cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rt714c5
title: Data from: Recording and reproducing the diurnal oviposition rhythms of wild populations of the soft- and stone- fruit pest Drosophila suzukii

description: Drosophila suzukii is a horticultural pest on a global scale which causes
 both yield and economic losses on a range of soft- and stone-fruit.
 Tackling this pest is problematic but exploiting behavioural rhythms could
 increase the impact of control. To do this, a better understanding of
 behavioural patterns is needed. Within this study we aimed to investigate
 rhythms in reproductive behaviour of wild D. suzukii under natural
 conditions in the field. Environmental parameters were also recorded to
 decipher how they influence these rhythms. Assays were then performed on
 laboratory cultures, housed under artificial conditions mimicking the
 temperature and light cycles, to see if these patterns were reproducible
 and rhythmic. We were able to promote field like oviposition patterns
 within the laboratory using realistic temperature and light cycles
 regardless of variations in other factors including substrate, humidity,
 and lighting type. Locomotion activity was also recorded under these
 mimicked conditions to identify how this behaviour interacts with
 oviposition rhythms. Both our field and laboratory assays show that
 oviposition behaviour is likely under the control of the circadian clock
 and primarily occurs during the day. However, consistent with prior
 reports we observed that these patterns become crepuscular when day-time
 temperature peaks exceeded 30°C. This was also found within locomotion
 rhythms. With an increased understanding of how these behaviours are
 influenced by environmental conditions, we highlight the importance of
 using realistic temperature and light cycles when investigating
 behavioural patterns. From an increased understanding of D. suzukii
 behaviour we increase our ability to target the pest in the field.
description: Oviposition
 dataData collected from all
 oviposition assays. This file includes both field and laboratory collected
 data under various conditions. Excel was used to generate this
 file.OvipositionData.xlsxLocomotionDataActivity counts of locomotion. Originally recorded in MatLab and Clocklab and exported to an excel file.
DOI: 10.5061/dryad.cm049
title: Data from: A global test for phylogenetic signal in shifts in flowering time under climate change

description: 1.Shifts in the timing of flowering are a conspicuous biological signal of
 climate change. These shifts have been documented across the globe for
 diverse communities. Although many species are flowering earlier, others
 have exhibited no shifts or delays in flowering. 2.How species respond
 phenologically will shape interactions both with other community members
 and with the abiotic environment, altering fitness, abundance, and
 ultimately persistence. 3.To understand if variability in phenological
 response is influenced by evolutionary history, we tested for phylogenetic
 signal in shifts in flowering onset for thirteen communities representing
 116 families across the Northern Hemisphere. We compared the fit of models
 of neutral evolution (Brownian Motion) with models that incorporate
 selection (Ornstein-Uhlenbeck). 4.We found significant signal in whether
 species had shifted and the magnitude of response, with both traits
 conforming to an Ornstein-Uhlenbeck model of trait evolution. 5.Synthesis.
 These results show there is global phylogenetic signal in the direction
 and magnitude of shifts in flowering onset and indicate selection has
 shaped flowering time responses of related species under climate change;
 thus, environmentally determined optima may constrain whether and to what
 degree species respond phenologically to climate change. Our findings
 further demonstrate the value of testing for phylogenetic signal across
 multiple communities and comparing multiple models of trait evolution.
description: Data on flowering time
 shift and slopeData compiled from the
 literature, from sources as indicated in the file, with species and family
 names. Shift indicates whether flowering onset has shifted significantly
 and in what direction; slope is the magnitude of the
 shift.Flowering_time_shift_slope_data_Dryad.xlsx
DOI: 10.5061/dryad.852
title: Data from: Phylogenetic Systematics and Evolution of Primate-Derived Pneumocystis Based on Mitochondrial or Nuclear DNA Sequence Comparison

description: [No abstract entered]
description: Appendices
 1-2-3Appendices.htm
DOI: 10.5061/dryad.v837k
title: Data from: Widespread chemical detoxification of alkaloid venom by formicine ants

