cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.zgmsbcc71
title: A comparison between mouse, in silico, and robot odor plume navigation reveals advantages of mouse odor-tracking

description: Localization of odors is essential to animal survival, and thus animals
 are adept at odor-navigation. In natural conditions animals encounter odor
 sources in which odor is carried by air flow varying in complexity. We
 sought to identify potential minimalist strategies that can effectively be
 used for odor-based navigation and asses their performance in an
 increasingly chaotic environment. To do so, we compared mouse, in silico
 model, and Arduino-based robot odor-localization behavior in a
 standardized odor landscape. Mouse performance remains robust in the
 presence of increased complexity, showing a shift in strategy towards
 faster movement with increased environmental complexity. Implementing
 simple binaral and temporal models of tropotaxis and klinotaxis, an in
 silico model and Arduino robot, in the same environment as the mice, are
 equally successful in locating the odor source within a plume of low
 complexity. However,  performance of these algorithms
 significantly drops when the chaotic nature of the plume is increased.
 Additionally, both algorithm-driven systems show more successful
 performance when using a strictly binaral model at a larger sensor
 separation distance and more successful performance when using a temporal
 and binaral model when using a smaller sensor separation distance. This
 suggests that with an increasingly chaotic odor environment, mice rely on
 complex strategies that allow for robust odor localization that cannot be
 resolved by minimal algorithms that display robust performance at low
 levels of complexity. Thus, highlighting that an animal’s ability to
 modulate behavior with environmental complexity is beneficial for odor
 localization.
description: <b>Extended Data 1.
 <i>In silico </i>MATLAB and Arduino codes.
 </b> Included are MATLAB codes to generate the
 center and corner odor plumes (file names: odorFun_plume_center.m,
 odorFun_plume_corner.m), test the <i>in silico</i> simulated
 robot using code A and Code B (filenames: SimRobot_test_A.m,
 SimRobot_test_B.m), and to test the <i>in silico </i>model
 with replicates (filenames: run_model_A_replicates.m,
 run_model_B_replicates.m). Additionally, the two Arduino codes for robot
 navigation (file names: Robot_CodeA.ino, Robot_CodeB.ino).
 Also included: robot STL files for 3D printing parts.
 Also included: Movies 1-19.  
description: Four minutes of near-surface acetone planar laser-induced
 fluorescence (PLIF) plume data from Connor et al 2018 was used as input
 for these models
 ('11282017_10cms_bounded.h5','/dataset7').The above
 models are deterministic. If they are synchronized with the first frame of
 the plume dataset, they will always generate the same trajectory. To
 simulate “random” complexity, each model evaluation initialized the plume
 dataset at a randomly chosen frame between 1 and 3600; the four-minute
 dataset was then allowed to loop continuously until the simulation
 concluded (<b>Movie 1</b>, <b>Movie
 2</b>).
DOI: 10.5061/dryad.4b8gtht8d
title: Recombination data for Wolbachia and Spiroplasma infected flies

description: Wolbachia pipientis is an intracellular alphaproteobacterium that infects
 40-60% of insect species and is well known for host reproductive
 manipulations. Although Wolbachia are primarily maternally transmitted,
 evidence of horizontal transmission can be found in incongruent
 host-symbiont phylogenies and recent acquisitions of the same Wolbachia
 strain by distantly related species. Parasitoids and predator-prey
 interactions may indeed facilitate the transfer of Wolbachia between
 insect lineages but it is likely that Wolbachia are acquired via
 introgression in many cases. Many hypotheses exist as to explain Wolbachia
 prevalence and penetrance such as nutritional supplementation, protection
 from parasites, protection from viruses, or straight up reproductive
 parasitism. Using classical genetics we show that Wolbachia increase
 recombination in infected lineages across two genomic intervals. This
 increase in recombination is titer dependent as the wMelPop variant, which
 infects at higher load in Drosophila melanogaster, increases recombination
 5% more than the wMel variant. In addition, we also show that Spiroplasma
 poulsonii, the other bacterial intracellular symbiont of Drosophila
 melanogaster, does not induce an increase in recombination. Our results
 suggest that Wolbachia infection specifically alters host recombination
 landscape in a dose dependent manner.
description: These are raw counts of flies extibiting phenotypes from
 recessive markers after backcrossing in Wolbachia or Spiroplasma infected
 or uninfected backgrounds.
DOI: 10.5061/dryad.2fqz612kk
title: Role of the intestinal microbiome in polyethylene degradation by caterpillar larva of the greater wax moth (Galleria mellonella)

