cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b8gtht7gr
title: Data from: Integrating machine learning with otolith isoscapes: reconstructing connectivity of a marine fish over four decades

description: Stable isotopes are an important tool to uncover animal migration.
 Geographic natal assignments often require categorizing the spatial domain
 through a nominal approach, which can introduce bias given the continuous
 nature of these tracers. Stable isotopes predicted over a spatial gradient
 (i.e., isoscapes) allow a probabilistic and continuous assignment of
 origin across space, although applications to marine organisms remain
 limited. We present a new framework that integrates nominal and continuous
 assignment approaches by (1) developing a machine-learning multi-model
 ensemble classifier using Bayesian model averaging (nominal); and (2)
 integrating nominal predictions with continuous isoscapes to estimate the
 probability of origin across the spatial domain (continuous). We applied
 this integrated framework to predict the geographic origin of the
 Northwest Atlantic mackerel (Scomber scombrus), a migratory pelagic fish
 comprised of northern and southern components that have distinct spawning
 sites off Canada (northern contingent) and the US (southern contingent),
 and seasonally overlap in US fished regions. The nominal approach based on
 otolith carbon and oxygen stable isotopes (δ13C/δ18O) yielded high
 contingent classification accuracy (84.9%). Contingent assignment of
 unknown-origin samples revealed prevalent, yet highly varied contingent
 mixing levels (12.5–83.7%) within the US waters over four decades
 (1975–2019). Nominal predictions were integrated into mackerel-specific
 otolith oxygen isoscapes developed independently for Canadian and US
 waters. The combined approach identified geographic nursery hotspots in
 known spawning sites, but also detected geographic shifts over
 multi-decadal time scales. This framework can be applied to other marine
 species to understand migration and connectivity at high spatial
 resolution, relevant to management of unit stocks in fisheries and other
 conservation assessments.
DOI: 10.5061/dryad.0rxwdbs4d
title: Data from: On the function of flower number: disentangling fertility from pollinator-mediated selection

description: FLODIS is an experimental research project which aims at understanding how
 artificially increased flower number (i.e. enhanced floral display)
 impacts male and female reproductive/mating success as well as
 sex-specific pattern of selection on floral traits, in the dioecious
 insect-pollinated species Silene dioica.
description: dataID_FLODIS: all data on floral traits and reproductive/mating
 success from individuals (males, OP females and HP females)
 allFruits_FLODIS: all fruits dissected in OP and HP females to
 assess seed and ovule number, seed weight, as well as mean+variance in
 seed size paternity_FLODIS: assigned father for each
 offspring from the paternity analysis on CERVUS
DOI: 10.5061/dryad.mkkwh7140
title: Data from: Supplementation of seasonal natural resources with year-round anthropogenic resources by coyotes in natural fragments within a high-density urban area

description: Coyotes (Canis latrans) in urban landscapes provide important food web
 functions and ecological services but can also trigger human-wildlife
 conflict when their diet includes anthropogenic resources or domestic
 pets. As adaptable omnivores, coyotes adjust their diet to their
 environment, routinely switching among food items to accommodate spatial
 and seasonal differences in availability. To evaluate coyotes’ potential
 impacts within the food web of urban Long Beach, California where
 human-wildlife conflict involving coyotes may occur, we analyzed 115 scat
 samples collected once every two weeks from two open space fragments
 inside the urban matrix. We hypothesized that differences in scat
 composition would correlate with seasonal and site differences, with
 greater use of anthropogenic resources during the dry season supplementing
 lower prey availability, and greater consumption of wild mammal prey
 during the wet season when rabbits and small mammals reproduce. We found
 coyote diet was predominately composed of natural prey and vegetation
 year-round. Mammals made up more of the coyote diet in the wet season than
 the dry, while arthropods and vegetation occurred more in dry season
 scats. Coyotes relied on rabbits as their main prey year-round across all
 sites. Domestic cats (Felis catus) were the third most common individual
 prey species found in coyote scats; we did not find evidence of domestic
 dog (Canis lupus familiaris) consumption. The overall frequency of
 mammalian remains did not differ across sites but did differ across sites
 for other prey types. While there is a potential for human-wildlife
 conflict in coyote’s consumption of feral or domestic cats, coyotes may
 also be providing an ecological service by reducing cats in natural
 habitat fragments.
DOI: 10.15468/dl.5u44hg
title: Occurrence Download

description: A dataset containing 12 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Galega lindblomii",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 12 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003343-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7syry8
title: Occurrence Download

description: A dataset containing 309 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dodona durga"
 ]
}

