cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.kd51c5bbd
title: Data from: Interplay between rainfall and hillslope hydrology determines drought resistance of tropical vegetation

description: Droughts are predicted to increase in both frequency and intensity by the
 end of the 21st century, but ecosystem response is not expected to be
 uniform. At the landscape scale, ecosystem response to drought is highly
 heterogeneous. Here we assess the importance of the hill-to-valley
 hydrologic gradient in shaping vegetation hydraulic properties related to
 drought resistance for three locations across a rainfall seasonality
 gradient in South America. For this, we use hydraulic traits related to
 xylem resistance to embolism and compare the functional composition and
 diversity of tree communities. We show that the hydrologic gradient
 systematically selects for community assemblages that are more vulnerable
 to embolism in valleys, regardless of rainfall. Under the same rainfall
 regime, diversity in resistance to embolism is higher on hills than
 valleys, suggesting that strategies to cope with drought are more
 important on hills. With increasing seasonality, diversity in embolism
 resistance increases on hills and decreases in valleys. Our
 results show that differential groundwater access from hilltops to valleys
 select for distinctive hydraulic properties, potentially explaining
 species turnover along topographical gradients. Incorporating this
 relationship might improve the representation of vegetation in climate
 models and the prediction of how different communities will respond to
 extreme droughts.
DOI: 10.5061/dryad.9ghx3ffnp
title: Bouts of rest and physical activity in C57BL/6J mice

description: The objective was to exploit the raw data output from a scalable home cage
 (type IIL IVC) monitoring (HCM) system (DVC®), to characterize the pattern
 of undisrupted rest and physical activity (PA) of C57BL/6J mice. The
 system’s tracking algorithm shows that mice in isolation spend 67% of the
 time in bouts of long rest (≥40s) and 59% of the time was interpreted as
 sleep. Twenty percent is physical activity (PA), split equally between
 local movements and locomotion. Decomposition revealed that a day contains
 ~6500 discrete bouts of short and long rest, and local and locomotor
 movements. Mice travel ~330m per day, mainly during the dark hours, while
 travelling speed is similar through the light-dark cycle. Locomotor bouts
 are usually &lt;0.2m and &lt;1% are &gt;1m. Tracking also
 revealed fits of abnormal behaviour. The starting positions of the bouts
 showed no preference for the rear over the front of the cage floor, while
 there was a strong bias for the peripheral (75%) over the central floor
 area. The composition of bouts has a characteristic circadian pattern,
 however, intrusive husbandry routines increased bout fragmentation by
 ~40%. Extracting electrode activations density (EAD) from the raw data
 yielded results close to those obtained with the tracking algorithm, with
 59% of the time in long rest (&lt;1 EAD s-1) and 20% in PA. We confirm
 that EAD correlates closely with movement distance (rs&gt;0.95) and
 the data agreed in ~96% of the file time. Thus, albeit EAD is less
 informative, it may serve as a proxy for PA and rest, enabling monitoring
 group-housed mice. The data show that a change in housing density from one
 to two, and up to three mice had the same effect size on EAD (~2) with no
 difference between sexes. The EAD deviated significantly from this
 stepwise increase with 4 mice per cage, suggesting a crowdedness stress
 inducing sex-specific adaptations. We conclude that informative metrics on
 rest and PA can be automatically extracted from the raw data flow in
 near-real time (&lt; 1 hrs). These metrics relay useful longitudinal
 information to those who use or care for the animals.
DOI: 10.5061/dryad.2bvq83bvk
title: Data for: Allometric relationships for eight species of 4–5 year old nitrogen-fixing and non-fixing trees

