cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5mkkwh76n
title: Lifetime reproductive output and life-history traits of lizards

description: Aim: Latitudinal gradients in life-history traits are apparent in
 many taxa and are expected to be strong for ectotherms that have
 temperature-driven constraints on performance and fitness. The strength of
 these gradients, however, should also be affected by diet. Because diet
 type (carnivory, omnivory, herbivory) influences accessibility to
 nutrition and assimilation efficiency, we aim to study how diet affects
 latitudinal gradients in lifetime reproductive output and the underlying
 life-history traits in ectotherms. Location: Global. Time
 period: Recent. Major taxa studied: Lizards (Reptilia,
 Squamata, Sauria). Methods: We used empirical (352 species) and
 phylogenetically imputed data (563 species) to analyse the interactive
 effects of latitude and diet on life-history traits (longevity, age at
 maturity, reproductive lifespan, hatchling mass, clutch/brood size,
 clutch/brood frequency, female mass) and lifetime reproductive output of
 lizards. Results: Lifetime reproductive output does not
 significantly differ in lizards across diet types, and only carnivores
 exhibit a small increase at higher latitudes. Diet type, however,
 influences latitudinal patterns of individual life-history traits.
 Carnivores exhibit a shift towards “slower-paced” life-histories at higher
 latitudes for most traits (increased longevity, age at maturity,
 reproductive lifespan, and decreased clutch frequency). By contrast,
 herbivores either display “faster-paced” life-histories (reduction in
 reproductive lifespan, hatchling mass, female mass) or no change (clutch
 frequency, clutch size, age at maturity) at higher latitudes. Omnivores
 exhibit intermediate and muted latitudinal patterns. Main
 conclusions: We suggest that the nutritional challenges of
 herbivory, compounded by thermal constraints at higher latitudes, may
 explain differences in life-history characteristics of herbivorous
 ectotherms. Intermediate patterns exhibited by omnivores highlight how
 flexibility in diet can buffer environmental challenges at higher
 latitudes. Our results indicate that lizards with different diet types
 display various trends in their life-histories across latitudes, which
 eventually balance out to result in similar reproductive outputs
 throughout their lifetime, with little benefits to carnivory.
DOI: 10.5061/dryad.1ns1rn8v2
title: Global patterns and drivers of herbivorous eriophyoid mite species diversity

description: Aim: Environmental drivers and host richness play key roles in affecting
 herbivore diversity. However, the relative effects of these factors and
 their effects on lineages characterized by high host specificity are not
 well known. In this study, we explored the extent to which contemporary
 climate, Quaternary climate change, habitat heterogeneity, and host plants
 determine the species richness and endemism patterns of herbivorous
 eriophyoid mites. Location: Global. Taxon: Eriophyoid mites (Acari:
 Eriophyoidea). Methods: We compiled a dataset comprising 4,278 eriophyoid
 mite species from 22,973 occurrence sites based on a comprehensive search
 of the published literature and the Global Biodiversity Information
 Facility (GBIF) as a basis for predicting their global distribution
 patterns. We measured the association of environmental variables and host
 plant richness with species richness and endemism of eriophyoid mites
 through multiple regression analyses using a simultaneous autoregressive
 (SAR) model, an ordinary least squares (OLS) model, and a random forest
 model. We examined the direct and indirect effects of these environmental
 variables and the host plant richness on eriophyoid mite diversity using
 structural equation models (SEMs). Results: The species richness and
 endemism patterns of eriophyoid mites are concentrated in temperate
 regions. Contemporary climate, Quaternary climate change, habitat
 heterogeneity, and host plants all significantly affected eriophyoid mite
 richness, while Quaternary climate change, habitat heterogeneity, and host
 plants contributed to the eriophyoid mite endemism. Abiotic factors
 indirectly influenced the species richness and endemism of eriophyoid
 mites, via biotic factors—host plants. Main conclusions: The species
 richness and endemism of eriophyoid mites peak in temperate regions,
 opposite to the patterns of plants and some other organisms. Complex
 interactions among biotic and abiotic factors shape the current eriophyoid
 mite species diversity.
DOI: 10.5061/dryad.mpg4f4r10
title: Theta oscillations coordinate grid-like representations between ventromedial prefrontal and entorhinal cortex

