cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bj70k
title: Data from: Population genetic structure of a sandstone specialist and a generalist heath species at two levels of sandstone patchiness across the Strait of Gibraltar

description: Many habitat specialist species are originally composed of small,
 discontinuous populations because their habitats are naturally fragmented
 or patchy. They may have suffered the long-term effects of natural
 patchiness. Mediterranean heathlands, a representative habitat in the
 Strait of Gibraltar region, are associated with nutrient-poor, acidic
 sandstone soils. Sandstone soil patches in the African side of the Strait
 (Tangier) are, in general, smaller and more scattered than in the European
 side (Algeciras). In this study, we analyze the effect of this sandstone
 patchiness on the population genetic diversity and structure of two Erica
 species from these Mediterranean heathlands that differ in their edaphic
 specificity, E. australis, sandstone specialist, and E. arborea,
 generalist. Average levels of within-population genetic diversity and gene
 flow between populations were significantly lower in Tangier (high
 sandstone patchiness) than in Algeciras (low patchiness) for the sandstone
 specialist, whereas no differences between both sides of the Strait were
 detected in the edaphic generalist. Since most endemic species in
 Mediterranean heathlands of the Strait of Gibraltar are sandstone
 specialists, these results highlight an increased vulnerability to loss of
 genetic diversity and local extinction of the heathland endemic flora in
 the Tangier side of the Strait of Gibraltar.
description: E_arborea__E_australis_GenotypesGenotypes for the populations of Erica arborea and Erica australis in Gil-López et al., 2014
DOI: 10.5061/dryad.334n3
title: Data from: Insecticides promote viral outbreaks by altering herbivore competition

description: While the management of biological invasions is often characterized by a
 series of single-species decisions, invasive species exist within larger
 food webs. These biotic interactions can alter the impact of
 control/eradication programs and may cause suppression efforts to
 inadvertently facilitate invasion spread and impact. We document the rapid
 replacement of the invasive Bemisia MEAM1 cryptic species by the cryptic
 MED species throughout China, and demonstrate that MED is more tolerant of
 insecticides and a better vector of tomato yellow leaf curl virus
 ('TYLCV') than MEAM1. While MEAM1 usually excludes MED under
 natural conditions, insecticide application reverses the MEAM1-MED
 competitive hierarchy and allows MED to exclude MEAM1. The
 insecticide-mediated success of MED has led to TYLCV outbreaks throughout
 China. Our work strongly supports the hypothesis that insecticide use in
 China reverses the MEAM1-MED competitive hierarchy and allows MED to
 displace MEAM1 in managed landscapes. By promoting the dominance of a
 Bemisia species that is a competent viral vector, insecticides thus
 increase the spread and impact of TYLCV in heterogeneous agroecosystems.
description: Bemisia sampling
 information and biotype compositionTable
 S1.pdfTYLCV infection in
 samples of B. tabaci MEAM1 and MED collected from tomato in China in
 2011S2.pdf
DOI: 10.5061/dryad.7p42b
title: Data from: Small spermatophore size and reduced female fitness in an isolated butterfly population

description: The Glanville fritillary butterfly (Melitaea cinxia) has a small
 population (Ne ~100) on the small island of Pikku Tytärsaari (PT) in the
 Gulf of Finland. The population has remained completely isolated for ~100
 generations, which has resulted in greatly reduced genetic variation and
 high genetic load (low fitness). In particular, females lay small egg
 clutches with low egg-hatching rate in comparison with a large reference
 population in the Åland Islands (ÅL). Here, we analyze to what extent egg
 clutch size and egg-hatching rate are influenced by male population and
 spermatophore size. Spermatophore size increases with male body size, is
 smaller after the first mating, and is smaller in the small PT population.
 In the ÅL population but not in the PT population, egg-hatching rate
 increases with spermatophore size. Egg-hatching rate of PT females is
 higher when mated with ÅL males than when mated with PT males (heterosis),
 but there is no such effect on clutch size. Clutch size of ÅL females is
 however reduced when mated with PT males. These results indicate that both
 male and female traits contribute to reduced reproductive fitness in the
 small isolated population.
description: Hatch
 RatesHatchRate-Spermatophore-Corrected.b.txtSpermatophore sizeSpermatophore-ALPT-2011+2012-8.xlsx
DOI: 10.5061/dryad.63vc5
title: Data from: Baseline C-reactive protein level and life prognosis in Parkinson disease

