cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.21223/p3/io6nav
title: Dataset for: Advanced clones of group LBHT cycle 1, population B (LBHT) in San Ramon-Peru

description: In anticipation of the effects of global warming on potato cultivation in both tropical and subtropical environments. Since 2004, efforts have turned to the development of a new group in Population B with improved adaptation to warm environments, resistance to late blight and virus, mid-season maturity (90 day growing period under short day length conditions), adaptation to mid elevations, low glycoalkaloids content, along with economically important traits such as high tuber yield, quality for table and industry. And so group LBHT of population B was developed, denominated LBHT because of its late blight and heat tolerance. All trials were conducted in randomized complete block design (RCBD) with 3-4 replicates or in simple lattice design, using Désirée as a heat tolerant control and Amarilis as a non-tolerant to heat control at San Ramon, located at 828 masl in Junin-Peru, a humid environment in mid elevation tropics.
DOI: 10.5061/dryad.d7wm37q54
title: Forestry influences on salmonid habitat in the North Thompson River Watershed, British Columbia

description: Freshwater ecosystems that support juvenile salmonids can be degraded by
 human pressures such as forestry. Forestry activities can alter water
 temperatures and the delivery and storage of water, nutrients, wood, and
 sediment in streams, resulting in changes to the habitat, growth, and
 survival of juvenile salmon. Previous research on forestry impacts on
 habitat has focused on small, intensively monitored coastal systems. Here
 we examined forestry impacts, watershed characteristics, physical habitat,
 and stream temperature for 28 midsized tributaries of the North Thompson
 River to examine relationships between forestry and juvenile coho stream
 habitat in interior watersheds. Forest harvest had a positive correlation
 to maximum summer stream temperature. Streams with 35% of the riparian
 area harvested since 1970 had maximum summer temperatures 3.7°C higher on
 average than those with 5% harvested. Stream gradient explained most of
 the variation in physical habitat and had negative correlations to pool
 cover, pool depth, and fine sediment cover. Taken together, these results
 indicate that watershed characteristics drive physical habitat, but
 forestry harvest can be a primary driver of water temperatures.
description: Data is comprised of measurements of physical habitat, watershed
 characteristics, and stream temperature collected by the authors. Details
 of the data collected are provided in the manuscript.
DOI: 10.5061/dryad.hmgqnk9mw
title: Data for: When does early-life telomere length predict survival? A case study and meta-analysis

description: Suboptimal conditions during development can shorten telomeres, the
 protective DNA caps on the end of chromosomes. Shorter early-life telomere
 length (TL) can indicate reduced somatic maintenance, leading to lower
 survival and shorter lifespan. However, despite some clear evidence, not
 all studies show a relationship between early-life TL and survival or
 lifespan, which may be due to differences in biology or study design
 (e.g., survival period measured). In superb fairy-wrens (Malurus cyaneus),
 we assessed whether early-life TL predicts mortality across different
 life-history stages (fledgling, juvenile, adult). However, in contrast to
 a similar study on a congener, early-life TL did not predict mortality
 across any life stage in this species. We then performed a meta-analysis
 including 32 effect sizes from 23 studies (15 birds and 3 mammals) to
 quantify the effect of early-life TL on mortality whilst taking into
 consideration potential sources of biological and methodological
 variation. Overall, the effect of early-life TL on mortality was
 significant, corresponding to a 15% reduction in mortality risk with each
 standard deviation increase in TL. However, the effect became weaker when
 correcting for publication bias. Contrary to our predictions, there was no
 evidence that effects of early-life TL on mortality varied with species
 lifespan or the period over which survival was measured. However, negative
 effects of early-life TL on mortality risk were pervasive throughout life.
 These results imply that effects of early-life TL on mortality are more
 likely context-dependent rather than age-dependent, although substantial
 power and publication bias issues highlight the need for more research.
DOI: 10.5061/dryad.k0p2ngfcj
title: Strength of the ‘island rule’ in birds is positively associated with absence of avian predators