description: Recently, a few insects, including the caterpillar larva of the greater
 wax moth Galleria mellonella, have been identified as avid
 "plastivores". Interestingly, these caterpillars are able to
 ingest and metabolize polyethylene at unprecedented rates. While it
 appears that G. mellonella plays an important role in the biodegradation
 process, the contribution of its intestinal microbiome remains poorly
 understood and contested. In a series of experiments, we present strong
 evidence of an intricate relationship between an intact microbiome, low
 density polyethylene (LDPE) biodegradation, and the production of glycol
 as a metabolic by-product. First, we biochemically confirmed that G.
 mellonella larvae consume and metabolize LDPE, as individual caterpillars
 fed on polyethylene excreted glycol, but those excretions are reduced by
 antibiotic treatment. Further, while the gut bacterial communities remain
 relatively stable regardless of diet, we show that during the early phases
 of feeding on LDPE (24-72 hrs), caterpillars exhibit increased microbial
 abundance relative to those starved or fed on their natural honeycomb
 diet. Finally, by isolating and growing gut bacteria with polyethylene as
 their exclusive carbon source for over one year, we identified
 microorganisms in the genus Acinetobacter that appear to be involved in
 this biodegradation process. Taken collectively, our study indicates that
 during short term exposure, the intestinal microbiome of G. mellonella is
 intricately associated with polyethylene biodegradation in vivo.
description: This dataset represents experiments exploring the role
 of <i>Galleria mellonella </i>microbiome in polyethylene
 degradation. 1- Glycol
 quantity: <i>Galleria
 mellonella</i> larvae<i> </i>were treated with broad
 spectrum antibiotic and fed polyethylene or their honeycomb diet, and we
 monitored glycol excretion as a metabolic by-product of polyethylene
 degradation. 2-Antibiotic
 effect: Using qPCR we established the relative microbial
 abundance in <i>Galleria mellonella</i> after 24
 hours<i>.</i> 3-Excreta and
 Bacterial Abundance: Using qPCR we quantified microbial
 abundance (16S) of <i>Galleria mellonella</i> fed on
 polyethylene that excreted vs. did not excrete glycol.
 4-Treatment Bacterial Abundance: We monitored
 bacterial abundance in waxworms under 3 feeding regimes: honeycomb,
 polyethylene and starvation for 24 and 72h.
DOI: 10.5061/dryad.2bvq83bm5
title: The role of sexual reproduction in the maintenance of established Zostera marina meadows

