cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f789n
title: Data from: Extensive mitochondrial introgression in North American Great Black-backed Gulls (Larus marinus) from the American Herring Gull (Larus smithsonianus) with little nuclear DNA impact

description: Recent genetic studies have shown that introgression rates among loci may
 greatly vary according to their location in the genome. In particular,
 several cases of mito-nuclear discordances have been reported for a wide
 range of organisms. In the present study, we examine the causes of
 discordance between mitochondrial (mtDNA) and nuclear DNA introgression
 detected in North American populations of the Great Black-backed Gull
 (Larus marinus), a Holarctic species, from the Nearctic North American
 Herring Gull (Larus smithsonianus). Our results show that extensive
 unidirectional mtDNA introgression from Larus smithsonianus into Larus
 marinus in North America cannot be explained by ancestral polymorphism but
 most likely results from ancient hybridization events occurring when Larus
 marinus invaded the North America. Conversely, our nuclear DNA results
 based on 12 microsatellites detected very little introgression from Larus
 smithsonianus into North American Larus marinus. We discuss these results
 in the framework of demographic and selective mechanisms that have been
 postulated to explain mito-nuclear discrepancies. We were unable to
 demonstrate selection as the main cause of mito-nuclear introgression
 discordance but cannot dismiss the possible role of selection in the
 observed pattern. Among demographic explanations, only drift in small
 populations and bias in mate choice in an invasive context may explain our
 results. As it is often difficult to demonstrate that selection may be the
 main factor driving the introgression of mitochondrial DNA in natural
 populations, we advocate that evaluating alternative demographic neutral
 hypotheses may help to indirectly support or reject hypotheses invoking
 selective processes.
description: Microsatellite data
 collected from L. marinus and L. smithsonianusData collected from 12
 microsatellite loci : Hg16, Hg18, Hg25 (Crochet et al. 2003), K16 (Tirard
 et al. 2002), LarZAP12, LarZAP19, LarSNX24, LarZAP26 (Gregory and Quinn
 2006), Rbg13, Rbg18, Rbg27 and Rbg29 (Given et al. 2002). Museum accession
 numbers and collection locality are included.MsatDataDyrad.xlsx
DOI: 10.5061/dryad.ps534
title: Data from: Marine ecosystem connectivity mediated by migrant–resident interactions and the concomitant cross-system flux of lipids

description: Accumulating research argues that migrants influence the functioning and
 productivity of local habitats and ecosystems along migration routes and
 potentially drive cross-system energy fluxes of considerable magnitude,
 yet empirical documentation of local ecological effects and descriptions
 of the underlying mechanisms are surprisingly rare. In this study, we
 discovered migrant–resident interactions and substantial cross-system
 lipid transportation in the transition zone between the Baltic Sea and the
 North Sea where a resident cod population (predators) was found to
 interact with a herring population (prey) on a seasonal basis. We traced
 the lipids, using fatty acid trophic markers (FATM), from the herring
 feeding grounds in the North Sea to the cod livers in the Western Baltic
 Sea. Time series analysis of population dynamics indicated that
 population-level production of cod is positively affected by the herring
 subsidies. However, the underlying mechanisms were more complicated than
 anticipated. During the herring season, large cod received most of its
 dietary lipids from the herring, whereas smaller cod were prevented from
 accessing the lipid pool due to a mismatch in predator–prey size ratio.
 Furthermore, while the herring were extremely rich in bulk energy, they
 were surprisingly poor in a specific functional fatty acid. Hence, our
 study was the first to illustrate how the magnitude cross-system fluxes of
 subsidies in migrant–resident systems are potentially constrained by the
 size structure of the resident predator population and the nutritional
 quality of the migrants.
description: Cod_lipid_proteinlipids, fatty acids, proteins in codCrab_lipid_proteinlipids, fattyacids, proteins in shore crabsHerring_lipid_proteinlipids, fatty acids, proteins in herringLiver_indexLiver index of codTime_seriesData used in the time series analysisData_Laboratory_experimentData from the Laboratory experiment: Three different treatments (SIL: herring; KRAB: crabs; MIX: mix og herring and crab) and the baseline samples
DOI: 10.5061/dryad.77h8fd8
title: Data from: Water, water everywhere: environmental DNA can unlock population structure in elusive marine species

