cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.x28d85
title: Occurrence Download

description: A dataset containing 1346651 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Quercus robur"
 ]
}

 The dataset includes 1346651 records from 3824 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0035132-251025141854904/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.88xwra
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "BasisOfRecord is one of (Human Observation, Machine Observation, Occurrence evidence, Observation)",
 "TaxonKey is one of (Lariscus insignis (F.Cuvier, 1821))",
 "Country is one of (Algeria, Angola, Benin, Botswana, British Indian Ocean Territory, Burkina Faso, Burundi, Cabo Verde, Cameroon, Central African Republic, Chad, Comoros, Congo, Congo, Democratic Republic of the, Côte d’Ivoire, Djibouti, Egypt, Equatorial Guinea, Eritrea, Eswatini, Ethiopia, French Southern Territories, Gabon, Gambia, Ghana, Guinea, Guinea-Bissau, Kenya, Lesotho, Liberia, Libya, Madagascar, Malawi, Mali, Mauritania, Mauritius, Mayotte, Morocco, Mozambique, Namibia, Niger, Nigeria, Réunion, Rwanda, Saint Helena, Ascension and Tristan da Cunha, Sao Tome and Principe, Senegal, Seychelles, Sierra Leone, Somalia, South Africa, South Sudan, Sudan, Tanzania, United Republic of, Togo, Tunisia, Uganda, Western Sahara, Zambia, Zimbabwe)"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0016271-250525065834625/datasets/export for details.
DOI: 10.15468/dl.he8d6n
title: Occurrence Download

description: A dataset containing 32549 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Trombidiformes",
 "Year 2005-2007",
 "Continent is Europe",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Machine Observation, Human Observation, Occurrence evidence, Observation)"
 ]
}

 The dataset includes 32549 records from 93 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049638-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.16882389
title: Scalability analysis of GlitchFlow with itwinai

description: Scalability analysis on JUWELS Booster of GlitchFlow use case (INFN, Virgo) from interTwin, using the itwinai library.

This data was used to generate the plots in the JOSS submission for itwinai
DOI: 10.5281/zenodo.16882390
title: Scalability analysis of GlitchFlow with itwinai

description: Scalability analysis on JUWELS Booster of GlitchFlow use case (INFN, Virgo) from interTwin, using the itwinai library.

This data was used to generate the plots in the JOSS submission for itwinai
DOI: 10.15468/dl.j87zhk
title: Occurrence Download

description: A dataset containing 11929 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Trombidiformes",
 "Year 2011-2013",
 "Continent is Europe",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Machine Observation, Human Observation, Occurrence evidence, Observation)"
 ]
}

 The dataset includes 11929 records from 98 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0049639-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.59zw3r2bp
title: Large scale eDNA monitoring of multiple aquatic pathogens as a tool to provide risk maps for wildlife diseases

description: Multiple parasites and pathogens cause disease in aquatic wildlife and in
 aquaculture species, generating a need for monitoring and management.
 Conventional disease monitoring methods involve laborious, costly and
 invasive capture and examination of host species, and require specialised
 expertise for every host and pathogen of interest. These restrictions
 could be alleviated by using pathogen detection techniques based on
 environmental DNA that provide simultaneous surveys of multiple aquatic
 pathogens across different host taxa. This would also be valuable for
 approaches employing parasite diversity as bioindicators of ecosystem
 disturbance, which suffer from similar restrictions. Here, we tested the
 potential for simultaneous detection of four wildlife pathogens in water
 samples from 280, mainly riverine, sites across Switzerland. We targeted
 the crayfish pathogen Aphanomyces astaci, the amphibian
 pathogen Batrachochytrium dendrobatidis, and the fish
 pathogens Saprolegnia
 parasitica and Tetracapsuloides bryosalmonae. The eDNA
 detection showed a widespread distribution of A.
 astaci, S. parasitica and T. bryosalmonae,
 although A. astaci and T.
 bryosalmonae were not detected in some alpine river
 catchments. B. dendrobatidis was detected only rarely, which was
 expected since the sampling did not target amphibian breeding sites.
 Co-detection rates were higher in rivers than in lakes, likely reflecting
 the habitat preferences and distributions of the host species. We discuss
 the advantages and limitations of eDNA-based pathogen monitoring and list
 a set of recommendations for managers. Our study illustrates how
 eDNA-based techniques can monitor several pathogen species concurrently,
 thus facilitating more comprehensive disease monitoring schemes. Combined
 with metabarcoding approaches in the future, eDNA based sampling and
 detection can facilitate the incorporation of parasite and pathogen
 occurrence and diversity as an indicator for aquatic ecosystem health, and
 for revealing the hidden biodiversity and structure of parasite
 communities.
DOI: 10.5061/dryad.wh70rxwrb
title: Data and analysis from: Body mass, temperature, and depth shape the maximum intrinsic rate of population increase in sharks and rays

