cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2r62k7s
title: Data from: The allometry of brain size in mammals

description: Why some animals have big brains and others do not has intrigued scholars
 for millennia. Yet, the taxonomic scope of brain size research is limited
 to a few mammal lineages. Here, we present a brain size dataset compiled
 from the literature for 1,552 species with representation from 28 extant
 taxonomic orders. The brain–body size allometry across all mammals is
 (Brain) = −1.26 (Body)^0.75. This relationship shows strong phylogenetic
 signal. Thus, we conducted additional allometries using median species
 values for each order, family, and genus to ensure evolutionary
 independence. Slopes from these analyses at different taxonomic levels all
 approximate ~0.75 scaling. Why brain size scales to the 3/4 power to body
 size across mammals is to our knowledge unknown. Slopes within taxonomic
 orders, exhibiting smaller size ranges, are generally shallower than 0.75
 and range from 0.24 to 0.81 with a median slope of 0.64. Published data on
 brain size are lacking for the majority of extant mammals (&gt; 70% of
 species) with strong bias in representation from Primates, Carnivora,
 Perissodactyla, and Australidelphian marsupials (orders Dasyuromorphia,
 Diprotodontia, Peramelemorphia). Several orders are particularly
 underrepresented. For example, data on brain size are available for less
 than 20% of species in each of the following speciose lineages:
 Soricomorpha, Rodentia, Lagomorpha, Didelphimorphia, and Scandentia. Use
 of museum collections can decrease the current taxonomic bias in mammal
 brain size data and tests of hypothesis.
description: Mammal brain size data
 for 1522 speciesBrain size (grams), body
 size (grams), sample size (when reported), and sex (when reported) for
 1522 species compiled from 54 published references.BrainAllometry_Supplement_Data.csvBrain Size ReferencesReferences for brain size data.BrainSize_supplement_refs.docx
DOI: 10.5061/dryad.b38k42m
title: Data from: The heritability of behavior: a meta-analysis

description: The contribution of genetic variation to phenotypes is a central factor in
 whether and how populations respond to selection. The most common approach
 to estimating this influences is via the calculation of heritabilities,
 which summarize the contribution of genetic variation to phenotypic
 variation. Heritabilities also indicate the relative affect of genetic
 variation on phenotypes versus that of environmental sources of variation.
 For labile traits like behavioral responses, life-history traits, and
 physiological responses, estimation of heritabilities is important as
 these traits are strongly influenced by the environment. Thus, knowing
 whether or not genetic variation is present within populations is
 necessary to understand whether or not these populations can evolve in
 response to selection. Here we report the results of a meta-analysis
 summarizing what we currently know about the heritability of behavior.
 Using phylogenetically controlled methods we assessed the average
 heritability of behavior (0.235)—which is similar to that reported in
 previous analyses of physiological and life-history traits—and examined
 differences among taxa, behavioral classifications, and other biologically
 relevant factors. We found that there was considerable variation among
 behaviors as to how heritable they were, with migratory behaviors being
 the most heritable. Interestingly, we found no effect of phylogeny on
 estimates of heritability. These results suggest, first, that behavior may
 not be particularly unique in the degree to which it is influenced by
 factors other than genetics and, second, that those factors influencing
 whether a behavioral trait will have low or high heritability require
 further consideration.
description: Analysis
 scriptThis file contains the
 annotated analysis script. Once the appropriate working directory is set
 and libraries loaded, this script will reproduce the results reported in
 the paper.Dochter_etal(h2_analysis)vR.1.RData for analysisContains all the data included in the meta-analysis. Column headers: Estimate.ID: unique ID for each estimate. Study.ID: unique ID associated with the source paper. Vert: vertebrate or invertebrate. Thermy: endo- or ectotherm. Phylum-species.epithet: Phylogenetic information for the species associated with the estimate. phylo: species name as it occurs in the phylogenetic tree. D.W.: domesticated or wild species. L.F.: estimate was made in lab or field conditions. Behavior: behavioral category corresponding to estimate. N: sample size at the highest hierarchical level. N.C.: alternative sample size to address whether inflated precision biased results. Heritability: h2 estimate. Zr: transformed estimate.Compiled2.csvJournalListList of articles included in analysis, including the associated study ID. Column names: Study ID: unique ID associated with each included paper. Year - Pages: bibliographic information.Phylogenetic treeNewick formatted phylogenetic tree allowing inclusion of phylogenetic structure in analysis.Dochter_etal(TREE).txt
DOI: 10.5281/zenodo.18390655
title: Strangford Lough surface water parameters 2014-2023