description: The ability to detoxify defensive compounds of competitors provides key
 ecological advantages that can influence community-level processes.
 Although common in plants and bacteria, this type of detoxification
 interaction is extremely rare in animals. Here, using laboratory
 behavioral assays and analyses of videotaped interactions in South
 America, we report widespread venom detoxification among ants in the
 subfamily Formicinae. Across both data sets, nine formicine species,
 representing all major clades, used a stereotyped grooming behavior to
 self-apply formic acid (acidopore grooming) in response to fire ant
 (Solenopsis invicta and S. saevissima) venom exposure. In laboratory
 assays, this behavior increased the survivorship of species following
 exposure to S. invicta venom. Species expressed the behavior when exposed
 to additional alkaloid venoms, including both compositionally similar
 piperidine venom of an additional fire ant species and the
 pyrrolidine/pyrroline alkaloid venom of a Monomorium species. In addition,
 species expressed the behavior following exposure to the uncharacterized
 venom of a Crematogaster species. However, species did not express
 acidopore grooming when confronted with protein-based ant venoms or when
 exposed to monoterpenoid-based venom. This pattern, combined with the
 specific chemistry of the reaction of formic acid with venom alkaloids,
 indicates that alkaloid venoms are targets of detoxification grooming.
 Solenopsis thief ants, and Monomorium species stand out as brood-predators
 of formicine ants that produce piperidine, pyrrolidine, and pyrroline
 venom, providing an important ecological context for the use of
 detoxification behavior. Detoxification behavior also represents a
 mechanism that can influence the order of assemblage dominance hierarchies
 surrounding food competition. Thus, this behavior likely influences
 ant-assemblages through a variety of ecological pathways.
description: Detoxification Behavior
 in Formicinae LeBrun et alThe data file has 6
 spreadsheets. Acido. Groom. - Sinvicta venom: For methods see - Acidopore
 grooming response - S. invicta venom. Acido. Groom. - other sp venom: For
 methods see - Acidopore grooming response - other venoms Detox. Capacity
 CO2 Anesthetiz.: For methods see - Detoxification capacity assay – S.
 invicta venom Detox Capacity Acidopor. Sealed: For methods see -
 Detoxification capacity assay – S. invicta venom Acid. Groom. S.A. Vid.
 Crufipes: For methods see - Video Analysis - South American Interactions
 Acid. Groom. S.A. Vid. Nfulva: For methods see - Video Analysis - South
 American Interactions
DOI: 10.5061/dryad.gd0hv
title: Data from: Feasting in fresh water: impacts of food concentration on freshwater tolerance and the evolution of food x salinity response during the expansion from saline into fresh water habitats

description: Saline to freshwater invasions have become increasingly common in recent
 years. A key hypothesis is that rates of freshwater invasions have been
 amplified in recent years by increased food concentration, yet this
 hypothesis has remained unexplored. We examined whether elevated food
 concentration could enhance freshwater tolerance, and whether this effect
 evolves following saline to freshwater invasions. We examined
 physiological response to salinity and food concentration in a 2 × 2
 factorial design, using ancestral brackish and freshwater invading
 populations of the copepod Eurytemora affinis. We found that high food
 concentration significantly increases low-salinity tolerance. This effect
 was reduced in the freshwater population, indicating evolution following
 the freshwater invasion. Thus, ample food could enable freshwater
 invasions, allowing subsequent evolution of low-salinity tolerance even
 under food-poor conditions. We also compared effects of food concentration
 on freshwater survival between two brackish populations from the native
 range. Impacts of food concentration on freshwater survival differed
 between the brackish populations, suggesting variation in functional
 properties affecting their propensity to invade freshwater habitats. The
 key implication is that high food concentration could profoundly extend
 range expansions of brackishwater species into freshwater habitats,
 potentially allowing for condition-specific competition between saline
 invaders and resident freshwater species.
description: Lee_EvolApp_2013Data
DOI: 10.5061/dryad.40jp4
title: Data from: Disentangling genetic and prenatal maternal effects on offspring size and survival

