cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d84hg87
title: Data from: Fluctuations in age structure and their variable influence on population growth

description: 1- Temporal fluctuations in growth rates can arise from both variation in
 age-specific vital rates and temporal fluctuations in age structure (i.e.,
 the relative abundance of individuals in each age-class). However,
 empirical assessments of temporal fluctuations in age structure and their
 effects on population growth rate are rare. Most research has focused on
 understanding the contribution of changing vital rates to population
 growth rates and these analyses routinely assume that: (i) populations
 have stable age distributions, (ii) environmental influences on vital
 rates and age structure are stationary (i.e., the mean and/or variance of
 these processes does not change over time), and (iii) dynamics are
 independent of density. 2- Here we quantified fluctuations in age
 structure and assessed whether they were stationary for four populations
 of free-ranging vertebrates: moose (observed for 48 years), elk (15
 years), tawny owls (15 years) and gray wolves (17 years). We also assessed
 the extent that fluctuations in age structure were useful for predicting
 annual population growth rates using models which account for
 density-dependence. 3- Fluctuations in age structure were of a similar
 magnitude to fluctuations in abundance. For three populations (moose, elk,
 owls), the mean and the skew of the age distribution fluctuated without
 stabilizing over the observed time periods. More precisely, the sample
 variance (interannual variance) of age structure indices increased with
 the length of the study period which suggests that fluctuations in age
 structure were non-stationary for these populations – at least over the
 15-48 year periods analysed. 4- Fluctuations in age structure were
 associated with population growth rate for two populations. In particular,
 population growth varied from positive to negative for moose and from near
 zero to negative for elk as the average age of adults increased over its
 observed range. 5- Non-stationarity in age structure may represent an
 important mechanism by which abundance becomes non-stationary – and
 therefore difficult to forecast – over time scales of concern to wildlife
 managers. Overall, our results emphasize the need for vertebrate
 populations to be modelled using approaches that consider transient
 dynamics and density-dependence, and that do not rely on the assumption
 that environmental processes are stationary.
description: Data for
 DryadFile contains estimates
 of abundance and three indices of age (mean age, and median age of adults
 and the proportion of adults in the population that were considered
 senescent) structure for each of the four study
 populations.
DOI: 10.5061/dryad.144h1s1
title: Data from: Extraocular motoneuron pools develop along a dorsoventral axis in zebrafish, Danio rerio

description: Both spatial and temporal cues determine the fate of immature neurons. A
 major challenge at the interface of developmental and systems neuroscience
 is to relate this spatiotemporal trajectory of maturation to circuit‐level
 functional organization. This study examined the development of two
 extraocular motor nuclei (nIII and nIV), structures in which a
 motoneuron's identity, or choice of muscle partner, defines its
 behavioral role. We used retro‐orbital dye fills, in combination with
 fluorescent markers for motoneuron location and birthdate, to probe
 spatial and temporal organization of the oculomotor (nIII) and trochlear
 (nIV) nuclei in the larval zebrafish. We describe a dorsoventral
 organization of the four nIII motoneuron pools, in which inferior and
 medial rectus motoneurons occupy dorsal nIII, while inferior oblique and
 superior rectus motoneurons occupy distinct divisions of ventral nIII.
 Dorsal nIII motoneurons are, moreover, born before motoneurons of ventral
 nIII and nIV. The order of neurogenesis can therefore account for the
 dorsoventral organization of nIII and may play a primary role in
 determining motoneuron identity. We propose that the temporal development
 of extraocular motoneurons plays a key role in assembling a functional
 oculomotor circuit.
description: Fig 3Raw data associated with
 Figure 3Fig 5All the data in Figure
 5Fig
 6-7Data found in BOTH
 figures 6-7 (the SR cells)Fig 7 part 1 of
 3All
 the data in Figure 7, part 1 of 3Fig 7 pt1 of
 3.zipFig 6All the data in Figure
 614dpf
 boundariesData that describes the
 boundaries of 14dpf fish. No associated figure.Fig 7 2 of
 3All
 the data in Figure 7, part 2 of 3Fig 7 pt2 of
 3.zipFig 7 part 3 of
 3All
 the data in Figure 7, part 3 of 3Fig 7 pt3 of
 3.zipFig 8
 1of2All the data in Figure
 8, part 1 of 2Fig 8 pt1 of
 2.zipFig 8
 2of2All the data in Figure
 8, part 2 of 2Fig 8 pt2 of
 2.zip
DOI: 10.5061/dryad.j2n1vq2
title: Data from: Shifts in woody plant defense syndromes during leaf development

