cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.t49hby
title: Occurrence Download

description: A dataset containing 5159 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Drosophila suzukii"
 ]
}

 The dataset includes 5159 records from 87 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001393-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.45fm6
title: Data from: Different genetic structures revealed resident populations of a specialist parasitoid wasp in contrast to its migratory host

description: Genetic comparisons of parasitoids and their hosts are expected to reflect
 ecological and evolutionary processes that influence the interactions
 between species. The parasitoid wasp, Cotesia vestalis, and its host
 diamondback moth (DBM), Plutella xylostella, provide opportunities to test
 whether the specialist natural enemy migrates seasonally with its host or
 occurs as resident population. We genotyped 17 microsatellite loci and two
 mitochondrial genes for 158 female adults of C. vestalis collected from 12
 geographical populations, as well as nine microsatellite loci for 127 DBM
 larvae from six separate sites. The samplings covered both the likely
 source (southern) and immigrant (northern) areas of DBM from China.
 Populations of C. vestalis fell into three groups, pointing to isolation
 in northwestern and southwestern China and strong genetic differentiation
 of these populations from others in central and eastern China. In
 contrast, DBM showed much weaker genetic differentiation and high rates of
 gene flow. TESS analysis identified the immigrant populations of DBM as
 showing admixture in northern China. Genetic disconnect between C.
 vestalis and its host suggests that the parasitoid did not migrate yearly
 with its host but likely consisted of resident populations in places where
 its host could not survive in winter.
description: Microsatellite loci,
 mitochondrial sequences and individual coordinatesmicrosatellite loci,
 mitochondrial sequences and individual coordinatesmicrosatellite loci and
 mitochondrial sequences and individual
 coordinates.zip
DOI: 10.5061/dryad.hj670t4
title: Data from: Genetic diversity, infection prevalence, and possible transmission routes of Bartonella spp. in vampire bats

description: Bartonella spp. are globally distributed bacteria that cause endocarditis
 in humans and domestic animals. Recent work has suggested bats as zoonotic
 reservoirs of some human Bartonella infections; however, the ecological
 and spatiotemporal patterns of infection in bats remain largely unknown.
 Here we studied the genetic diversity, prevalence of infection across
 seasons and years, individual risk factors, and possible transmission
 routes of Bartonella in populations of common vampire bats (Desmodus
 rotundus) in Peru and Belize, for which high infection prevalence has
 previously been reported. Phylogenetic analysis of the gltA gene for a
 subset of PCR-positive blood samples revealed sequences that were related
 to Bartonella described from vampire bats from Mexico, other Neotropical
 bat species, and streblid bat flies. Sequences associated with vampire
 bats clustered significantly by country but commonly spanned Central and
 South America, implying limited spatial structure. Stable and nonzero
 Bartonella prevalence between years supported endemic transmission in all
 sites. The odds of Bartonella infection for individual bats was unrelated
 to the intensity of bat flies ectoparasitism, but nearly all infected bats
 were infested, which precluded conclusive assessment of support for
 vector-borne transmission. While metagenomic sequencing found no strong
 evidence of Bartonella DNA in pooled bat saliva and fecal samples, we
 detected PCR positivity in individual saliva and feces, suggesting the
 potential for bacterial transmission through both direct contact (i.e.,
 biting) and environmental (i.e., fecal) exposures. Further investigating
 the relative contributions of direct contact, environmental, and
 vector-borne transmission for bat Bartonella is an important next step to
 predict infection dynamics within bats and the risks of human and
 livestock exposures.
description: Becker et al PLoS
 NTD_dataIndividual-level data on
 Bartonella infection status as determined by PCR targeting gltA and
 relevant vampire bat covariates.
DOI: 10.5061/dryad.6qn08
title: Data from: Experimentally increased reproductive effort alters telomere length in the blue tit (Cyanistes caeruleus)

