cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t77f1p4
title: Data from: History matters: contemporary versus historic population structure of bobcats in the New England region, USA

description: Habitat fragmentation and genetic bottlenecks can have substantial impacts
 on the health and management of wildlife species by lowering diversity and
 subdividing populations. Population genetic comparisons across time
 periods can help elucidate temporal changes in populations and the
 processes responsible for the changes. Bobcats (Lynx rufus) are
 wide-ranging carnivores and are currently increasing in abundance across
 an expanding range. Bobcat populations in New England have fluctuated in
 the past century in response to changes in their prey base, harvest
 pressure, and landscape development. We genotyped contemporary (2010–2017)
 and historic (1952–1964) bobcats from New England and Quebec, Canada at a
 suite of microsatellite loci and tested for differences in diversity,
 effective population size, and gene flow. Over 20 generations separated
 the sampling periods, and the intervening years were marked by drastic
 changes in land use and species management regimes. We found a general
 decrease in genetic diversity and differing population genetic structure
 through time. Effective population size decreased at the end of the
 historic period, coincident with a spike in harvest, but rebounded to
 greater numbers in the contemporary period. Our results suggest that
 bobcat populations in the region are robust, but development and range
 dynamics may play a significant role in population structure. Our study
 also highlights the benefits of a historical perspective in interpreting
 contemporary population genetic data.
description: Microsatellite data for
 contemporary (2009-2017) and historic (1952-1964)
 bobcatsEach row contains a
 unique individual ID, sex, year of collection, state and town of capture,
 XY coordinates for the town centroid (NH state plane coordinate system),
 and genetic data formatted as allele1_allele2. Column names are
 microsatellite loci.BobcatData.xlsx
DOI: 10.5061/dryad.98sp59j
title: Data from: Chromosomal inversions in the Atlantic cod genome: implications for management of Canada’s Northern cod stock

description: Following stock collapse and over twenty years of moratoria, the state of
 Canada’s Northern Atlantic cod (Gadus morhua) remains precarious. To test
 if recent stock growth was of endogenous or exogenous origin, we performed
 a whole genome scan (ddRAD) on 135 adults captured in 2015 at three
 offshore spawning locations spanning the range of the offshore stock along
 the northeastern Newfoundland and Labrador shelf (Hawke Channel, Notre
 Dame Channel and Bonavista Corridor), with an additional 105 adults from
 three more southern locations (St. Anns Bank, Browns Bank and Bay of
 Fundy). Population structure analysis using 5,077 single nucleotide
 polymorphisms (SNPs) detected a distinct genetic break off the coast of
 Nova Scotia near 45 °N. Gene flow between groups north and south of this
 divide appears to be limited despite the presence of several northern-type
 and admixed individuals present in the southern area. North of the genetic
 divide, allele frequencies of neutral loci were indicative of a panmictic
 population. Several outlier SNPs were found to be associated with
 ecologically relevant physical characteristics (visual pigments, fin
 development, response to hypoxia, and various metabolic processes), which
 may be indicative of different ecological niches.
description: Puncher_2019_NorthernSpawningCod_240IND_5077SNPGenepop file containing genotypes (5,077 SNPs) of 240 adult Atlantic Cod (Gadus morhua) captured in the Northeastern Atlantic Ocean (2J3KL4VX). DNA was prepared using a ddRAD protocol and 125PE sequenced 60-96 individuals/lane on an Illumina HiSeq2500. SNPs were selected using STACKS and various software described in "Chromosomal inversions in the Atlantic cod genome: implications for management of Canada’s Northern cod stock." Please refer to publication for individual codes.SNP_flanking_sequences and alleles_from_GadMor_May2010_alignmentSNP flanking sequences and alleles from GadMor_May2010_alignment (Star B, et al. Nature 2011 Aug 10).SNP_flanking_sequences_and_alleles_from_gadMor2_alignmentSNP flanking sequences and alleles from alignment with gadMor2 annotated genome assembly by Tørresen et al. 2017 (https://doi.org/10.6084/m9.figshare.3408247.v3).
DOI: 10.5061/dryad.tn73h20
title: Data from: Thermal plasticity of a freshwater cnidarian holobiont: detection of trans-generational effects in asexually reproducing hosts and symbionts

