cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2jm63xst8
title: Coordination of economics spectra in leaf, stem and root within the genus Artemisia along a large environmental gradient in China

description: Aim: The plant economics spectrum provides a fundamental framework for
 understanding functional trait variation along environmental gradients.
 However, it is unclear whether there is a general whole-plant economics
 spectrum across organs at the finer taxonomic scale (e.g. within genera),
 and if there is, which factors affect the trait coordination of the
 different organs. Here, we examined whether resource economics spectra of
 different organs (i.e. leaf, stem and root) can be integrated at the
 whole-plant level within a single genus, and how environment,
 intraspecific variation and taxonomic scale shape the whole-plant
 spectrum. Location: China. Time period: 2018. Major taxa studied:
 Artemisia. Results: Pairwise trait correlations and the trade-off patterns
 along the resource economic axis were consistent at both organ and
 whole-plant levels. Environmental gradients did not strongly affect the
 correlations among leaf, stem and root economics spectra, i.e. the
 intraspecific variation weakened but did not mask this coordination.
 Taxonomic scale did not affect the degree of trait coordination as the
 genus-wide whole-plant economics spectrum also emerged within each of the
 three subgenera. Main conclusions: Our results support the hypothesis that
 the coordination of economics spectra across organs forms a whole-plant
 economics spectrum representing “fast-slow” resource management strategy,
 which is robust to recent evolution (genotypic variation, even for species
 within a single genus) and present-day environmental variation. Further
 studies should elucidate in which circumstances or phylogenetic branches
 the coordinated pattern found for Artemisia is representative of other
 widely distributed genera.
description: We sampled 1,022 individuals
 of 62 Artemisia species from 81 sites across eastern and central China
 in late July and August 2018. We quantified 15 economic
 traits that were associated with plant resource economic strategies. The
 whole plants were harvested for trait measurements. Oven-dried leaves, stems and roots were ground
 to fine powders and then examined for total carbon (C,
 mg
 g-1) and nitrogen (N,
 mg
 g-1) concentrations using
 an elemental analyser (Vario EL III, Elementar, Hanau, Germany).
 Subsamples of the fine powders of leaves, stems and roots were used to
 measure total phosphorus (P, g kg-1) concentrations. The 50 mg fine powder was
 solubilized in a Teflon cylinder using a 1:4 mixture of HClO4 (60%) and
 HNO3 (60%), then 3% HClO4 was added to reach a final volume of 10 ml. The
 final solution was digested in a MARS 5 microwave digestion system (CEM
 GmbH, Kamp-Lintfort, Germany), and then P concentration was measured using
 the Thermo Scientific iCAP 6300 (Thermo Fisher Scientific Inc., Waltham,
 MA, USA).
DOI: 10.5061/dryad.v15dv420f
title: Data for: An invasive ant increases deformed wing virus loads in honey bees

description: The majority of invasive species are best known for their effects as
 predators. However, many introduced predators may also be substantial
 reservoirs for pathogens. Honey bee-associated viruses are found in
 various arthropod species including invasive ants. We examined how the
 globally invasive Argentine ant (Linepithema humile), which can reach high
 densities and infest beehives, is associated with pathogen dynamics in
 honey bees. Viral loads of Deformed wing virus (DWV), which has been
 linked to millions of beehive deaths around the globe, and black queen
 cell virus significantly increased in bees when invasive ants were
 present. Microsporidian and trypanosomatid infections, which are more
 bee-specific, were not affected by ant invasion. The bee virome in autumn
 revealed that DWV was the predominant virus with the highest infection
 levels and that no ant-associated viruses were infecting bees. Viral
 spillback from ants could increase infections in bees. In addition, ant
 attacks could pose a significant stressor to bee colonies that may affect
 virus susceptibility. These viral dynamics are a hidden effects of ant
 pests, which could have a significant impact on disease emergence in an
 economically important pollinator. Our study contributes to unravel a
 perhaps overlooked effect of species invasions: changes in pathogen
 dynamics.
description: In the austral summer of January 2019, 18 beehives from an
 Argentine ant-free apiary were moved into six sites in the Northland
 region, New Zealand, half with known Argentine ant incursions, placing
 three hives in each site. Monthly collections of adult worker bees from
 brood frames took place from January until August, except July.
 Quantitative PCR (qPCR) data was generated from reverse
 transcribed total RNA extracted from honey bees or Argentine ants on a
 StepOne™ Real-Time PCR cycler or a QuantStudio 7 Real-Time PCR System,
 respectively. Survival data was generated from field
 observations. RNA-seq data originates from Illumina 1.9
 Hi-seq 100 base pair (bp) paired-end sequencing of total RNA from honey
 bees. Reads were aligned to the honey bee reference genome (Amel_HAv3.1)
 in HISAT2 2.1.0 to exclude host-derived reads. Unaligned reads were de
 novo assembled in Trinity 2.9.1 and transcript counts generated using a
 pipeline integrated with the Trinity package (www.github.com/trinityrnaseq/trinityrnaseq/blob/master/util/abundance_estimates_to_matrix.pl). Further details of the experimental setup and method used can be found in the accompanying manuscript.
description: Files ending in .matrix can be opened in R (r-project.org) using
 DESEQ2 and files ending in .csv can, for instance, be opened in Microsoft
 Excel or Cal in the LibreOffice suite.
DOI: 10.5061/dryad.00000006t
title: Navigating agricultural landscapes: Responses of critically endangered giant tortoises to farmland vegetation and infrastructure

