cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d5dt7d0
title: Data from: Effects of forest management on vertebrates: synthesizing two decades of data from hardwood forests in Missouri, USA

description: Modern forest management seeks to balance multiple social, economic, and
 ecological goals. Different management approaches create different types
 of disturbances in a forest ecosystem, and thus also differ in their
 impacts on plants, animals, and insects. Understanding these impacts is
 important for conservation of forest ecosystem function, but challenging
 due to the large spatial and temporal scale over which management occurs.
 Most past research has focused on relatively small areas, short time
 scales, and/or a small number of species. To address this, we examined the
 effects of two common silvicultural systems (even- and uneven-aged) on
 abundance and richness of three vertebrate taxa (birds, small mammals, and
 herpetofauna) over a two-decade period in a temperate hardwood forest in
 Missouri, USA. The two systems removed a similar amount of biomass
 overall, but differed in the intensity, number, and configuration of
 harvests applied. We found that vertebrate population responses varied by
 taxa, occurred at multiple spatial scales, and were concentrated in the
 period following the first harvest entry. Birds generally had the largest
 changes in relative abundance, both positive and negative, following
 management. Small mammals and reptiles had smaller, but generally
 positive, responses; amphibians were mixed. Bird species tended to respond
 in the same way to both silvicultural systems, while small mammals and
 herpetofauna did not respond consistently. Thus, for birds, the total
 amount of harvest disturbance across the landscape drives population
 responses, while for others the size and configuration of individual
 harvests is likely more important. Synthesizing results across the
 vertebrate community at large spatial and temporal scales allows managers
 to better understand tradeoffs when making decisions that will affect
 wildlife in contrasting ways.
description: R and Stan code for
 analysisContains R and Stan code
 for cleaning, processing, analyzing, and visualizing data on vertebrate
 abundance and richness at the Missouri Ozark Forest Ecosystem
 Project.Kellner_MOFEP_paper_code.zip
DOI: 10.5061/dryad.g5b5q70
title: Data from: Fine scale hierarchical genetic structure and kinship analysis of the ascidian Pyura chilensis in the southeastern Pacific

description: Studying population structure and genetic diversity at fine spatial scales
 is key for a better understanding of demographic processes that influence
 population connectivity. This is particularly important in marine benthic
 organisms that rely on larval dispersal to maintain connectivity among
 populations. Here, we report the results of a genetic survey of the
 ascidian Pyura chilensis from three localities along the southeastern
 Pacific. This study follows up on a previous report that described a
 genetic break in this region among localities only 20 km apart. By
 implementing a hierarchical sampling design at four spatial levels and
 using ten polymorphic microsatellite markers, we test if differences in
 fine-scale population structure explain the previously reported genetic
 break. We compared genetic spatial autocorrelations, as well as kinship
 and relatedness distributions within and among localities adjacent to the
 genetic break. We found no evidence of significant autocorrelation at the
 scale up to 50 m despite the low dispersal potential of P. chilensis that
 has been reported in the literature. We also found that the proportion of
 related individuals in close proximity (&lt; 1 km) was higher than the
 proportion of related individuals further apart. These results were
 consistent in the three localities. Our results suggest that the spatial
 distribution of related individuals can be nonrandom at small spatial
 scales and suggests that dispersal might be occasionally limited in this
 species or that larval cohorts can disperse in the plankton as clustered
 groups. Overall, this study sheds light on new aspects of the life of this
 ascidian as well as confirms the presence of a genetic break at 39 ° S
 latitude. Also, our data indicate there is not enough evidence to confirm
 that this genetic break can be explained by differences in fine-scale
 genetic patterns among localities.
description: Multilocus
 microsatellite genotype fileMicrosatellite
 multilocus genotypes for 903 individuals of Pyura chilensis collected in
 the southern Pacific coasts of Chile. Each row contains multilocus
 genotypic data for one individual. The first column contains the sampling
 site code, the second column contains the Point ID code, the third column
 contains the Percha ID code, the fourth column contains the Individual ID
 and the fifth column contains the sampling locality name. Details can be
 found in the main text of the associated article.
DOI: 10.5061/dryad.cq0nt70
title: Data from: Prospective validation of the PML risk biomarker L-Selectin and influence of natalizumab extended intervals

