cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4mw6m9081
title: Data from: Genomic signatures of convergent adaptation to Alpine environments in three Brassicaceae species

description: It has long been discussed to what extent related species develop similar
 genetic mechanisms to adapt to similar environments. Most studies
 documenting such convergence have either used different lineages within
 species or surveyed only a limited portion of the genome. Here, we
 investigated whether similar or different sets of orthologous genes were
 involved in genetic adaptation of natural populations of three related
 plant species to similar environmental gradients in the Alps. We used
 whole-genome pooled population sequencing to study genome-wide SNP
 variation in 18 natural populations of three Brassicaceae (Arabis alpina,
 Arabidopsis halleri, and Cardamine resedifolia) from the Swiss Alps. We
 first de novo assembled draft reference genomes for all three species. We
 then ran population and landscape genomic analyses with ~3 million SNPs
 per species to look for shared genomic signatures of selection and
 adaptation in response to similar environmental gradients acting on these
 species. Genes with a signature of convergent adaptation were found at
 significantly higher numbers than expected by chance. The most closely
 related species pair showed the highest relative over-representation of
 shared adaptation signatures. Moreover, the identified genes of convergent
 adaptation were enriched for non-synonymous mutations, suggesting
 functional relevance of these genes, even though many of the identified
 candidate genes have hitherto unknown or poorly described functions based
 on comparison with Arabidopsis thaliana. We conclude that
 adaptation to heterogeneous Alpine environments in related species is
 partly driven by convergent evolution, but that most of the genomic
 signatures of adaptation remain species-specific.
description: See Methods section of the mansucript.
description: See read me file.
DOI: 10.5061/dryad.xksn02vdb
title: PIV data of straight blade and swept blade wind turbine

description: In large wind farms, the wake behind the upstream wind turbine affects the
 performance of the downstream turbines which reduces the overall power
 output. The geometry of the wind turbine blades has significant effects on
 the mechanical efficiency of this process. Here, we suggest to utilize a
 bio-inspired blade based on the common swift wing. Common swift is known
 to be a long-distance flyer, able to stay aloft for long periods of time
 by maintaining high lift and low drag. We study the near wake flow
 characteristics of a horizontal turbine model with swept blades and its
 aerodynamic loads. These are compared with a straight-bladed turbine. The
 experiments were conducted in a water flume using particle image
 velocimetry (PIV) technique. Both blades were studied for four different
 speeds with freestream Reynolds numbers ranging from 23,000 to 41,000. Our
 results show that the near wake developed behind the swept-back blade was
 significantly different from the straight blade configuration. The near
 wake developed behind the swept-back blade exhibited relatively lower
 momentum loss and suppressed turbulent activity (mixing and production)
 compared to the straight blade. Comparing the aerodynamic characteristics,
 though the swept-back blade generated relatively less lift than the
 straight blade, the drag was relatively lower as well. Thus, the
 swept-back blade produced 2-3 times higher lift-to-drag ratio than the
 straight blade. Based on the observations, we suggest that, with improved
 design optimizations, using the swept-back configuration in wind turbine
 blades can positively help to improve the energy loss in downstream wind
 turbines in wind farms and can increase the overall energy efficiency.
description: This dataset was collected using PIV (particle image
 velocimetry), then it was processed using Insight
 4G<sup>TM</sup> global image acquisition, analysis and display
 software to obtain vector files.
description: In the file names 30Hz, 40Hz, 50Hz, 60Hz refers to 0.12m/s,
 0.15m/s, 0.18m/s, 0.21m/s freestream velocity respectively.
DOI: 10.5061/dryad.jq2bvq87b
title: Spatial segregation between wild ungulates and livestock outside protected areas in the lowlands of Nepal

