cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pnvx0k6kk
title: Native biodiversity collapse in the Eastern Mediterranean

description: Global warming causes the poleward shift of the trailing edges of marine
 ectotherm species distributions. In the semi-enclosed Mediterranean Sea,
 continental masses and oceanographic barriers do not allow natural
 connectivity with thermophilic species pools: as trailing edges retreat, a
 net diversity loss occurs. We quantify this loss on the Israeli shelf,
 among the warmest areas in the Mediterranean, by comparing current native
 molluscan richness with the historical one obtained from surficial death
 assemblages. We recorded only 12% and 5% of historically present native
 species on shallow subtidal soft and hard substrates, respectively. This
 is the largest climate-driven regional-scale diversity loss in the oceans
 documented to date. In contrast, assemblages in the intertidal, more
 tolerant to climatic extremes, and in the cooler mesophotic zone show ~50%
 of the historical native richness. Importantly, ~60% of the recorded
 shallow subtidal native species do not reach reproductive size, making the
 shallow shelf a demographic sink. We predict that, as climate warms, this
 native biodiversity collapse will intensify and expand geographically,
 counteracted only by Indo-Pacific species entering from the Suez Canal.
 These assemblages, shaped by climate warming and biological invasions,
 give rise to a ‘novel ecosystem’ whose restoration to historical baselines
 is not achievable.
description: The dataset origins from the collection of samples of benthonic
 living molluscs and empty shells from the Mediterranean Israeli coastline
 (ESM2). Additionally, the dataset contains the maximum size of a subset of
 species collected alive (ESM3) and the radiocarbon ages used to quantify
 death assemblage time-averaging (ESM4). Last, four R scripts to analyse
 the data are provided. Details on the methods can be found in the
 published paper.
DOI: 10.5061/dryad.s4mw6m95h
title: Pieris brassicae geometric morphometric data

description: By adopting a longitudinal study design and through geometric
 morphometrics methods, we investigated size and shape regulation in the
 head capsule during the larval development of the cabbage butterfly Pieris
 brassicae under laboratory conditions. We found evidence of size
 regulation by compensatory growth, although not equally effective in all
 larval stages. Size compensation is not attained through the regulation of
 developmental timing, but rather through the modulation of per-time growth
 rate. As for the shape, neither the variance of the symmetric component of
 shape, nor the level of fluctuating asymmetry show any evidence of
 increase across stages, either at the population or individual level,
 which is interpreted as a mark of ontogenetic shape regulation. In
 addition, also the geometry of individual asymmetry is basically conserved
 across stages. While providing specific documentation on the ontogeny of
 size and shape variation in this insect, this study may contribute to a
 more general understanding of developmental regulation and its influence
 on phenotypic evolution.
DOI: 10.5061/dryad.zcrjdfn99
title: Effects of diet fermentability and supplementation of 2-hydroxy-(4-methylthio) butanoic acid and isoacids on milk fat depression: 2. Ruminal fermentation, fatty acid, and bacterial community structure