description: Context: Interactions between wildlife and anthropogenic infrastructure,
 such as roads, fences, and dams, can influence wildlife movement, and
 potentially cause human-wildlife conflict. In the Galapagos archipelago,
 two species of critically endangered giant tortoise encounter
 infrastructure and human-modified vegetation in farms, which could
 influence movement choices. Objectives: We investigated factors
 influencing tortoise movement and habitat selection in the agricultural
 landscape of Santa Cruz Island, Galapagos. Methods: We examined the
 movement of 27 tortoises collected using GPS tracking between 2014 and
 2020, in relation to the location of vegetation, ponds, fences, and roads.
 Results: We found that tortoises preferred pasture over native vegetation,
 but there was little difference among their preferences for native
 vegetation, crops, or invasive vegetation. Tortoises also travelled slower
 in pasture, and faster in invasive vegetation, compared to crops and
 native vegetation. Tortoises were more likely to be found closer to ponds
 than predicted by chance. Our results indicated that most fences were
 porous to tortoises, with limited impact on their movement. Tortoises were
 more likely to use areas near roads with low-traffic. Conclusions:
 Pastures and ponds are important habitats for tortoises in farms and are
 likely to be used preferentially by tortoises. Overall, fences and roads
 did not strongly obstruct tortoise movements, however, this may lead to
 potential injury to tortoises on roads and property damage for farmers. To
 best identify priority areas for managing wildlife on farms, we recommend
 evaluating the combined effects of multiple anthropogenic landscape
 features on wildlife movements.
description: To first determine the structural attributes of fences in
 farmland, we conducted 205 “fence surveys” in 2019 in the east (82
 surveys) and west (123 surveys) of the Santa Cruz highlands, Galapagos
 Islands. At each fence survey, we selected a random 10-m section and
 recorded the fence’s material, and the land-use associated with the fence
 as ‘crop’ (which included transitory or permanent crops or, rarely,
 housing) or ‘non-crop’ (which included paddocks for livestock, abandoned
 land, and land for tourism, forestry, or national park). For each fence,
 we recorded the distance between the ground and first wire, distance
 between posts, and height to the nearest mm, measured in three places
 along the 10-m survey (between 0 and 1 m, 4–5 m, and 9–10 m)
description: Microsoft Excel, or R
DOI: 10.15468/dl.ev9f6s
title: Occurrence Download

description: A dataset containing 44 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((5.91246 43.89781,5.87129 43.87363,5.88349 43.86483,5.94754 43.85604,6.1229 43.89341,6.24184 43.92966,6.32723 43.87693,6.37145 43.84394,6.44922 43.87583,6.46295 43.91868,6.466 43.99662,6.41568 44.07007,6.3684 44.09636,6.27539 44.035,6.19762 44.01746,6.13357 43.98345,6.07563 43.94613,5.99786 43.91429,5.91246 43.89781))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Bidens frondosa"
 ]
}