description: 1. Herbivores target young leaves in forests worldwide. How this strong
 and predictable selection pressure has shaped plant defense syndromes
 remains unclear. Specifically, whether young leaf herbivory has led to
 general global patterns of shifting leaf defences during lead development
 (i.e. ontogenetic trajectories) remains unknown but likely. 2. Using
 meta-analysis, we have synthesized developmental shifts in chemical,
 physical, and indirect defence traits, as well as leaf nutrient content,
 during leaf expansion and maturation across 124 woody plant species. Leaf
 traits were compared for immature young leaves versus mature leaves within
 studies, and these developmental shifts were then compared across studies
 to characterize general patterns. 3. Traits shifted strongly during leaf
 maturation, giving rise to discrete defence syndromes, with young leaves
 having significantly greater nutrient and secondary chemistry
 concentrations but reduced toughness and indirect defence traits than
 mature leaves. These patterns corroborate a growing consensus on the
 importance of ontogeny in plant defences, illustrating ontogenetic
 trajectories at the scale of leaves. 4. Trait developmental shifts were
 stronger in species with synchronous than asynchronous leaf flushing, but
 whether this reflects variation across biomes remains unclear. 5. Future
 research on under-studied traits, such as alkaloids, cyanogenesis, leaf
 phosphorus content, and indirect defence traits, and in a more
 biogeographic context will provide additional insights into the generality
 of shifts in defence syndromes during leaf development.
description: Barton_Leaf_Development_Defence_Syndrome_DataLog response ratio data for complete meta-analysis.
DOI: 10.5061/dryad.gr68f2j
title: Data from: Temperature accounts for the biodiversity of a hyperdiverse group of insects in urban Los Angeles

description: The urban heat island effect is a worldwide phenomenon that has been
 linked to species’ distributions and abundances in cities. However,
 effects of urban heat on biotic communities are nearly impossible to
 disentangle from effects of land cover in most cases because hotter urban
 sites also have less vegetation and more impervious surfaces than cooler
 sites within cities. We sampled phorid flies, one of the largest, most
 biologically diverse families of true flies (Insecta: Diptera: Phoridae),
 at 30 sites distributed within the central Los Angeles Basin, where we
 found that temperature and the density of urban land cover are decoupled.
 Abundance, richness, and community composition of phorids inside urban Los
 Angeles were most parsimoniously accounted for by mean air temperature in
 the week preceding sampling. Sites with intermediate mean temperatures had
 more phorid fly individuals and higher richness. Communities were more
 even at urban sites with lower minimum temperatures and sites located
 further away from natural areas, suggesting that communities separated
 from natural source populations may be more homogenized. Species
 composition was best explained by minimum temperature. Inasmuch as warmer
 areas within cities can predict future effects of climate change, phorid
 fly communities are likely to shift non-linearly under future climates in
 more natural areas. Exhaustive surveys of biotic communities within
 cities, such as the one we describe here, can provide baselines for
 determining the effects of urban and global climate warming as they
 intensify.
description: Locations of BioSCAN 1
 sitesThe physical locations
 of the sites used for sampling, with resolution limited to protect the
 privacy of the community participants in the project.dis_CPAD.csvFly species occurrences and associated weather dataSpecies occurrences from each sampling eventfly_data_with_weather.csvRemote sensing data from BioSCAN sitesThese are the remote sensing data that were used for the analyses in this manuscript.site_ndvi_imperv.csvWeekly weather data in 2014These are the weekly weather data, collected from the weather station at each sampling site. Minor gaps in the data have been replaced using linear modeling as described in the associated manuscript.weather_data_compiled_weekly_res.csv
DOI: 10.5061/dryad.r9m0f6r
title: Data from: Sex-differences in nutrient intake can reduce the potential for sexual conflict over fitness maximisation by female and male crickets