description: Telomeres have recently been suggested to play important role in ageing
 and are considered to be a reliable ageing biomarkers. The life history
 theory predicts that costs of reproduction should be expressed in terms of
 accelerated senescence, and some empirical studies do confirm such
 presumption. Thus, a link between reproductive effort and telomere
 dynamics should be anticipated. Recent studies have indeed demonstrated
 that reproduction may trigger telomere loss, but actual impact of
 reproductive effort has not received adequate attention in experimental
 studies. Here, we experimentally manipulated reproductive effort by
 increasing the brood size in the wild blue tit (Cyanistes caeruleus). We
 show that parents attending enlarged broods experienced larger yearly
 telomere decay in comparison to control birds attending unaltered broods.
 In addition, we demonstrate that the change in telomere length differs
 between sexes, but this effect was independent from our treatment. To our
 knowledge, this is the first experimental study in the wild revealing that
 telomere dynamics may be linked to reproductive effort. Thus, telomere
 shortening may constitute one of the potential proximate mechanisms
 mediating the costs of reproduction.
description: Sudykaetal
DOI: 10.5061/dryad.5pv1k
title: Data from: Pinpointing genes underlying annual/perennial transitions with comparative genomics

description: Background: Transitions between perennial and an annual life history occur
 often in plant lineages, but the genes that control whether a plant is an
 annual or perennial are largely unknown. To identify genes that confer
 differences between annuals and perennials we compared the gene content of
 four pairs of sister lineages (Arabidopsis thaliana/Arabidopsis lyrata,
 Arabis montbretiana/Arabis alpina, Arabis verna/Aubrieta parviflora and
 Draba nemorosa/Draba hispanica) in the Brassicaceae in which each pair
 contains one annual and one perennial, plus one extra annual species
 (Capsella rubella). Results: After sorting all genes in all nine species
 into gene families, we identified five families in which well-annotated
 genes are present in the perennials A. lyrata and A. alpina, but are not
 present in any of the annual species. For the eleven genes in perennials
 in these families, an orthologous pseudogene or otherwise highly diverged
 gene was found in the syntenic region of the annual species in six cases.
 The five candidate families identified encode: a kinase, an
 oxidoreductase, a lactoylglutathione lyase, a F-box protein and a zinc
 finger protein. By comparing the active gene in the perennial to the
 pseudogene or heavily altered gene in the annual, dN and dS were
 calculated. The low dN/dS values in one kinase suggest that it became
 pseudogenized more recently, while the other kinase, F-box, oxidoreductase
 and zinc-finger became pseudogenized closer to the divergence between the
 annual-perennial pair. Conclusions: We identified five gene families that
 may be involved in the life history switch from perennial to annual.
 Considering the dN and dS data and whether syntenic pseudogenes were found
 and the potential functions of the genes, the F-box family is considered
 the most promising candidate for future functional studies to determine if
 it affects life history.
description: ForDryadAlnThe file is the alignment of the ITS and trnLF loci from the following species: Arabidopsis thaliana, Arabidopsis lyrata, Arabis montbretiana, Arabis alpina, Draba hispanica, Draba nemorosa, Arabis verna and Aubrieta parviflora. This alignment was used to make the phylogeny in the associated paper
DOI: 10.5061/dryad.1pj4302
title: Data from: Male competition drives song divergence along an ecological gradient in an avian ring species

description: Sexual selection operates via female choice and male competition, which
 can act independently, in concert, or in opposition. Female choice is
 typically considered the stronger selective force, but how these two
 processes interact to shape phenotypic divergence is poorly understood. I
 tested the hypothesis that variation in sexual selection in different
 habitats drives song divergence in the greenish warbler ring species. I
 evaluated the strength, direction, and targets of female choice and male
 competition in three populations spanning 2400km of latitude. Average song
 length increased with latitude, concomitant with a decline in population
 density. Within populations, males sang longer songs when females were
 fertile and shorter songs during territory establishment. Females
 consistently preferred males with longer songs and larger song
 repertoires. By contrast, playback experiments showed that males used
 short songs in territory defense. Songs were shortest at high densities,
 and in the highest density population only, song traits preferred by
 females correlated with male territoriality. Stronger male competition at
 high population densities likely constrains maximum song length, whereas
 weaker competition at low densities allows expression of female choice for
 long songs. Interactions between male competition and ecology may be a
 crucial but oft-overlooked component of phenotypic divergence and
 speciation.
description: fitness_data_scordato2018File including fitness and phenotype datafitness_scordato_dryad.csvPlayback_data_Scordato2018Responses to playback experimentsPB_expts_scordato.csv
DOI: 10.5061/dryad.p53t7
title: Data from: Small N e of the isolated and unmanaged horse population on Sable Island

