cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8m0t6
title: Data from: Hybridization of Southern Hemisphere blue whale subspecies and a sympatric area off Antarctica: impacts of whaling or climate change?

description: Understanding the degree of genetic exchange between subspecies and
 populations is vital for the appropriate management of endangered species.
 Blue whales (Balaenoptera musculus) have two recognized Southern
 Hemisphere subspecies that show differences in geographic distribution,
 morphology, vocalizations and genetics. During the austral summer feeding
 season the pygmy blue whale (B. m. brevicauda) is found in temperate
 waters and the Antarctic blue whale (B. m. intermedia) in polar waters.
 Here we used genetic analyses to report on several cases of hybridization
 between the two recognized blue whale Southern Hemisphere subspecies in a
 previously unconfirmed feeding season sympatric area off Antarctica. The
 pygmy blue whales utilizing waters off Antarctica may migrate then breed
 during the austral winter with the Antarctic subspecies. Alternatively,
 the subspecies may interbreed off Antarctica outside the expected austral
 winter breeding season. The genetically estimated recent migration rate
 from the pygmy to Antarctic subspecies was greater than evolutionary
 migration rate estimates and previous estimates based on morphology of
 whaling catches. This discrepancy may be due to differences in the methods
 or an increase in the proportion of pygmy blue whales off Antarctica
 within the last four decades. Potential causes for the latter are whaling,
 anthropogenic climate change or a combination of these, and may have led
 to hybridization between the subspecies. Our findings challenge the
 current knowledge about the breeding behaviour of the world’s largest
 animal and provide key information that can be incorporated into
 management and conservation practices for this endangered species.
description: Microsatellite and sex
 dataMicrosatellite_and_sex_data.txt
DOI: 10.5061/dryad.d5f53
title: Data from: Fishing, fast growth, and climate variability increase the risk of collapse

description: Species around the world have suffered collapses, and a key question is
 why some populations are more vulnerable than others. Traditional
 conservation biology and evidence from terrestrial species suggest that
 slow-growing populations are most at risk, but interactions between
 climate variability and harvest dynamics may alter or even reverse this
 pattern. Here, we test this hypothesis globally. We use boosted regression
 trees to analyse the influences of harvesting, species traits and climate
 variability on the risk of collapse (decline below a fixed threshold)
 across 154 marine fish populations around the world. The most important
 factor explaining collapses was the magnitude of overfishing, while the
 duration of overfishing best explained long-term depletion. However, fast
 growth was the next most important risk factor. Fast-growing populations
 and those in variable environments were especially sensitive to
 overfishing, and the risk of collapse was more than tripled for
 fast-growing when compared with slow-growing species that experienced
 overfishing. We found little evidence that, in the absence of overfishing,
 climate variability or fast growth rates alone drove population collapse
 over the last six decades. Expanding efforts to rapidly adjust harvest
 pressure to account for climate-driven lows in productivity could help to
 avoid future collapses, particularly among fast-growing species.
description: Explanatory and response
 variables for fish stock dynamicsfinal_data_2015-06-30.csv
DOI: 10.5061/dryad.65jr5
title: Data from: Abandoned pastures cannot spontaneously recover the attributes of old-growth savannas

