cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9b407
title: Data from: Seasonal shifts along the oviparity-viviparity continuum in a cold-climate lizard population

description: Because squamate embryos require weeks of high temperature to complete
 development, cool climatic areas are dominated by viviparous taxa (in
 which gravid females can sun-bask to keep embryos warm) rather than
 oviparous taxa (which rely on warm soil to incubate their eggs). How,
 then, can some oviparous taxa reproduce successfully in cool climates –
 especially late in summer, when soil temperatures are falling? Near the
 northern limit of their distribution (in Sweden), sand lizards (Lacerta
 agilis) shift tactics seasonally, such that the eggs in late clutches
 complete development more quickly (when incubated at a standard
 temperature) than do those of early clutches. That acceleration is
 achieved by a reduction in egg size, and by an increase in the duration of
 uterine retention of eggs (especially, after cool weather). Our results
 clarify the ability of oviparous reptiles to reproduce successfully in
 cool climates, and suggest a novel advantage to reptilian viviparity in
 such conditions: by maintaining high body temperatures, viviparous females
 may escape the need to reduce offspring size in late-season litters.
description: Lacerta agilis data
 Shine et al.Data from free-ranging
 sand lizards on reproductive biologyLacerta agilis for
 Dryad.xlsx
DOI: 10.5061/dryad.2r6m4
title: Data from: Extending glacial refugia for a European tree: genetic markers show that Iberian populations of white elm are native relicts and not introductions

description: Conservation policies usually focus on in situ protection of native
 populations, a priority that requires accurate assessment of population
 status. Distinction between native and introduced status can be
 particularly difficult (and at the same time, is most important) for
 species whose natural habitat has become both rare and highly fragmented.
 Here we address the status of the white elm (Ulmus laevis Pallas), a
 European riparian tree species whose populations have been fragmented by
 human activity and is protected wherever it is considered native. Small
 populations of this species are located in Iberia, where they are
 unprotected because they are considered introductions due to their rarity.
 However, Iberia and neighbouring regions in south-western France have been
 shown to support discrete glacial refuge populations of many European
 trees, and the possibility remains that Iberian white elms are native
 relicts. We used chloroplast RFLPs and nuclear microsatellites to
 establish the relationship between populations in Iberia and the Central
 European core distribution. Bayesian approaches revealed significant
 spatial structure across populations. Those in Iberia and south-western
 France shared alleles absent from Central Europe, and showed spatial
 population structure within Iberia common in recognised native taxa.
 Iberian populations show a demographic signature of ancient population
 bottlenecks, while those in Central European show a signature of recent
 population bottlenecks. These patterns are not consistent with historical
 introduction of white elm to Iberia, and instead strongly support native
 status, arguing for immediate implementation of conservation measures for
 white elm populations in Spain and contiguous areas of southern France.
description: PFU_Ulaevis_Dryad_data
DOI: 10.5061/dryad.1h268g3
title: Data from: Within-species tradeoffs in plant-stimulated soil enzyme activity and growth, flowering and seed size

description: 1. Soil microbial communities affect species demographic rates of plants.
 In turn, plants influence the composition and function of the soil
 microbiome, potentially resulting in beneficial feedbacks that alter their
 fitness and establishment. For example, differences in the ability to
 stimulate soil enzyme activity among plant lineages may affect plant
 growth and reproduction. 2. We used a common garden study to test
 differences in plant-stimulated soil enzyme activity between lineages of
 the same species across developmental stages. 3. Lineages employed
 different strategies whereby growth, days to flowering and seed size
 traded-off with plant-stimulated soil enzyme activity. Specifically, the
 smaller seeded lineage stimulated more enzyme activity at the early stage
 of development and flowered earlier while the larger seeded lineage
 sustained lower but consistent enzyme activity through development. 4. We
 suggest that these lineages, which are both successful invaders, employ
 distinct strategies (a colonizer and a competitor) and differ in their
 influence on soil microbial activity. Synthesis. The ability to influence
 the soil microbial community by plants may be an important trait that
 trades-off with other growth, flowering and seed size for promoting plant
 establishment, reproduction and invasion.
description: CompiledDataContains all data on plant biomass, harvest times and soil enzyme assays with a metadata sheet.CompiledSeedDataContains all data on seed number and weight with a metadata sheet.
DOI: 10.5061/dryad.cm675
title: Data from: Fine partitioning of epiphyte habitat within Johansson zones in tropical Australian rainforest trees

