cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ghx3ffbkm
title: Construction of a chromosome-scale long-read reference genome assembly for potato

description: Background: Worldwide, the cultivated potato, Solanum tuberosum L., is the
 number one vegetable crop and a critical food security crop. The genome
 sequence of DM1-3 516 R44, a doubled monoploid clone of S. tuberosum Group
 Phureja, was published in 2011 using a whole-genome shotgun sequencing
 approach with short read sequence data. Current advanced sequencing
 technologies now permit generation of near-complete, high-quality
 chromosome-scale genome assemblies at a minimal cost. Findings: Here, we
 present an updated version of the DM1-3 516 R44 genome sequence (v6.1)
 using Oxford Nanopore Technologies long reads coupled with
 proximity-by-ligation scaffolding (Hi-C) yielding a chromosome-scale
 assembly. The new (v6.1) assembly represents 741.6 Mb of sequence (87.8 %)
 of the estimated 844 Mb genome, of which, 741.5 Mb is non-gapped with
 731.2 Mb anchored to the 12 chromosomes. Use of Oxford Nanopore
 Technologies full-length cDNA sequencing enabled annotation of 32,917
 high-confidence protein-coding genes encoding 44,851 gene models that had
 a significantly improved representation of conserved orthologs compared to
 the previous annotation. The new assembly has improved
  contiguity with a 595-fold increase in N50 contig size, 99%
 reduction in the numbersof contigs, a 44-fold increase in N50 scaffold
 size, and an LTR Assembly Index score of 13.56, placing it in the category
 of reference genome quality. The improved assembly also permitted
 annotation of the centromeres via alignment to sequencing reads derived
 from CENH3 nucleosomes. Conclusions: Access to advanced sequencing
 technologies and improved software permitted generation of a high-quality,
 long-read, chromosome-scale assembly and improved annotation dataset for
 the reference genotype of potato that will facilitate research aimed at
 improving agronomic traits and understanding genome evolution.
description: See attached DM_1-3_516_R44_potato.v6.1.README.pdf for additional
 information.
DOI: 10.5061/dryad.xksn02vck
title: European bird declines: do we need to rethink approaches to the management of abundant generalist predators?

description: Bird species are declining across Europe. Current European policy, i.e.
 the Birds and Habitats Directives, focus on habitat management as a way of
 halting the declines. This paper explores the role of predation in causing
 bird population declines and asks if we need to reconsider our approach to
 the management of generalist predators.  We analysed bird
 population trends and distribution changes across Europe, Britain and
 Ireland, reflecting an increasing gradient of generalist predator
 abundance (principally red fox Vulpes vulpes and species
 of the family Corvidae). We tested if ground-nesting
 bird species, considered more vulnerable to predation,were in
 greater decline compared to other nesting strategies. We also
 compared Annex I designated species to non-designated species as a proxy
 for habitat management. We found that across Europe, 74% of ground-nesting
 bird species were in decline, compared to 41% of other species. This was
 especially evident in Britain, where the pattern was 66% compared to 31%,
 and in Ireland, 71% compared to 20%. Ground-nesting species were
 significantly more likely to be declining than other species. These
 patterns are consistent with the idea that population declines are at
 least partially related to the increased abundance of generalist
 predators. In Britain, ground-nesting species were less likely to be in
 decline if covered by Annex I designation. However, in Europe and Ireland,
 Annex I status did not mitigate the effect of nesting strategy. 
 Policy implications. Current legislation is clearly insufficient to
 prevent widespread declines in ground-nesting birds, and this is the case
 across Europe, in Britain and Ireland. Ignoring the role of generalist
 predators in modern landscapes may lead to further declines and losses. We
 urgently need large-scale experiments to establish causality in the impact
 of generalist predators on ground-nesting birds in different landscapes.
 If we value our ground-nesting bird species, consideration needs to be
 given to the control of widespread generalist predators, at least until
 landscapes are restored.
DOI: 10.15468/dl.gs74q3
title: Occurrence Download