description: An important challenge in ecology is to understand variation in species’
 maximum intrinsic rate of population increase, ????, not least because
 ???? underpins our understanding of the limits of fishing, recovery
 potential, and ultimately extinction risk. Across many vertebrate species,
 terrestrial and aquatic, body mass and environmental temperature are
 important correlates of ????. In sharks and rays, specifically, ???? is
 known be lower in larger species, but also in deep-sea ones. We use an
 information-theoretic approach that accounts for phylogenetic relatedness
 to evaluate the relative importance of body mass, temperature and depth on
 ????. We show that both temperature and depth have separate effects on
 shark and ray ???? estimates, such that species living in deeper waters
 have lower ????. Furthermore, temperature also correlates with changes in
 the mass scaling coefficient, suggesting that as body size increases,
 decreases in ???? are much steeper for species in warmer waters. These
 findings suggest that there are (as-yet understood) depth-related
 processes that limit the maximum rate at which populations can grow in
 deep sea sharks and rays. While the deep ocean is associated with colder
 temperatures, other factors that are independent of temperature, such as
 food availability and physiological constraints, may influence the low
 ???? observed in deep sea sharks and rays. Our study lays the foundation
 for predicting the intrinsic limit of fishing, recovery potential, and
 extinction risk species based on easily accessible environmental
 information such as temperature and depth, particularly for data-poor
 species. This repository contains the data and a minimum working example
 of the model-fitting process used for the article "Body mass,
 temperature, and depth shape productivity in sharks and rays", which
 is currently in press at Ecology and Evolution.
description: Analyses are reproducible using version 3.3.2 or above (R Core
 Team 2016). Files needed for reproducing the analyses
 are: chond-data.csv: Data frame with 63 rows (species)
 and 11 variables. Some of these variables are based on the same life
 history trait but are transformed for ease of interpretation and
 analysis. stein-et-al-single.tree: Phylogenetic tree
 with scaled branch lengths from Stein et al. (2018) used in analyses.
 These are freely downloadable from
 &lt;http://vertlife.org/sharktree/&gt;.
 rmax-scaling-analysis.R: R code with minimum working example of
 how to load data files, fit models phylogenetic linear models using the
 `pgls` function in the `caper` package, run information-theoretic
 comparisons, and check diagnostics.
DOI: 10.5061/dryad.bnzs7h4f0
title: Data from: Strong phylogenetic congruence between Tulasnella fungi and their associated Drakaeinae orchids