description: 1.Active restoration strategies have been recommended to recover
 Neotropical savannas in abandoned lands, but no studies have investigated
 the trajectories and speeds of spontaneous recovery for these systems.
 Research into the dynamics of degraded savannas is urgently needed to
 guide restoration decision-making. 2.We analysed the dynamics of secondary
 savannas in the Brazilian Cerrado by sampling 29 abandoned pastures (time
 since abandonment ranging from 3 to 25 years) and applying the
 space-for-time substitution method. We modelled the temporal changes in
 plant community attributes and estimated the time (years) required for
 these attributes to match those of two reference ecosystems (three
 replicates each), old-growth savanna and a forest-type savanna, which had
 encroached following fire suppression (encroached savanna). We also
 analysed the plant community composition of the study sites. 3.Our models
 showed that tree canopy cover, richness and density rapidly increased with
 time since pasture abandonment, easily surpassing the values of the
 old-growth savanna (28 years) and reaching the values of encroached
 savanna 49 years after abandonment. The cover and richness of the ground
 layer increased at a much slower pace. Since the species in this layer,
 including the exotic grasses, are shade intolerant, they will be
 eliminated by canopy closure over time. 4.Up to 25 years after
 abandonment, secondary savannas continued to lack many (37%) old-growth
 savanna species, mostly from the ground layer (82% of grasses absent).
 This period was also not sufficient for the secondary savannas to become
 floristically similar to the encroached savannas, which are dominated by
 shade-tolerant tree species. 5.Synthesis and applications. Despite the
 reported high natural regeneration of Neotropical savanna vegetation,
 abandoned pastures will not spontaneously return to an old-growth savanna
 state. Protected from fire and lacking the native ground layer, the end
 state of secondary savannas will be a low-diversity forest. If restoration
 goals include the recovery of old-growth savanna biodiversity and
 structure, interventions are required to prevent woody encroachment and
 reintroduce native grasses, forbs and shrubs. However, if the desirable
 endpoint is a low-diversity forest, passive restoration (non-intervention)
 and fire protection are appropriate.
description: Data from_Cava et al
 2017_Abandoned pastures cannot spontaneously recover the attributes of
 old-growth savannas
DOI: 10.5061/dryad.g16gv
title: Data from: Vigor and skill in the acrobatic mating displays of a Neotropical songbird

description: Animal social behaviors are often mediated by signals that provide
 information about signaler attributes. Although some signals are
 structurally simple, others are temporally dynamic and multifaceted. In
 such cases, exaggeration of some display components is likely to curtail
 the expression of others. We quantified features of the acrobatic,
 multimodal “leap display” of blue-black grassquits (Volatinia jacarina),
 which appears to entail moderate-to-high performance levels in terms of
 vigor and skill. We video recorded and quantified leap parameters (height,
 duration, rotation angle, launch velocity, and number of wing beats) and
 assessed how these parameters covaried with each other and with vocal
 parameters, display rates, and body mass index. Our analyses revealed
 correlations among multiple performance variables: leap height, duration,
 launch velocity, and number of wing beats. Leap height also correlated
 positively with song duration. By contrast, no leap parameters covaried
 with rotation angle. Our analyses also revealed a trade-off in vigor and
 skill-based leap attributes: birds with a lower body mass index showed a
 negative relationship between leap heights and the proportion of displays
 that included leaps (vs. perched vocalizations only). Our results identify
 directions of display evolution subject to mechanical or timing
 constraints and provide evidence that display attributes that emphasize
 vigor and skill may limit one another. Our results also support a key
 expectation of handicap models of display evolution, which is that costs
 of display execution should be borne disproportionately by signalers of
 lower quality.
description: Manica et al BE
 2016_DryadSubmissionThis data file describes
 motor and acoustic display parameters and body mass index of male
 blue-black grassquits (Volatinia jacarina).
DOI: 10.5061/dryad.7384037h
title: Data from: Nonadditive indirect effects of group genetic diversity on larval viability in Drosophila melanogaster imply key role of maternal decision-making