description: For over three decades, the Johansson zones have been widely used in
 epiphyte studies as a way of stratifying the host tree into habitat zones,
 however, the usefulness of this system has been questioned. We test the
 effectiveness of the Johansson zones by grouping epiphyte species by the
 substrate and microclimatic attributes of their individual occurrences and
 assessing the fidelity of these groups to the Johansson zones. Habitat
 characteristics were recorded for every individual epiphyte on 30 trees in
 the lower montane rainforests of north-eastern Australia. Twenty-four
 epiphyte species were agglomerated into four groups using Ward’s method.
 Group 4 was highly distinct and included shade loving species and nomadic
 vines from the lower zones of the host trees. Group 3 contained species
 from the most exposed habitats. Group 1 had higher light levels and lower
 substrate thickness than Group 2, yet both groups had close to identical
 distributions over the Johansson zones. This suggests that groups of
 epiphyte species may utilise different micro-sites within the same zone.
 While the Johansson zones are a useful tool in epiphyte studies, finer
 partitioning of habitat within the host tree may be missed.
description: SangerKirkpatrick_BiotropicaEpiphyte observations and host tree infomation
DOI: 10.5061/dryad.6b650
title: Data from: Watershed versus within-lake drivers of nitrogen: phosphorus dynamics in shallow lakes

description: Research on lake eutrophication often identifies variables affecting
 amounts of phosphorus (P) and nitrogen (N) in lakes, but understanding
 factors influencing N:P ratios is important given its influence on species
 composition and toxin production by cyanobacteria. We sampled 80 shallow
 lakes in Minnesota (USA) for three years to assess effects of watershed
 size, proportion of watershed as both row crop and natural area, fish
 biomass, and lake alternative state (turbid versus clear) on total N:
 total P (TN:TP), ammonium, total dissolved phosphorus (TDP), and seston
 stoichiometry. We also examined N:P stoichiometry in 20 additional lakes
 that shifted states during the study. Lastly, we assessed importance of
 denitrification by measuring denitrification rates in sediment cores from
 a subset of 34 lakes, and by measuring seston δ15N in four additional
 experimental lakes before and after they were experimentally manipulated
 from turbid to clear states. Results showed alternative state had the
 largest influence on overall N:P stoichiometry in these systems, as it had
 the strongest relationship with TN:TP, seston C:N:P, ammonium, and TDP.
 Turbid lakes had higher N at given levels of P than clear lakes, with TN
 and ammonium two-fold and 1.4-fold higher in turbid lakes, respectively.
 In lakes that shifted states, TN was three-fold higher in turbid lakes,
 while TP was only two-fold higher, supporting the notion N is more
 responsive to state shifts than is P. Seston δ15N increased after lakes
 shifted to clear states, suggesting higher denitrification rates may be
 important for reducing N levels in clear states, and potential
 denitrification rates in sediment cores were among the highest recorded in
 the literature. Overall, our results indicate lake state was a primary
 driver of N:P dynamics in shallow lakes, and lakes in clear states had
 much lower N at a given level of P relative to turbid lakes, likely due to
 higher denitrification rates. Shallow lakes are often managed for the
 clear-water state due to increased value as wildlife habitat. However, our
 results indicate lake state also influences N biogeochemistry, such that
 managing shallow lakes for the clear-water state may also mitigate excess
 N levels at a landscape scale.
description: 15N seston
 dataData used to test for
 changes in 15N in seston as lakes shifted.chla macro all lakes
 three yearsData used to classify
 lakes as clear, shifting, or turbid all 3 years.denitrification
 dataData used to assess
 denitrifcation rates in subset of lakes.effects of changing fish
 mass on lakesData used to test
 whether changes in fish biomass caused changes in
 lakes.effects of changing TP
 on NPData used to test
 whether changes in TP changed NP.N and P data lakes that
 shifted statesN and P data for lakes
 that shifted states.seston isotope data two
 yearsSeston CNP data for 2
 years.stable lakes data 3
 yearsData for stable lakes
 that didnt shift over three years.
DOI: 10.5061/dryad.b786c
title: Data from: Male competition fitness landscapes predict both forward and reverse speciation

