cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.nq2j7
title: Data from: Functional diversity loss with increasing livestock grazing intensity in drylands: the mechanisms and their consequences depend on the taxa

description: 1. Overgrazing is one of the main drivers of desertification in drylands,
 and livestock production is expected to increase in the next decades. The
 analysis of functional diversity can clarify the effects of increasing
 livestock grazing on ecosystem functioning. 2. We assess the effect of
 livestock grazing intensity on the relationship between taxonomic (TDH)
 and functional diversity (FDQ) of plants, ants and small mammals, as well
 as on within-trait diversity. We compared results using two indices of
 taxonomic diversity (Shannon and Simpson). We used structural equation
 modelling (SEM) to assess the causal relationship between grazing
 intensity, TDH, FDQ and decomposition rate for each taxa. 3. Correlation
 between TDH vs. FDQ varied across assemblages and seasons, but was
 consistent between different indices of taxonomic diversity. A similar
 trajectory of TDH vs. FDQ under land-use intensification was found for all
 taxa, with a correlated loss of species and functional traits. Also,
 within-trait diversity was negatively affected by increasing grazing
 pressure. Vegetation and small mammal SEM models show that increasing
 grazing intensity had a strong and direct effect on decomposition rate.
 The ant SEM model was the only one that showed an indirect effect of
 grazing on decomposition through FDQ. TDH had no effect on decomposition
 for either taxa. 4. We found higher niche differentiation in animal than
 in plant assemblages. In vegetation, several species seem to have similar
 trait diversity (i.e. redundancy), perhaps due to a dominant role of
 environmental constraints. These results were consistent among diversity
 indices. But increasing disturbance negatively affected TDH vs. FDQ in all
 assemblages in a similar way. Livestock grazing affected decomposition
 rate directly, and indirectly only through the effect of ants FDQ. 5.
 Synthesis and applications. Under increasing grazing intensity all plant
 and animal assemblages respond with a mirrored reduction in taxonomic and
 functional diversity, although vegetation seems to have higher functional
 redundancy. Our results are robust to diversity indices, showing that
 several taxa respond similarly to land-use intensification, despite
 differences in the mechanism behind it. This may facilitate sustainable
 management. Notably, increasing grazing intensity affects decomposition
 rate through a stronger direct than indirect effect. The stronger direct
 effect of livestock on decomposition rate, rather than indirectly through
 functional diversity, suggests that changes in structure may be more
 important than changes in community composition.
description: Chillo et
 al_DataSampling sites
 locations, Index values for every sampling site, R scripts for SEM
 analyses and TDvsFD trajectory analysesChillo et
 al_data.zip
DOI: 10.5061/dryad.1476
title: Data from: Ecological partitioning among parapatric cryptic species

description: Geographic range differences among species may result from differences in
 their physiological tolerances. In the intertidal zone, marine and
 terrestrial environments intersect to create a unique habitat, across
 which physiological tolerance strongly influences range. Traits to cope
 with environmental extremes are particularly important here because many
 species live near their physiological limits and environmental gradients
 can be steep. The snail Melampus bidentatus occurs in coastal salt marshes
 in the western Atlantic and the Gulf of Mexico. We used sequence data from
 one mitochondrial (COI) and two nuclear markers (histone H3 and a
 mitochondrial carrier protein, MCP) to identify three cryptic species
 within this broad-ranging nominal species, two of which have partially
 overlapping geographic ranges. High genetic diversity, low population
 structure, and high levels of migration within these two overlapping
 species suggest that historical range limitations do not entirely explain
 their different ranges. To identify microhabitat differences between these
 two species, we modeled their distributions using data from both marine
 and terrestrial environments. Although temperature was the largest factor
 setting range limits, other environmental components explained features of
 the ranges that temperature alone could not. In particular, the
 interaction of precipitation and salinity likely sets physiological limits
 that lead to range differences between these two cryptic species. This
 suggests that the response to climatic change in these snails will be
 mediated by changes to multiple environmental factors, and not just to
 temperature alone.
description: AliceDennis_sequences.zipAlignment files in FASTA format. There are 4 species and three genes, each in an individual file. The 4 species are: (1) Melampus coffeus, (2) Melampus bidentatus cryptic species NORTH, (3) Melampus bidentatus cryptic species SOUTH, (4) Melampus bidentatus cryptic species GULF. The 3 genes are: (1) Histone H3 (2) Cytochrome oxidase I (CO1) and (3) MCP, which has been Probable mitochondrial phosphate carrier protein.
DOI: 10.5061/dryad.f57g6h5
title: Data from: Female mate choice is a reproductive isolating barrier in Heliconius butterflies