description: Genetic variation can have important consequences for populations: high
 population genetic diversity is typically associated with ecological
 success. Some mechanisms that account for these benefits assume that local
 social groups with high genetic diversity are more successful than
 low-diversity groups. At the same time, active decision-making by
 individuals can influence group genetic diversity, a behavioral process
 not generally incorporated into discussions of population-level diversity
 effects. Here, we examine how maternal decisions that determine group
 genetic diversity influence the viability of Drosophila melanogaster
 larvae. Our groups contained wildtype larvae, whose genetic diversity we
 manipulated; and genetically-marked “tester” larvae, whose genotype and
 frequency were identical in all trials. We measured wildtype and tester
 viability for each group. Surprisingly, the viability of wildtype larvae
 did not depend on group genetic diversity. However, the viability of the
 tester genotype was substantially depressed in large, high-diversity
 groups. Further, not all high-diversity groups produced this effect:
 certain combinations of wildtype genotypes were deleterious to tester
 viability, while other groups of the same diversity—but containing
 different wildtype genotypes—were not deleterious. These deleterious
 combinations of wildtype genotypes could not be predicted by observing the
 performance of the same tester and wildtype genotypes in low-diversity
 groups. Taken together, these results suggest that non-additive
 interactions among genotypes, rather than genetic diversity per se,
 account for between-group differences in viability in D. melanogaster; and
 that predicting the consequences of genetic diversity at the population
 level may not be straightforward.
description: data for
 dryadThe attending
 spreadsheet contains data from all 3 levels of diversity and 2 group
 sizes. Data were collected by JBS, ETA, JG, MH, and NM. The “diversity”
 column refers to the level of wildtype genetic diversity in the group (L=
 low, M= medium, H= high). “Number of tester survivors” and “number of
 wildtype survivors” are the number of tester and wildtype individuals,
 respectively, who eclosed from that group. Groups in which either the
 number of wildtype or tester survivors was 0 were excluded from the
 analysis. “Date” is the date the vial was created. “Genotype combination”
 describes the complement of wildtype genotypes present in the group;
 information about specific genotype combinations is available in the
 Supplemental Information to the paper. “Group size” is the number of
 first-instar larvae originally added to the vial (72 for small groups, 144
 for large groups).
DOI: 10.5061/dryad.742cc92
title: Geographic patterns in morphometric and genetic variation for coyote populations with emphasis on southeastern coyotes

description: Prior to 1900, coyotes (Canis latrans) were restricted to the western and
 central regions of North America, but by the early 2000s coyotes became
 ubiquitous throughout the eastern United States. Information regarding
 morphological and genetic structure of coyote populations in the
 southeastern United States is limited, and where data exist, they are
 rarely compared to those from other regions of North America. We assessed
 geographic patterns in morphology and genetics of coyotes with special
 consideration of coyotes in the southeastern United States. Mean body mass
 of coyote populations increased along a west-to-east gradient, with
 southeastern coyotes being intermediate to western and northeastern
 coyotes. Similarly, principal component analysis of body mass and linear
 body measurements suggested that southeastern coyotes were intermediate to
 western and northeastern coyotes in body size but exhibited shorter tails
 and ears from other populations. Genetic analyses indicated that
 southeastern coyotes represented a distinct genetic cluster that
 differentiated strongly from western and northeastern coyotes. We
 postulate that southeastern coyotes experienced lower immigration from
 western populations than did northeastern coyotes, and over time,
 genetically diverged from both western and northeastern populations.
 Coyotes colonizing eastern North America experienced different selective
 pressures than did stable populations in the core range and we offer that
 the larger body size of eastern coyotes reflect an adaptation that
 improved dispersal capabilities of individuals in the expanding range.
description: Coyote Body
 MeasurementsFile contains body
 measurements for coyotes
DOI: 10.5061/dryad.3n216
title: Data from: Mid-Cretaceous megaspore floras from Maryland, USA