 The dataset includes 309 records from 18 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003344-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.x3ffbg7p5
title: Data for: Sex matters: Predator presence induces sexual dimorphism in a monomorphic prey, from stress genes to morphological defenses

description: Inducible defences allow prey to increase survival chances when predators
 are present while avoiding unnecessary costs in their absence. Many
 studies report considerable inter-individual variation in
 inducible-defence expression, yet what underlies this variation is poorly
 understood. A classic vertebrate example of a predator‐induced
 morphological defence is the increased body depth in crucian carp
 (Carassius carassius), which reduces the risk of predation from gape‐size
 limited predators. Here, we report that among-individual variation in
 morphological defence expression can be linked to sex. We documented
 sexual dimorphism in lakes in which crucian carp coexisted with predators,
 where females showed shallower relative body depths than males, but not in
 a predator-free lake. When exposing crucian carp from a population without
 predators to perceived predation risk in a laboratory environment
 (presence/absence of pike, Esox lucius), we found that males expressed
 significantly greater morphological defence than females, causing sexual
 dimorphism only in the presence of predators. We uncovered a correlative
 link between the sex-specific inducible phenotypic response and gene
 expression patterns in major stress-related genes (POMC, MC3R, MC4R).
 Together, our results highlight that sex-specific responses may be an
 important, yet underappreciated, component underlying inter-individual
 differences in the expression of inducible defences, even in species
 without pronounced sexual dimorphism.
DOI: 10.5061/dryad.b8gtht7gs
title: Data from: Estimating potential global sources and secondary spread of freshwater invasions under historical and future climates

description: Aim: We employ a climate-matching method to evaluate potential source
 regions of freshwater invasive species to an introduced region and their
 potential secondary spread under historical and future climates. Location:
 Global source regions, with primary introductions to the Laurentian Great
 Lakes and secondary introductions throughout North America Methods: We
 conducted a climate-match analysis using the CLIMATE algorithm to estimate
 global source freshwater ecoregions under historical and future climates
 with an ensemble of general circulation models for climate change scenario
 SSP5-8.5. Given existing research, we use a climate match of ≥ 71.7%
 between ecoregions to indicate climatic conditions that will not inhibit
 the survival of introduced freshwater organisms. Further, we estimate the
 secondary spread of freshwater invaders to the ecoregions of North America
 under historical and future climates. Results: We identified 54 global
 freshwater ecoregions with a climate match ≥ 71.7% to the recipient
 Laurentian Great Lakes under historical climatic conditions and 11
 additional ecoregions were predicted to exceed the threshold under climate
 change. Three of the 11 ecoregions were located in South America, a
 continent where no matches existed under historical climates and eight
 were located in the southern United States, southern Europe, Japan, and
 New Zealand. Further, we identify 34 North American ecoregions of
 potential secondary spread of freshwater invasions from the Great Lakes
 under historical climatic conditions, and five ecoregions were predicted
 to exceed the threshold under climate change. Main conclusion: We provide
 a climate-match method that can be employed to assess the sources and
 spread of freshwater invasions under historical and future climate
 scenarios. Our climate-match method predicted increases in climate match
 between the recipient region and several potential source regions, and
 changes in areas of potential spread under climate change. The identified
 ecoregions are candidates for detailed biosecurity risk assessments and
 related management actions. The identified ecoregions are candidates for
 detailed biosecurity risk assessments and related management actions.
description: We accessed downscaled historical climate data and climate change
 projections via the Worldclim database (worldclim.org; Fick and Hijmans
 2017).  Freshwater ecoregion delineations are from
 Abell et al. (2008). We used the CLIMATE algorithm
 (also known as climatch; Pheloung 1996; Crombie et al. 2008) in the
 provided scripts to model climate match between ecoregions (see article
 methods for details on which ecoregions).
description: All scripts are coded in R.
DOI: 10.5061/dryad.2v6wwpzsg
title: Evolutionary responses of energy metabolism, development, and reproduction to artificial selection for increasing heat tolerance in Drosophila subobscura

description: Adaptation to warming conditions involves increased heat tolerance and
 metabolic changes to reduce maintenance costs and maximize biological
 functions close to fitness. Evidence shows that energy metabolism evolves
 in response to warming conditions, but we know little about how heat
 stress intensity determines the evolutionary responses of metabolism and
 life history traits. Here, we evaluated the evolutionary responses of
 energy metabolism and life-history traits to artificial selection for
 increasing heat tolerance in Drosophila subobscura, using two protocols to
 measure and select heat tolerance: slow and fast ramping protocols. We
 found that the increase in heat tolerance was associated with reduced
 activity of the enzymes involved in the glucose-6-phosphate branchpoint,
 but no changes in the metabolic rate in selected lines. We also found that
 the evolution of increased heat tolerance increased the early fecundity in
 selected lines and increased the egg-to-adult viability only in the
 slow-ramping selected lines. This work shows heat tolerance can evolve
 under different thermal scenarios but with different evolutionary outcomes
 on associated traits depending on the heat stress intensity. Therefore,
 spatial and temporal variability of thermal stress intensity should be
 taken into account to understand and predict the adaptive response to
 ongoing and future climatic conditions.
DOI: 10.15468/dl.karkc7
title: Occurrence Download

description: A dataset containing 233 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Germany",
 "TaxonKey is Cloeon simile"
 ]
}