description: Allometric equations are often used to estimate plant biomass allocation
 to different tissue types from easier-to-measure quantities. Biomass
 allocation, and thus allometric equations, often differs by species and
 sometimes varies with nutrient availability. We measured biomass
 components for five nitrogen-fixing tree species (Robinia pseudoacacia,
 Gliricidia sepium, Casuarina equisetifolia, Acacia koa, Morella faya) and
 three non-fixing tree species (Betula nigra, Psidium cattleianum, Dodonaea
 viscosa) grown in field sites in New York and Hawaii for 4–5 years and
 subjected to four fertilization treatments. We measured total aboveground
 biomass, foliar biomass, main stem biomass, secondary stem biomass, and
 twig biomass in all species, and belowground biomass in Robinia
 pseudoacacia and Betula nigra, along with basal diameter, height, and
 canopy dimensions. The individuals spanned a wide size range (&lt;1 to
 16 cm basal diameter and 0.24 to 8.8 m height). For each biomass
 component, aboveground biomass, belowground biomass, and total biomass, we
 determined the following four allometric equations: the most parsimonious
 (lowest AIC) overall, the most parsimonious without a fertilization
 effect, the most parsimonious without canopy dimensions, and an equation
 with basal diameter only. For some species, the most parsimonious overall
 equation included fertilization effects, but fertilization effects were
 inconsistent across fertilization treatments. We therefore concluded that
 fertilization does not clearly affect allometric relationships in these
 species, size classes, and growth conditions. Our best-fit allometric
 equations without fertilization effects had the following R2 values:
 0.91–0.99 for aboveground biomass (the range is across species), 0.95 for
 belowground biomass, 0.80–0.96 for foliar biomass, 0.94–0.99 for main stem
 biomass, 0.77–0.98 for secondary stem biomass, and 0.88–0.99 for twig
 biomass. Our equations can be used to estimate overall biomass and biomass
 of tissue components for these size classes in these species, and our
 results indicate that soil fertility does not need to be considered when
 using allometric relationships for these size classes in these species.
DOI: 10.6086/d1tq2h
title: Dataset for: Diets of two non-native praying mantids (Tenodera sinensis and Mantis religiosa) show consumption of arthropods across all ecological roles

description: These data are from a comparative diet analysis which reveals many
 ecological guilds are consumed by nonnative mantids in old-field
 ecosystems. We observed low diet overlap between mantid species and
 overall high diet variability across samples. 
description: Mantids were collected in the field. We dissected their gut
 contents and used metabarcoding approaches to identify major diet
 components.
DOI: 10.5061/dryad.0cfxpnw6z
title: A toolkit for precise, multigene control in Saccharomyces cerevisiae

description: Systems that allow researchers to precisely control the expression of
 genes are fundamental to biological research, biotechnology, and synthetic
 biology. However, few inducible gene expression systems exist that can
 enable simultaneous, multi-gene control in the important model organism
 and chassis, Saccharomyces cerevisiae. Here, we repurposed ligand binding
 domains (LBDs) from mammalian Type I nuclear receptors to establish a
 family of up to five orthogonal synthetic gene expression systems in
 yeast. Our systems enable tight, independent, multi-gene control through
 the addition of inert hormones, and are capable of driving robust gene
 expression outputs. As a proof-of-principle, we placed expression of four
 enzymes from the violacein biosynthetic pathway under independent
 expression control to selectively route pathway flux. Our results
 establish a modular, versatile, and potentially expandable toolkit for
 multidimensional control of gene expression in yeast that can be used to
 construct and control naturally-occurring and synthetic gene networks.
description: These data were generated to support the development and
 characterization of a toolkit used to construct orthogonal, small
 molecule-inducible genetic programs in yeast. The toolkit is based on
 synthetic transcription factors derived from human type I nuclear
 receptors fused to zinc finger DNA binding domains and transcription
 activation domains. In the published work, we extensively characterized
 synthetic transcription factor performance and orthogonality. As a
 proof-of-concept, we modulated flux through the violacein biosynthetic
 pathway by selectively inducing expression of combinations of pathway
 enzymes.  Our datasets, comprised of data gathered
 using flow cytometry and high-performance liquid chromatography, support
 the four major figures of our manuscript: 
 The mechanism of action, features, and design of synthetic
 transcription factors for genetic circuit construction in
 yeast. The characterization of maximum induction,
 basal expression, and dose curve response for the toolkit
 elements. The characterization of cross-reactivity
 and orthogonality among the synthetic transcription factors.
 The application of the engineered toolkit to the violacein
 biosynthetic pathway as a proof-of-principle. 
 The arranged datasets for each figure are included in .xlsx
 files, named “Fig#_arranged,” and the processed data are presented in
 .pzfx files, named “Fig#_processed.” They are accompanied by the relevant
 raw dataset files. Please refer to the README file for
 a more detailed description of the data and file structure.
description: The raw datasets require FlowJo to
 open, and the processed data files require GraphPad Prism.
DOI: 10.5061/dryad.qnk98sfms
title: Data from: Predicting regional carbon price in China based on multi-factor HKELM by combining secondary decomposition and ensemble learning

