cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3ds11g5
title: Data from: Hyperabundant herbivores limit habitat availability and influence nest-site selection of Arctic-breeding birds

description: 1. Understanding an organism’s habitat selection and behavioural
 flexibility in the face of environmental change can help managers plan for
 future conservation of that species. Hyperabundant tundra-nesting geese
 are influencing Arctic environments through their foraging activities.
 Goose-induced habitat change in Arctic wetlands may influence the
 availability of habitat for numerous shorebird species that breed
 sympatrically with geese. 2. Here, we explore whether goose-induced
 habitat alteration affects shorebird breeding density and nest-site
 selection. Using habitat data collected at sites with high, moderate, and
 low goose influence, and samples collected during two periods separated by
 11 years, we document the habitat characteristics influenced by geese. We
 describe the habitat characteristics preferred by shorebirds and relate
 their availability to goose influence and shorebird density. Finally, we
 examine whether shorebird nest-site selection has changed over time and
 whether shorebirds select nest sites differently in habitat influenced by
 geese. 3. We report spatial and temporal changes in sedge meadow habitat
 and lateral concealment relating to goose influence. The availability of
 sedge meadow habitat and the degree of lateral concealment declined with
 increasing goose influence, and also declined at two sites over the 11
 years of the study. 4. Densities of both cover- and open-nesting
 shorebirds were highest where goose influence was lowest. At sites with
 low goose influence, cover-nesting shorebirds selected nest sites with
 more sedge meadow and concealment than at sites with moderate and high
 goose influence, presumably because these high quality sites were more
 available. 5. Synthesis and applications. Our results suggest that
 goose-induced habitat alteration is influencing the availability of
 preferred habitat, and the densities of sympatric-nesting shorebirds.
 Cover-nesting species that prefer moist sedge habitat may be especially
 susceptible to goose-induced alteration, while upland specialists may be
 unaffected. Our results underscore the need for management of Arctic goose
 populations to reduce their impacts on sedge meadow habitats. Studies
 examining the degree to which these effects scale up to impact the
 population sizes of declining shorebirds should be considered a future
 research priority.
description: Proportional cover and
 dominant habitat type surveysHabitat surveys
 conducted at all shorebird nests and random sites. Includes proportional
 cover of different habitat types and dominant habitat
 type.dryas_1.csvCover types and heights of cover typesCover types and heights of all cover types measured at random sitesdryas_2.csv
DOI: 10.5061/dryad.43cp5
title: Data from: Comparative multi-locus phylogeography of two Palaearctic spruce bark beetles: influence of contrasting ecological strategies on genetic variation

description: While phylogeographic patterns of organisms are often interpreted through
 past environmental disturbances, mediated by climate changes, and
 geographic barriers, they may also be strongly influenced by
 species-specific traits. To investigate the impact of such traits, we
 focused on two Eurasian spruce bark beetles that share a similar
 geographic distribution, but differ in their ecology and reproduction. Ips
 typographus is an aggressive tree-killing species characterized by strong
 dispersal, whereas Dendroctonus micans is a discrete inbreeding species
 (sib mating is the rule), parasite of living trees and a poor disperser.
 We compared genetic variation between the two species over both beetles’
 entire range in Eurasia with five independent gene fragments, to evaluate
 whether their intrinsic differences could have an influence over their
 phylogeographic patterns. We highlighted widely divergent patterns of
 genetic variation for the two species and argue that the difference is
 indeed largely compatible with their contrasting dispersal strategies and
 modes of reproduction. In addition, genetic structure in I. typographus
 divides European populations in a northern and a southern group, as was
 previously observed for its host plant, and suggests past allopatric
 divergence. A long divergence time was estimated between East Asian and
 other populations of both species, indicating their long-standing presence
 in Eurasia, prior to the last glacial maximum. Finally, the strong
 population structure observed in D. micans for the mitochondrial locus
 provides insights into the recent colonization history of this species,
 from its native European range to regions where it was recently
 introduced.
description: Structure input file for
 Ips typographusInput file for the
 genetic structure analysis of the European populations of I. typographus
 by applying the Bayesian procedure implemented in STRUCTURE
 v2.3.3Ips_typographus_Structure_FileAligned sequencesAligned sequences for Ips typographus (COI, EF1a, G6PD, AK, Wg) and for Dendroctonus micans (COI)AlignedSequences.ziphaplotype composition for individuals of Ips typographushaplotype composition for individuals of Ips typographus (Table S19)Table_S19.xlsxhaplotype composition for individuals of Dendroctonus micanshaplotype composition for individuals of Dendroctonus micans (Table S20)Table_S20.xlsxGenBank accession number associated to each haplotypeGenBank accession number associated to each haplotype (Table S18)Table_S18.xlsx
DOI: 10.5061/dryad.d12t1
title: Data from: Arctic greening from warming promotes declines in caribou populations