description: In sexually reproducing organisms, speciation involves the evolution of
 reproductive isolating mechanisms that decrease gene flow. Premating
 reproductive isolation, often the result of mate choice, is a major
 obstacle to gene flow between species because it acts earlier in the life
 cycle than other isolating barriers. While female choice is often
 considered the default mode in animal species, research in the butterfly
 genus Heliconius, a frequent subject of speciation studies, has focused on
 male mate choice. We studied mate choice by H. cydno females by pairing
 them with either conspecific males or males of the closely related species
 H. pachinus. Significantly more intraspecific trials than interspecific
 trials resulted in mating. Because male courtship rates did not differ
 between the species when we excluded males that never courted, we
 attribute this difference to female choice. Females also performed more
 acceptance behaviours towards conspecific males. Premating isolation
 between these two species thus entails both male and female mate choice,
 and female choice may be an important factor in the origin of Heliconius
 species.
description: female.choice.dataCSV file with data from each female choice trial (including those that had to be excluded from the results due to no courtship). README file contains descriptions of each variable/column.female.choice.analysisR code for analyzing female choice data, as in paper.
DOI: 10.15468/dl.tbt72r
title: Occurrence Download

description: A dataset containing 18726 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Chinese Taipei",
 "OccurrenceStatus is Present",
 "TaxonKey is Papilionidae",
 {
 "or" : [
 "Year 2013-2025",
 "Year 2013-2025"
 ]
 }
 ]
}

 The dataset includes 18726 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001370-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.f20v3
title: Data from: Population dynamics of a northern-adapted mammal: disentangling the influence of predation and climate change

description: Community structure and interspecific interactions are particularly
 vulnerable to rapidly changing climatic regimes. Recent changes in both
 climate and vertebrate community assemblages have created a unique
 opportunity to examine the impacts of two dynamic forces on population
 regulation. We examined the effects of warming winter conditions and the
 reestablishment of a previously extirpated predator, the fisher (Martes
 pennanti), on regulatory mechanisms in a northern-adapted mammal, the
 porcupine (Erethizon dorsatum), along their southern range boundary. Using
 a long-term (17-year) capture–recapture data set, we (1) quantified the
 impacts of climate change and increased fisher predation on the survival
 of adult porcupines at their regional southern terminus, (2) assessed
 recruitment (via both adult fecundity and juvenile survival) of
 porcupines, and (3) modeled the relative importance of predation and
 winter conditions on the demography and population growth rate (λ). Severe
 winters and abundant predators interacted synergistically to reduce adult
 survivorship by as much as 44%, while expanding predator populations led
 to near reproductive failure among porcupines. Increasing predatory
 pressure, disruptions in this community module, and more frequent extreme
 winter weather events led to predicted extirpation within 50 years,
 whereas in the absence of predators, the population was viable. Our
 results provide a mechanistic understanding behind distributional shifts
 resulting from climate change and may be broadly relevant for predicting
 future distributional shifts in other northern-adapted mammalian species.
description: Capture
 MatrixAnnual capture histories
 for porcupines at Sandhill Wildlife Area, WI from 1996 to
 2013.Spring_fall_KM_datafileWeekly monitoring record radio-collared juvenile and adult porcupines at Sandhill Wildlife Area from 23 April through 15 October 2012.
DOI: 10.5061/dryad.4qb79
title: Data from: Ecological speciation of bacteriophage lambda in allopatry and sympatry