description: This dataset contains iEEG neural recordings and behavior movement
 direction in a navigation task from human subjects undergoing inpatient
 monitoring for seizure localization. The experimental design, including an
 explanation of metrics of interest, is detailed in Chen et
 al (2018) Current Biology and Chen et al (2021) Science
 Advances. EXAMPLE electrode data from the vmPFC and EC ROIs are included.
 These data are used for grid-like modulation of theta power in vmPFC and
 EC.
description: A series of MATLAB scripts were used for extracting data,
 processing, calculating. A number of functions are called within
 scripts. just run the Main script to get grid
 modulation of the electrode. the Main.m code helps you
 run glm fitting to get grid-like modulation beta from electrode.
 for every electrode, we include raw data in a matrix: the 1st
 line is movement direction; 2nd line is session; 3rd line is oscillation
 power of theta band; GLM_parametric.m is a key function
 to fit glm to get beta of every fold
 divide_algin_misalgin.m is a key function to divide
 move-directions  into align or misalign according to grid angle
DOI: 10.5061/dryad.3n5tb2rj9
title: Pollinator sharing, copollination, and speciation by host shifting among six closely related dioecious fig species

description: The obligate pollination mutualism between figs (Ficus, Moraceae) and
 pollinator wasps (Agaonidae, Hymenoptera) is a classic example of
 cospeciation. However, examples of phylogenetic incongruencies between
 figs and their pollinators suggest that pollinators may speciate by host
 shifting. To investigate the mechanism of speciation by host shifting, we
 examined the phylogenetic relationships and population genetic structures
 of six closely related fig species and their pollinators from southern
 China and Taiwan-Ryukyu islands using various molecular markers. The
 results revealed 1) an extraordinary case of pollinator sharing, in which
 five distinct fig species share a single pollinator species in southern
 China; 2) two types of copollination, namely, sympatric copollination by
 pollinator duplication or pollinator migration, and allopatric
 copollination by host migration and new pollinator acquisition; 3) fig
 species from southern China have colonized Taiwan repeatedly and one of
 these events has been followed by host shifting, host specificity
 reestablishment, and pollinator speciation, in order. Based on our
 results, we propose a model for pollinator speciation by host shifting in
 which reestablishment of host-specificity plays a central role in the
 speciation process. These findings provide important insights into
 understanding the mechanisms underlying pollinator speciation and host
 specificity in obligate pollination mutualism.
DOI: 10.5061/dryad.47d7wm3dp
title: An innovative approach combining metabarcoding and ecological interaction networks for selecting candidate biological control agents

description: Classical biological control (CBC) can be used to decrease the density of
 invasive species to below an acceptable ecological and economic threshold.
 Natural enemies specific to the invasive species are selected from its
 native range and released into the invaded range. This approach has
 drawbacks, despite the performance of specificity tests to ensure its
 safety, because the fundamental host range defined under controlled
 conditions does not represent the actual host range in natura, and these
 tests omit indirect interactions within community. We focus on Sonchus
 oleraceus (Asteraceae), a weed species originating from Western Palearctic
 that is invasive in many countries and notably in Australia. We explore
 how analyses of interaction network within its native range can be used to
 1) inventory herbivores associated to the target plant, 2) characterize
 their ecological host ranges, and 3) guide the selection of candidate
 biocontrol agents considering interactions with species from higher
 trophic levels. Arthropods were collected from plant community sympatric
 to S. oleraceus, in three bioclimatic regions, and interactions were
 inferred by a combination of molecular and morphological approaches. The
 networks reconstructed were structured in several trophic levels from
 basal species (plant community), to intermediate and top species
 (herbivorous arthropods and their natural enemies). The subnetwork
 centered on S. oleraceus related interactions contained 116 taxa and 213
 interactions. We identified 47 herbivores feeding on S. oleraceus, 15 of
 which were specific to the target species. Some discrepancies with respect
 to published findings or conventional specificity tests suggested possible
 insufficient sampling effort for the recording of interactions or the
 existence of cryptic species. Among potential candidate agents, 6
 exhibited interactions with natural enemies. Synthesis and applications:
 Adopting a network approach as prerequisite step of the classical
 biological control program can provide a rapid screening of potential
 agents to be tested in priority. Once ecological host range defined, we
 suggest that priority should be given to agent used by a minimum species,
 and, when they exist, to agents that possess enemies from the most distant
 taxonomical group from those occurring in the range of introduction.
description: Arthropods were collected from plant community sympatric to
 <em>S. oleraceus</em>, in three bioclimatic regions, and
 interactions were inferred by a combination of molecular and morphological
 approaches. For more details, please refer to the materials and methods
 section of the associated paper.
description: No additional knowlegde needed.
DOI: 10.5061/dryad.wstqjq2n3
title: Metadata collected from 500 articles in the field of ecology and evolution

description: The submitted dataset contains the metadata collected from 500 articles in
 the field of ecology and evolution. This includes articles from the
 following journals: Ecology and Evolution, PLoS One, Proceedings of the
 Royal Society B, Ecology and the preprint server bioRxiv. Direct
 identifiers have been removed from the dataset. These included the first
 and last names of authors. No more than three indirect identifiers have
 been provided. Information found herein includes article titles, number of
 authors and ECR status, among others. A README file has been attached to
 provide greater details about the dataset.
DOI: 10.5061/dryad.02v6wwq41
title: Social effects on annual fitness in red squirrels

