cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pq624
title: Data from: A multispecies occupancy model for two or more interacting species

description: Species occurrence is influenced by environmental conditions and the
 presence of other species. Current approaches for multispecies occupancy
 modelling are practically limited to two interacting species and often
 require the assumption of asymmetric interactions. We propose a
 multispecies occupancy model that can accommodate two or more interacting
 species. We generalize the single-species occupancy model to two or more
 interacting species by assuming the latent occupancy state is a
 multivariate Bernoulli random variable. We propose modelling the
 probability of each potential latent occupancy state with both a
 multinomial logit and a multinomial probit model and present details of a
 Gibbs sampler for the latter. As an example, we model co-occurrence
 probabilities of bobcat (Lynx rufus), coyote (Canis latrans), grey fox
 (Urocyon cinereoargenteus) and red fox (Vulpes vulpes) as a function of
 human disturbance variables throughout 6 Mid-Atlantic states in the
 eastern United States. We found evidence for pairwise interactions among
 most species, and the probability of some pairs of species occupying the
 same site varied along environmental gradients; for example, occupancy
 probabilities of coyote and grey fox were independent at sites with little
 human disturbance, but these two species were more likely to occur
 together at sites with high human disturbance. Ecological communities are
 composed of multiple interacting species. Our proposed method improves our
 ability to draw inference from such communities by permitting modelling of
 detection/non-detection data from an arbitrary number of species, without
 assuming asymmetric interactions. Additionally, our proposed method
 permits modelling the probability two or more species occur together as a
 function of environmental variables. These advancements represent an
 important improvement in our ability to draw community-level inference
 from multiple interacting species that are subject to imperfect detection.
description: Data and code for
 fitting multi-species occupancy model.Camera trap detection /
 non-detection data for bobcats, coyotes, gray foxes, and red foxes from 6
 mid-Atlantic states and the District of Columbia, USA; associated
 site-level covariates; and R and Stan code for fitting a multi-species
 occupancy model. See ReadMe for detailed file
 descriptions.Data.zip
DOI: 10.5061/dryad.500dm
title: Data from: Fragmentation can increase spatial genetic structure without decreasing pollen-mediated gene flow in a wind-pollinated tree

description: Fragmentation reduces population sizes, increases isolation between
 habitats, and can result in restricted dispersal of pollen and seeds.
 Given that diploid seed dispersal contributes more to shaping fine-scale
 spatial genetic structure than haploid pollen flow, we tested whether
 fine-scale SGS can be sensitive to fragmentation even if extensive pollen
 dispersal is maintained. Castanopsis sclerophylla (Lindley &
 Paxton) Schottky (Fagaceae), a wind-pollinated and gravity seed-dispersed
 tree, was studied in an area of Southeast China where its populations have
 been fragmented to varying extents by human activity. Using different age
 classes of trees in areas subject to varying extents of fragmentation, we
 found no significant difference in genetic diversity between pre- and
 post-fragmentation C. sclerophylla subpopulations. Genetic differentiation
 among post-fragmentation subpopulations was also only slightly lower than
 among post-fragmentation subpopulations. In the most fragmented habitat,
 selfing rates were significantly higher than zero in pre-fragmentation,
 but not post-fragmentation, cohorts. These results suggest that
 fragmentation had not decreased gene flow among these populations and that
 pollen flow remains extensive. However, significantly greater fine-scale
 SGS was found in post-fragmentation subpopulations in the most fragmented
 habitat, but not in less fragmented habitats. This alteration in SGS
 reflected more restricted seed dispersal, induced by changes in the
 physical environments and the prevention of secondary seed dispersal by
 rodents. An increase in SGS can therefore result from more restricted seed
 dispersal, even in the face of extensive pollen flow, making it a
 sensitive indicator of the negative consequences of population
 fragmentation.
description: data file of Castanopsis
 sclerophylla spatial genetic structure in a fragmented
 landscape
DOI: 10.5061/dryad.hd3s3
title: Data from: Root and shoot glucosinolate allocation patterns follow optimal defence allocation theory