description: Determining management units for natural populations is critical for
 effective conservation and management. However, collecting the requisite
 tissue samples for population genetic analyses remains the primary
 limiting factor for a number of marine species. The harbor porpoise
 (Phocoena phocoena), one of the smallest cetaceans in the Northern
 Hemisphere, is a primary example. These elusive, highly mobile small
 animals confound traditional approaches of collecting tissue samples for
 genetic analyses, yet their nearshore habitat makes them highly vulnerable
 to fisheries bycatch and the effects of habitat degradation. By exploiting
 the naturally shed cellular material in seawater and the power of next
 generation sequencing, we develop a novel approach for generating
 population-specific mitochondrial sequence data from environmental DNA
 (eDNA) using surface seawater samples. Indications of significant genetic
 differentiation within a currently recognized management stock highlights
 the need for dedicated eDNA sampling throughout the population’s range in
 southeast Alaska. This indirect sampling tactic for characterizing stock
 structure of small and endangered marine mammals has the potential to
 revolutionize population assessment for otherwise inaccessible marine
 taxa.
description: Phocoena_CR_sequences_Dryad_040418Control region sequences resolved from Alaska harbor porpoise.
DOI: 10.5061/dryad.2d8c3
title: Data from: Reconsidering the phosphorus limitation of soil microbial activity in tropical forests

description: 1. It has long been believed that soil microbial activity in tropical
 forest ecosystems is limited by phosphorus (P) rather than nitrogen (N)
 availability. In this study, we reviewed the methods used to determine the
 limiting nutrients and evaluated the validity of the widespread
 P-limitation hypothesis in tropical forest soils. 2. The most commonly
 used analysis method entails testing whether fertilization increased
 microbial biomass or soil respiration. Fertilization using microbial
 biomass as an indicator was not a satisfactory method because standing
 microbial biomass does not always signal microbial activity. An increase
 in soil respiration after fertilization was also an insufficient indicator
 because the negative response shown by organic matter decomposition to
 nutrient addition can also be driven by nutrient shortage (nutrient
 mining). Nutrient amendment can also shift microbial communities toward
 more copiotrophic organisms, which may exhibit lower microbial respiration
 rates. 3. We suggest that P addition may accelerate soil organic matter
 decomposition compared with N, which is independent of the nutrient
 limitation of soil microbial activity. The negative response of organic
 matter decomposition to N addition through nutrient mining is driven by N
 shortage, which is less likely to occur with P. N addition inhibits
 microbial activity via chemical reactions, whereas P addition may
 stimulate activity through replacement by C bound to sorption sites in the
 soil, improving C availability. Thus, the P-limitation hypothesis must be
 reconsidered because of the contrasting effects of exogenous N and P
 addition on soil microbial activity, which could lead to misdetection of P
 limitation on soil microbial activity in tropical forest ecosystems. 4. We
 recommend caution in applying the statement that soil microbial activity
 in tropical forest ecosystems is limited by P until a novel method is
 established to accurately determine the nutrients limiting soil microbial
 activity at the ecosystem level. We propose alternative ways to describe
 nutrient shortage for soil microbes.
description: Data used for
 meta-analysisData used for
 calculating weighted response ratio of N fertilization on microbial
 biomass and soil respiration, and of P fertilization on microbial biomass
 and soil respiration.Data.csvReference listReferences that data were extracted to calculate weighted response ratio of N fertilization on microbial biomass and soil respiration, and of P fertilization on microbial biomass and soil respiration.
DOI: 10.5061/dryad.2kp51
title: Data from: Invasive seaweeds transform habitat structure and increase biodiversity of associated species

