cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b2387
title: Data from: Cryptic diversity and gene flow among three African agricultural pests: Ceratitis rosa, Ceratitis fasciventris and Ceratitis anonae (Diptera, Tephritidae)

description: The ‘Ceratitis FAR complex’ is a species complex of African fruit flies
 (Diptera, Tephritidae) including the major agricultural pest Ceratitis
 rosa and the morphologically similar Ceratitis fasciventris and Ceratitis
 anonae. To resolve their intra- and interspecific genetic relationships
 and to estimate gene flow within this complex, we surveyed allelic
 variation at 16 microsatellite loci in 27 African populations of the three
 morphospecies. Interpopulation genetic distances and individual Bayesian
 assignments distinguished five genotypic clusters: two involving C. rosa
 (R1, R2; that may occur in sympatry), two involving C. fasciventris (F1,
 F2; with parapatric distributions) and one involving C. anonae (A). Intra-
 and interspecific patterns of genetic differentiation were not
 hierarchically structured and genetic differentiation between conspecific
 clusters (F1–F2 and R1–R2) was higher or comparable with differentiation
 between heterospecific clusters (e.g. F1-A or R2-A). In some cases, gene
 flow estimates among morphospecies or among heterospecific genotypic
 clusters were significantly different from zero, showing the lack of
 reproductive isolation. Genetic differentiation between genotypic clusters
 was partly supported by morphological differences observed a posteriori in
 male secondary sexual characters. These results suggest important
 revisions to current models of ecological niche requirements and invasion
 risk of the major agricultural pest C. rosa and provide a basis for a
 taxonomic re-interpretation of the FAR complex.
description: Virgilio_et_al_microsat_genotypesIndividual multilocus genotypes (as resulting from the analysis of 16 microsatellite markers) of 621 specimens of Ceratitis fasciventris, C. anonae, C. rosa.MIGRATE parmfileMIGRATE parmfileVirgilio_et_al_MIGRATE_parmfile
DOI: 10.5061/dryad.2f1k2
title: Data from: Thin Al1-xGaxAs0.56Sb0.44 diodes with extremely weak temperature dependence of avalanche breakdown

description: When using avalanche photodiodes (APDs) in applications, temperature
 dependence of avalanche breakdown voltage is one of the performance
 parameters to be considered. Hence, novel materials developed for APDs
 require dedicated experimental studies. We have carried out such a study
 on thin Al1–xGaxAs0.56Sb0.44 p–i–n diode wafers (Ga composition from 0 to
 0.15), plus measurements of avalanche gain and dark current. Based on data
 obtained from 77 to 297 K, the alloys Al1−xGaxAs0.56Sb0.44 exhibited weak
 temperature dependence of avalanche gain and breakdown voltage, with
 temperature coefficient approximately 0.86–1.08 mV K−1, among the lowest
 values reported for a number of semiconductor materials. Considering no
 significant tunnelling current was observed at room temperature at typical
 operating conditions, the alloys Al1−xGaxAs0.56Sb0.44 (Ga from 0 to 0.15)
 are suitable for InP substrates-based APDs that require excellent
 temperature stability without high tunnelling current.
description: Data from: Thin
 Al1-xGaxAs0.56Sb0.44 diodes with extremely weak temperature dependence of
 avalanche breakdownThis file includes all
 the raw data for figures in Manuscript (Thin Al1-xGaxAs0.56Sb0.44 diodes
 with extremely weak temperature dependence of avalanche breakdown)
 submitted to Royal Society Open Science.Data
 file_25thJan17.xls
DOI: 10.5061/dryad.8cn82
title: Data from: Differential responses to related hosts by nesting and non-nesting parasites in a brood-parasitic duck