description: 1. Optimal defence allocation theory (ODT) is one of the most prominent
 theoretical frameworks to explain the allocation of defence compounds
 within plants. It predicts that the most valuable and vulnerable plant
 organs have the highest levels of chemical defence. The ODT has been well
 worked out and experimentally tested for shoot defences, but not for root
 defences. To assess if ODT principles apply similarly to roots and shoots,
 we examined glucosinolates in aboveground and belowground organs of nine
 plant species belonging to two families. 2. In order to evaluate whether
 ODT equally applies to shoot and root organs, we designed a conceptual
 model in which aboveground and belowground organs were assigned to orders
 of importance to plant performance. We hypothesized that organs
 constituting the plant’s core structure are better protected than more
 distal organs. 3. The nine plant species were cultivated, and their roots
 and shoots were harvested and divided in three orders for glucosinolate
 analysis. Using a specialist (Delia radicum) and a generalist (Amphimallon
 solstitiale) root herbivore, we also experimentally tested the hypothesis
 that the generalist herbivore prefers to feed on fine roots with a low
 glucosinolate concentration, while the specialist prefers taproots with a
 high glucosinolate concentration. 4. We found that both in roots and
 shoots the higher-ordered core structural organs (taproots and stems) had
 the highest levels of glucosinolates. Belowground, taproots and lateral
 roots were better protected than the more distal, and less costly, fine
 roots in seven out of nine species tested. The specialist root herbivore
 preferred feeding on the highly defended taproots, which is in line with
 what has been found for aboveground specialist herbivores. Moreover, the
 glucosinolate concentration in roots overall was significantly higher than
 that in shoots. 5. Synthesis. These results support the hypothesis that
 ODT generally applies to glucosinolate allocation in aboveground and
 belowground organs and may mainly serve to maintain the integrity of the
 main plant structure. Moreover, it suggests that aboveground and
 belowground insect herbivores independently exert similar selection
 pressures on defence allocation patterns in roots and shoots.
description: Glucosinolate and insect
 feeding preference dataData.xlsx
DOI: 10.5061/dryad.288ft
title: Data from: A revision of African helmeted terrapins (Testudines: Pelomedusidae: Pelomedusa), with descriptions of six new species

description: Using nearly range-wide sampling, we analyze up to 1848 bp of
 mitochondrial DNA of 183 helmeted terrapins and identify a minimum of 12
 deeply divergent species-level clades. Uncorrected p distances of these
 clades equal or clearly exceed those between the currently recognized
 species of Pelusios, the genus most closely related to Pelomedusa. We
 correlate genetic discontinuities of Pelomedusa with data on morphology
 and endoparasites and describe six new Pelomedusa species. Moreover, we
 restrict the name Pelomedusa subrufa (Bonnaterre, 1789) to one genetic
 lineage and resurrect three further species from its synonymy, namely P.
 galeata (Schoepff, 1792), P. gehafie (Rüppell, 1835), and P. olivacea
 (Schweigger, 1812). In addition to these ten Pelomedusa species, we
 identify two further clades from Cameroon and Sudan with similar levels of
 genetic divergence that remain unnamed candidate species. We also note
 that some problematical terrapins from South Africa and Somalia may
 represent two additional candidate species. Some of the Pelomedusa species
 are morphologically distinctive, whilst others can only be identified by
 molecular markers and are therefore morphologically cryptic taxa.
description: Pelomedusa_Supporting-Information_Reference_AlignmentREFERENCE ALIGNMENT. 12S rRNA sequences (fasta format) for Pelomedusa species.Pelomedusa_Supporting-Information_Table_S1TABLE S1. Used samples, GenBank sequences and their accession numbers. Mitochondrial lineages sensu Vargas-Ramírez et al. (2010) and Fritz et al. (2014) indicated.Supporting-Information_Table_S1.xlsPelomedusa_Supporting-Information_Table_S2TABLE S2. Evolutionary models selected by the Bayesian Information Criterion in PARTITIONFINDER (Lanfear et al. 2012).
DOI: 10.5061/dryad.k4p48
title: Data from: Quantitative genetic variance and multivariate clines in the Ivyleaf morning glory, Ipomoea hederacea

