cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5j56v
title: Data from: Shifting baselines on a tropical forest frontier: extirpations drive declines in local ecological knowledge

description: The value of local ecological knowledge (LEK) to conservation is
 increasingly recognised, but LEK is being rapidly lost as indigenous
 livelihoods change. Biodiversity loss is also a driver of the loss of LEK,
 but quantitative study is lacking. In our study landscape in SW China, a
 large proportion of species have been extirpated. Hence, we were
 interested to understand whether species extirpation might have led to an
 erosion of LEK and the implications this might have for conservation. So
 we investigated peoples' ability to name a selection of birds and
 mammals in their local language from pictures. Age was correlated to
 frequency of forest visits as a teenager and is likely to be closely
 correlated to other known drivers of the loss of LEK, such as declining
 forest dependence. We found men were better at identifying birds overall
 and that older people were better able to identify birds to the species as
 compared to group levels (approximately equivalent to genus). The effect
 of age was also stronger among women. However, after controlling for these
 factors, species abundance was by far the most important parameter in
 determining peoples' ability to name birds. People were unable to
 name any locally extirpated birds at the species level. However, contrary
 to expectations, people were better able to identify extirpated mammals at
 the species level than extant ones. However, extirpated mammals tend to be
 more charismatic species and several respondents indicated they were only
 familiar with them through TV documentaries. Younger people today cannot
 experience the sights and sounds of forest animals that their parents grew
 up with and, consequently, knowledge of these species is passing from
 cultural memory. We suggest that engaging older members of the community
 and linking the preservation of LEK to biodiversity conservation may help
 generate support for conservation.
description: Analysis
 codeR
 code for analysis conducted in our studyAnalysis_final.RData file for birdsComma separated text file of the bird dataBirds.csvData file for mammalsComma separated text file of mammal dataMammals.csv
DOI: 10.5061/dryad.gn714
title: Data from: Do cities represent sources, sinks or isolated islands for urban wild boar population structure?

description: Urban sprawl has resulted in the permanent presence of large mammal
 species in urban areas, leading to human–wildlife conflicts. Wild boar Sus
 scrofa are establishing a permanent presence in many cities in Europe,
 with the largest German urban population occurring in Berlin. Despite
 their relatively long-term presence, there is little knowledge of
 colonization processes, dispersal patterns or connectivity of
 Berlin's populations, hampering the development of effective
 management plans. We used 13 microsatellite loci to genotype 387 adult and
 subadult wild boar from four urban forests, adjacent built-up areas and
 the surrounding rural forests. We applied genetic clustering algorithms to
 analyse the population genetic structure of the urban boar. We used
 approximate Bayesian computation to infer the boar's colonization
 history of the city. Finally, we used assignment tests to determine the
 origin of wild boar hunted in the urban built-up areas. The animals in
 three urban forests formed distinct genetic clusters, with the remaining
 samples all being assigned to one rural population. One urban cluster was
 founded by individuals from another urban cluster rather than by rural
 immigrants. The wild boar that had been harvested within urban built-up
 areas was predominantly assigned to the rural cluster surrounding the
 urban area, rather than to one of the urban clusters. Synthesis and
 applications. Our results are likely to have an immediate impact on
 management strategies for urban wild board populations in Berlin, because
 they show that there are not only distinct urban clusters, but also
 ongoing source–sink dynamics between urban and rural areas. It is
 therefore essential that the neighbouring Federal States of Berlin and
 Brandenburg develop common hunting plans to control the wild boar
 population and reduce conflicts in urban areas.
description: Wild boar Berlin
 datasetPopulation genetic data
 from 13 microsattelite loci for 387 adult and subadult wild boar from
 Berlin and the Federal State Bandenburg which were collected between 2012
 and 2015.Datafile_Dryad.txt
DOI: 10.5061/dryad.1c700
title: Data from: Characterizing behavioural ‘characters’: an evolutionary framework