description: Understanding factors affecting the susceptibility of organisms to thermal
 stress is of enormous interest in light of our rapidly changing climate.
 When adaptation is limited, thermal acclimation and deacclimation
 abilities of organisms are critical for population persistence through a
 period of thermal stress. Holobionts (hosts plus associated symbionts) are
 key components of various ecosystems, such as coral reefs, yet the
 contributions of their two partners to holobiont thermal plasticity are
 poorly understood. Here, we tested thermal plasticity of the freshwater
 cnidarian Hydra viridissima (green hydra) using individual behavior and
 population responses. We found that algal presence initially reduced hydra
 thermal tolerance. Hydra with algae (symbiotic hydra) had comparable
 acclimation rates, deacclimation rates, and thermal tolerance after
 acclimation to those without algae (aposymbiotic hydra) but they had
 higher acclimation capacity. Acclimation of the host (hydra) and/or
 symbiont (algae) to elevated temperatures increased holobiont thermal
 tolerance and these effects persisted for multiple asexual generations. In
 addition, acclimated algae presence enhanced hydra fitness under prolonged
 sublethal thermal stress, especially when food was limited. Our study
 indicates while less intense but sublethal stress may favor symbiotic
 organisms by allowing them to acclimate, sudden large, potentially lethal
 fluctuations in climate stress likely favor aposymbiotic organisms. It
 also suggests that thermally stressed colonies of holobionts could
 disperse acclimated hosts and/or symbionts to other colonies, thereby
 reducing their vulnerability to climate change.
description: Acclimation &
 deacclimmation in green hydraEach tab contains the
 data correspondent to figures in the paper
DOI: 10.5518/1500
title: Data associated with "Analysing the Photo-Physical Properties of Liquid Crystals"

description: Data associated with ''Analysing the Photo-Physical Properties of Liquid Crystals". Data collated is for all the data present in the figures with the exception of figure 6 due to its arbitrary nature.
DOI: 10.5061/dryad.kc4m7p2
title: Data from: Species richness mediates within-species nutrient resorption: implications for the biodiversity-productivity relationship

description: 1.Between-species variation in nutrient resorption is one of the
 mechanisms explaining the positive relationship between biodiversity and
 primary productivity. Yet, the role of within-species variations in
 nutrient resorption in mediating the relationship between biodiversity and
 productivity remains unclear. 2.We examined how within-species nutrient
 resorption, and ultimately productivity, respond to changes in species
 richness by using four traits related to nitrogen and phosphorus use in
 four dominant species from different plant functional groups in a
 biodiversity removal experiment in the temperate steppe. 3.Nitrogen and
 phosphorus concentrations in both green and senesced leaves in all species
 significantly decreased with increasing plant species richness, suggesting
 that plants used those limiting nutrients more efficiently with increasing
 biodiversity. Plants in higher-diversity communities resorbed more
 nutrients during senescence, which may facilitate reproduction and
 vegetative regrowth in the next year. 4.Synthesis. Our results highlight
 the importance of considering within-species variation in nutrient
 resorption as an important underlying mechanism explaining the positive
 effects of biodiversity on primary productivity and ecosystem carbon
 accumulation.
description: Data of Plant Nutrient
 Characters in a Biodiversity ExperimentThe data include soil
 available nutrients, aboveground primary productivity, nitrogen and
 phosphorus concentrations in four dominant plant species from a plant
 species removal experiment in the temperate steppe of northern
 China.Data
 submission.xlsx
DOI: 10.5061/dryad.b32pf80
title: Data from: Increasing plant diversity of experimental grasslands alters the age and growth of Plantago lanceolata from younger and faster to older and slower