description: A dataset containing 220 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Austrodolichos errabundus",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 220 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002398-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.9kd51c5dq
title: Data from: Vessel noise levels drive behavioural responses of humpback whales with implications for whale-watching

description: Disturbance from whale-watching can cause significant behavioural changes
 with fitness consequences for targeted whale populations. However, the
 sensory stimuli triggering these responses are unknown, preventing
 effective mitigation. Here, we test the hypothesis that vessel noise level
 is a driver of disturbance, using humpback whales (Megaptera novaeangliae)
 as a model species. We conducted controlled exposure experiments (n= 42)
 on resting mother-calf pairs on a resting ground off Australia, by
 simulating whale-watch scenarios with a research vessel (range 100 m,
 speed 1.5 knts) playing back vessel noise at control/low (124/148 dB),
 medium (160 dB) or high (172 dB) LF-weighted source levels (re 1 μPa
 RMS@1m). Compared to control/low treatments, during high noise playbacks
 the mother’s proportion of time resting decreased by 30%, respiration rate
 doubled and swim speed increased by 37%. We therefore conclude that vessel
 noise is an adequate driver of behavioural disturbance in whales and that
 regulations to mitigate the impact of whale-watching should include noise
 emission standards.
description: Controlled exposure experiments, focal follows from unmanned
 aerial vehicles (UAVs). The supplementary video provides 3 examples of
 control, medium and high noise controlled exposure experiments.
DOI: 10.5061/dryad.x0k6djhgh
title: Data from: Vessel noise levels drive behavioural responses of humpback whales with implications for whale-watching

description: Disturbance from whale-watching can cause significant behavioural changes
 with fitness consequences for targeted whale populations. However, the
 sensory stimuli triggering these responses are unknown, preventing
 effective mitigation. Here, we test the hypothesis that vessel noise level
 is a driver of disturbance, using humpback whales (Megaptera novaeangliae)
 as a model species. We conducted controlled exposure experiments (n= 42)
 on resting mother-calf pairs on a resting ground off Australia, by
 simulating whale-watch scenarios with a research vessel (range 100 m,
 speed 1.5 knts) playing back vessel noise at control/low (124/148 dB),
 medium (160 dB) or high (172 dB) LF-weighted source levels (re 1 μPa
 RMS@1m). Compared to control/low treatments, during high noise playbacks
 the mother’s proportion of time resting decreased by 30%, respiration rate
 doubled and swim speed increased by 37%. We therefore conclude that vessel
 noise is an adequate driver of behavioural disturbance in whales and that
 regulations to mitigate the impact of whale-watching should include noise
 emission standards.
description: Controlled exposure experiments
DOI: 10.5061/dryad.v15dv41tc
title: Lightning-caused disturbance in the Peruvian Amazon

description: Lightning is a major agent of disturbance in tropical terrestrial
 ecosystems, but its effects often are overlooked or misidentified in
 lowland forests.  We used an unmanned aerial vehicle (i.e.,
 drone) to locate 12 probable lightning strike sites in ca. 47 ha of forest
 in the Peruvian Amazon.  Subsequent ground-based surveys of the
 10 accessible sites revealed 7 that were unambiguously caused by
 lightning.  The seven sites included 121 lightning-damaged trees,
 45 of which were dead.  Large trees (&gt;60 cm in diameter)
 were disproportionately affected by lightning.  The numbers of
 trees damaged and their size distribution were comparable to results from
 a comprehensive study of lightning damage in Panama.  By
 contrast, post hoc surveys of lightning gaps in Brazil and Malaysia
 documented 3-5 times more dead trees per strike, suggesting that
 gap-focused surveys are biased towards larger disturbances. 
 These findings contribute to a growing body of evidence that lightning is
 an important disturbance pantropically, and that accurately documenting
 the effects of lightning requires reliable identification of lightning
 strike locations.
DOI: 10.5061/dryad.dncjsxkwq
title: Multiple phenotypes conferred by a single insect symbiont are independent

