cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9ghx3ffgn
title: A sparse observation model to quantify species distributions and their overlap in space and time

description: Camera traps and acoustic recording devices are essential tools to
 quantify the distribution, abundance and behavior of mobile species.
 Varying detection probabilities among device locations must be accounted
 for when analyzing such data, which is generally done using occupancy
 models. We introduce a Bayesian Time-dependent Observation Model for
 Camera Trap data (Tomcat), suited to estimate relative event densities in
 space and time. Tomcat allows to learn about the environmental
 requirements and daily activity patterns of species while accounting for
 imperfect detection. It further implements a sparse model that deals well
 will a large number of potentially highly correlated environmental
 variables. By integrating both spatial and temporal information, we extend
 the notation of overlap coefficient between species to time and space to
 study niche partitioning. We illustrate the power of Tomcat through an
 application to camera trap data of eight sympatrically occurring duiker
 (Cephalophinae) species in the the savanna - rainforest ecotone in the
 Central African Republic and show that most species pairs show little
 overlap. Exceptions are those for which one species is very rare, likely
 as a result of direct competition.
DOI: 10.5061/dryad.dncjsxkzn
title: Bound within boundaries: How well do protected areas match movement corridors of their most mobile protected species?

description: Conserving and managing large portions of land to connect wildlife
 reserves is an increasingly used strategy to maintain and restore
 connectivity among wildlife populations. Boundaries of such conservation
 areas are often determined based on expert opinion and socio-political
 constraints, yet the extent to which they match species’ movement
 corridors is rarely examined. This is mainly due to a lack of data,
 particularly on wide-ranging movement behavior such as dispersal.
 Nevertheless, empirically assessing the adequacy of protected areas is key
 for the implementation of targeted management actions and efficient use of
 limited conservation funds. Between 2011 and 2019, we collected
 high-resolution GPS data on 16 dispersing African wild dog (Lycaon pictus)
 coalitions from a free-ranging population in the Kavango-Zambezi
 Transfrontier Conservation Area (KAZA-TFCA). Spanning five countries and
 520’000 km2 the KAZA-TFCA is the world’s largest transboundary
 conservation area and a prime example for international conservation
 efforts. We used integrated step selection analysis to estimate habitat
 selection of dispersers and to create a permeability surface for the
 KAZA-TFCA. We compared landscape permeability across different regions
 within the KAZA-TFCA as well as outside its boundaries. Lastly, we
 calculated least-cost paths and corridors to verify that major movement
 routes were adequately encompassed within the KAZA-TFCA. Permeability
 within the boundaries of the KAZA-TFCA was more than double compared to
 areas outside it. Furthermore, we observed a five-fold permeability
 difference among the five KAZA-TFCA countries. We also showed that major
 movement corridors of wild dogs ran within the KAZA-TFCA, although some
 minor routes remained formally unprotected. Differences in permeability
 were mainly related to different degrees of human activities across
 regions, and to the presence or absence of rivers, swamps and open water.
 The relationship between permeability and other landscape features was
 less pronounced. Synthesis and Applications: In this study, we showed how
 pertinent dispersal data of a highly mobile species can be used to
 empirically evaluate the adequacy of already-existing or planned protected
 areas. Furthermore, we observed regional differences in landscape
 permeability that highlight the need for a coordinated effort towards
 maintaining or restoring connectivity, especially where transboundary
 dispersal occurs.
description: GPS_Dryad.csv: This file contains the lon-lat GPS locations of
 the dispersing African wild dogs. For protection reasons, coordinates were
 rounded to two decimal degrees. Animal ID and Timestamps are linked to
 each random "identifier" and available upon request to the
 leading author.
DOI: 10.5061/dryad.z08kprrc4
title: Are evolutionary transitions in sexual size dimorphism related to sex determination in reptiles? - Electronic supplementary material