description: Low L-selectin (CD62L) on CD4+ T cells after cryopreservation has been
 introduced in 2013 as a risk biomarker for the development of progressive
 multifocal leukoencephalopathy (PML) during natalizumab treatment1 or HIV
 infection.2 The biomarker has been reproduced retrospectively in some
 international cohorts,3,4 but not in others,5 potentially because of its
 sensitivity to biomaterial quality, assay protocols, and the time point of
 testing. With regard to current approaches to PML risk reduction,
 natalizumab extended interval dosing is thought to improve immune
 surveillance and reduce PML risk, whereas clinical efficacy seems
 unaffected.6
description: tables
 e-1-3table_e1-3.zip
DOI: 10.5061/dryad.3g1r4v3
title: Data from: Variation in migration pattern, broodstock origin, and family productivity of coho salmon hatchery populations in British Columbia, Canada derived from parentage-based tagging.

description: In salmonid parentage-based tagging (PBT) applications, entire hatchery
 broodstocks are genotyped, and subsequently progeny can be non-lethally
 sampled and assigned back to their parents using parentage analysis, thus
 identifying their hatchery of origin and brood year (i.e. age). Inter- and
 intra-population variability in migration patterns, life history traits,
 and fishery contributions can be determined from PBT analysis of samples
 derived from both fisheries and escapements (portion of a salmon
 population that does not get caught in fisheries and returns to its natal
 river to spawn). In the current study of southern British Columbia coho
 salmon (Oncorhynchus kisutch) populations, PBT analysis provided novel
 information on intra-population heterogeneity among males in the total
 number of progeny identified in fisheries and escapements, the proportion
 of progeny sampled from fisheries versus escapement, the proportion of
 two-year old progeny (jacks) produced, and the within-season return time
 of progeny. Fishery recoveries of coho salmon revealed heterogeneity in
 migration patterns among and within populations, with recoveries from
 north and central coast fisheries distinguishing ‘northern migrating’ from
 ‘resident’ populations. In northern-migrating populations, the mean
 distance between fishery captures of sibs (brothers and sisters) was
 significantly less than the mean distance between non-sibs, indicating the
 possible presence of intra-population genetic heterogeneity for migration
 pattern. Variation among populations in productivity and within
 populations in fish catchability indicated that population selection and
 broodstock management can be implemented to optimize harvest benefits from
 hatcheries. Application of PBT provided valuable information for
 assessment and management of hatchery-origin coho salmon in British
 Columbia.
description: 2017 Coho PBT
 BaselineGenotypes of the 2017
 coho Brood stock, collected from BC hatcheries at the time of spawning.
 This is a compressed text file in rubias format.coho_2017_PBT_baseline_2019_01_20.gz
DOI: 10.5061/dryad.97g891f
title: Data from: Genetic benefits of extreme sequential polyandry in a terrestrial-breeding frog

