cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6b6k8b83
title: Data from: Habitat selection predicts genetic relatedness in an alpine ungulate

description: Landscape heterogeneity plays an integral role in shaping ecological and
 evolutionary processes. Despite links between the two disciplines,
 ecologists and population geneticists have taken different approaches to
 evaluating habitat selection, animal movement, and gene flow across the
 landscape. Ecologists commonly use statistical models such as resource
 selection functions (RSFs) to identify habitat features disproportionately
 selected by animals, while population genetic approaches model genetic
 differentiation according to the distribution of habitat variables. We
 combined ecological and genetic approaches by using RSFs and
 step-selection functions (SSFs) to predict genetic relatedness across a
 heterogeneous landscape. We constructed sex and season-specific resistance
 surfaces based on RSFs and SSFs estimated using data from 102 GPS
 radiocollared mountain goats (Oreamnos americanus) in southeast Alaska.
 Based on mountain goat ecology, we hypothesized that summer and male
 surfaces would be the best predictors of relatedness. All individuals were
 genotyped at 22 microsatellite loci, which we used to estimate genetic
 relatedness. Summer resistance surfaces derived from RSFs were the best
 predictors of genetic relatedness, and winter models the poorest. Male and
 female specific surfaces were similar, except for winter where male
 habitat selection better predicted genetic relatedness. The null models of
 isolation-by-distance and barrier only outperformed the winter models.
 This study merges high-resolution individual locations through GPS
 telemetry and genetic data, that can be used to validate and parameterize
 landscape genetics models, and further elucidates the relationship between
 landscape heterogeneity and genetic differentiation.
description: Shafer_LG_data_DRYAD_2011_1021_subIntroductory information: Mountain goat (Oreamnos americanus) capture and genotype data. Collected by Kevin White (Alaska Department of Fish and Game) and Aaron Shafer (University of Alberta). Please contact either Kevin White (kevin.white@alaska.gov) or Aaron Shafer (shafer@ualberta.ca) with any questions of location and genotype data, respectively. Row 1 - Headings (descriptions in subheadings): Identification – lab ID, capture ID, capture date, sex, and estimated age of animal; Capture Location - latitude and longitude; Home Range centroid location - latitude and longitude (of 100% Minimum Convex Polygon); Loci - names of microsatellite loci analyzed. Row 2 - Subheadings: Lab ID - ID number used in lab; Capture ID - ID number used in field; Capture Date – Day-Month-Year; Sex – male or female; Est. Age – estimated age based on horn annuli; Latitude, Longitude - latitude (Y) and longitude (X) coordinates (datum = WGS84) of capture and home range centroid; Name of Loci - 21 in total, two alleles provided per loci in adjacent columns, missing data given a zero. Row 3 - Data.
DOI: 10.5061/dryad.505d9
title: Data from: Negative effects of litter richness on root decomposition in the presence of detritivores

description: 1. Decomposition is a vital process underlying many ecosystem functions.
 Although a growing number of studies have tested how litter richness
 affects the decomposition of aboveground plant organs, knowledge remains
 limited about the decomposition of root mixtures. Here, we used a field
 experiment in a subtropical forest to investigate how species richness in
 root litter mixtures (air-dried fresh fine roots) affects the
 decomposition of root litter material. 2. Based on the concept of resource
 complementarity, we hypothesized that root litter would decompose faster
 as the richness of the root litter mixture increased. In addition, we
 expected the presence of detritivores to modify the effect of root
 richness on mass loss, because detritivores might experience bottom-up
 effects from specific plant species and might affect microbial decomposer
 communities. 3. We found that the richness level of root litter mixtures
 did not affect mass loss in the absence of detritivores. In the presence
 of detritivores, all root litter types decomposed faster. Notably, the
 positive effect of detritivores was stronger at low root litter richness
 than at high root litter richness, particularly during the early stages of
 decomposition (the first two sampling points) when litter mass loss was
 roughly double at low root litter richness compared to that at high root
 litter richness. The composition of the root fungal community measured at
 the last sampling point did not differ significantly across root richness
 levels, and was not affected by the presence of detritivores. 4.
 Synthesis. Our findings demonstrate that detritivores modify the
 relationship between root litter diversity and root litter decomposition
 in subtropical forest ecosystems. This highlights an importance of cascade
 effects between different trophic organisms on ecosystem functioning.
description: Massloss of root
 mixtures in a subtropical forestHere, we used a field
 experiment in a subtropical forest to investigate how species richness in
 root litter mixtures (air-dried fresh fine roots) affects the
 decomposition of root litter material. The data are the root massloss of
 multiple species mixtures.massloss of root mixtures in a
 subtropical forest_data.csvInitial root chemicals
 in a subtropical forestHere, we used a field
 experiment in a subtropical forest to investigate how species richness in
 root litter mixtures (air-dried fresh fine roots) affects the
 decomposition of root litter material. The data are the initial chemicals
 of these root materials.initial root chemicals in a
 subtropical forest_data.csv
DOI: 10.5061/dryad.969j137
title: Data from: Climate-woodland effects on population genetics for two congeneric lichens with contrasting reproductive strategies