description: The study of congruency between phylogenies of interacting species can
 provide a powerful approach for understanding the evolutionary history of
 symbiotic associations. Orchid mycorrhizal fungi can survive independently
 of orchids making cospeciation unlikely, leading us to predict that any
 congruence would arise from host-switches to closely related fungal
 species. The Australasian orchid subtribe Drakaeinae is an iconic group of
 sexually-deceptive orchids that consists of approximately 66 species. In
 this study, we investigated the evolutionary relationships between
 representatives of all six Drakaeinae orchid genera (39 species) and their
 mycorrhizal fungi. We used an exome capture dataset to generate the first
 well-resolved phylogeny of the Drakaeinae genera. A total of 10 closely
 related Tulasnella Operational Taxonomic Units (OTUs) and previously
 described species were associated with the Drakaeinae orchids. Three of
 them were shared among orchid genera, with each genus associating with 1–7
 Tulasnella lineages. Cophylogenetic analyses show Drakaeinae orchids and
 their Tulasnella associates exhibit significant congruence (P &lt;
 0.001) in the topology of their phylogenetic trees. An event-based method
 also revealed significant congruence in Drakaeinae-Tulasnella
 relationships, with duplications (35), losses (25), and failure to diverge
 (9) the most frequent events, with minimal evidence for cospeciation (1)
 and host-switches (2). The high number of duplications suggests that the
 orchids speciate independently from the fungi, and the fungal species
 association of the ancestral orchid species is typically maintained in the
 daughter species. For the Drakaeinae-Tulasnella interaction, a pattern of
 phylogenetic niche conservatism rather than coevolution likely led to the
 observed phylogenetic congruency in orchid and fungal phylogenies. Given
 that many orchid genera are characterized by sharing of fungal species
 between closely related orchid species, we predict that these findings may
 apply to a wide range of orchid lineages.
description: Bayesian inference analyses were conducted using MrBayes 3.2.6
 (Huelsenbeck & Ronquist, 2001; Ronquist & Huelsenbeck,
 2003) to construct phylogenetic trees, with 25 % burn-in, 2,500,000
 generations, a tree was sampled every 200 generations with four chains,
 using the GTR+G model of nucleotide substitution. Convergence of runs was
 confirmed when the average standard deviation of split frequencies was
 &lt;0.01 with effective sample sizes &gt;200.
 <em>Tulasnella</em> phylogenetic trees were visualized in
 Figtree 1.4.3 (Rambaut, 2016) and midpoint rooted.
DOI: 10.5061/dryad.w6m905qsj
title: A test for plasticity in sperm motility activation

description: Evolutionary theory predicts that selection will favour phenotypic
 plasticity in sperm traits that maximise fertilisation success in dynamic
 fertilisation environments. In species with external fertilisation,
 osmolality of the fertilisation medium is known to play a critical role in
 activating sperm motility, but evidence for osmotic-induced sperm
 plasticity is limited to euryhaline fish and marine invertebrates. Whether
 this capacity extends to freshwater taxa remains unknown. Here, we provide
 the first test for plasticity in sperm-motility activation in response to
 osmotic environment in an anuran amphibian. Unexpectedly, there was no
 detectable shift in the optimal osmolality for sperm-motility activation
 after approximately 13 weeks of acclimation (a period reflecting the
 duration of the winter breeding season). However, in both the low and high
 acclimation treatments, the optimal osmolality for sperm-motility
 activation mirrored the osmolality at the natural breeding site,
 indicating a phenotypic match to the local environment. Previously it has
 been shown that C. signifera display among-population covariation between
 environmental osmolality and sperm performance. Coupled with this finding,
 the results of the present study suggest that inter-population differences
 reflect genetic divergence and local adaptation.  We discuss the
 need for experimental tests of osmotic-induced sperm plasticity in more
 freshwater taxa to better understand the environmental and evolutionary
 contexts favouring adaptive plasticity in sperm-motility activation.
description: Male common eastern froglets (<em>Crinia
 signifera</em>) were acclimated to either low (0 mOsmol kg-1) or
 high (50 mOsmol kg-1) environmental osmolality and using a split-sample
 experimental design sperm were activated across a range of osmolality
 treatments (0, 25, 50, 75, 100 and 200 ± 2 mOsmol kg-1).
DOI: 10.5061/dryad.rv15dv49z
title: Spatial variation in the evolutionary potential and constraints of basal metabolic rate and body mass in a wild bird