description: The migratory tundra caribou herds in North America follow decadal
 population cycles, and browsing from abundant caribou could be expected to
 counteract the current climate-driven expansion of shrubs in the
 circumpolar tundra biome. We demonstrate that the sea ice cover in the
 Arctic Ocean has provided a strong signal for climate-induced changes on
 the adjacent caribou summer ranges, outperforming other climate indices in
 explaining the caribou-plant dynamics. We found no evidence of a negative
 effect of caribou abundance on vegetation biomass. On the contrary, we
 found a strong bottom-up effect in which a warmer climate related to
 diminishing sea ice has increased the plant biomass on the summer
 pastures, along with a paradoxical decline in caribou populations. This
 result suggests that this climate-induced greening has been accompanied by
 a deterioration of pasture quality. The shrub expansion in Arctic North
 America involves plant species with strong antibrowsing defenses. Our
 results might therefore be an early signal of a climate-driven shift in
 the caribou-plant interaction from a system with low plant biomass
 modulated by cyclic caribou populations to a system dominated by nonedible
 shrubs and diminishing herds of migratory caribou.
description: Data Fauchald et al.
 SciAdv 2017Excel sheets including
 caribou population data, NDVI, sea-ice, temperature and snow
 cover.Data_Fauchald_et_al_SciAdv_2017.xlsx
DOI: 10.5061/dryad.b96j3
title: Data from: The evolution of vertebrate eye size across an environmental gradient: phenotype does not predict genotype in a Trinidadian killifish

description: Vertebrates exhibit substantial variation in eye size. Eye size correlates
 positively with visual capacity and behaviors that enhance fitness, such
 as predator avoidance. This foreshadows a connection between predation and
 eye size evolution. Yet, the conditions that favor evolutionary shifts in
 eye size, besides the well-known role for light availability, are unclear.
 We tested the influence of predation on the evolution of eye size in
 Trinidadian killifish, Rivulus hartii. Rivulus are located across a series
 of communities where they coexist with visually oriented piscivores (‘high
 predation’ sites), and no predators (‘Rivulus-only’ sites). Wild-caught
 Rivulus from high predation sites generally exhibited a smaller relative
 eye size than communities that lack predators. Yet, such differences were
 inconsistent across rivers. Second-generation common garden reared fish
 revealed repeatable decreases in eye size in Rivulus from high predation
 sites. We performed additional experiments that tested the importance of
 light and resources on eye size evolution. Sites that differ in light or
 resource availability did not differ in eye size. Our results argue that
 differences in predator-induced mortality underlie genetically-based
 shifts in vertebrate eye size. We discuss the drivers of eye size
 evolution in light of the nonparallel trends between the phenotypic and
 common garden results.
description: Eye size
 dataEyeData.xlsx
DOI: 10.5061/dryad.n4h17
title: Data from: Characterization of recruitment through tandem running in an Indian queenless ant Diacamma indicum