description: The persistence of plant populations depends on the ability of individuals
 to cope with the conditions provided by the community. So far, it is not
 known whether differences in the diversity and composition of plant
 communities affect the age structure of plant populations or the
 expression of stem anatomical traits reflecting investment into plant
 growth and storage. We analyzed annual growth rings in the secondary xylem
 and measured stem anatomical traits in individuals from 18 populations of
 Plantago lanceolata growing in a 12-year old grassland biodiversity
 experiment (Jena Experiment). Plant individuals of P. lanceolata were on
 average older and reproduced later with increasing species richness.
 Individuals of P. lanceolata were slightly younger and the age
 distribution within populations skewed to younger individuals in the
 presence of grasses. The presence of legumes did not affect mean age, but
 led to a more even age distribution within populations. The width of
 growth-related tissues (xylem, phloem, phellem) decreased with increasing
 species richness. Plant diversity-effects on storage-related tissues
 (pith, cortex) were less consistent, as pith showed increasing width with
 species richness, while cortex did not change with plant diversity. Our
 results imply that plant diversity effects on population age structure and
 the expression of stem anatomical traits of P. lanceolata reflect a
 trade-off: growth and turnover is fast at low diversity (younger age,
 higher allocation to growth-related tissue, faster generative
 reproduction), while it is slow at high diversity (older age, higher
 allocation to storage-related tissue, later generative reproduction).
description: Data_GrowthRingAnalysisThis file contains data on plant age, stem anatomical traits and shoot biomass of Plantago lanceolata collected in a grassland biodiversity experiment (Jena Experiment) in plant communities of different species richness.Data_SeedlingsThis file contains data on seedling numbers of Plantago lanceolata counted in plots of a grassland biodiversity experiment (Jena Experiment), where this species belongs to the sown species combinations.
DOI: 10.5061/dryad.5k586p0
title: Data from: Decreasing predator density and activity explain declining predation of insect prey along elevational gradients

description: Predation, which is a fundamental force in ecosystems, has been found to
 decrease in intensity with elevation and latitude. The mechanisms behind
 this pattern, however, remain unaddressed. Using visual sampling of
 potential predators and live flies as baits, we assessed predation
 patterns along 4000-meter elevation transects on either side of the
 equatorial Andes. We found that at the lower elevations around eighty
 percent of predation events on our insect baits were due to ants. The
 decline in predation with elevation was mainly driven by a decline in the
 abundance of ants, whose importance relative to other predators also
 declined. We show that both predator density and activity (predation rate
 per individual predator) decreased with elevation, thus ascribing specific
 mechanisms to known predation patterns. We suggest that changes in these
 two mechanisms may reflect changes in primary productivity and metabolic
 rate with temperature, factors of potential relevance across latitudinal
 and other macroecological gradients, in particular for ectotherm predators
 and prey.
description: Predation across
 elevational gradientsData consists of two CSV
 files, which contain data pertinent to different analyses. Code for the
 analyses are included. All data collected in the field with the exception
 of temperature data, which was extracted from WorldClim. The variable
 'TEMP' (temperature) was obtained from WorldClim v 1.4 at
 http://worldclim.org/version1 If you reuse data from WorldClim, please
 cite the original data source and the associated publication Hijmans,
 R.J., S.E. Cameron, J.L. Parra, P.G. Jones and A. Jarvis, 2005. Very high
 resolution interpolated climate surfaces for global land areas.
 International Journal of Climatology 25: 1965-1978.data&code.zip
DOI: 10.5061/dryad.7mq2q24
title: Data from: Competition suppresses shrubs during early, but not late, stages of arid grassland-shrubland state transition