description: The experiment was conducted to understand ruminal effects of diet
 modification during moderate milk fat depression (MFD) and ruminal effects
 of HMTBa and isoacids on alleviating MFD. Five ruminally cannulated cows
 were used in a 5 × 5 Latin square design with the following 5 dietary
 treatments (dry matter basis): HF-C, a high forage and low starch control
 diet with 1.5% safflower oil; LF-C, a low forage and high starch control
 diet with 1.5% safflower oil; LF-HMTBa, the LF-C diet supplemented with
 HMTBa (0.11%; 28 g/d); LF-IA, the LF-C diet supplemented with isoacids
 (0.24%; 60 g/d; IA); and LF-COMB, the LF-C diet supplemented with HMTBa
 and IA. The experiment consisted of 5 periods with 21 d per period (14-d
 diet adaptation and 7-d sampling). Ruminal samples were collected to
 determine fermentation characteristics (0, 1, 3, and 6 h after feeding),
 long chain fatty acids (FA) profile (6 h after feeding), and bacterial
 community structure by analyzing 16S gene amplicon sequences (3 h after
 feeding). Data were analyzed using the MIXED procedure of SAS in a Latin
 square design. Preplanned comparison between HF-C and LF-C were conducted
 and the main effects of HMTBa and IA and their interaction within the LF
 diets were examined. The LF-C diet decreased ruminal pH and the ratio of
 acetate to propionate, with no major changes detected in ruminal FA
 profile compared with HF-C. The alpha diversity for LF-C was lower
 compared with HF-C, and beta diversity also differed between LF-C and
 HF-C. The relative abundance of bacterial phyla and genera associated
 indirectly with fiber degradation was influenced by LF-C versus HF-C. As
 the main effect of HMTBa within the LF diets, HMTBa increased the ratio of
 acetate to propionate and butyrate molar proportion. Ruminal saturated FA
 were increased and unsaturated FA concentration were decreased by HMTBa,
 with minimal changes detected in ruminal bacterial diversity and
 community. As the main effect of IA, IA supplementation increased ruminal
 concentration of all branched chain volatile FA and valerate and increased
 the percentage of trans-10 C18 isomers in total FA. In addition, alpha
 diversity and the number of functional features were increased for IA.
 Changes in the abundances of bacterial phyla and genera were minimal for
 IA. Interactions between HMTBa and IA were observed for ruminal variables
 and some bacterial taxa abundances. In conclusion, increasing trans-10 C18
 isomers did not decrease milk fat yield for LF-C versus HF-C when dietary
 PUFA level was similar. Supplementation of HMTBa increased
 biohydrogenation capacity, and supplemental IA increased bacterial
 diversity, possibly alleviating MFD. The combination of HMTBa and IA had
 no associative effects in the rumen and need further studies to understand
 the interactive mechanism.
DOI: 10.5061/dryad.rn8pk0p89
title: Abundance of herbaceous bamboos in Central Amazonia

description: Density and growth of Olyra latifolia L. and Taquara micrantha
 (Kunth) I.L.C. Oliveira & R.P. Oliveira were sampled in
 November 2017 in the municipality of Autazes, Amazonas, Brazil.
 This data was used in "Forest Fires Facilitate Growth of Herbaceous
 Bamboos in Central Amazonia" (Ziccardi et al., 2020). The dataset is
 composed by 14 variables and 36 cases (rows). Is combines data
 from canopy openness (collected with a hemispheric camera) with remote
 sensing (Vertical distance to channel network) and bamboo abundance
 (density and growth). The density of these herbaceous bamboos was
 represented by the density of clumps (clumps ha-1) and of culms (culms
 ha-1), while bamboo growth was expressed as culms per clump and the
 average height of clumps. The values are extrapolated to hectare and each
 row represents a sampled sub-plot.  
description: See in "Forest Fires Facilitate Growth of Herbaceous Bamboos
 in Central Amazonia" (Ziccardi et al., 2020).
DOI: 10.5061/dryad.d7wm37q0g
title: Abundances of xylobiont beetles in the Leipzig floodplain forest 2016

description: The dataset includes abundance data from xylobiont beetles, captured in
 the Leipzig floodplain forest between March and October 2016. We sampled
 three strata and three tree species. The strata were the understory with 2
 traps, the lower canopy with 12 traps and the upper canopy with 12 traps.
 The 24 traps in the lower and upper canopy can further be assigned to the
 tree species Quercus robur, Tilia cordata and Fraxinus excelsior. Each
 tree was sampled with 8 traps, 4 in the lower and 4 in the upper canopy.
 The dataset includes 5187 individuals, belonging to 279 beetle species of
 51 families and further 553 individuals which couldn't be determined
 to species level.
description: The beetles were captured using omnidirectional window flight
 intercept traps, consisting of  an upper sampling unit, a lower sampling
 unit and two inter-crossed plexiglass panels. The chosen sampling liquid
 was diethylene glycol. A canopy crane was used to access the lower and
 upper canopy.
description: The assignment of the trap numbers to the strata and tree species
 can be taken from the additional file
 "Metadata_XylobiontBeetles_Leipzig_2016.csv". Due to a storm two
 traps of one tree of  <em>F. excelsior</em> were lost,
 resulting in missing data for these traps between 21.07.2016 and
 04.08.2016.
DOI: 10.5061/dryad.0p2ngf205
title: Effects of social structure and management on risk of disease establishment in wild pigs

