cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2fqz612r8
title: Community composition of bacteria isolated from Swiss banknotes varies depending on collection environment

description: Humans interact constantly with surfaces and associated microbial
 communities in the environment. The factors shaping the composition of
 these communities are poorly understood: some proposed explanations
 emphasize the influence of local habitat conditions (niche-based
 explanations), while others point to geographic structure and the distance
 among sampled locations (dispersal-based explanations). However, the
 relative roles of these different drivers for microbial community assembly
 on human-associated surfaces are not clear. Here, we used a combination of
 sampling, sequencing (16S rRNA) and culturing to show that the
 composition of banknote-associated bacterial communities varies depending
 on the local collection environment. Using banknotes collected from
 various locations and types of shops across Switzerland, we found
 taxonomic diversity dominated by families such
 as Pseudomonadaceae and Staphylococcaceae, but
 with banknote samples from particular types of shops (especially butcher
 shops) having distinct community structure. By contrast, we found no
 evidence of geographic structure: similarity of community composition did
 not decrease with increasing distance among sampled locations. These
 results show that microbial communities associated with banknotes, one of
 the most commonly encountered and exchanged human-associated surfaces, can
 reflect the local environmental conditions (in this case, the type of
 shop), and the signal for this type of variation was stronger than that
 for geographic structure among the locations sampled here.
description: In daily life, currency is one of the most frequently and
 actively exchanged commodities among humans. We collected banknotes from
 50 locations in Switzerland (10 towns, five different shops in each town),
 with the aim to investigate the drivers behind variations in the bacterial
 communities on Swiss banknotes, specifically to assess if the microbiome
 associated with banknotes differs with geographic distance and/or the type
 of shop the banknote originated from (collection environment).
 Each of the 50 banknotes was processed as follows: (1) we swabbed
 front and back of the each banknote with one sampling swab; (2) we plated
 a dilution of the sample on chromatic agar; (3) we extracted DNA from each
 swab tip; (4) we performed 16S rRNA amplicon sequencing on extracted DNA
 samples.
DOI: 10.5061/dryad.cz8w9gj5m
title: Uncovering the effects of Müllerian mimicry on the evolution of conspicuousness in colour patterns

description: Variation in the conspicuousness of colour patterns is observed within and
 among defended prey species. The evolution of conspicuous colour pattern
 in defended species can be strongly impaired because of increased
 detectability by predators. Nevertheless, such evolution of the colour
 pattern can be favoured if changes in conspicuousness result in Müllerian
 mimicry with other defended prey. Here, we develop a model describing the
 population dynamics of a conspicuous defended prey species, and we assess
 the invasion conditions of derived phenotypes that differ from the
 ancestral phenotype by their conspicuousness. Such change in
 conspicuousness may then modify their level of mimicry with the local
 community of defended species. Derived colour pattern displayed in this
 focal population can therefore be either exactly similar, partially
 resembling or completely dissimilar to the local mimicry ring displaying
 the ancestral colour pattern. We assume that predation risk depends (1) on
 the number of individuals sharing a given colour pattern within the
 population, (2) on the occurrence of co-mimetic defended species, and (3)
 on the availability of alternative edible prey. Using a combination of
 analytical derivations and numerical simulations, we show that colour
 patterns that are less conspicuous than the ancestral one are generally
 favoured within mimicry rings, unless reduced conspicuousness impairs
 mimicry. By contrast, when a mutation affecting the colour pattern leads
 to a shift toward a better protected mimicry ring, a more conspicuous
 colour pattern can be favoured. The selected aposematic pattern then
 depends on the local communities of defended and edible prey, as well as
 on the detectability, memorability and level of mimicry of the colour
 patterns.
description: Code C++ and R Code C++ to run simulations and to
 produce the raw data, and code R to draw the same figures as in the
 manuscript.
DOI: 10.6078/d1070p
title: The effect of diet on colony recognition and cuticular hydrocarbon profiles of the invasive Argentine ant, Linepithema humile

