cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.12jm63xv7
title: Data from: Human disturbance and the activity patterns and temporal overlap of tapirs and jaguars in reserves of NW Belize.

description: Human disturbance from tourism and other non-consumptive activities in
 protected areas may be stressful to wildlife. Animals may move away in
 space or time to avoid human interaction. For species of particular
 conservation concern, such as Baird’s tapirs (Tapirus bairdii) and jaguars
 (Panthera onca), a better understanding of how they respond to different
 levels and types of disturbance is needed in order to manage human
 visitation to parks in ways that minimize negative outcomes for wildlife.
 We describe the overlap of activity patterns of tapirs, jaguars, and
 humans at logged and unlogged sites and at places with low versus high
 human visitation using camera survey data from protected areas of
 northwest Belize, 2013-2016. Tapirs were nocturnal in all study sites,
 with &gt;80 percent of all tapir detections occurring between 1900 h
 and 0500 h. Their activity patterns were not different in unlogged versus
 logged sites and did not change with increased human traffic. Jaguars were
 cathemeral across sites, but had more nocturnal activity at the site with
 the most human impact. Activity pattern overlap between tapirs and jaguars
 did not differ significantly between logged and unlogged sites, nor
 between areas with low and high human activity. Human traffic increased
 from 2013-2016 at most of the study locations. In conclusion, this camera
 trap dataset suggests that non-consumptive human disturbance does not
 alter the activity patterns of tapirs and jaguars in protected areas
 lacking hunting pressure.
description: These data were collected from a long-term camera-trapping study
 of jaguar movements and habitat occupancy in Belize.  This study was
 conducted at four locations in the Orange Walk District of NW Belize:
 Yalbac (YB), La Milpa (LM), Gallon Jug (GJ), and Hill Bank (HB).  At each
 location, cameras were placed in a grid formation approximately 2-3 km
 apart to maximize detection of individual jaguars, which have larger home
 ranges than tapirs.  Cameras were placed on tree trunks or stakes about 35
 cm off the ground and were not baited.  Cameras remained active 24 h/d and
 were set to take 3 photos when triggered by motion with a 15 sec delay
 between trigger events.  Date and timestamp data were collected from the
 photo detections of tapirs, jaguars, and humans and used to analyze
 activity patterns of these species.
description: R scripts are titled by the kind of comparison being made: Logged
 vs. Unlogged.R is for activity overlap of tapirs, jaguars, and humans in
 logged and unlogged areas, HighLow.R is for activity overlap of the three
 species at camera stations of high and low frequency of human activity,
 and BySite.R is for activity overlap of the three species at each of the
 four study sites.  The two species being compared for each overlap
 calculation are abbreviated together as tapjag (tapir and jaguar
 activity), taphum (tapir and human activity), or jaghum (jaguar and human
 activity).
DOI: 10.5061/dryad.9ghx3fff6
title: Data from: In the foothill zone - Sabanejewia balcanica (Karaman 1922), in the lowland zone - Sabanejewia bulgarica (Drensky 1928): myth or reality?

description: The status of golden loaches (genus Sabanejewia) in the region of Central
 Europe and Balkans is still ambiguous. The greatest controversy is caused
 by species Sabanejewia balcanica and S. bulgarica, whose distinguishing
 features are often difficult to prove and their occurrence in some river
 sections is often mentioned as sympatric. Previous phylogenetic studies
 aimed at the resolving of their taxonomic status did not include samples
 from their type localities and so led to a lack of their true distribution
 in this region. Therefore, the main aim of this study was to identify the
 taxonomic status of golden loaches populations in this area on the model
 territory of Slovakia. For this purpose, we used a novelty approach
 (morphological, molecular and microhabitat) and we also included the
 missing samples from the type localities of both species. Based on mtDNA
 all the Slovakian samples reflected haplotype richness revealed on the
 type locality of S. bulgarica, although the genetic distances from other
 representatives of the genus Sabanejewia occurring are not significant.
 Within the morphology, we have revealed a great measure of variability in
 studied populations, which is largely caused by different habitat
 conditions and thus representing a phenotypic plasticity of these fish.
description: Table_S1 Detail list of all studied taxa, their haplotype
 classification to sampling sites, haplotype frequencies and GenBank
 accession numbers. Table_S2 Summary of genetic
 diversity indices and results of neutrality tests in the cyt b
 dataset Table_S3 Support values of the nodes according
 to two delimitation methods and three phylogenetic analyses
DOI: 10.5061/dryad.fqz612jqc
title: Data from: An ECF-type transporter scavenges heme to overcome iron-limitation in Staphylococcus lugdunensis

