes in climate may
 benefit such populations. If species are unable to disperse to new habitat
 on their own, assisted migration may need to be considered to prevent the
 widespread loss of vulnerable species.
DOI: 10.5061/dryad.k98sf7m3r
title: Upper Columbia River Steelhead Capture-Recapture-Recovery data (2008-2018)

description: In the Columbia River basin, USA, predation by Caspian terns (Hydroprogne
 caspia) on U.S. Endangered Species Act (ESA)-listed juvenile salmonids
 (smolts; Oncorhynchus spp.) has led to predator management actions to
 reduce predation; however, the assumption that reduced predation
 translates into greater salmonid survival, either within the life stage
 where predation occurs or across their lifetime, has remained untested. To
 address this critical uncertainty, we analyzed a long-term (2008-2018)
 mark-recapture-recovery dataset of ESA-listed steelhead trout (O. mykiss)
 that were tagged (n = 78,409) and subsequently exposed to predation during
 smolt out-migration through multiple river reaches (spatial-scales),
 jointly estimating weekly probabilities of steelhead survival, mortality
 due to bird predation, and mortality due to other causes. This concurrent
 estimation across time-stratified cohorts allowed for the direct
 measurement of the strength, magnitude, and direction of relationships
 between survival and Caspian tern predation. Results of our analysis
 provided novel evidence that predation by Caspian terns may have been a
 super additive source of mortality during the smolt life-stage and a
 partially additive source of mortality to the adult life-stage. The
 estimated levels of compensation have important implications for predator
 management actions aimed at increasing the survival of endangered
 salmonids, and the modelling approach developed herein provides a
 framework to directly quantify the impacts of source-specific mortality
 factors on prey populations.
DOI: 10.5061/dryad.kwh70rz1f
title: Data from: Using three-dimensional geometric morphometric and dental topographic analyses to infer the systematics and paleoecology of fossil treeshrews (Mammalia, Scandentia)

description: Treeshrews are small, Indomalayan mammals closely related to primates.
 Previously, three-dimensional geometric morphometric analyses were used to
 assess patterns of treeshrew lower second molar morphology, which showed
 that the position of molar landmarks covaries with intraordinal
 systematics. Another analysis used dental topographic metrics to test
 patterns of functional dental morphology and found that molar curvature,
 complexity, and relief were an effective means for examining patterns of
 variation in treeshrew dietary ecology. Here, we build on these analyses
 by adding two fossil taxa; Prodendrogale yunnanica, from the Miocene of
 China and Ptilocercus kylin from the Oligocene of China. Our results show
 that Pr. yunnanica had a dental bauplan more like that of a tupaiid than
 that of a ptilocercid, but that the extant tupaiids, including Tupaia and
 Dendrogale, are more similar to one another in this regard than any are to
 Prodendrogale. This is contrary to our expectations as Prodendrogale is
 hypothesized to be most closely related to Dendrogale. Ptilocercus kylin,
 which has been proposed to be the sister taxon of Pt. lowii, is
 characterized by dental morphology like that of Pt. lowii in crest and
 cuspal position but is interpreted to have been more frugivorous. It has
 been claimed that Ptilocercus has undergone little morphological change
 through time. Our results suggest that Pt. kylin was more ecologically
 distinct from Pt. lowii than previously proposed, providing a glimpse into
 a more complex evolutionary history of that group than had been inferred.
description: We collected landmark and topographic data from surface files
 segmented from micro-ct scans of both fossil and extant treeshrew taxa
 using Avizo.
DOI: 10.5061/dryad.z08kprr99
title: Multiple environmental stressors induce an adaptive maternal effect

description: Evolution of adaptation requires predictability and recurrence of
 functional contexts. Yet, organisms live in multi-faceted environments
 that are dynamic and ever-changing, making it difficult to understand how
 complex adaptations evolve. This problem is particularly apparent in the
 evolution of adaptive maternal effects, which are often assumed to require
 reliable and discrete cues that predict conditions in the offspring
 environment. One resolution to this problem is if adaptive maternal
 effects evolve through pre-existing, generalized maternal pathways that
 respond to many cues and also influence offspring development. Here, we
 assess whether an adaptive maternal effect in western bluebirds is
 influenced by maternal stress pathways across multiple challenging
 environments. Combining seventeen years of hormone sampling across diverse
 environmental contexts with an experimental manipulation of the
 competitive environment, we show that multiple environmental factors
 influenced maternal corticosterone levels which, in turn, influenced the
 maternal effect on aggression of sons in adulthood. Together, these
 results support the idea that multiple stressors can induce a known
 maternal effect in this system. More generally, it suggests that
 activation of general pathways, such as the HPA axis, may simplify and
 facilitate the evolution of adaptive maternal effects by integrating
 variable environmental conditions into pre-existing maternal physiological
 systems.
DOI: 10.5061/dryad.44j0zpcb5
title: Chromosome-level clam genome helps elucidate the molecular basis of adaptation to a buried lifestyle