description: Host-parasite relatedness may facilitate the evolution of conspecific
 brood parasitism (CBP), but empirical support for this contention remains
 inconclusive. One reason for this disparity may relate to the diversity of
 parasitic tactics, a key distinguishing feature being whether the parasite
 has a nest of her own. Previous work suggests that parasites without nests
 of their own may be of inferior phenotypic quality, but due to
 difficulties in identifying these parasitic individuals, little is known
 about their host selection criteria. We used high-resolution molecular
 maternity tests to assign parasitic offspring to known parasites with and
 without their own nests in a population of Barrow’s goldeneyes (Bucephala
 islandica). We determined whether parasite nesting status, host-parasite
 relatedness, and distance between host and parasite nests affected the
 probability of parasitizing a host and the number of eggs laid per host.
 We also investigated whether nesting parasites, conventionally nesting
 females and non-nesting parasites differed regarding their age, structural
 size, body condition, nesting phenology or total brood size. The
 probability of engaging in parasitism increased with host-parasite
 relatedness and spatial proximity to host nests for nesting and
 non-nesting females alike. However, nesting parasites increased the number
 of eggs donated with relatedness to the host, while non-nesting parasites
 did not do so. Non-nesting parasites laid fewer eggs in total, but did not
 differ by any of the other quality measures from conventional nesters or
 nesting parasites. Our study provides the first demonstration that nesting
 and non-nesting parasites from the same population may use different host
 selection criteria.
description: Genotypes
 2006-200719 loci genotypes of the
 individuals in the study.
DOI: 10.5061/dryad.6s444
title: Data from: The jack-of-all-trades is master of none: a pathogen's ability to infect a greater number of host genotypes comes at a cost of delayed reproduction.

description: A trade-off between a pathogen's ability to infect many hosts and its
 reproductive capacity on each host genotype is predicted to limit the
 evolution of an expanded host range, yet few empirical results provide
 evidence for the magnitude of such trade-offs. Here, we test the
 hypothesis for a trade-off between the number of host genotypes that a
 fungal pathogen can infect (host genotype range) and its reproductive
 capacity on susceptible plant hosts. We utilized strains of the oat crown
 rust fungus that carried widely varying numbers of virulence (avr) alleles
 known to determine host genotype range. We quantified total spore
 production and the expression of four pathogen life history stages:
 infection efficiency, time until reproduction, pustule size, and spore
 production per pustule. In support of the trade-off hypothesis, we found
 that virulence level, the number of avr alleles per pathogen strain, was
 correlated with significant delays in the onset of reproduction and with
 smaller pustule sizes. Modeling from our results, we conclude that
 trade-offs have the capacity to constrain the evolution of host genotype
 range in local populations. In contrast, long term trends in virulence
 level suggests that the continued deployment of resistant host lines over
 wide regions of the USA has generated selection for increased host
 genotype range.
description: Crown rust
 trait-measurementsThe excel file contains
 P. coronata life history measurements of all 348 individual inoculated
 plants. The data for each individual replicate is shown in a single row. A
 description of the column names can be found in the second excel
 sheet.trait-measurements.xls
DOI: 10.5061/dryad.6tv0f
title: Data from: Warming advances top-down control and reduces producer biomass in a freshwater plankton community

description: Global warming has been shown to affect ecosystems worldwide. Warming may,
 for instance, disrupt plant herbivore synchrony and bird phenology in
 terrestrial systems, reduce primary production in oceans, and promote
 toxic cyanobacterial blooms in freshwater lakes. Responses of communities
 will not only depend on direct species-specific temperature effects, but
 also on indirect effects related to bottom-up and top-down processes.
 Here, we investigated the impact of warming on freshwater phytoplankton
 community dynamics, and assessed the relative contribution of nutrient
 availability, fungal parasitism, and grazing therein. For this purpose, we
 performed an indoor mesocosm experiment following seasonal temperature
 dynamics of temperate lakes and a warmed (+4°C) scenario from early spring
 to late summer. We assessed phytoplankton biomass, C:N:P stoichiometry and
 community composition, dissolved nutrient availabilities, fungal parasite
 (i.e., chytrid) prevalence, and zooplankton abundance. Warming led to an
 overall reduction in phytoplankton biomass as well as lower C:P and N:P
 ratios, while phytoplankton community composition remained largely
 unaltered. Warming resulted in an earlier termination of the diatom spring
 bloom, and an epidemic of its fungal parasite ended earlier as well.
 Furthermore, warming advanced zooplankton phenology, leading to an earlier
 top-down control on phytoplankton in the period after the spring bloom.
 Linear model analysis showed that most of the observed variance in
 phytoplankton biomass was related to seasonal temperature dynamics in
 combination with zooplankton abundance. Our findings showed that warming
 advanced grazer phenology and reduced phytoplankton biomass, thereby
 demonstrating how bottom-up and top-down related processes may shape
 future phytoplankton dynamics.
description: Velthuisetal2017EcosphereDatasets and R scriptsData from Velthuis et al., 2017 Ecosphere.zip
DOI: 10.5061/dryad.4552m
title: Data from: Genetic diversity and multiple origins of polyploid Atriplex nummularia Lindl. (Chenopodiaceae).