description: Energy-coupling factor type (ECF-transporters) represent trace nutrient
 acquisition systems. Substrate binding components of ECF-transporters are
 membrane proteins with extraordinary affinity, allowing them to scavenge
 trace amounts of ligand. A number of molecules have been described as
 substrates of ECF-transporters, but an involvement in iron-acquisition is
 unknown. Host-induced iron limitation during infection represents an
 effective mechanism to limit bacterial proliferation. We identified the
 iron-regulated ECF-transporter Lha in the opportunistic bacterial pathogen
 Staphylococcus lugdunensis and show that the transporter is specific for
 heme. The recombinant substrate-specific subunit LhaS accepted heme from
 diverse host-derived hemoproteins. Using isogenic mutants and recombinant
 expression of Lha, we demonstrate that its function is independent of the
 canonical heme acquisition system Isd and allows proliferation on human
 cells as sources of nutrient iron. Our findings reveal a unique strategy
 of nutritional heme acquisition and provide the first example of an
 ECF-transporter involved in overcoming host-induced nutritional
 limitation.
DOI: 10.5061/dryad.pk0p2ngkd
title: Genome-wide patterns of divergence and introgression after secondary contact between Pungitius sticklebacks

description: Speciation is a continuous process. Although it is known that differential
 adaptation can initiate divergence even in the face of gene flow, we know
 relatively little about the mechanisms driving complete reproductive
 isolation and the genomic patterns of divergence and introgression at the
 later stages of speciation. Sticklebacks contain many pairs of sympatric
 species differing in levels of reproductive isolation and divergence
 history. Nevertheless, most previous studies have focused on young species
 pairs. Here, we investigated two sympatric stickleback species, Pungitius
 pungitius and P. sinensis, whose habitats overlap in eastern Hokkaido;
 these species show hybrid male sterility, suggesting that they may be at a
 late stage of speciation. Our demographic analysis using whole genome
 sequence data showed that these species split 1.73 million years ago and
 came into secondary contact 37,200 years ago after a period of allopatry.
 This long period of allopatry might have promoted the evolution of
 intrinsic incompatibility. Although we detected on-going gene flow and
 signatures of introgression, overall genomic divergence was high, with
 considerable heterogeneity across the genome. The heterogeneity was
 significantly associated with variation in recombination rate. This
 sympatric pair provides new avenues to investigate the late stages of the
 stickleback speciation continuum.
description: A reference genome sequence of Pungitius sinensis was determined.
 Using fastsimcoal2, past demography was inferred.
DOI: 10.5061/dryad.qrfj6q5cp
title: Resolution of the house mouse (Mus musculus) phylogeny by integration over isolation-with-migration histories

description: The three main subspecies of house mice, Mus musculus castaneus, Mus
 musculus domesticus , and Mus musculus musculus, are estimated to have
 diverged ~325-500KYA. Resolution of the details of their evolutionary
 history is complicated by their relatively recent divergence, ongoing gene
 flow among the subspecies, and complex demographic histories. Previous
 studies have been limited to some extent by the number of loci surveyed
 and/or by the scope of the method used. Here we apply a method (IMa3) that
 provides an estimate of a population phylogeny while allowing for complex
 histories of gene exchange. Results strongly support a topology with M. m.
 domesticus as sister to M. m. castaneus and M. m. musculus . In addition,
 we find significant evidence of reciprocal gene flow between all pairs of
 subspecies. Our estimates of another key set of parameters, effective
 population size ( N e ), support previous results that the N e of M. m.
 castaneus is larger than that of the other two subspecies.
DOI: 10.5061/dryad.0vt4b8gwg
title: Cranial endocast of the stem lagomorph Megalagus and brain structure of basal Euarchontoglires

