cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.nn514kg
title: Data from: Bt rice plants may protect neighbouring non-Bt rice plants against the striped stem borer, Chilo suppressalis

description: The area planted with insect-resistant genetically engineered crops
 expressing Bacillus thuringiensis (Bt) genes has greatly increased in many
 areas of the world. Given the nearby presence of non-Bt crops (including
 those planted as refuges) and non-crop habitats, pests targeted by the Bt
 trait have a choice between Bt and non-Bt crops or weeds, and their host
 preference may greatly affect insect management and management of pest
 resistance to Bt proteins. In this study we examined the oviposition
 preference of the target pest of Bt rice, Chilo suppressalis, for Bt vs.
 non-Bt rice plants as influenced by previous damage caused by C.
 suppressalis larvae. The results showed that C. suppressalis females had
 no oviposition preference for undamaged Bt or non-Bt plants but were
 repelled by conspecific-damaged plants whether Bt or non-Bt. Consequently,
 C. suppressalis egg masses were more numerous on Bt plants than on
 neighbouring non-Bt plants both in greenhouse and in field experiments due
 to the significantly greater conspecific damage on non-Bt plants. We also
 found evidence of poorer performance of C. suppressalis larvae on
 conspecific-damaged rice plants when compared to undamaged plants. GC-MS
 analyses showed that larval damage induced the release of volatiles that
 repelled mated C. suppressalis females in wind tunnel experiments. These
 findings suggest that Bt rice could act as a dead-end trap crop for C.
 suppressalis and thereby protect adjacent non-Bt rice plants. The results
 also indicate that the oviposition behavior of target pest females should
 be considered in the development of Bt resistance management strategies.
description: Wind tunnel-female moth
 preferenceThe results from wind
 tunnel experiments showing preference of females for undamaged or
 caterpillar-damaged Bt or non-Bt riceGreenhouse cage
 experiment-female moth ovipositon preferenceResults from greenhouse
 cage experiments showing oviposition preference of females for undamaged
 or caterpillar-damaged Bt or non-Bt riceFeild experiment-female
 moth ovipositionThe results from a feild
 experiment showing egg densities of C. suppressalis on Bt and non-Bt rice
 under field conditionsField experiment-female moth
 oviposition.xlsFeeding
 bioassy-caterpillar performanceResusts from a feeding
 bioasssay showing performance of caterpillars on damaged rice plants in a
 climate-controlled chamberFeeding bioassay-caterpillar
 performance.xlsGC-MS test-caterpillar
 induced rice volatilesThe results from GC-MS
 test showing volatiles released by rice plants that have been damaged by
 caterpilalr or left intact.GC-MS-caterpillar induced rice
 volatiles.xlsNon-choice wind
 tunnel-response of female males to volatilesThe results from
 non-choice wind tunnel tests showing response of female C. suppressalis to
 caterpillar-induced nocturnal plant volatilesNon-choice wind tunnel-response
 of female moths to volatiles.xls
DOI: 10.5061/dryad.9jj428f
title: Data from: Stochastic character mapping of state-dependent diversification reveals the tempo of evolutionary decline in self-compatible Onagraceae lineages

description: A major goal of evolutionary biology is to identify key evolutionary
 transitions that correspond with shifts in speciation and extinction
 rates. Stochastic character mapping has become the primary method used to
 infer the timing, nature, and number of character state transitions along
 the branches of a phylogeny. The method is widely employed for standard
 substitution models of character evolution. However, current approaches
 cannot be used for models that specifically test the association of
 character state transitions with shifts in diversification rates such as
 state-dependent speciation and extinction (SSE) models. Here we introduce
 a new stochastic character mapping algorithm that overcomes these
 limitations, and apply it to study mating system evolution over a
 time-calibrated phylogeny of the plant family Onagraceae. Utilizing a
 hidden state SSE model we tested the association of the loss of
 self-incompatibility with shifts in diversification rates. Confirming long
 standing theory, we found that self-compatible lineages have higher
 extinction rates and lower net diversification rates compared to
 self-incompatible lineages. Furthermore, these results provide empirical
 evidence for the "senescing" diversification rates predicted in
 highly selfing lineages: our mapped character histories show that the loss
 of self-incompatibility is followed by a short-term spike in speciation
 rates, which declines after a time lag of several million years resulting
 in negative net diversification. Lineages that have long been
 self-compatible such as Fuchsia and Clarkia are in a previously
 unrecognized and ongoing evolutionary decline. Our results demonstrate
 that stochastic character mapping of SSE models is a powerful tool for
 examining the timing and nature of both character state transitions and
 shifts in diversification rates over the phylogeny.
description: Freyman_OnagraceaeThis zip file contains all data and scripts used to perform the analyses in Freyman, W.A. and S. Höhna (2018) "Stochastic character mapping of state-dependent diversification reveals the tempo of evolutionary decline in self-compatible lineages"
DOI: 10.5061/dryad.cg0gn
title: Data from: Developmental environment effects on sexual selection in male and female Drosophila melanogaster