description: Abstract 1.For clonal plants the role of sexual reproduction in the
 maintenance of populations can vary widely. Some species are dependent on
 repeated seedling recruitment. For other species, interactions between
 adults and seedlings within existing populations can affect seedling
 survival and limit sexual reproduction in existing populations. Genetic
 studies of seagrass populations increasingly suggest sexual reproduction
 is important for the resilience and stability of their populations, but as
 of yet little observational data supports these findings. Because seagrass
 populations provide important ecosystem services and are threatened with
 increasing anthropogenic impacts, understanding their reliance on sexual
 reproduction is evolutionarily and ecologically important. 2.The goals of
 this study were to determine: 1. if seedlings of a marine angiosperm,
 Zostera marina, establish and recruit within existing Z. marina meadows;
 2. if interactions between seedlings and surrounding adult shoots
 influence the survival of established seedlings. To meet these goals,
 surveys estimated seedling establishment and tracked seedling survival
 within multiple populations. Manipulative experiments then tested the
 impact of neighboring adult shoots on seedling survival and the overall
 trajectory of experimental plots with and without sexual reproduction. 3.
 A three-year survey identified established seedlings within Z. marina
 meadows each year. Additionally, concurrent seed addition experiments
 indicated seed supply could influence seedling establishment rates. A
 survey tracking the survival of tagged seedlings, as well as the height
 and density of surrounding adult shoots, showed adult shoots may
 negatively impact seedling survival. Experiments then demonstrated that
 seedlings without neighboring shoots survived longer than those with
 neighboring shoots. Lastly, two transplant garden experiments comparing
 the survival of plots with and without seeds highlighted that seedling
 recruitment is likely most important to maintain bottom cover where
 disturbances generate gaps in the adult population. 4. Synthesis. This
 study demonstrates that seedlings do establish within existing seagrass
 meadows, and that some survive to recruit into the adult population.
 Competition with existing vegetation, however, can be a factor
 compromising seedling survival. Sexual reproduction may thus most likely
 occur in, and be most important for, clonal plant populations that
 experience seasonal disturbance.
description: These datasets evaluate the presence and survival of Zostera
 marina seedlings in Z. marina meadows from 2016-2018 in the coastal waters
 of Virginia.
DOI: 10.15468/dl.fbnepu
title: Occurrence Download

description: A dataset containing 690 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Auchenoceros punctatus",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 1950",
 "Year is less than or equal to 2014"
 ]
}

 The dataset includes 690 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002169-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.fj6q573qp
title: Data from: Multiple scales of spatial heterogeneity control soil respiration responses to precipitation across a dryland rainfall gradient

description: Aims – Soil respiration (Rs) is a major pathway for releasing fixed carbon
 back to the atmosphere. However, controls over Rs are poorly understood in
 arid and hyper-arid systems where microbial activity is frequently
 constrained by moisture. We addressed key uncertainties in Rs: 1) How do
 short-term rainfall pulses affect Rs at sites that differ in long-term
 precipitation inputs?, 2) how do Rs responses to short and long-term
 rainfall differ across soil surfaces?, and 3) how are Rs responses
 affected by local-scale attributes? Methods – We measured Rs responses to
 rainfall pulses over a 48 h period. Working across a climate gradient, we
 compared Rs responses on two contrasting soil surfaces which both had two
 vegetation/soil morphology patch types that differed in organic matter
 inputs and accumulation. Results – Rates of Rs were low, but highly
 responsive to rainfall pulses. Stimulation of Rs by rainfall was generally
 greater in areas with higher annual rainfall. However, patterns for Rs
 responses to rainfall differed greatly on the two soil surfaces and among
 patch types. Conclusions – The strong role of patch type and soil surface
 in controlling Rs points to the need to carefully consider small-scale
 spatial and temporal variation when interpreting dryland biogeochemical
 fluxes.
description: See manuscript details.
DOI: 10.15468/dl.848kyq
title: Occurrence Download

description: A dataset containing 6 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "PublishingOrg is one of (c2ecae57-6701-485e-9ebd-5f87b2945cb2, f9b67ad0-9c9b-11d9-b9db-b8a03c50a862, 6ea87510-0561-11d8-b851-b8a03c50a862)",
 "TaxonKey is Melanoplus coreyi",
 "Year 1900-2026"
 ]
}

