cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vs08j
title: Data from: Evolutionary melting pots: a biodiversity hotspot shaped by ring diversifications around the Black Sea in the Eastern tree frog (Hyla orientalis)

description: Hotspots of intraspecific genetic diversity, which are of primary
 importance for the conservation of species, have been associated with
 glacial refugia, that is areas where species survived the Quaternary
 climatic oscillations. However, the proximate mechanisms generating these
 hotspots remain an open issue. Hotspots may reflect the long-term
 persistence of large refugial populations; alternatively, they may result
 from allopatric differentiation between small and isolated populations,
 that later admixed. Here, we test these two scenarios in a widely
 distributed species of tree frog, Hyla orientalis, which inhabits Asia
 Minor and southeastern Europe. We apply a fine-scale phylogeographic
 survey, combining fast-evolving mitochondrial and nuclear markers, with a
 dense sampling throughout the range, as well as ecological niche
 modelling, to understand what shaped the genetic variation of this
 species. We documented an important diversity centre around the Black Sea,
 composed of multiple allopatric and/or parapatric diversifications, likely
 driven by a combination of Pleistocene climatic fluctuations and complex
 regional topography. Remarkably, this diversification forms a ring around
 the Black Sea, from the Caucasus through Anatolia and eastern Europe, with
 terminal forms coming into contact and partially admixing in Crimea. Our
 results support the view that glacial refugia generate rather than host
 genetic diversity and can also function as evolutionary melting pots of
 biodiversity. Moreover, we report a new case of ring diversification,
 triggered by a large, yet cohesive dispersal barrier, a very rare
 situation in nature. Finally, we emphasize the Black Sea region as an
 important centre of intraspecific diversity in the Palearctic with
 implications for conservation.
description: Microsatellite genotypes
 of Hyla orientalis samplesThe file includes
 genotypes from 12 microsatellite loci in 521 samples of H. orientalis. For
 all loci but Ha-T53, genotypes of 150 samples were generated by Dufresnes
 et al. 2015, BMC Evol Biol and re-analyzed for this study. NA: missing
 data.msats_genotypes.xlsxMitochondrial cytochrome-b sequence alignmentSequence alignment of mitochondrial cytochrome-b (cyt-b), from 407 H. orientalis samples.cytB_alignment.fas
DOI: 10.5061/dryad.b7jh4
title: Data from: The influence of gene flow on species tree estimation: a simulation study

description: Gene flow among populations or species and incomplete lineage sorting
 (ILS) are two evolutionary processes responsible for generating gene tree
 discordance and therefore hindering species tree estimation. Numerous
 studies have evaluated the impacts of ILS on species tree inference, yet
 the ramifications of gene flow on species trees remain less studied. Here,
 we simulate and analyze multilocus sequence data generated with ILS and
 gene flow to quantify their impacts on species tree inference. We
 characterize species tree estimation errors under various models of gene
 flow, such as the isolation-migration model, the n-island model, and gene
 flow between non-sister species or involving ancestral species, and
 species boundaries crossed by a single gene copy (allelic introgression)
 or by a single migrant individual. These patterns of gene flow are
 explored on species trees of different sizes (4 vs. 10 species), at
 different time scales (shallow vs. deep), and with different migration
 rates. Species trees are estimated with the multispecies coalescent model
 using Bayesian methods (BEST and *BEAST) and with a summary statistic
 approach (MPEST) that facilitates phylogenomic-scale analysis. Even in
 cases where the topology of the species tree is estimated with high
 accuracy, we find that gene flow can result in overestimates of population
 sizes (species tree dilation) and underestimates of species divergence
 times (species tree compression). Signatures of migration events remain
 present in the distribution of coalescent times for gene trees, and with
 sufficient data it is possible to identify those loci that have crossed
 species boundaries. These results highlight the need for careful sampling
 design in phylogeographic and species delimitation studies as gene flow,
 introgression, or incorrect sample assignments can bias the estimation of
 the species tree topology and of parameter estimates such as population
 sizes and divergence times.
description: Supplemental
 MaterialsSupplemental
 Materials.
DOI: 10.5061/dryad.6m1m6
title: Data from: Morphological drivers of trophic cascades