description: Sequential polyandry may evolve as an insurance mechanism to reduce the
 risk that females choose mates that are genetically inferior (intrinsic
 male quality hypothesis) or genetically incompatible (genetic
 incompatibility hypothesis). The prevalence of such indirect benefits
 remains controversial, however, because few studies have estimated the
 contributions of additive and non-additive sources of genetic variation to
 offspring fitness in species with sequential polyandry. Here, we use
 artificial fertilisation techniques combined with a cross-classified
 breeding design (North Carolina Type II) to simultaneously test the ‘good
 genes hypothesis’ and the ‘genetic incompatibility hypothesis’ in the
 brown toadlet (Pseudophryne bibronii); a terrestrial breeding species with
 extreme sequential polyandry. Our results revealed no significant additive
 or non-additive genetic effects on fertilisation success. Moreover, they
 revealed no significant additive genetic effects, but highly significant
 non-additive genetic effects (sire by dam interaction effects), on
 hatching success and larval survival to initial and complete
 metamorphosis. Taken together, these results indicate that offspring
 viability is significantly influenced by the combination of parental
 genotypes, and that negative interactions between parental genetic
 elements manifest during embryonic and larval development. More broadly,
 our findings provide novel quantitative genetic evidence that insurance
 against genetic incompatibility favours the evolution and maintenance of
 sequential polyandry.
description: Byrne et al. Evolution
 data 2019.This data file contains
 data from three IVF blocks (blocks 1, 2 and 3).Byrne et al data for
 Dryad.xls
DOI: 10.5061/dryad.4gg39k6
title: Data from: Taxonomy of Arabian Temnothorax Mayr (Formicidae: Myrmicinae) with description of a new species enhanced by x-ray microtomography

description: Temnothorax elmenshawyi sp. n., a new ant species from the Asir Mountains
 of the southwestern region of the Kingdom of Saudi Arabia, is described
 based on the worker caste. The new species is a member of the T. exilis
 species group and is distinguished from the other species included in this
 group by the impressed metanotal groove, the short, acute and
 broadly-based propodeal spines, the finely punctate posterior half of
 cephalic surface, and absence of a median clypeal carina. Despite
 extensive collecting by the authors at the type locality, only two
 specimens are available for description, suggesting that this species may
 be rare and likely endemic to the Asir Mountains. The species description
 is complemented by still images of volume renderings of a 3D model and a
 3D rotation video of the holotype based on x-ray microtomography
 (micro-CT), allowing remote in-depth examination of the specimen. The
 virtual micro-CT data is provided as cybertype dataset and freely
 available online, as well as 3D surface model (Sketchfab.com,
 https://skfb.ly/6HYRz). An updated identification key to the Arabian
 species is presented.
description: Cybertype
 dataset_Temnothorax elmenshawfi_CASENT0790240Cybertype dataset for
 Temnothorax elmenshawyi (CASENT0790240) paratype worker: complete micro-CT
 scanning raw dataset (in DICOM format - 964 slices), 3D surface (in ply
 format), 3D rotation video (in mp4 format), 3D model volume rendering
 snapshots (in tiff format), and stacked colour photos (in tiff
 format).Cybertype
 dataset_T.elmenshawfi_CASENT0790240_.zip
DOI: 10.5061/dryad.17r4585
title: Data from: Standardization and validation of a panel of cross-species microsatellites to individually identify the Asiatic wild dog (Cuon alpinus)