description: Temperature, salinity, dissolved oxygen and turbidity data from Strangford Lough, Co. Down, Northern Ireland.

Data collected by Agri-Food and Biosciences Institute, Belfast as part of Marine Inshore Water Quality Monitoring programme (Department of Agriculture, Environment and Rural Affairs funded) using multiparameter sondes deployed on a buoy :- position 54 31.567N; 5 38.136W.
DOI: 10.5281/zenodo.18390656
title: Strangford Lough surface water parameters 2014-2023

description: Temperature, salinity, dissolved oxygen and turbidity data from Strangford Lough, Co. Down, Northern Ireland.

Data collected by Agri-Food and Biosciences Institute, Belfast as part of Marine Inshore Water Quality Monitoring programme (Department of Agriculture, Environment and Rural Affairs funded) using multiparameter sondes deployed on a buoy :- position 54 31.567N; 5 38.136W.
DOI: 10.5061/dryad.jv2hd72
title: Data from: Disturbance, microclimate and historical habitat connectivity determine the population performance of the threatened grassland specialist Carex caryophyllea in remnant grasslands

description: Many grassland specialist plant populations in Europe have been restricted
 to remnant habitats. The performance of these populations depends on both
 species-specific traits and local and landscape level aspects of habitat
 quality. Understanding which specific local or landscape level conditions
 determine the performance of grassland species populations in remnant
 habitats would help design the restoration of the habitats and to detect
 the conditions that favour the long-term persistence of grassland species
 in them. Such information is especially needed in urbanised landsapes,
 where remnant habitats engulfed by urban land use types types may
 experience increased erosion, higher temperatures and invasion by alien
 species. This study investigates the population performance determinants
 of Carex caryophyllea (VU), a grassland specialist, in 43 remnant
 grasslands in an urban-rural gradient in Finland. The population
 performance was assessed with metrics of persistence, establishment and
 reproduction, and related to environmental conditions with generalized
 additive models and redundancy analysis. The most important positive
 determinants for the performance of C. caryophyllea populations were
 disturbance through management or ground erosion, a warm microclimate,
 large habitat area and high historical connectivity to suitable grassland
 habitats. Present connectivity to other C. caryophyllea populations had a
 weak and near-significant positive relationship with population
 performance. Urbanisation of the surrounding landscape correlated with
 population performance as well, possibly due to the high historical cover
 of grasslands in presently urbanised landscapes. The results imply that
 the most effective restoration method of remnant C. caryophyllea
 populations would be reinstating disturbance regimes in overgrown habitats
 with warm microclimates close to suitable habitats and other existing
 populations, whether urban or rural. This would counteract the species
 future decline due to possible extinction debts and help the species
 persist in the study area in the long term.
description: Population performance
 and environmental conditions of 43 Carex caryophyllea -populations in
 southern FinlandData_Lampinen_J_2019_NJBot.csv
DOI: 10.5061/dryad.rs776p3
title: Data from: A comparative analysis of common methods to identify waterbird hotspots

