cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sg77240
title: Data from: Transgenic Aedes aegypti mosquitoes transfer genes into a natural population

description: In an attempt to control the mosquito-borne diseases yellow fever, dengue,
 chikungunya, and Zika fevers, a strain of transgenically modified Aedes
 aegypti mosquitoes containing a dominant lethal gene has been developed by
 a commercial company, Oxitec Ltd. If lethality is complete, releasing this
 strain should only reduce population size and not affect the genetics of
 the target populations. Approximately 450 thousand males of this strain
 were released each week for 27 months in Jacobina, Bahia, Brazil. We
 genotyped the release strain and the target Jacobina population before
 releases began for &gt;21,000 single nucleotide polymorphisms (SNPs).
 Genetic sampling from the target population six, 12, and 27–30 months
 after releases commenced provides clear evidence that portions of the
 transgenic strain genome have been incorporated into the target
 population. Evidently, rare viable hybrid offspring between the release
 strain and the Jacobina population are sufficiently robust to be able to
 reproduce in nature. The release strain was developed using a strain
 originally from Cuba, then outcrossed to a Mexican population. Thus,
 Jacobina Ae. aegypti are now a mix of three populations. It is unclear how
 this may affect disease transmission or affect other efforts to control
 these dangerous vectors. These results highlight the importance of having
 in place a genetic monitoring program during such releases to detect
 un-anticipated outcomes.
description: SNP data, Table
 S1The
 genotype data used for this study in PLINK map/ped format and Table
 S1tosubmit.zip
DOI: 10.5061/dryad.5v3s28v
title: Data from: What's stirring in the reservoir? modelling mechanisms of henipavirus circulation in fruit bat hosts

description: Pathogen circulation among reservoir hosts is a precondition for zoonotic
 spillover. Unlike the acute, high morbidity infections typical in
 spillover hosts, infected reservoir hosts often exhibit low morbidity and
 mortality. Although it has been proposed that reservoir host infections
 may be persistent with recurrent episodes of shedding, direct evidence is
 often lacking. We construct a generalised SEIR (susceptible, exposed,
 infectious, recovered) framework encompassing 46 sub-models representing
 the full range of possible transitions among those four states of
 infection and immunity. We then use likelihood-based methods to fit these
 models to nine years of longitudinal data on henipavirus serology from a
 captive colony of Eidolon helvum bats in Ghana. We find that reinfection
 is necessary to explain observed dynamics; that acute infectious periods
 may be very short (hours to days); that immunity, if present, lasts about
 1-2 years; and that recurring latent infection is likely. Although
 quantitative inference is sensitive to assumptions about serology,
 qualitative predictions are robust. Our novel approach helps clarify
 mechanisms of viral persistence and circulation in wild bats, including
 estimated ranges for key parameters such as the basic reproduction number
 and the duration of the infectious period. Our results inform how future
 field-based and experimental work could differentiate the processes of
 viral recurrence and reinfection in reservoir hosts.
description: Captive Eidolon helvum
 serologySample dates, bat ID
 numbers, and NiVsG mean fluorescence index (MFI) values from Luminex
 assays applied to blood samples from captive Eidolon
 helvum.Bat_data_PTRSB.csv
DOI: 10.5061/dryad.087g0k7
title: Data from: Landing maneuvers of houseflies on vertical and inverted surfaces