description: Early lagomorphs are central to our understanding of how the brain evolved
 in Glires (rodents, lagomorphs and their kin) from basal members of
 Euarchontoglires (Glires + Euarchonta, the latter grouping primates,
 treeshrews, and colugos). Here we report the first virtual endocast of the
 fossil lagomorph Megalagus turgidus, from the Orella Member of the Brule
 Formation, early Oligocene, Nebraska, USA. The specimen represents one of
 the oldest nearly complete lagomorph skulls known. Primitive aspects of
 the endocranial morphology in Megalagus include large olfactory bulbs,
 exposure of the midbrain, a small neocortex, and a relatively low
 encephalization quotient. Overall, this suggest a brain morphology closer
 to that of other basal members of Euarchontoglires (e.g., plesiadapiforms
 and ischyromyid rodents) than to that of living lagomorphs. However, the
 well-developed petrosal lobules in Megalagus, comparable to the condition
 in modern lagomorphs, suggest early specialization in that order for the
 stabilization of eye movements necessary for accurate visual tracking. Our
 study sheds new light on the reconstructed morphology of the ancestral
 brain in Euarchontoglires and fills a critical gap in the understanding of
 palaeoneuroanatomy of this major group of placental mammals.
description: The skull of <i>Megalagus turgidus</i> was micro-CT
 scanned in a high resolution Phoenix v|tome|x L 240 scanner (GE
 Measurement & Control Solutions) at the American Museum of Natural
 History (New York, NY, USA) with the following parameters: voltage 155 kV,
 current 145 mA, and 0.2 mm Cu filter. To accommodate the length of the
 specimen, the skull was scanned as a multiscan in four parts. The total of
 4501 images were acquired at a resolution of 22.54 μm (isotropic voxels)
 with 0.33 sec of exposure. Raw data were reconstructed with Phoenix
 datos|x 2.0 software resulting in 16-bit TIFFs (1977x1000 pixel in size).
 The CT-data of the endocranial cavity of <i>Megalagus</i>
 <i>turgidus </i>were manually segmented in Avizo 9.0.1
 (Visualization Science Group, 1995–2015) using a WACOM Cintiq 21UX tablet
 in each of the three parts that contain the cranial cavity, then the three
 resulting datasets were merged.
description: The file format is STL.
DOI: 10.5061/dryad.z8w9ghx8m
title: The role of infarct location in DWI-ASPECTS 0-5 acute stroke patients treated with thrombectomy

description: Objective: To determine whether hemisphere involvement and infarct
 location on the Alberta Stroke Program CT Score (ASPECTS) score template
 should serve as predictors of 90-day clinical outcome in acute ischemic
 stroke patients with pretreatment diffusion-weighted imaging (DWI)-ASPECTS
 0-5 treated with thrombectomy. Methods: We analyzed data of all
 consecutive patients included in the Endovascular Treatment in Ischemic
 Stroke (ETIS) registry between January 1, 2012 and January 31, 2018 who
 presented with a pretreatment DWI-ASPECTS 0-5 score and underwent
 thrombectomy. Multivariable analyses were performed in order to identify
 the role of infarct location and hemisphere involvement on good outcome
 defined by a modified Rankin Scale (mRS) score 0-2 at 90 days and on the
 whole distribution of mRS (shift analysis). Results: 344 patients with a
 DWI-ASPECTS 0-5 (median 4, IQR, 3-5) were included. Neither infarct
 location nor hemisphere involvement were found to be independent
 predictors of good outcome. Involvement of the M6 region in right-sided
 strokes (adjusted odds ratio [aOR] 2.6, 99% confidence interval [CI]
 1.14-5.8; P=0.003) and the internal capsule in left-sided strokes (aOR
 2.6, 99% CI 0.8-7.9; P&lt; 0.020) independently predicted increased
 disability on the mRS distribution in the affected subpopulations.
 Conclusions: The results of our study suggests that neither hemisphere nor
 infarct location should be considered as exclusion criteria for
 endovascular thrombectomy in DWI-ASPECTS 0-5 patients. Nonetheless, the
 involvement of specific ROIs resulted associated with increased
 disability. They may provide valuable information regarding stroke
 management options and neurological recovery of use for caregivers in the
 post-acute phase.
description: We analyzed data of all consecutive anterior circulation stroke
 patients with a baseline DWI-ASPECTS 0-5 treated with thrombectomy from
 January 1st, 2012 to January 31st, 2018, included in the on-going
 prospective multicentric real-world ETIS (Endovascular Treatment in
 Ischemic Stroke) registry<b> </b>(NCT03776877).
DOI: 10.5061/dryad.4qrfj6q7k
title: Data from: Evaluating community effects of a keystone ant, Azteca sericeasur, on Inga micheliana leaf litter decomposition in a shaded coffee agro-ecosystem