description: 1. Transitions from grass to woody plant dominance, widely reported in
 arid systems, are typically attributed to changes in disturbance regimes
 in combination with abiotic feedbacks, whereas biotic mechanisms such as
 competition and facilitation are often overlooked. Yet, research in
 semi-arid and sub-humid savannas indicates that biotic interactions are
 important drivers in systems at risk for state transition. We sought to
 bridge this divide by experimentally manipulating grass-on-shrub and
 shrub-on-shrub interactions in early and late stages of
 grassland-shrubland state transition, respectively, and to assess the
 extent to which these interactions might influence arid land state
 transition dynamics. 2. Target Prosopis glandulosa shrubs had surrounding
 grasses or conspecific neighbors left intact or killed with foliar
 herbicide, and metrics of plant performance were monitored over multiple
 years for shrubs with and without grass or shrub neighbors. 3.
 Productivity of small shrubs was enhanced by grass removal in years with
 above-average precipitation, a result not evident in larger shrubs or
 during dry years. Proxy evidence based on nearest-neighbor metrics
 suggested shrub-shrub competition was at play, but our experimental
 manipulations revealed no such influence. 4. Competition from grasses
 appears to attenuate the rate at which shrubs achieve the size necessary
 to modify the physical environment in self-reinforcing ways, but only
 during the early stages of shrub encroachment. Our results further suggest
 that at late stages of grassland-to-shrubland state transitions,
 shrub-shrub competition will not slow the rate of shrub expansion, and
 suggest that maximum shrub cover is regulated by something other than
 density-dependent mechanisms. We conclude that grass effects on shrubs
 should be included in assessments of desert grassland state transition
 probabilities and rates, and that desertification models in arid
 ecosystems that traditionally focus on disturbance and abiotic feedbacks
 should be broadened to incorporate spatial and temporal variations in
 competitive effects.
description: Pierce et al.
 dataPierce
 et al data.zip
DOI: 10.5061/dryad.d20221b
title: Data from: The influence of potential stressors on oviposition site selection and subsequent growth, survival and emergence of the non-biting midge (Chironomus tepperi)

description: Theory predicts that animals should prefer habitats where their fitness is
 maximized but some mistakenly select habitats where their fitness is
 compromised, that is, ecological traps. Understanding why this happens
 requires knowledge of the habitat selection cues animals use, the habitats
 they prefer and why, and the fitness costs of habitat selection decisions.
 We conducted experiments with a freshwater insect, the non‐biting midge
 Chironomus tepperi to ask: (a) whether females respond to potential
 oviposition cues, (b) to explore whether oviposition is adaptive in
 relation to metal pollution and conductivity, and (c) whether individuals
 raised in poor quality sites are more likely to breed in similarly poor
 locations. We found the following: (a) females responded to some cues,
 especially conductivity and conspecifics, (b) females preferred sites with
 higher concentrations of bioavailable metals but suffered no consequences
 to egg/larval survival, (c) females showed some avoidance of high
 conductivities, but they still laid eggs resulting in reduced egg
 hatching, larval survival, and adult emergence, and (d) preferences were
 independent of natal environment. Our results show that C. tepperi is
 susceptible to ecological traps, depending on life stage and the relative
 differences in conductivities among potential oviposition sites. Our
 results highlight that (a) the fitness outcomes of habitat selection need
 to be assessed across the life cycle and (b) the relative differences in
 preference/suitability of habitats need to be considered in ecological
 trap research. This information can help determine why habitat preferences
 and their fitness consequences differ among species, which is critical for
 determining which species are susceptible to ecological traps.
description: conduc_emerg_analysisEmergence rates of Chironomus tepperi across different conductivity treatmentsConductivity natal experiment Run 1 - trialsOivposition of Chironomus tepperi raised in two natal environments to four conductivity treatmentsconspecific_analysisOviposition of Chironomus tepperi in relation to visual and chemical cues from conspecificsegg_hatching_NSW_popnEgg hatching of Chironomus tepperi across a gradient of conductivitieshumic acid analysisOviposition of Chironomus tepperi in response to humic acidlarval_growth_analysisGrowth of larval Chironomus tepperi in different conductivitieslarval_survival_analysisSurvival of larval Chironomus tepperi across different conductivitieswetland_choice_analysisOviposition of Chironomus tepperi in water collected from four stormwater wetlands
DOI: 10.5061/dryad.524cv34
title: Data from: Stochastic and deterministic processes drive wetland community assembly across a gradient of environmental filtering

