cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bb6f284
title: Data from: Bunching up the background betters bias in species distribution models

description: Sets of presence records used to model species’ distributions typically
 consist of observations collected opportunistically rather than
 systematically. As a result, sampling probability is geographically
 uneven, which may confound the model’s characterization of the species’
 distribution. Modelers frequently address sampling bias by manipulating
 training data: either subsampling presence data or creating a similar
 spatial bias in non-presence background data. We tested a new method,
 which we call “background thickening,” in the latter category. Background
 thickening entails concentrating background locations around presence
 locations in proportion to presence location density. We compared
 background thickening to two established sampling bias correction methods
 — target group background selection and presence thinning — using
 simulated data and data from a case study. In the case study, background
 thickening and presence thinning performed similarly well, both producing
 better model discrimination than target group background selection, and
 better model calibration than models without correction. In the
 simulation, background thickening performed better than presence thinning
 when the number of simulated presence locations was low, and vice versa.
 We discuss drawbacks to target group background selection, why background
 thickening and presence thinning are conservative but robust sampling bias
 correction methods, and why background thickening is better than presence
 thinning for small sample sizes. Particularly, background thickening is
 advantageous for treating sampling bias when data are scarce because it
 avoids discarding presence records.
description: Zip file archive of
 code, data, and outputecog04503.zip
DOI: 10.5061/dryad.67k2q1t
title: Data from: The effect of multiple natural enemies on a shared herbivore prey

description: 1. Natural enemy diversity is thought to be important for effective
 suppression of herbivores in production systems. Studies investigating the
 importance of the diversity and composition of the natural enemy complex
 often use within year empirical studies or experimental exclusion set-ups.
 2. However, within year population suppression might not translate in long
 term population regulation. Therefore, I used a combination of long-term
 data collection and an exclusion experiment to investigate mechanisms
 behind year-to-year population changes and potential effects of
 disturbance of the natural enemy complex. 3. Using the holly leaf miner
 study system in Wytham woods, I find that the dominant predator in the
 system does not necessarily contribute the most to the reduction in
 year-to-year changes in mine density or within-patch fluctuations. Using
 the exclusion experiment, it becomes clear that parasitism later in the
 prey life cycle, can to a certain level compensate for disruption of
 mortality in the earlier life stage of the prey. 4. Thus, for host
 suppression in perennial systems the mortality pressure over the whole the
 life-cycle is important and disturbance during one part of the life cycle
 might not necessarily be buffered by mortality in other parts of the life
 cycle, especially if the natural enemy complex consists of multiple
 predator guilds.
description: Long term data
 collection; Holly network Wytham WoodsThe data is collected
 using standardized methods for 9 years as described in the publication.
 The data comprises the number of mined leaves and total number of leaves
 counted, holly leaf miner survival data, pupal and larval parasitism
 rates, bird predation and miscellaneous mortality. The data also comprises
 the patch characteristics as used in the analyses, connectivity, patch
 size and patch ID, year and the numbers of years the data was collected
 for each patch.data.years.csvexclusion experiment dataThe data for the covered and uncovered trees is collected in the same way as the long term data.The dataset comprises the number of survived holly leaf miners adults. The number of each parasitoid species that has hatched. The total hatched mined and the total hatched parasitoids and the total mined leaves and total leaves counted. The experimental treatment, year of data collected and patch ID and patch characteristics are included in the datasetexclusion.csv
DOI: 10.5061/dryad.3p84s7s
title: Data from: Infrastructure expansion challenges sustainable development in Papua New Guinea