description: Understanding how wildlife interacts with human activities across
 non-protected areas are critical for conservation. This is especially true
 for ungulates that inhabit human-dominated landscapes outside the
 protected area system in Nepal, where wildlife often coexist with
 livestock. Here we investigated how elevation, agricultural land, distance
 from roads, and the relative abundance of livestock influenced wild
 ungulate (chital (Axis axis), nilgai, barking deer (Muntiacus muntjak),
 wild boar (Sus scrofa) and sambar (Rusa unicolor)) abundance and
 occurrence. We counted all individuals of wild ungulates and livestock
 along 35 transects conducted between November 2017 and March 2018 in Bara
 and Rautahat forests in the lowlands of Nepal. We assessed abundance and
 occurrence relation to covariates using Generalized Linear
 Models.  We found that livestock outnumbered wild ungulates 6 to
 1. Wild boar was the most abundant wild ungulate, followed by nilgai,
 chital, barking deer and sambar. We found that elevation and livestock
 abundance were the most important covariates affecting the overall
 abundance of wild ungulates and the distribution of each individual
 ungulate species.  Our results suggest spatial segregation
 between wild ungulates, which occur mainly on highlands, and livestock
 that concentrate across lowland habitats. Our results provide critical
 information to improve conservation in community forest areas of Nepal,
 where wildlife interacts with people and their livestock. Finding better
 strategies to allow the coexistence of ungulates with people and their
 livestock is imperative if they are to persist into the future.
DOI: 10.5061/dryad.n02v6wwvk
title: Experimental predator intrusions in a cooperative breeder reveal threat-dependent task partitioning

description: In cooperatively breeding species, non-breeding individuals provide
 alloparental care and help in territory maintenance and defence.
 Antipredator behaviours of subordinates can enhance offspring survival,
 which may provide direct and indirect fitness benefits to all group
 members. Helping abilities and involved costs and benefits, risks and
 outside options (e.g. breeding independently) usually diverge between
 group members, which calls for status-specific differentiated behavioural
 responses. Such role differentiation within groups may generate
 task-specific division of labour, as exemplified by eusocial animals. In
 vertebrates, little is known about such task differentiation among group
 members. We show how breeders and helpers of the cooperatively breeding
 cichlid Neolamprologus savoryi partition predator defence depending on
 intruder type and the presence of dependent young. In the field, we
 experimentally simulated intrusions by different fish species posing a
 risk either specifically to eggs, young, or adults. We used intrusions by
 harmless algae-eaters as a control. Breeders defended most when dependent
 young were present, while helper investment hinged mainly on their body
 size and on the potential threat posed by the respective intruders.
 Breeders and helpers partitioned defence tasks primarily when dependent
 young were exposed to immediate risk, with breeders investing most in
 antipredator defence, while helpers increased guarding and care in the
 breeding chamber. Breeders’ defence likely benefits helpers as well, as it
 was especially enhanced in the treatment where helpers were also at risk.
 These findings illustrate that in a highly social fish different group
 members exhibit fine-tuned behavioural responses in dependence of
 ecological and reproductive parameter variation.
DOI: 10.5061/dryad.6t1g1jwx4
title: The BHMT-Betaine methylation pathway epigenetically modulates oligodendrocyte maturation

description: Research into the epigenome is of growing importance as a loss of
 epigenetic control has been implicated in the development of
 neurodegenerative diseases. Previous studies have implicated aberrant DNA
 and histone methylation in multiple sclerosis (MS) disease
 pathogenesis.  We have previously reported that the
 methyl donor betaine is depleted in MS and is linked to changes in histone
 H3 trimethylation (H3K4me3) in neurons.  We have also
 shown that betaine increases histone methyltransferase activity by
 activating chromatin bound betaine homocysteine S-methyltransferase
 (BHMT).  Here, we investigated the role of the
 BHMT-betaine methylation pathway in
 oligodendrocytes.  Immunocytochemistry in the human
 MO3.13 cell line, primary rat oligodendrocytes, and tissue from MS
 postmortem brain confirmed the presence of the BHMT enzyme in the nucleus
 in oligodendrocytes.  BHMT expression is increased
 2-fold following oxidative insult, and qRT-PCR demonstrated that betaine
 can promote an increase in expression of oligodendrocyte maturation genes
 SOX10 and NKX-2.2 under oxidative conditions.  Chromatin
 fractionation provided evidence of a direct interaction of BHMT on
 chromatin and co-IP analysis indicates an interaction between BHMT and
 DNMT3a.  Our data show that both histone and DNA
 methyltransferase activity are increased following betaine
 administration.  Betaine effects were shown to be
 dependent on BHMT expression following siRNA knockdown of
 BHMT.  This is the first report of BHMT expression in
 oligodendrocytes and suggests that betaine acts through BHMT to modulate
 histone and DNA methyltransferase activity on
 chromatin.  These data suggest that methyl donor
 availability can impact epigenetic changes and maturation in
 oligodendrocytes. 
description: A ReadMe file is included with the dataset.
DOI: 10.5061/dryad.p5hqbzkn1
title: Microcystin production by Nostoc in Greenlandic lakes