description: The visual landscape of marine and terrestrial systems is changing as a
 result of anthropogenic factors. Often these shifts involve introduced
 species that are morphologically dissimilar to native species, creating a
 unique biogenic structure and habitat for associated species within the
 landscape. While community level changes as a result of introduced species
 have been documented in both terrestrial and marine systems, it is still
 unclear how long-term shifts in species composition will affect habitat
 complexity or its potential to influence the biodiversity of species that
 occur at the base of the food web. We analysed quadrat photos collected at
 several subtidal sites in the Gulf of Maine over a 30+ year period, and
 collected individual seaweed species to determine their complexity and the
 biodiversity of meso-invertebrates associated with each species. By
 coupling the relationship of 30+ years of shifts in seaweed assemblages,
 morphological structure of the seaweed assemblage, and their
 meso-invertebrates, we determined introduced seaweeds have increased by up
 to 90%, corresponding to a rise in two-dimensional (2D) structure, and a
 decline in canopy height of subtidal rocky habitats. The highly complex
 two-dimensional habitat provided by introduced filamentous red seaweeds
 supports 2 to 3 times more meso-invertebrate individuals and species that
 form the base of the food web than simpler forms of morphological habitat.
 Synthesis: The present study demonstrates a long-term shift in foundation
 species towards a dominance of invasive seaweeds that directly reduce
 canopy height and increase the 2D biogenic structure of the habitat. These
 introduced seaweeds harbour greater biodiversity of species found at the
 base of the food web than seaweeds with simpler forms such as the native
 kelp species. Such shifts in habitat structure will propagate to food-webs
 by influencing the structure of lower trophic level meso-invertebrates and
 indirectly upper trophic level species that feed on these invertebrates
 and use the seaweed structure as refuge.
description: Seaweed complexity and
 meso-invertebratesComplexity of individual
 seaweed species. Count and species richness of associated
 meso-invertebratesDataDryadMC.xlsxPercent Cover DataPercent cover data for each speciesDataDryadPCD.xlsx
DOI: 10.5061/dryad.f36h3n1
title: Data from: Ranking stressor impacts on periphyton structure and function with mesocosm experiments and environmental-change forecasts

description: Streams are being subjected to physical, chemical, and biological stresses
 stemming from both natural and anthropogenic changes to the planet. In the
 face of limited time and resources, scientists, resource managers, and
 policy makers need ways to rank stressors and their impacts so that we can
 prioritize them from the most to least important (i.e., perform
 'ecological triage'). We report results from an experiment in
 which we established a periphyton community from the Huron River
 (Michigan, USA) in 84 experimental 'flumes' (stream mesocosms).
 We then dosed the flumes with gradients of six common stressors (increased
 temperature, taxa extinctions, sedimentation, nitrogen, phosphorus, and
 road salt) and monitored periphyton structure and function. A set of a
 priori deterministic functions were fit to each stressor-endpoint response
 and model averaging based on AICc weights was used to develop
 concentration-response best-fit predictions. Model predictions from
 different stressors were then compared to forecasts of future
 environmental change to rank stressors according to the potential
 magnitude of impacts. All of the stressors studied altered at least one
 characteristic of the periphyton; however, the extent (i.e., structural
 and functional changes) and magnitude of effects expected under future
 forecasts differed significantly among stressors. Elevated nitrogen
 concentrations are projected to have the greatest combined effect on
 stream periphyton structure and function. Extinction, sediment, and
 phosphorus all had similar but less substantial impact on the periphyton
 (e.g., affected only structure not function, smaller magnitude change).
 Elevated temperature and salt both had measurable effects on periphyton,
 but their overall impacts were much lower than any of the other stressors.
 For periphyton in the Huron River, our results suggest that, among the
 stressors examined, increased N pollution may have the greatest potential
 to alter the structure and function of the periphyton community, and
 managers should prioritize reducing anthropogenic sources of nitrogen. Our
 study demonstrates an experimental approach to ecological triage that can
 be used as an additional line of evidence to prioritize management
 decisions for specific ecosystems in the face of ecological change.
description: flume_communityWater chemistryWater chemistry (pH, nitrate, ammonium, soluble reactive phosphorus) in each flume at the end of the experiment.flume_EOE_waterchem.csvPeriphyton photosynthetic rate and chemistryEnd of experiment rates of photosynthesis and chemistry (C, N, and P) of periphytonflume_photosyn_chemistry.csv
DOI: 10.5061/dryad.8424c
title: Data from: Females manipulate behavior of caring males via prenatal maternal effects