description: Worldwide, local anthropogenic extinctions have recently been reported to
 induce trophic cascades, defined as perturbations of top consumers that
 propagate along food chains down to primary producers. This focus on the
 effects of top-consumer extinction (i.e. of species presence) ignores
 potential cascading effects of the rapid morphological changes that may
 precede extinction. Here, we show in an experimental, three-level food
 chain including medaka fish, herbivorous zooplankton and unicellular algae
 that varying body length of a single fish from large (36.3 mm) to small
 (11.5 mm) induced a stronger trophic cascade than varying an average-sized
 (23.8 mm) fish from being present to absent. The strength of fish
 predation on zooplankton scaled quasi linearly (not with a power exponent)
 with fish body length and associated gape width, suggesting that the
 resultant trophic cascade was morphology (not metabolism)-dependent. The
 effect of fish body length was stronger on phyto- than on zooplankton,
 because large-sized fish had the unique ability to suppress large-sized
 herbivores, which in turn had high grazing capacities. Hence, our results
 show that consumer body size, by setting diet breadth, can both drive and
 magnify the strength of trophic cascades. In contrast, fish body shape had
 no significant effect on fish predatory performances when its allometric
 component (the effect of size on shape) was removed. In the wild,
 human-induced body downsizing of top consumers is widespread, and
 mitigating the resultant perturbations to ecosystem function and services
 will require a paradigm shift from preserving species presence towards
 preserving species size structure.
description: Data tables for
 Morphological drivers of trophic cascadesHere we provide the data
 files used in the article Morphological drivers of trophic cascades. The
 Read me document provides details about the columns of each data
 files.OikosData.zip
DOI: 10.5061/dryad.bd6v0
title: Data from: On the origin of sweet potato (Ipomoea batatas (L.) Lam) genetic diversity in New Guinea, a secondary centre of diversity

description: New Guinea is considered the most important secondary centre of diversity
 for sweet potato (Ipomoea batatas). We analysed nuclear and chloroplast
 genetic diversity of 417 New Guinea sweet potato landraces, representing
 agro-morphological diversity collected throughout the island, and compared
 this diversity with that in tropical America. The molecular data reveal
 moderate diversity across all accessions analysed, lower than that found
 in tropical America. Nuclear data confirm previous results, suggesting
 that New Guinea landraces are principally derived from the Northern
 neotropical genepool (Camote and Batata lines, from the Caribbean and
 Central America). However, chloroplast data suggest that South American
 clones (early Kumara line clones or, more probably, later reintroductions)
 were also introduced into New Guinea and then recombined with existing
 genotypes. The frequency distribution of pairwise distances between New
 Guinea landraces suggests that sexual reproduction, rather than somaclonal
 variation, has played a predominant role in the diversification of sweet
 potato. The frequent incorporation of plants issued from true seed by
 farmers, and the geographical and cultural barriers constraining crop
 diffusion in this topographically and linguistically heterogeneous island,
 has led to the accumulation of an impressive number of variants. As the
 diversification of sweet potato in New Guinea is primarily the result of
 farmers’ management of the reproductive biology of their crop, we argue
 that on-farm conservation programmes that implement distribution of core
 samples (clones representing the useful diversity of the species) and
 promote on-farm selection of locally adapted variants may allow local
 communities to fashion relatively autonomous strategies for coping with
 ongoing global change.
description: data
 Hereditythe "data
 heredity" file provides the chloroplast and nuclear genetic data from
 the 417 New Guinea varieties analyzed in the present study. It also
 includes their full passeport data (names of ex situ collections, full
 geographical origin data and local landrace names). ND means not
 determined.
DOI: 10.5061/dryad.6r1t61j
title: Data from: Phylogeographic pattern of the plane leaf miner, Phyllonorycter platani (STAUDINGER, 1870) (Lepidoptera: Gracillariidae) in Europe

