cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p9f07
title: Data from: Regime shifts in marine communities: a complex systems perspective on food web dynamics

description: Species composition and habitats are changing at unprecedented rates in
 the world’s oceans, potentially causing entire food webs to shift to
 structurally and functionally different regimes. Despite the severity of
 these regime shifts, elucidating the precise nature of their underlying
 processes has remained difficult. We address this challenge with a new
 analytic approach to detect and assess the relative strength of different
 driving processes in food webs. Our study draws on complexity theory, and
 integrates the network-centric Exponential Random Graph Modeling (ERGM)
 framework developed within the social sciences with community ecology. In
 contrast to previous research, this approach makes clear assumptions of
 direction of causality and accommodates a dynamic perspective on the
 emergence of food webs. We apply our approach in analysing food webs of
 the Baltic Sea before and after a previously reported regime shift. Our
 results show that the dominant food web processes have remained largely
 the same, although we detect changes in their magnitudes. The results
 indicate that the reported regime shift may not be a system-wide shift,
 but instead involve a limited number of species. Our study emphasizes the
 importance of community-wide analysis on marine regime shifts and
 introduces a novel approach to examine food webs.
description: Food web
 dataFood webs used for the
 ERGM analysis.Yletyinen & al
 data.xlsx
DOI: 10.5061/dryad.35h47
title: Data from: Human–wildlife conflict, benefit sharing and the survival of lions in pastoralist community-based conservancies

description: Like many wildlife populations across Africa, recent analyses indicate
 that African lions are declining rapidly outside of small fenced areas.
 Community conservancies – privately protected areas that engage community
 members in conservation – may potentially maintain wildlife populations in
 unfenced pastoralist regions, but their effectiveness in conserving large
 carnivores has been largely unknown until now. We identify drivers of lion
 survival in community conservancies within the Masai Mara ecosystem,
 Kenya, applying mark–recapture analyses to continuous sight–resight
 surveys. We use the number of livestock and human settlements as proxies
 for potential human–lion conflict whilst controlling for environmental
 variables and lion socioecology. Average lion densities within the Mara
 conservancies between 2008 and 2013 (11·87 lions 100 km−2) were 2·6 times
 higher than those previously reported in 2003. Survival rates varied
 amongst prides and were highest for lions utilizing central regions of
 conservancies. The number of livestock settlements (bomas [corrals] and
 manyattas) that were not members of a conservancy, and that fell within a
 pride home-range, had a large negative effect on female survival and was
 the most influential external predictor in models. These non-conservancy
 settlements accounted for 37·2% of total observed variation in survival,
 whereas conservancy settlements, which benefit financially from wildlife
 through their membership, had no effect on lion survival. Internal drivers
 of survival agreed with known ecology and social behaviour including age
 plus a negative effect of male takeovers on cub survival &lt;6 months.
 Vegetation cover, prey availability and the density of grazing livestock
 within a pride's range did not explain patterns in lion survival.
 Synthesis and applications. We show that lion densities have increased
 substantially within the Mara conservancies over the last decade and
 suggest that the creation of community conservancies has benefitted their
 survival. This suggests that lions can survive outside of fenced areas
 within pastoral regions if communities gain benefits from wildlife. We
 highlight the importance of expanding existing conservancies beyond their
 current geographical and political scope and forming buffer zones if
 wildlife ranges outside them. We suggest that changing attitudes to
 predators should be a key goal of community-based conservancies. Further
 work is recommended to identify what specific aspects of conservancy
 membership promote lion survival.
description: Capture histories for
 lions Panthera leoGender, DOB, Pride
 membership and location by conservancy of lions within community
 conservancies north of the Masai Mara, Kenya. Presence/absence (1/0) and
 age category also given for 6 month periods to generate capture history
 (column AB) for mark-recapture analysis with MARK.Dryad
 data.xlsx
DOI: 10.5061/dryad.46d37
title: Data from: Effects of ovarian fluid and genetic differences on sperm performance and fertilization success of alternative reproductive tactics in Chinook salmon