description: Sex determination systems are highly variable in vertebrates, although
 neither the causes nor the implications of this diversity are fully
 understood. Theory suggests that sex determination is expected to relate
 to sexual size dimorphism, because environmental sex determination
 promotes sex-specific developmental bias in embryonic growth rates.
 Furthermore, selection for larger size in one sex or the other has been
 proposed to drive the evolution of different genetic sex determination
 systems. Here we investigate whether sex determination systems relate to
 adult sexual size dimorphism, using 250 species of reptiles (Squamata,
 Testudines, Crocodylia) representing 26 families. Using phylogenetically
 informed analyses, we find that sexual size dimorphism is associated with
 sex determination: species with TSDIa sex determination (i.e. in which the
 proportion of female offspring increases with incubation temperature),
 have more female-biased size dimorphism than species with TSDII (i.e.,
 species in which males are produced at mid temperatures). We also found a
 trend that species with TSD ancestors had more male-biased size dimorphism
 in XY sex-chromosome systems than in ZW sex-chromosome systems. Taken
 together, our results support the prediction that sexual size dimorphism
 is linked to sex-dependent developmental variations caused by
 environmental factors and also by sex chromosomes. Since the extent of
 size dimorphism is related to various behavioural, ecological and
 life-history differences between sexes, our results imply profound impacts
 of sex determination systems for vertebrate diversity.
DOI: 10.5061/dryad.qv9s4mwdb
title: Eutrophic status influences the impact of pesticide mixtures and predation on Daphnia pulex populations

description: Pesticides, nutrients, and ecological stressors such as competition or
 predation co-occur in freshwater ecosystems impacted by agricultural
 pollution. The extent to which combinations of these stressors affect
 aquatic populations and the role of nutrients availability in modulating
 these responses requires further understanding. In this study, we assessed
 how pesticides affecting different taxonomic groups and predation
 influence the response of Daphnia pulex populations under different
 trophic conditions. An outdoor experiment was designed following a
 factorial design, with the insecticide chlorpyrifos, the herbicide diuron,
 and predation by Notonecta sp. individuals as key stressors. The single
 impact of each of these stressors, and their binary and tertiary
 combinations were evaluated on D. pulex abundance and population structure
 under mesotrophic and eutrophic conditions for 21 days. Data were analysed
 using generalized linear mixed models estimated by means of a novel
 Bayesian shrinkage technique. Our study shows a significant influence of
 each of the evaluated stressors on D. pulex abundance, however, the
 impacts of the herbicide and predation were lower under eutrophic
 conditions as compared to the mesotrophic ones. We found that binary
 stressor interactions were generally additive in the mesotrophic scenario,
 except for the herbicide-predation combination, which resulted in
 synergistic effects. The impacts of the binary stressor combinations in
 the eutrophic scenario were classified as antagonistic, except for the
 insecticide-herbicide combination, which was additive. The tertiary
 interaction resulted in significant effects on several sampling dates,
 however, those were rather antagonistic and resembled the most important
 binary stressor combination in each trophic scenario. Our study shows that
 the impact of pesticides on freshwater populations depends on the
 predation pressure, and demonstrates that the combined effect of
 pesticides and ecological stressors is influenced by the food availability
 and organism fitness related to the trophic status of freshwater
 ecosystems.
DOI: 10.5061/dryad.cvdncjt3q
title: Testing small scale ecological gradients and intraspecific differentiation for hundreds of kelp forest species using haplotypes from metabarcoding