description: Few studies have described the genetic diversity within and between
 populations of polyploid plant species despite the general acceptance of
 the importance of polyploidy in plant diversification and speciation. The
 genus Atriplex has a complex evolutionary history in Australia that has
 included polyploidy and hybridization among perennial forms. The
 octoploid, dioecious species Atriplex nummularia is proposed to have
 evolved from an octoploid ancestor in the coastal semi-arid fringe of
 south-western Australia, and to have spread east and diversified into taxa
 which occupy edaphically different habitats. Despite interest in the
 diversification of the genus, and the ecological and economic importance
 of A. nummularia, there are no descriptions of the genetic structure of
 the species. Nuclear microsatellite markers and principal coordinate
 analysis, analysis of molecular variance, Bayesian and phenetic analyses
 were used to investigate the diversity and taxonomic relationships of two
 common subspecies of A. nummularia. Genetic diversity was high overall (A
 = 509, A′ = 42.4, Ho = 0.824, H′ = 2.8), but values were significantly
 lower in the western subspecies, A. nummularia ssp. spathulata. As in
 other outbreeding, perennial species, most of the genetic diversity was
 within populations (FST = 0.125). Clear divergence of subspecies was
 evident in principal coordinate analysis, neighbor-joining and Bayesian
 clustering analyses and the differentiation of populations was very low
 within subspecies (FSC = 0.048). These findings support the taxonomic
 separation of the two subspecies. Clustering patterns based on Bayesian
 analyses suggested that the polyploid subspecies of A. nummularia have
 multiple origins.
description: AtriplexPOLYSAT
DOI: 10.5061/dryad.c770013c
title: Data from: Limitations on orchid recruitment: not a simple picture

description: Mycorrhizal fungi have substantial potential to influence plant
 distribution, especially in specialized orchids and mycoheterotrophic
 plants. However, little is known about environmental factors that
 influence the distribution of mycorrhizal fungi. Previous studies using
 seed packets have been unable to distinguish whether germination patterns
 resulted from the distribution of appropriate edaphic conditions or the
 distribution of host fungi, as these cannot be separated using seed
 packets alone. We used a combination of organic amendments, seed packets,
 and molecular assessment of soil fungi required by three terrestrial
 orchid species to separate direct and indirect effects of fungi and
 environmental conditions on both seed germination and subsequent protocorm
 development. We found that locations with abundant mycorrhizal fungi were
 most likely to support seed germination and greater growth for all three
 orchids. Organic amendments affected germination primarily by affecting
 the abundance of appropriate mycorrhizal fungi. However, fungi associated
 with the three orchid species were affected differently by the organic
 amendments and by forest successional stage. The results of this study
 help contextualize the importance of fungal distribution and abundance to
 the population dynamics of plants with specific mycorrhizal requirements.
 Such phenomena may also be important for plants with more general
 mycorrhizal associations.
description: Amendment seed packets
 and fungi_allwood_amended_seedpackets_1998-2001_all
DOI: 10.5061/dryad.78nt1
title: Data from: The energetics of life on the deep seafloor

