cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d0bq0
title: Data from: Landscape simplification reduces classical biological control and crop yield

description: Agricultural intensification resulting in the simplification of
 agricultural landscapes is known to negatively impact the delivery of key
 ecosystem services such as the biological control of crop pests. Both
 conservation and classical biological control may be influenced by the
 landscape context in which they are deployed; yet studies examining the
 role of landscape structure in the establishment and success of introduced
 natural enemies and their interactions with native communities are
 lacking. In this study, we investigated the relationship between landscape
 simplification, classical and conservation biological control services and
 importantly, the outcome of these interactions for crop yield. We showed
 that agricultural simplification at the landscape scale is associated with
 an overall reduction in parasitism rates of crop pests. Additionally, only
 introduced parasitoids were identified, and no native parasitoids were
 found in crop habitat irrespective of agricultural landscape
 simplification. Pest densities in the crop were lower in landscapes with
 greater proportions of semi natural habitats. Furthermore, farms with less
 semi-natural cover in the landscape and consequently, higher pest numbers,
 had lower yields than farms in less agriculturally dominated landscapes.
 Our study demonstrates the importance of landscape scale agricultural
 simplification in mediating the success of biological control programs and
 highlights the potential risks to native natural enemies in classical
 biological control programs against native insects. Our results represent
 an important contribution to an understanding of the landscape-mediated
 impacts on crop yield which will be essential to implementing effective
 policies that simultaneously conserve biodiversity and ecosystem services.
description: Grab et al. Landscape
 influences pest control and yieldThis data file contains
 site level information on the abundance of the pest Lygus lineolaris, the
 parasitism rates of Lygus nymphs, yield of the focal crop strawberry and
 surrounding land cover at multiple scales for each of three collection
 periods during fruit ripening across 13 farms in the finger lakes region
 of New York State
DOI: 10.5061/dryad.4p2781m
title: Data from: Molecular evidence for the paraphyly of Scolecophidia and its evolutionary implications

description: The phylogenetic relationships between the three main clades of worm
 snakes remain controversial. This question is, however, crucial to
 elucidate the origin of the successful snake radiation, as these burrowing
 and miniaturized wormlike organisms represent the earliest branching
 clades among the snake tree. The present molecular phylogenetic study,
 intended to minimize the amount of missing data, provides fully resolved
 inter-subfamilial relationships among Typhlopidae. It also brings robust
 evidence that worm snakes (Scolecophidia) are paraphyletic, with the
 scolecophidian family Anomalepididae recovered with strong support as
 sister clade to the “typical snakes” (Alethinophidia). Ancestral state
 reconstructions applied to three different traits strongly associated to a
 burrowing life-style (scolecoidy, absence of retinal cones and microstomy)
 provide results in favour of a burrowing origin of snakes, and suggest
 that worm snakes might be the only extant fossorial representatives of
 that primordial snake incursion toward an underground environment.
description: BI tree (chimaeric
 assemblage).nexBI tree (chimaeric
 assemblage)BI tree (without
 chimaeric assemblage)BI tree (without
 chimaeric assemblage)RAxML_bipartitions
 (chimaeric assemblage)RAxML_bipartitions
 (chimaeric assemblage)RAxML_bipartitions (no
 chimaeric assemblage)RAxML_bipartitions (no
 chimaeric assemblage)ASTRAL
 treeASTRAL
 tree
DOI: 10.5061/dryad.47mq9
title: Data from: Fish prey change strategy with the direction of a threat