description: DNA metabarcoding has been increasingly used to detail distributions of
 hundreds of species. Most analyses focus on creating molecular operation
 taxonomic units (MOTUs) from complex mixtures of DNA sequences, but much
 less common is use of the sequence diversity within these MOTUs. Here we
 use the diversity of COI haplotypes within MOTUs from a California kelp
 forest to infer patterns of population abundance, dispersal and population
 history from 527 species of animals and algae from 106 samples of benthic
 habitats in Monterey Bay. Using haplotypes as a unit we show fine-grained
 differences of abundance across locations for 15 species, and marked
 aggregation from sample to sample for most of the common species of plants
 and animals. Previous analyses could not distinguish these patterns from
 artefacts of amplification or sequence bias. Our haplotype data also
 reveal strong population genetic differentiation over small spatial scales
 for 48 species of red algae, sponges, and Bryozoa. Last, phylogenetic
 analysis of mismatch frequencies among haplotypes show a wide variety of
 demographic histories from recent expansions to long, stable population
 sizes. These analyses show that abundant, small bodied marine species that
 are often overlooked in ecological surveys can have strikingly different
 patterns of ecological and genetic structure leading to population,
 ecological, and perhaps adaptive differences between habitats. MOTU
 diversity data from the same sequencing efforts that generate
 species-level analyses, and can greatly increase the scope and value of
 metabarcoding studies.
description: This dataset is a reanalysis of DNA metabarcoding data from Shum
 et al (2019, https://doi.org/10.1111/1755-0998.13067) to extract haplotypes using JAMP (https://github.com/VascoElbrecht/JAMP) and carry out demographic genetic analysis for hundreds of kelp forest species.
description: <strong>HaploCOBB_table.xlsx</strong>
 This file contains the raw output of haplotypes from JAMP, the
 filtered haploCOBB dataset, Aggregation analysis (Figure S2) and mismatch
 analysis (Figure 9).
 <strong>Rscript.zip</strong> This
 zipped folder contain the R code (haploCOBB__Rscripts.txt) to recreate
 Figures in the main manuscript including the data files.
 <strong>PopGen.zip</strong> This
 zipped folder contains the HaploCOBB population genetic datasets of 527
 MOTUs in fasta format including filter1 and filter2 datasets. .out files
 contain the DNAsp output of all datasets.
 <strong>haploCOBB19_pipeline.zip</strong>
 This zipped folder contains the bioinformatic workflow
 (haploCOBB_pipeline.txt) to generate haplotypes using OBITools and JAMP,
 including the generation of population genetic datasets from DNA
 metabarcoding data. The information containing the samples, barcodes and
 primers are contained in file ngsfilter.txt used to demultiplex the
 data.
DOI: 10.5061/dryad.m0cfxpp33
title: Midlife Plasma AB and Latelife Risk of MCI/Dementia Supplemental Material

description: Objective. To evaluate the association between midlife plasma amyloid-beta
 (Aβ1-42, Aβ1-40, Aβ42:Aβ40) and risk of MCI and dementia. Plasma Aβ42 and
 Aβ40 were retrospectively measured using a fluorimetric bead-based
 immunoassay in a subsample of the Atherosclerosis Risk in Communities
 study (n=2284) at the third (1993-95, mean age=59.2±5.2, 57% female, 22%
 Black) and fifth in-person visits (2011-13, mean age=77.0±5.3). We
 investigated the relationship of plasma Aβ42, Aβ40, and Aβ42:Aβ40 ratio
 measured in midlife, late-life, and the change from midlife to late-life,
 to risk of MCI, dementia, and combined MCI/dementia outcomes in late-life
 (from 2011-19). We used multinomial logistic regressions estimating
 relative risk ratios (RRR) of these cognitive outcomes vs cognitively
 normal adjusted for age, sex, education, site-race, APOE, hypertension,
 diabetes, and body mass index. Each doubling of midlife Aβ42:Aβ40 was
 associated with 37% lower risk of MCI/dementia (RRR=0.63, 95% CI: 0.46,
 0.87), but only up to approximately the median (spline model threshold
 0.20). Every standard deviation increase in plasma Aβ42 (10 pg/mL) was
 associated with 13% lower risk of MCI/dementia (RRR=0.87, 95% CI: 0.77,
 0.98), whereas every standard deviation increase in plasma Aβ40 (67 pg/mL)
 was associated with 15% higher risk of MCI/dementia (RRR=1.15, 95% CI:
 1.01, 1.29). Associations were comparable, but slightly weaker
 statistically, when repeating models using late-life plasma Aβ predictors.
 Aβ42 and Aβ40 increased from midlife to late-life, but changes were not
 associated with cognitive outcomes. Midlife measurement of plasma Aβ may
 have utility as a blood-based biomarker indicative of risk for future
 cognitive impairment.
DOI: 10.5061/dryad.t76hdr80f
title: Integrating high-speed videos in capture-mark-recapture studies of insects

description: Capture-mark-recapture (CMR) studies have been used extensively in ecology
 and evolution. While it is feasible to apply CMR in some animals, it is
 considerably more challenging in small fast-moving species such as
 insects. In these groups, low recapture rates can bias estimates of
 demographic parameters, thereby, handicapping effective analysis and
 management of wild populations. Here we use high-speed videos (HSV) to
 capture two large dragonfly species, Anax junius and Rhionaeschna
 multicolor, that rarely land and, thus, are particularly challenging for
 CMR studies. We test whether HSV, compared to conventional “eye”
 observations, increases the “resighting” rates and, consequently, improves
 estimates of both survival rates and the effects of demographic covariates
 on survival. We show that the use of HSV increases the number of resights
 by 64% in A. junius and 48% in R. multicolor. HSV improved our estimates
 of resighting and survival probability which were either under- or
 overestimated with the conventional observations. Including HSV improved
 credible intervals for resighting rate and survival probability by 190%
 and 130% in A. junius and R. multicolor, respectively. Hence, it has the
 potential to open the door to a wide range of research possibilities on
 species that are traditionally difficult to monitor with distance
 sampling, including within insects and birds.
description: Please read the method section of the article.
DOI: 10.5061/dryad.pvmcvdnk9
title: Dwarf emu eggs retained large size: Supplementary material