description: Background: C-reactive protein (CRP) is a biomarker of inflammation, and
 high levels of CRP correlate with vascular death. Chronic inflammation is
 considered to be involved in neurodegeneration, although there is no
 evidence linking it with the process of neurodegenerative diseases.
 Objective: To determine the role of baseline CRP levels in the prognosis
 of patients with Parkinson disease (PD). Methods: A cohort of 313 patients
 with a mean age of 69.1 and mean PD duration of 7.9 years was
 retrospectively followed for a mean observation time of 1,753 days. CRP
 was measured when patients were not diagnosed with any infections, and
 levels were repetitively measured to investigate a tendency of “regression
 to mean.” The primary outcome measure was a survival time from study
 enrollment to death. Results: During the observation period 56 patients
 died. Baseline CRP was log-linearly associated with a risk of death in PD.
 Mean survival time was 3,149 (95% confidence interval; 3,009-3,289) days
 in patients with CRP ≤ 0.8mg/L (lower two thirds) and 2,620 (2,343-2,897)
 days in those with CRP &gt; 0.8 mg/L (top third, p &lt; 0.001,
 log-rank test). The adjusted hazard ratio (HR) per two-fold higher CRP
 concentration for all deaths was 1.29 (1.10-1.52), and after excluding
 PD-unrelated deaths, such as cancer or stroke, HR was 1.23 (1.01-1.49)
 (adjusted for age, sex, PD duration, modified Hohen-Yahr stages, MMSE
 scores, and serum albumin). Conclusions: Baseline CRP concentrations were
 associated with the risk of death and predicted life prognosis of patients
 with PD. The associations were independent from PD duration, PD severity,
 cognitive function, ages, and nutritional conditions, suggesting the
 possibility that subclinical chronic inflammation is associated with a
 neurodegenerative process in PD.
description: data
 set
DOI: 10.5061/dryad.pn371m9
title: Data from: Variation in coexisting birds to exploit spatial heterogeneity in small mammal activity

description: Breeding nest site selection is often the first defense against nest
 predation risk. To be effective, this mechanism requires site-specific
 spatial heterogeneity in predator abundance which produces predator-poor
 space, prey's ability to assess spatial heterogeneity in risk, and
 few or weak constraints on the ability to settle in within predator-poor
 space. We used a 15-year dataset on forested grids that provided extensive
 records of fledging success of veeries (Catharus fuscescens) and ovenbirds
 (Seiurus aurocapilla) in relation to areas of low and high spatial
 clustering of an important nest predator, the eastern chipmunk (Tamias
 striatus). Ovenbird nests were built in locations with significantly lower
 chipmunk clustering at a scale of 900m2, relative to random locations
 within our study grids. In contrast, veery nests were built at sites with
 significantly higher chipmunk clustering relative to random locations.
 Veery nest site preference for dense shrub patches may increase their
 vulnerability to chipmunks seeking shrubs to reduce their own
 vulnerability to predators. Despite interspecific differences in nest
 placement and avoidance of chipmunk clusters, for both species fledging
 success was unaffected by surrounding chipmunk activity. This study
 highlights key differences in the use of predator-poor space among
 coexisting species, and highlights the need to consider constraints due to
 other habitat preferences and large predator communities.
description: Data_Schmdit et al.
 JAB01946Summary data for
 chipmunk annual aggregation, local cluster indices, and cluster indices at
 the 9-trap neighborhoods surrounding veery and ovenbird
 nestsData_Emmering et al.
 JAB01946.xlsx
DOI: 10.5061/dryad.8q4b9
title: Data from: Changes in Bivalve functional and assemblage ecology in response to environmental change in the Caribbean Neogene