description:             Our research examined the effect of Azteca sericeasur, a keystone arboreal ant, on the decomposition of leaf litter of the shade tree, Inga micheliana, in coffee agro-ecosystems. This interaction is important in understanding the spatial heterogeneity in decomposition. We hypothesized that A. sericeasur could affect leaf litter decomposition by excluding other ants, which could release decomposers, like collembolans, from predation pressure. Determining the relative strengths of these interactions can illuminate the importance of A. sericeasur in decomposition and nutrient cycling processes. We assessed the ant and arthropod communities surrounding 10 pairs of trees, where each pair included one shade tree with an established A. sericeasur nest. Tuna baits were used in conjunction with pitfall traps to assess the ant and arthropod community, and litterbags with I. micheliana leaf litter were used to assess decomposition. The species richness of ants did not change in proximity to A. sericeasur nests, though the ant communities were distinct. Abundance of collembola and community composition of other invertebrates did not change with the presence of an A. sericeasur nest and there were no differences in leaf litter decomposition rates. This contradicts past studies that suggests A. sericeasur reduces species richness in its territory. We suggest that other ants may avoid A. sericeasur by moving within and beneath the leaf litter. Our results indicate there is no net effect of A. sericeasur on leaf litter decomposition.
description: The data was collected using 3 methods -- tuna baiting, pitfall
 traps and litterbags. Site data was taken at paired sites and is included
 in the data set. Methods are described in full in the
 manuscript.
description: Tuna baits were used to describe the ant community. The full list
 of morpho-species is given in the manuscript's supplementary
 material. Abbreviations are used in the dataset.
 Pitfall traps were sorted to order and ants were described to
 morpho-species. Again, abbreviations are used, but the full list is given
 in the supplementary material. Litterbags with
 <em>Inga micheliana </em>litter were in the field for a
 year.
DOI: 10.5061/dryad.gf1vhhmm0
title: Data from: The effects of nutrient enrichment and invasive mollusks on freshwater environments

description: The effects of invasive species might be altered by anthropogenic
 activities such as nutrient pollution or the presence of additional
 invasive species with similar or unique traits. Using experimental
 mesocosms, we tested the separate and combined effects of three invasive
 mollusks (zebra mussels, Asian clams, and banded mystery snails) on
 freshwater environments in nutrient-poor and nutrient-enriched conditions.
 We predicted that in nutrient-poor conditions, single mollusk species
 would reduce the abundance of algae and zooplankton, but nutrient
 enrichment would mitigate these effects. Regardless of nutrient additions,
 paired bivalve species would reduce phytoplankton and zooplankton
 abundance, increasing periphyton biomass. Bivalves and snails paired
 together would reduce periphyton, phytoplankton, and zooplankton compared
 to communities with paired bivalve species. Finally, nutrient enrichment
 would increase the survival or biomass of paired bivalves and snails.
 Single, paired, and three co-occurring invasive mollusks did not affect
 algae or zooplankton abundance. Banded mystery snails reduced nutrient
 concentrations in high-nutrient conditions more than other invasive
 species, but the reduced nutrients did not affect algal abundance. Paired
 invasive species did not affect the survival or biomass of other invasive
 species. Nutrient enrichment increased the biomass of zebra mussels and
 mystery snails, but not Asian clams. Additionally, zebra mussel
 reproduction increased in the high nutrient treatment when banded mystery
 snails were present, but not when all three species were together. We
 conclude that human-induced trophic states might determine the effects
 that single and multiple invasive species have in freshwater
 environments.
DOI: 10.5061/dryad.k0p2ngf5s
title: Data from: Genome-wide SNP identification and association mapping for seed mineral concentration in Mung bean (Vigna radiata L.)

