cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5q783
title: Data from: Experimental evidence that parasites drive eco-evolutionary feedbacks

description: Host resistance to parasites is a rapidly evolving trait that can
 influence how hosts modify ecosystems. Eco-evolutionary feedbacks may
 develop if the ecosystem effects of host resistance influence selection on
 subsequent host generations. In a mesocosm experiment, using a recently
 diverged (&lt;100 generations) pair of lake and stream three-spined
 sticklebacks, we tested how experimental exposure to a common fish
 parasite (Gyrodactylus spp.) affects interactions between hosts and their
 ecosystems in two environmental conditions (low and high nutrients). In
 both environments, we found that stream sticklebacks were more resistant
 to Gyrodactylus and had different gene expression profiles than lake
 sticklebacks. This differential infection led to contrasting effects of
 sticklebacks on a broad range of ecosystem properties, including
 zooplankton community structure and nutrient cycling. These ecosystem
 modifications affected the survival, body condition, and gene expression
 profiles of a subsequent fish generation. In particular, lake juvenile
 fish suffered increased mortality in ecosystems previously modified by
 lake adults, whereas stream fish showed decreased body condition in stream
 fish-modified ecosystems. Parasites reinforced selection against lake
 juveniles in lake fish-modified ecosystems, but only under oligotrophic
 conditions. Overall, our results highlight the overlapping timescales and
 the interplay of host–parasite and host–ecosystem interactions. We provide
 experimental evidence that parasites influence host-mediated effects on
 ecosystems and, thereby, change the likelihood and strength of
 eco-evolutionary feedbacks.
description: EcoEvoParasite_rawData_Dryadphysiological measurements and gene expression data from all fish in the experiment plus ecosystem dataEcoEvoParasite_Data_Dryad.xlsx
DOI: 10.5061/dryad.6rs6q
title: Data from: The importance of naming cryptic species and the conservation of endemic subterranean amphipods

description: Molecular taxonomy often uncovers cryptic species, reminding us that
 taxonomic incompleteness is even more severe than previous thought. The
 importance of cryptic species for conservation is poorly understood.
 Although some cryptic species may be seriously threatened or otherwise
 important, they are rarely included in conservation programs as most of
 them remain undescribed. We analysed the importance of cryptic species in
 conservation by scrutinizing the South European cryptic complex of the
 subterranean amphipod Niphargus stygius sensu lato. Using uni- and
 multilocus delineation methods we show that it consists of 15 parapatric
 and sympatric species, which we describe using molecular diagnoses. The
 new species are not mere “taxonomic inflation” as they originate from
 several distinct branches within the genus and coexist with no evidence of
 lineage sharing. They are as evolutionarily distinct as average nominal
 species of the same genus. Ignoring these cryptic species will
 underestimate the number of subterranean endemics in Slovenia by 12 and in
 Croatia by four species, although alpha diversity of single caves remains
 unchanged. The new taxonomy renders national Red Lists largely obsolete,
 as they list mostly large-ranged species but omit critically endangered
 single-site endemics. Formal naming of cryptic species is critical for
 them to be included in conservation policies and faunal listings.
description: COI_alnCAOSCOI alignment used to determine diagnostic nucleotides using CAOS softwareCOIcaos.fasta28SrRNA_alnCAOS28S rRNA alignment used to determine diagnostic nucleotides using CAOS software28Scaos.fastaITS_alnCAOSInternal Transcribed Spacer (ITS) alignment used to determine diagnostic nucleotides using CAOS softwareITScaos.fasta
DOI: 10.5061/dryad.q8p95mg
title: Data from: Bean yield and economic response to fertilizer in eastern and southern Africa