description: Landing maneuvers of flies are complex behaviors which can be conceptually
 decomposed into sequences of modular actions, including body-deceleration,
 leg-extension, and body rotations. These behavioral ‘modules’ must be
 coordinated to ensure well-controlled landing. The composite nature of
 these behaviors induces kinematic variability, making it difficult to
 identify the central rules that govern landing. Many previous studies have
 relied on tethered preparations to study landing behaviors, but tethering
 induces experimental artefacts by forcing some behaviors to operate in
 open-feedback control loop while others remain closed-loop. On the other
 hand, freely-flying insects are harder to precisely control, and hence
 inherently prone to behavioral variability. One approach towards
 understanding general mechanisms of landing is to determine the common
 elements of their kinematics on surfaces of different orientations. We
 conducted a series of experiments in which the houseflies, Musca
 domestica, were lured to land on vertical (vertical landings) or inverted
 (inverted landings) substrates, while their flight was recorded with
 multiple high-speed cameras. We observed that, in both cases,
 well-controlled landings occurred when the distance at which flies
 initiated deceleration was proportional to flight velocity component in
 the direction of substrate. The ratio of substrate distance and velocity
 at onset of deceleration (tau) was conserved, despite substantial
 differences in mechanics of vertical vs. inverted landings. When these
 conditions were not satisfied, their landing performance was compromised,
 causing their heads to collide into the substrate. Unlike
 body-deceleration, leg-extension in flies was independent of substrate
 distance or approach velocity. Thus, the robust reflexive visual
 initiation of deceleration is independent of substrate orientation, and
 combines with a more variable initiation of leg-extension which depends on
 surface orientation. Together, these combinations of behaviors enable
 flies to land in a versatile manner on substrates of various orientations.
description: Balebail_Raja_and_Sane_2019Contains videos of landings on vertical and inverted surfaces. Also contains the xyz coordinate files, and the MATLAB codes used to compute kinematic variables.
DOI: 10.5061/dryad.1sn2352
title: Data from: A framework for linking competitor ecological differences to coexistence

description: 1. Not all ecological differences among competing species affect their
 ability to locally coexist. Rather, the differences that promote stable
 coexistence can be those which cause each species to experience stronger
 intraspecific than interspecific competition. Recent approaches have
 established how to detect the demographic signature of these competitive
 effects, but alone they cannot elucidate the ecological differences among
 species that yield these patterns. 2. Here, we present a unifying
 experimental and observational framework that identifies potential
 ecological differences among species shaping their responses to intra- and
 interspecific competition. We first describe a conceptual model
 establishing why the strength of intra- and interspecific competitive
 interactions should vary along environmental gradients related to species
 ecological differences. We then show how to apply the framework using
 Enallagma damselflies, a diverse group of predatory aquatic insects. 3. To
 determine how species responded to intra- and interspecific competition
 along environmental gradients, we experimentally manipulated the relative
 abundances of three species and replicated this across five lakes which
 varied in environmental conditions affecting larval damselfly per capita
 growth and mortality rates – key vital rates regulating their populations.
 4. Results suggest Enallagma are ecologically differentiated in ways that
 in some communities can result in intraspecific competition exceeding
 interspecific competition. However, in many cases the opposite was true,
 or the effects of intra- and interspecific competition were equivalent via
 growth and mortality responses. Moreover, these effects tended to be weak
 and asymmetrical among competitors, which suggests that differential
 responses of larval growth and mortality to intra- and interspecific
 competition may not contribute strongly to the maintenance of Enallagma
 diversity. Different environmental factors appear to shape these
 demographic responses to competition, providing insight into the
 ecological mechanisms regulating damselfly assemblages. 5. This framework
 can be broadly applied to identify the ecological differences among
 species that may promote coexistence, advancing knowledge of the
 mechanisms underlying coexistence, and overcoming some limitations of
 purely phenomenological approaches.
description: Ousterhout_et_al_Competition_dataResults from the experiment manipulating Enallagma species relative abundances across lakes. Shown are lakes (all in AR), Date the cages were pulled, cage number, species acronym (see meta-data), head width, and whether these are the initial for final measurements.
DOI: 10.5061/dryad.4b08gn8
title: Data from: Habitat enhancements rescue bee body size from the negative effects of landscape simplification