description: Organizational processes during prenatal development can have long-term
 effects on an individual’s phenotype. Because these early developmental
 stages are sensitive to environmental influences, mothers are in a unique
 position to alter their offspring’s phenotype by differentially allocating
 resources to their developing young. However, such prenatal maternal
 effects are difficult to disentangle from other forms of parental care,
 additive genetic effects, and/or other forms of maternal inheritance,
 hampering our understanding of their evolutionary consequences. Here we
 used divergent selection lines for high and low prenatal maternal
 investment and their reciprocal line crosses in a precocial bird—the
 Japanese quail (Coturnix japonica)—to quantify the relative importance of
 genes and prenatal maternal effects in shaping offspring phenotype.
 Maternal but not paternal origin strongly affected offspring body size and
 survival throughout development. Although the effects of maternal egg
 investment faded over time, they were large at key life stages.
 Additionally, there was evidence for other forms of maternal inheritance
 affecting offspring phenotype at later stages of development. Our study is
 among the first to successfully disentangle prenatal maternal effects from
 all other sources of confounding variation and highlights the important
 role of prenatal maternal provisioning in shaping offspring traits closely
 linked to fitness.
description: Pick_et_al_2016_AmNat_dataData of body mass, size and survival throughout development of Japanese quail chicks originating from reciprocal crosses of divergent artificial selection lines for prenatal maternal investmentdata_for_dryad.csv
DOI: 10.5061/dryad.82kv2
title: Data from: Geographical barriers and climate influence demographic history in narrowleaf cottonwoods

description: Studies of genetic variation can clarify the role of geography and
 spatio-temporal variation of climate in shaping demography, particularly
 in temperate zone tree species with large latitudinal ranges. Here, we
 examined genetic variation in narrowleaf cottonwood, Populus angustifolia,
 a dominant riparian tree. Using multi-locus surveys of polymorphism in 363
 individuals across the species’ 1800 km latitudinal range, we found that,
 first, P. angustifolia has stronger neutral genetic structure than many
 forest trees (simple sequence repeat (SSR) FST=0.21), with major genetic
 groups corresponding to large apparent geographical barriers to gene flow.
 Second, using SSRs and putatively neutral sequenced loci, coalescent
 simulations indicated that populations diverged before the last glacial
 maximum (LGM), suggesting the presence of population structure before the
 LGM. Third, the LGM and subsequent warming appear to have had different
 influences on each of these distinct populations, with effective
 population size reduction in the southern extent of the range but major
 expansion in the north. These results are consistent with the hypothesis
 that climate and geographic barriers have jointly affected the demographic
 history of P. angustifolia, and point the importance of both factors as
 being instrumental in shaping genetic variation and structure in
 widespread forest trees.
description: Populus angustifolia
 locations and SSR dataThis file contains all
 the SSR data collected for all unique P. angustifolia genotypes, formatted
 for the program STRUCTURE. It also contains the latitude, longitude, and
 elevation of the collections.PopulusAngustifoliaSSR.xlsx
DOI: 10.5061/dryad.1d24c
title: Data from: Convergent evolution of phenotypic integration and its alignment with morphological diversification in Carribean Anolis ecomorphs

description: The adaptive landscape and the G-matrix are keys concepts for
 understanding how quantitative characters evolve during adaptive
 radiation. In particular, whether the adaptive landscape can drive
 convergence of phenotypic integration (i.e., the pattern of phenotypic
 variation and covariation summarized in the P-matrix) is not well studied.
 We estimated and compared P for 19 morphological traits in eight species
 of Caribbean Anolis lizards, finding that similarity in P among species
 was not correlated with phylogenetic distance. However, greater similarity
 in P among ecologically similar Anolis species (i.e., the trunk-ground
 ecomorph) suggests the role of convergent natural selection. Despite this
 convergence and relatively deep phylogenetic divergence, a large portion
 of eigenstructure of P is retained among our 8 focal species. We also
 analyzed P as an approximation of G to test for correspondence with the
 pattern of phenotypic divergence in 21 Caribbean Anolis species. These
 patterns of covariation were coincident, suggesting that either genetic
 constraint has influenced the pattern of among-species divergence or,
 alternatively, that the adaptive landscape has influenced both G and the
 pattern of phenotypic divergence among species. We provide evidence for
 convergent evolution of phenotypic integration for one class of Anolis
 ecomorph, revealing yet another important dimension of evolutionary
 convergence in this group.
description: 21 species
 meansMean values for the 16
 morphological traits for the 21 Anolis species.P (correlation
 matrices)Phenotypic correlation
 matrices for 18 morphological traits for the 8 Anolis species and pooled
 P.P (covariance
 matrices)Phenotypic covariance
 matrices for 18 morphological traits for the 8 Anolis species and pooled
 P.
DOI: 10.5061/dryad.1bk06
title: Data from: Evolutionary patterns of adaptive acrobatics and physical performance predict expression profiles of androgen receptor – but not oestrogen receptor – in the forelimb musculature