description: In many species, sperm velocity affects variation in the outcome of male
 competitive fertilization success. In fishes, ovarian fluid (OF) released
 with the eggs can increase male sperm velocity and potentially facilitate
 cryptic female choice for males of specific phenotypes and/or genotypes.
 Therefore, to investigate the role of OF on fertilization success, we
 measured sperm velocity and conducted in vitro competitive fertilizations
 with paired Chinook salmon (Oncorhynchus tshawytscha) males representing
 two alternative reproductive tactics, jacks (small sneaker males) and
 hooknoses (large guarding males), in the presence of river water alone and
 OF mixed with river water. To determine the role of genetic differences on
 fertilization success, we genotyped fish at neutral (microsatellites) and
 functional [major histocompatibility complex (MHC) II ß1] markers. We
 found that when sperm were competed in river water, jacks sired
 significantly more offspring than hooknoses, however, in OF there was no
 difference in paternity between the tactics. Sperm velocity was
 significantly correlated with paternity success in river water but not in
 ovarian fluid. Paternity success in OF, but not in river water alone, was
 correlated with genetic relatedness between male and female, where males
 that were less related to the female attained greater paternity. We found
 no relationship between MHC II ß1 divergence between mates and paternity
 success in water or OF. Our results indicate that OF can influence the
 outcome of sperm competition in Chinook salmon, where OF provides both
 male tactics with fertilization opportunities, which may in part explain
 what maintains both tactics in nature.
description: Sperm performance and
 fertilization in jack and hooknose Chinook salmonData sheet 1: Male
 metrics: Includes sperm metrics (velocity in water, velocity in ovarian
 fluid and sperm density) as well as paternity success (water and ovarian
 fluid) for each male. Data sheet 2: Difference between males: Includes
 differences between males in a pair (Jack vs. Hooknose) for sperm density,
 sperm velocity (water and ovarian fluid), paternity, relatedness between
 mates and amino acid divergence (MHC II B1) between mates. Data sheet 3:
 Relatedness and AA divergence: Relatedness and amino acid divergence for
 all male-female combinations used in the study. Data sheet 4: Genotypes:
 Microsatellite and MHC II B1 genotypes. Data sheet 5: MH sequences: DNA
 sequence and GenBank reference for six MHC II B1 alleles found in the
 study.JEB_ART_SpermComp_Lehnert.xlsx
DOI: 10.5061/dryad.g791n
title: Data from: Climatic niche differences between diploid and tetraploid cytotypes of Chamerion angustifolium (Onagraceae)

description: Premise of the study: Polyploidy—the possession of more than two copies of
 each chromosome in the nucleus—is common in flowering plants. Polyploid
 plants can occupy different geographic ranges than their diploid
 progenitors, but the factors responsible for maintaining these range
 differences are poorly understood. Polyploidy can have significant
 physiological consequences, and the present study aims to determine
 whether previously described physiological differences between cytotypes
 are correlated with climatic niches and geographic distributions. Methods:
 Prior research indicates that tetraploid Chamerion angustifolium
 (Onagraceae) are more tolerant of drought and less tolerant of freezing
 than diploids, which suggests that they should occupy a niche that is
 warmer and drier than that of diploids. We extracted climate data for 134
 C. angustifolium populations classified as pure diploid, pure tetraploid,
 or mixed-ploidy. We compared climatic conditions between these population
 categories, and generated ecological niche models to compare their
 geographic distribution with prior qualitative estimates. Key results:
 Pure tetraploid populations occupy habitats that are warmer and drier than
 pure diploid populations. Mixed-ploidy populations occur in habitats that
 are not strictly intermediate between pure diploid and pure tetraploid
 populations, but are as cold as pure diploid populations and have
 intermediate soil moisture deficits. Our niche models were similar to
 previous qualitative estimates of cytotype geographic distribution.
 Conclusions: The correspondence between the physiological tolerances of
 cytotypes, their climatic niches, and their geographic distributions
 suggests that physiological traits are at least partially responsible for
 differences in the realized climatic niches of diploid and tetraploid C.
 angustifolium.
description: ChamerionPopulationDataPopulation information for 134 populations of Chamerion angustifolium sampled across North America, Greenland, Iceland. Includes Lat/Long, Ploidy (Diploid, Mixed-Ploidy, Tetraploid), Information about previous publication, climate data, and PCA axis scores.2014-04-16-NichePaperDryad.xlsx
DOI: 10.5061/dryad.1n834
title: Data from: Sustained costs of growth and the trajectory of recovery

description: 1. Large body size is associated with many fitness advantages. Despite
 this, most species do not grow at their physiological maximum, suggesting
 costs to rapid growth. There are now many empirical examples of trade-offs
 with growth. 2. Despite the ubiquity of physiological delays, few studies
 have evaluated the duration over which growth costs occur. To address this
 question, we measured swimming ability in growth-manipulated Atlantic
 silversides (Menidia mendia). Fish were manipulated to grow at their
 maximum for two weeks and then were put on restricted rations so they grew
 slowly. We then compared swimming ability with fish that had always grown
 slowly. 3. Fast-grown fish had significantly poorer swimming ability, and
 continued to show a prolonged cost of this early period of rapid growth.
 We found that fish fully recovered normal swimming ability after ~1 month
 of growing slowly. Most surprisingly, the trajectory of recovery was not
 monotonic; performance actually decreased before it improved. 4. We
 conclude with a suggestion to develop a better understanding of the
 mechanisms linking growth to performance trade-offs. Our results suggest
 that reduced swimming performance following fast growth is unlikely to be
 completely explained by bioenergetic constraints. Additionally, there is
 need for more nuanced life history theory that incorporates prolonged
 growth costs to increase accuracy of growth rate prediction.
description: Perez and
 Munch_Data_Sustained costs of growth and the trajectory of
 recovery
DOI: 10.5061/dryad.mk58d
title: Data from: Population structure and genetic diversity of native and invasive populations of Solanum rostratum (Solanaceae)