description: Organismal energy budget is strongly related to resource consumption,
 performance, and fitness. Hence, understanding the evolution of key
 energetic traits, such as basal metabolic rate (BMR), in natural
 populations is central for understanding life-history evolution and
 ecological processes. Here we used quantitative genetic analyses to study
 evolutionary potential of BMR in two insular populations of the house
 sparrow (Passer domesticus). We obtained measurements of BMR and body mass
 (Mb) from 911 house sparrows on the islands of Leka and Vega along the
 coast of Norway. These two populations were the source populations for
 translocations to create an additional third, admixed “common garden”
 population in 2012. With the use of a novel genetic group animal model
 concomitant with a genetically determined pedigree, we differentiate
 genetic and environmental sources of variation, thereby providing insight
 into the effects of spatial population structure on evolutionary
 potential. We found that the evolutionary potential of BMR was similar in
 the two source populations, whereas the Vega population had a somewhat
 higher evolutionary potential of Mb than the Leka population. BMR was
 genetically correlated with Mb in both populations, and the
 conditional evolutionary potential of BMR (independent of body mass) was
 41% (Leka) and 53% (Vega) lower than unconditional estimates. Overall, our
 results show that there is potential for BMR to evolve independently of
 Mb, but that selection on BMR and/or Mb may have different evolutionary
 consequences in different populations of the same species.
description: Phenotypic data were collected during winters (February-Marc) in
 2012–2015. Wild house sparrows were captured, and their metabolic rates
 were measured as oxygen consumption rates (mL O<sub>2</sub>
 h<sup>-1</sup>) during evening-night, and the lowest 20-minute
 running average oxygen consumption rate was recorded as the basal
 metabolic rate (BMR). Simultaneously, body mass was measured to the
 nearest 0.1 g. A blood sample (approx 25 μL) was obtained by brachial
 venipuncture and stored in absolute ethanol. The blood samples were used
 for genetic analyses, by genotyping 603 SNP markers that were used for
 pedigree reconstruction using the R package sequoia. The data and code
 sections provided in this archive provide further analyses of these
 data. 
description: All analyses were performed in R (version 4.1.0), using the
 packages MCMCglmm, nadiv, pedantics, tidyverse and boot.
DOI: 10.5061/dryad.34tmpg4p8
title: Intraspecific competition and temperature drive habitat-based resource polymorphism in brook charr

description: Intra- and interspecific competition, two density-dependent processes, are
 the two main driving forces suggested to promote habitat-based resource
 polymorphism, but very few studies have provided empirical support for
 this hypothesis. Furthermore, external drivers like temperature, an
 important environmental constraint in ectotherms, are often omitted when
 studying density-dependent habitat selection. Specifically, ambient
 temperature may have important effects on habitat-based resource
 polymorphism in ectotherms. Using mixed-effects modelling and isodar
 analyses, we quantified the effects of water temperature as well as intra-
 and interspecific competition on abundance and density-dependent habitat
 selection of brook charr (Salvelinus fontinalis) between littoral and
 pelagic habitats in 27 Canadian Shield lakes. We found that interspecific
 competition with white sucker (Catostomus commersonii) reduced brook charr
 abundances in both habitats but did not affect their density-dependent
 habitat selection. In contrast, the isodar analysis showed
 density-dependent habitat selection, confirming that intraspecific
 competition is a driver of brook charr habitat use in this system.
 Furthermore, brook charr preferred the littoral habitat at water
 temperatures below 20.8°C, but preferred the pelagic habitat above this
 threshold and no longer used the littoral habitat when its temperature was
 above ~22.2°C. By incorporating an external driver in the
 density-dependent habitat selection model, we show how the littoral
 temperature can shape brook charr distribution patterns between the
 littoral and pelagic habitats by acting as a thermal barrier and thus
 limiting the willingness of fish to use resources in the littoral habitat.
 This result suggests that global warming could constrain the diversifying
 effect of intraspecific competition and prevent resource polymorphism, a
 phenomenon that promotes adaptive radiation and speciation.
DOI: 10.5061/dryad.tx95x6b21
title: LiDAR reveals a preference for intermediate visibility by a forest-dwelling ungulate species: Code and LiDAR data