description: With frigid temperatures and virtually no in situ productivity, the deep
 oceans, Earth’s largest ecosystem, are especially energy-deprived systems.
 Our knowledge of the effects of this energy limitation on all levels of
 biological organization is very incomplete. Here we use the Metabolic
 Theory of Ecology to examine the relative roles of carbon flux and
 temperature in influencing metabolic rate, growth rate, lifespan, body
 size, abundance, biomass, and biodiversity for life on the deep seafloor.
 We show that the relative impacts of thermal and chemical energy change
 across organizational scales. Results suggest that individual metabolic
 rates, growth, and turnover proceed as quickly as temperature-influenced
 biochemical kinetics allow, but that chemical energy limits higher-order
 community structure and function. Understanding deep-sea energetics is a
 pressing problem because of accelerating climate change and the general
 lack of environmental regulatory policy for the deep oceans.
description: DS_Energetics_MetabolismDS_Energetics_GrowthDS_Energetics_TurnoverDS_Energetics_StandingStockDS_Energetics_Diversity
DOI: 10.5061/dryad.mk870
title: Data from: Application of circulating tumor DNA as a non-invasive tool for monitoring the progression of colorectal cancer

description: Background: Liquid biopsy has been proposed to be a promising noninvasive
 tool to obtain information on tumor progression. Through a clinical
 observation of a case series of 6 consecutive patients, we aim to
 determine the value of circulating tumor DNA (ctDNA) for monitoring the
 tumor burden during the treatment of colorectal cancer (CRC). Materials
 and methods: We used capture sequencing of 545 genes to identify somatic
 alternations in primary tumor tissues of the six CRC patients who
 underwent radical surgery and in 23 plasma samples collected at serial
 time points. We compared the mutation patterns and variant allele
 frequencies (VAFs) between the matched tissue and the plasma samples and
 evaluated the potential advantage of using ctDNA as a better tumor load
 indicator to detect disease relapse over carcinoembryonic antigen (CEA),
 cancer antigen (CA) 19-9 and imaging studies. Results: We identified
 low-frequency mutations with a mean VAF of 0.88% (corresponding to a mean
 tumor burden of 0.20ng/mL) in the preoperative plasmas of four patients
 with locally advanced CRC and a subset of mutations shared by their
 primary tumors. The tumor loads appeared a sudden decrease upon surgery or
 other adjuvant treatments and then generally maintained at low levels
 (0.092ng/mL) until disease recurred. ctDNA increased by 13-fold when
 disease relapsed in one patient while the CEA and CA 19-9 levels remained
 normal. In this patient, all six somatic mutations identified in the
 preoperative plasma were detected in the recrudescent plasma again, with
 five mutations showing allele fraction increase. Conclusions: We described
 a multi-time-point profile of ctDNA of CRC patients during the course of
 comprehensive treatment and observed a correlation of ctDNA level with the
 clinically evaluated tumor progression. This demonstrated a new strategy
 by analyzing the heterogeneous ctDNA to evaluate and monitor the tumor
 burden in the treatment and follow-up of CRC patients, with potentially
 better potency than conventional biomarkers.
description: QC files of all
 samplesQC files of all
 samplesQC.zipRaw_variationsRaw variations of all samples including the tissue and plasmaraw_variations.zip
DOI: 10.5061/dryad.qk835
title: Data from: Quantifying physiological influences on otolith microchemistry