description: As females and males have different roles in reproduction, they are
 expected to require different nutrients for the expression of reproductive
 traits. However, due to their shared genome, both sexes may be constrained
 in the regulation of nutrient intake that maximises sex specific fitness.
 Here, we used the Geometric Framework for nutrition to examine the effect
 of macronutrient and micronutrient intakes on lifespan, fecundity, and
 cuticular hydrocarbons (CHCs) that signal mate quality to prospective
 mates in female field crickets, Teleogryllus oceanicus. In addition, we
 contrasted nutritional effects on life-history traits between males and
 females to determine how sex differences influence nutrient regulation. We
 found that carbohydrate intake maximised female lifespan and protein
 intake influenced CHC expression, while early life fecundity (cumulative
 fecundity at Day 21) and lifetime fecundity were dependent on both
 macronutrient and micronutrient intakes. Fecundity required different
 nutrient blends to those required to optimise sperm viability in males,
 generating the potential for sexual conflict over macronutrient intake.
 The regulation of protein (P) and carbohydrate (C) intakes by virgin and
 mated females initially matched that of males, but females adjusted their
 intake to a higher P:C ratio, 1P:2C, that maximised fecundity as they
 aged. This suggests that a sex-specific, age-dependent change in intake
 target for sexually mature females, regardless of their mating status,
 adjusts protein consumption in preparation for oviposition. Sex
 differences in the regulation of nutrient intake to optimise critical
 reproductive traits in female and male T. oceanicus, provides an example
 of how sexual conflict over nutrition can shape differences in foraging
 between the sexes.
description: Ng et al_2019_J Evol
 Biol_raw dataExcel spreadsheet
 containing the individual data of female life history traits with their
 protein, carbohydrate and micronutrient intakes.
DOI: 10.5061/dryad.pt2624c
title: Data from: Complex conductivity of graphitic schists and sandstones

description: Spectral Induced Polarization spectra were carried out on 3 graphitic
 schists and 2 graphitic sandstones. The microstructural arrangement of
 graphite of two graphitic schists was studied with thin sections using
 transmitted and reflected light optical and electron microscopic methods.
 Chemical maps of selected areas confirm the presence of carbon. The
 complex conductivity spectra were measured in the frequency range 10 mHz
 to 45 kHz and in the temperature range +20°C down to -15°C. The measured
 spectra are fitted with a double Cole Cole complex conductivity model with
 one component associated with the polarization of graphite and the second
 component associated with the Maxwell Wagner polarization. The Cole Cole
 exponent and the chargeability are observed to be almost independent of
 temperature including in freezing conditions. The conductivity and
 relaxation time are dependent on the temperature in a predictable way. As
 long as the temperature decreases, the electrical conductivity decreases
 and the relaxation time increases. A finite element model is able to
 reproduce the observed results. In this model, we consider an intra-grain
 polarization mechanism for the graphite and a change of the conductivity
 of the background material modeled with an exponential freezing curve. One
 of the core sample (a black schist), very rich in graphite, appears to be
 characterized by a very high conductivity (approximately 30 S m-1). Two
 induced polarization profiles are discussed in the area of Thorens. The
 model is applied to the chargeability data to map the volumetric content
 of graphite.
description: Revil
 archiveSpectral induced
 polarization data of rocks and porous media with
 graphite
DOI: 10.5061/dryad.pp045j3
title: Data from: Does an early spring indicate an early summer? relationships between intra-seasonal growing degree day thresholds

description: Spring heat accumulation plays a major role in the timing of events such
 as leaf-out, leaf expansion, flowering, and insect hatch in temperate
 systems. Accordingly, heat accumulation can serve as a proxy for the
 timing of plant and insect phenological activity and can be used in a
 predictive way when the timing of heat accumulation thresholds being
 reached can be anticipated. This has strong value for a host of planning
 and management applications. If relationships exist between earlier- and
 later-season thresholds at a location, then the timing of later-season
 phenological events that are forced by the accumulation of warmth could be
 anticipated based on when earlier-season thresholds are met. Using
 high-resolution daily temperature data, we calculated the coherence in
 pairs of spring-season heat accumulation (growing degree day) threshold
 anomalies over 1948-2016. Overall, relationships between thresholds
 spanning the entire spring season were relatively low, while later season
 thresholds exhibited much higher correlations. This pattern is generally
 the result of decreasing variability in heat accumulation with season
 progression. However, correlation strengths did not follow latitudinal or
 gradients, revealing that within-season heat accumulation and interannual
 variability in threshold timing are unique to the specified base
 temperature and thresholds being compared. We show that the relationships
 between earlier- and later-season heat accumulation thresholds were
 sufficient to accurately predict the timing of phenological events in
 plants in two case examples.
description: Data from: Does an Early
 Spring Indicate an Early Summer? Relationships between Intra-seasonal
 Growing Degree Day ThresholdsNetCDF files containing
 day-of-year a growing degree day threshold was met for two base
 temperatures (0C, 10C) and three thresholds (50, 250, 450). A link to the
 R script used to create these data files from the original TopoWx gridded
 temperature data is also provided in the README file.TOPOWX_GDD_JGR_CRIMMINS2019.zip
DOI: 10.5061/dryad.d12k64m
title: Data from: Adaptation to temperature stress by Vibrio fischeri facilitates this microbe's symbiosis with the Hawaiian bobtail squid (Euprymna scolopes)

