cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7pr65
title: Data from: Time constraint effects on phenology and life history synchrony in a damselfly along a latitudinal gradient

description: In organisms with complex life cycles living in seasonal environments, the
 synchronisation of phenological events is important from the ecological
 and evolutionary perspectives. Life history transitions should be
 synchronised to a greater degree at northern latitudes. We quantified
 hatching and emergence timing and synchrony in the obligate univoltine
 damselfly Lestes sponsa along a latitudinal gradient covering its entire
 north–south range in Europe. In our first experiment, populations from
 different latitudes were grown in separate climate chambers simulating
 temperature and photoperiod conditions occurring at their sites of origin.
 Northern populations expressed early and high synchronous hatching and
 emergence, central populations intermediate, and southern populations late
 and low synchronous hatching and emergence. This pattern was expressed at
 both population and full-sibling family levels, indicating stronger
 selection for timing and synchronisation in the north compared to the
 south. In our second experiment, populations from all latitudes were
 reared in conditions simulating an average temperature and photoperiod
 over the latitudinal gradient. Interestingly, the pattern of timing and
 synchronisation was reversed with respect to latitude when compared to the
 pattern shown in the first experiment, indicating the importance of
 environmental factors in shaping phenological events. Our results indicate
 strong selection for timing and synchronisation of life history events at
 northern latitudes, caused by time constraints. Our results also show that
 it is important to use as natural conditions as possible in experiments on
 life history shifts in organisms with complex life cycles in order to
 achieve a correct understanding of these shifts.
description: Śniegula et
 al._dataContains data used for
 analyses in experiment 1 and experiment 2
DOI: 10.5061/dryad.3cs6v
title: Data from: Direct behavioral and neurophysiological evidence for retronasal olfaction in mice

description: The neuroscience of flavor perception is hence becoming increasingly
 important to understand food flavor perception that guides food selection,
 ingestion and appreciation. We recently provided evidence that rats can
 use the retronasal mode of olfaction, an essential element of human flavor
 perception. We showed that in rats, like humans, odors can acquire a
 taste. We and others also defined how the input of the olfactory bulb (OB)
 -not functionally imageable in humans- codes retronasal smell in
 anesthetized rat. The powerful awake transgenic mouse, however, would be a
 valuable additional model in the study of flavor neuroscience. We used a
 go/no-go behavioral task to test the mouse's ability to detect and
 discriminate the retronasal odor amyl acetate. In this paradigm a
 tasteless aqueous odor solution was licked by water-restricted head-fixed
 mice from a lick spout. Orthonasal contamination was avoided. The
 retronasal odor was successfully discriminated by mice against pure
 distilled water in a concentration-dependent manner. Bulbectomy removed
 the mice's ability to discriminate the retronasal odor but not
 tastants. The OB showed robust optical calcium responses to retronasal
 odorants in these awake mice. These results suggest that mice, like rats,
 are capable of smelling retronasally. This direct neuro-behavioral
 evidence establishes the mouse as a useful additional animal model for
 flavor research.
description: Rebello_2014_retronasal
 detection_DryadBehavioral data from
 go-nogo task to determine detestability of retronasal odors by
 mice.
DOI: 10.5061/dryad.n244p
title: Data from: Testing hypotheses of mitochondrial gene-tree paraphyly: unraveling mitochondrial capture of the Streak-breasted Scimitar Babbler (Pomatorhinus ruficollis) by the Taiwan Scimitar Babbler (P. musicus)

