cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q83bk3jjw
title: What is the best fitness measure in wild populations? A case study on the power of short-term fitness proxies to predict reproductive value

description: Fitness is at the core of evolutionary theory, but it is difficult to
 measure accurately. One way to measure long-term fitness is by calculating
 the individual’s reproductive value, which represents the expected number
 of allele copies an individual passes on to distant future generations.
 However, this metric of fitness is scarcely used because the estimation of
 individual’s reproductive value requires long-term pedigree data, which is
 rarely available in wild populations where following individuals from
 birth to death is often impossible. Wild study systems therefore use
 short-term fitness metrics as proxies, such as the number of offspring
 produced. This study obtained three frequently used short-term proxies for
 fitness obtained at different offspring life stages (eggs, hatchlings,
 fledglings and recruits), and compared their ability to predict
 reproductive values derived from the genetic pedigree of a wild passerine
 bird population. We used twenty years of precise field observations and a
 near-complete genetic pedigree to calculate reproductive success,
 individual growth rate and de-lifed fitness as lifetime fitness measures,
 and as annual de-lifed fitness. We compared the power of these metrics to
 predict reproductive values and lineage survival to the end of the study
 period. The three short-term fitness proxies predict the reproductive
 values and lineage survival only when measured at the recruit stage. There
 were no significant differences between the different fitness proxies at
 the same offspring stages in predicting the reproductive values and
 lineage survival. Annual fitness at one year old predicted reproductive
 values equally well as lifetime de-lifed fitness. However, none of the
 short-term fitness proxies was strongly associated with the reproductive
 values. In summary, the commonly short-term fitness proxies capture
 long-term fitness with intermediate accuracy at best, if measured at
 recruitment stage. As lifetime fitness measured at recruit stage and
 annual fitness in the first year of life were the best proxies of
 long-term fitness, we encourage their future use.
DOI: 10.57760/sciencedb.ecodb.00241
title: A dataset of carbon and water fluxes at the Changling paddy field flux observation site from 2019 to 2020
title: 2019-2020年长岭稻田生态系统碳水通量观测数据集

description: The raw observation data acquired by the eddy covariance system at the Changling paddy field flux observation site from 2019 to 2020 were processed based on the ChinaFLUX data processing standards to produce this standardized dataset of ecosystem carbon and water fluxes and key meteorological elements. The site was established by Shanxi University. It is located in Changling county, Jilin province, representing a typical agricultural ecosystem in Northeast China with rice as the crop type. In this dataset, the annual data includes 8 Excel data files, divided into two categories: LITE, which includes major fluxes and meteorological variables, and ALL, which adds data quality and interpolation indicators on the basis of LITE. Each category has four data files, including data files at four scales: half-hour (HH), day (DD), month (MM), and year (YY). 
description: The raw observation data acquired by the eddy covariance system at the Changling paddy field flux observation site from 2019 to 2020 were processed based on the ChinaFLUX data processing standards to produce this standardized dataset of ecosystem carbon and water fluxes and key meteorological elements. The site was established by Shanxi University. It is located in Changling county, Jilin province, representing a typical agricultural ecosystem in Northeast China with rice as the crop type. In this dataset, the annual data includes 8 Excel data files, divided into two categories: LITE, which includes major fluxes and meteorological variables, and ALL, which adds data quality and interpolation indicators on the basis of LITE. Each category has four data files, including data files at four scales: half-hour (HH), day (DD), month (MM), and year (YY).
DOI: 10.5061/dryad.95x69p8mj
title: Data from: Genomic data clarify Aquarana systematics and reveal isolation-by-distance dominates phylogeography of the wide-ranging frog Rana clamitans