description: The membership of social insect colonies is defined by chemical pheromones
 on the bodies of colony members. In nearly all ant species that have been
 studied, these pheromones have been shown to be genetically based. In some
 cases, however, environmentally derived odors have been implicated as
 colony recognition cues. The widely introduced and invasive Argentine ant
 is well known for forming massive “supercolonies” in its introduced
 ranges. Previous studies have implicated both genetic and diet-derived
 chemicals in the colony recognition systems of introduced populations.
 Here, we perform feeding experiments, in both realistic field settings and
 the lab, and show that dietary changes do not cause behavioral changes in
 the field, as well as under most laboratory conditions. However, one
 exception was found, in which reduced aggression was recorded in one of
 the laboratory feeding treatments (with crickets as the dietary item),
 but, nevertheless, not of sufficient magnitude to explain the unusual
 colony structure of introduced Argentine ants. We conclude that dietary
 shifts during introduction to new ranges do not account for the origin of
 Argentine ant supercolonies.
description: Necessary information included in README file.
DOI: 10.5061/dryad.0gb5mkm3d
title: A new, narrowly endemic species of swamp-dwelling dusky salamander (Plethodontidae: Desmognathus) from the Gulf Coastal Plain of Mississippi and Alabama

description: We describe a new, narrowly endemic species of swamp-dwelling dusky
 salamander (Plethodontidae: Desmognathus pascagoula sp. nov.) from the
 Gulf Coastal Plain of southeastern Mississippi and southwestern Alabama
 based on linear morphometrics, mitochondrial DNA, and single nucleotide
 polymorphisms from 881 loci produced using genotype-by-sequencing. Some
 populations of the new species were historically referred to as D.
 auriculatus, a polyphyletic assemblage of at least three species in the
 Atlantic and Gulf Coastal Plain from Texas to North Carolina. Populations
 of D. auriculatus from the Gulf Coastal Plain in Louisiana and Mississippi
 were recently described as D. valentinei. The new species includes
 populations that were tentatively referred to D. valentinei, but we find
 it is morphologically, genetically, and geographically distinct. It is
 smaller, has a more defined dorsal color pattern, more irregular whitish
 “portholes” in up to three rows on the lateral surfaces of the body and
 tail, and a brighter orange or yellowish orange postocular stripe. At
 present, the new species is known from only six extant populations in the
 lower Pascagoula, Escatawpa, and Mobile drainages. The latter represents a
 distinct phylogeographic lineage. We also refer a historical collection
 from the northeastern side of the Mobile-Tensaw River Delta to this
 species, suggesting a much broader range in the past. We suspect that more
 populations remain to be discovered in the area, and their potential
 species-level distinctiveness should be tested further. This discovery
 increases knowledge of the biodiversity in the southeastern United States
 Coastal Plain, a candidate region meeting the global criteria for a
 “biodiversity hotspot,” and underscores the amount of cryptic diversity
 likely remaining to be discovered and described in Nearctic salamanders.
description: COI Sanger sequencing, GBS genotype-by-sequencing, linear
 morphometrics
description: GBS folder: output from ipyrad with clustering value of
 88% COI folder: alignment, partitions, and treefile
 from ND2/COI Sanger sequencing data analyzed in IQTREE-2
 Appendix S1: Excel spreadsheet of specimen data and accession
 numbers Appendix S2: Excel spreadsheet of linear
 morphometric data in mm
DOI: 10.5061/dryad.fj6q573x8
title: Data from: Sensitivity to line-of sight in tolerant versus despotic macaques (Macaca sylvanus and Macaca mulatta)