description: 1. The negative effects of landscape simplification on bee communities are
 well documented. To reverse these effects, flowering habitat enhancements
 are designed to provide supplemental nutritional resources for wild bees
 and are particularly important when few resources are available in the
 surrounding landscape. Yet, it is not known whether or how habitat
 enhancements support bee populations under varying landscape contexts.
 Body size is a morphological trait that is strongly linked to foraging
 ability, immune function, and fitness in bees. Landscape simplification
 has been associated with size declines across bee taxa, and smaller body
 size can be an early indicator of environmental stress. 2. To determine
 whether the negative effects of landscape simplification on body size can
 be improved by adding floral resources to farm landscapes, we measured the
 body size of ten wild bee species collected at 70 sites with or without
 habitat enhancements in Michigan and New York. Bees were collected at
 sites with varying amounts of agriculture in the surrounding landscape,
 allowing us to test whether morphological responses to enhancements are
 affected by landscape simplification. 3. Half of the bee species measured
 exhibited declining body size across the landscape gradient. Among these
 species, declines were buffered by the presence of habitat enhancements
 suggesting this response is the result of improved nutrition, reduced need
 for long-distance foraging, enhanced recruitment of larger individuals or
 a combination of these mechanisms. 4. Declines in body size were strongest
 in both the smallest and the largest species. Large and medium sized
 species exhibited the greatest response to flowering habitat enhancements.
 Synthesis and applications. Our findings suggest that the presence of
 flowering habitat enhancements can support pollinators experiencing stress
 from intensively managed agricultural landscapes across multiple cropping
 systems and regions.
description: Michigan Bee and Site
 Datadata file in csv format
 containing the specimen level data on body size measures: intertegular
 distance (ITD) and head capsule width (head). Also includes locality data
 including local treatment, land cover and planting
 metrics.MI_size_data.csvNew York Bee and Site Datadata file in csv format containing the specimen level data on body size measures: intertegular distance (ITD) and head capsule width (head). Also includes locality data including local treatment, land cover and planting metrics.NY_size_data.csv
DOI: 10.5061/dryad.b7t80m5
title: Data from: Loss and gain of sexual reproduction in the same stick insect

description: The outcome of competition between different reproductive strategies
 within a single species can be used to infer selective advantage of the
 winning strategy. Where multiple populations have independently lost or
 gained sexual reproduction it is possible to investigate whether the
 advantage is contingent on local conditions. In the New Zealand stick
 insect Clitarchus hookeri, three populations are distinguished by recent
 change in reproductive strategy and we determine their likely origins. One
 parthenogenetic population has established in the United Kingdom and we
 provide evidence that sexual reproduction has been lost in this
 population. We identify the sexual population from which the
 parthenogenetic population was derived, but show that the UK females have
 a post-mating barrier to fertilisation. We also demonstrate that two
 sexual populations have recently arisen in New Zealand within the natural
 range of the mtDNA lineage that otherwise characterizes parthenogenesis in
 this species. We infer independent origins of males at these two locations
 using microsatellite genotypes. In one population, a mixture of local and
 non-local alleles suggested males were the result of invasion. Males in
 another population were most likely the result of loss of an X chromosome
 that produced a male phenotype in situ. Two successful switches in
 reproductive strategy suggest local competitive advantage for outcrossing
 over parthenogenetic reproduction. Clitarchus hookeri provides remarkable
 evidence of repeated and rapid changes in reproductive strategy, with
 competitive outcomes dependent on local conditions.
description: stick insect genotypes
 for dryadGenotypes for stick
 insect population samples for 10 microsatellite loci are provided.
 Collection location, code and sex of each individual stick insect is
 provided. Loci codes are explained in Myers et al. 2017
 (https://doi.org/10.1111/jbi.13004) All specimens are Clitarchus hookeri,
 a species endemic to New Zealand, but with a newly established population
 in the UK.aligned mtDNA sequences
 for 125 stick insectsFragments of COI and
 COII mtDNA sequence from 125 individuals of the New Zealand stick insect
 Clitarchus hookeri. This FASTA format file is the full alignment used for
 phylogenetic reconstruction. Subsets of the data used for molecular clock
 analysis and network analysis. Codes identify individuals, location
 information provided in the associated paper. Representatives of unique
 haplotypes are on genbank.Full dataset Clitarchus
 alignment 125.fasta
DOI: 10.5061/dryad.vc80r13
title: Data from: Long-term responses of desert ant assemblages to climate