description: 1. Contact heterogeneity among hosts determines invasion and spreading
 dynamics of infectious disease, thus its characterization is essential for
 identifying effective disease control strategies. Yet, little is known
 about the factors shaping contact networks in many wildlife species and
 how wildlife management actions might affect contact networks. 2. Wild
 pigs in North America are an invasive, socially-structured species that
 pose a health concern for domestic swine given their ability to transmit
 numerous devastating diseases such as African swine fever (ASF). Using
 proximity loggers and GPS data from 48 wild pigs in Florida and South
 Carolina, USA, we employed a probabilistic framework to estimate weighted
 contact networks. We determined the effects of sex, social group, and
 spatial distribution (monthly home range overlap and distance) on wild pig
 contact. We also estimated the impacts of management-induced perturbations
 on contact and inferred their effects on ASF establishment in wild pigs
 with simulation. 3. Social group membership was the primary factor
 influencing contacts. Between-group contacts depended primarily on space
 use characteristics, with fewer contacts among groups separated by
 &gt;2 km and no contacts among groups &gt;4 km apart within a
 month. 4. Modeling ASF dynamics on the contact network demonstrated that
 indirect contacts resulting from baiting (a typical method of attracting
 wild pigs or game species to a site to enhance recreational hunting)
 increased the risk of disease establishment by ~33% relative to direct
 contact. Low-intensity population reduction (&lt;5.9% of the
 population) had no detectable impact on contact structure but reduced
 predicted ASF establishment risk relative to no population reduction. 5.
 We demonstrate an approach for understanding the relative role of spatial,
 social, and individual-level characteristics in shaping contact networks
 and predicting their effects on disease establishment risk, thus providing
 insight for optimizing disease control in spatially- and
 socially-structured wildlife species.
DOI: 10.5061/dryad.pnvx0k6km
title: Inter- and intra-archipelago dynamics of population structure and gene flow in a Polynesian bird

description: Islands are separated by natural barriers that prevent gene flow between
 terrestrial populations and promote allopatric diversification. Birds in
 the South Pacific are an excellent model to explore the interplay between
 isolation and gene flow due to the region’s numerous archipelagos and
 well-characterized avian communities. The wattled honeyeater complex
 (Foulehaio spp.) comprises three allopatric species that are widespread
 and common across Fiji, Tonga, Samoa, and Wallis and Futuna. Here, we
 explored patterns of diversification within and among these lineages using
 genomic and morphometric data. We found support for three clades of
 Foulehaio corresponding to three recognized species. Within F.
 carunculatus, population genetic analyses identified nine major lineages,
 most of which were composed of sub-lineages that aligned nearly perfectly
 to individual island populations. Despite genetic structure and great
 geographic distance between populations, we found low levels of gene flow
 between populations in adjacent archipelagos. Additionally, body size of
 F. carunculatus varied randomly with respect to evolutionary history (as
 Ernst Mayr predicted), but correlated negatively with island size,
 consistent with the island rule. Our findings support a hypothesis that
 widespread taxa can show population structure between immediately adjacent
 islands, and likely represent many independent lineages loosely connected
 by gene flow.
description: The data was collected using Illumina sequence of libraries
 enriched for tetrapod ultraconserved elements. It was then processed using
 common pipelines for the data (namely phyluce and a variant of seqcap_pop)
 before input files were generated for population genomic
 analyses.
description: The descriptions for all files can be found in
 "README.txt". Each category of file (script, morphometric data,
 pop gen input, and phylogenetic tree files) has it's own zipped
 folder.
DOI: 10.15468/dl.bmzdh8
title: Occurrence Download

description: A dataset containing 13 species occurrences available in GBIF matching the query:
{
 "and" : [
 "OccurrenceStatus is Present",
 "TaxonKey is Hopea mollissima"
 ]
}