description: Background: The plane leaf miner, Phyllonorycter platani is a widely
 distributed insect species on plane trees and has a well-documented
 colonisation history in Europe over the last century. However,
 phylogeographic data of the species are lacking. Results: We analysed 284
 individuals from 38 populations across Europe, Asia, and North America. A
 1242bp fragment of the mitochondrial COI gene and an 893bp fragment of the
 28S rDNA has been Sanger sequenced. Twenty-four haplotypes were detected
 on the COI gene, and two alleles were identified on the 28S rDNA. We
 revealed two distinct clades for both markers reflecting the geographic
 origins, Asia and Europe. The genetic distance between the two main clades
 is 2.08% on the COI gene and 0.10% on the nuclear DNA. An overlapping zone
 of the two clades was found across Eastern Europe and the Anatolian
 Peninsula. We detected heterozygote individuals of the 28S rDNA gene in
 Moldavia, Ukraine and in the southern part of Turkey. These suggest that
 the two clades can hybridise. Furthermore, the presence of European type
 homozygote individuals has been confirmed in the southern part of Turkey
 as well. Conclusions: We have shown that both post-glacial recolonization
 and recent expansion events influenced the present genetic structure of P.
 platani. The genetic patterns revealed at least two refugia during the
 last ice age: one in the Balkan Peninsula and the other in the Caucasus
 region. Recent expansion was detected in some European and Central Asian
 populations. The two main clades (Europe/Asia) show definite genetic
 differences; however, several hybrid individuals were found in the
 overlapping zone as well (stretching over Eastern Europe and the Anatolian
 Peninsula). Discrepancies in mitochondrial and nuclear data indicate
 introgressions in the southern part of the Anatolian Peninsula.
description: jmodeltest_ppPhyllonorycter platoon COI HT jmodeltest resultsPP_COIPhyllonorycter platani samples basic data COIsamplesPhyllonorycter platani voucher data
DOI: 10.25934/pr00012540.0
title: Available datapackage for study 'Adapting Community-Based Task-Shifting for the COVID-19 Response Among Underserved Populations in Piedmont, North Carolina (ACT UP)'

description: Vivli is an independent, non-profit organization that has developed a global data-sharing and analytics platform to serve all elements of the international research community. Our mission is to promote, coordinate, and facilitate scientific sharing and reuse of clinical research data through the creation and implementation of a sustainable global data-sharing enterprise. The Vivli platform includes an independent data repository, in-depth search engine and a cloud-based, secure analytics platform.
DOI: 10.5061/dryad.5m6p3
title: Data from: Allocation to male vs. female floral function varies by currency and responds differentially to density and moisture stress