description: We documented changes in the relative abundance of bivalve genera and
 functional groups in the southwest Caribbean over the past 11 Myr to
 determine their response to oceanographic changes associated with the
 closure of the Central American Seaway ca. 3.5 Ma. Quantitative bulk
 samples from 29 localities yielded 106,000 specimens in 145 genera. All
 genera were assigned to functional groups based on diet, relationship to
 the substrate, and mobility. Ordinations of assemblages based on
 quantitative data for functional groups demonstrated strong shifts in
 community structure, with a stark contrast between assemblages older than
 5 Ma and those younger than 3.5 Ma. These changes are primarily due to an
 increase in the abundance of attached epifaunal bivalves (e.g., Chama,
 Arcopsis, and Barbatia) and a decrease in infaunal bivalves (e.g.,
 Varicorbula and Caryocorbula). Taxa associated with seagrasses, including
 deposit-feeding and chemosymbiotic bivalves (e.g., Lucina), also increased
 in relative abundance compared to suspension feeders. The composition of
 bivalve assemblages is correlated with the carbonate content of sediments
 and the percentage of skeletal biomass that is coral. Our results strongly
 support the hypothesis that increases in the extent of coral reefs and
 Thalassia communities were important drivers of biologic turnover in
 Neogene Caribbean benthic communities.
description: Leonard-Pingel
 paleobiology SOMThese spreadsheet give
 numerical abundance data for bivalve genera found in the paleontological
 bulk samples collected for the associated research. One spreadsheet gives
 the abundance data for each genus by faunule (location), the other
 spreadsheet lists the abundance of each bivalve genus by individual bulk
 sample.
DOI: 10.5061/dryad.vs671
title: Data from: Individual variation in energy-saving heterothermy affects survival and reproductive success

description: Given fundamental energetic trade-offs among growth, maintenance and
 reproduction, individual differences in energy saving should have
 consequences for survival and reproductive success. Many endotherms use
 periodic heterothermy to reduce energy and water requirements and
 individual variation in heterothermy should have fitness consequences.
 However, attempts to disentangle individual- and population-level
 variation in heterothermy are scarce. Here, we quantified patterns of
 heterothermy of 55 free-ranging eastern chipmunks (Tamias striatus),
 food-hoarding hibernators. Over five hibernation periods, we obtained a
 total of 7108 daily individual heterothermy indices (median: 118 per
 individual). Based on an individual reaction norm approach, we found that
 the use of heterothermy was repeatable and varied among individuals of the
 same population under similar environmental conditions. This
 among-individual variation had consequences for winter survival and
 reproductive success. Individuals using less heterothermy at the beginning
 of the winter had decreased survival in resource-rich but not in
 resource-poor years and higher reproductive success in the subsequent
 breeding season. These results support the hypothesis that fluctuating
 selection maintains heterothermic diversity and suggest that
 individualized ecophysiology can contribute to a more thorough
 understanding of the evolution of energy-saving strategies in endotherms.
description: Raw
 dataThe data was collected
 in the field. All details are mentioned in the associated
 publication.Dammhahn_etal_FE-2016-00579R1_data.xlsx
DOI: 10.5061/dryad.53k260v
title: Data from: Multivariate species boundaries and conservation of harlequin poison frogs

description: In this paper we present an iterative method for delimiting species under
 the general lineage concept (GLC) based on the multivariate clustering of
 morphological, ecological, and genetic data. Our rationale is that
 distinct multivariate groups correspond to evolutionarily independent
 metapopulation lineages because they reflect the common signal of
 different secondary defining properties (environmental and genetic
 distinctiveness, phenotypic diagnosability, etc.) that imply the existence
 of barriers preventing or limiting gene exchange. We applied this method
 to study a group of endangered poison frogs, the Oophaga histrionica
 complex. In our study case, we used next generation targeted amplicon
 sequencing to obtain a robust genetic dataset that we combined with
 patterns of morphological and ecological divergence. Our analyses revealed
 the existence of at least five different species in the histrionica
 complex (three of them new to science), some of them, occurring in small
 isolated populations outside any protected areas. The lineage delimitation
 proposed here has important conservation implications as it revealed that
 some of the Oophaga species should be considered amongst the most
 vulnerable of the Neotropical frogs. More broadly, our study exemplifies
 how multiple -amplicon and multivariate statistical techniques can be
 integrated to successfully identify species and their boundaries.
description: Morphology and
 coloration dataMorphology, pattern of
 coloration and coloration intensity variables (as described in Table S3)
 for morphological clusteringMorpho_Data_Oophaga_Final.xlsxClimatic Data Oophaga populationsHigh resolution (30 arc-seconds) environmental data from 19 bioclimatic variables (www.worldclim.org) along with altitude data (STRM901 http://srtm.csi.cgiar.org/) for climatic clustering analysis.Climatic_Data_Oophaga_Final.xlsxTranscriptome Markers OophagaGenotyping of Oophaga individuals based on transcriptome-derived haplotypes described in Table S1Transcriptome_Markers_Oophaga_Final.xlsxGenotypes Microsatellites OophagaGenotyping of Oophaga individuals based on Microsatellite markers described in Table S1Microsatellites_Oophaga_Final.xlsx
DOI: 10.5061/dryad.vb44k
title: Data from: Evolution of the plastid genomes in diatoms