description: Accurately predicting carbon price is crucial for risk avoidance in the
 carbon financial market. In light of the complex characteristics of the
 regional carbon price in China, this paper proposes a model to forecast
 carbon price based on the multi-factor hybrid kernel-based extreme
 learning machine (HKELM) by combining secondary decomposition and ensemble
 learning. Variational mode decomposition (VMD) is first used to decompose
 the carbon price into several modes, and range entropy is then used to
 reconstruct these modes. The multi-factor HKELM optimized by the sparrow
 search algorithm is used to forecast the reconstructed subsequences, where
 the main external factors innovatively selected by maximum information
 coefficient and historical time-series data on carbon prices are both
 considered as input variables to the forecasting model. Following this,
 the improved complete ensemble-based empirical mode decomposition with
 adaptive noise and range entropy are respectively used to decompose and
 reconstruct the residual term generated by VMD. Finally, the nonlinear
 ensemble learning method is introduced to determine the predictions of
 residual term and final carbon price. In the empirical analysis of
 Guangzhou market, the root mean square error (RMSE), mean absolute error
 (MAE) and mean absolute percentage error (MAPE) of the model are 0.1716,
 0.1218 and 0.0026, respectively. The proposed model outperforms other
 comparative models in predicting accuracy. The work here extends the
 research on forecasting theory and methods of predicting the carbon price.
description: Please see the README document
 and the accompanying published article: Predicting regional carbon price in China based
 on multi-factor HKELM by combining secondary decomposition and ensemble
 learning. Accepted. DOI:
 10.1371/journal.pone.0285311
DOI: 10.5061/dryad.gqnk98st8
title: Elevation and phylogeny shape herbaceous seed dormancy in a biodiversity hotspot of southwest China

description: Seed dormancy contributes greatly to successful establishment and
 community stability and shows large variation over a continuous status
 scale in mountain ecosystems. Although empirical studies have shown that
 seed dormancy status (SDS) is shaped by elevation and phylogenetic history
 in mountain ecosystems, few studies have quantified their combined effects
 on SDS. Here, we collected mature seeds from 51 populations of 11
 Impatiens species (Balsaminaceae) along an elevational gradient in the
 Gaoligong Mountains of southwest China and estimated SDS using mean
 dormancy percentage of fresh seeds germinated at three constant
 temperatures (15, 20, and 25 °C). We downloaded 19 bioclimatic variables
 from WorldClim v.2.1 for each Impatiens population and used internal
 transcribed spacer (ITS), atpB-rbcL, and trnL-F molecular sequences from
 the GenBank nucleotide database to construct a phylogenetic tree of the 11
 species of Impatiens. Logistic regression model analysis was performed to
 quantify the effects of phylogeny and environment on SDS. Results
 identified a significant phylogenetic SDS signal in the Impatiens species.
 Furthermore, elevation and phylogeny accounted for 63.629% of the total
 variation in SDS among the Impatiens populations. The best logistic model
 indicated that temperature was the main factor influencing variation in
 SDS among the Impatiens species, and model residuals were significantly
 correlated with phylogeny, but not with elevation. Our results indicated
 that seed dormancy is phylogenetically conserved, and climate drives
 elevational patterns of SDS variation in mountain ecosystems. This study
 provides new insights into the response of seed plant diversity to climate
 change.
DOI: 10.5061/dryad.bzkh189f6
title: Parasite infection and the movement of the aquatic snail Potamopyrgus antipodarum along a depth cline