description: Genetic variation is expected to be influenced by the interaction between
 reproductive mode and dispersal traits on the one hand, and environmental
 and habitat setting affecting establishment success on the other. We
 evaluated how environmental/habitat setting affect population genetic
 variation (i.e. variation in genetic diversity and structure) when
 regulated by contrasting dispersal traits. We used fungus-specific
 microsatellite markers to examine genetic diversity and structure of two
 closely related epiphytic lichen fungi that differ in their primary
 reproductive mode: Nephroma laevigatum (sexually reproducing, N = 191, ten
 microsatellites) and N. parile (asexually, N = 182, twelve
 microsatellites), along a steep climatic gradient in Scotland. Despite
 their reproductive differences, we found a high proportion of clones in
 both species and a background pattern of genetic structure related to
 climatic gradients. We also demonstrated that woodland connectivity,
 rather than geographic distance, explained genetic diversity in both
 species. Environmental/habitat setting, modulated by the reproductive mode
 of the species, affects genetic diversity and structure, but the putative
 dissimilarity in their reproductive mode is less important than has been
 previously assumed. We reinforce the importance of protecting highly
 connected populations, positioned along a gradient capturing the
 segregation of gene pool differences in response to climatic variation.
description: Microsatellite markers
 NephromaThis data set contains
 raw genotypes of 14 microsatellite markers for Nephroma parile and 12
 microsatellite markers for Nephroma laevigatum at 14 localites in
 Scotland. When using this data, please cite the original publication:
 Belinchón, Ellis, and Yahr (2018). Climate-woodland effects on population
 genetics for two congeneric lichens with contrasting reproductive
 strategies. FEMS Microbiology Ecology
 doi.org/10.1093/femsec/fiy159Belinchón et al.,
 2018.xlsx
DOI: 10.5061/dryad.bt612
title: Data from: Laboratory colonisation and genetic bottlenecks in the tsetse fly Glossina pallidipes