description: Bulk maceration of unconsolidated Potomac Group sediments collected from
 12 samples of middle – late Albian and early Cenomanian age on the Elk
 Neck Peninsula, Maryland, yielded 14 genera and 18 species of megaspores.
 The identified megaspores have affinities to both heterosporous ferns,
 e.g., Arcellites and Molaspora, and to heterosporous lycopsids, e.g.,
 Erlansonisporites, Minerisporites, and Paxillitriletes. Morphological
 variation within species is high, and most morphotypes differ from
 established taxa in one or more characters. Two new species —
 Dijkstraisporites praetextus and Verrutriletes diversus—are proposed. The
 composition of these middle–late Albian and early Cenomanian floras is a
 mixture of taxa previously recorded from Aptian and Santonian floras in
 North America. In addition, a fragmentary strobilus of selaginellalean
 affinity containing a megaspore and microspores is described.
description: SupplemntalData01Locality Register
DOI: 10.5061/dryad.70m5h
title: Data from: iTRAQ-based quantitative proteomic analysis on S100 calcium binding protein A2 in metastasis of laryngeal cancer

description: Laryngeal cancer is the most frequent neoplasm in the head and neck
 region, with the vast majority of tumors originating from squamous cells.
 The survival rate of patients with laryngeal cancer has not improved
 substantially over the past 25 years. To acquire further knowledge
 regarding the molecules responsible for laryngeal cancer oncogenesis and,
 in turn, to improve target therapy，iTRAQ and mass spectrometry analysis
 were utilized to detect differences in protein expression from 15 paired
 laryngeal cancer and adjacent non-cancerous tissue samples. Using mass
 spectrometry analysis, the expression levels of 100 proteins in laryngeal
 cancer samples were distinct from the non-tumor, non-cancerous samples.
 Further validation of the differentially expressed proteins S100A2, KRT16,
 FGB and HSPB1 were carried out using quantitative real-time RT-PCR,
 immunoblot and immunohistochemistry. Functional analysis of one of the
 highly expressed proteins, S100 calcium binding protein A2 (S100A2), was
 performed using RNA interference. As a consequence, attenuated S100A2
 expression enhanced the ability of HEp-2 cell lines to migrate and invade
 in vitro. Our investigation complements the current understanding of
 laryngeal cancer progression. Furthermore, this study supports the concept
 that enhanced expression of S100A2 may be a promising strategy in
 developing novel cancer therapeutic drugs.
description: The data underlying the
 findings of the studySupplementary data 1:
 Patient demographic and clinical characteristics. Supplementary data 2:
 The list of proteins found to be expressed at different levels between
 laryngeal carcinoma samples and paired non-cancerous samples by iTRAQ
 analysisa. a118:117 and 121:119 refer to relative level of protein
 expression in laryngeal carcinoma samples with respect to non-cancerous
 samples. Statistical calculation for iTRAQ-based detection and relative
 quantification were calculated using the Paragon Algorithm in the
 ProteinPilot software. Supplementary data 3: The biological processes of
 differentially expressed proteins. Supplementary data 4: The protein
 classes of differentially expressed proteins. Supplementary data 5: The
 molecular functions of differentially expressed proteins. a118:117 and
 121:119 refer to relative level of protein expression in laryngeal
 carcinoma samples with respect to non-cancerous samples. Statistical
 calculation for iTRAQ-based detection and relative quantification were
 calculated using the Paragon Algorithm in the ProteinPilot software.
 Supplementary data 3: The biological processes of differentially expressed
 proteins. Supplementary data 4: The protein classes of differentially
 expressed proteins. Supplementary data 5: The molecular functions of
 differentially expressed proteins.
DOI: 10.5061/dryad.53g68
title: Data from: Phenotype-associated inbreeding biases estimates of inbreeding depression in a wild bird population