description: The similar characteristics shared by island environments have been shown
 to lead to common patterns of adaptations in island species, commonly
 referred to as the "insularity syndrome". A well-known example
 is the "island rule", where large species become smaller on
 islands and small species become larger, leading to well-known cases of
 dwarfism and gigantism. This pattern was recently verified on a global
 scale, but the mechanisms underlying it have been poorly investigated.
 Here, we focused on the role of released pressure from predation and
 competition experienced by island birds. Using 120 pairs of endemic island
 species and their mainland sister relatives, we first verified that the
 island rule was detected in our dataset, and then evaluated the effects of
 the numbers of raptors and inter-specific competitors on the evolution of
 the insular species' body mass. We found a strong effect of predation
 on body mass evolution, with a stronger island rule for species occurring
 on islands with no raptors, while the pattern disappears in their
 presence. However, we did not find an effect of competition on this
 pattern. Our study shows the importance of considering ecological
 interactions for understanding patterns of body size evolution, and the
 exceptions to those patterns.
DOI: 10.25338/b84060
title: Data and model code for: Habitat use patterns suggest that climate-driven vegetation changes will negatively impact mammal communities in the Amazon (ACV)

description: The dataset contains species detection/non-detection data from 5
 camera-trap surveys, carried out in 4 protected areas, in the southern
 Brazilian Amazon, along with camera-specific covariate and effort data.
 Also provided is R and Nimble code to implement the two community
 occupancy models described in the main text in Rocha and Sollmann (2023),
 Habitat use patterns suggest that climate-driven vegetation changes will
 negatively impact mammal communities in the Amazon, Animal Conservation,
 in press.
description: Please see description in the publication.
description: Viewing data requires R; running models requires R package
 Nimble.
DOI: 10.5061/dryad.zkh1893dv
title: Data for: Experimentally advancing morning emergence time does not increase extra-pair siring success in blue tit males

description: Extra-pair paternity occurs frequently in socially monogamous birds, but
 there is substantial variation in extra-pair siring success among males.
 Several studies have shown that siring success relates to the timing of
 morning activity, with the earliest active males being more successful,
 which suggests that early activity is important for acquiring extra-pair
 copulations. However, these studies are correlational, and it therefore
 remains unclear whether the relationship between timing and extra-pair
 siring success is causal. An alternative explanation is that successful
 extra-pair sires tend to be active earlier (e.g. because they are of high
 quality or in good condition), but that early activity in itself does not
 increase siring success. We experimentally advanced the emergence time of
 male blue tits by exposing them to light about half an hour before their
 natural emergence time. Although males that were exposed to the light
 treatment emerged from their roost substantially earlier than males that
 were exposed to a control treatment, light-treated males were not more
 likely to sire extra-pair offspring. Furthermore, whereas control males
 showed the expected relation between emergence time and siring success
 (although not statistically significant), there was no relation between
 emergence time and extra-pair siring success among light-treated males.
 Our results challenge the hypothesis that the timing of morning activity
 per se is an important factor underlying extra-pair siring success.
DOI: 10.5061/dryad.kwh70rz80
title: Bridging the gap: Optimising connectivity solutions for an arboreal gliding mammal