description: With gene prediction and functional annotation, a final nonredundant
 consensus gene set for C. sinensis was obtained, and 27,564 protein-coding
 genes were predicted in the final assembled genome. Finally, 27,344
 protein-coding genes were annotated, accounting for 99.2% of all the
 predicted genes.
description: The prediction of genes in the <i>C. sinensis</i>
 genome was performed using a combination of three approaches:
 homolog-based, <i>de novo</i>, and transcriptome-based
 predictions.
DOI: 10.15468/dl.4gq7da
title: Occurrence Download

description: A dataset containing 1597 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Nyctiphanes australis",
 "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 1597 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002356-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3n5tb2rdd
title: Data from: “A cleaner break”: genetic divergence between geographic groups and sympatric phenotypes revealed in ballan wrasse (Labrus bergylta)

description: Capture and long-distance translocation of cleaner fish to control lice
 infestations on marine salmonid farms has the potential to influence wild
 populations via overexploitation in source regions, and introgression in
 recipient regions. Knowledge of population genetic structure is therefore
 required. We studied the genetics of ballan wrasse, a phenotypically
 diverse and extensively used cleaner fish, from 18 locations in Norway and
 Sweden, and from Galicia, Spain. We detected two very distinct genetic
 groups in Scandinavia, northwest and southeast. These groups were split by
 a stretch of sandy beaches in southwest Norway, representing a habitat
 discontinuity for this rocky shore associated benthic egg laying species.
 The Galician sample was highly differentiated from all Scandinavian
 samples, but overall closer to northwestern samples. . Distinct genetic
 differences were observed between sympatric spotty and plain phenotypes in
 Galicia, but not in Scandinavia. The mechanisms underlying the
 geographical patterns between phenotypes are discussed, but not
 identified. We conclude that extensive aquaculture-mediated translocation
 of ballan wrasse from Sweden and southern Norway, to western and middle
 Norway, has the potential to mix genetically distinct populations. These
 results question the sustainability of the current cleaner fish practice.
description: Genotype results for Scandinavian and Galician ballan wrasse
 <em>(Labrus bergylta</em>) genotyped for panel of 82 randomly
 selected SNPs.  The dataset was the basis
 for population structure analysis and subsequent comparison between
 sampling locations in Scandinavia and Galicia, Spain, as well as between a
 subset of phenotype sorted samples from some Scandinavian locations and
 from Galicia.  Dataset resulting from SNP genotyping on
 an Agena iPlex Platform, called in TyperAnalyzer
DOI: 10.15468/dl.vhbmhj
title: Occurrence Download

description: A dataset containing 2009 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Arachis hypogaea",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 2009 records from 202 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002358-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d82nwh
title: Occurrence Download

description: A dataset containing 17 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Canada",
 "EstablishmentMeans is introduced",
 "OccurrenceStatus is Present",
 "StateProvince is Alberta",
 "TaxonKey is Plantae"
 ]
}

 The dataset includes 17 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002357-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.fttdz08q0
title: Genotypes of Swan Geese Anser cygnoides using 17 nuclear microsatellite loci at 14 locations.

description: Dispersal affects the spatial distribution and population structure of
 species.Dispersal is often male-biased in mammals while female-biased in
 birds, with the notable exception of the Anatidae. In this study, we
 tested genetic evidence for sex-biased dispersal (SBD) in the Swan Goose
 Anser cygnoides, an Asian endemic and IUCN vulnerable species, which has
 been increasingly restricted to breeding on Mongolian steppe wetlands. We
 analyzed the genotypes of 278 Swan Geese samples from 14 locations at 14
 microsatellite loci. Results from assignment indices, analysis of
 molecular variance and five other population descriptors all failed to
 support significant SBD signals for the Swan Goose at the landscape level.
 Although overall results showed significantly high relatedness within
 colonies (suggesting high levels of philopatry in both sexes), local male
 genetic structure at the 1,050 km distance indicated greater dispersal
 distance for females from the eastern sector of the breeding range. Hence,
 local dispersal is likely scale-dependent and female-biased within the
 eastern breeding range. These findings are intriguing considering the
 prevailing expectation for there to be female fidelity in most goose
 species. We suggest that while behaviour-related traits may have
 facilitated the local genetic structure for the Swan Goose, several
 extrinsic factors, including the decreasing availability of the nesting
 sites and the severe fragmentation of breeding habitats, could have
 contributed to the absence of SBD at the landscape level. The
 long-distance molt-migration that is typical of goose species such as the
 Swan Goose may also have hampered our ability to detect SBD. Hence, we
 urge further genetic sampling from other areas in summer to extend our
 results, complemented by field observations to confirm our DNA analyses
 conclusions about sex-specific dispersal patterns at different spatial
 scales in this species.
DOI: 10.15468/dl.a9bnpy
title: Occurrence Download