description: Mung bean (Vigna radiata L.) quality is dependent on seed chemical
 composition, which in turn determines the benefits of mung bean
 consumption for human health. While rich in a range of nutritional
 components, such as protein, macro- and micro- nutrients, carbohydrates
 and vitamins, mung bean remains less well studied than other legume crops.
 Mung bean genomics and genetic resources are relatively sparse. To further
 improve nutritional levels of mung bean grain requires genome-wide marker
 system tools. The objectives of this research were to develop these tools
 and conduct nutrient analysis in order to 1) identify single nucleotide
 polymorphisms (SNPs) using genotyping by sequencing (GBS) and to 2)
 perform genome-wide association studies (GWAS) for levels of calcium,
 iron, potassium, manganese, phosphorous, sulfur, and zinc in mung bean
 grain produced over two years of field experiment. A total of 112 GWAS
 models were explored using 6,486 high quality SNPs discovered in 92
 cultivated mung bean accessions chosen from USDA core collection that
 represented 13 countries. The data obtained allowed for the identification
 of 43 associated SNPs and 20 main genomic regions that explained on
 average 22 % of the overall variation in seed macro- and micro- nutrients
 concentration on the basis of a multiple-year analysis. Most of the
 regions discovered in this study provide valuable candidate gene to use in
 future breeding of new varieties of mung bean with novel nutritional
 properties. Identification of the underlying genes will help to
 reveal the genetic control of mung bean seed nutritional property. Other
 SNPs identified in this study will serve as important resources to enable
 marker-assisted selection (MAS) in the species V. radiata, including wide
 and narrow crosses with / between cultivated and wild mung bean.
DOI: 10.5061/dryad.2ngf1vhkd
title: Data from: Tree litter functional diversity and nitrogen concentration enhance litter decomposition via changes in earthworm communities

description: Biodiversity is a major driver of numerous ecosystem functions. However,
 consequences of changes in forest biodiversity remain difficult to predict
 because of limited knowledge about how tree diversity influences ecosystem
 functions. Litter decomposition is a key process affecting nutrient
 cycling, productivity and carbon storage, and can be influenced by plant
 biodiversity. Leaf litter species composition, environmental conditions,
 and the detritivore community are main components of the decomposition
 process, but their complex interactions are poorly understood. In this
 study, we tested the effect of tree functional diversity (FD) on litter
 decomposition in a field experiment manipulating tree diversity, and
 partitioned the effects of litter physio-chemical diversity and the
 detritivore community. We used litterbags with different mesh sizes to
 separate the effects of microorganisms and microfauna, mesofauna, and
 macrofauna, and monitored soil fauna using pitfall traps and earthworm
 extractions. We hypothesized that higher tree litter FD accelerates litter
 decomposition due to the availability of complementary food components and
 higher activity of detritivores. Although we did not find direct effects
 of tree FD on litter decomposition, we identified key litter traits and
 macro-detritivores that explained part of the process. Litter mass loss
 was found to decrease with an increase in leaf litter carbon:nitrogen
 ratio. Moreover, litter mass loss increased with an increasing density of
 epigeic earthworms, with most pronounced effects in litterbags with a
 smaller mesh size, indicating indirect effects. Higher litter FD and
 litter nutrient content were found to increase the density of surface
 dwelling macrofauna and epigeic earthworm biomass. Based on structural
 equation modeling, we conclude that tree FD has a weak positive effect on
 soil surface litter decomposition by increasing the density of epigeic
 earthworms, and that litter nitrogen-related traits play a central role in
 tree composition effects on soil fauna and decomposition.
description: See Methods in Patoine et al. 2020
description: DATA_Patoineetal_EcolEvol_2020.csv Data file
 from the BIOTREE-FD decomposition experiment, for each plot and litterbag
 mesh size. When data is at the plot level, values are duplicated across
 rows for each mesh size. The variables include data about litter
 decomposition, tree community and litter traits, soil fauna and soil
 chemical and microbial properties.
 README_Patoineetal_EcolEvol_2020.csv
 Description file of the columns from DATA.