description: Clinal variation is commonly interpreted as evidence of adaptive
 differentiation, although clines can also be produced by stochastic
 forces. Understanding whether clines are adaptive therefore requires
 comparing clinal variation to background patterns of genetic
 differentiation at presumably neutral markers. Although this approach has
 frequently been applied to single traits at a time, we have comparatively
 fewer examples of how multiple correlated traits vary clinally. Here, we
 characterize multivariate clines in the Ivyleaf morning glory, examining
 how suites of traits vary with latitude, with the goal of testing for
 divergence in trait means that would indicate past evolutionary responses.
 We couple this with analysis of genetic variance in clinally varying
 traits in 20 populations to test whether past evolutionary responses have
 depleted genetic variance, or whether genetic variance declines
 approaching the range margin. We find evidence of clinal differentiation
 in five quantitative traits, with little evidence of isolation by distance
 at neutral loci that would suggest non-adaptive or stochastic mechanisms.
 Within and across populations, the traits that contribute most to
 population differentiation and clinal trends in the multivariate phenotype
 are genetically variable as well, suggesting that a lack of genetic
 variance will not cause absolute evolutionary constraints. Our data are
 broadly consistent theoretical predictions of polygenic clines in response
 to shallow environmental gradients. Ecologically, our results are
 consistent with past findings of natural selection on flowering phenology,
 presumably due to season-length variation across the range.
description: Raw phenotypic
 datadryad_univariate.txtLine meansLine means for the raw phenotypic datadryad_line_means.txt
DOI: 10.5281/zenodo.17460214
title: Steady Collapse of Uranus' Exosphere After 1998 to the Present Decade

description: This contains all the data and programs used to generate the plots in both the main body of the manuscript and the supplementary material. The manuscript is about the analysis of HST Lyman alpha observations of Uranus and is titled "Steady Collapse of Uranus' Exosphere After 1998 to the Present Decade".
DOI: 10.5281/zenodo.18382186
title: Steady Collapse of Uranus' Exosphere After 1998 to the Present Decade

description: This contains all the data and programs used to generate the plots in both the main body of the manuscript and the supplementary material. The manuscript is about the analysis of HST Lyman alpha observations of Uranus and is titled "Steady Collapse of Uranus' Exosphere After 1998 to the Present Decade".
DOI: 10.5061/dryad.qq304
title: Data from: Attraction to and learning from social cues in fruitfly larvae

description: We examined the use of social information in fruitfly larvae, which
 represent an ideal model system owing to their robust learning abilities,
 small number of neurons and well-studied neurogenetics. Focal larvae
 showed attraction to the distinct odour emanating from food occupied by
 other larvae. In controlled learning experiments, focal larvae preferred
 novel odours previously paired with food occupied by other larvae over
 novel odours previously paired with unoccupied food. When we gave groups
 of larvae a choice between food patches differing in quality, more larvae
 aggregated on the higher-quality food, suggesting that attraction to and
 learning about cues associated with other larvae can be beneficial.
 Furthermore, larvae were more likely to find the best available food patch
 in trials when that food patch was occupied by other larvae than in trials
 when that food patch was unoccupied. Our data suggest, however, that the
 benefits from joining others may be at least partially offset by the
 fitness costs of increased competition, because larvae reared in isolation
 did as well as or better than larvae reared in groups on three key fitness
 parameters: developmental rate, survival rate and adult dry body mass. Our
 work establishes fruitfly larvae as a highly tractable model species for
 further research on the mechanisms that modulate behaviour and learning in
 a social context.
description: Dryad_Experiment_1Data for Experiment 1A-1E. Collected in the lab. Created in microsoft excel.Dryad_Experiment_2Covers Experiments 2A-2C. Collected in the lab. Created in Microsoft Excel.Dryad_Experiment_3Covers Experiments 3A and 3B. Collected in the lab. Created in Microsoft excel.Dryad_Experiment_4Data for Experiments 4A-4C.
DOI: 10.5061/dryad.vn77k
title: Data from: Polygamy slows down population divergence in shorebirds