description: Tandem running is a primitive recruitment method employed by many ant
 genera. This study characterizes this behaviour during the recruitment of
 colony mates to a new nest in an Indian ant Diacamma indicum. Tandem
 leaders who have knowledge of the new nest lead a single follower at a
 time, to the destination by maintaining physical contact. In order to
 characterize tandem running, we captured and analysed 621 invitations, 217
 paths and 226 termination events. Remarkably, not a single colony member
 was lost. While invitations were stereotypic in behaviour, termination was
 not. Analysis of speed revealed that the average transport speed was
 4.2 cm s−1. Coupled adult-brood transport was slower than other transports
 but was more efficient than individual trips. Comparing tandem running
 with other popular recruitment methods in ants allows us to postulate that
 even though tandem running is primitive it is probably just another means
 to achieve the same end.
description: Characterization of
 tandem running data filesBasic details of the
 colonies used, the data for initiation, path, speed analysis and
 termination is listed in the excel file.TR-IPT data
 files.xlsx
DOI: 10.5061/dryad.9k19f
title: Data from: Differentiation within the endemic burrowing skink Pamelaescincus gardineri, across the Seychelles islands, assessed by mitochondrial and nuclear markers

description: Unveiling patterns of genetic differentiation across insular distributions
 is relevant for biogeographic and conservation reasons. In the Indian
 Ocean, surprisingly, little is known regarding the genetic structure of
 many taxa across the Seychelles Islands, despite their importance as old
 Gondwanic islands, part of the western Indian Ocean biodiversity hotspot.
 In recent molecular studies, a northeastern–southwestern subdivision
 pattern across the granitic islands has been uncovered within some
 species. Pamelaescincus gardineri, a Seychelles endemic skink and possibly
 one of the deepest lineages of Afro-Malagasy ‘scincines’, is another
 species widespread across these islands, within which undescribed
 variation may occur. Both nuclear (c-mos and MC1R) and mitochondrial
 (Cyt-b) DNA data were used to address this issue. Mitochondrial DNA shows
 a marked northeastern–southwestern structure of two highly divergent
 clades, similar to the pattern previously described in other reptile
 species. Nuclear DNA seems to corroborate this pattern, although these
 markers were much less informative. Migration between the two island
 groups was identified, and gene flow between the two mtDNA lineages is
 likely, the extent of which remains to be fully explored. This will
 require more variable nuclear markers and more detailed sampling across
 the island of Mahé. A suitable assessment of morphological variation is
 also needed prior to any taxonomic revision of this species. From a
 conservation point of view, however, these lineages should already be
 treated as two distinct evolutionary units.
description: citb_pam_outgroup_haps.nex.conconsensus tree file from mrbayes phylogenetic analyses (BI)citb_pam_outgroup_haps_phy_phyml_treetree file from maximum likelihood analysis with bootstrapscmos_inferred_haplotypesNuclear haplotypes from C-mos gene fragment inferred using PHASE (see details in article) and used for haplotype network constructionmc1r_inferred_haplotypesNuclear haplotypes inferred using PHASE (see details in publication) for the MC1R dataset and used for haplotype network construction
DOI: 10.5061/dryad.p3c75
title: Data from: Moderation is best: effects of grazing intensity on plant-flower visitor networks in Mediterranean communities

description: The structure of pollination networks is an important indicator of
 ecosystem stability and functioning. Livestock grazing is a frequent land
 use practice that directly affects the abundance and diversity of flowers
 and pollinators and, therefore, may indirectly affect the structure of
 pollination networks. Here we studied how grazing intensity affected the
 structure of plant-flower visitor networks along a wide range of grazing
 intensities by sheep and goats, using data from 11 Mediterranean
 plant-flower visitor communities from Lesvos Island, Greece. We
 hypothesized that intermediate grazing might result in higher diversity as
 predicted by the Intermediate Disturbance Hypothesis, which could in turn
 confer more stability to the networks. Indeed, we found that networks at
 intermediate grazing intensities were larger, more generalized, more
 modular, and contained more diverse and even interactions. Despite general
 responses at the network level, the number of interactions and
 selectiveness of particular flower visitor and plant taxa in the networks
 responded differently to grazing intensity, presumably as a consequence of
 variation in the abundance of different taxa with grazing. Our results
 highlight the benefit of maintaining moderate levels of livestock grazing
 by sheep and goats to preserve the complexity and biodiversity of the rich
 Mediterranean communities, which have a long history of grazing by these
 domestic animals.
description: SummaryNetLevelDryadNetwork-level characteristics for the 33 study networksStandardNetwDryadNetwork-level characteristics for the standardized networksGuildDryadDegree and d' for each insect species in the study networksFamiliPlantsDryadDegree and d' for the plant species in the study networks
DOI: 10.5061/dryad.1324
title: Data from: History and evolution of alpine plants endemic to the Qinghai-Tibetan Plateau: Aconitum gymnandrum (Ranunculaceae)