description: For microorganisms cycling between free-living and host-associated stages,
 where reproduction occurs in both of these lifestyles, an interesting
 inquiry is whether adaptation to stress during the free-living stage can
 impact microbial fitness in the host. To address this topic, the mutualism
 between the Hawaiian bobtail squid (Euprymna scolopes) and the marine
 bioluminescent bacterium Vibrio fischeri was utilized. Using microbial
 experimental evolution, V. fischeri was selected to low (8⁰C), high
 (34⁰C), and fluctuating temperature stress (8⁰C/34⁰C) for 2,000
 generations. The temperatures 8⁰C and 34⁰C were the lower and upper growth
 limits, respectively. V. fischeri was also selected to benign temperatures
 (21⁰C and 28⁰C) for 2,000 generations, which served as controls. V.
 fischeri demonstrated significant adaptation to low, high, and fluctuating
 temperature stress. V. fischeri did not display significant adaptation to
 the benign temperatures. Adaptation to stressful temperatures facilitated
 V. fischeri’s ability to colonize the squid host relative to the ancestral
 lines. Bioluminescence levels also increased. Evolution to benign
 temperatures did not manifest these results. In summary, microbial
 adaptation to stress during the free-living stage can promote coevolution
 between hosts and microorganisms.
description: ArchivedDataBioluminescence data
DOI: 10.6073/pasta/0fc0c9a999f36615740c79b2debfce32
title: Fall 2024 plant monitoring survey -- biomass calculated from shoot height and flowering status of plants in permanent plots at GCE sampling sites 1-10

description: The biomass of plants surveyed in permanent plots at 10 GCE LTER sampling sites in October 2024 was estimated based on allometric relationships between biomass and shoot height and flowering status derived for each site, zone, and species in October 2002 and October 2008. Biomass was calculated for dominant species, including Spartina alterniflora, S. cynosuroides, Juncus roemerianus, and Zizaniopsis miliacea, as well as rarer species including Scirpus spp, Panicum spp. And Typha angustifolia. This data set is based on GCE plant monitoring survey data set PLT-GCEM-2111a, and allometric relationships were based on GCE data sets PLT-GCEM-0211b, PLT-GCEM-0711, and PLT-GCEM-2011.
DOI: 10.5061/dryad.1nn0206
title: Data from: Evidence for sympatric speciation in a Wallacean ancient lake