description: Benthic primary producers are recognized for their important role in
 contributing to ecosystem productivity and nutrient cycling in lake and
 stream ecosystems, particularly in polar environments. In Arctic lakes,
 benthic producers often comprise mats or colonies of cyanobacteria capable
 of producing cyanotoxins. However, the extent to which benthic communities
 contribute cyanotoxins in polar regions remains poorly described. We
 evaluated the potential for benthic colonies of the cyanobacterium Nostoc
 pruniforme from lakes in Kangerlussuaq, Greenland, to contribute
 microcystins (MCs) to lake water using three approaches. First, we
 dissected field-collected Nostoc colonies and measured MCs within multiple
 layers of fresh colony tissue. Second, we conducted a laboratory
 experiment to evaluate the temporal dynamics of MC release by incubated,
 intact colonies. Finally, we quantified whether MC concentrations in water
 and sediment samples in the field were higher in and above dense bands of
 benthic Nostoc as compared to bare sediment. Field-collected Nostoc
 colonies contained MCs throughout the colony tissue, suggesting that
 damage to colonies from grazers or physical disturbance could facilitate
 the release of toxins into the water. Undamaged Nostoc colonies incubated
 in high-nutrient conditions in the laboratory leaked MCs into the
 surrounding water at a steady mass-specific rate over the course of seven
 days. MC concentrations in water and sediment from two Greenlandic lakes
 were highly variable, but slightly higher in lake water immediately above
 dense bands of Nostoc than in water immediately above bare sediments,
 suggesting that benthic Nostoc colonies contribute cyanotoxins to lake
 water and that MCs vary at very fine, 1-2 m spatial scales. Benthic
 cyanobacteria may be important in releasing MCs into aquatic ecosystems,
 especially in systems where benthic producers dominate, such as polar
 environments.
description: Description of Data Files:
 "NostocLeakage" - Release of microcystin from incubated
 Nostoc colonies   "NostocDissection" -
 Spatial distributon of MC concentrations within dissected Nostoc
 colonies  "NostocBands" - Microcystin
 concentrations in water and sediment samples in two Greenlandic
 lakes
DOI: 10.5061/dryad.bvq83bk6s
title: Data from: Crops and their wild progenitors recruit beneficial and detrimental soil biota in opposing ways

description: Aims Conventional agriculture promotes negative feedbacks of soil microbes
 on crop performance (plant soil feedbacks, PSFs) by stimulating
 species-specific pathogens. Crop traits, modified by domestication, also
 influence PSFs. Therefore, we asked if crop cultivars and their wild
 progenitors promote soil pathogens and mutualists differently, and thus
 trigger different PSFs. Methods We studied PSFs in cultivated varieties
 and wild progenitors of ten crops. In a first season, we grew all
 genotypes separately in a common soil to obtain genotype-specific soil
 inocula (‘trained soil’) for a second season. In season two, we examined
 the effects of the trained soil on plant interactions with arbuscular
 mycorrhizal fungi and with root-feeding nematodes, and on plant
 performance. Results Mycorrhizal colonization was lower, and nematode
 infection rate was higher, in plant roots growing on soils previously
 trained by domesticated plants. Moreover, domesticated plants showed lower
 mycorrhizal colonization, and higher nematode infection rates than their
 wild progenitors, irrespective of previous soil training. The response of
 plant performance to soil training was species-specific and unrelated to
 cultivated vs wild status. Conclusions Soil legacies differed between
 cultivated varieties and their wild progenitors, suggesting an impact of
 domestication on the way rhizosphere organisms are recruited, on the
 resistance of plants to herbivores, and on their interactions with root
 mutualists.
description: Data are free to use. A readme file with metadata can be found in
 the Excel file.
DOI: 10.15468/dl.32pgcc
title: Occurrence Download

description: A dataset containing 245 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Biodiversity Survey of Echuya forest, Year 2012"
 ]
}