description: Connectivity modelling tools are important for developing mitigation
 strategies to alleviate negative impacts on animal movement caused by road
 networks. Arboreal gliding mammals are especially vulnerable to road
 widening as they are unable to cross gaps beyond their gliding capacity.
 However, there are limitations of conventional raster-based modelling
 techniques when applied on this group. We developed and applied a
 new model that quantifies the changes in connectivity for an arboreal
 gliding species, the Sunda colugo, in Singapore using information on
 species-specific glide performance through a vector-based GIS approach. We
 also incorporated a genetic algorithm to determine optimal locations for
 sets of glide poles that could be installed to improve
 connectivity.  Expectedly, connectivity was heavily
 impacted by the road widening works, with a 93.3% decrease in the total
 number of feasible glide paths connecting roadside trees. Nine
 glide poles installed during the construction phase of the project were
 initially uninformed by the connectivity model and they provided 26
 additional connections only. Comparatively, the top nine pole locations
 identified through the genetic algorithm provided 247 additional
 connections, almost 10 times more than the amount supplied by the initial
 nine glide pole locations determined through qualitative
 methods. The multi-objective capacity of the genetic algorithm
 also reduced large connectivity gaps post-development, with simulated
 glide poles increasing the percentage of pixels covered with connectivity
 from 16.1% to 27.7%.  Synthesis and applications: Our model fills
 a knowledge gap in connectivity modelling for arboreal gliding mammals
 whose movements are affected by varying habitat alterations. We
 demonstrated that locations of mitigation structures greatly influence the
 success of mitigation efforts and the locations can be optimized by
 incorporating the glide performance of the species into the genetic
 algorithm. Given limited conservation resources, this approach would
 benefit managers in formulating cost-effective efforts for arboreal
 gliding mammals.
description: Information on colugo glide performance was obtained through
 nocturnal visual surveys. Tree surveys were conducted prior to development
 works to identify tree species, measure tree height, and mark their
 locations. Relevant information on road plans was provided by Mandai
 Wildlife Group.
description: All analyses were performed in
 the R statistical programming platform. The shapefiles could also be
 opened using GIS software such as QGIS.
DOI: 10.5061/dryad.n02v6wx1r
title: Coexisting mangrove-coral habitat use by reef fishes in the Caribbean

description: We conducted visual fish surveys in coexisting mangrove-coral (CMC)
 habitats in Panama to analyze the effect of coral presence in mangrove
 habitats on the fish assemblage. Our study revealed that CMC habitats
 harbor distinct fish assemblages compared to mangrove habitats without
 coral, with greater species richness and increased herbivore abundance.
description: This study took place from March 13 to 27, 2019 in Bocas del
 Toro, Panama. Visual surveys were conducted in two types of mangrove
 habitat (six sites per habitat): CMC and non-CMC habitats. Each site was
 surveyed five times; six sites were sampled per day (CMC sites were
 sampled one day, then non-CMC the next) for a total of 10 days over the
 sampling period. To study the fish assemblage, we used the visual
 “belt-transect” method, snorkeling a 30 m-long transect parallel to the
 mangrove fringe while looking 2 m landward from the submerged prop root
 edge and recording species, number, and estimated size (total length, cm)
 of the fish taxa encountered. The entire fish assemblage was surveyed
 except cryptic species (Clinidae, Gobiidae). Small, silvery, fork-tailed
 fishes that tend to inhabit the water column in large schools (e.g.,
 Atherinidae, Clupeidae, Engraulidae) were placed into a single group
 (“small pelagic forage fishes”), and these fishes were analyzed separately
 due to sporadic sightings in high densities. All surveys were conducted
 and standardized between 1000 and 1600 h to reduce possible diel rhythm
 effects, and transect locations were chosen at nonfixed points. At each
 site, we measured water temperature, salinity, dissolved oxygen, pH, and
 total chlorophyll using a YSI EXO2 multiparameter sonde and light
 intensity using a HOBO MX2202 data logger. We also measured depth, prop
 root density, and epibiont prop root diameter within 1-m2 quadrats (10
 quadrats per site evenly spaced along a 30-m transect). Depth was measured
 to the mean low tide line using a 1-m long polyvinyl chloride pole marked
 every 5 cm. Prop root density was measured by counting the number of prop
 roots within each quadrat. Epibiont prop root diameter was measured by
 using a tape to measure the maximum diameter of the attached organism
 assemblage on each root within the quadrat (one maximum diameter per
 root). Prior to data analysis, we pooled fish species abundances for each
 site. To distinguish between juveniles and adults, we considered fishes to
 be juveniles when they were smaller than one third of the maximum species
 length obtained from FishBase.
DOI: 10.5061/dryad.v9s4mw70x
title: Data from: Heat stress increases risk taking in foraging shorebirds

