cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.584d64s
title: Data from: Ants, fire and bark traits affect how African savanna trees recover following damage

description: Bark damage resulting from elephant feeding is common in African savanna
 trees with subsequent interactions with fire, insects and other pathogens
 often resulting in tree mortality. Yet, surprisingly little is known about
 how savanna trees respond to bark damage. We addressed this by
 investigating how the inner bark of marula (Sclerocarya birrea), a
 widespread tree species favoured by elephants, recovers after bark damage.
 We used a long-term fire experiment in the Kruger National Park to measure
 bark recovery with and without fire. At 24 months post-damage, mean wound
 closure was 98, 92, and 72% respectively in annual and biennial burns and
 fire exclusion treatments. Fire exclusion resulted in higher rates of ant
 colonisation of bark wounds, and such ant colonisation resulted in
 significantly lower bark recovery. We also investigated how ten common
 savanna tree species respond to bark damage and tested for relationships
 between bark damage, bark recovery and bark traits while accounting for
 phylogeny. We found phylogenetic signal in bark dry matter content, bark N
 and bark P, but not in bark thickness. Bark recovery and damage was
 highest in species which had thick moist inner bark and low wood densities
 (Anacardiaceae), intermediate in species which had moderate inner bark
 thickness and wood densities (Fabaceae) and lowest in species which had
 thin inner bark and high wood densities (Combretaceae). Elephants prefer
 species with thick, moist inner bark, traits that also appear to result in
 faster recovery rates.
description: Bark_recoveryRecovery rates of the species in the paperDryad_recovery.xlsxBark nutrients_DryadNutrient content of species in the studyRecovery_traits_DryadRecovery and traits of species in the study
DOI: 10.5061/dryad.33874bj
title: Data from: A novel accessory respiratory muscle in the American alligator (Alligator mississippiensis)

description: The muscles that effect lung ventilation are key to understanding the
 evolutionary constraints on animal form and function. Here, through
 electromyography, we demonstrate a newly discovered respiratory function
 for the iliocostalis muscle in the American alligator (Alligator
 mississippiensis). The iliocostalis is active during expiration when
 breathing on land at 28C and this activity is mediated through the
 uncinate processes on the vertebral ribs. There was also an increase in
 muscle activity during the forced expirations of alarm distress
 vocalisations. Interestingly we did not find any respiratory activity in
 the iliocostalis when the alligators were breathing with their body
 submerged in water at 18C, which resulted in a reduced breathing
 frequency. The iliocostalis is an accessory breathing muscle that
 alligators are able to recruit in to assist expiration under certain
 conditions.
description: Codd et al_gator EMG
 analysisraw and processed EMG
 data filesCodd et al_suppl.
 dataraw and processed EMG
 data files
DOI: 10.5061/dryad.g60vv21
title: Data from: Detrital traits affect substitutability of a range-expanding foundation species across latitude

description: Climate-driven range shifts of foundation species could alter ecosystem
 processes and community composition by providing different resources than
 resident foundation species. Along the US Atlantic coast, the northward
 expanding foundation species, black mangrove, Avicennia germinans, is
 replacing the dominant salt marsh foundation species, marsh cordgrass,
 Spartina alterniflora. These species have distinct detrital attributes
 that ostensibly provide different resources to epifauna. We experimentally
 examined how detritus of these species affects decomposition and community
 composition in different habitat contexts at regional and local scales.
 First, we manipulated detritus identity (Avicennia, Spartina) at 13 sites
 across a 5° latitudinal gradient spanning mangrove, mixed marsh-mangrove,
 and salt marsh habitats. Across latitude, we found that Avicennia detritus
 decomposed 2-4 times faster than Spartina detritus, suggesting that
 detrital turnover will increase with mangrove expansion. Epifaunal
 abundance and richness increased 2-7 times from south to north (mangrove
 to salt marsh) and were equivalent between Avicennia and Spartina detritus
 except for crabs, a dominant taxonomic group that preferred Spartina
 detritus. Second, to examine the whether changing habitat context affected
 regional patterns, we manipulated detritus identity and surrounding
 habitat type (mangrove, salt marsh) at a single mixed site, also including
 inert mimics to separate structural and nutritional roles of detritus.
 Epifaunal richness was similar between the two detrital types, but crabs
 were 2-7 times more abundant in Spartina detritus, due to its structural
 attributes. Surrounding habitat type did not influence decomposition rate
 or community patterns, which suggests that latitudinal influences, not
 surrounding habitat, drove the regional community patterns in the first
 experiment. Overall, mangrove expansion could alter epifaunal communities
 due to the lower structural value and faster turnover of mangrove
 detritus. As species shift with changing climate, understanding foundation
 species substitutability is critical to predict community change, but we
 must account for concomitant environmental changes that also modify
 communities.
description: Dryad_data_Smith_et_al_2019This file explains all of the variables in each of the datasets that accompany the following publication: R.S. Smith, T.Z. Osborne, I. Feller, J. E. Byers. Detrital traits affect substitutability of a range-expanding foundation species across latitude. Oikos. 2019.
DOI: 10.5061/dryad.85b47d1
title: Data from: Fallow management increases habitat suitability for endangered steppe bird species through changes in vegetation structure