description: 1. Hotspot analysis is a commonly used method in ecology and conservation
 to identify areas of high biodiversity or conservation concern. However,
 delineating and mapping hotspots is subjective and various approaches can
 lead to different conclusions with regard to the classification of
 particular areas as hotspots, complicating long-term conservation
 planning. 2. We present a comparative analysis of recent approaches for
 identifying waterbird hotspots, with the goal of developing insights about
 the appropriate use of these methods. We selected four commonly used
 measures to identify persistent areas of high use: kernel density
 estimation, Getis-Ord Gi*, hotspot persistence, and hotspots conditional
 on presence, which represent the range of quantitative hotspot estimation
 approaches used in waterbird analyses. We applied each of the methods to
 aerial survey waterbird count data collected in the Great Lakes from
 2012-2014. For each approach, we identified areas of high use for seven
 species/species groups and then compared the results across all methods
 and with mean effort-corrected counts. 3. Our results indicate that formal
 hotspot analysis frameworks do not always lead to the same conclusions.
 The kernel density and Getis-Ord Gi* methods yielded the most similar
 results across all species analyzed and were generally correlated with
 mean effort-corrected count data. We found that these two models can
 differ substantially from the hotspot persistence and hotspots conditional
 on presence estimation approaches, which were not consistently similar to
 one another. The hotspot persistence approach differed most significantly
 from the other methods but is the only method to explicitly account for
 temporal variation. 4. We recommend considering the ecological question
 and scale of conservation or management activities prior to designing
 survey methodologies. Deciding the appropriate definition and scale for
 analysis is critical for interpretation of hotspot analysis results as is
 inclusion of important covariates. Combining hotspot analysis methods
 using an integrative approach, either within a single analysis or
 post-hoc, could lead to greater consistency in the identification of
 waterbird hotspots.
description: alldata_attributed_v04122017More information can be found on the Midwest Avian Data Center, a regional node of the Avian Knowledge Network, hosted by Point Blue Conservation Science (http://data.pointblue.org/partners/mwadc/) or through the Zipkin Quantitative Ecology Lab GitHub page (https://zipkinlab.github.io/).
DOI: 10.5061/dryad.4bq41sg
title: Data from: Unexpected spatial population ecology of a widespread terrestrial salamander near its southern range edge

description: Under the current amphibian biodiversity crisis, common species provide an
 opportunity to measure population dynamics across a wide range of
 environmental conditions while examining the processes that determine
 abundance and structure geographic ranges. Studying species at their range
 limits also provides a window for understanding the dynamics expected in
 future environments under increasing climate change and human
 modification. We quantified patterns of seasonal activity, density, and
 space use in the Eastern red-backed salamander (Plethodon cinereus) near
 its southern range edge and compare the spatial ecology of this population
 to previous findings from the core of their range. This southern
 population shows the expected phenology of surface activity based on
 temperature limitations in warmer climates, yet maintains unexpectedly
 high densities and large home ranges during the active season. Our study
 suggests that ecological factors known to strongly affect amphibian
 populations (e.g., warm temperature, forest fragmentation) do not
 necessarily constrain this southern population. Our study highlights the
 utility of studying a common amphibian as a model system for investigating
 population processes in environments under strong selective pressure.
description: Plethodon cinereous
 encounter history dataIndividual-level data
 for spatial capture recapture analysis in R package
 oSCRHernandez-Pacheco_et_al_edf.csvTrap deployment data for cover board array in Site 1, Session 1Data frame containing information of each trap and their corresponding session, site, and day covariateHernandez-Pacheco_et_al_tdf1.csvTrap deployment data for cover board array in Site 2, Session 1Data frame containing information of each trap and their corresponding session, site, and day covariateHernandez-Pacheco_et_al_tdf2.csvTrap deployment data for cover board array in Site 3, Session 1Data frame containing information of each trap and their corresponding session, site, and day covariateHernandez-Pacheco_et_al_tdf3.csvTrap deployment data for cover board array in Site 1, Session 2Data frame containing information of each trap and their corresponding session, site, and day covariateHernandez-Pacheco_et_al_tdf4.csvTrap deployment data for cover board array in Site 2, Session 2Data frame containing information of each trap and their corresponding session, site, and day covariateHernandez-Pacheco_et_al_tdf5.csvTrap deployment data for cover board array in Site 3, Session 2Data frame containing information of each trap and their corresponding session, site, and day covariateHernandez-Pacheco_et_al_tdf6.csvR codes for running red-backed salamander spatial capture-recapture analysis using package oSCRHernandez_Pacheco_et_al_codes.R
DOI: 10.5061/dryad.438t5kg
title: Data from: Disturbance history mediates climate change effects on subtropical forest biomass and dynamics