description: Speciation is facilitated when selection generates a rugged fitness
 landscape such that populations occupy different peaks separated by
 valleys. Competition for food resources is a strong ecological force that
 can generate such divergent selection. However, it is unclear whether
 intrasexual competition over resources that provide mating opportunities
 can generate rugged fitness landscapes that foster speciation. Here we use
 highly variable male F2 hybrids of benthic and limnetic threespine
 sticklebacks, Gasterosteus aculeatus Linnaeus, 1758, to quantify the male
 competition fitness landscape. We find that disruptive sexual selection
 generates two fitness peaks corresponding closely to the male phenotypes
 of the two parental species, favouring divergence. Most surprisingly, an
 additional region of high fitness favours novel hybrid phenotypes that
 correspond to those observed in a recent case of reverse speciation after
 anthropogenic disturbance. Our results reveal that sexual selection
 through male competition plays an integral role in both forward and
 reverse speciation.
description: Stickleback Male
 Competition DatasetThis zipped file
 contains both the data file (Stickleback Male Comp Data.csv) and metadata
 explaining the data columns (Stickleback Male Comp
 Metadata.csv).Stickleback Male
 Comp.zipAggression R
 ScriptThis is the script we
 used to process JWatcher files to ultimately calculate a summary
 aggression score for each male. The script is commented, but note that it
 is currently very specific to our purposes.Aggression
 Script.RAll the R
 FunctionsThis provides R
 functions to aid analysis of selection. They were written fairly
 generically so should be easy to utilize in your
 research.All the
 Functions.RREADME.txtREADME file for Dryad Digital Repository files associated with Keagy, J., Lettieri, L., and Boughman, J.W. 2015. “Male competition fitness landscapes predict both forward and reverse speciation”. Ecology Letters.
DOI: 10.5061/dryad.70sj1
title: Data from: Empirical evaluation of neutral interactions in host-parasite networks

description: While niche-based processes have been invoked extensively to explain the
 structure of interaction networks, recent studies propose that neutrality
 could also be of great importance. Under the neutral hypothesis, network
 structure would simply emerge from random encounters between individuals
 and thus would be directly linked to species abundance. We investigated
 the impact of species abundance distributions on qualitative and
 quantitative metrics of 113 host-parasite networks. We analysed the
 concordance between neutral expectations and empirical observations at
 interaction, species and network levels. We found that species abundance
 accurately predicts network metrics at all levels. Despite host-parasite
 systems being constrained by physiology and immunology, our results
 suggest that neutrality could also explain, at least partially, their
 structure. We hypothesize that trait-matching would determine potential
 interactions between species, while abundance would determine their
 realization.
description: Occurence of host and
 parasite species in localities in timeMatrices of species
 occurence (in row) in sites at each time (in column). The 26 host species
 (rodents) are identified as H1, H2, ..., H26. The 61 parasite species
 (ectoparasites) are identified as P1, P2, ..., P61. The 13 localities are
 identified by a letter (A, C, D, E, ect) and the temporal repetition by a
 number. For example, the locality A have been checked 15 times in all, and
 the locality D 7 times. Then, at locality A, for the second temporal
 repetition, more than 50% of host individuals collected were from the
 species H2 (relative abundance = 0.512) for a total of 5 host
 species.Matrix_list_spxsitextempo.txtInteractions_matricesList of interactions matrices recorded at each locality at each time, with relative interaction strengths between host and parasite species (i.e. relative abundance of parasite species on each host species).
DOI: 10.5061/dryad.vs078
title: Data from: Sexual selection reinforces a higher flight endurance in urban damselflies