 The dataset includes 245 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002569-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.kh189323r
title: Data from: Global origins of invasive brown rats (Rattus norvegicus) in the Haida Gwaii archipelago

description: Brown rats (Rattus norvegicus) have commensally spread from northern China
 and Mongolia to become among the most invasive species on the planet.
 Understanding the proximate source(s) of invasion can inform biosecurity
 plans and eradication strategies for preventing or mitigating impacts to
 native biodiversity. The Haida Gwaii archipelago, located off the coast of
 British Columbia, Canada, is a significant nesting site for 1.5 million
 seabirds across 12 species, half of which are now threatened by brown
 rats. Local knowledge points to a European origin in the late 1800’s to
 early 1900’s, though the true source(s) and firm date(s) of invasion
 remain unknown. To fill these knowledge gaps, we analyzed genotypic data
 (16,598 SNPs) for 280 brown rats sampled throughout Haida Gwaii relative
 to a published global database of potential source populations. Principle
 component analysis and population assignment tests supported multiple
 potential invasion sources from Europe and North America. Likewise,
 demographic modelling best supported two invasions into the islands. The
 first invasion likely occurred in the early 1900’s into the south-central
 archipelago from Western Europe followed by a more recent invasion in the
 early 2000’s from Vancouver, British Columbia, into northern Haida Gwaii.
 The northern invasion of Haida Gwaii could also be indicative of
 contemporary gene flow between Haida Gwaii and the mainland, representing
 a significant biosecurity risk. Our results will inform management
 strategies for invasive rats in Haida Gwaii, and serve as a guide for
 studies in other isolated systems worldwide.
description: HG_GlobalRef_17k.vcf: genotypic data for 582 brown rats (Rattus
 norvegicus) at 16,598 SNPs originally generated via ddRAD; referred to as
 "17K" dataset in manuscript HG_GlobalRef_5k.
 vcf: genotypic data for 582 brown rats (Rattus norvegicus) at 5,000 SNPs
 originally generated via ddRAD; referred to as "5K" dataset in
 manuscript
DOI: 10.15468/dl.nwhsyp
title: Occurrence Download

description: A dataset containing 37 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cascaronia astragalina",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 37 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002566-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.msbcc2fwh
title: Relationships of mass properties and body proportions to locomotor habit in terrestrial Archosauria

description: Throughout their 250 Myr history, archosaurian reptiles have exhibited a
 wide array of body sizes, shapes and locomotor habits, especially in
 regard to terrestriality. These features make Archosauria a useful clade
 with which to study the interplay between body size, shape and locomotor
 behaviour, and how this interplay may have influenced locomotor evolution.
 Here, digital volumetric models of 80 taxa are used to explore how mass
 properties and body proportions relate to each other and locomotor posture
 in archosaurs. One-way, non-parametric, multivariate analysis of variance,
 based on the results of principal components analysis, shows that bipedal
 and quadrupedal archosaurs are largely distinguished from each other on
 the basis of just four anatomical parameters (P &lt; 0.001): mass,
 centre of mass position and relative forelimb and hindlimb lengths. This
 facilitates the development of a quantitative predictive framework that
 can help assess gross locomotor posture in understudied or controversial
 taxa, such as the crocodile-line Batrachotomus (predicted quadruped) and
 Postosuchus (predicted biped). Compared to quadrupedal archosaurs, bipedal
 species tend to have relatively longer hindlimbs and a more caudally
 positioned whole-body centre of mass, and collectively exhibit greater
 variance in forelimb lengths. These patterns are interpreted to reflect
 differing biomechanical constraints acting on the archosaurian bauplan in
 bipedal versus quadrupedal groups, which may have shaped the evolutionary
 histories of their respective members.
description: All files and their usage are described in the main supplementary
 text document.
DOI: 10.25338/b8m32v
title: Selectin-targeting glycosaminoglycan-peptide conjugate limits neutrophil-mediated cardiac reperfusion injury