description: Diatoms are a monophyletic group of eukaryotic, single-celled heterokont
 algae. Despite years of phylogenetic research, relationships among major
 groups of diatoms remain uncertain. Here we assess diatom phylogenetic
 relationships using the plastid genome (plastome). The 22 previously
 published diatom plastomes showed variable genome size, gene content and
 extensive rearrangement. We report another 18 diatom plastome sequences
 ranging in size from 119,120 to 201,816 bp. Plagiogramma staurophorum had
 the largest plastome sequenced so far due to large inverted repeats and a
 2971 bp group II intron insertion in petD. The previously reported loss of
 psaE, psaI and psaM genes in Rhizosolenia imbricata also occurred in the
 closely related species Rhizosolenia fallax. In the largest genome-scale
 phylogeny yet published for diatoms based on 103 shared plastid-coding
 genes from 40 diatoms and Triparma laevis as the outgroup, Leptocylindrus
 was recovered as sister to the remaining diatoms and the clade of Attheya
 plus Biddulphia was recovered as sister to pennate diatoms, strongly
 rejecting monophyly of two of the three proposed classes of diatoms. Our
 study also revealed extensive gene loss and a strong positive correlation
 between sequence divergence and gene order change in diatom plastomes.
description: Supplementary
 Information for the evolution of the plastid genomes in
 diatomsThis file contains
 supplementary information for the book chapter. Table A to G contains
 additional information of the genome size, genome rearrangement, and
 correlation between genome rearrangement etc.SupplementaryInformation.xlsx
DOI: 10.5061/dryad.7pd8q
title: Data from: Is floral divergence sufficient to maintain species boundaries upon secondary contact in Mediterranean food-deceptive orchids?

description: Analysing the processes that determine whether species boundaries are
 maintained upon secondary contact may shed light on the early phase of
 speciation. In Anacamptis morio and A. longicornu, two Mediterranean
 orchid sister-species, we used molecular and morphological analyses,
 together with estimates of pollination success and experimental crosses,
 to assess whether floral isolation can shelter the species' genomes
 from genetic admixture upon secondary contact. We found substantial
 genetic and morphological homogenization in sympatric populations in
 combination with an apparent lack of postmating isolation. We further
 detected asymmetric introgression in the sympatric populations and an
 imbalance in cytotype representation, which may be due either to a
 difference in flowering phenology or else be a consequence of cytonuclear
 incompatibilities. Estimates of genetic clines for markers across
 sympatric zones revealed markers that significantly deviated from neutral
 expectations. We observed a significant correlation between spur length
 and reproductive success in sympatric populations, which may suggest that
 directional selection is the main cause of morphological differentiation
 in this species pair. Our results suggest that allopatric divergence has
 not led to the evolution of sufficient reproductive isolation to prevent
 genomic admixture upon secondary contact in this orchid species pair.
description: AFLP
 matrixcpDNA restriction
 haplotypesMorphological Data
 MatrixSeed viability
 data
DOI: 10.5061/dryad.r0v20
title: Data from: Light and nutrient dependent responses in secondary metabolites of Plantago lanceolata offspring are due to phenotypic plasticity in experimental grasslands