description: Inbreeding depression is usually quantified by regressing individual
 phenotypic values on inbreeding coefficients, implicitly assuming there is
 no correlation between an individual's phenotype and the kinship
 coefficient to its mate. If such an association between parental phenotype
 and parental kinship exists, and if the trait of interest is heritable,
 estimates of inbreeding depression can be biased. Here we first derive the
 expected bias as a function of the covariance between mean parental
 breeding value and parental kinship. Subsequently, we use simulated data
 to confirm the existence of this bias, and show that it can be accounted
 for in a quantitative genetic animal model. Finally, we use long-term
 individual-based data for white-throated dippers (Cinclus cinclus), a bird
 species in which inbreeding is relatively common, to obtain empirical
 estimate of this bias. We show that during part of the study period,
 parents of inbred birds had shorter wings than those of outbred birds, and
 as wing length is heritable, inbred individuals were smaller, independent
 of any inbreeding effects. This resulted in the overestimation of
 inbreeding effects. Similarly, during a period when parents of inbred
 birds had longer wings, we found that inbreeding effects were
 underestimated. We discuss how such associations may have arisen in this
 system, and why they are likely to occur in others, too. Overall, we
 demonstrate how less biased estimates of inbreeding depression can be
 obtained within a quantitative genetic framework, and suggest that
 inbreeding and additive genetic effects should be accounted for
 simultaneously whenever possible.
description: Becker-et-al_JEB_pedigreePedigree Data White-throated dipper (Cinclus cinclus), Pruned Pedigree, Long-term Study Zurich, Switzerland.Becker-et-al_JEB_wing-dataMorphological Data, White-throated dipper (Cinclus cinclus), Long-term Study Zurich, Switzerland. See file for more information.
DOI: 10.5061/dryad.b7f53
title: Data from: Arbuscular mycorrhizal fungi increase organic carbon decomposition under elevated CO2

description: The extent to which terrestrial ecosystems can sequester carbon to
 mitigate climate change is a matter of debate. The stimulation of
 arbuscular mycorrhizal fungi (AMF) by elevated atmospheric carbon dioxide
 (CO2) has been assumed to be a major mechanism facilitating soil carbon
 sequestration by increasing carbon inputs to soil and by protecting
 organic carbon from decomposition via aggregation. We present evidence
 from four independent microcosm and field experiments demonstrating that
 CO2 enhancement of AMF results in considerable soil carbon losses. Our
 findings challenge the assumption that AMF protect against degradation of
 organic carbon in soil and raise questions about the current prediction of
 terrestrial ecosystem carbon balance under future climate-change
 scenarios.
description: chengsupp2_datasets 1-4
 for the meta-analysis studyThe data sets 1-4 for
 the meta-analysis study.
DOI: 10.5061/dryad.12n6v
title: Data from: Sex-dependent carry-over effects on timing of reproduction and fecundity of a migratory bird

description: Life of many organisms flows as a sequence of annual cycles. Timing of
 cyclical events is shaped by natural selection also via the domino effects
 that any life history stage has on the stages that follow. Such
 ‘carry-over effects’ have major consequences for evolutionary, ecological
 and demographic processes, but the causes that generate their
 individual-level variation, including the effect of sex, are poorly
 understood. We used light-level geolocators to study carry-over effects on
 the year-round life cycle of the long-distance migratory barn swallow
 (Hirundo rustica) and sex-dependent variation in their strength.
 Correlation analyses showed that timing of breeding influenced departure
 time for autumn migration in females but not in males. In addition,
 strong, time-mediated carry-over effects of timing of departure from the
 wintering areas in sub-Saharan Africa for spring migration on timing of
 arrival to the breeding grounds in Italy and Switzerland operated in both
 sexes. However, carry-over effects of spring migration phenology on
 breeding date and seasonal fecundity were observed among females but not
 among males. We used partial least squares path modelling to unveil the
 complex carry-over effects of phenology during the non-breeding season in
 combination with the ecological conditions experienced by individual
 swallows in the wintering area, as gauged by Normalized Difference
 Vegetation Index values (NDVI), on breeding performance. Phenology during
 the non-breeding season combined with NDVI during wintering accounted for
 as much as 65–70% of variation in subsequent seasonal fecundity in
 females, while such carry-over effects on breeding success of males were
 weaker. Intense, sex-specific carry-over effects can have impacted on
 evolutionary processes, including sexual selection, and affected
 phenological response to climate change, causing the large population
 decline observed in this species.
description: Carryover effects
 supporting dataData
 file