description: 1. Superior physical competence is vital to the adaptive behavioural
 routines of many animals, particularly those that engage in elaborate
 sociosexual displays. How such traits evolve across species remains
 unclear. 2. Recent work suggests that activation of sex steroid receptors
 in neuromuscular systems is necessary for the fine motor skills needed to
 execute physically elaborate displays. Thus, using passerine birds as
 models, we test whether interspecific variation in display complexity
 predicts species differences in the abundance of androgen and oestrogen
 receptors (AR and ER-α) expressed in the forelimb musculature and spinal
 cord. 3. We find that small-scale evolutionary patterns in physical
 display complexity positively predict expression of AR in the main muscles
 that lift and retract the wings. No such relationship is detected in the
 spinal cord, and we do not find a correlation between display behaviour
 and neuromuscular expression of ER-α. Also, we find that AR expression
 levels in different androgen targets throughout the body – namely the wing
 muscles, spinal cord and testes – are not necessarily correlated,
 providing evidence that evolutionary forces drive AR expression in a
 tissue-specific manner. 4. These results suggest co-evolution between the
 physical prowess necessary for display performance and levels of AR
 expression in avian forelimb muscles. Moreover, this relationship appears
 to be both specific to muscle and AR-mediated signalling. 5. Given that
 prior work suggests that activation of muscular AR is a necessary
 component of physical display performance, our current data support the
 hypothesis that sexual selection shapes levels of AR expressed in the
 forelimb skeletal muscles to help drive the evolution of adaptive motor
 abilities.
description: Musclemuscular AR and ER
 expressionSpinal
 Cordspinal cord AR and ER
 expressionGonadgonad AR
 expressionSpecies
 Meansaverage species AR and
 ER expression
DOI: 10.5061/dryad.5f1f8
title: Data from: Ecological and genetic determinants of plasmid distribution in Escherichia coli

description: Bacterial plasmids are important carriers of virulence and antibiotic
 resistance genes. Nevertheless, little is known of the determinants of
 plasmid distribution in bacterial populations. Here the factors affecting
 the diversity and distribution of the large plasmids of Escherichia coli
 were explored in cattle grazing on semi-natural grassland, a set of
 populations with low frequencies of antibiotic resistance genes.
 Critically, the population genetic structure of bacterial hosts was
 chararacterized. This revealed structured E. coli populations with high
 diversity between sites and individuals but low diversity within cattle
 hosts. Plasmid profiles, however, varied considerably within the same E.
 coli genotype. Both ecological and genetic factors affected plasmid
 distribution: plasmid profiles were affected by site, E. coli diversity,
 E. coli genotype and the presence of other large plasmids. Notably 3/26 E.
 coli serotypes accounted for half the observed plasmid-free isolates
 indicating that within species variation can substantially affect carriage
 of the major conjugative plasmids. The observed population structure
 suggest that most of the opportunities for within species plasmid transfer
 occur between different individuals of the same genotype and support
 recent experimental work indicating that plasmid–host coevolution, and
 epistatic interactions on fitness costs are likely to be important in
 determining occupancy.
description: Raw bacteria plasmid
 association dataExcel sheet containing
 data on bacterial abundance, genotype, replicon profiles associated with
 pat and site.Medaney raw plasmid
 distribution data.xlsx
DOI: 10.5061/dryad.71q1n
title: Data from: Century-long tree population dynamics in a deciduous forest stand in central Sweden