description: A few studies in the past have shown that plant diversity in terms of
 species richness and functional composition can modify plant defense
 chemistry. However, it is not yet clear to what extent genetic
 differentiation of plant chemotypes or phenotypic plasticity in response
 to diversity-induced variation in growth conditions or a combination of
 both is responsible for this pattern. We collected seed families of
 ribwort plantain (Plantago lanceolata) from six-year old experimental
 grasslands of varying plant diversity (Jena Experiment). The offspring of
 these seed families was grown under standardized conditions with two
 levels of light and nutrients. The iridoid glycosides, catalpol and
 aucubin, and verbascoside, a caffeoyl phenylethanoid glycoside, were
 measured in roots and shoots. Although offspring of different seed
 families differed in the tissue concentrations of defensive metabolites,
 plant diversity in the mothers' environment did not explain the
 variation in the measured defensive metabolites of P. lanceolata
 offspring. However secondary metabolite levels in roots and shoots were
 strongly affected by light and nutrient availability. Highest
 concentrations of iridoid glycosides and verbascoside were found under
 high light conditions, and nutrient availability had positive effects on
 iridoid glycoside concentrations in plants grown under high light
 conditions. However, verbascoside concentrations decreased under high
 levels of nutrients irrespective of light. The data from our greenhouse
 study show that phenotypic plasticity in response to environmental
 variation rather than genetic differentiation in response to plant
 community diversity is responsible for variation in secondary metabolite
 concentrations of P. lanceolata in the six-year old communities of the
 grassland biodiversity experiment. Due to its large phenotypic plasticity
 P. lanceolata has the potential for a fast and efficient adjustment to
 varying environmental conditions in plant communities of different species
 richness and functional composition.
description: data-Miehe-Steier&al
DOI: 10.5061/dryad.qj5ck
title: Data from: Morphological variability in propagules of a desert annual as a function of rainfall patterns at different temporal and spatial scales

description: 1.Organisms living in highly variable environments have to display
 integrated strategies to deal with both systematic and random variation
 occurring at different temporal and spatial scales. Two predictions were
 tested by analysing geographic-scale patterns of seed size and seed
 retention (serotiny) in Chorizanthe rigida, a strict winter desert annual
 that delays seed dispersal and releases propagules after rainfall events:
 (a) Adaptation to systematic environmental cues occurs by means of changes
 in morphology, and (b) within-individual variation in seed size allows a
 differential response to rainfall cues: while some seeds germinate rapidly
 others are retained for future rainfall events. 2.We quantified
 morphological variation and performed germination experiments on C. rigida
 propagules (involucres + achenes) from six populations distributed
 throughout the Mojave and Sonoran deserts covering: (a) a systematic,
 west-to-east, winter-to-bi-seasonal (summer and winter) precipitation
 gradient, and (b) a winter-rain unpredictability gradient inferred from
 long-term climatic data. 3.The propagule retention structure (i.e., base
 area of the pedicel) of C. rigida individuals experiencing bi-seasonal
 rainfall are double the size of those that have evolved under a strict
 winter rainfall regime, showing that populations living in bi-seasonal
 environments have higher seed retention which allows them to avoid
 releasing seeds to a summer rainfall cue. 4.Within-individual variance of
 propagule size varied significantly between populations and was correlated
 with winter rainfall variability in each site. 5.Germination varied as a
 function of propagule size; smaller seeds germinated more readily than
 larger seeds. Increased variability in propagule size might result in a
 more variable germination response. 6.Under common experimental conditions
 germination varied significantly among sites and was negatively correlated
 with mean winter effective precipitation, suggesting that propagules from
 populations in drier sites have lower germination moisture thresholds.
 7.Synthesis. C. rigida propagules have larger bases in deserts with
 biseasonal rainfall, which allows them to avoid seed release during summer
 rainfall cues, and display within-individual seed variance associated to
 rainfall unpredictability, a trait often interpreted as a bet-hedging
 strategy. Our study provides empirical evidence of an integrated strategy
 that allows to cope with both random and systematic rainfall variation.
description: FE_morph_crigidaFE_germ_crigida