description: 1. Animals often face a trade-off between food acquisition and
 predation/disturbance avoidance. Yet the extent to which this trade-off is
 affected by modulating factors such as thermal risk and foraging
 opportunities has been largely overlooked. 2. Here, we examined the
 influence of temporal and environmental gradients on the flight initiation
 distance (FID, the distance at which animals flee from an approaching
 human-simulated predator) and escape mode (flying/low risk versus
 running/low cost) in 16 species of shorebirds foraging on tidal flats of
 the Bijagós Archipelago, Guinea-Bissau. We measured escape responses
 throughout the low tide period during wet and dry seasons and
 simultaneously recorded microclimate variables and occurrence of
 heat-reduction behaviour (ptiloerection). Furthermore, we measured
 corticosterone metabolites (CORTm) from droppings in red knots Calidris
 canutus to assess whether ptiloerection is associated to a physiological
 stress response to hot conditions. 3. Overall, birds tolerated a closer
 approach at higher environmental temperatures and when showing
 ptiloerection. They also had shorter FIDs during the dry season and
 towards the start/end of the low tide period. FIDs also increased with
 body mass and decreased in areas with more human presence. In red knots,
 individuals showing ptiloerection had higher levels of CORTm,
 demonstrating a link between physiological and behavioural stress coping
 responses to heat events. 4. Our results suggest that heat-stressed
 shorebirds take greater risks, supporting the idea of a
 thermoregulation–predation risk trade-off. They also indicate that
 shorebirds adjust risk taking to tidal and seasonal cycles, generally
 reducing FIDs when the energetic costs of escape are expected to be large.
 Finally, they suggest that shorebirds habituate to non-lethal human
 presence and respond to perceived predation risk in accordance with the
 predictions of optimal escape theory. 5. These results are relevant to
 many animals that face a tight window for foraging activity while being
 exposed to predation/disturbance and heat during the day. We discuss
 management implications of our results in the context of global change.
description: All analyses were performed in
 R 4.0.2 (R Core Team,
 2020). All data files (.csv) can be opened with R or
 other programs.
DOI: 10.5061/dryad.qbzkh18nd
title: Data from: Summary tests of introgression are highly sensitive to rate variation across lineages

description: The evolutionary implications and frequency of hybridization and
 introgression are increasingly being recognized across the tree of life.
 To detect hybridization from multi-locus and genome-wide sequence data, a
 popular class of methods is based on summary statistics from subsets of 3
 or 4 taxa. However, these methods often carry the assumption of a constant
 substitution rate across lineages and genes, which is commonly violated in
 many groups. In this work, we quantify the effects of rate variation on
 the D test (also known as ABBA-BABA test), the D3 test, and HyDe. All
 three tests are used widely across a range of taxonomic groups, in part
 because they are very fast to compute. We consider rate variation across
 species lineages, across genes, their lineage-by-gene interaction, and
 residual variation across gene-tree edges. We do so by simulating gene
 trees within species networks according to a birth-death-hybridization
 process so as to capture a range of realistic species phylogenies. For all
 three methods tested, we found a marked increase in the false discovery of
 reticulation (type-1 error rate) when there is rate variation across
 species lineages. The D3 test was the most sensitive, with around 80%
 type-1 error, such that D3 appears to be more sensitive to a departure
 from the clock than to the presence of reticulation. For all three tests,
 the power to detect hybridization events decreased as the number of
 hybridization events increased, indicating that multiple hybridization
 events can obscure one another if they occur within a small subset of
 taxa. Our study highlights the need to consider rate variation when using
 site-based summary statistics and points to the advantages of methods that
 do not require assumptions on evolutionary rates across lineages or across
 genes.
DOI: 10.5061/dryad.pg4f4qrv1
title: Data and code for: When origin, reproduction ability, and diet define the role of birds in invasions