description: When resources are limited, mean fitness is constrained and competition
 can cause genes and phenotypes to enhance an individual’s own fitness
 while reducing the fitness of their competitors. Negative social effects
 on fitness have the potential to constrain adaptation, but the interplay
 between ecological opportunity and social constraints on adaptation
 remains poorly studied in nature. Here, we tested for evidence of
 phenotypic social effects on annual fitness (survival and reproductive
 success) in a long-term study of wild North American red squirrels
 (Tamiasciurus hudsonicus) under conditions of both resource limitation and
 super-abundant food resources. When resources were limited, populations
 remained stable or declined, and there were strong negative social effects
 on annual survival and reproductive success. That is, mean fitness was
 constrained and individuals had lower fitness when other nearby
 individuals had higher fitness. In contrast, when food resources were
 super-abundant, populations grew and social constraints on reproductive
 success were greatly reduced or eliminated. Unlike reproductive success,
 social constraints on survival were not significantly reduced when food
 resources were super-abundant. These findings suggest resource-dependent
 social constraints on a component of fitness, which have important
 potential implications for evolution and adaptation.
description: Data were collected on individuallly marked North American red
 squirrels between 1989 and 2019.
DOI: 10.5061/dryad.w0vt4b8s1
title: Leopard (Panthera pardus) occupancy in the Chure range of Nepal

description: Conservation of large carnivores like leopards requires large and
 interconnected habitats. Despite the wide geographic range of the leopard
 globally, only 17% of their habitat is within protected areas. Leopards
 are widely distributed in Nepal but their population status and occupancy
 is poorly understood. We carried out the sign-based leopard occupancy
 survey across the entire Chure range (~19,000 km2)to understand the
 habitat occupancy along with the covariates affecting their occupancy.
 Leopard signs were obtained from in 70 out of 223 grids surveyed, with a
 naïve leopard occupancy of 0.31. The model-averaged leopard occupancy was
 estimated to be 0.5732 (SE 0.0082) with a replication level detection
 probability of 0.2554 (SE 0.1142). The top model shows the additive effect
 of wild boar, ruggedness, presence of livestock and human population
 density positively affecting the leopard occupancy. The detection
 probability of leopard was higher outside the protected areas, less in the
 high NDVI (normalized difference vegetation index) areas, and higher in
 the areas with livestock presence. Presence of wild boar was strong
 predictor of leopard occupancy followed by presence of livestock,
 ruggedness and human population density. Leopard occupancy was higher in
 west Chure (0.70±SE 0.047) having five protected areas compared to east
 Chure (0.46 ±SE0.043) with no protected areas. Protected areas and prey
 species had positive influence on leopard occupancy in west Chure range.
 Similarly in the east Chure, the leopard occupancy increased with prey,
 NDVI, and terrain ruggedness. Enhanced law enforcement and mass awareness
 activities are necessary to reduce poaching/killing of wild ungulates and
 leopards in the Chure range to increase leopard occupancy. In addition,
 maintaining the sufficient natural prey base can contribute to minimize
 the livestock depredation and hence, decrease the human-leopard conflict
 in the Chure range. 
description: The study area was divided into blocks, grids, and sub grids
 (Chure range, 19000 km<sup>2</sup>) (details in the paper).
 Each grid was 10 km x 10 km in size. Furthermore, each grid was subdivided
 into 16 sub-grids, each measuring 2 km by 2 km. The presence and absence
 of leopards within each sub-grid were collected. The leopard's
 occupancy was estimated using the software PRESENCE (details in the
 paper).
description: Due to logistical constraints, the survey effort across the grids
 varies due to the rough terrain of the Chure range. As a result, we were
 unable to survey all of the sub-grids in the Chure range. In the
 datasheet, these missing sub-grids are referred to as 'null,'
 i.e. 1= leopard presence, 0= leopard absence, null= unsurveyed
 grids.
DOI: 10.5061/dryad.zs7h44j9f
title: Measuring phylogenetic information of incomplete sequence data

description: Widely used approaches for extracting phylogenetic information from
 aligned sets of molecular sequences rely upon probabilistic models of
 nucleotide substitution or amino-acid replacement. The phylogenetic
 information that can be extracted depends on the number of columns in the
 sequence alignment and will be decreased when the alignment contains gaps
 due to insertion or deletion events. Motivated by the measurement of
 information loss, we suggest assessment of the Effective Sequence Length
 (ESL) of an aligned data set. The ESL can differ from the actual number of
 columns in a sequence alignment because of the presence of alignment gaps.
 Furthermore, the estimation of phylogenetic information is affected by
 model misspecification. Inevitably, the actual process of molecular
 evolution differs from the probabilistic models employed to describe this
 process. This disparity means the amount of phylogenetic information in an
 actual sequence alignment will differ from the amount in a simulated data
 set, which motivated us to develop a new test for model adequacy. Via
 theory and empirical data analysis, we show how to disentangle the effects
 of gaps and model misspecification. By comparing the Fisher information of
 actual and simulated sequences, we identify which alignment sites and tree
 branches are most affected by gaps and model misspecification.
DOI: 10.5281/zenodo.16314545
title: World EEZ v12

description: The purpose of Marine Regions is therefore to create a standard, relational list of geographic names, coupled with information and maps of the geographic location of these features. This will improve access and clarity of the different geographic, marine names such as seas, sandbanks, ridges and bays and display univocally the boundaries of marine biogeographic or managerial marine areas.