description: Predation is a fundamental interaction between species, yet it is unclear
 what escape strategies are effective for prey survival. Classical theory
 proposes that prey should either escape in a direction that conforms to a
 performance optimum or that is random and therefore unpredictable. Here,
 we show that larval zebrafish (Danio rerio) instead use a mixed strategy
 that may be either random or directed. This was determined by testing
 classic theory with measurements of the escape direction in response to a
 predator robot. We found that prey consistently escaped in a direction
 contralateral to the robot when approached from the side of the
 prey's body. At such an orientation, the predator appeared in the
 prey's central visual field and the contralateral response was
 consistent with a model of strategy that maximizes the distance from the
 predator. By contrast, when the robot approached the rostral or caudal
 ends of the body, and appeared in the prey's peripheral vision, the
 escape showed an equal probability of a contralateral or ipsilateral
 direction. At this orientation, a contralateral response offered little
 strategic advantage. Therefore, zebrafish larvae adopt an escape strategy
 that maximizes distance from the threat when strategically beneficial and
 that is otherwise random. This sensory-mediated mixed strategy may be
 employed by a diversity of animals and offers a new paradigm for
 understanding the factors that govern prey survival.
description: preyStrategy_kinematicDataKinematic data in Matlab-binary file.
DOI: 10.5061/dryad.5j1k1
title: Data from: Atypical residency of short-beaked common dolphins (Delphinus delphis) to a shallow, urbanized embayment in south-eastern Australia

description: Short-beaked common dolphins (Delphinus delphis) are typically considered
 highly mobile, offshore delphinids. This study assessed the residency of a
 small community of short-beaked common dolphins in the shallow, urbanized
 Port Phillip Bay, south-eastern Australia. The ability to identify common
 dolphins by their dorsal fin markings and coloration using
 photo-identification was also investigated. Systematic and non-systematic
 boat surveys were undertaken between 2007 and 2014. Results showed that 13
 adult common dolphins and their offspring inhabit Port Phillip Bay, of
 which 10 adults exhibit residency to the bay. The majority of these adults
 are reproductively active females, suggesting that female philopatry may
 occur in the community. Systematic surveys conducted between 2012 and 2014
 revealed that the dolphins were found in a median water depth of 16 m and
 median distance of 2.2 km from the coast. The shallow, urbanized habitat
 of this resident common dolphin community is atypical for this species. As
 a result, these common dolphins face threats usually associated with
 inshore bottlenose dolphin communities. We suggest that the Port Phillip
 Bay common dolphin community is considered and managed separate to those
 outside the embayment and offshore to ensure the community's
 long-term viability and residency in the bay.
description: Common dolphin atypical
 residency - location dataExcel spreadsheet of
 sighting information including location, depth and distance to shore of
 resident common dolphin in the Port Phillip embayment, Victoria,
 Australia. Location data collected in field. Depth and distance to shore
 calculated in ArcGIS
DOI: 10.5061/dryad.3ds26
title: Data from: Genetic composition of social groups influences male aggressive behaviour and fitness in natural genotypes of Drosophila melanogaster

description: Indirect genetic effects (IGEs) describe how an individual’s
 behaviour—which is influenced by his or her genotype—can affect the
 behaviours of interacting individuals. IGE research has focused on dyads.
 However, insights from social networks research, and other studies of
 group behaviour, suggest that dyadic interactions are affected by the
 behaviour of other individuals in the group. To extend IGE inferences to
 groups of three or more, IGEs must be considered from a group perspective.
 Here, I introduce the “focal interaction” approach to study IGEs in
 groups. I illustrate the utility of this approach by studying aggression
 among natural genotypes of Drosophila melanogaster. I chose two natural
 genotypes as “focal interactants”: the behavioural interaction between
 them was the “focal interaction.” One male from each focal interactant
 genotype was present in every group, and I varied the genotype of the
 third male—the “treatment male.” Genetic variation in the treatment male’s
 aggressive behaviour influenced the focal interaction, demonstrating that
 IGEs in groups are not a straightforward extension of IGEs measured in
 dyads. Further, the focal interaction influenced male mating success,
 illustrating the role of IGEs in behavioural evolution. These results
 represent the first manipulative evidence for IGEs at the group level.
description: second-order
 IGEsThis file includes all
 data from the paper, Genetic composition of social groups influences male
 aggressive behaviour and fitness in natural genotypes of Drosophila
 melanogaster." The columns "A_col" and "B_col"
 describe which paint color was received by A and B males. Columns labelled
 "X_onpatch" describe whether or not the male was on the patch.
 For example, "A_onpatch" describes whether the A male landed on
 the patch during the 30-minute observation period; if so, a 1 is recorded
 in that column, or a 0 if not. Columns labelled "XatY_lunge"
 describe the number of times that the genotype X male lunged at the
 genotype Y male. For example, the column labelled "AatB_lunge"
 records the number of times that the A male lunged at the B male during
 the 30-minute observation period.data for
 dryad.xlsx
DOI: 10.5061/dryad.p4sk4
title: Data from: Sexual selection of male parental care in giant water bugs