description: Parasite species that use two or more host species during their life cycle
 depend on successful transmission between these species. These successive
 host species may have different habitat requirements; for example, one
 host species can be aquatic while the other is terrestrial. To overcome
 this complicating factor in transmission, a wide diversity of parasite
 species have adaptations that alter habitat preference in one host species
 in order to facilitate transmission to the next host species. Two common
 trematode parasites from New Zealand, Atriophallophorus winterbourni and
 Notocotylus spp., both have a two-host life‑cycle. The aquatic snail
 Potamopyrgus antipodarum is the intermediate host, from which the
 parasites require transmission to dabbling ducks or other waterfowl. Of
 these parasites, A. winterbourni is most frequently found in snails from
 the shallow-water margin, which may indicate parasite-induced movement of
 infected snails to the foraging habitat of dabbling ducks. To test if the
 parasites manipulate the snails to move to shallow water, we stretched
 tubular mesh cages across depth-specific ecological habitat zones in a
 lake. Both infected and healthy snails were released into the cages. After
 eleven days, significantly higher infection frequencies of A. winterbourni
 were retrieved from the shallowest end of the cages, while Notocotylus
 spp. frequencies did not vary with depth. The hypothesis that
 A. winterbourni induces its snail host to move toward the
 shallow-water habitat cannot be rejected based on the results from the
 experiment. Although additional research will be needed to address
 alternative explanations, the depth preference of infected snails may be a
 parasite adaptation that facilitates trophic transmission of parasites to
 dabbling ducks.
DOI: 10.5061/dryad.f4qrfj718
title: Three-dimensional morphology of the biramous appendages in Isoxys from the early Cambrian of South China, and its implications for early euarthropod evolution

description: Early euarthropod evolution involved a major transition from
 lobopodian-like taxa to organisms featuring a segmented, well-sclerotized
 trunk (arthrodization) and limbs (arthropodization). However, the precise
 origin of a completely arthrodized trunk and arthropodized ventral
 biramous appendages remain controversial, as well as the early onset of
 anterior-posterior limb differentiation in stem-group euarthropods. New
 fossil material and micro-computed tomography inform the detailed
 morphology of the arthropodized biramous appendages in the
 carapace-bearing euarthropod Isoxys curvirostratus from the early Cambrian
 Chengjiang biota. In addition to well-developed grasping frontal
 appendages. I. curvirostratus possesses two batches of morphologically and
 functionally distinct biramous limbs. The first batch consists of four
 pairs of short cephalic appendages with robust endites with a feeding
 function, whereas the second batch has more elongate trunk appendages for
 locomotion. Critically, our new material shows that the trunk of I.
 curvirostratus was not arthrodized. The results of our phylogenetic
 analyses recover isoxyids as some of the earliest branching sclerotized
 euarthropods, and strenghens the hypothesis that arthropodized biramous
 appendage evolved before full body arthrodization.
description: Anatomical data are collected by photos from a Keyence VHX 6000
 and Leica M205AF stereomicroscope, a GE Phoenix Nanotom cone beam scanner
 and a Zeiss Xradia 520 Versa X-ray microscope. And we
 analysed it in MrBayes v.3.2.7.
description: Nexus (.nex) is a common file type for phylogenetic data, and the
 required runfile to use MrBayes for phylogenetic analysis.
 .p are sampled parameter files from MrBayes analysis, output for
 each run specigied. Newick (.tre) files are
 phylogenetic tree outputs, which can be visualized directly e.g. with
 Figtree. .tnt is a file type for phylogenetic data,
 specifically the required runfile to conduct maximum parsimony
 phylogenetic analysis in TNT.
DOI: 10.5061/dryad.83bk3j9wk
title: Data for: Female foraging strategy co-evolve with sexual harassment intensity in the Trinidadian guppy