description: 1. Productivity is a key driver of ecosystem structure and function, so
 long-term studies are critical to understanding ecosystems with high
 temporal variation in productivity. In some deserts, productivity, driven
 by moisture availability, varies immensely over time (rainfall) and space
 (landscape factors). At high productivity, species richness is expected to
 be driven in opposing directions by abundance (More Individuals Hypothesis
 – MIH), and competition. While studies investigating the impacts of
 spatial variation in productivity on community structure are common, the
 impacts of temporal variability on productivity are poorly understood. 2.
 We tested how well rainfall predicted the activity, species numbers and
 assemblage composition of ants and if responses were moderated by
 landscape position. We also asked whether the number of species (richness
 per sampling unit and estimated species richness) responded directly to
 rainfall or was moderated by ant activity or competition from dominant
 ants. 3. Over a 22-year period, when annual rainfall fluctuated between 79
 mm and 570 mm, we sampled ants using pitfall traps in paired dune and
 swale habitats in the Simpson Desert, Australia. We used climate records
 over this period to model changes in ant assemblages. 4. Activity of
 dominant ants responded primarily to long-term rainfall, increasing
 exponentially, while subordinate ants responded to short-term weather and
 time. Consistent with the MIH, the number of ant species was best
 predicted by activity, particularly that of subordinate ants. Activity of
 dominant ants had a declining positive effect on numbers of species.
 Landscape position strongly predicted species composition, while long-term
 rainfall determined composition at genus- but not species-level. Over
 time, species composition fluctuated, but several genera consistently
 increased in activity.
description: Simpson Desert Ants
 1992-2013Includes data on ants
 collected during pitfall trapping in the Simpson Desert, northern
 Australia, 1992-2013. The "Activity data" sheet details
 abundance and richness and environmental variables. The "Composition
 data" sheet includes species abundance data and links to the
 "Activity data" sheet through the "code". A
 "Metadata" sheet is supplied to explain the
 columns.Gibb et al. Journal of Animal
 Ecology - Data.xlsx
DOI: 10.5061/dryad.23420f6
title: Data from: From canopy to seed: loss of snow drives directional changes in forest composition

description: Climate change is altering the conditions for tree recruitment, growth,
 and survival, and impacting forest community composition. Across southeast
 Alaska, USA, and British Columbia, Canada, Callitropsis nootkatensis
 (Alaska yellow-cedar) is experiencing extensive climate change-induced
 canopy mortality due to fine root death during soil freezing events
 following warmer winters and the loss of insulating snowpack. Here, we
 examine the effects of ongoing, climate-driven canopy mortality on
 regeneration and identify potential shifts in stand trajectories due to
 loss of a single canopy species. We sampled canopy and regenerating
 communities across the extent of C. nootkatensis decline in southeast
 Alaska to identify the drivers of C. nootkatensis canopy mortality and
 regeneration as well as post-decline regenerating community composition.
 Across the plot network, C. nootkatensis exhibited significantly higher
 mortality than co-occurring conifers across all size classes and
 locations. Regenerating community composition was highly variable but
 closely related to the severity of C. nootkatensis mortality. Callitropsis
 nootkatensis canopy mortality on the plot network was correlated with
 winter temperatures and precipitation as well as soil drainage, with C.
 nootkatensis regeneration abundances and regenerating community
 composition best explained by available seed source. In areas of high C.
 nootkatensis mortality, C. nootkatensis regeneration was low and was
 replaced by Tsuga. Our study suggests that climate-induced forest
 mortality is driving alternate successional pathways in forests where C.
 nootkatensis was once a major component. These pathways are likely to lead
 to long-term shifts in forest community composition and stand dynamics.
 Our analysis fills a critical knowledge gap on forest ecosystem response
 and rearrangement following the climate-driven decline of a single
 species, providing new insight into stand dynamics in a changing climate.
 As tree species across the globe are increasingly stressed by climate
 change-induced alteration of suitable habitat, identifying the
 autecological factors contributing to successful regeneration, or lack
 thereof, will provide key insight into forest resilience and persistence
 on the landscape.
description: Callitropsis
 nootkatensis southeast Alaska decline raw plot data
 (2011-2016)Callitropsis
 nootkatensis canopy mortality and regeneration field-collected data from
 plots across southeast Alaska, USA.YCregen_manuscript_PlotData.xlsxCallitropsis nootkatensis southeast Alaska decline summary plot data (2011-2016)Callitropsis nootkatensis canopy mortality and regeneration field-collected data from plots across southeast Alaska, USA, summarized to the plot level. Additionally, this file includes extracted plot-level climate data (ClimateWNA).YCregen_manuscript_SummaryData.xlsx
DOI: 10.5061/dryad.c806hk2
title: Data from: Cell migration through three-dimensional confining pores: speed accelerations by deformation and recoil of the nucleus