description: Understanding the conditions that allow speciation to occur is difficult
 because most research has focused on either long-lived organisms or
 asexual microorganisms. We propagated bacteriophage λ, a virus with rapid
 generations and frequent recombination, on two Escherichia coli host
 genotypes that expressed either the LamB or OmpF receptor. When supplied
 with either single host (allopatry), λ improved its binding to the
 available receptor while losing its ability to use the alternative. When
 evolving on both hosts together (sympatry), the viruses split into two
 lineages with divergent receptor preferences. Although the level of
 divergence varied among replicates, some lineages evolved reproductive
 isolation via genetic incompatibilities. This outcome indicates that,
 under suitable conditions, allopatric and sympatric speciation can occur
 with similar ease.
description: Meyer Science 2016 Fig
 1AData collected for
 results shown in figure 1a, see notes within the file and the manuscript
 for further guidance.Meyer Science 2016 Fig
 1BData collected for
 results shown in figure 1b, see notes within the file and the manuscript
 for further guidance.Meyer Science 2016 Fig
 2Data
 collected for results shown in figure 2, see notes within the file and the
 manuscript for further guidance.Meyer Science 2016 Fig
 3Data
 collected for results shown in figure 3, see notes within the file and the
 manuscript for further guidance.Meyer Science 2016 Fig
 4CData collected for
 results shown in figure 4c, see notes within the file and the manuscript
 for further guidance.Meyer Science 2016 Fig
 S1Data collected for
 results shown in figure S1, see notes within the file and the manuscript
 for further guidance.
DOI: 10.5061/dryad.q4222
title: Data from: Decline and recovery of a large carnivore: environmental change and long-term trends in an endangered brown bear population

description: Understanding what factors drive fluctuations in the abundance of
 endangered species is a difficult ecological problem but a major
 requirement to attain effective management and conservation success. The
 ecological traits of large mammals make this task even more complicated,
 calling for integrative approaches. We develop a framework combining
 individual-based modelling and statistical inference to assess alternative
 hypotheses on brown bear dynamics in the Cantabrian range (Iberian
 Peninsula). Models including the effect of environmental factors on
 mortality rates were able to reproduce three decades of variation in the
 number of females with cubs of the year (Fcoy), including the decline that
 put the population close to extinction in the mid-nineties, and the
 following increase in brown bear numbers. This external effect prevailed
 over density-dependent mechanisms (sexually selected infanticide and
 female reproductive suppression), with a major impact of climate driven
 changes in resource availability and a secondary role of changes in human
 pressure. Predicted changes in population structure revealed a nonlinear
 relationship between total abundance and the number of Fcoy, highlighting
 the risk of simple projections based on indirect abundance indices. This
 study demonstrates the advantages of integrative, mechanistic approaches
 and provides a widely applicable framework to improve our understanding of
 wildlife dynamics.
description: AppendixE
DOI: 10.5061/dryad.451c4s2
title: Data from: Experimental study on diesel engine EGR performance and Optimum EGR Rate Determination Method

description: In order to study deeply the Exhaust gas recirculation（EGR）performance of
 marine diesel engines，a venturi high-pressure exhaust gas recirculation
 device was established to overcome the exhaust gas reflow problem in a
 certain type turbocharged diesel engine. With the device, the EGR
 performance test is accomplished and an optimal EGR decision-making
 optimization method based on grey correlation coefficient modified is
 proposed. The results show that the venturi tube EGR can basically meet
 the injection requirements of high-pressure exhaust gas and makes good
 results to the diesel engine . Through the venturi tube EGR, the NOX
 emissions reduces significantly with the maximum drop of 30.6%. The
 explosive pressure in cylinder reduces with the EGR rate increases, and
 the cylinder pressure curve shows a single peak at low-speed conditions
 and double peaks at high-speed condition. However, the fuel consumption
 rate, NO, and smoke have been negatively affected. Due to small samples,
 the traditional evaluation method is difficult to determine the optimal
 EGR rate reasonably, while the proposed method can effectively solve this
 problem. It can weaken the shortcomings of subjective judgment and greatly
 improve the rationality of decision-making results.
description: experimental
 dataexperiment
 data.xlsx
DOI: 10.5061/dryad.1pm64
title: Data from: Parallel evolution of behaviour during independent host-shifts following maize introduction into Asia and Europe