description: Visibility (viewshed) plays a significant and diverse role in animals’
 behavior and fitness. Understanding how visibility influences animal
 behavior requires the measurement of habitat visibility at spatial scales
 commensurate to individual animal choices. However, measuring habitat
 visibility at a fine spatial scale over a landscape is a challenge,
 particularly in highly heterogeneous landscapes (e.g., forests). As a
 result, our ability to model the influence of fine-scale visibility on
 animal behavior has been impeded or limited. In this study, we demonstrate
 the application of the concept of 3D cumulative viewshed in the study of
 animal spatial behavior at a landscape level. Specifically, we employed a
 newly described approach that combines terrestrial and airborne LiDAR to
 measure fine-scale habitat visibility (3D cumulative viewshed) on a
 continuous scale in forested landscapes. We applied the LiDAR-derived
 visibility to investigate how visibility in forests affects the summer
 habitat selection and the movement of 20 GPS-collared female red
 deer Cervus elaphus in a temperate forest in
 Germany. We used integrated step selection analysis to determine whether
 red deer show any preference for fine-scale habitat visibility and whether
 visibility is related to the rate of movement of red deer. We found that
 red deer selected intermediate habitat visibility. Their preferred level
 of visibility during the day was substantially lower than that of night
 and twilight, whereas the preference was not significantly different
 between night and twilight. In addition, red deer moved faster in
 high-visibility areas, possibly mainly to avoid predation and
 anthropogenic risk. Furthermore, red deer moved most rapidly between
 locations in the twilight. For the first time, the preference for
 intermediate habitat visibility and the adaption of movement rate to
 fine-scale visibility by a forest-dwelling ungulate species at a landscape
 scale was revealed. The LiDAR technique used in this study offers
 fine-scale habitat visibility at the landscape level in forest ecosystems,
 which would be of broader interest in the fields of animal ecology and
 behavior.
description: Please see detailed description as to how these data were
 colleced and processed in the paper "LiDAR reveals a preference for
 intermediate visibility by a forest-dwelling ungulate
 species".
description: The datasets are used for demonstrating the method to generate
 the fine-scale LiDAR-based visibility, which is elaborated in the paper
 "LiDAR reveals a preference for intermediate visibility by a
 forest-dwelling ungulate species". The detailed specifications of
 these datasets are described in the README file. The R and C++ codes
 implementing this method are also attached. The detailed steps as to the
 usage of these code scripts are described in the README file contained in
 3DViewshed codes.rar.
DOI: 10.5061/dryad.2bvq83btg
title: Data from: Extra-pair paternity correlates with genetic diversity, but not breeding density, in a Neotropical passerine, the Black Catbird

description: The frequency of extra-pair paternity (EPP) varies widely across socially
 monogamous birds, but the proximate mechanisms driving this variation
 remain unclear. In this study, we tested two major factors hypothesized to
 influence extra-pair mating—breeding density and genetic diversity—by
 comparing genetic mating patterns in two populations of black catbirds
 Melanoptila glabrirostris. This Neotropical songbird is endemic to the
 Yucatán Peninsula, including eastern Mexico, and its offshore islands. We
 sampled one mainland (Sian Ka’an Biosphere Reserve) and one island (Isla
 Cozumel) population and used single-nucleotide polymorphisms (SNPs) to
 quantify heterozygosity and genetic parentage over two breeding seasons.
 Moderate levels of EPP occurred in both populations (9.5 – 35% of
 offspring and 17 – 45% of nests). Contrary to predictions, breeding
 density did not affect EPP: although breeding densities were much higher
 on the mainland than on the island, EPP rates did not differ between
 populations, and local breeding density was not correlated with EPP at
 individual nests. In contrast, partial support emerged for the hypothesis
 that genetic diversity influences EPP: extra-pair offspring were more
 heterozygous than within-pair offspring. However, the two populations did
 not differ in genetic diversity, and neither the heterozygosity of social
 fathers nor within-pair relatedness predicted EPP. These results are
 consistent with recent comparative studies suggesting that breeding
 density is not a critical driver of EPP rates, and that not all tropical
 songbirds exhibit low rates of EPP.
description: Please see the README document
 ("README_Dataset-BlackCatbirdPaternity_v0.1.0.txt") and the
 accompanying published article: LaPergola, J.B., C. Riehl, J.E.
 Martínez-Gómez, B. Roldán-Clarà, and R.L. Curry. 2022. Extra-pair
 paternity correlates with genetic diversity, but not breeding density, in
 a Neotropical passerine, the Black Catbird. Journal of Avian Biology.
 Accepted. DOI: 10.1111/jav.03034
description: Please see the README document
 ("README_Dataset-BlackCatbirdPaternity_v0.1.0.txt") and the
 accompanying published article: LaPergola, J.B., C. Riehl, J.E.
 Martínez-Gómez, B. Roldán-Clarà, and R.L. Curry. 2022. Extra-pair
 paternity correlates with genetic diversity, but not breeding density, in
 a Neotropical passerine, the Black Catbird. Journal of Avian Biology.
 Accepted. DOI: 10.1111/jav.03034