description: For small, isolated populations 2 common conservation concerns relate to
 genetic threats: inbreeding and negative consequences associated with loss
 of genetic diversity due to drift. Mitigating these threats often involves
 conservation actions that can be controversial, such as translocations or
 captive breeding programs. Although such actions have been successful in
 some situations, in others they have had undesirable outcomes. Here, we
 estimated the effective population size (N e) of the Sable Island horses
 to assess the risk to this population of these genetic threats. We found
 surprising consistency of N e estimates across the 5 different methods
 used, with a mean of 48 effective individuals. This estimate falls below
 the 50 criterion of the “50/500 rule,” below which inbreeding depression
 is a concern for population viability. However, simulations and knowledge
 of population history indicate that this population is still in its early
 stages of approaching equilibrium between mutation, drift, and genetic
 diversity; and no negative consequences have been identified that could be
 associated with inbreeding depression. Therefore, we do not recommend
 taking management action (such as translocations) at this stage. Rather,
 we propose continued monitoring of genetic diversity and fitness over time
 so that trends and any substantial changes can be detected. This
 represents one of the few unmanaged horse populations in the world, and
 therefore these data will not only alert us to serious concerns regarding
 their conservation status, but will also provide a wealth of information
 about how natural processes drive patterns of reproduction, mortality, and
 population growth over time.
description: Horse
 GenotypesGenotypes of Sable
 Island horses at 10 microsatellite loci. Samples are from two time
 periods: 1987/1988 and 2011. File includes sample name, time period, and
 genotypes for all analyzed samples.horsegenotypes.csv
DOI: 10.5061/dryad.n7b7d
title: Data from: Allometric scaling of intraspecific space use

description: Allometric scaling relationships enable exploration of animal space-use
 patterns, yet interspecific studies cannot address many of the underlying
 mechanisms. We present the first intraspecific study of home range (HR)
 allometry relative to energetic requirements over several orders of
 magnitude of body mass, using as a model the predatory fish, pike Esox
 lucius. Analogous with interspecific studies, we show that space use
 increases more rapidly with mass (exponent = 1.08) than metabolic scaling
 theories predict. Our results support a theory that suggests increasing HR
 overlap with body mass explains many of these differences in allometric
 scaling of HR size. We conclude that, on a population scale, HR size and
 energetic requirement scale allometrically, but with different exponents.
description: Rosten et al
 dataset
DOI: 10.5061/dryad.96n62
title: Data from: Cumulative frequency-dependent selective episodes allow for rapid morph cycles and rock-paper-scissors dynamics in species with overlapping generations

description: Rock-paper-scissors (RPS) dynamics, which maintain genetic polymorphisms
 over time through negative frequency-dependent (FD) selection, can evolve
 in short-lived species with no generational overlap, where they produce
 rapid morph frequency cycles. However, most species have overlapping
 generations and thus, rapid RPS dynamics are thought to require stronger
 FD selection, the existence of which yet needs to be proved. Here, we
 experimentally demonstrate that two cumulative selective episodes, FD
 sexual selection reinforced by FD selection on offspring survival,
 generate sufficiently strong selection to generate rapid morph frequency
 cycles in the European common lizard Zootoca vivipara, a multi-annual
 species with major generational overlap. These findings show that the
 conditions required for the evolution of RPS games are fulfilled by almost
 all species exhibiting genetic polymorphisms and suggest that RPS games
 may be responsible for the maintenance of genetic diversity in a wide
 range of species.
description: Juvenile_survivalSiring_success
DOI: 10.5061/dryad.4194c
title: Data from: Fight evolution with evolution: plasmid-dependent phages with a wide host range prevent the spread of antibiotic resistances