description: Wide-ranging species are often polytypic, span geographic dispersal
 barriers, and experience opportunities for divergence via genetic drift or
 natural selection. Such conditions can be favorable for speciation and
 wide-ranging taxa are frequently subdivided into multiple species by
 modern molecular studies. However, with wide-ranging species, it is
 important to explicitly test for isolation-by-distance (IBD) which can
 produce continuous genetic variation that may be misinterpreted as
 discrete population structure or even distinct species. Here we examine
 the Green Frog (Rana clamitans), a wide-ranging species of the Aquarana
 clade distributed across much of North America. Although Rana clamitans is
 phenotypically variable enough to previously merit description of two
 subspecies, patterns of genetic diversity remain unclear. Additionally,
 the broader phylogenetic context for R. clamitans is poorly understood,
 particularly its relationship with the closely related and IUCN Vulnerable
 Bog Frog (Rana okaloosae). Using genome-wide ddRAD markers, we largely
 resolve relationships within Aquarana and unambiguously identify R.
 okaloosae as the sister lineage to R. clamitans. Within R. clamitans we
 find two well-supported and geographically divided clades which are
 identified as distinct species by a widely used genetic species
 delimitation method, BPP. However, the two clades exhibit low genealogical
 divergence and population genetic analyses reveal that genetic variation
 within R. clamitans is best described by a pattern of IBD rather than
 independently evolving lineages. We conclude that R. clamitans is indeed a
 single species and the subspecies concept is of limited use. Our analysis
 emphasizes how existing approaches can erroneously split species
 characterized by continuous genetic variation and highlights the power of
 combining population genetic and phylogenetic perspectives to better
 understand diversity within wide-ranging taxa.
DOI: 10.5061/dryad.gtht76hnm
title: Fishing, predation, and temperature drive herring decline in a large marine ecosystem

description: Since 1960, landings of Atlantic herring have been the greatest of any
 marine species in Canada, surpassing Atlantic cod and accounting for 24%
 of the total seafood harvested in Atlantic Canada. The Scotian Shelf-Bay
 of Fundy herring fisheries (NAFO Division 4VWX) is among Canada’s oldest
 and drives this productivity, accounting for up to 75% of the total
 herring catch in some years. The stocks' productivity and overall
 health have declined since 1965. Despite management measures to promote
 recovery implemented since 2003, biomass remains low and is declining. The
 factors that drive the productivity of 4VWX herring are primarily
 unresolved, likely impeding the effectiveness of management actions on
 this stock. We evaluated potential drivers of herring variability by
 analyzing 52 time-series that describe the temporal and spatial evolution
 of the 4VWX herring population and the physical, ecological, and
 anthropogenic factors that could affect them using structural equation
 models. Variation in herring biomass was best accounted for by the
 exploitation rate's negative effect and the geographic distribution
 of fishing and recruitment. Thermal phenology and temperature adversely
 and egg predation positively impacted the early life stage mortality rate
 and, ultimately, adult biomass. These findings are broadly relevant to
 fisheries management, but particularly for 4VWX herring, where the current
 management approach does not consider their early life stage dynamics or
 assess them within the ecosystem or climate change contexts.
description: We assembled data that included spatial and temporal variation in
 NAFO Division 4VWX herring across different life stages, the exploitation
 dynamics, and the biological and environmental factors that may influence
 herring. Data sources related to changes in the mean states, seasonal
 dynamics (timing, amplitude), and community composition of the plankton or
 larval assemblages that herring interact with, the type and intensity of
 fishing pressure, predation and competition were obtained or calculated
 from the stock assessments, peer-reviewed publications, at-sea surveys,
 ships of opportunity, and remote sensing are listed in Table 1. From these
 data, 52 time series were developed (Table 2).  Five of the series
 describe the temporal variability in larval, juvenile, and adult herring
 dynamics; the remaining 47 describe the environmental, biological, and
 anthropogenic factors that could drive them. A full description of the
 data sources and methods to calculate these indices are in the
 Supplementary Information (SI). The indices are organized within eight
 categories (Table 2): 1) Intrinsic (Herring; n=5); 2) Anthropogenic (n=5);
 3) Competition (n=1); 4) Predation (n=6); 5) Plankton (n=4); 6) Physical
 (n=22); 7) Prey (n=2); 8) Phenology (n=7). Both raw and imputed datasets
 are provided.
DOI: 10.5061/dryad.612jm644q
title: GWAS results conditioned on coding variants