description: Background: The IAEA colony is the only one available for mass rearing of
 Glossina pallidipes, a vector of human and animal African trypanosomiasis
 in eastern Africa. This colony is the source for Sterile Insect Technique
 (SIT) programs in East Africa. The source population of this colony is
 unclear and its genetic diversity has not previously been evaluated and
 compared to field populations. Methodology/Principal Findings: We examined
 the genetic variation within and between the IAEA colony and its potential
 source populations in north Zimbabwe and the Kenya/Uganda border at 9
 microsatellites loci to retrace the demographic history of the IAEA
 colony. We performed classical population genetics analyses and also
 combined historical and genetic data in a quantitative analysis using
 Approximate Bayesian Computation (ABC). There is no evidence of
 introgression from the north Zimbabwean population into the IAEA colony.
 Moreover, the ABC analyses revealed that the foundation and establishment
 of the colony was associated with a genetic bottleneck that has resulted
 in a loss of 35.7% of alleles and 54% of expected heterozygosity compared
 to its source population. Also, we show that tsetse control carried out in
 the 1990's is likely reduced the effective population size of the
 Kenya/Uganda border population. Conclusions/Significance: All the analyses
 indicate that the area of origin of the IAEA colony is the Kenya/Uganda
 border and that a genetic bottleneck was associated with the foundation
 and establishment of the colony. Genetic diversity associated with traits
 that are important for SIT may potentially have been lost during this
 genetic bottleneck which could lead to a suboptimal competitiveness of the
 colony males in the field. The genetic diversity of the colony is lower
 than that of field populations and so, studies using colony flies should
 be interpreted with caution when drawing general conclusions about G.
 pallidipes biology.
description: G. pallidipes
 microsatellites data - Busia, Rukomeshi, IAEA - Ciosi et al 2014 - PLOS
 NTDThe file
 "2013-06-10 BUS+IAEA2012-2013+Zim_ALPHA&BETA.xlsx" contains
 the genotypes of 121 Glossina pallidipes individuals from two field
 population samples (Busia and Rukomeshi) and from two samples from the
 IAEA laboratory colony. These genotypic data have been used in the
 publication by Ciosi et al. 2014 PLOS Neglected Tropical Diseases untitled
 "Laboratory colonisation and genetic bottlenecks in the tsetse fly
 Glossina pallidipes"2013-06-10
 BUS+IAEA2012-2013+Zim_ALPHA&BETA.xlsx
DOI: 10.5061/dryad.47j89
title: Data from: Sunrise in the city: disentangling drivers of the avian dawn chorus onset in urban greenspaces

description: Urban systems are known to have a number of effects on avian richness,
 density, and morphological and behavioral traits. However, no study to
 date has simultaneously examined the wide range of urban variables in
 relation to the avian dawn chorus, a complex behavioral phenomenon.
 Previous studies investigating adjustments of the dawn chorus onset in
 urban settings have mainly been confined to relationships with noise and
 light levels. In addition to noise and light levels, in this study we
 included other potentially related environmental characteristics
 describing vegetation structure, urban infrastructure, and human activity,
 all of which have been shown to be drivers of bird diversity in urban
 areas. We conducted dawn chorus surveys at 38 Los Angeles urban
 greenspaces and used a classification and regression tree analysis to
 identify specific urban scenarios that best explained timing differences
 in the dawn chorus onset. Our results show that light level was the most
 important variable related to the dawn chorus onset time, in which,
 counter-intuitively, bird communities in greenspaces with higher light
 levels had later onsets. In addition, noise was an important factor for
 the chorus onset in greenspaces with higher light levels. Although our
 results differ from those of previous studies, these findings highlight
 the importance of noise and light levels in explaining dawn chorus onset
 variation, indicating the need for further research in untangling this
 complex and ecologically important phenomenon.
description: Lee et al. 2017_Dawn
 Chorus and Environmental Variables DataThis Microsoft Excel
 spreadsheet contains the raw values of all variables that were measured
 and used to identify specific environmental variables (describing
 vegetation structure, urban infrastructure, human activity, noise levels,
 light levels, and bird species) that best explained timing differences in
 the dawn chorus onset. This data was obtained in the Los Angeles
 intra-urban area by one of the coauthors (JG-HL) and a trained field
 assistant (S. A. Bressler) from early-July to early-August 2016. Further
 information pertaining to this data set and analyses is available in the
 published paper.
DOI: 10.5061/dryad.d5n0d
title: Data from: Genetic variability and structuring of Arctic charr (Salvelinus alpinus) populations in northern Fennoscandia

description: Variation in presumably neutral genetic markers can inform us about
 evolvability, historical effective population sizes and phylogeographic
 history of contemporary populations. We studied genetic variability in 15
 microsatellite loci in six native landlocked Arctic charr (Salvelinus
 alpinus) populations in northern Fennoscandia, where this species is
 considered near threatened. We discovered that all populations were
 genetically highly (mean FST ≈ 0.26) differentiated and isolated from each
 other. Evidence was found for historical, but not for recent population
 size bottlenecks. Estimates of contemporary effective population size (Ne)
 ranged from seven to 228 and were significantly correlated with those of
 historical Ne but not with lake size. A census size (NC) was estimated to
 be approximately 300 individuals in a pond (0.14 ha), which exhibited the
 smallest Ne (i.e. Ne/NC = 0.02). Genetic variability in this pond and a
 connected lake is severely reduced, and both genetic and empirical
 estimates of migration rates indicate a lack of gene flow between them.
 Hence, albeit currently thriving, some northern Fennoscandian populations
 appear to be vulnerable to further loss of genetic variability and are
 likely to have limited capacity to adapt if selection pressures change.
description: Genotype
 dataMicrosatellite genotypes
 for 15 loci in six charr populations
DOI: 10.5061/dryad.m5r87
title: Data from: Elevated success of multispecies bacterial invasions impacts community composition during ecological succession