description: Sexual selection may act as a promotor of speciation since divergent mate
 choice and competition for mates can rapidly lead to reproductive
 isolation. Alternatively, sexual selection may also retard speciation
 since polygamous individuals can access additional mates by increased
 breeding dispersal. High breeding dispersal should hence increase gene
 flow and reduce diversification in polygamous species. Here we test how
 polygamy predicts diversification in shorebirds using genetic
 differentiation and subspecies richness as proxies for population
 divergence. Examining microsatellite data from 79 populations in ten
 plover species (Genus: Charadrius) we found that polygamous species
 display significantly less genetic structure and weaker
 isolation-by-distance effects than monogamous species. Consistent with
 this result, a comparative analysis including 136 shorebird species showed
 significantly fewer subspecies for polygamous than for monogamous species.
 By contrast, migratory behaviour neither predicted genetic differentiation
 nor subspecies richness. Taken together, our results suggest that
 dispersal associated with polygamy may facilitate gene flow and limit
 population divergence. Therefore, intense sexual selection, as occurs in
 polygamous species, may act as a brake rather than an engine of speciation
 in shorebirds. We discuss alternative explanations for these results and
 call for further studies to understand the relationships between sexual
 selection, dispersal and diversification.
description: Polygamy slows
 diversification in shorebirds_rawdataThis file contains all
 of the raw microsatellite data for ten species of plover. Kittlitz's
 plover and white-fronted plover are divided into two datasets which
 represent 1) mainland African populations and 2) Madagascan populations.
 Details of the microsatellite markers and PCR conditions can be found in
 the paper. Killdeer plover has one marker identified as having a high
 estimate of null alleles, this is marked in grey
 shading.shorebird_subspeciesThis file contains breeding system, breeding range size, subspecies richness and migratory behaviour information for 136 shorebird species. This is the datafile used to test the hypotheses described in the paper using a PGLS approach implemented in R.
DOI: 10.5061/dryad.v577v
title: Data from: Bony traits and genetics drive intraspecific variation in vertebrate elemental composition

description: Interspecific variation in elemental composition is well known and often
 leads to predictable differences in ecosystem interactions, but little is
 known about the extent, causes and importance of intraspecific variation
 in elemental composition. If intraspecific variation is substantial and
 has a genetic basis, it may underlie an important mechanism of
 evolutionary interplay with ecology as individuals compensate for
 evolutionary changes in elemental demand. To investigate the extent and
 causes of intraspecific elemental variation in vertebrates, we sampled
 evolutionary model species Gasterosteus aculeatus (Threespine Stickleback)
 from 12 locations in British Columbia, Canada. Fish were phenotyped,
 genotyped for Eda alleles underlying lateral plate variation and assayed
 for elemental content (C, N, P). We found stickleback vary widely in
 elemental composition (2.2 – 6.5%P; 3.0 – 9.4:1 N:P). Phenotypic models
 explained the majority of this variation using bony armour traits (pelvis
 length, lateral plate count), bone mineralization, body size and
 condition. Subsequent genetic models found allelic variation at Eda
 generates a 7-14% change in whole organism N:P. As Eda allele frequencies
 are commonly changed through strong natural selection in freshwater
 habitats, we infer that stickleback elemental composition can evolve
 rapidly. Further, as genetics are known to drive variation in many of the
 other influential traits, we conclude that genetic variation constitutes a
 major source of variation in the elemental composition of Gasterosteus
 aculeatus. As such, we find that elemental composition has a large
 evolutionary potential which may underlie important evo-eco interactions.
description: Durston and El-Sabaawi -
 Stickleback CompositionFrom Durston and
 El-Sabaawi 2017, this file contains morphological, genetic, environmental
 and elemental data for 375 Threespine Stickleback from 12 populations. The
 file contains separate tabs for data from all locations, Kennedy and
 Miami. The Kennedy and Miami data is also present in the all locations
 tab, but the size adjustment and standardization are
 different.Durston-STKB-Comp-Dryad.xlsx
DOI: 10.5061/dryad.1sm54
title: Data from: Evolution and comparative ecology of parthenogenesis in haplodiploid arthropods