description: The research detailed in Connally et al. 2021
 (https://www.medrxiv.org/content/10.1101/2021.06.08.21258515v2) requires
 GWAS summary statistics for non-coding variants without the effects of
 nearby coding variants.
description: For GWAS on type II diabetes (Mahajan et al. 2018), Crohn disease
 (Liu et al. 2015, Goyette et al. 2015), ulcerative colitis (Liu et al.
 2015, Goyette et al. 2015), and breast cancer (Zhang et al. 2020), the
 effects of coding variants were removed from summary statistics using
 conditional and joint analysis (COJO, Yang et al. 2012). For LDL
 cholesterol, HDL cholesterol, and height, GWAS were run from UKBB data
 using coding variants as covariates. The coding SNPs to condition on are
 selected as described in Connally et al. (2021).
description: These GWAS do not measure all associations, only those of
 non-coding variants.
DOI: 10.5061/dryad.31zcrjdn4
title: Identifying relationships between multi-scale social-ecological factors to explore ungulate health in a Western Kazakhstan rangeland

description: 1. Rangelands are multi-use landscapes which are socially and ecologically
 important in different ways. Among other interactions, shared use
 of rangelands by wildlife and livestock can lead to disease transmission.
 Understanding wildlife and livestock health and managing disease
 transmission in rangelands requires an integration of social and
 ecological knowledge. 2. Using the example of Western Kazakhstan, home to
 two types of ungulate hosts, the critically-endangered saiga antelopes,
 Saiga tatarica, and livestock, we conducted a cross-scale analysis of
 social-economic, ecological and climatic factors that contribute to
 transmission of diseases. We focused on Gastro-intestinal Nematodes (GINs)
 because they are transmitted between hosts that share pasture and they
 affect ungulate fitness. We used an interdisciplinary
 social-ecological methods approach which included conducting fecal egg
 counts of GINs in saigas and livestock, semi-structured interviews and
 focus group discussions with livestock owners and herders in the region,
 and triangulation of information through secondary sources. 3. Livestock
 rearing was done in two ways a) village-based livestock and b) outlying
 farms. The latter overlapped more with saigas. Village-based livestock had
 significantly higher worm burdens than those on outlying farms, which had
 comparable burdens to saigas. Various factors exacerbate GIN
 prevalence and transmission: Veterinary services are minimal; both saiga
 and livestock numbers are increasing; and changing climate is increasing
 farmers' dependence on shared pastures for hay production. It will be
 crucial for saiga conservationists to engage in multi-pronged conservation
 interventions, which are evaluated and adapted through the lens of rural
 livelihoods and the livestock health on which they depend. 4. Synthesis
 and Application: Our work provides researchers and practitioners
 with an avenue to better understand complex inter-relationships
 and plan interventions within rangelands, while viewing host health from
 an interdisciplinary perspective - ultimately working towards wildlife
 conservation whilst safeguarding livelihoods across the world’s
 rangelands.
DOI: 10.5061/dryad.vt4b8gtt5
title: Data from: Invasive herbaceous respond more negatively to elevated ozone concentration than native species