description: Successful microbial invasions are determined by a species’ ability to
 occupy a niche in the new habitat whilst resisting competitive exclusion
 by the resident community. Despite the recognised importance of biotic
 factors in determining the invasiveness of microbial communities, the
 success and impact of multiple concurrent invaders on the resident
 community has not been examined. Simultaneous invasions might have
 synergistic effects, for example if resident species need to exhibit
 divergent phenotypes to compete with the invasive populations. We used
 three phylogenetically diverse bacterial species to invade two
 compositionally distinct communities in a controlled, naturalised in vitro
 system. By initiating the invader introductions at different stages of
 succession, we could disentangle the relative importance of resident
 community structure, invader diversity and time pre-invasion. Our results
 indicate that multiple invaders increase overall invasion success, but do
 not alter the successional trajectory of the whole community.
description: Colony counts for
 invaders and communitiesData file including all
 of the colony counts for each of the different timepoints, communities and
 replicates, formatted for direct import into R. See README file for
 definitions of the columns.InvasionData.csvOperational Taxonomic Unit tableOTU table, concatenated by genus, non-normalised, with singletons. The first column is matched to the first column in the InvasionData.csv file to align composition and invasion data.OTUgenus.csv
DOI: 10.5061/dryad.v3546
title: Data from: Association between severity of MERS-CoV infection and incubation period

description: We analyzed data for 170 patients in South Korea who had
 laboratory-confirmed infection with Middle East respiratory syndrome
 coronavirus. A longer incubation period was associated with a reduction in
 the risk for death (adjusted odds ratio/1-day increase in incubation
 period 0.83, 95% credibility interval 0.68–1.03).
description: MERS data in South
 KoreaThis data file contains
 individual information on laboratory-confirmed MERS cases in South Korea
 in 2015.data_mers.csvRead me (data file explanations)Scripts of simple MCMC functionsR syntax to define the MCMC functions to be used in other scriptsmcmc_function_incubation.rTechnical Appendix Table 1 scriptsTable_1.rTechnical Appendix Table 2 scripts (part 1)Table_2.1.rTechnical Appendix Table 2 scripts (part 2)Table_2.2.rTechnical Appendix Table 3 scriptsTable_3.rFigure scriptsFigure.r
DOI: 10.5061/dryad.5j38fm7
title: Data from: Community-level economics spectrum of fine-roots driven by nutrient limitations in subalpine forests

description: 1. Fine-root traits show remarkable variation with plant community
 structure and environmental shifts, but there is limited understanding of
 how trait covariation that exists among fine-root traits shifts among
 different communities, especially in forests. We explored links among the
 fine-root traits of forest communities to determine whether community root
 traits shift predictably according to an economics framework along
 environmental gradients. 2. Measurements of root morphology, nitrogen,
 phosphorus and carbon concentrations, and measures of standing root
 densities were collected on fine roots (diameter ≤ 2 mm) from 129 forest
 plots in five subalpine forests. 3. This study demonstrates an existence
 of a community-level fine-root economics spectrum (REScom) in the
 subalpine forests, in which specific root length was strongly and
 positively related to root nitrogen and phosphorusconcentrations, but
 negatively related to root diameter. Soil nutrient limitation was a major
 driver of the REScom as changes in soil [N], [P] and [C] contents were
 related to changes in SRL, root [N], root [P]. Variables related to
 standing fine-root length and mass were independent of the REScom and was
 primarily related to forest community structure, particularly in tree
 closure and herbaceous plant mass. 4. These results indicate two distinct
 functional dimensions of community fine-root trait variation: resource-use
 efficiency via changes in root structure and construction, and separately
 via changes in the standing root system. Identifying shifts in allocation
 to and investment in fine roots enhances our understanding of a root and
 whole-plant economics spectrum and community functioning.
description: Data JEcol-2018-0505
 LiVariable definitions
 included in a separate Excel sheet.
DOI: 10.5061/dryad.4p3s0
title: Data from: Invasive alien plants benefit more from clonal integration in heterogeneous environments than natives