description: The responses of forest communities to interacting anthropogenic
 disturbances like climate change and logging are poorly known. Subtropical
 forests have been heavily modified by humans and their response to climate
 change is poorly understood. We investigated the nine year-change observed
 in a mixed conifer-hardwood Atlantic forest mosaic that included both
 mature and selectively-logged forest patches in subtropical South America.
 We used demographic monitoring data within 10 1 ha plots that were
 subjected to distinct management histories (plots logged until 1955, until
 1987, and unlogged) to test the hypothesis that climate change affected
 forest structure and dynamics differentially depending on past
 disturbances. We determined the functional group of all species based on
 life-history affinities as well as many functional traits like leaf size,
 specific leaf area, wood density, total height, stem slenderness, and seed
 size data for the 66 most abundant species. Analysis of climate data
 revealed that minimum temperatures and rainfall have been increasing in
 the last few decades of the 20th century. Floristic composition differed
 mainly with logging history categories, with only minor change over the
 nine annual census intervals. Aboveground biomass increased in all plots,
 but increases were higher in mature unlogged forests, which showed signs
 of forest growth associated with increased CO2, temperature, and
 rainfall/treefall gap disturbance at the same time. Logged forests showed
 arrested succession as indicated by reduced abundances of Pioneers and
 biomass-accumulators like Large Seeded Pioneers and Araucaria, as well as
 reduced functional diversity. Management actions aimed at creating
 regeneration opportunities for long-lived pioneers are needed to restore
 community functional diversity, and ecosystem services such as increased
 aboveground biomass accumulation. We conclude that the effects of climate
 drivers on the dynamics of Brazilian mixed Atlantic forests vary with
 land-use legacies, and can differ importantly from the ones prevalent in
 better known tropical forests.
description: Souza & Longhi 2019
 - Ecology and Evolution Dryad DataA zipped file
 containing: 1) a .txt file containing rainfall data for São Francisco de
 Paula between 1945-2006 2) a spreadsheet containing climatic data for São
 Francisco de Paula for the same period including CRU data 3) a spreadsheet
 containing species x plot data used to run the NMDS ordination, and 4) a
 spreadsheet containing plot-level forest structure variables. (English
 translations for data: historico = historic; ano = year; chuva = rain;
 media = average; anual = yearly; temperada = temperate)
DOI: 10.5061/dryad.j35fq7r
title: Data from: Inter-annual monitoring improves diversity estimation of tropical butterfly assemblages

description: Monitoring programs for diverse tropical butterfly assemblages are scarce
 and temporal diversity patterns in these assemblages are poorly
 understood. We adopted an additive partitioning approach to determine how
 temporal butterfly species richness was structured at the levels of days,
 months, and years in five tropical/subtropical sites across three
 continents covering up to nine years of monitoring. We found that observed
 butterfly richness was not uniformly distributed across temporal extents.
 Butterfly species composition differed across months and years,
 potentially accounting for the fact that temporal butterfly species
 richness contributed a high proportion to total species richness. We
 further examined how species richness of common and uncommon species
 (&gt; and &lt;0.5 percent of total abundance, respectively) were
 structured across temporal extents. The results showed that the common
 species relative contribution to total species richness was higher at
 lower-temporal levels, whereas uncommon species contributed more at
 higher-temporal resolutions. This suggests that long-term sampling will be
 more effective in capturing patterns of rare species and the total species
 pool while lower-temporal level sampling (e.g. daily or weekly) may be
 more useful in examining common species demographic patterns. We therefore
 encourage careful consideration of temporal replication at different
 extents in developing butterfly monitoring schemes. Long-term monitoring
 is essential for improvement in the resolution of species estimation and
 diversity patterns for tropical ecosystems.
description: TropicalTropical butterfly monitoring data collected over two to nine consecutive years in five tropical/subtropical forest sites under standardized monitoring protocolsbutterfly data to upload.xlsx
DOI: 10.5061/dryad.c3269fc
title: Data from: Efferocytosis perpetuates substance accumulation inside macrophage populations