description: Complex social life is considered important to the evolution of cognition
 in primates. One key aspect of primate social interactions concerns the
 degree of competition that individuals face in their social group. To
 examine how social tolerance versus competition shapes social cognition,
 we experimentally assessed capacities for flexible gaze-following in more
 tolerant Barbary macaques (Macaca sylvanus) and compared to previous data
 from despotic rhesus macaques (Macaca mulatta). Monkeys experienced one of
 two possible conditions. In the barrier condition, they observed an actor
 look upwards into an overheard barrier, so they could not directly see the
 target of the actor's gaze without reorienting. In the no barrier
 condition, they observed an actor look upwards without a barrier blocking
 her line-of-sight, so they could observe the target of the actor's
 gaze by also looking upwards. Both species (N = 58 Barbary macaques, 64
 rhesus macaques) could flexibly modulate their gaze responses to account
 for the demonstrator’s line of sight, looking up more often when no
 barrier was present, and this flexible modulation declined with age in
 both species. However, neither species preferentially approached to look
 inside the barrier when their view of the target location was obscured,
 although rhesus macaques approached more overall. This pattern suggests
 that both tolerant and despotic macaques exhibit similar capacities to
 track other’s line of sight and do not preferentially reorient their
 bodies to observe what an actor looks at in this situation. This contrasts
 with other work indicating that competitive primates are especially adept
 at some aspects of theory of mind. Thus, it is important to understand
 both the similarities and differences in the social–cognitive abilities of
 primates with different social styles.
description: See manuscript for all methodological details regarding this
 dataset.
description: The data file includes a key defining all variables.
DOI: 10.5061/dryad.x3ffbg7mv
title: Meta-analysis suggests variable, but pCO2-specific, effects of ocean acidification on crustacean biomaterials

description: Crustaceans comprise an ecologically and morphologically diverse taxonomic
 group. They are typically considered resilient to many environmental
 perturbations found in marine and coastal environments, due to effective
 physiological regulation of ions and hemolymph pH, and a robust
 exoskeleton. Ocean acidification can affect the ability of marine
 calcifying organisms to build and maintain mineralized tissue and poses a
 threat for all marine calcifying taxa. Currently, there is no consensus on
 how ocean acidification will alter the ecologically-relevant exoskeletal
 properties of crustaceans. Here, we present a systematic review and
 meta-analysis on the effects of ocean acidification on the crustacean
 exoskeleton, assessing both exoskeletal ion content (calcium and
 magnesium) and functional properties (biomechanical resistance and cuticle
 thickness). Our results suggest that the effect of ocean acidification on
 crustacean exoskeletal properties varies based upon seawater pCO2 and
 species identity, with significant levels of heterogeneity for all
 analyses. Calcium and magnesium content were significantly lower in
 animals held at pCO2 levels of 1500-1999 μatm as compared to those under
 ambient pCO2. At lower pCO2 levels, however, statistically significant
 relationships between changes in calcium and magnesium content within the
 same experiment were observed: a negative relationship between calcium and
 magnesium content at pCO2 of 500-999 μatm and a positive relationship at
 1000-1499 μatm. Exoskeleton biomechanics, such as resistance to
 deformation (microhardness) and shell strength, also significantly
 decreased under pCO2 regimes of 500-999 μatm and 1500-1999 μatm,
 indicating functional exoskeletal change coincident with decreases in
 calcification. Overall, these results suggest that the crustacean
 exoskeleton can be susceptible to ocean acidification at the biomechanical
 level, potentially predicated on changes in ion content, when exposed to
 high influxes of CO2. Future studies will need to accommodate the high
 variability of crustacean responses to ocean acidification, as well as
 ecologically-relevant ranges of pCO2 conditions, when designing
 experiments with conservation-level endpoints. --
description: Data was collected as either raw values from the main or
 supplementary text of a primary research article, or extracted from a
 visual figure using WebPlotDigitizer. Values were coded in Excel, saved to
 a CSV file, and then processed in R using the 'metafor'
 package.
description: CSV files are usable with provided R code. If any issues arise,
 please contact Kyle R. Siegel at siegel.kyle9@gmail.com
DOI: 10.5061/dryad.m37pvmd47
title: Residual force enhancement is reduced in permeabilized fiber bundles from mdm muscles