description: Species-level paraphyly inferred from mitochondrial gene trees is a
 prevalent phenomenon in taxonomy and systematics, but there are several
 potential causes that are not easily explained by currently used methods.
 The present study aims to test the underlying causes behind the observed
 paraphyly of Streak-breasted Scimitar Babbler (Pomatorhinus ruficollis)
 via statistical analyses of four mitochondrial (mtDNA) and nine nuclear
 (nuDNA) genes. Mitochondrial gene trees show paraphyly of P. ruficollis
 with respect to the Taiwan Scimitar Babbler (P. musicus), but nuclear
 genealogies support a sister-group relationship. Predictive coalescent
 simulations imply several hypothetical explanations, the most likely being
 mitochondrial capture of P. ruficollis by P. musicus for the observed
 cyto-nuclear incongruence. Further Approximate Bayesian Computation
 suggests a unidirectional introgression model with substantial level of
 gene flow from P. ruficollis to P. musicus during their initial divergence
 during the Late Pleistocene. This specific observation frames several
 potential causes for incongruent outcomes of mitochondrial and nuclear
 introgression in general, and on the whole, our results underscore the
 strength of multiple independent loci for species delimitation and
 importance of testing hypotheses that explain disparate causes of
 mitochondrial gene-tree paraphyly.
description: 1.raw sequence dataset
 of nulcear loci2.complete genetypic
 dataset of nuclear loci_for ABC analysis3.partial genetypic
 dataset of nuclear loci_for multilocus network analysis4. partial genetypic
 dataset of nuclear loci for species tree analysis5.dataset for
 evolutionary rate estimation6. mitochondrial raw
 sequences and haplotypic dataset
DOI: 10.5061/dryad.5t55d
title: Data from: Big wigs and small wigs: Time, sex, size and shelter affect cohabitation in the maritime earwig (Anisolabis maritima)

description: Animal aggregations can occur for a variety of abiotic factors, such as
 resource limitation, or biotic factors, including group foraging and
 protection from predators. In our study, we examined whether time, sex,
 body size or shelter availability affected aggregation behavior of the
 maritime earwig, Anisolabis maritima (Order Dermaptera), an insect found
 globally at high densities under driftwood. Specifically, we monitored the
 distribution of two individuals in arenas with either two shelters (no
 habitat limitation) or one shelter (habitat limitation) to determine their
 propensity for cohabitation at times of peak activity and times of
 quiescence. Females, whose high levels of aggression are often associated
 with maternal care, were particularly averse to cohabitation, whereas
 males were generally more tolerant of other earwigs. Females initially
 preferred not to cohabitate when placed with a male, but were more
 tolerant of cohabitation later, regardless of the number of shelters.
 Same-sex pairs, on the other hand, were less likely to cohabitate with
 only one shelter present, but males were again more tolerant of
 conspecifics than females regardless of habitat limitation. When
 competition for one shelter did not lead to cohabitation, the lone
 occupant was more likely to be the larger individual in same-sex trials
 and females in mixed-sex trials. Understanding the tolerance for close
 proximity under these varying conditions may provide insight into
 aggregative behavior and spatial distribution patterns in the maritime
 earwig.
description: HackIyengar2017 - Data
 TablesThis document contains
 tables of the raw numbers for cohabitation among the different
 trials.HackIyengar2017-PLOS_ONE-DataTables(Word).docxHackIyengar2017 - Data FileThis Excel file contains the raw data for cohabitation among the different trials.HackIyengar2017-PLOS_ONE-DataFile(Excel).xlsxHackIyengar2017 - Full GLMThis text file contains the results of the Full GLM analyses based on the data.HackIyengar2017-PLOS_ONE-FullGLM.txtHackIyengar2017 - Final GLMThis text file contains the results of the Final GLM analyses, with non-significant interactions removed, based on the data.HackIyengar2017-PLOS_ONE-FinalGLM.txtHackIyengar2017 - Posthoc TestsThis text file contains the results of the Posthoc (Tukey) tests based on the GLM analyses.HackIyengar2017-PLOS_ONE-PosthocTests.txt
DOI: 10.5061/dryad.898t03g
title: Data from: Soil erodibility differs according to heritable trait variation and nutrient-induced plasticity in the salt marsh engineer Spartina alterniflora