description: In both cells and animals, cannibalism can transfer harmful substances
 from the consumed to the consumer. Macrophages are immune cells that
 consume their own dead via a process called cannibalistic efferocytosis.
 Macrophages that contain harmful substances are found at sites of chronic
 inflammation, yet the role of cannibalism in this context remains
 unexplored. Here we take mathematical and experimental approaches to study
 the relationship between cannibalistic efferocytosis and substance
 accumulation in macrophages. Through mathematical modelling, we deduce
 that substances which transfer between individuals through cannibalism
 will concentrate inside the population via a coalescence process. This
 prediction was confirmed for macrophage populations inside a closed
 system. We used image analysis of whole slide photomicrographs to measure
 both latex microbead and neutral lipid accumulation inside murine bone
 marrow-derived macrophages (104-105 cells) following their stimulation
 into an inflammatory state ex vivo. While the total number of phagocytosed
 beads remained constant, cell death reduced cell numbers and efferocytosis
 concentrated the beads among the surviving macrophages. % from small to
 large numbers per cell. Since lipids are also conserved during
 efferocytosis, these cells accumulated lipid derived from the membranes of
 dead and consumed macrophages (becoming macrophage foam cells).
 Consequently, enhanced macrophage cell death increased the rate and extent
 foam cell formation. Our results demonstrate that cannibalistic
 efferocytosis perpetuates exogenous (e.g. beads) and endogenous (e.g.
 lipids) substance accumulation inside macrophage populations. As such,
 cannibalism has similar detrimental consequences in both cells and
 animals.
description: BeadDataRaw images of the experiments for bead accumulation in macrophageBead Experiments.zipLipidDataRaw images of the experiments for lipid accumulation in macrophagesLipid Experiments.zip
DOI: 10.5061/dryad.24p1k82
title: Data from: Genetic homogenization of indigenous sheep breeds in Northwest Africa

description: Northwest-African sheep represent an ideal case-study for assessing the
 potential impact of genetic homogenization as a threat to the future of
 traditional breeds that are adapted to local conditions. We studied ten
 Algerian and Moroccan breeds of sheep, including three transboundary
 breeds, distributed over a large part of the Maghreb region, which
 represents a geographically and historically coherent unit. Our analysis
 of the dataset that involved carrying out Genome-wide SNP genotyping,
 revealed a high level of homogenization (ADMIXTURE, NetView, fineSTRUCTURE
 and IBD segments analyses), in such a way that some breeds from different
 origins appeared genetically undistinguished: by grouping the eight most
 admixed populations, we obtained a mean global FST value of 0.0024. The
 sPCA analysis revealed that the major part of Morocco and the Northern
 part of Algeria were affected by the phenomenon, including most of the
 breeds considered. Unsupervised cross-breeding with the popular
 Ouled-Djellal breed was identified as a proximate cause of this
 homogenization. The issue of transboundary breeds was investigated, and
 the Hamra breed in particular was examined via ROH fragments analysis.
 Genetic diversity was considered in the light of historical archives and
 anthropological works. All of these elements taken together suggest that
 homogenization as a factor affecting the Maghrebin sheep stock, has been
 particularly significant over the last few decades, although this process
 probably started much earlier. In particular, we have identified the
 policies set by the French administration during the colonial period of
 the region’s history as a causal factor that probably contributed
 significantly to this process. The genetic homogenization that we have
 observed calls into question the integrity of the farm animal genomic
 resources represented by these local breeds, whose conservation is of
 critical importance to the future of the livestock sector.
description: Algerian sheep genotypes
 (.map file)Genotypes obtained with
 the Illumina OvineSNP50K Genotyping BeadChip (markers files by
 chromosomes) for two Algerian sheep breeds in a Plink
 format.AlgerianSheepSidaounHamra.mapAlgerian sheep genotypes (.ped file)Genotypes obtained with the Illumina OvineSNP50K Genotyping BeadChip (genotype files) for two Algerian sheep breeds in a Plink format.AlgerianSheepSidaounHamra.ped