description: Biologists often study phenotypic evolution assuming that phenotypes
 consist of a set of quasi-independent units that have been shaped by
 selection to accomplish a particular function. In the evolutionary
 literature, such quasi-independent functional units are called
 ‘evolutionary characters’, and a framework based on evolutionary
 principles has been developed to characterize them. This framework mainly
 focuses on ‘fixed’ characters, i.e. those that vary exclusively between
 individuals. In this paper, we introduce multi-level variation and thereby
 expand the framework to labile characters, focusing on behaviour as a
 worked example. We first propose a concept of ‘behavioural characters’
 based on the original evolutionary character concept. We then detail how
 integration of variation between individuals (cf. ‘personality’) and
 within individuals (cf. ‘individual plasticity’) into the framework gives
 rise to a whole suite of novel testable predictions about the evolutionary
 character concept. We further propose a corresponding statistical
 methodology to test whether observed behaviours should be considered
 expressions of a hypothesized evolutionary character. We illustrate the
 application of our framework by characterizing the behavioural character
 ‘aggressiveness’ in wild great tits, Parus major.
description: dataData necessary to
 replicate all the analyses.
DOI: 10.5061/dryad.3d00d
title: Data from: Shifts in plant functional strategies over the course of wheat domestication

description: 1. Human selection, changes in environmental conditions and management
 practices drove the phenotypic trajectory of crops during domestication.
 The characterization of the crop domestication syndrome lies mostly on
 reproductive characters. However, biophysical and ecophysiological
 constraints during vegetative growth are also at play and can strongly
 impact crop phenotypes. It has been argued that a broadened examination of
 crop phenotypes through a functional trait-based lens should improve our
 understanding of the domestication syndrome. 2. We used a collection of 39
 genotypes representative of key steps during tetraploid wheat
 domestication, and grew them in a common garden experiment. We quantified
 the vegetative phenotype of each genotype through the measurements of 13
 functional traits related to root, leaf and whole-plant dimensions. 3. In
 modern cultivars, compared to ancestral forms, leaf longevity was shorter
 while net photosynthetic rate, leaf production rate and nitrogen content
 were higher. Modern cultivars had a shallower root system and exhibited a
 larger proportion of fine roots, preferring to invest biomass above rather
 than below ground. We found ancestral forms to be integrated phenotypes
 characterized by coordination between above- and below-ground functioning.
 Conversely, in modern forms, human selection appeared to have broken this
 coordination and to have generated a new type of network of trait
 covariations. 4. Synthesis and applications. The examination of leaf,
 root, and whole-plant traits of wheat accessions indicated a strong shift
 in plant functional strategies over the course of domestication. Elite
 genotypes tended to better optimize resource-use acquisition strategies
 than ancestral ones. The characterization of the crop phenotype based on
 vegetative traits thus suggests a much more complete domestication
 syndrome. Our findings highlight the benefits of using a functional
 trait-based characterization of crop phenotypes to document the extent of
 domestication syndrome and to further advance the agroecological
 management of cereals.10-Oct-2017
description: MiLES16
 datasetThe MiLES16 database is
 a dataset of 15 root, leaf and plant functional traits compiled from our
 own experiment in 2016. Data are provided for 39 accessions from 3
 sub-species of Triticum turgidum. It contains a copy of the main data
 files used for this paper, as well as a description of the studied
 variables (see below).MiLES2016.xls
DOI: 10.5061/dryad.p0t7770
title: Data from: Interacting stressors matter: diet quality and virus infection in honey bee health

description: Honey bee population declines have been linked to multiple stressors,
 including reduced diet diversity and increased exposure to understudied
 viral pathogens. Despite interest in these factors, few experimental
 studies explored the interaction between diet diversity and viral
 infection in honey bees. Here, we used a mixture of laboratory cage and
 small semi-field nucleus hive experiments to determine how these factors
 interact. We found that high quality diets (polyfloral pollen and high
 quality single-source pollen) have the potential to reduce mortality in
 the face of infection with Israeli acute paralysis virus (IAPV).). There
 was a significant interaction between diet and virus infection on
 mortality, even in the presence of high virus titers, suggesting that good
 diets can help bees tolerate virus infection. Further, we found that
 extreme stress in the form of pollen starvation in conjunction with IAPV
 infection increase exiting behavior from small experimental hives.
 Finally, we showed that higher quality pollen diets have significantly
 higher iron and calcium content, suggesting micronutrient deficiencies
 could be an under explored area of bee nutrition.
description: Dolezal_virusnutrition
 data archive
DOI: 10.5061/dryad.7p2cv
title: Data from: Priority effects are interactively regulated by top-down and bottom-up forces: evidence from wood decomposer communities