description: A dataset containing 191761 records in GBIF matching the query:
SELECT
 '431' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 41.89415215079384
 AND decimalLatitude &lt;= 46.479780028101516
 AND decimalLongitude &gt;= -94.41597137694312
 AND decimalLongitude &lt;= -83.91704653307544
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 191761 records were derived from 300 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002342-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.6djh9w0xw
title: Siderophore-mediated interactions determine the disease suppressiveness of microbial consortia

description: Interactions between plant pathogens and root-associated microbes play an
 important role in determining disease outcomes. While several studies have
 suggested that steering these interactions may improve plant health, such
 approaches have remained challenging in practice. Because of low iron
 availability in most soils, competition for iron via secreted siderophore
 molecules might influence microbial interaction outcomes.Here we tested if
 bacterial interactions mediated by iron-scavenging
 siderophores can be used to predict the disease suppressiveness
 of microbial consortia against soil-borne Ralstonia solanacearum bacterial
 pathogen in tomato rhizosphere. Iron availability significantly affected
 the interactions within inoculated consortia and between the consortia and
 the pathogen. We observed contrasting effects of siderophores and other
 non-siderophore metabolites on the pathogen growth, while the siderophore
 effects were relatively much stronger. Specifically, disease incidence was
 reduced in vivo when the inoculated consortia produced siderophores that
 the pathogen could not use for its own growth. Employing
 siderophore-mediated interactions to engineer functionally robust
 microbial inoculants show promise in protecting plants from soil-borne
 pathogens.
description: All data were collected from indoor and greenhouse pot
 experiments, please check the corresponding article for details.
description: General linear mixed models were used to examine the siderophore
 and non-siderophore metabolite effects on the pathogen and consortia
 member growth in mono, pairwise and consortia co-cultures. In these
 analyses, we conducted separate models to explore consortia community
 richness, composition and strain identity effects (presence and absence of
 certain strain) on strain interactions. Differences in disease incidence
 was explained by three quantitative factors that were measured in vitro:
 consortia siderophore production, consortia siderophore-mediated effect on
 the pathogen growth and siderophore-mediated interactions between
 inoculated consortia members. All variables were fitted as continuous
 variables and one separate model was used for each variable. All analyses
 were performed using R 3.3.1 program (www.r-project.org).
DOI: 10.5061/dryad.0cfxpnvzg
title: Data from: Co-introduction of native mycorrhizal fungi and plant seeds accelerates restoration of post-mining landscapes

description: 1. Grasslands are among the most threatened terrestrial biomes, and
 habitat conservation alone will be insufficient to meet biodiversity
 goals. While restoration of indigenous grasslands is a priority, conflict
 with economic objectives means that incorporation of alternative habitats
 is necessary to offset grassland loss. With up to 800,000 km² of land
 affected by mining globally, there is an opportunity to create additional
 grassland habitat in post-mining landscapes. 2. We aimed to assess whether
 co-introduction of native arbuscular mycorrhizal (AM) fungi and plants is
 an efficient means of initializing species rich vegetation recovery in
 barren post-mining landscapes. We established an experiment in three
 post-mining areas in Estonia, where we seeded plots with native plant
 seeds and inoculated them with trap cultured native AM fungi from a
 similar habitat. We measured the abundance and composition of soil AM
 fungal and aboveground plant communities in two consecutive years using
 relevés, high-throughput sequencing and fatty acid profiling. 3. Our
 results demonstrate that co-introduction of native plants and AM fungi is
 an effective way to establish species rich vegetation in post-mining
 areas. Co-introduction of symbiotic partners resulted in higher richness,
 diversity and abundance of plants and AM fungi than when either partner
 was introduced individually. However, the plant and AM fungal communities
 in sown and inoculated plots were not distinct from those in uninoculated
 treatments; they rather formed a subset of all taxa present on the sites
 but exhibited higher diversity than uninoculated plots. 4. Synthesis and
 applications: This study shows that managing the below-ground microbiome
 is an essential part of vegetation restoration. The availability of
 symbiotic partners can be considered a key aspect determining the
 diversity of restored vegetation. Targeted inoculations with native and
 habitat-specific AM fungi could therefore increase restoration
 success.28-Apr-2020
description: Please refer to Vahter et al., 2020 in Journal of Applied Ecology
 for details on data collection and handling.
description: All relevant information is given in the first row of the
 document.