description: The island of New Guinea hosts the third largest expanse of tropical
 rainforest on the planet. Papua New Guinea—comprising the eastern half of
 the island—plans to nearly double its national road network (from 8,700 to
 15,000 km) over the next three years, to spur economic growth. We assessed
 these plans using fine-scale biophysical and environmental data. We
 identified numerous environmental and socioeconomic risks associated with
 these projects, including the dissection of 54 critical biodiversity
 habitats and diminished forest connectivity across large expanses of the
 island. Key habitats of globally endangered species including Goodfellow’s
 tree-kangaroo (Dendrolagus goodfellowi), Matchie’s tree kangaroo (D.
 matschiei), and several birds of paradise would also be bisected by roads
 and opened up to logging, hunting, and habitat conversion. Many planned
 roads would traverse rainforests and carbon-rich peatlands, contradicting
 Papua New Guinea’s international commitments to promote low-carbon
 development and forest conservation for climate-change mitigation. Planned
 roads would also create new deforestation hotspots via rapid expansion of
 logging, mining, and oil-palm plantations. Our study suggests that several
 planned road segments in steep and high-rainfall terrain would be
 extremely expensive in terms of construction and maintenance costs. This
 would create unanticipated economic challenges and public debt. The net
 environmental, social, and economic risks of several planned projects—such
 as the Epo-Kikori link, Madang-Baiyer link, Wau-Malalaua link, and some
 other planned projects in the Western and East Sepik Provinces—could
 easily outstrip their overall benefits. Such projects should be
 reconsidered under broader environmental, economic, and social grounds,
 rather than short-term economic considerations.
description: protected
 areasPeatlandsRoad development corridor
DOI: 10.5061/dryad.7r1p25r
title: Data from: Speciation and subsequent secondary contact in two edaphic endemic primroses driven by Pleistocene climatic oscillation

description: Climatic perturbation during the Pleistocene era has played a major role
 in plant evolutionary history by altering species distribution range.
 However, the relative roles of climatic and geographic factors in the
 distribution dynamics remains poorly understood; in particular, the
 edaphic endemics. In this paper, we examine the evolutionary history of
 two ultramafic primroses, Primula hidakana and P. takedana. These species
 are ecologically and morphologically distinct with disjunct distributions
 on Hokkaido Island, Japan. Primula hidakana is found on various rocks in
 southern Hokkaido and P. takedana in serpentine areas in northern
 Hokkaido. We performed population genetics analyses on nuclear and
 chloroplast data sets and tested alternative phylogenetic models of
 divergence using approximate Bayesian computation (ABC) analyses. Nuclear
 microsatellite loci clearly distinguished the two sister taxa. In
 contrast, chloroplast sequence variations were shared between P. takedana
 and P. hidakana. ABC analyses based on nuclear data supported a secondary
 contact scenario involving asymmetrical gene flow from P. hidakana to P.
 takedana. Paleodistribution modeling also supported the divergence model,
 and predicted their latitudinal range shifts leading to past secondary
 contact. Our findings highlight the importance of the distribution
 dynamics during the Pleistocene climatic oscillations in the evolution of
 serpentine plants, and demonstrate that tight species cohesion between
 serpentine and non-serpentine sister taxa has been maintained despite past
 interspecific gene flow across soil boundaries.
description: Genotypes of Primiula
 hidakana and P. takedanaGenotypes based on 12
 microsatellite loci.Yamamoto_etal_2019.txt
DOI: 10.5061/dryad.1ch4264
title: Data from: Using radio telemetry to study behavioural thermoregulation in insects under field conditions

description: 1. Thermoregulation is a central aspect of animal physiology. Mobile
 ectotherms have the potential to influence their temperature through their
 location and orientation. Behavioural thermoregulation has been
 extensively studied in insects, particularly in the migratory locust
 (Locusta migratoria). However, most field studies are confined to daytime
 observations typically using invasive thermocouples with obvious potential
 to disrupt natural behaviour. 2. We demonstrate that miniature
 radio-transmitters represent an alternative and less invasive method to
 study insect thermoregulation. We discuss how this method can be used to
 study the thermal behaviour of free-ranging animals for extended periods.
 Specifically, we show that there is a close correlation between
 temperature recordings from implanted thermocouples in locusts (L.
 migratoria) and externally mounted radio transmitters on the same animals.
 3. Our experiments match earlier observations of locust thermoregulatory
 behaviour confirming that the locusts with transmitters exhibit “normal”
 thermoregulatory responses to feeding and to infections (behavioural
 fever). 4. Finally, we demonstrate the practicality of a radio-transmitter
 based system by recording natural thermoregulatory behaviour of locusts in
 a semi-field setting. Our field study showed locusts actively chose warm
 microclimates during the day and cold microclimates at night. We conclude
 that the use of radio-telemetry in studies of behavioural thermoregulation
 in wild insects could provide unique continuous recordings of body
 temperature over several days. Such data will provide researchers with a
 more complete understanding of how insects use behavioural
 thermoregulation in nature.
description: Description of raw
 dataA
 word file explaining the structure of the data in the assoiated Excel
 fileRaw
 dataExcel file with the data
 used to construct figures
DOI: 10.5061/dryad.g3h1444
title: Data from: Inter-population spread of a parasitic B chromosome is unlikely through males in the grasshopper Eyprepocnemis plorans