description: Aims: We investigate native and introduced populations of Solanum
 rostratum, an annual, self-compatible plant that has been introduced
 around the globe. This study is the first to compare the genetic diversity
 of Solanum rostratum between native and introduced populations. We aim to
 (1) determine the level of genetic diversity across the studied regions;
 (2) explore the likely origins of invasive populations in China; and (3)
 investigate whether there is the evidence of multiple introductions into
 China. Methods: We genotyped 329 individuals at 10 microsatellite loci to
 determine the levels of genetic diversity and to investigate population
 structure of native and introduced populations of S. rostratum. We studied
 five populations in each of three regions across two continents: Mexico,
 the U.S.A. and China. Important Findings: We found the highest genetic
 diversity among Mexican populations of S. rostratum. Genetic diversity was
 significantly lower in Chinese and U.S.A. populations, but we found no
 regional difference in inbreeding coefficients (FIS) or population
 differentiation (FST). Population structure analyses indicate that Chinese
 and U.S.A. populations are more closely related to each other than to
 sampled Mexican populations, revealing that introduced populations in
 China share an origin with the sampled U.S.A. populations. The
 distinctiveness between some introduced populations indicates multiple
 introductions of S. rostratum into China.
description: Genotype
 data-PONE-D-13-20610This file includes
 genotype data of the paper, “Population structure and genetic diversity of
 native and invasive populations of Solanum rostratum (Solanaceae)."
 We genotyped 329 individuals at 10 microsatellite loci to determine the
 levels of genetic diversity and to investigate population structure of
 native and introduced populations of S. rostratum. We studied five
 populations in each of three regions across two continents: Mexico, the
 U.S.A. and China.
DOI: 10.15468/dl.8kwwvj
title: Occurrence Download

description: A dataset containing 3666461 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Aves",
 "Country is Japan",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3666461 records from 112 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001000-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4jn05
title: Data from: Genetic variation in the shape of cold survival curves in a single fly population suggests potential for selection from climate variability

description: Temperature variation is one of the primary challenges facing ectotherms,
 and the ability to tolerate a range of thermal environments is critical
 for setting current and future species distributions. Low temperature is
 particularly challenging for ectotherms because winter conditions have
 strong latitudinal and temporal variation. Lower lethal temperature (LLT)
 is a common metric of cold tolerance used in studies of local adaptation
 and plasticity. Comparisons of LLT across groups typically assume parallel
 S-shaped survival curves, but genetic variation in the shape of survival
 vs. temperature curves has not been assessed. Here, we measured the
 ability of 36 lines of the Drosophila Genetic Reference Panel (DGRP) to
 survive a 1 h cold shock at seven ecologically relevant low temperatures
 (-1 to -7°C) to create a high resolution response curve for each genotype.
 We observed surprising variation both in the magnitude of survival and the
 shapes of the response curves, with the curves clustering into four
 distinct shapes. To encompass variation in the shapes of these survival
 curves, we developed a new cold tolerance metric, Cumulative Cold
 Tolerance (CCT). By comparing our survival data with climatological data,
 we propose that variation in the shapes of cold survival curves arose from
 weak selection pressure to survive intermediate subzero temperatures in
 this mid-latitude population of flies. Using publicly available genome
 sequence and transcript expression data for these lines, we identified
 several candidate genes associated with CCT, and using transgenic RNAi we
 confirmed a functional role for many of these genes.
description: Teets and Hahn Cold
 Tolerance DataThe spreadsheet has two
 tabs. The first tab includes raw cold tolerance data for the DGRP Core 40.
 Each line was exposed to temperatures from -1 to -7 deg. C in 1 deg. C
 increments. For each line, each temperature was replicated a minimum of
 four times, with each replicate consisting of a vial of ~20 female flies.
 The second tab contains cold tolerance data and cross information for the
 RNAi experiment. F1 Females from each cross were tested for cold tolerance
 at -2, -4, and -6 deg. C. In the table to the right, the lines used for
 each cross are denoted. The "driver line" is the GAL4 line,
 while the "effector line" is the line UAS-RNAi (or control)
 line. The line numbers refer to Bloomington Drosophila Stock Center stock
 numbers.Teets Dryad
 Data.xlsx
DOI: 10.5061/dryad.f468h
title: Data from: No evidence for strong cytonuclear conflict over sex allocation in a simultaneously hermaphroditic flatworm