description: The Asiatic wild dog or dhole (Cuon alpinus) is a highly elusive,
 monophyletic, forest dwelling, social canid distributed across south and
 Southeast Asia. Severe pressures from habitat loss, prey depletion,
 disease, human persecution and interspecific competition resulted in
 global population decline in dholes. Despite a declining population trend,
 detailed information on population size, ecology, demography and genetics
 is lacking. Generating reliable information at landscape level for dholes
 is challenging due to their secretive behaviour and monomorphic physical
 features. Recent advances in non-invasive DNA-based tools can be used to
 monitor populations and individuals across large landscapes. In this
 paper, we describe standardization and validation of faecal DNA-based
 methods for individual identification of dholes. We tested this method on
 249 field-collected dhole faeces from five protected areas of the central
 Indian landscape in the state of Maharashtra, India. Results We tested a
 total of 18 cross-species markers and developed a panel of 12 markers for
 unambiguous individual identification of dholes. This marker panel
 identified 101 unique individuals from faecal samples collected across our
 pilot field study area. These loci showed varied level of amplification
 success (57-88%), polymorphism (3-9 alleles), heterozygosity (0.23-0.63)
 and produced a cumulative misidentification rate or PID(unbiased) and
 PID(sibs) value of 4.7x10-10 and 1.5x10-4, respectively, indicating a high
 statistical power in individual discrimination from poor quality samples.
 Conclusion Our results demonstrated that the selected panel of 12
 microsatellite loci can conclusively identify dholes from poor quality,
 non-invasive biological samples and help in exploring various population
 parameters. This genetic approach would be useful in dhole population
 estimation across its range and will help in assessing population trends
 and other genetic parameters for this elusive, social carnivore.
description: Co-dominant marker
 allelic raw dataData generation was done
 for scat samples of Asiatic wild odg collected from field using codominant
 microsatellite markers. Post amplification, 2 μl of PCR product was mixed
 with HiDi formamide and LIZ 500 size standard and genotyped in an ABI
 genetic analyzer. The fragment lengths were scored manually using the
 program GENEMARKER (Softgenetics Inc., Pennsylvania, 196 Unites States).
 Each reaction was repeated three times to ensure good data quality. The
 uploaded file is the consensus allele call for three repeats of each 101
 sample.Dhole genotype Raw
 Data.xlsx
DOI: 10.5061/dryad.tq63tp2
title: Data from: Metabolism and foraging strategies of mid-latitude mesozooplankton during cyanobacterial blooms as revealed by fatty acids, amino acids and their stable carbon isotopes

description: Increasing sea surface temperatures (SST) and blooms of lipid-poor,
 filamentous cyanobacteria can change mesozooplankton metabolism and
 foraging strategies in marine systems. Lipid shortage and imbalanced diet
 may challenge the build-up of energy pools of lipids and proteins, and
 access to essential fatty acids (FAs) and amino acids (AAs) by copepods.
 The impact of cyanobacterial blooms on individual energy pools was
 assessed for key species, temperate Temora longicornis and boreal
 Pseudo-/Paracalanus spp. that dominated field mesozooplankton communities
 isolated by seasonal stratification in the central Baltic Sea during the
 hot and the cold summer. We looked at (1) total lipid and protein levels;
 (2) FA trophic markers and AA composition, and (3) compound-specific
 stable carbon isotopes (δ13C) in bulk mesozooplankton and in a subset of
 parameters in particulate organic matter. Despite lipid-poor
 cyanobacterial blooms, the key species were largely able to cover both
 energy pools, yet a tendency of lipid reduction was observed in surface
 animals. Omni- and carnivory feeding modes, FA trophic makers, and δ13C
 patterns in essential compounds emphasized that cyanobacterial FAs and AAs
 have been incorporated into mesozooplankton mainly via feeding on mixo-
 and heterotrophic (dino-) flagellates and detrital complexes during
 summer. Foraging for essential highly unsaturated FAs from (dino-)
 flagellates may have caused night migration of Pseudo-/Paracalanus spp.
 from the deep sub-halocline waters into the upper waters. Only in the hot
 summer (SST&gt;19.0°C) was T. longicornis sub-merged in the colder
 sub-thermocline water (~4°C). Thus, the continuous warming trend and
 simultaneous feeding can eventually lead to competition on the preferred
 diet by key copepod species below the thermocline in stratified systems. A
 comparison of δ13C patterns of essential AAs in surface mesozooplankton
 across sub-basins of low and high cyanobacterial biomasses revealed the
 potential of δ13C-AA isoscapes for studies of commercial fish feeding
 trails across the Baltic Sea food webs.
description: Supplement_ECE-2018-11-01372_E&ERawData_Eglite et al.2019Raw data that were used in Figures and Tables of the Main Document. Results of fatty acids, amino acids, stable carbon isotopes in zooplankton and particulate organic matter.
DOI: 10.15468/dl.fsjak3
title: Occurrence Download

description: A dataset containing 163716 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "Geometry POLYGON((-79.16283 0.57727,-79.72006 -0.51922,-79.70928 -1.1124,-79.55586 -1.85462,-79.14582 -2.28713,-78.38752 -2.25343,-77.96063 -1.89394,-77.14602 -0.73492,-77.7392 0.28607,-79.16283 0.57727))",
 "IucnRedListCategory is one of (CR, EN, VU, NT)"
 ]
}