description: The near-neutral model of B chromosome evolution predicts that population
 invasion is quite fast. To test this prediction, in 1994, we introduced
 males of the grasshopper Eyprepocnemis plorans from a B-carrying
 population into a B-lacking population and monitored the evolution of B
 chromosome frequency up to 2013. We observed fluctuating very low B
 frequency across years but, remarkably, the B chromosome introduced (the
 B2 variant) was found up to 1996 only, whereas the B1 variant was present
 from 1996 onwards, presumably introduced by fishermen using E. plorans
 males as bait. Effective introgression of genetic material from the donor
 population was evidenced by the presence of a satellite DNA on autosome 9
 (up to 1999) and the presence of one individual in 2006 showing an ISSR
 marker profile being highly similar to that found in the donor population.
 This indicated that the males introduced by us effectively mated with
 resident females, but donor genes rapidly decreased in frequency after
 this non-recurrent migration event. Taken together, our results indicated:
 i) that the non-recurrent migration event had a slight, transient genetic
 effect on the recipient population which was diluted in only a few
 generations; and ii) that even with recurrent migration (forced by
 fishermen) the B chromosome failed to increase in frequency. Bearing in
 mind that B chromosomes in this species drive through females only, we
 hypothesize that B chromosomes most likely failed invasion in both
 migration events because the migrating sex shows no B-drive.
description: ISSR_dataset E.plorans
 in SouthEast SpainThe file contains the
 ISSR marker genotypes for all individuals from 7 natural populations
 collected at South-East Spain in 2006ISSR_dataset.xls
DOI: 10.5061/dryad.56br7f7
title: Data from: Resilience of ecosystem processes: a new approach shows that functional redundancy of biological control services is reduced by landscape simplification

description: Functional redundancy can increase the resilience of ecosystem processes
 by providing insurance against species loss and the effects of abundance
 fluctuations. However, due to the difficulty of assessing individual
 species’ contributions and the lack of a metric allowing for a
 quantification of redundancy within communities, few attempts have been
 made to estimate redundancy for individual ecosystem processes. We present
 a new method linking interaction metrics with metabolic theory that allows
 for a quantification of redundancy at the level of ecosystem processes.
 Using this approach, redundancy in the predation on aphids and other prey
 by natural enemies across a landscape heterogeneity gradient was
 estimated. Functional redundancy of predators was high in heterogeneous
 landscapes, low in homogeneous landscapes, and scaled with predator
 specialisation. Our approach allows quantifying functional redundancy
 within communities and can be used to assess the role of functional
 redundancy across a wide variety of ecosystem processes and environmental
 factors
description: MGCA, community
 composition and landscape dataData file used for the
 calculation of functional redundancy in natural predator communities.
 Treatment: C = conventional, O = organic; Abundance = activity density
 corrected by metabolic rate; H' = Shannon diversity of the landscape
 at 500 and 1000 m radius, respectively; Border = cumulative length of
 borders between habitat patches; Patches = number of distinct habitat
 patches within 1000 m radius.Raw
 data.csv
DOI: 10.5061/dryad.n8065tv
title: Data from: Insights into the origin and evolution of plant sigma factors