description: Many microbial symbionts have multiple phenotypic consequences for their
 animal hosts. However, the ways in which different symbiont-mediated
 phenotypes combine to affect fitness are not well understood. We
 investigated whether there are correlations between different
 symbiont-mediated phenotypes. We used the symbiont Spiroplasma, a striking
 example of a bacterial symbiont conferring diverse phenotypes on insect
 hosts. We took 11 strains of Spiroplasma infecting pea aphids
 (Acyrthosiphon pisum) and assessed their ability to provide protection
 against the fungal pathogen Pandora neoaphidis and the parasitoids
 Aphidius ervi and Praon volucre. We also assessed effects on male
 offspring production for five of the Spiroplasma strains. All but one of
 the Spiroplasma strains provided very strong protection against the
 parasitoid P. volucre. As previously reported, variable
 protection against P. neoaphidis and A. ervi was also
 present; male-killing was likewise a variable phenotype. We find no
 evidence of any correlation, positive or negative, between the different
 phenotypes, nor was there any evidence of an effect of symbiont phylogeny
 on protective phenotype. We conclude that multiple symbiont-mediated
 phenotypes can evolve independently from one another without trade-offs
 between them.
description: Dataset comprises the raw data collected for the associated
 published manuscript, and methods are as described in that
 publication.
description: <strong>Resistance to <i>Aphidius
 ervi: </i></strong>Spiroplasma_Aphidius_data_txt
 Raw data collected on effects of <i>Spiroplasma</i>
 strains on aphid resistance to <i>Aphidius ervi</i>. The
 heading 'block' refers to the temporal block and
 'replicate' to a single dish of aphids attacked by a single
 female parasitoid.  <strong>Resistance to
 <i>Pandora
 neoaphidis: </i></strong>Spiroplasma_Pandora_data_txt Raw data collected on effects of <i>Spiroplasma</i> strains on aphid resistance to <i>Pandora neoaphidis. </i><strong>D0 = </strong>number of aphids exposed to fungus; <strong>D2, D4 ... D8 = </strong>number of aphids surviving on day 2, day 4 ... day 8 post-exposure. <strong>Resistance to <i>Praon volucre: </i></strong>Spiroplasma_Praon_data_txt Raw data collected on effects of <i>Spiroplasma</i> strains on aphid resistance to <i>Praon volucre</i>. The heading 'block' refers to the temporal block and 'replicate' to a single dish of aphids attacked by a single female parasitoid.  <strong>Male-killing: </strong>Spiroplasma_male_killing_da... Raw data collected on effects of <i>Spiroplasma</i> strains on male offspring production.
DOI: 10.5061/dryad.j6q573nb0
title: Hypoxia inducible factor-1α knockout does not impair acute thermal tolerance or heat hardening in zebrafish

description: The rapid increase in critical thermal maximum (CTmax) in fish (or other
 animals), previously exposed to critically high temperature is termed
 ‘heat hardening’, which likely represents a key strategy to cope with
 increasingly extreme environments. The physiological mechanisms that
 determine acute thermal tolerance, and the underlying pathways
 facilitating heat hardening, remain debated. It has been posited, however,
 that exposure to high temperature is associated with tissue hypoxia and
 may be associated with increased expression of hypoxia-inducible factor-1
 (Hif-1). We studied acute thermal tolerance in zebrafish lacking
 functional Hif-1α paralogs (Hif-1aa and Hif-1ab double knockout;
 Hif-1α-/-), which are known to exhibit markedly reduced hypoxia tolerance.
 We hypothesised that Hif-1α-/- zebrafish would suffer reduced acute
 thermal tolerance relative to wild-types and that the heat hardening
 ability would be lost. On the contrary, we observed that Hif-1α-/- and
 wild-type fish did not differ in CTmax, and both genotypes exhibited heat
 hardening of a similar degree when CTmax was re-tested 48 h later. Despite
 exhibiting impaired hypoxia tolerance (based on loss of equilibrium
 experiments), Hif-1α-/- zebrafish display unaltered thermal tolerance,
 suggesting that these traits are not necessarily functionally associated.
 Hif-1α is accordingly not required for short-term acclimation in the form
 of heat hardening.
description: Critical thermal maximum (CTmax) trials in wild-type and Hif-1a
 knockout zebrafish. CTmax2 was conducted 48 h after CTmax1. Hypoxia
 tolerance determined as time to loss of equilibrium during hypoxia
 expsoure.
DOI: 10.5061/dryad.9cnp5hqfm
title: Data from: Ten-year survival trends of neovascular age-related macular degeneration at first presentation