description: Aim: Many studies show that increase in ground-level ozone (O3) has
 adverse effects on plant growth. Due to high phenotypic plasticity,
 invasive species is considered to be more adaptable to elevated O3 than
 native species. This idea is only tested by the very limited studies
 comparing invasive weeds with crops. However, whether it holds remains
 unclear when comparing invasive species with their co-occurring native
 species in natural systems. Location: China Methods: We performed an
 open-top chamber experiment growing six congeneric pairs of invasive and
 native species with and without competition under ambient (approximately
 43 ppb) and elevated O3 (approximately 89 ppb) concentrations to test
 whether the growth responses to elevated O3 concentrations differ between
 invasive and native species. Results: Our results revealed that elevated
 O3 had a significant negative effect on both invasive and native species.
 In particular, elevated O3 reduced the aboveground biomass and damaged the
 leaves of invasive species significantly more than those of native
 species. Main conclusions: Our study indicates that elevated O3
 concentration has a stronger adverse effect on invasive species than on
 native species. Therefore, increasing O3 pollution might suppress plant
 invasion, and thus invasive species might expand their distribution more
 easily to the area with lower O3 pollution in the future.
description: All data were collected from this experiment.
description: The terms of 'NA' in the dataset represents the missing
 values. Two pots of plants
 experienced drought in the
 experiment, which were also
 indicated in the dataset (see the 'Note' column). The unit of
 biomass is gram. The unit of height is centimeter. Regarding any question on the data, please contact Dr. Yan Li (yan.li@uni-konstanz.de) or Dr. Yanjie Liu (liuyanjie@iga.ac.cn).
DOI: 10.5061/dryad.ns1rn8pv6
title: Raw holograms frames of Bacillus Subtilis at different temperatures

description: We describe a system for high-temperature investigations of bacterial
 motility using a digital holographic microscope completely submerged in
 heated water. Temperatures above 90 ºC could be achieved, with a constant
 5 ºC offset between the sample temperature and the surrounding water bath.
 Using this system, we observed active motility in Bacillus subtilis up to
 66 ºC. As temperatures rose, most cells became immobilized on the surface,
 but a fraction of cells remained highly motile at distances of &gt;
 100 µm above the surface. Suspended non-motile cells showed Brownian
 motion that scaled consistently with temperature and viscosity. A novel
 open-source automated tracking package was used to obtain 2D tracks of
 motile cells and quantify motility parameters, showing that swimming speed
 increased with temperature until ~40 ºC, then plateaued. These findings
 are consistent with the observed heterogeneity of B. subtilis populations,
 and represent the highest reported temperature for swimming in this
 species. This technique is a simple, low-cost method for quantifying
 motility at high temperatures and could be useful for investigation of
 many different cell types, including thermophilic archaea.
description: Data were acquired using a custom, open-source software package,
 DHMx (https://github.com/dhm-org/dhm_suite). The
 holograms for each recording were either median subtracted (as we
 described previously (Bedrossian et al., 2020)) or frame-to-frame
 subtracted then reconstructed in amplitude using Fiji
 (ImageJ)(RRID:SCR_002285) (Schindelin et al., 2012).  Reconstructions were
 performed using the angular spectrum method (Mann et al., 2005)
 implemented in a custom plug-in described in detail elsewhere (Cohoe et
 al., 2019) and available from our update site
 (https://github.com/sudgy/). Bacteria were tracked using a custom
 software package, Holographic Examination for Life-like Motility (HELM)
 (https://github.com/JPLMLIA/OWLS-Autonomy), which was developed to autonomously detect, track, and characterize motile cells
description: Datasets used in this study <strong>33 degrees (corrected to
 28)</strong> 2.07
 17-04 3-27 
 12-47 <strong>39 degrees (corrected to
 34)</strong> From
 2-07  14-22 From 3-27
 13-48 From 3/21
 14-04 <strong>49
 degrees (corrected to 44)</strong> 02/07 18-05 03/21 14-33 <strong>66 degrees (corrected to
 61)</strong> 02/07
 19-10 03/21 15-39
 <strong>70 degrees (corrected
 to 66)</strong> From
 2.07 19-25 From 3/21
 15-53 <strong>89
 degrees (corrected to 84)</strong> From 2.07 21-02 Heat shock 3/27 15-48 (51 deg) 3/27 16-51 60 deg Dead Cells: 2/14 14:32 (34deg corrected to
 29) 2/14 14:46 (39deg
 corrected to 34) 2/14 15:36
 (54deg corrected to 49) 2/14 16<em>:</em>16 (64deg
 corrected to 59) 2/14 16:59
 (74deg corrected to 69) 2/14 18:24 (88deg corrected to
 83)
DOI: 10.5061/dryad.b8gtht7dm
title: Data from: A new species of genus Russula subsect. Ilicinae (Russulaceae) from Kashmir Himalaya based on morphology and molecular phylogeny