description: In the face of the dramatic worldwide decline of farmland bird
 populations, the preservation of fallow fields is a conservation measure
 encouraged through subsidies (e.g. agri‐environmental schemes, AES).
 Beyond the general benefits of increasing fallow availability for
 endangered steppe bird populations, there is a lack of knowledge on how
 fallow management can contribute to meeting species‐specific habitat
 requirements. We used occurrence data from three steppe bird species
 protected at the EU level (Stone Curlew Burhinus oedicnemus, Little
 Bustard Tetrax tetrax, and Calandra Lark Melanocorypha calandra), framed
 in a quasi‐experimental approach covering an unprecedented spatio‐temporal
 scale that included 612 fallow fields over a three‐year study period in an
 agricultural Mediterranean landscape (Spain). We used path analysis to
 explore the mechanisms by which common agricultural practices affected
 species‐specific occurrence. We examined partial effects of agricultural
 practices on vegetation structure and food availability, and the partial
 effect of these variables on bird occurrence compared to control fields
 (no agricultural practices applied). Agricultural practices had a
 significant effect on the presence of the three studied species. Through
 changes in the vegetation structure, Shredding + Herbicide and Tillage
 increased the occurrence of the Stone Curlew and Shredding increased the
 occurrence of the Little Bustard. The occurrence of Calandra Lark was
 mostly affected by landscape variables. Synthesis and applications. Our
 study highlights that, in addition to the acknowledged positive role of
 fallow availability, applying a limited number of specific agricultural
 practices before the breeding season can further increase bird occurrence
 by changing the vegetation structure. Using path analysis, we explored the
 mechanisms driving the occurrence of three steppe bird species under
 different agricultural practices. Such information is key to providing
 specific recommendations for future conservation management of endangered
 species within agri‐environmental schemes.
description: Data used to perform
 path analysisPresence/absence data of
 the studied species in different fallow fields, associated to the
 variables collected in the field and obtained from digital maps. All
 variables are standardized.Data_path_analysis.xlsx
DOI: 10.15468/dl.uy4frq
title: Occurrence Download

description: A dataset containing 169533 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Philippines",
 "GadmGid is PHL",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Tracheophyta"
 ]
}

 The dataset includes 169533 records from 161 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001666-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.13gv04f
title: Data from: Maladapted prey subsidize predators and facilitate range expansion