description: Urbanisation is among the most important and globally rapidly increasing
 anthropogenic processes, and is known to drive rapid evolution. Habitats
 in urbanised areas typically consist of small, fragmented and isolated
 patches, which is expected to select for a better locomotor performance,
 along with its underlying morphological traits. This, in turn, is expected
 to cause differentiation in selection regimes, as populations with
 different frequency distributions for a given trait will span different
 parts of the species’ fitness function. Yet, very few studies considered
 differentiation in phenotypic traits associated with patterns in habitat
 fragmentation and isolation along urbanisation gradients, and none
 considered differentiation in sexual selection regimes. We investigated
 differentiation in flight performance and flight-related traits, and
 sexual selection on these traits across replicated urban and rural
 populations of the scrambling damselfly Coenagrion puella. To disentangle
 direct and indirect paths going from phenotypic traits over performance to
 mating success, we applied a path analysis approach. We report for the
 first time direct evidence for the expected better locomotor performance
 in urban compared to rural populations. This matches a scenario of spatial
 sorting, whereby only the individuals with the best locomotor abilities
 colonise the isolated urban populations. The covariation patterns and
 causal relationships among the phenotypic traits, performance and mating
 success strongly depended on the urbanisation level. Notably, we detected
 sexual selection for a higher flight endurance only in urban populations,
 indicating that the higher flight performance of urban males was
 reinforced by sexual selection. Taken together, our results provide a
 unique proof of the interplay between sexual selection and adaptation to
 human-altered environments.
description: urban_flight_endurance_EVA
DOI: 10.5061/dryad.pn6jr
title: Data from: Robust extraction of quantitative structural information from high-variance histological images of livers from necropsied Soay sheep

description: Quantitative information is essential to the empirical analysis of
 biological systems. In many such systems, spatial relations between
 anatomical structures is of interest, making imaging a valuable data
 acquisition tool. However, image data can be difficult to analyse
 quantitatively. Many image processing algorithms are highly sensitive to
 variations in the image, limiting their current application to fields
 where sample and image quality may be very high. Here, we develop robust
 image processing algorithms for extracting structural information from a
 dataset of high-variance histological images of inflamed liver tissue
 obtained during necropsies of wild Soay sheep. We demonstrate that
 features of the data can be measured in a fully automated manner,
 providing quantitative information which can be readily used in
 statistical analysis. We show that these methods provide measures that
 correlate well with a manual, expert operator-led analysis of the same
 images, that they provide advantages in terms of sampling a wider range of
 information and that information can be extracted far more quickly than in
 manual analysis.
description: Widefield
 imagesImages from 81 sheep
 livers taken at the widefield and that were analysed both by the human
 operator and the algorithm.4x.zipNarrowfield imagesImages from 88 sheep livers taken at the narrowfield and that were analysed both by the human operator and the algorithm.10x.zipData_RSOS_widefieldThis file contains the values of the different measures produced using the algorithm, and by the human operator reading of the images. Each row contains the ID of an idividual sheep ('Sheep' column). All other columns have a measure name followed by "_human" for the human operator or "_comp" for the computer algorithm.Data_RSOS_narrowfieldThis file contains the values of the different measures produced using the algorithm, and by the human operator reading of the images, at the narrowfield. Each row contains the ID of an idividual sheep ('Sheep' column). All other columns have a measure name followed by "_human" for the human operator or "_comp" for the computer algorithm.
DOI: 10.5061/dryad.4rj3ks0
title: Data from: Regional paleoclimates and local consequences: Integrating GIS analysis of diachronic settlement patterns and process-based agroecosystem modeling of potential agricultural productivity in Provence (France)