description: Plant sigma factors (SIGs) are key regulators of chloroplast gene
 expression and chloroplast differentiation. Despite their functional
 importance, the evolutionary history of these factors remains unclear.
 Using newly available genomic and transcriptomic data, we conducted a
 detailed and comprehensive phylogenetic analysis of SIG homologues from
 land plants and algae. Our results reveal that plants have acquired sigma
 factors from ancestor cyanobacteria via endosymbiotic gene transfers,
 forming four major clades, namely, super-SIG2 (SIG2/3/4/6/SIG2-like),
 SIG1, SIG5 and SIGX. The super-SIG2 clade was confirmed to have evolved
 from cyanobacterial SIGA factors, and a novel clade (SIGX) specific to
 non-angiosperms was revealed here. Gene duplications (mainly whole genome
 duplications) within lineages and species have contributed to the
 expansion of sigma factors in plants, especially flowering plants. We
 hypothesize that plant sigma factors originated from different
 endosymbiotic ancestors and evolved diverse functions. This not only sheds
 new light on the evolution of plant SIG genes but also paves the way for
 understanding the functional diversification of these genes.
description: SIG_proteins_matrixProtein matrix for Fig. S1.SIG_proteins_treesTree files for Fig. S1super_SIG2_proteins_matrixProtein matrix for Fig. S2super_SIG2_proteins_treesTree files for Fig. S2SIG1_proteins_matrixProtein matrix for Fig. S3SIG1_proteins_treesTree files for Fig. S3SIG5_proteins_matrixProtein matrix for Fig. S4SIG5_proteins_treesTree files for Fig. S4SIGX_proteins_matrixProtein matrix for Fig. S5SIGX_proteins_treesTree files for Fig. S5
DOI: 10.5061/dryad.0r852nm
title: Data from: Ecological constraints coupled with deep-time habitat dynamics predict the latitudinal diversity gradient in reef fishes

description: We develop a spatially explicit model of diversification based on
 paleohabitat to explore the predictions of four major hypotheses
 potentially explaining the latitudinal diversity gradient (LDG), namely,
 the ‘time-area’, ‘tropical niche conservatism’, ‘ecological limits’ and
 ‘evolutionary speed’ hypotheses. We compare simulation outputs to observed
 diversity gradients in the global reef fish fauna. Our simulations show
 that these hypotheses are non-mutually exclusive and that their relative
 influence depends on the time scale considered. Indeed, simulations
 suggest that reef habitat dynamics produced the LDG during deep geological
 time, while ecological constraints shaped the modern LDG, with a strong
 influence of the reduction in the latitudinal extent of tropical reefs
 during the Neogene. Overall, this study illustrates how mechanistic models
 in ecology and evolution can provide a temporal and spatial understanding
 of the role of speciation, extinction and dispersal in generating
 contemporary biodiversity patterns.
description: Presence Absence Matrix
 of Acanthomorph speciesThis rdata file contains
 a matrix of presence/absence within 1° cells. The two first columns are
 the coordinates and the others are the presence/absence of
 species.PA_acanth.rda
DOI: 10.5061/dryad.gv0p9n4
title: Data from: Pollen limitation and autonomous selfing ability interact to shape variation in outcrossing rate across a species range