description: The ecological impacts of invasive alien species (IAS) are increasingly
 documented, however, they are usually studied through the lens of either
 the IAS or the species that suffer from them (IAS-threatened species). A
 clear understanding of how both protagonists of biological invasions are
 characterized is still lacking. We investigated the morphology,
 life-history, and ecology of birds involved in biological invasions.
 Evaluating the disposal of 450 IAS-threatened birds and 400 alien birds in
 a functional space, we found that both groups harbored various strategies.
 Aliens had larger clutches and were more herbivorous than IAS-threatened
 and worldwide birds, while IAS-threatened birds were more insular endemic
 from the Australia region than alien and worldwide birds. IAS-threatened
 species showed opposite strategies to alien birds regarding traits related
 to diet, origin, and reproduction. Further exploring traits associated
 with impact magnitude, we found that alien birds with high impact had a
 generalist behavior and an animal-based diet. Although traits were a
 strong basis to distinguish aliens from IAS-threatened birds, they did not
 differentiate the impact type. In conclusion, by emphasizing differences
 relating to the density distribution of bird groups in a functional space,
 we opened new opportunities to identify the role of birds in biological
 invasions.
description: Scripts and data for reproducing the results
 obtained by Marino & Bellard (2023) in the paper "When
 origin, reproduction ability, and diet define the role of birds in
 invasions" The first script
 computes the axes of the multidimensional functional space based on the
 traits of both alien and IAS-threatened birds. The second script performs
 the statistical analyses based on the functional space and creates figures
 1 and 4. The third script performs the trait-by-trait analysis and creates
 figures 2 and 3. The last script describes the steps implemented for
 evaluating the prediction of impact type based on the position of birds in
 the functional space. The dataset
 has been collected as described in the method section of the associated
 paper.
DOI: 10.6084/m9.figshare.31169113
title: Figures Autophagy

description: Autophagy-deficient fission yeast cells display mating defects and are unable to recover from amino acid starvation, even when external amino acids are available. We investigated the interplay between TORC1 signaling, autophagy, and stress adaptation, to understand these phenotypes. Amino acid or nitrogen starvation, as well as oxidative stress, inactivate TORC1, and translation inhibition through eIF2α phosphorylation occurs during all stresses. We show that both major phenotypes of autophagy-deficient cells - their failure to resume growth after amino acid starvation and their mating defects - are alleviated by genetic or environmental enhancement of intracellular amino acid pools. Regarding leucine starvation, deletion of <i>any1</i> rescues the growth defect of <i>atg1</i>Δ mutants by maintaining amino acid transporters at the plasma membrane, promoting amino acid uptake. Regarding mating defects, TORC1 inactivation by nitrogen depletion drives cell cycle remodeling for meiotic entry, and autophagy is specifically required for the final G2-to-G1 arrest, which correlates with accumulation of the CDK inhibitor Rum1. Metabolomic analyses reveal that intracellular amino acid pools decrease sharply during nitrogen starvation, especially in autophagy-deficient cells, and supplementation with trace amino acids restores their ability to complete the final G2-to-G1 transition. Overall, our findings demonstrate that autophagy sustains intracellular amino acid pools during prolonged stress, enabling TORC1 reactivation and cell cycle remodeling required for mating and meiosis.
DOI: 10.6084/m9.figshare.31169113.v1
title: Figures Autophagy

description: Autophagy-deficient fission yeast cells display mating defects and are unable to recover from amino acid starvation, even when external amino acids are available. We investigated the interplay between TORC1 signaling, autophagy, and stress adaptation, to understand these phenotypes. Amino acid or nitrogen starvation, as well as oxidative stress, inactivate TORC1, and translation inhibition through eIF2α phosphorylation occurs during all stresses. We show that both major phenotypes of autophagy-deficient cells - their failure to resume growth after amino acid starvation and their mating defects - are alleviated by genetic or environmental enhancement of intracellular amino acid pools. Regarding leucine starvation, deletion of <i>any1</i> rescues the growth defect of <i>atg1</i>Δ mutants by maintaining amino acid transporters at the plasma membrane, promoting amino acid uptake. Regarding mating defects, TORC1 inactivation by nitrogen depletion drives cell cycle remodeling for meiotic entry, and autophagy is specifically required for the final G2-to-G1 arrest, which correlates with accumulation of the CDK inhibitor Rum1. Metabolomic analyses reveal that intracellular amino acid pools decrease sharply during nitrogen starvation, especially in autophagy-deficient cells, and supplementation with trace amino acids restores their ability to complete the final G2-to-G1 transition. Overall, our findings demonstrate that autophagy sustains intracellular amino acid pools during prolonged stress, enabling TORC1 reactivation and cell cycle remodeling required for mating and meiosis.