description: Maize was introduced into opposite sides of Eurasia 500 years ago, in
 Western Europe and in Asia. This caused two host-shifts in the
 phytophagous genus Ostrinia, O. nubilalis (the European corn borer; ECB)
 and O. furnacalis (the Asian corn borer; ACB) are now major pests of maize
 worldwide. They originated independently from Dicot-feeding ancestors,
 similar to O. scapulalis (the Adzuki bean borer; ABB). Unlike other
 host-plants, maize is yearly harvested, and harvesting practices impose
 severe mortality on larvae found above the cut-off line. Positive geotaxis
 in the ECB has been proposed as a behavioural adaptation to harvesting
 practices, allowing larvae to move below the cut-off line and thus escape
 harvest-mortality. Here we test whether the same behavioural adaptation
 evolved independently in Europe and in Asia. We sampled eight genetically
 differentiated ECB, ACB and ABB populations in France and China and
 monitored geotaxis through the entire larval development in artificial
 stacks mimicking maize stems. We find that all ECB and ACB populations
 show a similar tendency to move down during the latest larval stages, a
 behaviour not observed in any European or Asian ABB population. The
 behaviour is robustly expressed regardless of larval density, development
 mode or environmental conditions. Our results indicate that maize
 introduction triggered parallel behavioural adaptations in Europe and
 Asia, harvest selection presumably being the main driver.
description: Raw data table for
 Calcagno et al. 2016 articleEach row in an
 artificial stacks. Cells contain counts of individuals (larvae and pupae,
 separately)Calcagno_et_al_2016_data.zip
DOI: 10.5061/dryad.0dk3n
title: Data from: Polygyny without wealth: popularity in gift games predicts polygyny in BaYaka Pygmies

description: The occurrence of polygynous marriage in hunter–gatherer societies, which
 do not accumulate wealth, remains largely unexplored since resource
 availability is dependent on male hunting capacity and limited by the lack
 of storage. Hunter–gatherer societies offer the greatest insight in to
 human evolution since they represent the majority of our species'
 evolutionary history. In order to elucidate the evolution of
 hunter–gatherer polygyny, we study marriage patterns of BaYaka Pygmies. We
 investigate (i) rates of polygyny among BaYaka hunter–gatherers; (ii)
 whether polygyny confers a fitness benefit to BaYaka men; (iii) in the
 absence of wealth inequalities, what are the alternative explanations for
 polygyny among the BaYaka. To understand the latter, we explore
 differences in phenotypic quality (height and strength), and social
 capital (popularity in gift games). We find polygynous men have increased
 reproductive fitness; and that social capital and popularity but not
 phenotypic quality might have been important mechanisms by which some male
 hunter–gatherers sustained polygynous marriages before the onset of
 agriculture and wealth accumulation.
description: Chaudhary et al. public
 dataData used for analysis
 in: Polygyny without wealth: popularity in gift games predicts polygyny in
 BaYaka Pygmies (Chaudhary et al. 2015).
DOI: 10.5061/dryad.3h12j8d3
title: Data from: Do secondary forests act as refuges for old growth forest animals? Recovery of ant diversity in the Atlantic forest of Brazil