description: Bean (Phaseolus vulgaris L.) is important in sub-Saharan Africa for human
 dietary protein. Low yields are attributed to biotic and abiotic
 constraints including inadequate nutrient availability. Research was
 conducted to determine nutrient response functions for bean production
 areas of Kenya, Mozambique, Rwanda, Tanzania, and Zambia. Mean trial
 yields ranged from 0.32 to 2.60 and 1.72 to 2.89 Mg ha-1 for bush and
 climbing bean, respectively. Response to N was common except in Kenya and
 Mozambique. The main effect of P and K increased yield in Rwanda only but
 P and K effects were inconsistent in Zambia. Mean yield increase with a
 diagnostic treatment containing Mg-S-Zn-B was 0.41 and 0.58 Mg ha-1 for
 bush and climbing bean, respectively, in Rwanda and 0.36 Mg ha-1 in
 Tanzania with no effects in other countries. In Rwanda, the economically
 optimal rates (EOR) of N, P and K were &gt;20 kg ha-1, but higher with
 less costly fertilizer. Variations in EOR for growth type varied with
 nutrient. The EOR of N in Tanzania and Zambia were generally &lt;10 kg
 ha-1, depending on fertilizer costs, but P and K application had profit
 potential only in Rwanda. Yield, agronomic efficiency and profit to cost
 ratio, averaged across nutrients, were -36, 54 and 96% greater,
 respectively, with nutrients applied at 50% compared with 100% of EOR.
 Profit potential for the EOR of N is high when expected yield is
 &gt;1.5 Mg ha-1 but responses to P, K and Mg-S-Zn-B vary with bean
 production area.
description: ESA Bean Nutrient
 Response DatasetThis data was generated
 from collaborative research in five countries of eastern and southern
 Africa using a similar treatment structure for determination of bean
 response functions to fertiizer N, P, and K and for the diagnosis of
 deficiencies for Mg, S, Zn and B.
DOI: 10.5061/dryad.1783
title: Data from: Strong population genetic structure in a broadcast-spawning Antarctic marine invertebrate

description: Although studies of population genetic structure are commonplace, a strong
 bias exists towards species from low latitudes and with relatively poor
 dispersal capabilities. Consequently, we used 280 Amplified Fragment
 Length Polymorphism (AFLP) bands to explore patterns of genetic
 differentiation among eight populations of a high latitude
 broadcast-spawning marine mollusc, the Antarctic limpet Nacella concinna.
 Over three hundred individuals were sampled along a latitudinal gradient
 spanning the Antarctic Peninsula from Adelaide Island to King George
 Island (67º–62º S), then to Signy Island (60ºS) and South Georgia (54ºS).
 Populations from the Antarctic Peninsula exhibited little genetic
 structure, but were themselves strongly differentiated from both Signy and
 South Georgia. This finding was analytically highly robust and implies the
 presence of significant oceanographic barriers to gene flow in a species
 long regarded as a classic example of a widely-dispersing
 broadcast-spawner.
description: Strong population
 genetic structure in a broadcast-spawning Antarctic marine
 invertebrateAFLP dataset comprising
 Nacella concinna Antarctic Peninsula populationsDryadsubmission200710.xlsx
DOI: 10.5061/dryad.k5st3
title: Data from: Studying long-term, large-scale grassland restoration outcomes to improve seeding methods and reveal knowledge gaps

description: Studies are increasingly investigating effects of large-scale management
 activities on grassland restoration outcomes. These studies are providing
 useful comparisons among currently used management strategies, but not the
 novel strategies needed to rapidly improve restoration efforts. Here we
 illustrate how managing restoration projects adaptively can allow
 promising management innovations to be identified and tested. We studied
 327 Great Plains fields seeded after coal mining. We modelled plant
 responses to management strategies to identify the most effective
 previously used strategies for constraining weeds and establishing desired
 plants. Then, we used the model to predict responses to new strategies our
 analysis identified as potentially more effective. Where established, the
 weed crested wheatgrass (Agropyron cristatum L.) increased through time,
 indicating a need to manage establishment of this grass. Seeding
 particular grasses reduced annual weed cover, and because these grasses
 appeared to become similarly abundant whether sown at low or high rates,
 low rates could likely be safely used to reduce seeding costs. More
 importantly, lower than average grass seed rates increased cover of
 shrubs, the plants most difficult to restore to many grassland ecosystems.
 After identifying grass seed rates as a driver, we formulated model
 predictions for rates below the range managers typically use. These
 predictions require testing but indicated atypically low grass seed rates
 would further increase shrubs without hindering long-term grass stand
 development. Synthesis and applications. Designing management around
 empirically based predictions is a logical next step towards improving
 ecological restoration efforts. Our predictions are that reducing grass
 seed rates to atypically low levels will boost shrubs without compromising
 grasses. Because these predictions derive from the fitted model, they
 represent quantitative hypotheses based on current understanding of the
 system. Generating data needed to test and update these hypotheses will
 require monitoring responses to shifts in management, specifically shifts
 to lower grass seed rates. A paucity of data for confronting hypotheses
 has been a major sticking point hindering adaptive management of most
 natural resources, but this need not be the case with degraded grasslands,
 because ongoing restoration efforts around the globe are providing
 continuous opportunities to monitor and manage processes regulating
 grassland restoration outcomes.
description: predictor and response
 dataData on environmental
 and management predictors and vegetation responses.full dataset formatted for
 others2.csv
DOI: 10.5061/dryad.dt3k0
title: Data from: Stochastic faunal exchanges drive diversification in widespread Wallacean and Pacific island lizards (Squamata: Scincidae: Lamprolepis smaragdina)