description: Question: We quantify tree dynamics over a century of free development in
 a small broadleaved forest dominated by Fraxinus excelsior and Ulmus
 glabra. What are the internal and external factors driving the changes,
 and how predictable are they? What were the time scale and effects of the
 spread of Dutch elm disease (DED)? Location: Vårdsätra, eastern central
 Sweden. Methods: The survival, growth and recruitment of all trees (≥ 12
 cm in girth) were monitored in 1912, 1967, 1988 and 2013 (more often for a
 part of the forest). Woody species in the field and shrub layers were
 surveyed in permanent plots in 1976 and 2012. We used transition matrix
 models to project changes in population sizes and species composition
 within the century and for 2050. Results: The results indicate that the
 forest was in a successional development during the first period. The
 species composition had stabilised by 1967, except for an expansion of
 Acer platanoides and the drastic effect of DED that struck the forest
 around 2000. It took only a decade to kill virtually all large elms in the
 forest, leading to strong decrease in stem density and basal area. The
 evidence for effects of DED is still weak, but there has been an increase
 in saplings, notably of Fraxinus, Prunus padus, Ulmus, and of shoots of
 Corylus avellana. Several species that are abundant in the vicinity and as
 seeds fail to establish (Picea abies, Betula spp., Quercus robur, Populus
 tremula). Projections for 2050 based on the third period (1988-2013) are
 probably unrealistic since also Fraxinus may disappear because of the
 recent arrival of the ash dieback. Conclusions: Slow dynamics in forests
 that could follow from climate change will locally probably be overruled
 by unforeseen catastrophes, such as invasions by forest pathogens. These
 initiate changes with long lag phases difficult to quantify. Still, a
 dense deciduous forest can resist invasion of colonist species and of
 regionally dominant conifers; the reason being unfavourable conditions for
 establishment rather than dispersal limitation
description: Data set
 1Data
 on tree individuals present in 1912, re-measured in 1953, 1976, 1988 and
 2013 in Area 1; Data set 1.Hytteborn2017_VN1912Data1.csvData set 2Data on tree individual measured in 1912, 1967, 1988, 2013 in Area 2; Data set 2.Hytteborn2017_VN12678813Data2.csvMatlab codeMatlab code for population matrix models based on Data 2Hytteborn2017_Matlab_code.txtRead meDescription of columns in the data filesHytteborn2017_ReadMe.csv
DOI: 10.5061/dryad.bb33v
title: Data from: Testing the influence of family structure and outbreeding depression on heterozygosity-fitness correlations in small populations

description: Theory predicts that positive Heterozygosity-Fitness Correlations (HFC)
 arise as a consequence of inbreeding, which is often assumed to have a
 strong impact in small, fragmented populations. Yet according to empirical
 data, HFC in such populations seem highly variable and impredictible. We
 here discuss two overlooked phenomena that may contribute to this
 variation. First, in a small population, each generation may consist of a
 few families. This generates random correlations between particular
 alleles and fitness (AFC, Allele-Fitness Correlations) and results in too
 liberal tests for HFC. Second, in some contexts, small populations
 receiving immigrants may be more impacted by outbreeding depression than
 by inbreeding depression, resulting in negative rather than positive HFC.
 We investigated these processes through a case study in tadpole cohorts of
 Pelodytes punctatus living in small ponds. We provide evidence for a
 strong family structure and significant AFC in this system, as well as an
 example of negative HFC. By simulations, we show that this negative HFC
 cannot be a spurious effect of family structure, and therefore reflects
 outbreeding depression in the studied population. Our example suggests
 that a detailed examination of AFC and HFC patterns can provide valuable
 insights into the internal genetic structure and sources of fitness
 variation in small populations.
description: data-manuscript-Jourdan-Pineau-EvolutionThis file contains the genotype data as well as the measured size of every sample. It also gives the geographic localization of the studied sites and the sampling dates.Script of program to simulate HFC in family-structured samplesThis is the script for our simulations (HFC in family structured samples).