description: In species with biparental care, there is sexual conflict as each parent
 is under selection to minimize its personal effort by shifting as much as
 possible of the workload over to the other parent. Most theoretical and
 empirical work on the resolution of this conflict has focused on
 strategies used by both parents, such as negotiation. However, because
 females produce the eggs, this might afford females with an ability to
 manipulate male behavior via maternal effects that alter offspring
 phenotypes. To test this hypothesis, we manipulated the prenatal
 conditions (i.e., presence or absence of the male), performed a
 cross-fostering experiment, and monitored the subsequent effects of
 prenatal conditions on offspring and parental performance in the burying
 beetle Nicrophorus vespilloides. We found that offspring were smaller at
 hatching when females laid eggs in presence of a male, suggesting that
 females invest less in eggs when expecting male assistance. Furthermore,
 broods laid in the presence of a male gained more weight during parental
 care, and they did so at the expense of male weight gain. Contrary to our
 expectations, males cared less for broods laid in the presence of a male.
 Our results provide experimental evidence that females can alter male
 behavior during breeding by adjusting maternal effects according to
 prenatal conditions. However, rather than increasing the male’s parental
 effort, females appeared to suppress the male’s food consumption, thereby
 leaving more food for their brood.
description: Female_manipulation_2017datadryad_PNAS.xlsx
DOI: 10.5061/dryad.8dc30
title: Data from: No association between sperm competition and sperm length variation across dung flies (Scathophagidae)

description: Sperm length is extremely variable across species, but a general
 explanation for this variation is lacking. However, when the risk of sperm
 competition is high, sperm length is predicted to be less variable within
 species, and there is some evidence for this in birds and social insects.
 Here, we examined intraspecific variation in sperm length, both within and
 between males, and its potential associations with sperm competition risk
 and variation in female reproductive tract morphology across dung flies.
 We used two measures of variation in sperm size, and testis size was
 employed as our index of sperm competition risk. We found no evidence of
 associations between sperm length variation and sperm competition or
 female reproductive tract variation. These results suggest that variation
 in sperm competition risk may not always be associated with variation in
 sperm morphology, and the cause(s) of sperm length variation in dung flies
 remains unclear.
description: Phenotypic means,
 between and within male coefficients of variation and variance estimates
 for testis area and sperm lengthPhenotypic means (±SE),
 along with between and within male coefficients of variation and variance
 estimates for the male characters (testis area and sperm length) used in
 the analyses. NA = no value. * Indicates species that could not be used
 for phylogenetic analysis and ° indicates those species for which
 between-male data could not be calculated. TA= testis area in mm2; MSL =
 mean sperm length (mm); BMVAR = between male variance; WMVAR = within male
 variance; BMCV = between male coefficient of variation and WMCV = within
 male coefficient of variation.Dryad_JEB-2013-00331.R1.docx
DOI: 10.5061/dryad.k3r47
title: Data from: Prevention of surgical site infection in lower limb skin lesion excisions with single dose oral antibiotic prophylaxis: a prospective randomised placebo-controlled double-blind trial

description: Objectives: To determine the effectiveness of a single perioperative
 prophylactic 2 g dose of cephalexin in preventing surgical site infection
 (SSI) following excision of skin lesions from the lower limb. Design:
 Prospective double-blinded placebo-controlled trial testing for difference
 in infection rates. Setting: Primary care in regional North Queensland,
 Australia. Participants: 52 patients undergoing lower limb skin lesion
 excision. Interventions: 2 g dose of cephalexin 30–60 min before excision.
 Main outcome measures: Incidence of SSI. Results: Incidence of SSI was
 12.5% (95% CI 2.7% to 32.4%) in the cephalexin group compared with 35.7%
 (95% CI 18.6% to 55.9%) in the placebo group (p=0.064). This represented
 an absolute reduction of 23.21% (95% CI −0.39% to 46.82%), relative
 reduction of 65.00% (95% CI −12.70% to 89.13%) and number-needed-to-treat
 of 4.3. Conclusions: Administration of a single 2 g dose of cephalexin
 30–60 min before skin lesion excision from the lower limb may produce a
 reduction in the incidence of infection; however, this study was
 underpowered to statistically determine this. Trial registration number:
 ACTRN12611000595910.
description: AntibioticProphylaxisDataDryadDe-identified Core data set from trial
DOI: 10.5061/dryad.1m8r2
title: Data from: Persistence of an extreme male-biased adult sex ratio in a natural population of polyandrous bird