 The dataset includes 6 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002170-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.905qfttgp
title: The role of evolutionary time, diversification rates and dispersal in determining the global diversity of a large radiation of passerine birds

description: Aim: Variation in species diversity among different geographic areas may
 result from differences in speciation and extinction rates, immigration
 and time for diversification. An area with high species diversity may be
 the result of a high net diversification rate, multiple immigration events
 from adjacent regions,anda long time available for the accumulation of
 species (know as the “time-for-speciation effect”). Here, we examine the
 relative importance of the three aforementionedprocesses in
 shaping the geographic diversity patterns of a large radiation of
 passerine birds. Location: Global Time period: Early Miocene to present
 Major taxa studied: Babblers (Aves: Passeriformes) Methods: Using
 a comprehensive phylogeny of extant species (~90% sampled) and
 distributions of the world’s babblers, we reconstructed their
 biogeographic history and analysed the diversification
 dynamics. We examined how species richness correlates
 with the timing of regional colonization, the number of
 immigration events and the rate of speciation within all 13 geographic
 distribution regions. Results: We found thatbabblers likely
 originated in the Sino-Himalayan Mountains (SHM) in the early Miocene,
 suggesting a long time for diversification and species accumulation within
 the SHM. Regression analyses showed the regional diversity of babblers can
 be well explained by the timing of the first colonization within
 of these areas, while differences in rates of speciation or immigration
 have far weaker effects. Nonetheless, the rapid speciation
 of Zosteropsduring the Pleistocene has accounted for the
 increased diversification and accumulation of species in the oceanic
 islands. Main conclusions: Our results suggest that the global diversity
 patterns of babblers have predominantly been shaped by the
 time-for-speciation effect. Our findings also support an origin centred in
 tropical and subtropical parts of the SHM, with a cradle of recent
 diversification in the oceanic islands of the Indo-Pacific region, which
 provides new insights into the generation of global biodiversity hotspots.
description: A near-complete phylogeny of babblers has been reconstructed in
 BEAST 1.8.4 based on 12 gene loci.
DOI: 10.5061/dryad.8kprr4xjm
title: Payoff of the Grain for Green policy

description: 1. To protect the global ecological environment and prevent threats to
 human safety and property, nations around the world have invested heavily
 in ecological restoration programmes. However, we don’t know
 whether these investments have been repaid by the resultant benefits. 2.
 To answer this question, we developed an improved method of quantifying
 costs and benefits that accounts for more of the costs associated with
 ecological restoration, thereby letting us calculate the
 net benefit. 3. To demonstrate this method, we analysed the Grain
 for Green Program, which is the world’s largest ecological restoration
 program. We found that the increase in net benefits amounted to a total of
 530.1×109 RMB·yr-1 in 2017. However, 11 of China’s 25
 provinces have incurred net losses due to high cost increases and low
 increases in benefits under the GGP. 4. Synthesis and applications.
 Because compensation payments to farmers and herders whose livelihoods
 were disrupted by implementation of the Grain for Green
 Program only accounted for 0.8% of the programme’s cost,
 improving compensation payments will be essential to its
 success. Assessing GGP the largest ecological
 restoration program in the world will provide guidance
 for ecological protection and restoration policies around the world. 1. To
 protect the global ecological environment and prevent threats to human
 safety and property, nations around the world have invested heavily in
 ecological restoration programmes. However, we don’t know whether
 these investments have been repaid by the resultant benefits. 2. To answer
 this question, we developed an improved method of quantifying costs and
 benefits that accounts for more of the costs associated with ecological
 restoration, thereby letting us calculate the net benefit. 3. To
 demonstrate this method, we analysed the Grain for Green Program, which is
 the world’s largest ecological restoration program. We found that the
 increase in net benefits amounted to a total of
 530.1×109 RMB·yr-1 in 2017. However, 11 of China’s 25
 provinces have incurred net losses due to high cost increases and low
 increases in benefits under the GGP. 4. Synthesis and applications.
 Because compensation payments to farmers and herders whose livelihoods
 were disrupted by implementation of the Grain for Green
 Program only accounted for 0.8% of the programme’s cost,
 improving compensation payments will be essential to its
 success. Assessing GGP the largest ecological
 restoration program in the world will provide guidance
 for ecological protection and restoration policies around the world.
description: The data of value of
 ecosystem services of Grain for Green Program are collected
 from monitoring sites under the authority of the Chinese Academy of
 Sciencesand China’s State Forestry Administration, and data of costs,
 value of products, compensation, area are from related statistical
 yearbooks.
DOI: 10.5061/dryad.z08kprr8v
title: A spatial genomic approach identifies time lags and historic barriers to gene flow in a rapidly fragmenting Appalachian landscape