 The dataset includes 44 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003414-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4f4qrfjgn
title: The geometry of evolutionary conflict

description: Conflicts of interest abound not only in human affairs but also in the
 biological realm. Evolutionary conflict occurs over multiple scales of
 biological organization, from genetic outlawry within genomes, to sibling
 rivalry within nuclear families, to collective-action disputes within
 societies. However, achieving a general understanding of the dynamics and
 consequences of evolutionary conflict remains an outstanding challenge.
 Here, we show that a development of R. A. Fisher’s classic “geometric
 model” of adaptation yields novel and surprising insights into the
 dynamics of evolutionary conflict and resulting maladaptation, including
 the discoveries that: (1) conflict can drive evolving traits arbitrarily
 far away from all parties’ optima and, indeed, if all mutations are
 equally likely then contested traits are more often than not driven
 outwith the zone of actual conflict (hyper-maladaptation); (2)
 evolutionary conflicts drive persistent maladaptation of orthogonal,
 non-contested traits (para-maladaptation); and (3) modular design greatly
 ameliorates conflict-driven maladaptation, thereby facilitating major
 transitions in individuality.
DOI: 10.5061/dryad.gmsbcc2s5
title: Data from: Kinematic and hydrodynamic analyses of turning manoeuvres in penguins: Body banking and wing upstroke generate the centripetal force

description: Penguins perform lift-based swimming by flapping their wings. Previous
 kinematic and hydrodynamic studies have revealed the basics of wing motion
 and force generation in penguins. Although these studies have focused on
 steady forward swimming, the mechanism of turning manoeuvres is not well
 understood. In this study, we examined the horizontal turning of penguins
 via 3D motion analysis and quasi-steady hydrodynamic analysis. Free
 swimming of gentoo penguins (Pygoscelis papua) at an aquarium was
 recorded, and body and wing kinematics were analysed. In addition,
 quasi-steady calculations of the forces generated by the wings were
 performed. Among the selected horizontal swimming manoeuvres, turning was
 distinguished from straight swimming by the body trajectory for each
 wingbeat. During the turns, the penguins maintained outward banking
 through a wingbeat cycle and utilized a ventral force during the upstroke
 as a centripetal force to turn. Within a single wingbeat during the turns,
 changes in the body heading and bearing also mainly occurred during the
 upstroke, while the subsequent downstroke accelerated the body forward. We
 also found contralateral differences in the wing motion; i.e., the inside
 wing of the turn became more elevated and pronated. Quasi-steady
 calculations of the wing force confirmed that the asymmetry of the wing
 motion contributes to the generation of the centripetal force during the
 upstroke and the forward force during the downstroke. The results of this
 study demonstrate that the hydrodynamic force of flapping wings, in
 conjunction with body banking, is actively involved in the mechanism of
 turning manoeuvres in penguins.
description: Please see the README document (“README.md”) and the accompanying
 published article: N. Harada and H. Tanaka. 2022. Kinematic and
 hydrodynamic analyses of turning manoeuvres in penguins: body banking and
 wing upstroke generate centripetal force. Journal of Experimental Biology.
 DOI: 10.1242/jeb.244124. Please see also the related
 article: N. Harada, T. Oura, M. Maeda, Y. Shen, D. M. Kikuchi and H.
 Tanaka. 2021. Kinematics and hydrodynamics analyses of swimming penguins:
 wing bending improves propulsion performance. Journal of Experimental
 Biology. DOI: 10.1242/jeb.242140.
description: The data files can be opened with spreadsheet software such as
 Microsoft Excel.
DOI: 10.5061/dryad.573n5tbbm
title: Data from: Freshwater fishes maintain multi-trait phenotypic stability across an environmental gradient in aqueous calcium

description: Reductions in a limiting nutrient might be expected to necessitate
 compromises in the functional traits that depend on that nutrient; yet
 populations existing in locations with low levels of such nutrients often
 do not show the expected degradation of functional traits. Indeed, we
 previously found that fish of three species, Logperch (Percina
 caprodes),Pumpkinseed Sunfish (Lepomis gibbosus), and Yellow
 Perch (Perca flavescens) residing in low-calcium water in the
 Upper St. Lawrence River nevertheless maintained levels of scale calcium
 comparable to those of conspecific populations in high-calcium water.
 However, it remains possible that the maintenance of one functional trait
 under nutrient-limited conditions could come at the expense of maintaining
 other functional traits that depend on that same nutrient. Hence, we here
 extend prior work by examining other calcium-dependent traits: skeletal
 element sizes and bone densities in the same fish species in the same
 area. Using radiographs of 101 fish from the three species across four
 locations (two in high-calcium water and two in low-calcium water), we
 document multi-trait “homeostasis” along the gradient of water calcium.
 That is, we did not detect any effect of calcium regime (low-calcium
 versus high-calcium) on any of the measured variables. Further, effect
 sizes for the skeletal traits were very low – lower even than effect sizes
 previously documented for scale calcium. Our results thus show that native
 fishes maintain phenotype stability across a suite of functional traits
 linked to calcium regulation, perhaps pointing to an “organismal-level
 homeostasis” scenario rather than a “trait-level homeostasis”
 scenario.
DOI: 10.5061/dryad.3ffbg79nk
title: A new fossil family of aculeate wasp sheds light on early evolution of Apoidea (Hymenoptera)