description: Sexual harassment is a widespread evolutionary outcome of sexual conflict
 over mating rates. Male harassment can impose costs on females, and
 females often change their behaviors to avoid unwanted attention. In
 Trinidadian guppies (Poecilia reticulata), females experience two
 potential sources of male harassment: coercive sneak mating behavior (more
 harmful, and common in high-predation populations) and courtship displays
 (less harmful, and common in low-predation populations). Here, we tested
 whether female foraging strategy co-evolves with decreasing levels of male
 harassment as guppies colonize low-predation environments. We set up
 outdoor stream mesocosms with ecologically naïve males and females from
 either a high- or a low-predation population in a 2x2 design and tested
 whether populations diverge in female response to male harassment. We
 found that low-predation males used more courtship and fewer sneak tactics
 than their natural high-predation ancestors. Male sneak behavior reduced
 female foraging efficiency, and this effect was stronger for
 high-predation females. We then tested whether a similar pattern evolved
 in a population where high-predation guppies were artificially introduced
 to a low-predation habitat 12 years ago. Unexpectedly, the introduced
 males had evolved decreased courtship and increased sneak tactics. Here,
 increased male courtship, but not increased sneak behavior, reduced female
 foraging efficiency, and this effect existed only in the introduced,
 low-predation population. Altogether, our results suggest that both male
 mating behaviors harass females to differing degrees; females evolve
 foraging behavior in response to divergence in male mating strategies, but
 populations may differ in strategies of enduring or ignoring unwanted
 attention.
description: Data was collected on a physical datasheet, entered into an Excel
 file, and processed in R. Saved as an Rda file.
description: Data is saved as Rda file, and code is organized in an R markdown
 file with annotation. R and R Studio is needed to open data file and
 code.
DOI: 10.5061/dryad.280gb5mtm
title: Biogeographic barriers and historical climate affect phylogeographic structure and demographic history of the common gartersnake

description: Aim: Current distributions of widespread North American (NA) species have
 been shaped by Pleistocene glacial cycles, latitudinal temperature
 gradients, sharp longitudinal habitat transitions, and the vicariant
 effects of major mountain and river systems that subdivide the continent.
 Within these transcontinental species, genetic diversity patterns might
 not conform to established biogeographic breaks compared to more spatially
 restricted taxa due to intrinsic differences (e.g., greater dispersal
 ability in generalist species) or spatiotemporal differences (e.g.,
 wide-ranging species predate younger barriers). In this study, we
 highlight the effects of these extrinsic variables on genetic structuring
 by investigating the phylogeographic history of a widespread generalist
 squamate found throughout NA.  Location: North America
 Taxon: Common gartersnake, Thamnophis sirtalis Methods: We
 evaluate the effects of major river basins and the forest-grassland
 transition into the Interior Plains on genetic structure patterns using
 phylogenetic, spatially informed population structure, and demographic
 analyses of SNP data, and address range expansion history with ecological
 niche modeling using locality and historic climate data. Results: We
 identify four phylogeographic lineages with varying degrees of
 connectivity between them. We find discordant population structure
 patterns between sex-linked and autosomal loci with respect to the
 relationship between the central NA lineage relative to coastal lineages.
 We find support for southeast Pleistocene refugia where recent secondary
 contact occurred during the Last Glacial Maximum and evidence for both
 northern and southern refugia in western NA. Main Conclusion: Our results
 provide strong evidence for a Middle Pliocene origin for Thamnophis
 sirtalis in central-southeastern NA preceding its rapid expansion across
 the continent prior to middle Pleistocene climate-mediated lineage
 formation. We implicate major riverine networks within the Mississippi
 watershed in likely repeated westward expansion events across the Interior
 Plains. Finally, we corroborate prior conclusions that phenotypic
 differences between subspecies do not reflect shared evolutionary history
 and note that the degree of separation between inferred lineages warrants
 further investigation before any taxonomic revisions are proposed.
DOI: 10.6084/m9.figshare.31169579
title: S5: Detrital zircon ages from the Palaeoproterozoic Tanque Novo–Ipirá Complex, Itabuna–Salvador–Curaçá Orogen, northern São Francisco Craton, Brazil: records from Kenorland and Columbia supercontinents

description: Table 2
DOI: 10.6084/m9.figshare.31169579.v1
title: S5: Detrital zircon ages from the Palaeoproterozoic Tanque Novo–Ipirá Complex, Itabuna–Salvador–Curaçá Orogen, northern São Francisco Craton, Brazil: records from Kenorland and Columbia supercontinents

description: Table 2