description: Holocene climate variability in the Mediterranean Basin is often cited as
 a potential driver of societal change, but the mechanisms of this putative
 influence are generally little explored. In this paper we integrate two
 tools - agro-ecosystem modeling of potential agricultural yields and
 spatial analysis of archaeological settlement pattern data - in order to
 examine the human consequences of past climatic changes. Focusing on a
 case study in Provence (France), we adapt an agro-ecosystem model to the
 modeling of potential agricultural productivity during the Holocene.
 Calibrating this model for past crops and agricultural practices and using
 a downscaling approach to produce high spatiotemporal resolution
 paleoclimate data from a Mediterranean Holocene climate reconstruction, we
 estimate realistic potential agricultural yields under past climatic
 conditions. These serve as the basis for spatial analysis of
 archaeological settlement patterns, in which we examine the changing
 relationship over time between agricultural productivity and settlement
 location. Using potential agricultural productivity (PAgP) as a measure of
 the human consequences of climate changes, we focus on the relative
 magnitudes of 1) climate-driven shifts in PAgP and 2) the potential
 increases in productivity realizable through agricultural intensification.
 Together these offer a means of assessing the scale and mechanisms of the
 vulnerability and resilience of Holocene inhabitants of Provence to
 climate change. Our results suggest that settlement patterns were closely
 tied to PAgP throughout most of the Holocene, with the notable exception
 of the period from the Middle Bronze Age through the Early Iron Age. This
 pattern does not appear to be linked to any climatically-driven changes in
 PAgP, and conversely the most salient changes in PAgP during the Holocene
 cannot be clearly linked to any changes in settlement pattern. We argue
 that this constitutes evidence that vulnerability and resilience to
 climate change are strongly dependent on societal variables.
description: LPJmL
 paleo-agroecological resultsThis dataset includes
 LPJmL (the Lund-Potsdam-Jena managed land model; see Bondeau et al. 2007
 for details) results for high and low assumptions (Par 1 and and Par 2,
 respectively) about agricultural intensity for two crop types (wheat and
 peas) over the period 8400 – 1400 BP. Parameterization of LPJmL for past
 agriculture is based on archaeological, historic, ethnographic, and
 experimental data about pre-industrial agriculture, detailed in Contreras
 et al. 2018. These 300m-pixel annual reconstructions of potential
 agricultural productivity are based on paleoclimate data downscaled (see
 Contreras et al. 2018b) from Guiot and Kaniewski’s Mediterranean-wide
 Holocene reconstruction (Guiot and Kaniewski 2015).LPJmL_results.tar.gz
DOI: 10.5061/dryad.311mm
title: Data from: A cost-efficient and simple protocol to enrich prey DNA from extractions of predatory arthropods for large-scale gut content analysis by Illumina sequencing

description: Molecular analysis of predator gut content is a popular tool to uncover
 food web structure and has greatly profited from the emergence of
 next-generation sequencing technology. However, the molecular recovery of
 prey spectra comes with many challenges, particularly the overabundance of
 predator DNA in extractions. When predator and prey are distantly related,
 predator-specific blocking primers can be used to preferentially amplify
 prey DNA. But this is difficult in the case of arthropods, where prey and
 predator are often closely related. Here, we present a simple and
 cost-efficient protocol for high-throughput analysis of the gut content of
 predatory arthropods without the need for blocking primers. We test
 several factors for their potential to enrich prey DNA from extractions of
 predators, including size selection of DNA, selection of different body
 parts for extraction, and variation in extraction lysis time and PCR
 fragment length. Using a locally abundant spider species (Hololena adnexa,
 Agelenidae), we show that prey DNA can be significantly enriched from
 predator extracts by selectively removing high molecular weight DNA and by
 extracting from the midgut and hindgut only. A comparison of our results
 with observational data from other agelenid spider species indicates a
 high efficiency of our approach. Our enrichment protocol allows for the
 parallel analysis of several hundred predators in a single MiSeq run,
 reducing the cost per specimen to only a few dollars and requiring a
 simple and minimal work flow. This will enable large-scale and
 ecosystem-wide analyses of niche differentiation and food web structure.
description: Illumina_Read_FilesIllumina_Reads.zip