description: Use of landform engineers for habitat restoration has often resulted in
 unanticipated outcomes. It is possible that departures from expectation
 arise because applications do not adequately account for the influence of
 heritable and non-heritable phenotypic variation on ecosystem attributes.
 In this study, we performed a common garden greenhouse experiment to
 determine whether soil shear strength—a characteristic linked to erosion
 resistance—varies according to heritable and plastic trait expression in
 Spartina alterniflora grown under contrasting nutrient regimes. We
 detected heritable variation across a broad spectrum of functional traits,
 including nutrient uptake. We also found that S. alterniflora exhibited
 trait-specific differences in nutrient-induced phenotypic plasticity.
 Heritable trait differences and plasticity together explained
 approximately 70% of the observed variation in soil shear strength. Soil
 shear strength increased when plants received more nutrients, but the
 influence of heritable variation on soil shear strength was equal to or
 larger than that of nutrient-induced plasticity. These findings illustrate
 that heritable and non-heritable trait expression can potentially govern
 the fate of marsh ecosystems, which suggests that consideration should be
 given to both factors when deploying landform engineers for coastal
 restoration.
description: Bernik-et-al-2018_S-alt-Greenhouse-GenoXNutrients-Trait-Soil-Data.csvBucket-level data collected in the greenhouse. See paper for methods and details.Bernik-et-al-2018_S-alt-Greenhouse-GenoXNutrients-ShootSubsampleData.csvShoot-level data sampled from buckets in the greenhouse experiment. See paper for methods and details.Bernik-et-al-2018_S-alt-Greenhouse-MicrosatelliteGenotypeData.csvMicrosatellite genotype data from greenhouse plants. See paper for methods and details.
DOI: 10.5061/dryad.mn6pm
title: Data from: Heterochrony in the evolution of Trinidadian guppy offspring size: maturation along a uniform ontogenetic trajectory

description: The size and maturity of Trinidadian guppy (Poecilia reticulata) offspring
 vary among populations adapted to environments of differential predation.
 Guppy offspring born to low-predation, high-competition environments are
 larger and more mature than their high-predation ancestors. Here we ask:
 what specific changes in developmental or birth timing occur to produce
 the larger, more mature neonates? We collected specimens across the
 perinatal window of development from five populations and quantified
 musculoskeletal maturation. We found that all populations undergo similar
 ontogenetic trajectories in skeletal and muscle acquisition; the only
 difference among populations is when neonates emerge along the trajectory.
 The smallest neonates are born with 20% of their skeleton ossified,
 whereas the largest neonates are born with over 70% of their skeleton
 ossified. The area of the major jaw-closing muscle is relatively larger in
 larger offspring, scaling with length as L2.5. The size range over which
 offspring are birthed among populations sits along the steepest part of
 the size–maturity relationship, which provides a large marginal increase
 in fitness for the high-competition female. Because of the functional
 effects of producing more mature offspring at birth, offspring size may be
 the first and most critical life-history trait selected upon in highly
 competitive environments.
description: Maturity
 Data
DOI: 10.5061/dryad.fb40c
title: Data from: Independent origins of resistance or susceptibility of parasitic wasps to a defensive symbiont

description: Insect microbe associations are diverse, widespread, and influential.
 Among the fitness effects of microbes on their hosts, defense against
 natural enemies is increasingly recognized as ubiquitous, particularly
 among those associations involving heritable, yet facultative, bacteria.
 Protective mutualisms generate complex ecological and co-evolutionary
 dynamics that are only beginning to be elucidated. These depend in part on
 the degree to which symbiont-mediated protection exhibits specificity to
 one or more members of the natural enemy community. Recent findings in a
 well-studied defensive mutualism system (i.e., aphids, bacteria,
 parasitoid wasps) reveal repeated instances of evolution of susceptibility
 or resistance to defensive bacteria by parasitoids. The present study
 searched for similar patterns in an emerging model system for defensive
 mutualisms: the interaction of Drosophila, bacteria in the genus
 Spiroplasma, and wasps that parasitize larval stages of Drosophila.
 Previous work indicated that three divergent species of parasitic wasps
 are strongly inhibited by the presence of Spiroplasma in three divergent
 species of Drosophila, including D. melanogaster. The results of this
 study uncovered two additional wasp species that are susceptible to
 Spiroplasma and two that are unaffected by Spiroplasma, implying at least
 two instances of loss or gain of susceptibility to Spiroplasma among
 larval parasitoids of Drosophila.
description: wasp_protection_round_2_simplified070715This file provides the raw data counts for each replicate (vial).
DOI: 10.5061/dryad.73p8s
title: Data from: Plant defense negates pathogen manipulation of vector behavior