description: What confers invasive alien plants a competitive advantage over native
 plants remains open to debate. Many of the world's worst invasive
 alien plants are clonal and able to share resources within clones (clonal
 integration), particularly in heterogeneous environments. Here, we tested
 the hypothesis that clonal integration benefits invasive clonal plants
 more than natives and thus confers invasives a competitive advantage. We
 selected five congeneric and naturally co-occurring pairs of invasive
 alien and native clonal plants in China, and grew pairs of connected and
 disconnected ramets under heterogeneous light, soil nutrient and water
 conditions that are commonly encountered by alien plants during their
 invasion into new areas. Clonal integration increased biomass of all
 plants in all three heterogeneous resource environments. However, invasive
 plants benefited more from clonal integration than natives. Consequently,
 invasive plants produced more biomass than natives. Our results indicate
 that clonal integration may confer invasive alien clonal plants a
 competitive advantage over natives. Therefore, differences in the ability
 of clonal integration could potentially explain, at least partly, the
 invasion success of alien clonal plants in areas where resources are
 heterogeneously distributed.
description: data-biomassdata of table 1 and Fig.1, biomass of clone, recipient and donor in three heterogeneous environments. data format is for R analysis.R-codeR code for Table 1 and Table S2data-root leaf and clonal organ massdata for Fig.S1 and Table S2
DOI: 10.5061/dryad.b273t
title: Data from: Apex predators and the facilitation of resource partitioning among mesopredators

description: Apex predators may influence carnivore communities through the suppression
 of competitively dominant mesopredators, however they also provide carrion
 subsidies that could influence foraging and competition among sympatric
 mesopredators when small prey is scarce. We assessed coyote Canis latrans
 and red fox Vulpes vulpes winter diet overlap and composition from scats
 collected in two study areas with &gt;3-fold difference in grey wolf
 Canis lupus density due to a wolf control program. We hypothesized that
 differences in diet composition would be driven by the use of carrion, and
 tested whether 1) apex predators facilitate resource overlap, or 2) apex
 predators facilitate resource partitioning. We estimated the available
 biomass of snowshoe hares and voles based on pellet density and vole
 capture rates in each study area. We used molecular analysis to confirm
 species identification of predator scats, and used microscopic evaluation
 of prey remains to analyze diet composition of 471 coyote and fox scats.
 Ungulate carrion, voles and snowshoe hares comprised 73% of coyote and fox
 diet, and differences in use of carrion and microtines accounted for
 nearly 60% of the dissimilarity in diet among these canids. Carrion was
 the top-ranked item in the coyote diet in both study areas, whereas
 carrion use by red foxes declined &gt;3-fold in the study area with
 higher wolf and small prey abundance. Diet overlap tended to be lower and
 diet diversity tended to be higher where wolves were more abundant, though
 these trends were not statistically significant. Taken together, our
 findings indicate that carrion provisions could facilitate resource
 partitioning in mesocarnivore communities by alleviating exploitation
 competition for small mammals.
description: Coyote and red fox scat
 contentsThis file contains data
 of percent volume of items found in 471 coyote and red fox scats collected
 in interior Alaska, winter 2013-2014. "Scat number" refers to
 the sample number, "Study area" refers to the study area from
 which the scat was collected, "Species" refers to the species
 that deposited the scat, as determined by molecular analyses. The
 remaining categories and values refer to the percent volume of each item
 found in that scat as determined by visual inspection of contents and
 microscopic evaluation of hair fragments. See methods of Sivy et al. 2017
 for further details.scat.xlsx