description: Aim: Widespread species found in disturbed habitats are often expected to
 be human commensals. In island systems, this association predicts that
 dispersal will be mediated by humans. We investigated the biogeographical
 relationships among populations of a widespread tree skink that inhabits
 coastal forest and human-cultivated plantations in Southeast Asia. We
 sought to determine whether populations of the emerald tree skink,
 Lamprolepis smaragdina, dis- persed via mechanisms that were not
 human-mediated (‘natural’ dispersal) or whether dispersal was mediated by
 humans. The latter scenario predicts low levels of genetic differentiation
 across a species’ range, coupled with a genetic signature of recent range
 expansion. Location: Southeast Asia, the Philippines, Wallacea and the
 south-western Pacific. Methods: We analysed sequences of mitochondrial DNA
 from 204 samples collected throughout the range of this species. We use
 phylogenetic and popu- lation genetic methods to distinguish between
 predicted geographical patterns of genetic variation that might indicate
 natural or human-mediated dispersal. Results: In contrast to predictions
 derived from similar studies of taxonomy and natural history, we found L.
 smaragdina to be characterized by highly structured and seemingly
 geographically stable mitochondrial gene lineages. Main conclusions: Our
 results demonstrate a novel pattern of widespread species distribution,
 never before observed in vertebrates of the Indo-Australian Archipelago.
 Although this widespread and highly dispersive species is capable of
 long-distance dispersal, and has a clear history of over-water dispersal,
 it exhibits sharp genetic differentiation across its range. Our results
 suggest that random waif dispersal has been a pervasive ongoing phenomenon
 throughout the evolutionary history of this species.
description: Lamprolepis nexus file
 for MrBayesAligned sequences of ND2
 gene for all samples with MrBayes blocks to run the different partitioning
 schemes presented in the paper.Lamp.JBioGeo.2013.nex
DOI: 10.5061/dryad.gq3fk
title: Data from: HS1BP3 negatively regulates autophagy by modulation of phosphatidic acid levels

description: A fundamental question is how autophagosome formation is regulated. Here
 we show that the PX domain protein HS1BP3 is a negative regulator of
 autophagosome formation. HS1BP3 depletion increased the formation of
 LC3-positive autophagosomes and degradation of cargo both in human cell
 culture and in zebrafish. HS1BP3 is localized to ATG16L1- and
 ATG9-positive autophagosome precursors and we show that HS1BP3 binds
 phosphatidic acid (PA) through its PX domain. Furthermore, we find the
 total PA content of cells to be significantly upregulated in the absence
 of HS1BP3, as a result of increased activity of the PA-producing enzyme
 phospholipase D (PLD) and increased localization of PLD1 to
 ATG16L1-positive membranes. We propose that HS1BP3 regulates autophagy by
 modulating the PA content of the ATG16L1-positive autophagosome precursor
 membranes through PLD1 activity and localization. Our findings provide key
 insights into how autophagosome formation is regulated by a novel
 negative-feedback mechanism on membrane lipids.
description: Compiled Lipidomics
 Data_NCOMMS-16-13893-ARaw data of MS
 lipidomics datasets used in Fig. 5a and Supplementary Fig. 4c. Data are
 from HEK cells treated with non-targeting (Control) or HS1BP3 siRNA
 starved for 2 hrs (mean +/- SEM., n = 6). See the Methods section for a
 full description of the Methods used.
DOI: 10.5061/dryad.nt7s243
title: Data from: A mechanistic assessment of the relationship between gut morphology and endozoochorous seed dispersal by waterfowl