description: Background: To describe 10-year trends in visual outcomes, anatomical
 outcomes, and treatment burden of patients receiving anti-vascular
 endothelial growth factor (VEGF) therapy for neovascular age-related
 macular degeneration (nAMD). Methods: Retrospective cohort study of
 treatment-naïve, first-affected eyes with nAMD started on ranibizumab
 before January 1, 2009. The primary outcome was time to best-corrected
 visual acuity (BCVA) falling ≤ 35 Early Treatment Diabetic Retinopathy
 Study (ETDRS) letters after initiating anti-VEGF therapy. Secondary
 outcomes included time to BCVA reaching ≥ 70 letters; proportion of eyes
 with BCVA ≥ 70 and ≤ 35 letters at 10 years; mean trend of BCVA and
 central retinal thickness (CRT) over 10 years; and mean number of
 injections. Results: For our cohort of 103 patients, Kaplan-Meier analyses
 demonstrated median time to BCVA reaching ≤35 and ≥70 letters were 37.8
 (95% CI 22.2-65.1) and 8.3 (95% CI 4.8-20.9) months after commencing
 anti-VEGF therapy, respectively. At the final follow-up, BCVA was ≤35
 letters and ≥70 letters in 41.1% and 21%, respectively, in first-affected
 eyes, whilst this was the case for 5.4% and 48.2%, respectively, in a
 patient’s better-seeing eye. Mean injection number was 37.0 ± 24.2 per eye
 and 53.6 ± 30.1 at patient-level (63.1% of patients required injections in
 both eyes).  Conclusions: The chronicity of nAMD disease and its
 management highlights the importance of long-term visual prognosis. Our
 analyses suggest that one in five patients will retain good vision (BCVA
 ≥70 ETDRS letters) in the first-affected eye at 10 years after starting
 anti-VEGF treatment; yet one in two patients will have good vision in
 their better-seeing eye. Moreover, our data suggest that early treatment
 of nAMD is associated with better visual outcomes.
description: Depersonalisation was carried out through hash function
 anonymisation of patient identification numbers, replacement of
 appointment dates with follow-up days to baseline. Age is not provided as
 a continuous variable as in original analysis to facilitate
 deidentification. The database is also comprehensive of lost to follow up
 patients' data. Approval of adequate depersonalisation was obtained
 by Moorfields Information Governance.
description: Moorfields_AMD_Database_10_years, the ReadMe file
 (Moorfields_AMD_Database_10_years_readme), and the related codes
 (anon_annualoutcomes and anon_survivalcurve) are provided.
DOI: 10.5061/dryad.9ghx3fff8
title: Data from: Polyandry and paternity affect disease resistance in eusocial wasps

description: One of several hypotheses proposed to explain polyandry in eusocial
 insects is the parasite–pathogen hypothesis (PPH), in which a colony of
 workers with multiple patrilines due to queen polyandry is less likely to
 fall victim to a parasite or pathogen threat because of genetic
 variability of the colony’s workforce. We challenged colonies with
 different strains of an entomopathogenic fungus to determine pathogen
 virulence and worker survival. We found that workers from different
 patrilines differed in their survival following the pathogen challenge,
 supporting the hypothesis that a major benefit of multiple mating by queen
 wasps is in disease resistance for the benefit of the colony. We infected
 isolated workers with the entomopathogenic fungus Beauveria bassiana and
 quantified their survival in the laboratory. We used five fungal strains
 (A–E) of B. bassiana for experiment 1, and then selected the two most
 lethal strains (A and C) for experiment 2. We used nine microsatellite
 markers to determine patriline membership, we analyzed microsatellite
 genotypes using the software Colony v2.0.6.5 (Wang 2004).
DOI: 10.5061/dryad.qfttdz0dq
title: A morphometric assessment of species boundaries in a widespread anole lizard (Squamata: Dactyloidae)