description: 1. Although many vector-borne plant pathogens can alter vector behavior to
 the pathogen's benefit, how plants might counter such manipulation is
 unknown. 2. In the Tomato yellow leaf curl virus (‘TYLCV’)-Bemisia
 tabaci-tomato interaction, TYLCV-mediated changes in Bemisia feeding
 improves viral uptake and transmission. We tested how jasmonic acid
 (‘JA’), a central regulator of plant anti-herbivore defenses, affected the
 ability of TYLCV to (A) manipulate Bemisia behavior; and (B) infect
 plants. 3. Viruliferous Bemisia fed much more than virus-free whiteflies
 on JA-deficient plants, more than virus-free whiteflies on controls, and
 similarly on high-JA plants. 4. When TYLCV was transmitted via whiteflies,
 infection levels were lower in high-JA plants relative to JA-deficient and
 control plants. When TYLCV was transmitted via direct injection,
 JA-overexpressed and JA-deficient plants had similar infection levels. The
 JA-mediated cessation of vector manipulation thus reduced infection and
 lessened pathogen impact. 5. The presence of the JA pathway in many plant
 species suggests that similar interactions may be widespread in nature.
description: Raw data for
 Liu_et_al_manuscript_Functional Ecology_FE-2016-00735This is the full set of
 raw data for Liu et al. manuscript of Functional Ecology_FE-2016-00735. It
 is a package containing 4 Microsoft Excel files.
DOI: 10.5061/dryad.b34d2
title: Data from: Trees as islands: canopy ant species richness increases with the size of liana-free trees in a Neotropical forest

description: The physical characteristics of habitats shape local community structure;
 a classic example is the positive relationship between the size of insular
 habitats and species richness. Despite the high density and proximity of
 tree crowns in forests, trees are insular habitats for some taxa.
 Specifically, crown isolation (i.e. crown shyness) prevents the movement
 of small cursorial animals among trees. Here, we tested the hypothesis
 that the species richness of ants (Sa) in individual, isolated trees
 embedded within tropical forest canopies increases with tree size. We
 predicted that this pattern disappears when trees are connected by lianas
 (woody vines) or when strong interactions among ant species determine tree
 occupancy. We surveyed the resident ants of 213 tree crowns in lowland
 tropical forest of Panama. On average, 9.2 (range = 2–20) ant species
 occupied a single tree crown. Average (± SE) Sa was ca 25% higher in trees
 with lianas (10.2 ± 0.26) than trees lacking lianas (8.0 ± 0.51). Sa
 increased with tree size in liana-free trees (Sa = 10.99A0.256), but not
 in trees with lianas. Ant species composition also differed between trees
 with and without lianas. Specifically, ant species with solitary foragers
 occurred more frequently in trees with lianas. The mosaic-like pattern of
 species co-occurrence observed in other arboreal ant communities was not
 found in this forest. Collectively, the results of this study indicate
 that lianas play an important role in shaping the local community
 structure of arboreal ants by overcoming the insular nature of tree
 crowns.
description: Adams et al 2016
 EcographyPresence-absence data
 for canopy ant species collected from 153 tree crowns in
 Panama
DOI: 10.5061/dryad.f79jb
title: Data from: Shell ornamentation as a likely exaptation: evidence from predatory drilling on Cenozoic bivalves