 The dataset includes 233 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003342-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.jwstqjqdh
title: Tolerance of coralline algae to ocean warming and marine heatwaves

description: Ocean warming (OW) and marine heatwaves (MHWs) rapidly transform marine
 ecosystems, especially when they impact keystone or foundation species.
 Foundation species such as kelps, fucoids and corals are highly sensitive
 to heat stress, which threatens the future of temperate seaweed forests
 and tropical reefs. However, functioning and resilience of these systems
 also rely on the less conspicuous coralline algae, whose thermal
 tolerances have gone largely untested. Here, we examined the sensitivity
 of four temperate coralline algal morphotypes from three different species
 to four realistic present-day and future OW and MHW scenarios (ambient
 [16°C constant]; ambient+MHW [16°C baseline + a symmetric two-week
 heatwave with a peak intensity of 18.7°C]; future [18.7°C constant];
 future+MHW [18.7°C baseline + a symmetric two-week heatwave with a peak
 intensity of 21.4°C]). Photo-physiology (e.g., Fv/Fm) and calcification
 physiology (e.g., proxies for calcifying fluid saturation state Ω CF )
 were generally unaffected by the treatments, implying a high
 thermo-tolerance of our study species compared to other important marine
 foundation species. We ascribe this mainly to their photosynthetic
 apparatus that, unlike in other photoautotrophs, continued to function
 under heat stress. Experimental evidence presented here and elsewhere
 implies that coralline algae are likely to continue to play their crucial
 ecological roles in a warming ocean. Yet, such predictions are fraught
 with uncertainty due to the substantial gaps in our knowledge. We attempt
 to highlight some of these gaps and aim to present potential physiological
 underpinnings of their thermo-tolerance.
description: Chlorophyll flourometry was used to obtain Fv/Fm (variable
 fluorescence [Fv] normalised to maximal fluorescence [Fm]), rETRmax
 (maximum relative elctron transport rate), Ek (minimum saturation
 intensity) and alpha (light use efficiency). Skeletal
 magnesium content in mol% and Full-Width-Half-Maximum were measured using
 confocal Raman spectroscopy. Chlorophyll a,
 phycoerything and phycocyanin content was calculated from absorbance
 readings (UV-vis spectrophotometer). Calcification
 rates were calculated from changes in weight (buoyant weight) which were
 normalised for surface area (cm-2) and time (d-1). 
description: Microsoft Excel or equivalent open-source software.
DOI: 10.15468/dl.57yzpk
title: Occurrence Download

description: A dataset containing 1309 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Euthalia lubentina"
 ]
}

 The dataset includes 1309 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003346-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3xsj3txkr
title: Data for: Space-for-time substitution reveals a hump-shaped distribution of dung beetles

description: Unravelling how climate change impacts the diversity and distribution
 patterns of organisms is a major concern in ecology, especially with
 climate-sensitive species, such as dung beetles. Often found in warmer
 weather conditions, beetles are used as bio-indicators of environmental
 conditions. By using an altitudinal gradient as a proxy for climate change
 (i.e., space-for-time substitution), we assessed how changes in climatic
 variables, such as temperature and precipitation, impact patterns of dung
 beetles diversity and distribution in the Peruvian Andes. We recorded dung
 beetles diversity using three different types of baits, feces, carrion,
 and fruits, distributed in 18 pitfall traps in five different altitudinal
 sites (from 900 to 2500 m, 400 m apart from each other) in the rainy and
 dry seasons. We found that (i) dung beetles richness and abundance were
 influenced by the climate gradient, (ii) seasonality influenced beetle
 richness, which was high in the wet season, but did not influence
 abundance, (iii) dung beetle richness and abundance fit to a hump-shaped
 distribution pattern along the altitudinal gradient, and (iv) species
 richness is the beta diversity component that best describes the
 composition of dung beetle species along the altitudinal gradient. Our
 data show that the distribution and diversity of dung beetles are
 different at larger scales, with different patterns resulting from the
 response of species to both abiotic and biotic factors.
description: Please see the README document
 ("README_Dataset-Dungbeetlesandeanmountain.txt") and the
 accompanying published article: Ancco‐Valdivia, F. G., Calixto, E. S.,
 & López‐Tejeda, E. (2022). Space‐for‐time substitution reveals a
 hump‐shaped distribution of dung beetles. Biotropica.  Accepted. DOI:
 10.1111/btp.13189
description: Please see the README document
 ("README_Dataset-Dungbeetlesandeanmountain.txt") and the
 accompanying published article: Ancco‐Valdivia, F. G., Calixto, E. S.,
 & López‐Tejeda, E. (2022). Space‐for‐time substitution reveals a
 hump‐shaped distribution of dung beetles. Biotropica.  Accepted. DOI:
 10.1111/btp.13189
DOI: 10.5061/dryad.rv15dv4b7
title: Data from: The influence of the number of tree searches on maximum likelihood inference in phylogenomics