description: In the present work, we describe a new fossil family of Apoidea supported
 by phylogenetic analyses involving both fossil and extant groups.
 †Burmasphecidae fam.n. is based on †Burmasphex Melo & Rosa, a
 genus described from Burmese amber. We include in this family the
 monotypic genus †Decasphex Zheng, Zhang & Rasnitsyn also from
 Burmese amber. Additionally, we describe two new genera and four new
 species in †Burmasphecidae fam.n.: †Burmasphex mirabilis sp.n.;
 †Simplisphex gen.n., containing S. scutellatus sp.n. and †S. burmensis
 sp.n.; and †Callisphex robustus gen. et sp.n. In our phylogenetic study,
 we extended a pre-existing matrix of morphological data and analyzed it
 under parsimony and Bayesian inference. In the Bayesian inference
 analyses, the morphological dataset was partitioned under a homoplasy
 criterion. We postulate the first phylogenetic hypotheses for the
 placement of †Angarosphecidae based on the type species, †Angarosphex
 myrmicopterus Rasnitsyn, plus a new Burmese amber taxon, †A. alethes sp.n.
 We demonstrate that †Burmasphecidae fam.n. clearly belongs to Apoidea and
 has a sister relationship with the other representatives of the
 superfamily. Our results indicate that †Burmasphecidae fam.n. and
 †Angarosphecidae are distinct lineages, with the second more derived than
 the first. We discuss the phylogenetic relationships of these fossil
 lineages with extant groups of both Apoidea and other Aculeata, and
 present for the first time morphological evidence supporting the clade
 Formicidae + Apoidea. Finally, we indicate some considerations about the
 paleoenvironment and the nature of the Burmese amber biota, suggesting an
 alternative hypothesis to the island endemism described in previous works.
description: # A new fossil family of aculeate wasps sheds light on the early evolution
 of Apoidea (Hymenoptera)
 [https://doi.org/10.5061/dryad.3ffbg79nk](https://doi.org/10.5061/dryad.3ffbg79nk) ## Description of the data and file structure #### Authors: Brunno B. Rosa* & Gabriel A. R. Melo *Corresponding author: [brunnobueno27@gmail.com](mailto:brunnobueno27@gmail.com) ### Files and variables #### File: Rosa\_\_\_Melo\_Matrix\_Burmasphecidae.nex **Description:** Data matrix #### File: Rosa\_\_\_Melo\_Tree\_A\_Burmasphecidae.tre **Description:** Bayesian tree with majority rule consensus with all-compatible groups added (Contype = allcompat) #### File: Rosa\_\_\_Melo\_Tree\_B\_Burmasphecidae.tre **Description:** Bayesian tree with 50% majority rule consensus (Contype = Halfcompat)
DOI: 10.5061/dryad.9zw3r22j5
title: Genetic restoration of black rhinoceroses in South Africa: conservation implications