 The dataset includes 13 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002672-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.zcrjdfn9b
title: Uncovering patterns of freshwater positive interactions using meta‐analysis: identifying the roles of common participants, invasive species and environmental context

description: General understanding of freshwater positive interactions has been far
 outpaced by knowledge of these important relationships in terrestrial and
 marine ecosystems. Positive interactions are sensitive to human impacts,
 necessitating synthetic approaches to elucidate broad patterns and predict
 future changes if these interactions are altered or lost.  We
 conducted a global meta-analysis to evaluate the magnitude of positive
 interactions across freshwater habitats. In 340 studies, we found
 substantial positive effects, with facilitators increasing beneficiaries
 by, on average, 81% across all taxa and response variables. Mollusks in
 particular were commonly studied as both facilitators and beneficiaries.
 Amphibians were one group benefiting the most from positive interactions,
 yet amphibians were not commonly studied. Invasive facilitators had
 stronger positive effects on beneficiaries than native facilitators. We
 compared positive effects between high and low stress conditions (n = 13)
 and found no difference in the magnitude of benefit. Future areas of
 research include understudied facilitators and beneficiaries, the stress
 gradient hypothesis, patterns across space or time, and the influence of
 declining taxa whose elimination would jeopardize fragile positive
 interaction networks. Freshwater positive interactions occur among a wide
 range of taxa, influence populations, communities, and ecosystem
 processes, and deserve further exploration
description: Please see <strong>readME.txt </strong>for associated
 metadata. The attached dataset includes both the full dataset used for the
 analysis (<strong>PositiveInteractionsF.csv</strong>), a small
 subset of the data used to evaluate the stress gradient hypothesis
 (<strong>PositiveInteractionsStress.csv</strong>), and
 geographical information on study locations
 (<strong>PositiveInteractionsLocs.csv</strong>).
DOI: 10.5061/dryad.hhmgqnkfp
title: Spatial and temporal dynamics of space use by free-ranging domestic dogs Canis familiaris in rural Africa

description: Variation in the spatial ecology of animals influences the transmission of
 infections and so understanding host behaviour can improve the control of
 diseases. Despite the global distribution of free-ranging domestic dogs
 Canis familiaris and their role as reservoirs for zoonotic diseases,
 little is known about the dynamics of their space use. We deployed GPS
 loggers on free-ranging dogs from six villages in rural Chad, and tracked
 the movements of 174 individuals in the dry season and 151 in the wet
 season. We calculated 95% and core home ranges using auto-correlated
 kernel density estimates (AKDE95 and AKDEcore), determined the degree to
 which their movements were predictable, and identified correlates of
 movement patterns. The median AKDE95 range in the dry season was 0.54km2
 and in the wet season was 0.31km2, while the median AKDEcore range in the
 dry season was 0.08km2 and in the wet season was 0.04km2. Seasonal
 variation was, in part, related to owner activities. Dogs from hunting
 households had ranges that were five times larger in the dry season. At
 least 70% of individuals were more predictably ‘at home’ (&lt;50m from
 the household) throughout the day in the dry season. 80% of dogs
 demonstrated periodicity in activity levels (speed) and just over half the
 dogs exhibited periodicity in location (repeated space use). In the wet
 season, dogs mostly exhibited 24-hour cycles in activity and location,
 with peaks at midday. In the dry season, dogs exhibited both 12 and
 24-hour cycles, with either a single peak at midday, or one peak between
 6am and 12 noon and a second between 6 and 10pm. Strategies to control
 canine-mediated zoonoses can be improved by tailoring operations to the
 local spatial ecology of free-ranging dogs. Interventions using a
 door-to-door strategy in rural Chad would best conduct operations during
 the dry season, when access to dogs around their household more reliably
 exceeds 70% throughout the day. Given the importance of use in hunting for
 explaining variation in dog space-use, targeting approaches to disease
 control at the household level on the basis of owner activities offers
 potential to improve access to dogs.
description: GPS tracking of a large sample of domestic dogs living in human
 households in rural Chad.
description: See ReadMe.txt file for details of data.
DOI: 10.5061/dryad.bzkh18979
title: Data from: Wild Goffin’s cockatoos flexibly manufacture and use tool sets