description: Russula indoilicis is proposed herein as a new mushroom taxon from the
 Union Territory of Jammu and Kashmir, India based on morphological
 features and ITS-based molecular phylogeny. This species belongs to
 Russula subg. Heterophyllidia subsect. Ilicinae. Russula indoilicis is
 characterized by light grey to greyish orange pileus, white lamellae
 turning light orange to golden yellow or golden brown to darker with age,
 basidiospores with isolated spines and small warts that never form any
 reticulum, ixotrichoderm nature of pileipellis (covered with thick gluten
 layer), hymenial cystidia mainly with appendiculate apex and
 ectomycorrhizal with Cedrus deodara dominated coniferous forests. A
 detailed description accompanied with colour photographs of the
 basidiomata, illustrations of the main anatomical features, nrITS-based
 molecular phylogeny and comprehensive comparisons with similar species is
 provided.
description: # Data from: A new species of genus Russula subsect. Ilicinae
 (Russulaceae) from Kashmir Himalaya based on morphology and molecular
 phylogeny
 [https://doi.org/10.5061/dryad.b8gtht7dm](https://doi.org/10.5061/dryad.b8gtht7dm) ## Description of the data and file structure This is the aligned file of Internal transcribed spacer region (nrITS) of Russula subject. Ilicinae. This is also .fas file. ## Sharing/Access information Data was derived from the following sources: * Sequences derived from dried mushrooms samples.
DOI: 10.5061/dryad.63xsj3v3n
title: Top-down effects override climate forcing on reproductive success in a declining sea duck

description: Population performance is predicted to be more strongly influenced by
 detrimental species interactions such as predation under benign climatic
 conditions, and by climate forcing under harsh conditions, reflected in
 geographical gradients in biotic interaction strength. Less appreciated is
 the potential for site-specific changes in drivers with the advent of
 anthropogenic alteration of predator-prey relationships, including apex
 predator restoration and spread of invasive predators. Particularly
 interesting is the relative impact of climate and biotic interactions on
 population performance when these conflict. In this 31-year study
 (1990-2020), we revisit a common eider (Somateria mollissima) population
 from SW Finland, Baltic Sea, fifteen years on from an earlier study
 showing that climate warming positively affected reproductive parameters
 and performance. However, the population is simultaneously exposed to
 increasing predation by the rapidly recovering native apex predator and
 invasive mammals. Based on the current population trend, we predicted (i)
 a weakening of the previously documented positive effects of a warming
 climate on vital rates, (ii) intensified predation, and (iii) increasing
 top-down control of vital rates and accompanying population decline. Five
 out of seven breeding parameters (annual spread in female body condition,
 breeding phenology and synchrony, interval between arrival and breeding,
 fledgling production) were best explained by predation indices, whereas
 climate signals (winter NAO, Baltic Sea maximum ice cover) on breeding
 parameters have weakened. Particularly intriguing is that the previous
 positive association between mild ice winters and subsequent reproductive
 output has disappeared during the past 15 years, highlighting the
 non-linear nature of climate change responses. Indirect predation effects
 (selective disappearance, changed reproductive strategies, nest-site
 selection and population age distribution) can potentially explain also
 the remaining breeding parameters (annual mean body condition and clutch
 size). The observed regime shift in predation risk appears to prevent this
 now endangered population from reaping the potential benefits of a warming
 climate.
description: The 31-year data set covers 1990-2020, but there are some missing
 values. Thus, data on eider breeding parameters were unavailable from the
 breeding population of common eiders from Tvärminne in 1992, a final brood
 count at Tvärminne was not conducted in 1993, and migration data from the
 Hanko Bird Observatory was lacking from 1990.