description: Allocation of finite resources to separate reproductive functions is
 predicted to vary across environments and affect fitness. Biomass is the
 most commonly measured allocation currency; however, in comparison with
 nutrients it may be less limited and express different environmental and
 evolutionary responses. Here, we measured carbon, nitrogen, phosphorus,
 and biomass allocation among floral whorls in recombinant inbred lines of
 Brassica rapa in multiple environments to characterize the genetic
 architecture of floral allocation, including its sensitivity to
 environmental heterogeneity and to choice of currency. Mass, carbon, and
 nitrogen allocation to female whorls (pistils and sepals) decreased under
 high density, whereas nitrogen allocation to male organs (stamens)
 decreased under drought. Phosphorus allocation decreased by half in
 pistils under drought, while stamen phosphorus was unaffected by
 environment. While the contents of each currency were positively
 correlated among whorls, selection to improve fitness through female (or
 male) function typically favored increased allocation to pistils (or
 stamens) but decreased allocation to other whorls. Finally, genomic
 regions underlying correlations among allocation metrics were mapped, and
 loci related to nitrogen uptake and floral organ development were located
 within mapped quantitative trait loci. Our candidate gene identification
 suggests that nutrient uptake may be a limiting step in maintaining male
 allocation. Taken together, allocation to male vs female function is
 sensitive to distinct environmental stresses, and the choice of currency
 affects the interpretation of floral allocation responses to the
 environment. Further, genetic correlations may counter the evolution of
 allocation patterns that optimize fitness through female or male function.
description: Brapa_2010_floral_allocationFloral allocation by whorl. This file includes genotypic values used for QTL mapping as well as replicate measures of whorl mass, carbon, nitrogen, and phosphorous allocation from Brassica rapa recombinant inbred lines (R500 x IMB211 RIL set) raised in three environmental treatments (control, high density, and moisture stress) at the University of Wyoming Agricultural Experiment Station.Brapa_2010_flr_allocation.xls
DOI: 10.5061/dryad.272gd5n
title: Data from: Single mechanosensory neurons encode lateral displacements using precise spike timing and thresholds

description: During locomotion, animals rely on multiple sensory modalities to maintain
 stability. External cues may guide behavior, but they must be interpreted
 in the context of the animal’s own body movements. Mechanosensory cues
 that can resolve dynamic internal and environmental conditions, like those
 from vertebrate vestibular systems or other proprioceptors, are essential
 for guided movement. How do afferent proprioceptor neurons transform
 movement into a neural code? In flies, modified hindwings known as
 halteres detect forces produced by body rotations, and are essential for
 flight. The mechanisms by which haltere neurons transform forces resulting
 from three-dimensional body rotations into patterns of neural spikes are
 unknown, however. We use intracellular electrodes to record from haltere
 primary afferent neurons during a range of haltere motions. We find that
 spike timing activity of individual neurons changes with displacement, and
 propose a mechanism by which single neurons can encode three-dimensional
 haltere movements during flight.
description: Haltere nerve spike
 timesThis file contains all
 of the spike and stimulus times and amplitudes for lateral displacement,
 cut-nerve, and voluntary haltere oscillation
 experimentscentipeded.zip
DOI: 10.5061/dryad.15kb3
title: Data from: Pervasive and strong effects of plants on soil chemistry: a meta-analysis of individual plant ‘Zinke’ effects

description: Plant species leave a chemical signature in the soils below them,
 generating fine-scale spatial variation that drives ecological processes.
 Since the publication of a seminal paper on plant-mediated soil
 heterogeneity by Paul Zinke in 1962, a robust literature has developed
 examining effects of individual plants on their local environments
 (individual plant effects). Here, we synthesize this work using
 meta-analysis to show that plant effects are strong and pervasive across
 ecosystems on six continents. Overall, soil properties beneath individual
 plants differ from those of neighbours by an average of 41%. Although the
 magnitudes of individual plant effects exhibit weak relationships with
 climate and latitude, they are significantly stronger in deserts and
 tundra than forests, and weaker in intensively managed ecosystems. The
 ubiquitous effects of plant individuals and species on local soil
 properties imply that individual plant effects have a role in plant–soil
 feedbacks, linking individual plants with biogeochemical processes at the
 ecosystem scale.
description: Zinke effect sizes and
 covariatesDataset used for
 meta-analysisZinke effect sizes for
 Dryad.xlsBibliographic
 informationList of references
 included in meta-analysisBibliographic
 info.docx
DOI: 10.5061/dryad.3877q7d
title: Data from: Population density mediates the interaction between pre- and post-mating sexual selection