description: Islands off southern Australia once harboured three subspecies of the
 mainland emu (Dromaius novaehollandiae), the smaller Tasmanian emu (D. n.
 diemenensis), and two dwarf emus, King Island emu (D. n. minor) and
 Kangaroo Island emu (D. n. baudinianus), which all became extinct rapidly
 after discovery by human settlers. Little was recorded about their
 life-histories and only a few historical museum specimens exist, including
 a number of complete eggs from Tasmania and a unique egg from Kangaroo
 Island. Here we present a detailed analysis of dwarf emu eggs, including a
 first record of an almost complete specimen from King Island. Our results
 show that despite the reduction in size of all island emus, especially the
 King Island emu that averaged 46% smaller than mainland birds, the egg
 remained virtually the same size and had slightly thinner eggshell, and we
 provide possible reasons why these phenomena occurred.
description: For intact eggs, all measurements were taken using dial calipers
 and rounded to the nearest 0.1 mm, with a micrometer rounded to the
 nearest 0.1 mm for eggshell thickness. Total length of complete eggs was
 taken along the long axis, and greatest width along the short axis at the
 widest medial point. Circulation of egg volume from museum eggs, including
 extinct taxa, used methodology described in [17]. Eggshell thickness was
 measured in the blowhole region of intact eggs, as described in [18], and
 recent museum and subfossil eggshell fragments were measured away from
 eroded or broken edges.<i> </i>
description: Table S1. Details of the museum and subfossil intact eggs used in
 this study, with location data and source information.
 Table S2. Details of the museum and subfossil eggshell fragments
 used in this study, with location data, measurement, age, source and
 registration information. Table S3. T-test for significance
 difference between mainland <i>Dromaius n. novaehollandiae
 </i>versus Tasmanian <i>D. n. diemenensis</i> for intact
 emu egg length, using two-tailed distribution and two-sampled unequal
 variance. P value = 0.05. Table S4. T-test for significance
 difference between mainland <i>Dromaius n. novaehollandiae
 </i>versus Tasmanian <i>D. n. diemenensis</i> for intact
 emu egg width, using two-tailed distribution and two-sampled unequal
 variance. P value = 0.05. Table S5. T-test for significance
 difference between mainland <i>Dromaius n. novaehollandiae
 </i>versus Tasmanian <i>D. n. diemenensis</i> for intact
 emu egg volume, using two-tailed distribution and two-sampled unequal
 variance. P value = 0.05. Table S6. T-test for significance
 difference between mainland <i>Dromaius n. novaehollandiae
 </i>versus Kangaroo Island <i>D. n. baudinianus</i> and
 King Island <i>D. n. minor</i> eggshell thickness, using
 two-tailed distribution and two-sampled unequal variance. P-value =
 0.05.
DOI: 10.5061/dryad.73n5tb2wh
title: Similar hibernation physiology in bats across broad geographic ranges

description: Species with broad geographic ranges may experience varied environmental
 conditions throughout their range leading to local adaptation. Variation
 among populations reflects potential adaptability or plasticity, with
 implications for populations impacted by disease, climate change, and
 other anthropogenic influences. However, behavior may counteract divergent
 selection among populations. We studied intraspecific variation in
 hibernation physiology of Myotis lucifugus (little brown
 myotis) and Corynorhinus townsendii (Townsend’s
 big-eared bat), two species of bats with large geographic ranges. We
 studied M. lucifugus at three hibernacula which spanned
 a latitudinal gradient of 1500 km, and C.
 townsendii from 6 hibernacula spread across 1200 km
 latitude and 1200 km longitude. We found no difference in torpid
 metabolic rate among populations of either species, nor was there a
 difference in the effect of ambient temperature among sites. Evaporative
 water loss was similar among populations of both species, with the
 exception of one C. townsendii pairwise site difference
 and one M. lucifugus site that differed from the others.
 We suggest the general lack of geographic variation is a consequence of
 behavioral microhabitat selection. As volant animals, bats can travel
 relatively long distances in search of preferred microclimates for
 hibernation. Despite dramatic macroclimate differences among populations,
 hibernating bats are able to find preferred microclimate conditions within
 their range, resulting in similar selection pressures among populations
 spread across wide geographic ranges.
DOI: 10.5061/dryad.3r2280gfg
title: Lean mass dynamics in hibernating bats and implications for energy and water budgets