description: Predation is an important process in modern oceans and in the evolutionary
 history of marine ecosystems. Consequently, it has been hypothesized that
 shelled prey modified their ornamentation in response to predation.
 However, bivalve ornamentation has also been argued to be important in
 maintaining a stable life position in the sediment and in burrowing. To
 test whether concentric ribs were effective against drilling by
 carnivorous gastropods, we examined drill hole position and completeness
 for four Cenozoic bivalve species that differ in rib strength (Astarte
 radiata, A. goldfussi, Lirophora glyptocyma, and L. latilirata). The
 percentage of drill holes located between the ribs increases with
 increasing rib strength, whereas the percentage of drill holes on top of
 ribs decreases. This result suggests that gastropods select the drill hole
 site more effectively as rib strength increases, thereby saving time and
 energy, and that natural selection favors gastropods that select drill
 hole sites between ribs. Because of this greater stereotypy, the
 percentage of drill holes that are incomplete is generally lower in
 strongly ribbed species. The proportion of drill holes located on top of
 ribs is greater for incomplete than complete holes, implying that ribs can
 be effective against predators, but only when selected as the drilling
 location. We show that ribs are most effective against drilling predation
 for bivalves with moderately sized ribs, between which gastropods have
 difficulty siting drill holes. Concentric ribs are unlikely to have
 evolved as an adaptation against drilling predation because concentric
 ribs evolved in the Paleozoic and were already common in the Mesozoic,
 whereas drilling frequency increased later, in the Late
 Cretaceous–Paleogene. Moreover, rib strength of North American Astarte did
 not change through this time interval. Thus, the ribs considered here are
 a likely exaptation to drilling given their effectiveness at deterring
 drilling predation on bivalves with moderate ribs.
description: Supplementary
 TableAstarte spp. and
 Lirophora shell length, completeness of drill hole, outer bore hole
 diameter, and position of drill hole on shell.
DOI: 10.5061/dryad.kb508
title: Data from: A high frequency of allopolyploid speciation in the gymnospermous genus Ephedra and its possible association with some biological and ecological features

description: The origin and evolution of polyploids have been studied extensively in
 angiosperms and ferns but very rarely in gymnosperms. With the exception
 of three species of conifers, all natural polyploid species of gymnosperms
 belong to Ephedra, in which more than half of the species show polyploid
 cytotypes. Here we investigate the origin and evolution of polyploids of
 Ephedra distributed in the Qinghai-Tibetan Plateau (QTP) and neighboring
 areas. Flow cytometry (FCM) was used to measure the ploidy levels of the
 sampled species that are represented by multiple individuals from
 different populations, and then two single-copy nuclear genes (LFY and
 DDB2) and two chloroplast DNA fragments were used to unravel the possible
 origins and maternal donors of the polyploids. The results indicate that
 the studied polyploid species are allopolyploids, and suggest that
 allotetraploidy is a dominant mode of speciation in Ephedra. The high
 percentage of polyploids in the genus could be related to some of its
 biological attributes such as vegetative propagation, a relatively high
 rate of unreduced gamete formation, and a small genome size relative to
 most other gymnosperms. Significant ecological divergences between
 allotetraploids and their putative progenitors were detected by PCA
 analyses and ANOVA and Tukey’s tests, with the exception of E. saxatilis.
 The overlap of geographical distributions and ecological niches of some
 diploid species could have provided opportunities for interspecific
 hybridization and allopolyploid speciation.
description: Alignment of the
 sequences and tree files upload to Dryad_WH_2015_8_7climate
 data
DOI: 10.5061/dryad.4pt8h
title: Data from: Sea level change and the area of shallow-marine habitat: implications for marine biodiversity

description: Analysis of a global elevation database to measure changes in
 shallow-marine habitat area as a function of sea-level reveals an
 unexpectedly complicated relationship. In contrast to prevailing views,
 sea-level rise does not consistently generate an increase in shelf area,
 nor does sea-level fall consistently reduce shelf area. Different
 depth-defined habitats on the same margin will experience different
 changes in area for the same sea-level change, and different margins will
 likewise experience different changes in area for the same sea-level
 change. Simple forward models incorporating a species-area relationship
 suggest that the diversity response to sea-level change will be largely
 idiosyncratic. The change in habitat area is highly dependent on the
 starting position of sea level, the amount and direction of sea-level
 change, and the habitat and region in question. Such an idiosyncratic
 relationship between diversity and sea-level reconciles the widespread
 evidence from the fossil record for a link between diversity and sea-level
 change with the lack of quantitative support for such a relationship
 throughout the Phanerozoic.
description: Supplementary
 MaterialsGMT and R code used in
 extracting and analyzing data.