description: Both top-down (grazing) and bottom-up (resource availability) forces can
 determine the strength of priority effects, or the effects of species
 arrival history on the structure and function of ecological communities,
 but their combined influences remain unresolved. To test for such
 influences, we assembled experimental communities of wood-decomposing
 fungi using a factorial manipulation of fungivore (Folsomia candida)
 presence, nitrogen availability, and fungal assembly history. We found
 interactive effects of all three factors on fungal species composition and
 wood decomposition 1 year after the fungi were introduced. The strength of
 priority effects on community structure was affected primarily by nitrogen
 availability, whereas the strength of priority effects on decomposition
 rate was interactively regulated by nitrogen and fungivores. These results
 demonstrate that top-down and bottom-up forces jointly determine how
 strongly assembly history affects community structure and function.
description: sample.dataContains sample metadata along with measurements related to wood decomposition during the experiment.species.prevalenceResults of LH-PCR characterization of fungal species prevalence. For each of the 10 fungal species used in the experiments, the number of wood-disc subsamples (out of 9) are indicated for each microcosm.collembola.csvCategorical observations of Collembola abundance before each harvest (0 = no individual in the microcosm; 1 = 1-10 individuals; 2 = 10-100 individuals; and 3 = more than 100 individuals).
DOI: 10.5061/dryad.2q2s4
title: Data from: Diversity and preserved shell coloration patterns of Miocene Conidae (Neogastropoda) from an exposure of the Gatun Formation, Colon Province, Panama

description: Extant members of the neogastropod family Conidae (cone snails) are
 renowned for their often dazzling shell coloration patterns and venomous
 feeding habits. Many cone snail species have also been described from the
 fossil record, but to date have been little used to understand the
 evolutionary history of extant clades. The cone snail fauna of the Miocene
 Gatun Formation of Colón Province, Panama is especially important for
 understanding the temporal and biogeographic history of tropical American
 Conidae. Intensive, focused collecting from an exposure of the lower Gatun
 Formation (deposited ca. 11-10 Ma) resulted in the discovery of nearly 900
 specimens of Conidae. Remarkably, many of these well-preserved specimens
 exhibit revealed coloration patterns when exposed to ultraviolet light.
 The fluorescing coloration patterns were used in conjunction with other
 features of shell morphology to differentiate species and, in most cases,
 evaluate their potential relationships to members of the extant tropical
 American fauna. Nine species are fully described from this locality, one
 of which is recognized as new: Conus (Stephanoconus) woodringi n. sp. At
 least one, and perhaps more, Conidae species are also present at the study
 locality. The diversity of this Conidae fauna is considered moderate
 relative to other recently analyzed tropical American fossil assemblages.
 The phylogenetic diversity of the assemblage, however, is noteworthy: six
 of the ten species can be confidently assigned to six different clades of
 extant Conidae, providing potentially useful calibration points for future
 phylogenetic studies.
description: Supplementary data set
 1.FLMNH specimen lots from
 UF locality YN020 that were studied as part of this investigation,
 including species assignment, catalog number, and number of specimens in
 each lot.Hendricks-SuppTable1.xlsxSupplementary data set 2.Shell measurement data for individual specimens; * indicates a measurement impacted by slight damage to specimen, ** indicates a measurement captured from a digital image.Hendricks-SuppTable2.xlsxSupplementary data set 3.Supplementary data set 3. Subsutural flexure measurement data for individual specimens.Hendricks-SuppTable3.xlsx
DOI: 10.5061/dryad.90r60
title: Data from: Population-dependent effects of ocean acidification