description: The emergence of pathogenic bacteria resistant to multiple antibiotics is
 a serious worldwide public health concern. Whenever antibiotics are
 applied, the genes encoding for antibiotic resistance are selected for
 within bacterial populations. This has led to the prevalence of
 conjugative plasmids that carry resistance genes and can transfer
 themselves between diverse bacterial groups. In this study, we
 investigated whether it is feasible to attempt to prevent the spread of
 antibiotic resistances with a lytic bacteriophage, which can replicate in
 a wide range of gram-negative bacteria harboring conjugative
 drug-resistance conferring plasmids. The counter-selection against the
 plasmid was shown to be effective, reducing the frequency of
 multi-resistant bacteria that formed via horizontal transfer by several
 orders of magnitude. This was true also in the presence of an antibiotic
 against which the plasmid provided resistance. Majority of the
 multi-resistant bacteria subjected to phage selection also lost their
 conjugation capability. Overall this study suggests that, while we are
 obligated to maintain the selection for the spread of the drug
 resistances, the ‘fight evolution with evolution’ approach could help us
 even out the outcome to our favor.
description: Ojala et al. (2013) -
 raw dataSee README.txt for
 instructions in interpreting the data.
DOI: 10.5061/dryad.c9s0g
title: Data from: RADseq underestimates diversity and introduces genealogical biases due to nonrandom haplotype sampling

description: Reduced representation genome-sequencing approaches based on restriction
 digestion are enabling large-scale marker generation and facilitating
 genomic studies in a wide range of model and nonmodel systems. However,
 sampling chromosomes based on restriction digestion may introduce a bias
 in allele frequency estimation due to polymorphisms in restriction sites.
 To explore the effects of this nonrandom sampling and its sensitivity to
 different evolutionary parameters, we developed a coalescent-simulation
 framework to mimic the biased recovery of chromosomes in restriction-based
 short-read sequencing experiments (RADseq). We analysed simulated DNA
 sequence datasets and compared known values from simulations with those
 that would be estimated using a RADseq approach from the same samples. We
 compare these ‘true’ and ‘estimated’ values of commonly used summary
 statistics, π, θw, Tajima's D and FST. We show that loci with missing
 haplotypes have estimated summary statistic values that can deviate
 dramatically from true values and are also enriched for particular
 genealogical histories. These biases are sensitive to nonequilibrium
 demography, such as bottlenecks and population expansion. In silico
 digests with 102 completely sequenced Drosophila melanogaster genomes
 yielded results similar to our findings from coalescent simulations.
 Though the potential of RADseq for marker discovery and trait mapping in
 nonmodel systems remains undisputed, our results urge caution when
 applying this technique to make population genetic inferences.
description: ms2radseqThis is a Perl script that takes output from the coalescent simulator ms and performs an "in silico" digest to mimic the recovery of chromosomes in a RADseq experiment.
DOI: 10.5061/dryad.nc88cg6
title: Data from: Evidence of degradation of hair corticosterone in museum specimens

description: Researchers increasingly rely on non-invasive physiological indices, such
 as glucocorticoid (GC) levels, to interpret how vertebrates respond to
 changes in their environment. Recently, hair GCs have been of particular
 interest, because they are presumed stable over long periods of storage,
 which may facilitate the study of large-scale spatial and temporal
 patterns of stress in mammals. In the current study, we evaluated the
 stability of hair corticosterone levels in museum specimens, and the
 potential effects of different museum curation treatments. Using deer
 mouse (Peromyscus maniculatus) specimens collected from Vancouver Island
 (11 sites, 82 individuals) over 76 years, we found that specimens
 collected earlier in the 20th century had lower hair corticosterone than
 more recently collected specimens. These results suggest that hair hormone
 levels may not be stable over decades of storage time. We then subjected
 hair samples collected from white-footed mouse (Peromyscus leucopus,
 n = 36) to 3 different museum curation treatments, and found that borax
 lowered hair corticosterone levels relative to control samples, but air
 drying samples, or treating them with turpentine had no effect. Our
 results present a source of concern for the use of museum specimens for
 hair hormone analysis, and for studying long term trends in glucocorticoid
 levels.
description: Museum specimen
 corticosterone dataFile contains
 corticosterone levels extracted from the hair of museum specimens of deer
 mouse (Peromyscus maniculatus), that had been collected over an
 approximately 75-year period.Corticosterone data
 following simulated curationFile contains data from
 an experiment in which skin sections from white-footed mouse (Peromyscus
 leucopus) were subjected to different museum curation techniques, to
 determine the effects of curation on hair corticosterone
 levels.
DOI: 10.5061/dryad.vr4k2
title: Data from: Phylogenetic beta diversity, similarity, and differentiation measures based on Hill numbers