description: Paternal care can be maintained under sexual selection, if it helps in
 attracting more mates. We tested the hypothesis in two giant water bug
 species, Appasus major and Appasus japonicus, that male parental care is
 sexually selected through female preference for caring males. Females were
 given an opportunity to choose between two males. In the first test of
 female mate choice, one male carried eggs on its back, while the other did
 not. The egg status was switched between these two males in the second
 test. The experiment revealed that females of both species preferred
 caring males (i.e. egg-bearing) to non-caring males. Nonetheless, the
 female mate preference for egg-bearing males was stronger in A. major than
 in A. japonicus. Our results suggest that sexual selection plays an
 important role in maintaining elaborate paternal care in giant water bugs,
 but the importance of egg-bearing by males in female mate choice varies
 among species.
description: ohba_RSOS_data
DOI: 10.5061/dryad.sd1hf16
title: Data from: Anther rubbing, a new mechanism that actively promotes selfing in plants

description: Self-fertilization has recurrently evolved in plants, involving different
 strategies and traits, often involving loss of attractive functions,
 collectively known as the selfing syndrome. However, few traits have been
 described that actively promote self-fertilization. Here we describe a
 novel mechanism promoting self-fertilization in the Brassicaceae species
 Erysimum incanum. This mechanism, which we called anther rubbing, consists
 of autonomous, repeated, and coordinated movements of the stamens over the
 stigma during flower opening. We have documented anther rubbing by
 time-lapse videos and experimentally show that it causes self-pollen
 deposition on stigmas and is sufficient to achieve maximal reproductive
 output in E. incanum. We predict that these movements should occur in
 species with limited inbreeding depression, and indeed we find that
 inbreeding depression in seed production is negligible in this species.
 While many studies have documented complex floral traits that promote
 outcrossing, the occurrence of anther rubbing demonstrates that plants can
 evolve elaborate and under-appreciated adaptations to promote
 self-fertilization.
description: Controlled-crosses_Anther rubbingResults of controlled crosses experiments
DOI: 10.5061/dryad.p9t05
title: Data from: Mother and offspring fitness in an insect with maternal care: phenotypic trade-offs between egg number, egg mass and egg care

description: Background: Oviparous females have three main options to increase their
 reproductive success: investing into egg number, egg mass and/or egg care.
 Although allocating resources to either of these three components is known
 to shape offspring number and size, potential trade-offs among them may
 have key impacts on maternal and offspring fitness. Here, we tested the
 occurrence of phenotypic trade-offs between egg number, egg mass and
 maternal expenditure on egg care in the European earwig, Forficula
 auricularia, an insect with pre- and post-hatching forms of maternal care.
 In particular, we used a series of laboratory observations and experiments
 to investigate whether these three components non-additively influenced
 offspring weight and number at hatching, and whether they were associated
 with potential costs to females in terms of future reproduction. Results:
 We found negative associations between egg number and mass as well as
 between egg number and maternal expenditure on egg care. However, these
 trade-offs could only be detected after statistically correcting for
 female weight at egg laying. Hatchling number was not determined by single
 or additive effects among the three life-history traits, but instead by
 pairwise interactions among them. In particular, offspring number was
 positively associated with the number of eggs only in clutches receiving
 high maternal care or consisting of heavy eggs, and negatively associated
 with mean egg mass in clutches receiving low care. In contrast, offspring
 weight was positively associated with egg mass only. Finally, maternal
 expenditure on egg care reduced their future reproduction, but this effect
 was only detected when mothers were experimentally isolated from their
 offspring at egg hatching. Conclusions: Overall, our study reveals
 simultaneous trade-offs between the number, mass and care of eggs. It also
 demonstrates that these factors interact in their impact on offspring
 production, and that maternal expenditure on egg care possibly shapes
 female future reproduction. These findings emphasize that studying
 reproductive success requires consideration of phenotypic trade-offs
 between egg-number, egg mass and egg care in oviparous species.
description: Full data
 setFull data
 setData set
 DRYAD.xlsx
DOI: 10.5061/dryad.p9v3q
title: Data from: Female density-dependent chemical warfare underlies fitness effects of group sex ratio in flour beetles