description: Understanding the response of marine fauna to this change is critical for
 understanding the effects of OA. Population level variation in OA
 tolerance is highly relevant and important in the determination of
 ecosystem resilience and persistence, but has received little focus to
 date. In this study, whether OA has the same biological consequences in
 high salinity-acclimated population vs a low-salinity acclimated
 population of the same species was investigated in the marine isopod
 Idotea balthica. The populations were found to have physiologically
 different responses to ocean acidification. While survival rate was
 similar between the two study populations at a future CO2 level of 1000
 ppm and both populations showed increased oxidative stress, the metabolic
 rate and osmoregulatory activity differed significantly between the two
 populations. The results of this study demonstrate that the physiological
 response to OA of populations from different salinities can vary.
 Population level variation, and the environment provenance of individuals
 used in OA experiments should be taken into account for the evaluation and
 prediction of climate change effects.
description: Wood et
 al.PRSB2016_Supporting dataRaw
 data
DOI: 10.5061/dryad.2hd320d
title: Data from: Unraveling the mechanisms underlying pulse dynamics of soil respiration in tropical dry forests

description: Tropical dry forests are already undergoing changes in the quantity and
 timing of rainfall, but there is great uncertainty over how these shifts
 will affect belowground carbon (C) cycling. While it has long been known
 that dry soils quickly release carbon dioxide (CO2) upon rewetting, the
 mechanisms underlying the so-called ‘Birch effect’ are still debated.
 Here, we quantified soil respiration pulses and their biotic predictors in
 response to simulated precipitation events in a regenerating tropical dry
 forest in Costa Rica. We also simulated the observed rewetting CO2 pulses
 with two soil carbon models: a conventional model assuming first-order
 decay rates of soil organic matter, and an enzyme- catalyzed model with
 Michaelis–Menten kinetics. We found that rewetting of dry soils produced
 an immediate and dramatic pulse of CO2, accompanied by rapid
 immobilization of nitrogen into the microbial biomass. However, the
 magnitude of the rewetting CO2 pulse was highly variable at fine spatial
 scales, and was well correlated with the size of the dissolved organic C
 pool prior to rewetting. Both the enzyme-catalyzed and conventional models
 were able to reproduce the Birch effect when respiration was coupled
 directly to microbial C uptake, although models differed in their ability
 to yield realistic estimates of SOC and microbial biomass pool sizes and
 dynamics. Our results suggest that changes in the timing and intensity of
 rainfall events in tropical dry forests will exert strong influence on
 ecosystem C balance by affecting the dynamics of microbial biomass growth.
description: Waring&Powers_ERL_for Dryad
DOI: 10.5061/dryad.9522r
title: Data from: Suppression of reproductive characteristics of the invasive plant Mikania micrantha by sweet potato competition

description: Background: As a means of biologically controlling Mikania micrantha
 H.B.K. in Yunnan, China, the influence of sweet potato [Ipomoea batatas
 (L.) Lam.] on its reproductive characteristics was studied. The trial
 utilized a de Wit replacement series incorporating six ratios of sweet
 potato and M. micrantha plants in 25 m2 plots over two years. Results:
 Budding of M. micrantha occurred at the end of September; flowering and
 fruiting occurred from October to February. Flowering phenology of M.
 micrantha was delayed (P&lt;0.05), duration of flowering and fruiting
 was reduced (P&lt;0.05) and duration of bud formation was increased
 (P&lt;0.05) with increasing proportions of sweet potato. Reproductive
 allocation, reproductive investment and reproductive index of M. micrantha
 were significantly reduced (P&lt;0.05) with increasing sweet potato
 densities. Apidae bees, and Calliphoridae or Syrphidae flies were the most
 abundant visitors to M. micrantha flowers. Overall flower visits decreased
 (P&lt;0.05) as sweet potato increased. Thus the mechanism by which
 sweet potato suppressed sexual reproduction in M. micrantha was
 essentially two-fold: causing a delay in flowering phenology and reducing
 pollinator visits. The number, biomass, length, set rate, germination
 rate, and 1000-grain dry weight of M. micrantha seeds were suppressed
 (P&lt;0.05) by sweet potato competition. With proportional increases
 in sweet potato, sexual and asexual seedling populations of M. micrantha
 were significantly reduced (P&lt;0.05). The mortality of both seedling
 types increased (P&lt;0.05) with proportional increases in sweet
 potato. Conclusions: These results suggest that sweet potato significantly
 suppresses the reproductive ability of the invasive species M. micrantha,
 and is a promising alternative to traditional biological control and other
 methods of control. Planting sweet potato in conjunction with other
 control methods could provide a comprehensive strategy for managing M.
 micrantha. The scenario of controlling M. micrantha by utilizing a crop
 with a similar growth form may provide a useful model for similar
 management strategies in other systems.
description: Data for suppression of
 reproductive characteristics of Mikania micrantha by sweet potato
 competitionData for the following
 parameters for Mikania micrantha in experiments when grown with sweet
 potato in different ratios (each set of parameters on a separate tab on
 the excel file): flowering phenology, pollinators, flowering
 characteristics, seeds, population
DOI: 10.15468/dl.gde55m
title: Occurrence Download