description: How Quaternary climatic oscillations affected range distributions and
 intraspecific divergence of alpine plants on the Qinghai-Tibetan Plateau
 (QTP) remains largely unknown. Here we report a survey of chloroplast (cp)
 and nuclear ribosomal (ITS) DNA variation aimed at exploring the
 phylogeographic history of the QTP alpine endemic Aconitum gymnandrum. We
 sequenced three cpDNA fragments (rpl20-rps12 intergenic spacer, the trnV
 intron and psbA-trnH spacer) and also the nuclear (ITS) region in 245
 individuals from 23 populations sampled throughout the species'
 range. Two distinct lineages with east and west geographical distributions
 respectively were identified from a phylogenetic analysis of ITS sequence
 variation and the divergence were estimated to be around 1.45 Ma. Nine
 chlorotypes that clustered into two major clades were broadly congruent in
 geographical distribution with the two ITS lineages, which was also
 supported by an analysis of molecular variance (AMOVA). Analysis of the
 spatial distribution of chlorotypes and coalescent simulation of
 chlorotype genealogies supported both an early Pleistocene origin of the
 two main cpDNA clades and the four-refugia hypothesis during the LGM. Two
 previous phylogeographic studies of QTP alpine plants indicated that such
 plants retreated to refugia at the eastern/south-eastern plateau edge
 during the LGM and/or previous glacial maxima. However, the results for A.
 gymnandrum suggest that at least some of these cold tolerant species may
 have also survived centrally on the QTP platform throughout the
 Quaternary.
description: ITS-1-20
 intragroup.nxsPreparing input file for
 A. gymnandrum and its close speciesITS-1-20
 intragroup.megFile include all
 different genotype within A. gymnandrumITS
 intersubgenera_20080420.nxsThis file contain ITS
 sequences of A. gymnandrum and its close speciesITS-1-20
 intragroup.nxs
DOI: 10.5061/dryad.6rp18
title: Data from: Height and clonality traits determine plant community responses to fertilization

description: Fertilization via agricultural inputs and nutrient deposition is one of
 the major threats to global terrestrial plant richness, yet we still do
 not fully understand the mechanisms by which fertilization decreases plant
 richness. Tall clonal species have recently been proposed to cause
 declines in plant species richness by increasing in abundance in response
 to fertilization and competing strongly with other species. We tested this
 hypothesis in a fertilization experiment in a low productivity grassland
 by using a novel experimental manipulation of the presence vs. absence of
 clonal species and by examining the role of height within these
 treatments. We found that fertilization decreased species richness more in
 the presence than absence of clonal species. We also found that only tall
 species increased in biomass in response to fertilization. In the absence
 of clonal species, fertilization increased biomass of tall nonclonal
 species. However, in the presence of clonal species, fertilization
 decreased tall nonclonal biomass and only tall clonal biomass increased.
 Fertilization caused almost all short species to be lost in the presence,
 but not the absence, of clonal species and caused greater declines in the
 mean and variance of light levels in the presence of clonal species. These
 results show that the traits of species in a community can determine the
 magnitude of species loss due to fertilization. The strongly negative
 effect of tall clonals on species richness in fertilized plots is likely a
 result of their capacity to decrease light levels to a greater extent and
 more uniformly than nonclonal species, and thereby drive the exclusion of
 short species. These results help clarify the mechanisms whereby
 fertilization decreases grassland plant species richness and suggest that
 efforts to prevent the loss of species under fertilized conditions may be
 most effective when they focus on controlling the biomass of tall clonal
 species.
description: Dickson_et_al_dataFile containing all data used in Dickson et al. (2014) Ecology paper entitled "Height and clonality traits determine plant community responses to fertilization"
DOI: 10.5061/dryad.sd0pm
title: Data from: Evolution of carotenoid pigmentation in caciques and meadowlarks (Icteridae): repeated gains of red plumage coloration by carotenoid C4-oxygenation