description: The use of different tools to achieve a single goal is considered unique
 to human and primate technology. To unravel the origins of such complex
 behaviors, it is crucial to investigate tool use that does not
 occur species wide. These cases can be assumed to have emerged
 innovatively and be applied flexibly, thus emphasizing creativity and
 intelligence. However, it is intrinsically challenging to record tool
 innovations in natural settings that do not occur species-wide. Here we
 report the discovery of two distinct tool
 manufacture methods and the use of tool sets in wild
 Goffin’s cockatoos (Cacatua goffiniana). Up to three types of wooden
 tools, differing in their physical properties and each serving a different
 function, were manufactured and employed to extract embedded
 seed matter of Cerbera manghas. While Goffin's
 cockatoos do not depend on tool-obtained resources, repeated observations
 of two temporarily kept wild birds and indications from free-ranging
 individuals suggest this behavior occurs in the wild, albeit not
 species-wide. The use of a tool set in a non-primate implies convergent
 evolution of advanced tool use. Furthermore, these observations
 demonstrate how a species without hands can achieve dexterity in a
 high-precision task. This finding of flexible use and manufacture of tool
 sets in animals distantly related to humans significantly diversifies the
 phylogenetic landscape of technology.
DOI: 10.5061/dryad.qrfj6q5dh
title: Data from: Harvest is associated with the disruption of social and fine-scale genetic structure among matrilines of a solitary large carnivore

description: Harvest can disrupt wildlife populations by removing adults with naturally
 high survival. This can reshape sociospatial structure, genetic
 composition, fitness, and potentially affect evolution. Genetic tools can
 detect changes in local, fine-scale genetic structure (FGS) and assess the
 interplay between harvest-caused social and FGS in populations. We used
 data on 1,614 brown bears, Ursus arctos, genotyped with 16
 microsatellites, to investigate whether harvest intensity (mean low: 0.13
 from 1990-2005, mean high: 0.28 from 2006-2011) caused changes in FGS
 among matrilines (8 matrilines; 109 females ≥ 4 years of age),
 sex-specific survival and putative dispersal distances, female spatial
 genetic autocorrelation, matriline persistence, and male mating patterns.
 Increased harvest decreased FGS of matrilines. Female dispersal distances
 decreased and male reproductive success was redistributed more evenly.
 Adult males had lower survival during high harvest, suggesting that higher
 male turnover caused this redistribution and helped explain decreased
 structure among matrilines, despite shorter female dispersal distances.
 Adult female survival and survival probability of both mother and daughter
 were lower during high harvest, indicating that matriline persistence was
 also lower. Our findings indicate a crucial role of regulated harvest in
 shaping populations, decreasing differences among ‘groups’, even for
 solitary-living species, and potentially altering the evolutionary
 trajectory of wild populations.
description: See "Methods" of main text and the "ReadMe"
 file.
description: See ReadMe file.
DOI: 10.5061/dryad.51c59zw72
title: Identification of determinants of pollen donor fecundity using the hierarchical neighborhood model

description: Individual differences in male reproductive success drive genetic drift
 and natural selection, altering genetic variation and phenotypic trait
 distributions in future generations. Therefore, identifying the
 determinants of reproductive success is important for understanding the
 ecology and evolution of plants. Here, based on the spatially-explicit
 mating model (the neighborhood model), we develop a hierarchical
 probability model that links co-dominant genotypes of offspring and
 candidate parents with the phenotypic determinants of male reproductive
 success. The model accounts for pollen dispersal, genotyping errors as
 well as individual variation in selfing, pollen immigration, and
 differentiation of immigrant pollen pools. Unlike the classic neighborhood
 model approach, our approach is specially designed to account for
 excessive variation (overdispersion) in male reproductive success. Using
 the Bayesian framework, we implemented the estimation method that, among
 others, allows the selection of phenotypic variables important for male
 reproductive success as well as the computation of the fraction of total
 variance in fecundity (R2) explained by selected variables. Computer
 simulations showed that our method outperforms both the classic
 neighborhood model and the two-step approach, where individual fecundities
 and the effects of phenotypic variables are estimated in separate steps.
 The analysis of two data examples showed that in wind-pollinated trees,
 male reproductive success depends on both the amount of produced pollen
 and the ability to pollen spread. However, despite that the tree size was
 positively correlated with male fecundity, it explained only a fraction of
 the total variance in reproductive success, indicating the presence of
 significant unmeasured factors. Finally, case studies highlighted the
 importance of accounting for pollen dispersal in the estimation of
 determinants of plant reproductive success.
description: Tree coordinates (XY) are given in meters. Microsatellite allele
 lengths are given in base pairs. Phenotypic measurements for trees are
 given as standardized values (mean=0 and standard deviation=1). Trees that
 can serve as pollen parents (hemraphrodites or male trees) are denoted
 with the variable "Pollen donor"=1.
description: Missing values are coded with NA.