description: Dispersal of prey from predator-free patches frequently supplies a trophic
 subsidy to predators by providing more prey than are produced locally.
 Prey arriving from predator-free patches might also have evolved weaker
 defenses against predators and thus enhance trophic subsidies by providing
 easily captured prey. Using local models assuming a linear or accelerating
 tradeoff between defense and population growth rate, we demonstrate that
 immigration of undefended prey increased predator abundances and decreased
 defended prey through eco-evolutionary apparent competition. In
 individual-based models with spatial structure, explicit genetics, and
 gene flow along an environmental gradient, prey became maladapted to
 predators at the predator’s range edge, and greater gene flow enhanced
 this maladaptation. The predator gained a subsidy from these easily
 captured prey, which enhanced its abundance, facilitated it's
 persistence in marginal habitats, extended its range extent, and enhanced
 range shifts during environmental changes, such as climate change. Once
 the predator expanded, prey adapted to it, and the advantage disappeared,
 resulting in an elastic predator range margin driven by eco-evolutionary
 dynamics. Overall, the results indicate a need to consider gene
 flow-induced maladaptation and species interactions as mutual forces that
 frequently determine ecological and evolutionary dynamics and patterns in
 nature.
description: PredPrey_src_submittedCode for individual-based model simulations
DOI: 10.5061/dryad.mm4qb48
title: Data from: Is black plumage an adaptation to high elevations in a cosmopolitan bird genus?

description: Black plumage is expected to absorb and retain more heat and provide
 better protection against UV radiation compared with lighter plumages.
 Black plumage is common in species of the genera Turdus and Platycichla
 that inhabit highlands across different regions of the world. Considering
 this geographical recurrent pattern we tested the hypothesis that black
 plumage in these two genera has evolved as a co-adaptive response to
 inhabiting highlands, reconstructing ancestral character states for
 plumage and altitudinal distribution using maximum-likelihood methods, and
 a Pagel's multistate discrete method. For these analyses, we used a
 phylogeny based on mitochondrial and nuclear DNA regions that included 60
 of the 66 recognized species in the genera Turdus and Platycichla. We
 found that black-plumage coloration evolved independently on eight
 occasions within these two genera, and species with black plumage occur
 more often at highlands. Our results support the hypothesis that
 black-plumage is adaptative in highlands; but, studies in other bird
 groups with black-plumage inhabiting at the same elevations will provide
 evidence for this adaptive hypothesis or if the evolution of black-plumage
 in other groups is explained by other evolutionary forces.
description: Appendix
 1Altitudinal distribution
 and main black color of plumage in males of 60 species and subspecies of
 thrushes used in the plumage reconstruction analysis. It is include the
 continent where each species inhabit and if have latitudinal migration
 (partial migration mean that all individuals from one species migrate to
 non-reproductive areas, but reproductive and non-reproductive areas
 overlap geographically). Information was obtained from Clement and Hathway
 (2000) and Collar (2005) reviews of the Turdidae
 family.
DOI: 10.5061/dryad.113j3h7
title: Data from: De novo sequencing, assembly, and annotation of four threespine stickleback genomes based on microfluidic partitioned DNA libraries

description: The threespine stickleback is a geographically widespread and ecologically
 highly diverse fish that has emerged as a powerful model system for
 evolutionary genomics and developmental biology. Investigations in this
 species currently rely on a single high-quality reference genome, but
 would benefit from the availability of additional, independently sequenced
 and assembled genomes. We present here the assembly of four new
 stickleback genomes, based on the sequencing of microfluidic partitioned
 DNA libraries. The base pair lengths of the four genomes reach 92–101% of
 the standard reference genome length. Together with their de novo gene
 annotation, these assemblies offer a resource enhancing genomic
 investigations in stickleback.
description: Stickleback genomes and
 annotationsThe content of this
 archive is described in the README fileSticklebackDeNovoGenomesAndAnnotations.zip
DOI: 10.5061/dryad.5f3s52r
title: Data from: Collagen vitrigel promotes hepatocytic differentiation of induced pluripotent stem cells into functional hepatocyte-like cells