description: Cryptic species - genetically distinct species that are morphologically
 difficult to distinguish - present challenges to systematists.
 Operationally, cryptic species are very difficult to identify and sole
 usage of genetic data or morphological data can fail to recognize
 evolutionarily isolated lineages. We use morphometric data to test species
 boundaries hypothesized with genetic data in the North Caribbean Bark
 Anole (Anolis distichus), a suspected species complex. We use univariate
 and multivariate analyses to test if candidate species based on genetic
 data can be accurately diagnosed. We also test alternate species
 delimitation scenarios with a model fitting approach that evaluates normal
 mixture models capable of identifying morphological clusters. Our analyses
 reject the hypothesis that the candidate species are diagnosable. Neither
 uni- nor multivariate morphometric data distinguish candidate species. The
 best supported model included two morphological clusters; however, these
 clusters were uneven and did not align with a plausible species divergence
 scenario. After removing two related traits driving this result, only one
 cluster was supported. Despite substantial differentiation revealed by
 genetic data, we recover no new evidence to delimit species and refrain
 from taxonomic revision. This study highlights the importance of
 considering other types of data along with molecular data when delimiting
 species.
description: This dataset contains 13 linear morphometric traits that were
 measured from 513 whole body specimens with digital calipers.
DOI: 10.5061/dryad.gmsbcc2jv
title: Ancient life and moving fluids

description: Over 3.7 billion years of Earth history, life has evolved complex
 adaptations to help navigate and interact with the fluid environment.
 Consequently, fluid dynamics has become a powerful tool for studying
 ancient fossils, providing insights into the paleobiology and -ecology of
 extinct organisms from across the tree of life. In recent years, this
 approach has been extended to the Ediacara biota, an enigmatic assemblage
 of Neoproterozoic soft-bodied organisms that represent the first major
 radiation of macroscopic eukaryotes. Reconstructing the ways in which
 Ediacaran organisms interacted with the fluids has provided new insights
 into how these organisms fed, moved, and interacted within communities. In
 this paper, we provide an in-depth review of fluid physics aimed at
 paleobiologists, in which we dispel misconceptions related to the Reynolds
 number and associated flow conditions, and specify the governing equations
 of fluid dynamics. We then review recent advances in Ediacaran
 paleobiology resulting from the application of computational fluid
 dynamics (CFD). We provide a worked example and account of best practice
 in CFD analyses of fossils, including the first large eddy simulations
 (LES) performed on extinct organisms. Lastly, we identify key questions,
 barriers, and emerging techniques in fluid dynamics, which will not only
 allow us to better understand the earliest animal ecosystems, but also
 help develop new paleobiological tools for studying ancient life.
description: CFD simulations were constructed in COMOSL Multiphysics 5.5.
 Original data model (Ernietta) embedded was constructed in COMSOL and
 subsquently smoothed using VG Studio Max. 
description: Requires COMSOL Multiphysics 5.5 or greater to run.
DOI: 10.5061/dryad.8931zcrn5
title: Appendix 1. List of different ethnozoological uses of mammals observed across tribes in Arunachal Pradesh

description: Many areas of biodiversity rich regions in South Asia are governed by
 local communities through norms and practices enforced by traditional
 community institutions. The role of traditional beliefs systems in
 wildlife conservation in such regions continues to be debated in
 contemporary conservation discourse. We examined the traditional beliefs
 and taboos of different tribal communities in the Eastern Himalaya
 Eco-region and their contribution to natural resource management and
 biodiversity conservation through semi-structured interviews (n = 299)
 conducted with indigenous communities. Among the 35 threatened mammals of
 IUCN Red List, 28 received some form of protection from taboos and
 traditional beliefs. We also explore the relevance of these informal
 institutions in contemporary society, in the contexts of ongoing
 socioeconomic changes and global demand for wildlife products. Informal,
 culturally mediated, self-regulation of communities reliant on natural
 resources for sustenance provides an opportunity to address the
 complexities of reconciling human needs with conservation goals.