description: 1. Trace element concentrations in fish earstones (“otoliths”) are widely
 used to discriminate spatially discrete populations or individuals of
 marine fish, based on a commonly held assumption that physiological
 influences on otolith composition are minor, and thus variations in
 otolith elemental chemistry primarily reflect changes in ambient water
 chemistry. 2. We carried out a long-term (1-yr) experiment, serially
 sampling seawater, blood plasma and otoliths of mature and immature
 European plaice (Pleuronectes platessa L.) to test relationships between
 otolith chemistry and environmental or physiological variables. 3.
 Seasonal variations in otolith elemental composition did not track
 seawater concentrations, but instead reflected physiological controls on
 metal transport and biokinetics, which are likely moderated by ambient
 temperature. The influence of physiological factors on otolith composition
 was particularly evident in Sr/Ca ratios, the most widely used elemental
 marker in applied otolith microchemistry studies. Reproduction also
 triggered specific variations in otolith and blood plasma metal chemistry,
 especially Zn/Ca ratios in female fish, which could potentially serve as
 retrospective spawning indicators. 4. The influence of physiology on the
 trace metal composition of otoliths may explain the success of
 microchemical stock discrimination in relatively chemically homogenous
 marine environments, but could complicate alternative uses for trace
 element compositions in biominerals of higher organisms.
description: Time series elemental
 and physiological data for experimental plaice serially sampled for 7-12
 monthsPlaice were serially
 sampled for 7-12 months under ambient but monitored conditions. Each fish
 was sampled approximately monthly. Measurements in the attached data file
 include physiological variables (e.g. plasma protein concentrations, age,
 weight, length, female gonadosomatic index), otolith growth rates and
 opacity, and blood plasma and otolith elemental concentrations.
 Environmental data (salinity, temperature and seawater elemental
 concentrations) are also displayed. Note that elemental concentrations and
 element/calcium ratios are denoted as X.El and X.El.Ca for concentrations
 of element (‘El’) in medium ‘X’, where ‘X’ is either seawater (SW), blood
 plasma (B) or otolith (O).OTODATA_for_Dryad.xlsx
DOI: 10.15468/dl.g5ytv4
title: Occurrence Download

description: A dataset containing 785 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is Human Observation",
 "Country is Mexico",
 "TaxonKey is Thamnophis cyrtopsis",
 "Year 1960-2026"
 ]
}

 The dataset includes 785 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000721-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5fn863j
title: Data from: Immigrant and extrinsic hybrid inviability contribute to reproductive isolation between lake and river cichlid ecotypes

description: Understanding how reproductive barriers evolve and which barriers
 contribute to speciation requires the examination of organismal lineages
 that are still in the process of diversification and the study of the full
 range of reproductive barriers acting at different life stages. Lake and
 river ecotypes of the East African cichlid fish Astatotilapia burtoni show
 habitat specific adaptations, despite different levels of genetic
 differentiation, and thus represent an ideal model to study the evolution
 of reproductive barriers. To evaluate the degree of reproductive isolation
 between genetically divergent lake and river populations, we performed a
 mesocosm mating experiment in a semi-natural setting at Lake Tanganyika.
 We assessed reproductive isolation in the presence of male–male
 competition by analysing survival and growth rates of introduced adults
 and their reproductive success from genetic parentage of surviving
 offspring. The genetically divergent river population showed reduced
 fitness in terms of survival, growth rate, and mating success in a
 lake-like environment. Hybrid offspring between different populations
 showed intermediate survival consistent with extrinsic postzygotic
 reproductive barriers. Our results suggest that both prezygotic (immigrant
 inviability) and postzygotic reproductive barriers contribute to
 divergence, and highlight the value of assessing multiple reproductive
 barriers acting at different stages and in natural contexts to understand
 speciation mechanisms.
description: Body shape
 dataTps file created using
 TPSDIG2 v.2.26 containing x and y coordinates of 17 homologous landmarks
 that were placed on the image of each fish. The ID contains the year,
 generation (pb - parents before the experiment, pa - parents after the
 experiment, F1- offspring), population or type of cross (KaL - Kalambo
 lake, NdL - Ndole lake, LfR - Lufubu river), individual ID and
 sex.Body_shape_morphometrics.tpsMeasurements, survival and number of matings for the introduced adultsStandard length (SL), total length (TL) and weight (W) of all the introduced (SL0, TL0, W0) and all the recovered (SL1, TL1, W1) adults .parents.txtMating data per female-male pairNumber of mating events and number of surviving free-swimming offspring per each female-male pairmatings.txt