description: Hibernation requires balancing energy and water demands over several
 months with no food intake for many species. Many studies have considered
 the importance of fat for hibernation energy budgets because it is energy
 dense and can be stored in large quantities. However, protein catabolism
 in hibernation has received less attention and whole animal changes in
 lean mass have not previously been considered. We used quantitative
 magnetic resonance body composition analysis to measure fat and lean mass
 in two systems of hibernating bats, emphasizing the importance of lean
 mass for energy and water budgets. For cave myotis ( Myotis velifer ),
 lean mass represented 38 and 25% (male and female respectively) of
 pre-hibernation mass gain. In Townsend’s big-eared bats ( Corynorhinus
 townsendii ), lean mass accounted for 18 – 35% of mass change during
 hibernation, but lean only contributed 3 – 7% of the energy budget. Water
 is produced from the catabolism of both fat and lean, but net water
 production is much less than gross water production when accounting for
 the water required to excrete urea. Although most mammals can’t rely on
 protein catabolism for metabolic water production due to the water cost of
 excreting urea, we propose a variation on the protein-for-water strategy
 whereby hibernators could temporally compartmentalize the benefits of
 protein catabolism to periods of torpor, and the water cost to periodic
 arousals when free drinking water is typically available. Combined, our
 analyses demonstrate that lean mass is dynamic in hibernation, with
 important functional consequences for both energy and water
 budgets.
DOI: 10.5061/dryad.9w0vt4bf0
title: Data from: Natal dispersal of whooping cranes in the reintroduced eastern migratory population

description: Natal dispersal is a key demographic process for evaluating population
 rate of change, especially for long-lived, highly mobile species. This
 process is largely unknown for reintroduced populations of endangered
 avian species. We evaluated natal dispersal distances (NDD) for male and
 female Whooping Cranes (Grus americana) introduced into two locations in
 central Wisconsin (Necedah National Wildlife Refuge, or NNWR, and the
 Eastern Rectangle, or ER) using a series of demographic, spatial, and life
 history related covariates. Data were analyzed using Gamma Regression
 models with a log-link function and compared using Akaike Information
 Criterion corrected for small sample sizes (AICc). Whooping Cranes
 released in the ER dispersed 261% further than those released into NNWR,
 dispersal distance increased 4% for each additional nesting pair,
 decreased about 24% for males as compared to females, increased for 21%
 for inexperienced pairs, and decreased 3% for each additional year of age.
 Natal philopatry, habitat availability, and competition for breeding
 territories may be influencing observed patterns of NDD. Whooping Cranes
 released in the ER may exhibit longer NDD due to fragmented habitat or
 conspecific attraction to established breeding pairs at NNWR.
 Additionally, sex-biased dispersal may be increasing in this population as
 there are more individuals from different natal sites forming breeding
 pairs. As the population grows and continues to disperse, the drivers of
 NDD patterns may evolve.
description: These long-term data were collected by members of the Whooping
 Crane Eastern Partnership, including staff of the International Crane
 Foundation, the Wisconsin Department of Natural Resources, and the U.S.
 Fish and Wildlife Service. Natal dispersal distances were measured using
 the 'Near' tool in ArcMap version 10.6.1. Coordinates of natal
 sites and nesting locations were not included to protect this territorial
 endangered species. All analyses were conducted in R 3.6.0. We used the
 following packages: 'stats' and 'MuMIn'. A more
 detailed description of methods can be found in the associated manuscript
 submitted for publication to Ecology and Evolution.
description: The README file explains each variable used and brief definitions
 of categorical variables. NA denotes missing data. A more detailed
 description of methods can be found in the associated
 manuscript.