description: Globally, wildlife populations are becoming increasingly small and
 isolated. Both processes contribute to an elevated risk of extinction,
 notably due to genetic factors related to inbreeding depression and a loss
 of adaptive potential. Wildlife translocation is a valuable conservation
 tool to reintroduce species to previously occupied areas, or augment
 existing populations with genetically divergent animals, thereby improving
 the viability of endangered populations. However, understanding the
 genetic implications of mixing gene pools is key to avoid the risk of
 outbreeding depression, and to maximise translocation effectiveness. In
 this study we used mitochondrial and microsatellite DNA collected from 110
 black rhinoceroses (Diceros bicornis minor) in Kruger National Park, South
 Africa, to determine levels of genetic diversity, inbreeding and
 relatedness. We compared this diversity with the two source populations
 (KwaZulu-Natal, South Africa and Zambezi River, Zimbabwe) using data from
 previously published studies, and assessed changes in the relative
 contribution of source lineages since their reintroduction in the 1970s.
 Our results show that Kruger’s black rhinoceroses are genetically more
 diverse than those from KwaZulu-Natal, with levels closer to those from
 the Zambezi Valley. Furthermore, our findings indicate a relative increase
 in the Zimbabwean lineage since reintroduction, suggesting a possible
 selective advantage. From a conservation perspective, our results
 demonstrate the benefits of mixing multiple source populations to restore
 gene flow, improve genetic diversity and thereby help protect small,
 isolated populations from extinction.
description: Blood samples (n=110; female = 60, male = 50) were collected from
 black rhinoceroses in southern Kruger (Fig. 1) from 2014–2019 during
 various management interventions, performed in accordance with South
 African National Parks (SANParks) Wildlife Capture Standard Operating
 Procedures. Sex, date and location were recorded at the time of capture.
  DNA was extracted using DNeasy Blood & Tissue Kits (Qiagen,
 Valencia, CA, USA), following the manufacturer’s instructions. A fragment
 of the mitochondrial DNA control region was sequenced by ZooOmics™ (Inqaba
 Biotec, Pretoria) using primers mt15996L (5’-TCCACCATCAGCACCCAAAGC-3’;
 Campbell et al. 1995) and mt16502H (5’-TTTGATGGCCCTGAAGTAAGAACCA-3’; Moro
 et al. 1998). Individuals were genotyped by ZooOmics™ using the standard
 rhinoceros forensic panel in South Africa (Harper et al. 2013) comprised
 of 23 microsatellite markers.
DOI: 10.6078/d1kh8r
title: Population-based heteropolymer design to mimic protein mixtures

description: Biological fluids, the most complex blends, have compositions that
 constantly vary and cannot be molecularly defined. Despite these
 uncertainties, proteins fluctuate, fold, function and evolve as
 programmed. We propose that in addition to the known monomeric sequence
 requirements, protein sequences encode multi-pair interactions at the
 segmental level to navigate random encounters; synthetic heteropolymers
 capable of emulating such interactions can replicate how proteins behave
 in biological fluids individually and collectively. Here, we extracted the
 chemical characteristics and sequential arrangement along a protein chain
 at the segmental level from natural protein libraries and used the
 information to design heteropolymer ensembles as mixtures of disordered,
 partially folded and folded proteins. For each heteropolymer ensemble, the
 level of segmental similarity to that of natural proteins determines its
 ability to replicate many functions of biological fluids including
 assisting protein folding during translation, preserving the viability of
 fetal bovine serum without refrigeration, enhancing the thermal stability
 of proteins and behaving like synthetic cytosol under biologically
 relevant conditions. Molecular studies further translated protein sequence
 information at the segmental level into intermolecular interactions with a
 defined range, degree of diversity and temporal and spatial availability.
 This framework provides valuable guiding principles to synthetically
 realize protein properties, engineer bio/abiotic hybrid materials and,
 ultimately, realize matter-to-life transformations.
DOI: 10.15468/dl.pkjbz9
title: Occurrence Download

description: A dataset containing 1572308 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "TaxonKey is Piranga olivacea",
 "Year 2000-2025"
 ]
}

 The dataset includes 1572308 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002647-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.hx3ffbgj9
title: Systematic paleontology of macroalgal fossils from the Tonian Mackenzie Mountains Supergroup

description: Proterozoic eukaryotic macrofossils are rarely preserved with enough
 morphological detail to inform their phylogeny. This dataset includes the
 measurements and descriptions of three size classes of filamentous fossils
 from the Dolores Creek Formation of the Mackenzie Mountain Supergroup in
 the Wernecke Mountains, Yukon. This data was used to systematically
 describe and interpret the middle size class specimens as green macroalgae
 with an unbranching, uniseriate thallus (with uniform width throughout;
 n=304, width = 0.20 to 0.85 mm) and elliptical to globose anchoring
 holdfast. Fossils from the smaller size class (n = 90, width = 0.03 to
 0.06 mm) retain too little morphological information to define properly.
 However, a third form is also documented, consisting of a ribbon-shaped
 thallus with a consistent width (n=19, width = 1.0 to 1.7 mm). The size
 range of these different, likely photoautotrophic, filaments supports the
 hypothesis of an increasing morphological complexity and overall
 diversification of macroalgae during the Tonian, setting the stage for
 dramatic changes to benthic marine ecosystems prior to the evolution of
 more complex ecosystems.
description: Measurements were collected using ImageJ.