 

More information can be found at https://www.marineregions.org/about.php
DOI: 10.5281/zenodo.16355917
title: World EEZ v12

description: The purpose of Marine Regions is therefore to create a standard, relational list of geographic names, coupled with information and maps of the geographic location of these features. This will improve access and clarity of the different geographic, marine names such as seas, sandbanks, ridges and bays and display univocally the boundaries of marine biogeographic or managerial marine areas.

 

More information can be found at https://www.marineregions.org/about.php
DOI: 10.5061/dryad.zkh1893bb
title: Relationship of insect biomass and richness with land use along a climate gradient

description: This dataset contains data from a field study conducted in 2019 and
 described in the paper "Relationship of insect biomass and richness
 with land use along a climate gradient" by Uhler et al. In this
 study, arthropod communities were collected by Malaisetraps along a land
 use and climate gradient and identified by Metabarcoding. Malaise traps
 are versatile passive net-traps, capable of catching a large spectrum of
 insect taxa and are very effective when the aim is to get a representative
 snapshot of the local insect community. Overall, 179 Malaise traps were
 set up in 2019 along a gradient of increasing land use intensity, ranging
 from forests, to meadows, to arable fields, and settlements. The analyzed
 sites were spatially distributed over 400km and covered an elevational
 gradient of 1000m. Generalized additive models were fitted to test for the
 effects of local and landscape-level land-use categories on insect biomass
 and species richness. We found the largest difference in biomass between
 semi-natural and urban environments (−42%), whereas  differences
 in total richness (−29%) and the richness of threatened species (−56%)
 were largest from semi-natural to agricultural environments. These results
 point to urbanization and agriculture as major drivers of decline. We also
 found that richness and biomass increase monotonously with increasing
 temperature, independent of habitat. The contrasting patterns of insect
 biomass and richness question the use of these indicators as mutual
 surrogates. Our study provides support for the implementation of more
 comprehensive measures aimed at habitat restoration in order to halt
 insect declines.
description: The data was collected during the course of a field experiment
 conducted in 2019. Malaisetraps were set up in 179 locations in Bavaria,
 Germany and emptied every two weeks. The biomass of insect samples was
 measured and a subset of samples were futher analyzed through
 meta-barcoding. For a complete summary of all methods used, see the
 methods section of the associated manuscript.
description: The ReadMe file contains an explanation of all variables of the
 main dataset used in the analyses and their measurement units. For easy
 access to all analyses and script outputs, see the attached html
 file.
DOI: 10.5061/dryad.3tx95x6gw
title: Conditional natal dispersal provides a mechanism for populations tracking resource pulses after fire

description: Animals that persist in spatially structured populations face the
 challenge of tracking the rise and fall of resources across space and
 time. To combat these challenges, theory predicts that species should use
 conditional dispersal strategies that allow them to emigrate from patches
 with declining resources and colonize new resource patches as they appear.
 We studied natal dispersal movements in the black-backed woodpecker
 (Picoides arcticus), a species known for its strong association with
 recent post-fire forests in western North America. We radio-tracked
 juveniles originating from seven burned areas and tested hypotheses that
 environmental and individual factors influence dispersal distance and
 emigration rates – investigating emigration while additionally accounting
 for imperfect detection with a novel Bayesian model. We found that
 juveniles were more likely to leave natal areas and disperse longer
 distances if they were heavier or hatched in older burned areas where
 resources are increasingly scarce. Juveniles were also more likely to
 leave their natal burn if they hatched in a nest closer to the fire
 perimeter. While dispersing across the landscape, black-backed woodpeckers
 selected for burned forest relative to unburned available habitat.
 Together, these results strongly support the hypothesis that black-backed
 woodpecker populations track resource pulses across fire-prone landscapes,
 with conditional natal dispersal acting as a mechanism for locating and
 colonizing newly burned areas. Lending empirical support to theoretical
 predictions, our findings suggest that changes in resource distribution
 may shape dispersal patterns and, consequently, the distribution and
 persistence of spatially structured populations. 
description: This data package includes several components:
 (1) Text files of JAGS model code. (2)
 .csv files with input data to run models and conduct the
 analysis. (3) A README file with definitions of
 variables.