description: Sympatric speciation has been demonstrated in few empirical case studies,
 despite intense searches, because of difficulties in testing the criteria
 for this mode of speciation. Here, we report a possible case of sympatric
 speciation in ricefishes of the genus Oryzias on Sulawesi, an island of
 Wallacea. Three species of Oryzias are known to be endemic to Lake Poso,
 an ancient tectonic lake in central Sulawesi. Phylogenetic analyses using
 RAD-seq-derived single nucleotide polymorphisms (SNPs) revealed that these
 species are monophyletic. We also found that the three species are
 morphologically distinguishable and clearly separated by
 population-structure analyses based on the SNPs, suggesting that they are
 reproductively isolated from each other. A mitochondrial DNA chronogram
 suggested that their speciation events occurred after formation of the
 tectonic lake, and existence of a historical allopatric phase was not
 supported by coalescent-based demographic inference. Demographic inference
 also suggested introgressive hybridization from an outgroup population.
 However, differential admixture among the sympatric species was not
 supported by any statistical tests. These results all concur with criteria
 necessary to demonstrate sympatric speciation. Ricefishes in this
 Wallacean lake provide a promising new model system for the study of
 sympatric speciation.
description: ND2 and cytb sequences
 of Sulawesi adrianichthyidsMitochondrial ND2 and
 cytb sequences of Sulawesi adrianichthyids1_ND2_cytb_Sulawesi_adrianichthyids.phyData for morphologyRaw data of morphological analyses of the three species of Poso Oryzias2_Morphology_data.xlsx3_Egg_size_dataRaw data of egg size of the three species of Poso Oryzias4_SNP_data_Poso_Oryzias_82indSNPs data in vcf for the 82 individuals of the three species of Poso Oryzias and their outgroup O. soerotoi5_Popmap_for_treemix_filesPopmap file for the TreeMix analyses of the three species of Poso Oryzias and their outgroup O. soerotoi6_Pop_order_for_treemixPopulation order file for the TreeMix analyses of the three species of Poso Oryzias and their outgroup O. soerotoi7_Data_for_NJ_treeConcatenated sequences of RAD loci used for the NJ phylogeny among the three species of Poso Oryzias and their outgroup O. soerotoi8_Data_for_SNAPPInput file for the SNAPP analysis of the three species of Poso species and their outgroup O. soerotoi9_JSFS_4sp_dataFolded JSFS (JSFS for minor allele) for fastcimcoal2 created using 3,188 RAD loci10_vcftosfs_jointCustom scripts for transforming the SNPs data into the folded JSFS11_SNP_data_Poso_Oryzias_Adrianichthys_92indSNPs data in vcf of the three species of Poso Oryzias, O. soerotoi, and two species of Poso Adrianichthys12_ND2_cytb_Poso_OryziasMitochondrial ND2 and cytb sequences of the three species of Poso Oryzias and their outgroup O. soerotoi
DOI: 10.5061/dryad.33bp0m3
title: Data from: Introduction history and population genetics of intracontinental scotch broom (Cytisus scoparius) invasion

description: Aim Biological invasions at the intracontinental scale are poorly studied,
 and intracontinental invasions often remain cryptic. Here, we investigate
 the recent range expansion of scotch broom (Cytisus scoparius) into Norway
 and clarify whether the genetic patterns support a natural spread or human
 introduction. Furthermore, we investigate whether plants were moved within
 the native range and how this influences invasion success. We also infer
 the level and structuring of genetic diversity within and between the
 putative native and introduced range. Location Europe Methods We analysed
 the chloroplast sequence variation in 267 scotch broom samples from its
 northern expansion front and from its native range across Europe,
 including herbarium samples dating back to 1835. For 37 populations, we
 analysed variation in nuclear single-nucleotide polymorphic markers to
 study gene flow and genetic diversity. Results We identified 20 different
 haplotypes, which lacked spatial and temporal distribution patterns in the
 recent expansion range in Norway. These also mostly lacked patterns across
 the native European range of scotch broom. The genetic diversity of
 nuclear genomic SNP markers across populations in the introduced range was
 similar to that of populations in the native range, with limited
 differentiation among populations. Main conclusions Scotch broom is alien
 to Norway and was introduced by humans on multiple occasions from diverse
 origins over a long period of time. High propagule pressure has probably
 maintained the high genetic diversity in the novel range through a
 combination of genetically diverse source populations and high gene flow
 among them. Within the native European range, our results suggest the
 presence of cryptic intraspecific admixture, most likely mediated by
 humans moving genotypes among the regions occupied by distinct native
 genotypes. Intracontinental invasions may easily go unnoticed and
 revealing these invasions and the factors driving them may be of great
 importance for the management of alien species.
description: Descrition of all
 samples of Cytisus scopariusAll samples used in the
 study, with information on their coordinates, the year and country they
 were collected in and their chloroplast haplotype.Samples.xlsxThe 20 different chloroplast haplotype sequencesThe five regions were concatenated, single nuclear repeats were coded with '?' and codes for the indels were added at the end.20_Chloroplast_sequences.xlsx36 nuclear SNP markerThe 36 nuclear sequences used for SNP calling in MassArray (AGENA Bioscience, San Diego, CA, United States).Nuclear SNPsNuclear SNPs for all 632 samples.