description: In animals, skewed sex ratios can affect individual fitness either via
 sexual (e.g. intersexual conflict or intrasexual mate competition) or
 non-sexual interactions (e.g. sex-specific resource competition). Because
 most analyses of sex ratio focus on sexual interactions, the relative
 importance of sexual vs. non-sexual mechanisms remains unclear. We tested
 both mechanisms in the flour beetle Tribolium castaneum, where male-biased
 sex ratios increase female fitness relative to unbiased or female-biased
 groups. Although flour beetles show both sexual and non-sexual (resource)
 competition, we found that sexual interactions did not explain female
 fitness. Instead, female fecundity was dramatically reduced even after a
 brief exposure to flour conditioned by other females. Earlier studies
 suggested that secreted toxins might mediate density-dependent population
 growth in flour beetles. We identified ethyl- and methyl- benzoquinone
 (EBQ and MBQ; “quinones”), as components of adult stink glands that
 regulate female fecundity. In female-biased groups (i.e. at high female
 density), females upregulated quinones and suppressed each other’s
 reproduction. In male-biased groups, low female density and associated low
 quinone levels maximized fecundity. Thus, females appear to use quinones
 as weapons for female-specific, density-dependent interference
 competition. Our results underscore the importance of non-sexual
 interference competition that may often underlie the fitness consequences
 of skewed sex ratios.
description: KhanEtal_AmNat_AllDataFilesRaw data for all figures in the manuscriptAllDataFiles.zip
DOI: 10.5061/dryad.351qg
title: Data from: Evolving from static to dynamic signals: evolutionary compensation between two communicative signals

description: Signals that convey related information may impose selection on each
 other, creating evolutionary links between different components of the
 communicative repertoire. Here, we ask about the consequences of the
 evolutionary loss of one signal (a colour patch) on another (a motion
 display) in Sceloporus lizards. We present data on male lizards of four
 species: two pairs of sister taxa representing two independent
 evolutionary losses of the static colour patch (S. cozumelae and S.
 parvus; S. siniferus and S. merriami). Males of the two species that have
 undergone an evolutionary loss of blue-belly patches (S. cozumelae, S.
 siniferus) were less active than their blue-bellied sister taxa (S.
 parvus, S. merriami), consistent with the suggestion that the belly
 patches were lost to reduce conspicuousness of species with high predation
 pressure. In contrast, the headbob display appears to have become more,
 rather than less, conspicuous over evolutionary time. The colour patch is
 exhibited primarily during aggressive encounters, whereas headbob displays
 are multifunction signals used in several different contexts, including
 aggressive encounters. Males of species that have lost the colour patch
 produced more motion displays, and the structure of those motion displays
 were more similar to those produced during combat. In both evolutionary
 episodes, a static colour signal appears to have been replaced by dynamic
 motion displays that can be turned off in the presence of predators and
 other unwanted receivers. The predominant pattern is one of evolutionary
 compensation and interactions between multiple signals that convey related
 information.
description: Martins et al 2015. Raw
 data.Behavioral data for four
 species of Sceloporus lizards.Martins et al
 Dynamic.csv
DOI: 10.5061/dryad.20cp7
title: Data from: Inferring species interactions in ecological communities: a comparison of methods at different levels of complexity