description: Residual force enhancement (RFE) is the increase in steady-state force
 after active stretch relative to the force after isometric contraction at
 the same final length. The mdm mutation in mice, characterized by a small
 deletion in N2A titin, has been proposed to prevent N2A titin-actin
 interactions so that active mdm muscles are more compliant than WT. This
 decrease in active muscle stiffness should be associated with reduced RFE.
 We investigated RFE in permeabilized soleus (SOL) and extensor digitorum
 longus (EDL) fiber bundles from wild type and mdm mice. On each fiber
 bundle, we performed active and passive stretch from an average sarcomere
 length of 2.6 - 3.0 &[mu]m at a slow rate of 0.04
 &[mu]m/s, as well as isometric contractions at the initial and
 final lengths. One-way ANOVA showed that SOL and EDL fiber bundles from
 mdm mice exhibited significantly lower RFE than WT (P &lt; 0.0001).
 This result is consistent with previous observations in single myofibrils
 and intact muscles. However, it contradicts the results from a previous
 study which appeared to show that compensatory mechanisms could restore
 titin force enhancement in single fibers from mdm psoas. We suggest that
 force enhancement measured previously in mdm single fibers was an artifact
 of the high variability in passive tension found in degenerating fibers,
 which begins after ~24 days of age. The results are consistent with the
 hypothesis that RFE is reduced in mdm skeletal muscles due to impaired
 Ca2+ dependent titin-actin interactions resulting from the small deletion
 in N2A titin.
description: No missing values.
DOI: 10.5061/dryad.g79cnp5rq
title: Spatially discrete disturbance processes enhance grassland floral resources

description: Grasslands provide essential floral resources for both managed and wild
 pollinators. However, grassland flowers in remaining native landscapes are
 threatened due to nonnative plant invasions and alterations to historic
 disturbance regimes such as fire and grazing. The potential for managed
 disturbance to promote grassland floral resources remains unclear. Fire
 and grazing historically occurred interactively, but uniform application
 of each may be a detriment to floral resources and the pollinators
 depending on them. Though fire can increase resources available to plants
 and stimulate flowering, it initially destroys floral resources and may
 delay flower availability. Similarly, grazing removes competitors of
 flowering plants, but destroys flower heads. To address this knowledge
 gap, we investigated the impacts patch-burn grazing with one and two
 seasons of fire per year versus season-long grazing with no fire on floral
 resources in mixed-grass prairie. In patch-burn treatments, part of each
 pasture is burned each year, which focuses grazing activity due to the
 high quality regrowth. We aimed to use fire to remove litter around
 flowering plants while also sheltering established flower heads from
 grazing pressure by directing cattle away from regenerating forbs in
 unburned portions of the landscape. Over two summers, we performed weekly
 flower surveys in season-long grazing and patch-burn grazing pastures. We
 analyzed total seasonal floral resources, maximum floral abundance, and
 seasonal species richness between treatments. Over two years, we surveyed
 1,238,241 ramets of 160 species, focusing on 36 common species for
 individual analysis. We found broad positive associations between
 patch-burn grazing and total seasonal flower abundance, maximum flower
 abundance, and species richness compared to traditional management. In
 most cases, patch-burn grazing with dormant and growing season fires
 produced higher floral abundance, total seasonal floral resources, and
 species richness than patch-burning with dormant season fires alone,
 suggesting benefits of increased levels of pyrodiversity. Synthesis and
 applications: Under increasing pressure to manage for declining
 pollinators, rangeland managers must consider strategies to enhance floral
 resources within the context of livestock production goals. The
 spatiotemporal interaction of cattle grazing and fire shows promise for
 promoting floral resource abundance and diversity.
DOI: 10.5061/dryad.x3ffbg7mw
title: Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH

description: Please contact Rongxin Fang (r3fang@fas.harvard.edu) for any question
 about the dataset. The human cerebral cortex has tremendous cellular
 diversity. How different cell types are organized in the human cortex and
 how cellular organization varies across species remain unclear. In this
 study, we performed spatially resolved single-cell profiling of 4000 genes
 using multiplexed error-robust fluorescence in situ hybridization
 (MERFISH), identified more than 100 transcriptionally distinct cell
 populations, and generated a molecularly defined and spatially resolved
 cell atlas of the human middle and superior temporal gyrus. We further
 explored cell-cell interactions arising from soma contact or proximity in
 a cell type–specific manner. Comparison of the human and mouse cortices
 showed conservation in the laminar organization of cells and divergence in
 somatic interactions across species. Our data revealed human-specific
 cell-cell proximity patterns and a marked increase in interaction
 enrichment between neurons and non-neuronal cells in the human cortex.
DOI: 10.5061/dryad.41ns1rngn
title: Demographic rates and stature of tree species in 13 sub-tropical forests: annual growth, annual survival, annual recruitment &gt;( 1 cm dbh), stature (max dbh)

description: Organisms of all species must balance their allocation to growth, survival
 and recruitment. Among tree species, evolution has resulted in different
 life-history strategies for partitioning resources to these key
 demographic processes. Life-history strategies in tropical forests have
 often been shown to align along a trade-off between fast growth and high
 survival, i.e. the well-known fast-slow continuum. In addition, an
 orthogonal trade-off has been proposed between tall stature – resulting
 from fast growth and high survival – and recruitment success, i.e. a
 stature−recruitment trade-off. However, it is not clear if these two
 independent dimensions of life-history variation structure tropical
 forests worldwide. We used data from 13 large-scale and long-term tropical
 forest monitoring plots in three continents to explore the principal
 trade-offs in annual growth, survival and recruitment as well as tree
 stature. These forests included relatively undisturbed forests as well as
 typhoon-disturbed forests. Life-history variation in twelve forests was
 structured by two orthogonal trade-offs, the growth−survival trade-off and
 the stature−recruitment trade-off. Pairwise Procrustes analysis revealed a
 high similarity of demographic relationships among forests. The small
 deviations were related to differences between African and Asian plots.
 Synthesis. The fast-slow continuum and tree stature are two independent
 dimensions structuring many, but not all tropical tree communities. Our
 discovery of the consistency of demographic trade-offs and life-history
 strategies across different forest types from three continents
 substantially improves our ability to predict tropical forest dynamics
 worldwide.
DOI: 10.5061/dryad.5x69p8d57
title: Geographic patterns in range sizes and their drivers of endemic angiosperms in China

description: Geographic range size of endemic species is the most important indicator
 of species’ vulnerability to extinction and conservation prioritization,
 yet variation in range size among species and across space has been
 relatively understudied. We investigated the variations and geographic
 patterns of the range sizes of 9,898 angiosperm species endemic to China
 and compared them with effects of historical and contemporary climate,
 physiological tolerances of species and species functional traits
 associated with dispersal ability (including growth form, fruit type and
 sexual system) on range size variations. Our results revealed that
 narrow-ranged species are clustered in Southwest China where angiosperm
 species richness peaks. Winter temperature had the strongest and most
 negative effects on the range size variations of narrow-ranged species
 across space and species, while climate seasonality had the strongest and
 most positive effects on the range size variations of wide-ranged species
 across space and species. Climate also influenced species range size
 indirectly via its effects on species' functional traits associated
 with dispersal ability. Range size of all species, narrow-ranged, and
 wide-ranged species showed little phylogenetic signal, suggesting that
 phylogenetic conservatism plays a very weak role in range size variations.
 Our results show that the range size of angiosperm species endemic to
 China is driven by both extrinsic spatio-temporal environmental factors
 and intrinsic species' traits that allow species to cope with
 environment change.