 The dataset includes 163716 records from 262 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001786-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.dn34vn2
title: Data from: Evolution of increased virulence is associated with decreased spite in the insect-pathogenic bacterium Xenorhabdus nematophila

description: Disease virulence may be strongly influenced by social interactions among
 pathogens, both during the time course of an infection and evolutionarily.
 Here we examine how spiteful bacteriocin production in the
 insect-pathogenic bacterium Xenorhabdus nematophila is evolutionarily
 linked to its virulence. Theory predicts a negative correlation between
 virulence and spite due to their inverse correlations with pathogen
 growth. We examined bacteriocin production and growth across 14
 experimentally evolved lineages that show faster host-killing relative to
 their ancestral population. Consistent with theory, these more virulent
 lineages showed reduced bacteriocin production and faster growth relative
 to the ancestor. Further, bacteriocin production was negatively correlated
 with growth across the examined lineages. These results strongly support
 an evolutionary trade-off between virulence and spiteful bacteriocin
 production and lend credence to the view that disease management can be
 improved by exploiting pathogen social interactions.
description: RawData_Bhattacharya et
 al. Biol_LettThis file contains all
 the raw data for the analyses described in the study. The data is provided
 across four sheets. An additional sheet titled 'Descriptions'
 provides more information about data on each sheet.AllDataInput_07.16.19.xlsxAnalyses_Codes_Bhattacharya et al. Biol_LettThis .txt file contains the SAS code used to conduct the statistical analyses described in the manuscript. Annotations are provided for the Input data from the Raw Data file used for specific analyses.AllAnalysesMasterFile_7.17.2019.rtf
DOI: 10.5061/dryad.n42p4k7
title: Data from: Adaptive limitations of white spruce populations to drought imply vulnerability to climate change in its western range

description: A cost-effective climate change adaptation strategy for the forestry
 sector is to move seed sources to more northern and higher elevation
 planting sites as part of ongoing reforestation programs. This is meant to
 match locally adapted populations with anticipated environments, but
 adaptive traits do not always show population differences suitable to
 mitigate climate change impacts. For white spruce, drought tolerance is a
 critical adaptive trait to prevent mortality and productivity losses.
 Here, we use a 40 year old provenance experiment that has been exposed to
 severe drought periods in 1999 and 2002 to retrospectively investigate
 drought response and the adaptive capacity of white spruce populations
 across their boreal range. Relying on dendrochronological analysis under
 experimentally controlled environments, we evaluate population differences
 in resistance, resilience and recovery to these extreme events. Results
 showed evidence for population differentiation in resistance and recovery
 parameters, but provenances conformed to approximately the same growth
 rates under drought conditions and had similar resilience metrics. The
 lack of populations with better growth rates under drought conditions is
 contrary to expectations for a wide-ranging species with distinct regional
 climates. Populations from the wettest environments in the northeastern
 boreal were surprisingly drought tolerant, suggesting that these
 populations would readily resist water deficits projected for the 2080s,
 and supporting the view that northeastern Canada will provide a refugium
 for boreal species under climate change. The findings also suggest that
 white spruce is sensitive to growth reductions under climate change in the
 western boreal. The study highlights that population differentiation in
 adaptive capacity is species and trait specific, and we provide a counter
 example for drought tolerance traits, where assisted migration
 prescriptions may be ineffective to mitigate climate change impacts. For
 resource managers and policy makers, we provide maps where planning for
 widespread declines of boreal white spruce forests may be unavoidable.
description: detrended_treeringTree-ring width measurements for white spruce provenance trail in Alberta, Canadatreering_width.csv