description: 1. Natural communities commonly contain many different species and
 functional groups, and multiple types of species interactions act
 simultaneously, such as competition, predation, commensalism or mutualism.
 However, experimental and theoretical investigations have generally been
 limited by focusing on one type of interaction at a time or by a lack of a
 common methodological and conceptual approach to measure species
 interactions. 2. We compared four methods to measure and express species
 interactions. These approaches are, with increasing degree of model
 complexity, an extinction-based model, a relative yield model and two
 generalized Lotka-Volterra (LV) models. All four approaches have been
 individually applied in different fields of community ecology, but rarely
 integrated. We provide an overview of the definitions, assumptions and
 data needed for the specific methods and apply them to empirical data by
 experimentally deriving the interaction matrices among 11 protist and
 rotifer species, belonging to three functional groups. Furthermore, we
 compare their advantages and limitations to predict multispecies community
 dynamics and ecosystem functioning. 3. The relative yield method is, in
 terms of final biomass production, the best method in predicting the
 11-species community dynamics from the pairwise competition experiments.
 The LV model, which is considering equilibrium among the species, suffers
 from experimental constraints given the strict equilibrium assumption, and
 this may be rarely satisfied in ecological communities. 4. We show how
 simulations of a LV stochastic community model, derived from an empirical
 interaction matrix, can be used to predict multispecies community dynamics
 across multiple functional groups. 5. Our work unites available tools to
 measure species interactions under one framework. This improves our
 ability to make management-oriented predictions of species
 coexistence/extinction and to compare ecosystem processes across study
 systems.
description: Interaction Matrices for
 the four different methodsThe excel file contains
 four tables corresponding to the interaction matrices, as in figure 2 of
 the associated publication. They are extracted with the four different
 methods ('EX'= extinction; 'RY'=Relative Yield;
 'EQ'= Lotka-Volterra equilibrium; 'LVD'=Lotka-Volterra
 dynamics). Species codes as in figure 2.Interaction_Matrices.xlsx
DOI: 10.5061/dryad.541g6
title: Data from: Signaling cascades and the importance of moonlight in coral broadcast mass spawning

description: Many reef-building corals participate in a mass-spawning event that occurs
 yearly on the Great Barrier Reef. This coral reproductive event is one of
 earth's most prominent examples of synchronised behavior, and coral
 reproductive success is vital to the persistence of coral reef ecosystems.
 Although several environmental cues have been implicated in the timing of
 mass spawning, the specific sensory cues that function together with
 endogenous clock mechanisms to ensure accurate timing of gamete release
 are largely unknown. Here, we show that moonlight is an important external
 stimulus for mass spawning synchrony and describe the potential mechanisms
 underlying the ability of corals to detect environmental triggers for the
 signaling cascades that ultimately result in gamete release. Our study
 increases the understanding of reproductive chronobiology in corals and
 strongly supports the hypothesis that coral gamete release is achieved by
 a complex array of potential neurohormones and light-sensing molecules.
description: Perl script that maps
 SAM reads to known Acropora genesThis perl script parse
 the output of TopHat alignment software (Trapnell et al., Bioinformatics,
 2009), which is given in the Sequence Alignment/Map (SAM) format
 (http://samtools.sourceforge.net/), and convert it into the raw number of
 reads aligned to each Acropora genemap_sam_reads_to_known_genes_rmdup.pl
DOI: 10.5061/dryad.p100g
title: Data from: Forward genetic screening for regulators involved in cholesterol synthesis using validation-based insertional mutagenesis

description: Somatic cell genetics is a powerful approach for unraveling the regulatory
 mechanism of cholesterol metabolism. However, it is difficult to identify
 the mutant gene(s) due to cells are usually mutagenized chemically or
 physically. To identify important genes controlling cholesterol
 biosynthesis, an unbiased forward genetics approach named validation-based
 insertional mutagenesis (VBIM) system was used to isolate and characterize
 the 25-hydroxycholesterol (25-HC)-resistant and SR-12813-resisitant
 mutants. Here we report that five mutant cell lines were isolated. Among
 which, four sterol-resistant mutants either contain a truncated
 NH2-terminal domain of sterol regulatory element-binding protein (SREBP)-2
 terminating at amino acids (aa) 400, or harbor an overexpressed SREBP
 cleavage-activating protein (SCAP). Besides, one SR-12813 resistant mutant
 was identified to contain a truncated COOH-terminal catalytic domain of
 3-hydroxy-3-methylglutaryl-coenzyme A reductase (HMG-CoA reductase). This
 study demonstrates that the VBIM system can be a powerful tool to screen
 novel regulatory genes in cholesterol biosynthesis.
description: SL-4 genome
 sequenceGene locus of SCAP in
 SL-4 mutant. This sequence is related to Fig.3SL-4 genome
 seq.docx