description: Until now, decomposition of abundance-sensitive gamma (regional)
 phylogenetic diversity measures into alpha and beta (within- and
 between-group) components has been based on an additive partitioning of
 phylogenetic generalized entropies, especially Rao's quadratic
 entropy. This additive approach led to a phylogenetic measure of
 differentiation between assemblages: (gamma − alpha)/gamma. We show both
 empirically and theoretically that this approach inherits all of the
 problems recently identified in the additive partitioning of
 non-phylogenetic generalized entropies. When within-assemblage (alpha)
 quadratic entropy is high, the additive beta and the differentiation
 measure (gamma − alpha)/gamma always tend to zero (implying no
 differentiation) regardless of phylogenetic structures and differences in
 species abundances across assemblages. Likewise, the differentiation
 measure based on the phylogenetic generalization of Shannon entropy always
 approaches zero whenever gamma phylogenetic entropy is high. Such critical
 flaws, inherited from their non-phylogenetic parent measures (Gini-Simpson
 index and Shannon entropy respectively), have caused interpretational
 problems. These flaws arise because phylogenetic generalized entropies do
 not obey the replication principle, which ensures that the diversity
 measures are linear with respect to species addition or group pooling.
 Furthermore, their complete partitioning into independent components is
 not additive (except for phylogenetic entropy). Just as in the
 non-phylogenetic case, these interpretational problems are resolved by
 using phylogenetic Hill numbers that obey the replication principle. Here
 we show how to partition the phylogenetic gamma diversity based on Hill
 numbers into independent alpha and beta components, which turn out to be
 multiplicative. The resulting phylogenetic beta diversity (ratio of gamma
 to alpha) measures the effective number of completely phylogenetically
 distinct assemblages. This beta component measures pure differentiation
 among assemblages and thus can be used to construct several classes of
 similarity or differentiation measures normalized onto the range [0, 1].
 We also propose a normalization to fix the traditional additive
 phylogenetic similarity and differentiation measures, and we show that
 this yields the same similarity and differentiation measures we derived
 from multiplicative phylogenetic diversity partitioning. We thus can
 achieve a consensus on phylogenetic similarity and differentiation
 measures, including N-assemblage phylogenetic generalizations of the
 classic Jaccard, Sørensen, Horn, and Morisita-Horn measures. Hypothetical
 and real examples are used for illustration.
description: rockfish-phylo_treeThe phylogenetic tree as a newick format, which is mirror from ELE_1344_sm_AppendixS4.txt (Pavoine et al. 2009).rockfish-dataThe rockfish relative abundances, modified from Pavoine et al. (2009)
DOI: 10.5061/dryad.m3g5jm6
title: Data from: Nitrogen addition does not reduce the role of spatial asynchrony in stabilizing grassland communities

description: While nitrogen (N) amendment is known to affect the stability of
 ecological communities, whether this effect is scale‐dependent remains an
 open question. By conducting a field experiment in a temperate grassland,
 we found that both plant richness and temporal stability of community
 biomass increased with spatial scale, but N enrichment reduced richness
 and stability at the two scales considered. Reduced local‐scale stability
 under N enrichment arose from N‐induced reduction in population stability,
 which was partly attributable to the decline in local species richness, as
 well as reduction in asynchronous local population dynamics across
 species. Importantly, N enrichment did not alter spatial asynchrony among
 local communities, which provided similar spatial insurance effects at the
 larger scale, regardless of N enrichment levels. These results suggest
 that spatial variability among local communities, in addition to local
 diversity, may help stabilise ecosystems at larger spatial scales even in
 the face of anthropogenic environmental changes.
description: zhang et al data Ecology
 Letters - ELE-00797-2018.R2