description: Premise of the study: Hermaphroditic plants commonly reproduce through a
 mixture of selfing and outcrossing. The degree to which outcrossing rates
 reflect the availability of outcross pollen, genetic differentiation in
 the ability to autonomously self-fertilize, or both is often unclear.
 Despite the potential for autonomy and the pollination environment to
 jointly influence outcrossing, this interaction is rarely studied.
 Methods: We reviewed literature testing whether the pollination
 environment or floral traits causing autonomous selfing predict
 outcrossing rate variation among populations. We also measured outcrossing
 rates in 23 populations of Campanula americana and examined associations
 with the pollination environment, autonomy, and their interaction. Key
 Results: Our review revealed that traits facilitating selfing were often
 negatively associated with outcrossing rates while most aspects of the
 pollination environment poorly predicted outcrossing. Populations of C.
 americana varied from mixed mating to highly outcrossing but variation was
 unrelated to population size, density, pollen limitation, or autonomous
 selfing ability. Outcrossing rate was significantly influenced by an
 interaction between autonomous selfing ability and pollen limitation. In
 highly autonomous populations, elevated pollen limitation was associated
 with reduced outcrossing, while there was no relationship for less
 autonomous populations. Conclusions: Both the ability to self autonomously
 and pollen limitation interact to shape outcrossing rates in C. americana.
 This work suggests autonomy affords mating system flexibility, though it
 is not ubiquitous in all populations across the species range.
 Interactions between traits influencing autonomy and pollen limitation are
 likely to explain variation in outcrossing rates among populations of
 flowering plants.
description: microsatellite
 datathe size and peak area
 of alleles generated in fragment analysis.microsatellite
 genotypesInferred tetraploid
 genotypes, using the MAC-PR method (Esselink et al.
 2004).MACPR R
 scriptR script that infers
 tetraploid genotypes given allele size and peak area
 data.MACPR.RMLTET_formatterR script that converts genotypic data (see microsatellite genotypes.csv) into MLTET formatMLTET_AL79AL79.datMLTET_AL2012AL2012.datMLTET_ALBGALBG.datMLTET_AR125AR125.datMLTET_IA10IA10.datMLTET_IN46IN46.datMLTET_IN77IN77.datMLTET_KS60KS60.datMLTET_KY51KY51.datMLTET_MI126MI126.datMLTET_MI127MI127.datMLTET_MN117MN117.datMLTET_MN118MN118.datMLTET_MO49MO49.datMLTET_MO57MO57.datMLTET_MO115MO115.datMLTET_MO116MO116.datMLTET_OH64OH64.datMLTET_OH119OH119.datMLTET_OK61OK61.datMLTET_PA27PA27.datMLTET_TN19TN19.datMLTET_WI128WI128.datREADME_final
DOI: 10.5061/dryad.r530142
title: Data from: Modelling variability in the fire-response of an endangered bird to improve fire-management

description: Conservation managers regularly burn vegetation to regenerate habitat for
 fire-dependent species. When determining the time-since-fire at which to
 burn, managers model change in a species’ occurrence over time, post-fire
 (fire-response curve) and identify the time-since-fire associated with
 decline in occurrence. However, where species exhibit variability in their
 fire-response across space, using a single fire-response curve to
 determine the timing of burns may lead to burning habitat at an
 inappropriate time-since-fire. We tested if elevation, local topography,
 soil properties, vegetation type or evapotranspiration affect the
 fire-response of the endangered mallee emu-wren Stipiturus mallee and its
 hummock-grass habitat Triodia scariosa in south-eastern Australia (n=
 217). Previous work on the mallee emu-wren found a unimodal fire-response
 with decline in occurrence at ~30-50 years-since-fire and a time-window of
 occurrence of ~30 years. We found that time-since-fire and elevation
 interact to affect the mallee emu-wren fire-response. At high elevations
 (55-98 m), mallee emu-wrens declined in occurrence at ~50
 years-since-fire, with a time-window of occurrence of 20-40 years.
 However, at low elevations (28-55 m), mallee emu-wrens showed no decline
 in occurrence with increasing time-since-fire with a time-window of
 occurrence of up to 107 years. Extent cover of Tall T. scariosa showed
 similar patterns to the mallee emu-wren, indicating that vegetation
 structure is a likely driver of variability in the mallee emu-wren
 fire-response. We speculate that the effect of low elevation is mediated
 by increased soil nutrient and water availability for key plants. We used
 our findings to map the appropriate time-since-fire at which to burn to
 regenerate habitat for the mallee emu-wren across the study-region. We
 recommend no burning for regeneration across one-third of potential
 habitat, because the mallee emu-wren showed no decline in occurrence in
 these areas. We recommend managers model variability in species’
 fire-responses across space to improve the timing of burns for
 regeneration.
description: Mallee emu-wren
 occurrence data with environmental co-variatespresence absence data
 for the mallee emu-wren at each study site. Each study site also has
 clearly labelled environmental co-variates associated with that
 site.MALLEE_EMU_WREN_DATA.csvTriodia data for each site with environmental co-variatesPercent cover of Triodia (&gt;45 cm tall) at each study site. Clearly labelled environmental co-variates are also included for each study site.TRIODIA_DATA.csv