description: The role of deterministic and stochastic processes in community assembly
 is a key question in community ecology. We evaluated the effect of an
 abiotic filter (hydroperiod) on the partitioned diversity of three
 taxonomic groups (birds, vegetation, macroinvertebrates) from prairie
 pothole wetlands in Alberta, Canada, which naturally vary in water
 permanence. We observed that alpha and gamma diversity were higher in
 permanent than temporary wetlands (16-25% and 34-47% respectively,
 depending on the taxon). This suggests an influence of deterministic
 constraints on the number of species a wetland can support. Taxa which
 cannot persist in shallow, temporary wetlands are excluded by the
 deterministic constraints that a shortened hydroperiod imposes. In
 contrast, we observed that beta diversity was significantly higher (2-12%)
 in temporary wetlands than permanent ones, and temporary wetlands
 supported more unique combinations of community composition than permanent
 wetlands, despite having a smaller regional species pool. This observation
 contradicts prior mesocosm studies that found beta diversity mirrored the
 pattern in gamma diversity along an environmental filtering gradient. We
 conclude that deterministic processes are more influential in more stable
 permanent wetlands, whereas stochastic processes play a more important
 role in assembly in dynamic temporary wetlands that must disassemble and
 re-establish annually. Considering three distinct taxonomic groups
 differing in their relative mobility, our large-scale field study
 demonstrates that both stochastic and deterministic processes act together
 to influence the assembly of multiple communities and that the relative
 importance of the two processes varies consistently along a gradient of
 environmental filtering.
description: Site Information &
 Community AbundancesThis spreadsheet
 contains the raw, stratified data we used in our analyses. The following
 lists the data contained in each sheet (1-4): 1) site information, 2) bird
 abundances, 3) plant percentage cover, 4) aquatic macroinvertebrate
 abundances.Daniel_Gleason_Rooney_Cottenie_Wetland Data.xlsx
DOI: 10.5061/dryad.5nb504n
title: Data from: A brief history of bird flu

description: In 1918, a strain of influenza A virus caused a human pandemic resulting
 in the deaths of 50 million people. A century later, with the advent of
 sequencing technology and corresponding phylogenetic methods, we know much
 more about the origins, evolution and epidemiology of influenza epidemics.
 Here we review the history of avian influenza viruses through the lens of
 their genetic makeup: from their relationship to human pandemic viruses,
 starting with the 1918 H1N1 strain, through to the highly pathogenic
 epidemics in birds and zoonoses up to 2018. We describe the genesis of
 novel influenza A virus strains by reassortment and evolution in wild and
 domestic bird populations, as well as the role of wild bird migration in
 their long-range spread. The emergence of highly pathogenic avian
 influenza viruses, and the zoonotic incursions of avian H5 and H7 viruses
 into humans over the last couple of decades are also described. The threat
 of a new avian influenza virus causing a human pandemic is still present
 today, although control in domestic avian populations can minimize the
 risk to human health.
description: SupplementaryText_DataThis file describes the subsampling procedure for compiling the sequence data sets, and the procedures for creating the phylogenetic trees. Additionally, links for visualisations of the tree data in the online program ITOL are provided.internals_subsampleThe files in this zip file contain Influenza A virus nucleotide sequence data, phylogenetic trees and data tables from segments = 1, 2, 3, 5, 7, 8 (the internal segments). See ReadMe.txt for more details.internals_subsample_for_displayThe files in this zip file contain Influenza A virus nucleotide sequence data, phylogenetic trees and data tables from segments = 1, 2, 3, 5, 7, 8 (the internal segments). This data was used to create Figure 1. Please see ReadMe.txt for more details.segment4_HA_H5The files in this zip file contain Influenza A virus nucleotide sequence data, phylogenetic trees and data tables from segment 4 (Hemagglutinin, HA) subtype H5N1-H5N9, including highly pathogenic and low pathogenic strains. This data was used to create Figure 5. Please see ReadMe.txt for more details.