description: The extent to which secondary forests occupying degraded and abandoned
 lands provide suitable habitat for forest-adapted species is an important
 conservation issue in times of vanishing old growth forests. We used ants
 (Hymenoptera: Formicidae), a functionally important and diverse group of
 invertebrates, to investigate the recovery of soil taxa during secondary
 forest succession in the Atlantic Forest of Southern Brazil. We compared
 the resilience of epigeic vs. hypogeic ant assemblages. For this purpose
 we established 27 sites that encompassed a chronosequence from pastures to
 old growth forests on two contrasting soil types. Our results are based on
 a collection of 35 508 individuals in 40 genera. Richness and composition
 of ant assemblages in secondary forests have recovered slowly and have not
 approached conditions typical of old growth forests. The distribution of
 genera along the successional stages was arranged in a nested pattern
 where ant genera of younger successional stages were a subset of genera
 present in older stages. Edaphic conditions had no influence on the
 recovery process. Overall, richness of ants was lower at study sites with
 water-logged soils than at sites where soils did not exhibit hydromorphic
 properties. The hypogeic ant assemblage recovered more slowly than the
 epigeic assemblage. Our results show that secondary forests do not act as
 refuges for many forest-adapted animals which are currently restricted to
 discontinuous patches of old growth forest in the highly endangered
 Atlantic Forest of Brazil. Moreover, estimated recovery times of 50 to
 several hundred years suggest it would take much longer than previously
 presumed for complete recolonization.
description: Ants_litterRelative abundance of ant genera collected from the leaf litter in 23 study sites.Ants_soilRelative abundance of ant genera collected from soil samples in 27 study sites.study_sites_coordinatesSpatial coordinates for 27 study sites. Coordinates are reported in Lat/Long decimal degrees, SAD69 (South_American_Datum_1969).
DOI: 10.5061/dryad.p2501
title: Data from: Predicting ecological and phenotypic differentiation in the wild: a case of piscivorous fish in a fishless environment

description: Environmental variation drives ecological and phenotypic change. How
 predictable is differentiation in response to environmental change?
 Answering this question requires the development and testing of
 multifarious a priori predictions in natural systems. We employ this
 approach using Gobiomorus dormitor populations that have colonized inland
 blue holes differing in the availability of fish prey. We evaluated
 predictions of differences in demographics, habitat use, diet, locomotor
 and trophic morphology, and feeding kinematics and performance between
 G. dormitor populations inhabiting blue holes with and without fish prey.
 Populations of G. dormitor independently diverged between prey regimes,
 with broad agreement between observed differences and a priori
 predictions. For example, in populations lacking fish prey, we observed
 male-biased sex ratios, a greater use of shallow-water habitat, and larger
 population diet breadths as a result of greater individual diet
 specialization. Furthermore, we found predictable differences in body
 shape, mouth morphology, suction generation capacity, strike kinematics,
 and feeding performance on different prey types, consistent with the
 adaptation of G. dormitor to piscivory when coexisting with fish prey and
 to feeding on small invertebrates in their absence. The results of the
 present study suggest great potential in our ability to predict population
 responses to changing environments, which is an increasingly important
 capability in a human-dominated, ever-changing world.
description: Gobiomorus dormitor
 divergence between prey regimesData associated with
 Gobiomorus dormitor populations inhabiting blue holes in the presence and
 absence of fish prey. Demographic and habitat data was collected using
 underwater survey techniques. Diet data was collected using gastric lavage
 and stomach dissections. Morphology data was taken from standardized
 photographs of live individuals and feeding/kinematics and performance
 data was calculated from video-taped lab trials. See “Predicting
 ecological and phenotypic differentiation in the wild: a case of
 piscivorous fish in a fishless environment, Martin, Ryan, McGee, Matthew,
 Langerhans, Brian” for a detailed description of the
 methods.sleeper
 data.xlsx
DOI: 10.5061/dryad.vj4vc
title: Data from: High-density native-range species affects the invasive plant Chromolaena odorata more strongly than species from its invasive range

description: Invasive plant species often form dense mono-dominant stands in areas they
 have invaded, while having only sparse distribution in their native
 ranges, and the reasons behind this phenomenon are a key point of research
 in invasive species biology. Differences in species composition between
 native and invasive ranges may contribute to the difference in
 distribution status. In this study, we found that the high-density
 condition had a more negative effect on C. odorata than the low-density
 condition when co-grown with neighbor plants from its native range in
 Mexico, while this pattern was not in evidence when it was grown with
 neighbors from its invasive range in China. Different competitive ability
 and coevolutionary history with C. odorata between native-range neighbors
 and invasive-range neighbors may lead to the inconsistent patterns.
description: Data from: High-density
 native-range species affects the invasive plant Chromolaena odorata more
 strongly than species from its invasive rangeData.xlsx