description: Changes from sexual reproduction to female-producing parthenogenesis
 (thelytoky) have great evolutionary and ecological consequences, but how
 many times parthenogenesis evolved in different animal taxa is unknown. We
 present the first exhaustive database covering 765 cases of
 parthenogenesis in haplodiploid arthropods, and estimate frequencies of
 parthenogenesis in different taxonomic groups. We show that the frequency
 of parthenogenetic lineages extensively varies among groups (0-38% among
 genera), that many species have both sexual and parthenogenetic lineages
 and that polyploidy is very rare. Parthenogens are characterized by broad
 ecological niches: parasitoid and phytophagous parthenogenetic species
 consistently use more host species, and have larger, polewards extended
 geographic distributions than their sexual relatives. These differences
 did not solely evolve after the transition to parthenogenesis. Extant
 parthenogens often derive from sexual ancestors with relatively broad
 ecological niches and distributions. As these ecological attributes are
 associated with large population sizes, our results strongly suggests that
 transitions to parthenogenesis are more frequent in large sexual
 populations and/or that the risk of extinction of parthenogens with large
 population sizes is reduced. The species database presented here provides
 insights into the maintenance of sex and parthenogenesis in natural
 populations that are not taxon specific and opens perspectives for future
 comparative studies.
description: List of species with
 obligate parthenogenesis.This list contains the
 species (with populations) that reproduce via obligate parthenogenesis
 (thelytoky).1-species_list_total.csvList of species with tychoparthenogenesis.This list contains the species for which asexual reproduction is likely tychoparthenogenesis.6-tychoparthenogenesis_list.csvList of species with facultative parthenogenesisThis is the list with species that are characterised by facultative parthenogenesis.7-facultativeparthenogenesis.csv
DOI: 10.5061/dryad.5c6d5
title: Data from: Edible dormice (Glis glis) avoid areas with a high density of their preferred food plant - the European beech

description: Background: Numerous species, especially among rodents, are strongly
 affected by the availability of pulsed resources. The intermittent
 production of large seed crops in northern hemisphere tree species (e.g.,
 beech Fagus spec.,oak Quercus spec., pine trees Pinus spec.) are prime
 examples of these resource pulses. Adult edible dormice are highly
 dependent on high energy seeds to maximize their reproductive output. For
 juvenile dormice the energy rich food is important to grow and fatten in a
 very short time period prior to hibernation. While these erratic, often
 large-scale synchronized mast events provide overabundant seed
 availability, a total lack of seed production can be observed in so-called
 mast failure years. We hypothesized that dormice either switch territories
 between mast and non-mast years, to maximize energy availability or select
 habitats in which alternative food sources are also available (e.g.,
 fleshy fruits, cones). To analyze the habitat preferences of edible
 dormice we performed environmental niche factor analyses (ENFA) for 9
 years of capture-recapture data. Results: As expected, the animals mainly
 used areas with high canopy closure and vertical stratification, probably
 to avoid predation. Surprisingly, we found that dormice avoided areas with
 high beech tree density,but in contrast preferred areas with a relatively
 high proportion of coniferous trees. Conifer cones and leaves can be an
 alternative food source for edible dormice and are less variable in
 availability. Conclusion: Therefore, we conclude that edible dormice try
 to avoid areas with large fluctuations in food availability to be able to
 survive years without mast in their territory.
description: dormice_distances_NBdistance analysis for capture events and moving tendenciesdormice_distances_NB_mastdata to analyse the tendencies of dormice to move in different mast situationsdormice_captures_environmentalcaptures under different environmental conditionsdormice_female_captures_environmentalcapture numbers under different environmental conditions for femalesdormice_male_captures_environmentalcapture numbers for different environmental conditions males