description: In a number of insects, fishes and birds the conventional sex roles are
 reversed: males are the main care provider whereas females focus on
 matings. The reversal of typical sex roles is an evolutionary puzzle,
 because it challenges the foundations of sex roles, sexual selection and
 parental investment theory. Recent theoretical models predict that biased
 parental care may be a response to biased adult sex ratios (ASRs).
 However, estimating ASR is challenging in natural populations, because
 males and females often have different detectabilities. Here we use
 demographic modelling with field data from 2101 individuals, including 579
 molecularly sexed offspring, to provide evidence that ASR is strongly
 male-biased in a polyandrous bird with male-biased care. The model
 predicts 6.1 times more adult males than females (ASR = 0.860, proportion
 of males) in the Kentish plover Charadrius alexandrinus. The extreme
 male-bias is consistent between years, and concordant with experimental
 results showing strongly biased mating opportunity toward females. Based
 on these results we conjecture that parental sex role reversal may occur
 in populations that exhibit extreme male-biased ASR.
description: chick_sexData to estimate brood sex ratio at fledging (BSR, see equation S1 in Supporting Information). Variables: BROOD - brood ID, MALE - number of male chicks in the brood, FEMALE - number of female chicks in the brood, MAHATCH - hatching date (number of days since 1 March), AGE - brood age at capture. BSR was estimated at the middle of the four periods: 49, 72, 95, 117.5 days since 1 March.fledging_successData to estimate fledging success (FS, see equation S2 in Supporting Information). Variables: BROOD - brood ID, MAHATCH - hatching date (number of days since 1 March), FLED - whether the brood fledged any chicks (1) or not (0). FS was estimated at the middle of the four periods: 49, 72, 95, 117.5 days since 1 March.brood_sizeData to estimate number of broods hatched (B) and average brood size (BS) for the four periods. Variables: BROOD - brood ID, MAHATCH - hatching date (number of days since 1 March), BROODSIZE - number of chicks hatched, PERIOD - categorical variable giving the four periods.
DOI: 10.5281/zenodo.18376509
title: Data for: Comparative Study of Nanosecond Laser Wavelengths for Improved LIBS Analysis of Soft Tissues
DOI: 10.5061/dryad.1ts48
title: Data from: Oral administration of Pantoea agglomerans-derived lipopolysaccharide prevents development of atherosclerosis in high-fat diet-fed apoE-deficient mice via ameliorating hyperlipidemia, pro-inflammatory mediators and oxidative responses

description: Pantoea agglomerans (P. agglomerans) is a Gram-negative bacterium that
 grows symbiotically with various edible plants, and the oral or sublingual
 administration of lipopolysaccharide derived from P. agglomerans (LPSp)
 have been suggested to contribute to prevention of immune-related
 diseases. Our previous study indicated that orally administered LPSp was
 shown to exhibit an LDL-lowering effect in hyperlipidemic volunteers;
 however, a preventive effect of LPSp on atherosclerosis is unclear. The
 present study attempted to evaluate the anti-atherosclerotic effect by
 LPSp in a mouse model of high-fat diet (HFD)-induced atherosclerosis. For
 16 weeks, apoE-deficient mice were fed an HFD and received drinking water
 containing LPSp (0.3 or 1 mg/kg body weight/day). The results showed that
 the orally administered LPSp decreased body weight. A significant
 reduction in atherosclerotic plaque deposition was observed even with the
 lower dose of LPSp. The biochemical analyses showed that LPSp markedly
 improved glucose tolerance and reduced plasma LDL and oxidized LDL levels.
 In addition, LPSp significantly reduced the production of pro-inflammatory
 mediators including MCP-1 (in the plasma), TNF-α and IL-6 (in the colon),
 and decreased the oxidative burst activities in the peripheral blood
 sample. Taken together, these results suggest the possibility that oral
 administration of LPSp can effectively ameliorate HFD-induced
 hyperlipidemia and inflammatory/oxidative responses to prevent
 atherosclerosis and related metabolic disorders.
description: Fig 8. Taxonomy
 SummaryFig8-Taxonomy
 Summary.xlsx
DOI: 10.5281/zenodo.18376508
title: Data for: Comparative Study of Nanosecond Laser Wavelengths for Improved LIBS Analysis of Soft Tissues