description: Many plants and invertebrates rely on internal transport by animals for
 long-distance dispersal. Their dispersal capacity is greatly influenced by
 interactions with the animal’s digestive tract. Omnivorous birds adjust
 their digestive tract morphology to seasonally variable diets. We
 performed feeding trials in waterfowl to unravel how changing organ size,
 in combination with seed size, affects dispersal potential. We subjected
 captive mallards to mimics of summer (animal-based), winter (plant-based)
 and intermediate diets, and analysed gut passage of seeds before and after
 the treatment (trials 1 and 2). To test the effect of gut morphology on
 seed digestion, we measured digestive organ size after euthanasia. Three
 hours before euthanasia, differently sized seeds were fed to test how seed
 size affects gut passage by determining their relative position in the
 digestive tract (trial 3). Trials 1 and 2 showed that intact seed passage
 was lower in the plant-based than in the animal-based diet group.
 Retention time changed only within groups, decreasing in the animal-based,
 and increasing in the plant-based diet group. No post-diet differences in
 organ size were detected, probably due to large between-individual
 variation within groups. Digestive tract measures did not explain
 variation in seed survival or retention time. Trial 3 revealed that small
 seeds pass the digestive tract rapidly, while large seeds are retained
 longer, particularly in the gizzard. Differential retention in the
 gizzard, the section where seeds can be destroyed, is likely why larger
 seeds have a lower probability to pass the digestive tract intact. These
 results confirm that rapid, flexible adaptation to diet shifts affects
 seed digestion in waterfowl, although we could not conclusively relate
 this to organ size. Large inter-individual variation in digestive
 efficiency between mallards feeding on the same diet may provide
 opportunities for seed dispersal in the field throughout the annual cycle.
description: Seed retrieval and gut
 morphology dataSeed retrieval data of
 three separate feeding trials in mallards before and after adaptation to
 experimental diets. Additionally includes post-experiment size
 measurements of mallard digestive tracts.Dataset_Kleyheeg_et_al_2018_Ecology_Evolution.xls
DOI: 10.5061/dryad.7c652r8
title: Data from: Do correlated responses to multiple environmental changes exacerbate or mitigate species loss?

description: Biological communities face multiple global changes simultaneously, and
 predicting how they will respond remains a key challenge. Co-tolerance
 theory offers a framework for understanding how species-level responses to
 multiple stressors affect community properties. Co-tolerance theory
 predicts that positive correlations in species responses (i.e., species
 that are susceptible to one stressor are more likely to be highly
 susceptible to a second) lessen total species loss, essentially because
 species cannot be eliminated from a community twice. However, it is
 unclear whether several of the tenets of co-tolerance theory describe
 real-world communities, and what consequences result from such deviations.
 Here, we use an empirical dataset of bird community response to land-use
 change over a climate gradient to examine co-tolerance theory’s tenet that
 environmental changes only harm species (not benefit them). We show that
 this tenet is not met, and then use simulations to examine how predictions
 of total species richness and community intactness vary when multiple
 environmental changes both harm and benefit particular species in the
 community. Finally, we conduct a sensitivity analysis, examining how the
 average species response to environmental change, as well as the variance
 among species, can further alter predictions. Overall, we find that
 predictions of co-tolerance theory can break down when communities contain
 species that benefit from some environmental changes. As a result, the
 presence of multiple environmental changes can either compound or mitigate
 species loss when species’ responses are positively correlated, preventing
 a one-size-fits-all statement regarding the effects of correlated
 responses. This finding highlights the need to carefully consider the
 underlying mechanisms of community change when making policy assessments
 regarding the consequences of correlations of species responses to
 environmental impacts.
description: Frishkoff_2018_Bird_DataZipped archive raw bird observation data collected in 2016 in Guanacaste peninsula, Costa Rica as well as point count information and species names in separate csv files.
DOI: 10.5061/dryad.58m67
title: Data from: Emissions and char quality of flame-curtain "Kon Tiki" kilns for farmer-scale charcoal/biochar production