description: Differentiation of stem cells to hepatocytes provides an unlimited supply
 of human hepatocytes and therefore has been vigorously studied. However,
 to date, the stem cell-derived hepatocytes were suggested to be of
 immature features. To obtain matured hepatocytes from stem cells, we
 tested the effect of culturing iPS cell-derived endoderm cells on collagen
 vitrigel membrane and compared with our previous reported nanofiber
 matrix. We cultured hiPS cell-derived endoderm cells on a collagen
 vitrigel membrane and examined the expression profiles, and tested the
 activity of metabolic enzymes. Gene expression profile analysis of
 hepatocytic differentiation markers revealed that upon culture on collagen
 vitrigel membrane, immature markers of AFP decreased, with a concomitant
 increase in the expression of mature hepatocyte transcription factors and
 mature hepatocyte markers such as ALB, ASGR1. Mature markers involved in
 liver functions, such as transporters, cytochrome P450 enzymes, phase II
 metabolic enzymes were also upregulated. We observed the upregulation of
 the liver markers for at least 2 weeks. Gene array profiling analysis
 revealed that hiPS cell-derived hepatocyte-like cells (hiPS-hep) resemble
 that of the primary hepatocytes. Functions of the CYP enzyme activities
 were tested in multi-institution and all revealed high CYP1A, CYP2C19,
 CYP2D6, CYP3A activity, which could be maintained for at least 2 weeks in
 culture. Taken together, the present approach identified that collagen
 vitrigel membrane provides a suitable environment for the generation of
 hepatocytes from hiPS cells that resemble many characteristics of primary
 human hepatocytes.
description: iPS-heps vs
 HepPre48hr_3mix_NormalizedDataMicroarray data for iPS
 cells and iPS cell-derived differentiated cells, iPS cell-derived
 hepatocytic cells, and primary hepatocytes harvested after 48hr culture (a
 mixture from 3 samples).
DOI: 10.5061/dryad.913qd93
title: Data from: Honey bee dietary neonicotinoid exposure is associated with pollen collection from agricultural weeds

description: Neonicotinoid insecticides have been linked to bee declines. However,
 tracking the primary exposure route for bees in the field has proven to be
 a major logistical challenge, impeding efforts to restore pollinator
 health in agricultural landscapes. We quantified neonicotinoid
 concentrations and botanical species composition in 357 pollen samples
 collected from 114 commercial honey bee colonies placed along a gradient
 of agricultural intensity between June and September. Neonicotinoid
 concentrations increased through the season, peaking at the end of August.
 As a result, concentrations in pollen were negatively associated with
 collection from woody and crop plants that flower early-mid season, and
 positively associated with collection from herbaceous plants that flower
 mid-late season. Higher clothianidin and thiamethoxam residues were
 correlated with samples containing a greater proportion of pollen
 collected from agricultural weeds. The percentage of agricultural land
 within 1,500 m was positively correlated with thiamethoxam concentration;
 however, this spatial relationship was far weaker than the relationship
 with the proportion of pollen collected from herbaceous plants. These
 results indicate that both plant species identity and agricultural
 dominance are important in determining honey bee neonicotinoid exposure
 through the pollen diet, but that uncultivated plants associated with
 agriculture are the source of the greatest acute exposure.
description: 1. Landscape composition
 data at 1500 m radiusLandscape composition
 data for the 24 selected sites at a 1500 m radius.2. Neonicotinoid
 residues detected in collected pollen samplesNeonicotinoid residues
 (thiamethoxam, clothianidin, and imidacloprid) detected in honey
 bee-collected pollen samples at both the sample and trapping event
 scale.3. Pollen composition
 dataIdentity and proportion
 data for the honey bee pollen loads4. Combined analysis
 file for impact of landscape and compositionAnalysis file combining
 site location, landscape composition, pollen composition, and
 neonicotinoid residue data.5. Analysis file for
 individual plant species composition on neonicotinoid
 concentrationAnalysis file containing
 neonicotinoid residue data and plant species composition of pollen load
 data.
DOI: 10.5061/dryad.hr6k12v
title: Data from: Rapid experimental evolution of reproductive isolation from a single natural population