description: Maximum likelihood (ML) phylogenetic inference is widely used in
 phylogenomics. As heuristic searches most likely find suboptimal trees, it
 is recommended to conduct multiple (e.g., ten) tree searches in
 phylogenetic analyses. However, beyond its positive role, how and to what
 extent multiple tree searches aid ML phylogenetic inference remains poorly
 explored. Here, we found that a random starting tree was not as effective
 as the BioNJ and parsimony starting trees in inferring ML gene tree and
 that RAxML-NG and PhyML were less sensitive to different starting trees
 than IQ-TREE. We then examined the effect of the number of tree searches
 on ML tree inference with IQ-TREE and RAxML-NG, by running 100 tree
 searches on 19,414 gene alignments from 15 animal, plant, and fungal
 phylogenomic datasets. We found that the number of tree searches
 substantially impacted the recovery of the best-of-100 ML gene tree
 topology among 100 searches for a given ML program. In addition, all of
 the concatenation-based trees were topologically identical if the number
 of tree searches was ≥ 10. Quartet-based ASTRAL trees inferred from 1 to
 80 tree searches differed topologically from those inferred from 100 tree
 searches for 6 /15 phylogenomic datasets. Lastly, our simulations showed
 that gene alignments with lower difficulty scores had a higher chance of
 finding the best-of-100 gene tree topology and were more likely to yield
 the correct trees.
description: FILE OVERVIEW The zip folder contains Supplementary Figures S1-S20,
 Supplementary Tables S1-S6, and Supplementary Text. File List: File 1
 Name: Supplementary Figures S1-S20.pdf File 1 Description: This file
 contains Supplementary Figures S1-S20. Each figure includes its respective
 legend. File 2 Name: Supplementary Tables S1-S6.xlsx File 2 Description:
 This file contains Supplementary Tables S1-S6. Each table includes its
 respective title. File 3 Name: Supplementary_Text.pdf File 3 Description:
 This file contains supplementary text detailing the parameters used for
 each phylogenetic analysis.
DOI: 10.5061/dryad.ghx3ffbsj
title: Data for: Visual guidance of honeybees approaching a vertical landing surface

description: Landing is a critical phase for flying animals, whereby many rely on
 visual cues to perform controlled touchdown. Foraging honeybees rely on
 regular landings on flowers to collect food, crucial for colony survival
 and reproduction. Here, we explore how honeybees utilize optical-expansion
 cues to regulate approach flight speed when landing on vertical surfaces.
 Three sensory-motor control models have been proposed for landings of
 natural flyers. Landing honeybees maintain a constant
 optical-expansion-rate set-point, resulting in a gradual decrease in
 approach velocity and gentile touchdown. Bumblebees exhibit a similar
 strategy, but they regularly switch to a new constant optic-expansion-rate
 set-point. Meanwhile, landing birds fly at a constant time-to-contact to
 achieve faster landings. Here, we re-examined the landing strategy of
 honeybee by fitting the three models to individual approach flights of
 honeybees landing on platforms with varying optic-expansion cues.
 Surprisingly, the landing model identified in bumblebees proves to be the
 most suitable for these honeybees. This reveals that honeybees adjust
 their optic-expansion-rate in a stepwise manner. Bees flying at low
 optic-expansion-rates tended to stepwise increase their set-point, while
 those flying at high optic-expansion-rates tend to stepwise decrease it.
 This modular landing control system enables honeybees to land rapidly and
 reliably under a wide range of initial flight conditions and visual
 landing platform patterns. The remarkable similarity between the landing
 strategies of honeybees and bumblebees suggests that this may also be
 prevalent among other flying insects. Furthermore, these findings hold
 promising potential for bioinspired guidance systems in flying robots.