description: Background: Cytoplasmic sex allocation distorters, which arise from
 cytonuclear conflict over the optimal investment into male versus female
 reproductive function, are some of the best-researched examples for
 genomic conflict. Among hermaphrodites, many such distorters have been
 found in plants, while, to our knowledge, none have been clearly
 documented in animals. Methods: Here we provide a quantitative test for
 cytonuclear conflict over sex allocation in the simultaneously
 hermaphroditic flatworm Macrostomum lignano. We used a quantitative
 genetic breeding design, employing pair-wise crosses of 2 × 15 independent
 inbred lines, to partition the phenotypic variance in several traits
 (including sex allocation) into its nuclear and cytoplasmic components.
 Results: Although the nuclear genetic background had a significant effect
 on all traits analyzed, we found significant cytoplasmic genetic variation
 only for ovary size, there explaining just 4.1% of the variance. A
 subsequent statistical power analysis showed that the experimental design
 had considerable power to detect cytonuclear interactions. Conclusion: We
 conclude that there were no strong effects of cytonuclear conflict in the
 studied populations, possibly because the usually compact mitochondrial
 genomes in animals have a lower evolvability than the large mitochondrial
 genomes in plants or because the sampled populations currently do not
 harbor variation at putative distorter and/or the restorer loci.
description: Vellnow et al. 2017 -
 Cytonuclear conflict DATA
DOI: 10.5061/dryad.964pf
title: Data from: Functional traits of marine macrophytes predict primary production

description: The relationship between community structure and the functioning of
 ecosystems is the subject of ongoing debate. Biological or functional
 trait-based approaches that capture life strategy, morphology and
 behavioural characteristics have received far less attention than
 taxonomic diversity in this context, despite their more intuitive link to
 ecosystem functioning. Macrophyte primary production underpins aquatic
 food webs, regulates benthic and pelagic ecosystems and is a key aspect of
 the global carbon cycle. This study spans a range of aquatic biomes across
 Europe and aims to examine potential for predicting primary production of
 macrophyte communities based on the functional traits of species and
 identify the traits that are the most informative indicators of macrophyte
 production. Macrophyte primary production was assessed based on the oxygen
 production of the whole community, linked to biomasses of selected
 biological traits derived of its component species and analysed using the
 novel boosted regression trees modelling technique. Results showed that
 functional traits derived from macrophyte community data explained most of
 the variation in primary production of macrophyte communities without the
 need to incorporate environmental data on the habitats. Macrophyte primary
 production was influenced by a combination of tolerance, morphology and
 life habit traits; however tolerance traits contributed most of
 variability in macrophyte primary production when all traits were analysed
 jointly. This study also showed the existence of trait clustering as the
 studied trait categories were not fully independent; strong interlinkages
 between and within trait categories emerged. Our study suggests that
 functional trait analysis captures different aspects of ecosystem
 functioning and thereby enables assessing primary production of macrophyte
 communities over geographically distinct areas without extensive taxonomic
 and environmental data. This could result in a novel framework through
 which a simplification of the general procedure of production estimations
 and comparisons across environmental gradients can be achieved.
description: Janes et al Functional
 traits predict production rawdataThis database includes
 the description of the study sites together with associated values of
 macroalgal community production and traits.
DOI: 10.5061/dryad.1984
title: Data from: Short- and long-term effects of egg size and feeding frequency on offspring quality in the collared flycatcher (Ficedula albicollis)

description: 1) Despite the central importance for life-history theory, egg-size
 effects on offspring fitness are still considered ambiguous. Most previous
 studies were only observational and consequently might suffer from
 uncontrolled correlations between egg size and parental/territory quality.
 Even after cross-fostering is performed, direct genetic effects and
 parental adjustment of postnatal care might confound our estimates of
 egg-size effects per se. 2) I performed a full cross-fostering experiment
 in the collared flycatcher (Ficedula albicollis) exchanging the whole
 clutches between pairs of nests. I statistically controlled for direct
 genetic effects and parental feeding frequencies. I followed young until
 recruitment to estimate the long-term effects of egg size and parental
 provisioning. In addition, I compared the effects obtained in the
 cross-fostering experiment with those obtained from a set of unmanipulated
 nests. 3) Egg size per se affected offspring morphology in both the short-
 and long-term, while having no effect on offspring survival and immunity.
 Egg-size effects were not confounded by parental postnatal care and direct
 genetic effects. 4) The number of care-givers was an influential predictor
 of nestling performance. Apart from the variation caused by this factor,
 feeding frequencies had no consistent effect on offspring performance. 5)
 Fitness benefits of large eggs may be difficult to establish due to
 variation of egg-size effects between years and habitats. Feeding
 frequency may affect offspring state but offspring state may also affect
 feeding frequency. Varying causality between feeding rate and offspring
 state may preclude the detection of a positive effect of the former on the
 latter.
description: dataset