description: Aims: One of the hallmarks of myocardial infarction (MI) is excessive
 inflammation. During an inflammatory insult, damaged endothelial cells
 shed their glycocalyx, a carbohydrate-rich layer on the cell surface which
 provides a regulatory interface to immune cell adhesion. Selectin-mediated
 neutrophilia occurs as a result of endothelial injury and inflammation. We
 recently designed a novel selectin-targeting glycocalyx mimetic (termed
 DS-IkL) capable of binding inflamed endothelial cells. This study examines
 the capacity of DS-IkL to limit neutrophil binding and platelet activation
 on inflamed endothelial cells, as well as the cardioprotective effects of
 DS-IkL after acute myocardial infarction.  In vitro, DS-IkL
 diminished neutrophil interactions with both recombinant selectin and
 inflamed endothelial cells, and limited platelet activation on inflamed
 endothelial cells. Our data demonstrated that DS-IkL localized to regions
 of vascular inflammation in vivo after 45 min of left anterior descending
 coronary artery ligation-induced MI. Further, findings from this study
 show DS-IkL treatment had short- and long-term cardioprotective effects
 after ischaemia/reperfusion of the left anterior descending coronary
 artery. Mice treated with DS-IkL immediately after ischaemia/reperfusion
 and 24 h later exhibited reduced neutrophil extravasation, macrophage
 accumulation, fibroblast and endothelial cell proliferation, and fibrosis
 compared to saline controls.  Our findings suggest that DS-IkL
 has great therapeutic potential after MI by limiting reperfusion injury
 induced by the immune response.
description: DS-IkL_Set1 and
 DS-IkL_Set2: Collected Jan 2018 – Jan 2020 Flow Cytometry Raw Data Files
 (zipped folders). Requires a flow cytometry analysis software (e.g.,
 FlowJo) to open. Raw data from the flow cytometry data shown in Figure 7.
 Data represents the expression of endothelial markers, fibroblast markers,
 neutrophil markers, macrophage/monocyte markers, and proliferation markers
 in non-myocyte cells in the hearts of I/R and sham mice.  IR_compiled_data_as_of_2020.09.05.pzfx and PMN_inhibition_compiled.pzfx: Collected Jan 2018-Aug 2020 Compiled experimental data from figures 1-7. Requires GraphPad PRISM to open. IR compiled data contains all data from the in vivo study. PMN inhibition compiled contains data from in vitro experiments.
DOI: 10.7280/d1m107
title: Comparing the individual and combined effects of ant attendance and wing formation on aphid body size and reproduction

description: Species employ multiple strategies to deal with stressful environments,
 but these strategies often incur costs. Aphids frequently utilize multiple
 predator avoidance strategies, including attracting mutualist ants for
 protection and dispersing by producing winged forms. While both strategies
 can be physiologically costly, the magnitudes of these costs have not been
 previously compared. In this study, we experimentally manipulated ant
 attendance in the field and measured the individual and interactive
 effects of ant attendance and wing formation on body size and reproduction
 of the ant-tended aphid Cinara schwarzii (Wilson) (Hemiptera: Aphididae).
 Aphid adult body size was smaller in the presence of ants (18%), but
 controlling for body size, there were no differences in embryo number or
 size. In contrast, wing formation did not affect adult body size but
 strongly reduced embryo number (46%) and size (8%). Although ant
 attendance reduced C. schwarzii wing formation, ant attendance and wing
 formation acted independently on aphid body size and reproduction. For
 comparison, we confirmed that the manipulation of ant presence had no
 effect on body size or reproduction of the untended co-existing congener
 Cinara solitaria (Gillette and Palmer). Complementing our empirical study,
 a meta-analysis of 78 responses from 24 publications showed that wing
 formation consistently and significantly reduces aphid body size and
 reproduction (37%), while the effects of ant attendance showed a mean
 positive effect (9%) that did not significantly differ from zero.
 Together, our empirical study and meta-analysis provide strong evidence
 for costs of wing formation but not ant attendance for aphids.