description: A dataset containing 1337 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Philadelphus sericanthus",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 1337 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001062-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.57027hc
title: Data from: Cross-species screening of microsatellite markers for individual identification of snow petrel Pagodroma nivea and Wilson’s storm petrel Oceanites oceanicus in Antarctica

description: Seabirds are important indicators of marine ecosystem health. Species
 within the order Procellariiformes are the most abundant seabird species
 group distributed from warm tropical to cold temperate regions including
 Antarctica. There is a paucity of information on basic biology of the
 pelagic seabird species nesting on the Antarctic continents, and long-term
 studies are required to gather data on their population demography,
 genetics and other ecological parameters. Under the ‘Biology and
 Environmental Sciences’ component of the Indian Antarctic programme,
 long-term monitoring of Antarctic biodiversity is being conducted. In this
 paper, we describe results of cross-species screening of a panel of 12 and
 10 microsatellite markers in two relatively little studied seabird species
 in Antarctica, the snow petrel Pagodroma nivea and the Wilson's storm
 petrel Oceanites oceanicus, respectively. These loci showed high
 amplification success and moderate levels of polymorphism in snow petrel
 (mean no. of alleles 7.08 ± 3.01 and mean observed heterozygosity 0.35 ±
 0.23), but low polymorphism in Wilson's storm petrel (mean no. of
 alleles 3.9 ± 1.3 and mean observed heterozygosity 0.28 ± 0.18). The
 results demonstrate that these panels can unambiguously identify
 individuals of both species (cumulative PIDsibs for snow petrel is 3.7 ×
 10−03 and Wilson's storm petrel is 1.9 × 10−02) from field-collected
 samples. This work forms a baseline for undertaking long-term genetic
 research of these Antarctic seabird species and provides critical insights
 into their population genetics.
description: Pande et
 al_2018_microsatelliteGenotype data generated
 from cross-species microsatellite markers for Snow Petrel and
 Wilson's Storm Petrel.
DOI: 10.5061/dryad.2cn83
title: Data from: Inbreeding promotes female promiscuity

description: The widespread phenomenon of polyandry (mating by females with multiple
 males) is an evolutionary puzzle, because females can sustain costs from
 promiscuity, while full fertility can be provided by a single male. Using
 the red flour beetle, Tribolium castaneum, we identify major fitness
 benefits of polyandry to females under inbreeding, when the risks of
 fertilization by incompatible male haplotypes are especially high. Fifteen
 generations after inbred populations had passed through genetic
 bottlenecks, we recorded increased levels of female promiscuity compared
 to non-inbred controls, most likely due to selection from prospective
 fitness gains through polyandry. These data illustrate how this common
 mating pattern can evolve if population genetic bottlenecks increase the
 risks of fitness depression due to fertilization by sperm carrying
 genetically incompatible haplotypes.
description: Tribolium - Inbreeding
 II - DRYADAll data used to
 generate statistics presented in the article.