description: Pyrolysis of organic waste or woody materials yields charcoal, a stable
 carbonaceous product that can be used for cooking or mixed into soil, in
 the latter case often termed "biochar". Traditional kiln
 technologies often used for charcoal production are slow and without
 treatment of the pyrolysis gases, . This resultings in emissions of gases
 (mainly methane and carbon monoxide) and aerosols that are both toxic and
 contributes to greenhouse gas emissions, the most important being methane,
 carbon monoxide and aerosols. In rRetort kilns where pyrolysis gases are
 led back to a combustion chamber. This are faster and can reduce emissions
 substantially, but isare costly and consumes a considerable amount of
 valuable ignition material such as wood during start-up. To overcome these
 problems, a novel type of technology, the Kon-Tiki flame curtain
 pyrolysisrocess, is proposed. This technology combines the simplicity of
 the traditional kiln with the combustion of pyrolysis gases in the flame
 curtain (similar toachieved in the retort kilns)., also avoiding use of
 external fuel for start-up. By adding feedstock layer by layer in an open
 cone-shaped kiln, the pyrolysis gases formed underneath the flame curtain
 are combusted, at the same time creating enough heat to avoid use of
 external fuel for start-up. The rResults from this aA field study in Nepal
 using various feedstocksmixtures of the ubiquitous invasive shrub
 Eupatorium, rice husk and wood as feedstocks showed char yields of 22 ± 5
 % on a dry weight basis and 40 ± 11 % on a C basis. Total pyrolysis time
 was one to four hours per m3 of produced biochar. Biochars with high C
 contents (76 ± 9%; n=57), average surface areas (11 to 215 m2 g-1), low
 EPA16 - PAHs (2.3 to 6.6 mg kg-1) and high CECs (43 to 217
 cmolc/kg)(average for all feedstocks, mainly woody shrubs) were obtained,
 in. Overall, the analytical data of all biocharsthe produced with this new
 technologybiochars complianceed with the European Biochar Certificate
 (EBC). The mMean emission factors for the flame curtain kilns found in
 this study were (in g kg-1 biochar for all feedstocks); carbon dioxide
 (CO2)= 4300 ± 1700, carbon monoxide (CO)= 54 ± 35, non-methane volatile
 organic compounds (NMVOC)= 6 ± 3, methane (CH4)= 30 ± 60, aerosols (total
 suspended particles, TSP, derived from (PM10) = 11 ± 15, total products of
 incomplete combustion (PIC)= 100 ± 83 and nitric oxides (NOx)= 0.4 ± 0.3.
 The Kon Tikiflame curtain kilns emitted statistically significantly
 (p&lt;0.05) lower amounts of CO, PIC and NOx than retort and
 traditional kilns, and higher amounts of CO2. With benefits such as high
 quality biochar, low emission, no need for start-up fuel, fast pyrolysis
 time and, importantly, easy and cheap construction and operation the flame
 curtain technology represent thus a promising possibility for sustainable
 rural biochar production.
description: Gas Emissions Feb 2016
 final_for-DryadMeasurement data of gas
 emissionsStatistical tests in
 R
DOI: 10.5061/dryad.56k55
title: Data from: Male-female coevolution in the wild: evidence from a time series in Artemia franciscana

description: Sexual conflicts are ubiquitous in nature and are expected to lead to an
 antagonistic coevolution between the sexes. This coevolutionary process is
 driven by selection on sexually antagonistic traits that can either be
 directional or fluctuating. In this study, we used dormant cysts of
 Artemia franciscana, collected in the same population in three different
 years over a 23-year period (corresponding to ~160 generations in this
 system), to investigate male-female coevolution in natural conditions over
 time. We performed a cross experiment study where reproduction of females
 mated to males from the past, present or future was monitored until death.
 In agreement with a model of ‘fluctuating selection’, we found that
 females survived better and had longer interbrood intervals when mated
 with their contemporary males compared to when mated with males from the
 future or the past. However, female weekly and lifetime reproductive
 successes displayed no differences between contemporary and
 non-contemporary matings. Finally, the coevolutionary patterns (‘arms race
 dynamics’ or ‘fluctuating selection dynamics’) possibly acting on female
 relative fitness could not be discriminated. This study is the first
 direct demonstration that the process of male – female coevolution,
 previously revealed by experimental evolution in laboratory artificial
 conditions, can occur in nature on a short evolutionary time scale.
description: Dataset Rode et al
 2011Experimental data in
 Excel format