description: Ecological speciation occurs when local adaptation generates reproductive
 isolation as a by-product of natural selection. Although ecological
 speciation is a fundamental source of diversification, the mechanistic
 link between natural selection and reproductive isolation remains poorly
 understood, especially in natural populations. Here, we show that
 experimental evolution of parasite body size over 4 y (approximately 60
 generations) leads to reproductive isolation in natural populations of
 feather lice on birds. When lice are transferred to pigeons of different
 sizes, they rapidly evolve differences in body size that are correlated
 with host size. These differences in size trigger mechanical mating
 isolation between lice that are locally adapted to the different sized
 hosts. Size differences among lice also influence the outcome of
 competition between males for access to females. Thus, body size directly
 mediates reproductive isolation through its influence on both intersexual
 compatibility and intrasexual competition. Our results confirm that
 divergent natural selection acting on a single phenotypic trait can cause
 reproductive isolation to emerge from a single natural population in real
 time.
description: Villa et
 al_PNAS_RawData_ExperimentalEvolVilla et
 al_PNAS_RawData_CommonGardenVilla et
 al_PNAS_RawData_CopulationAssayVilla et
 al_PNAS_RawData_EggLayingAssayVilla et
 al_PNAS_RawData_LiveBirdAssayVilla et
 al_PNAS_RawData_CompetitionAssay
DOI: 10.5061/dryad.9p2j626
title: Data from: Evolution of asexual Daphnia pulex in Japan: variations and covariations of the digestive, morphological and life history traits

description: Background Several genetic lineages of obligate parthenogenetic Daphnia
 pulex, a common zooplankton species, have invaded Japan from North
 America. Among these, a lineage named JPN1 is thought to have started
 colonization from a single genotype several hundred to thousand years ago
 and subsequently produced many genotypes in Japan. To examine the
 phenotypic variations due to ecological drivers diverging the genotypes in
 new habitats, we measured heritability and variation in 17 traits,
 including life history, morphology and digestive traits, and the genetic
 distance among the D. pulex JPN1 genotypes in Japan. Results We found that
 most of the traits measured varied significantly among the genotypes and
 that heritability was highest in the morphological traits, followed by the
 digestive and life history traits. In addition, 93% of the variation in
 these traits was explained by the first three components in the principal
 component analysis, implying that variations of these heritable traits are
 not random but rather converged into a few directions. These relations
 among traits revealed the potential importance of predation pressures and
 food conditions as factors for diverging and selecting different
 genotypes. However, the magnitude of the difference in any single trait
 group did not correlate with the genetic distance. Conclusions Our
 findings show that the divergent traits evolved within D. pulex JPN1
 without genetic recombination since their ancestral clone invaded Japan.
 Large variations and covariations of the phenotypic traits, irrespective
 of the genetic distance among the genotypes, support the view that the
 invasive success of D. pulex JPN1 was promoted by a genetic architecture
 that allowed for large phenotypic variations with a limited number of
 functionally important mutations without recombination.
description: Data_Xiofei_20190531
DOI: 10.5061/dryad.9pc85c0
title: Data from: Comparing thermal performance curves across traits: how consistent are they?

description: Thermal performance curves (TPCs) are intended to approximate the
 relationship between temperature and fitness, and are commonly integrated
 into species distributional models for understanding climate change
 responses. However, TPCs may vary across traits because selection and
 environmental sensitivity (plasticity) differ across traits or because the
 timing and duration of the temperature exposure, here termed time-scale,
 may alter trait variation. Yet the extent to which TPCs vary temporally
 and across traits is rarely considered in assessments of climate change
 responses. Using a common garden approach, we estimate TPCs for standard
 metabolic rate (SMR), and activity in Drosophila melanogaster at three
 test temperatures (16, 25 and 30 ˚C), using flies from each of six
 developmental temperatures (16, 18, 20, 25, 28 and 30 ˚C). We examined the
 effects of time-scale of temperature exposure (mins/hours vs days/weeks)
 in altering the TPC shape, position and commonly used descriptors of the
 TPC- thermal optimum (TOPT), thermal limits (TMIN and TMAX) and thermal
 breadth (TBR). In addition we collated previously published estimates of
 TPCs for fecundity and egg-to-adult viability in D. melanogaster. We found
 that the descriptors of the TPCs varied across traits (egg-to-adult
 viability, SMR, activity and fecundity), but variation in TPCs within
 these traits was small across studies when measured at the same
 time-scales. The time-scale at which traits were measured contributed to
 greater variation in TPCs than the observed variance across traits,
 although the relative importance of time-scale differed depending on the
 trait (activity vs fecundity). Variation in the TPC across traits and
 time-scales suggests that TPCs using single traits may not be an accurate
 predictor of fitness and thermal adaptation across environments.
description: Raw data of metabolic
 rate and activitydryad.xlsx