description: Many animals use carotenoid pigments to produce yellow, orange, and red
 coloration. In birds, at least 10 carotenoid compounds have been
 documented in red feathers; most of these are produced through metabolic
 modification of dietary precursor compounds. However, it is poorly
 understood how lineages have evolved the biochemical mechanisms for
 producing red coloration. We used high-performance liquid chromatography
 to identify the carotenoid compounds present in feathers from 15 species
 across two clades of blackbirds (the meadowlarks and allies, and the
 caciques and oropendolas; Icteridae), and mapped their presence or absence
 on a phylogeny. We found that the red plumage found in meadowlarks
 includes different carotenoid compounds than the red plumage found in
 caciques, indicating that these gains of red color are convergent. In
 contrast, we found that red coloration in two closely related lineages of
 caciques evolved twice by what appear to be similar biochemical
 mechanisms. The C4-oxygenation of dietary carotenoids was responsible for
 each observed transition from yellow to red plumage coloration, and has
 been commonly reported by other researchers. This suggests that the
 C4-oxygenation pathway may be a readily evolvable means to gain red
 coloration using carotenoids.
description: Friedman et al
 Data
DOI: 10.5061/dryad.368nr
title: Data from: Male-biased fitness effects of spontaneous mutations in Drosophila melanogaster

description: In populations with males and females, sexual selection may often
 represent a major component of overall selection. Sexual selection could
 act to eliminate deleterious alleles in concert with other forms of
 selection, thereby improving the fitness of sexual populations.
 Alternatively, the divergent reproductive strategies of the sexes could
 promote the maintenance of sexually-antagonistic variation, causing sexual
 populations to be less fit. The net impact of sexual selection on fitness
 is not well understood, due in part to limited data on the sex-specific
 effects of spontaneous mutations on total fitness. Using a set of mutation
 accumulation lines of Drosophila melanogaster, we found that mutations
 were deleterious in both sexes and had larger effects on fitness in males
 than in females. This pattern is expected to reduce the mutation load of
 sexual females and promote the maintenance of sexual reproduction.
description: Fitness
 measuresData on the fitness of
 different lines, following mutation accumulation, for either juveniles,
 males, or females of that genotype. Group: the trait measured, either
 juvenile egg-to-adult viability, male reproductive success, or female
 reproductive success. MA_generation: the number of generations since lines
 were initiated; juvenile fitness was assessed at 16, 30, and 46, adult
 traits at 52. Treatment: whether the replicate is of a line that underwent
 mutation accumulation (mutant), or is from one of three control
 populations (controlX, controlY, controlZ). Line: an arbitrary replicate
 number, i.e. a mutant or control genotype. Note that mutant lines are
 consistent across generations, whereas control genotypes in a given
 generation are independent of those in another generation. Offspring: a
 measure of fitness. For juveniles, the number of focal individuals
 emerging as adults, in the presence of standard competitors. For adults
 (males, females), the number of offspring sired/produced in the presence
 of standard competitors.SharpAgrawalEvolutionData.xlsx
DOI: 10.5281/zenodo.18382701
title: Example data for FluoResFM.

description: The example data for FluoResFM (a foundation model for multi-task cross-distribution restoration of fluorescence microscopy image) algorithm, including:



checkpoint of FluoResFM.

checkpoint of image and text encoder.

database used for image retrival.

example data uased for plugin demonstrations.
DOI: 10.5281/zenodo.18382702
title: Example data for FluoResFM.

description: The example data for FluoResFM (a foundation model for multi-task cross-distribution restoration of fluorescence microscopy image) algorithm, including:



checkpoint of FluoResFM.

checkpoint of image and text encoder.

database used for image retrival.

example data uased for plugin demonstrations.