description: Directional cell migration in dense three-dimensional (3D) environments
 critically depends upon shape adaptation and is impeded depending on the
 size and rigidity of the nucleus. Accordingly, the nucleus is primarily
 understood as a physical obstacle, however, its pro-migratory functions by
 step-wise deformation and reshaping remain unclear. Using atomic force
 spectroscopy, time-lapse fluorescence microscopy and shape change analysis
 tools, we determined nuclear size, deformability, morphology and shape
 change of HT1080 fibrosarcoma cells expressing the Fucci cell cycle
 indicator or being pre-treated with chromatin-decondensating agent TSA. We
 show oscillating peak accelerations during migration through 3D collagen
 matrices and microdevices that occur during shape reversion of deformed
 nuclei (recoil), and increase with confinement. During G1 cell cycle
 phase, nucleus stiffness was increased and yielded further increased speed
 fluctuations together with sustained cell migration rates in confinement
 as compared to interphase populations, or to periods of intrinsic nuclear
 softening in the S/G2 cell cycle phase. Likewise, nuclear softening by
 pharmacological chromatin decondensation or after lamin A/C depletion
 reduced peak oscillations in confinement. In conclusion, deformation and
 recoil of the stiff nucleus contributes to saltatory locomotion in dense
 tissues.
description: Krause et al, raw data
 for all graphsThis file contains all
 data points for all the displayed graphs in the article Krause et
 al.Krause
 et al raw data for all graphs_final.xlsx
DOI: 10.5061/dryad.7c2g5rn
title: Data from: Effects of altitude, land use and microsites on the early-life performance of a high mountain tree: insights from an in situ sowing experiment.

description: Aim. Understanding the forces that drive range shifts in forest landscapes
 is imperative for predicting species distributions under anthropogenic
 climate and land use change. However, empirical studies exploring how
 these components jointly influence critical early-life stages of mountain
 tree species across environmental gradients are scarce. We used the
 high-mountain tree Polylepis australis as model species to investigate the
 relative importance of altitude and associated climatic conditions, land
 use for livestock and microsite characteristics on early-life performance.
 Location. Córdoba Sierras, central Argentina. Methods. We set up an
 extensive in situ sowing experiment with a robust split-plot design that
 integrated spatial scales ranging from 0.4 m2 subplots at the microsite
 level (associated with vegetative and micro-topographic structures), to
 livestock exclosure and enclosure plots of several hectares, to an
 altitudinal gradient of 1000 m. Components of early-life performance were
 monitored across two subsequent growing seasons. Results. Microsite
 characteristics played a fundamental role in P. australis establishment,
 whereby interactions with altitude and/or land use suggested alternate
 mechanisms: facilitation (likely reduced desiccation) dominated at low
 altitude while at high altitude abiotic stress (likely intensive frost and
 radiation) overruled any microsite effects. At mid altitude benefits of
 competition release prevailed over facilitation and microsite effects
 gained importance under livestock presence. Inconsistencies between pre-
 and post- emergence responses illustrated potential tradeoffs between
 beneficial and detrimental effects of microsite conditions upon
 performance throughout early life: a favorable location for seeds may
 abruptly turn adverse for seedlings. Main conclusions. We unravel how
 changes in altitude, anthropogenic disturbances and microsite
 characteristics jointly modulate P. australis performance across stages of
 early establishment. Such information is fundamental when categorizing
 specific microhabitats as “safe sites” for tree regeneration especially in
 mountain environments with high spatiotemporal heterogeneity.
description: Field_exp_1stYearField_exp_1Year.xlsxField_exp_1Year (metadata).txtField_exp_2YearSurvival_cleandata_2Year