description: The resolution offered by genomic data sets coupled with recently
 developed spatially informed analyses are allowing researchers to quantify
 population structure at increasingly fine temporal and spatial scales.
 However, both empirical research and conservation measures have been
 limited by questions  regarding the impacts of data set size,
 data quality thresholds, and the time scale at which barriers to gene flow
 become detectable. Here, we used restriction site associated DNA
 sequencing to generate a 2,140 SNP data set for the copperhead snake
 (Agkistrodon contortrix) and address the population genomic impacts of
 recent and widespread landscape modification across an approximately 1000
 km2 region of eastern Kentucky, USA. Nonspatial population-based
 assignment and clustering methods supported little to no population
 structure. However, using individual-based spatial autocorrelation
 approaches we found evidence for genetic structuring which closely follows
 the path of a historically important highway which experienced high
 traffic volumes from ca. 1920 to 1970 before losing most traffic to a
 newly constructed alternate route. We found no similar spatial genomic
 signatures associated with more recently constructed highways or surface
 mining activity, though a time lag effect may be responsible for the lack
 of any emergent spatial genetic patterns. Subsampling of our SNP data set
 suggested that similar results could be obtained with as few as 250 SNPs,
 and a range of thresholds for missing data exhibited limited impacts on
 the spatial patterns we detected. While we were not able to estimate
 relative effects of land uses or precise time lags, our findings highlight
 the importance of temporal factors in landscape genetics approaches, and
 suggest the potential advantages of genomic data sets and fine-scale,
 spatially informed approaches for quantifying subtle genetic patterns in
 temporally complex landscapes.
DOI: 10.5061/dryad.wpzgmsbhh
title: Structural defence is coupled with the leaf economic spectrum across saplings of spiny species

description: Given that the rate of resource capture constrains plant growth and
 defence, understanding the linkage between the leaf economic spectrum
 (LES) and defence and how it contributes to growth is central to
 predicting species performance. In spite of the prevalence of spiny plants
 in many plant communities, little is known about how the LES relates to
 defence and growth rate across these species. We grew 42 spiny species,
 from diverse environments, under common garden conditions for 15 weeks and
 measured LES (leaf N, SLA and assimilation rate), defence and growth
 traits. We assessed general relationships between LES and growth rate and
 tested whether structural defences (spines, leaf fibre and lignin content)
 and quantitative chemical defences (condensed tannins) are linked to the
 LES and growth and if different spine types (i.e. leaf spines, stipular
 spines, prickles and thorns), with distinct anatomical origins, partition
 out across the LES. We observed two independent trait axes that together
 explained ~68% of trait variation across species. The first axis showed
 that structural defences (spines, leaf fibre and lignin content) trade off
 with leaf productivity along the LES. Axis 2 revealed that condensed
 tannins is orthogonal and less integrated with the LES-structural defence
 axis. Bivariate trait analyses disclosed positive covariations between LES
 traits and sapling growth rate. All structural defence traits were
 negatively related to sapling growth. Across spine types, species with
 leaf spines were associated with the conservative end of the LES,
 characterized by  high structural defences and lower leaf
 productivity relative to other spine types. Our study shows that the LES
 and structural defences are coupled in spiny species such that
 constitutive growth – defence strategies range from fast-growing species
 with low allocation to defences to slow-growing species that invest
 heavily in structural defences (dominated by leaf spiny species).
description: See companion article for details of data collection.