description: When females mate with more than one male, sexual selection acts both
 before and after mating. The interaction between pre- and post-mating
 episodes of selection is expected to be context dependent, but few studies
 have investigated how total sexual selection changes under different
 ecological conditions. We examined how population density mediates the
 interaction between pre- and post-mating sexual selection by establishing
 replicate populations of the horned dung beetle Onthophagus taurus at low,
 medium, and high densities, and using microsatellite-based parentage
 analyses to measure male fitness. We found that mating success and
 fertilization success were positively correlated at all three densities,
 but the strength of the correlation decreased with increasing density. We
 also found a shift from negative to positive linear selection on testes
 mass as density increased, and opposing selection on weapons and testes at
 high densities. These patterns suggest that the importance of post-mating
 processes increases with increasing population density, which reduces the
 selective advantage of weapons for pre-mating contest competition, and
 increases the selective advantage of large ejaculates for post-mating
 sperm competition. We expect that density-dependent selection on testes
 mass has contributed to the phenotypic variation observed between natural
 populations of O. taurus that differ in density.
description: Male fitness and
 phenotype dataFitness and phenotype
 data for all males included in our experimental
 populationsMale and female Bateman
 gradientsComplete data on the
 number of offspring and number of mates for males and females in our
 experimental populationsBateman_gradients_both_sexes.xlsxOnthophagus taurus P2 dataDistribution of P2 values for O. taurus males using the irradiated male techniqueVariance partitioning estimatesPopTools simulation for calculating the 95% confidence intervals for the variance partitioning estimates of each fitness componentVariance_partitioning_all_3_densities_M,B,F.xlsxEstimating spurious correlationPopTools simulation for estimating the spurious correlation between mating success and fertilization successEstimating_spurious_correlation_coefficient_all_3_densities.xlsx
DOI: 10.5061/dryad.cf2kd
title: Data from: Old-growth forests buffer climate-sensitive bird populations from warming

description: Aim: Habitat loss and climate change constitute two of the greatest
 threats to biodiversity worldwide, and theory predicts that these factors
 may act synergistically to affect population trajectories. Recent evidence
 indicates that structurally complex old-growth forest can be cooler than
 other forest types during spring and summer months, thereby offering
 potential to buffer populations from negative effects of warming. Old
 growth may also have higher food and nest-site availability for certain
 species, which could have disproportionate fitness benefits as species
 approach their thermal limits. Location: Pacific Northwestern United
 States. Methods: We predicted that negative effects of climate change on
 30-year population trends of old-growth-associated birds should be
 dampened in landscapes with high proportions of old-growth forest. We
 modelled population trends from Breeding Bird Survey data for 13 species
 as a function of temperature change and proportion old-growth forest.
 Results: We found a significant negative effect of summer warming on only
 two species. However, in both of these species, this relationship between
 warming and population decline was not only reduced but reversed, in
 old-growth-dominated landscapes. Across all 13 species, evidence for a
 buffering effect of old-growth forest increased with the degree to which
 species were negatively influenced by summer warming. Main conclusions:
 These findings suggest that old-growth forests may buffer the negative
 effects of climate change for those species that are most sensitive to
 temperature increases. Our study highlights a mechanism whereby management
 strategies to curb degradation and loss of old-growth forests—in addition
 to protecting habitat—could enhance biodiversity persistence in the face
 of climate warming.
description: Breeding Bird Survey
 trendsFile containing the
 Breeding Bird Survey trends analysis results published by the Patuxent
 Wildlife Research Center on the following website:
 www.mbr-pwrc.usgs.gov/bbs/. Each trends is associated with a species'
 abundance and monitoring route.BBS_birdtrends.csvEnvironmental variablesEnvironmental predictor variables used in analysis describing location, forest cover, and topography of BBS routes.predictors.csvR code for analysisThis file contains annotated R code for the main analyses in the manuscript. These are 1) Determining which month for temperature change is the best predictor for each species' trend (June or July), 2) Trend ~ Temperature change * old-growth forest models for each species, 3) Global trend models for Wilson's warbler and hermit warbler that include additional interaction terms, & 4) Calculation of % change in trend per increase in June/July temperature for Wilson's warbler and hermit warbler.Betts_et_al_D&D_analysis_code.R