description: The developmental environment can potentially alter the adult social
 environment and influence traits targeted by sexual selection such as body
 size. In this study, we manipulated larval density in male and female
 Drosophila melanogaster, which results in distinct adult size phenotypes -
 high (low) densities for small (large) adults - and measured sexual
 selection in experimental groups consisting of adult males and females
 from high, low, or a mixture of low and high larval densities. Overall,
 large adult females (those reared at low larval density) had more matings,
 more mates and produced more offspring than small females (those reared at
 high larval density). The number of offspring produced by females was
 positively associated with their number of mates (i.e. there was a
 positive female Bateman gradient) in social groups where female size was
 experimentally varied, likely due to the covariance between female
 productivity and mating rate. For males, we found evidence that the larval
 environment affected the relative importance of sexual selection via mate
 number (Bateman gradients), mate productivity, paternity share, and their
 covariances. Mate number and mate productivity were significantly reduced
 for small males in social environments where males were of mixed sizes,
 versus social environments where all males were small, suggesting that
 social heterogeneity altered selection on this subset of males. Males are
 commonly assumed to benefit from mating with large females, but in
 contrast to expectations we found that in groups where both the male and
 female size varied, males did not gain more offspring per mating with
 large females. Collectively, our results indicate sex-specific effects of
 the developmental environment on the operation of sexual selection, via
 both the phenotype of individuals, and the phenotype of their competitors
 and mates.
description: Developmental
 environment effects on sexual selection in Drosophila
 melanogasterThe data is divided into
 three different tabs, according to the experiments performed (see paper).
 For any queries, suggestions or corrections please contact the authors. We
 provide an explanation of the data in the attached
 file.FullDataset-Morimotoet.al2016.xlsx
DOI: 10.5061/dryad.6dd04
title: Data from: Temperature effects on life-history trade-offs, germline maintenance and mutation rate under simulated climate warming

description: Mutation has a fundamental influence over evolutionary processes, but how
 evolutionary processes shape mutation rate remain less clear. In asexual
 unicellular organism, increased mutation rates have been observed in
 stressful environments and the reigning paradigm ascribes this increase to
 selection for evolvability. However, this explanation does not apply in
 sexually reproducing species, where little is known about how the
 environment affects mutation rate. Here we challenged experimental lines
 of seed beetle, evolved at ancestral temperature or under simulated
 climate warming, to repair induced mutations at ancestral and stressful
 temperature. Results show that temperature stress causes individuals to
 pass on a greater mutation load to their grand-offspring. This suggests
 that stress-induced mutation rates, in unicellular and multicellular
 organisms alike, can result from compromised germline DNA repair in low
 condition individuals. Moreover, lines adapted to simulated climate
 warming had evolved increased longevity at the cost of reproduction, and
 this allocation decision improved germline repair. These results suggest
 that mutation rates can be modulated by resource allocation trade-offs
 encompassing life-history traits and the germline and have important
 implications for rates of adaptation and extinction as well as our
 understanding of genetic diversity in multicellular organisms.
description: Raw data, longevity,
 repr effort and mutation loadContains all three data
 files: Sheet 1: F0 male longevity, Sheet 2: F0 Reproductive effort, Sheet
 3: F2 adult offspring counts.Dryad data
 ProcB2017.xlsx
DOI: 10.5061/dryad.f55c5
title: Data from: Nymphalid eyespot serial homologs originate as a few individualized modules

description: Serial homologues are repeated traits that share similar development but
 occur in different parts of the body. Variation in number of repeats
 accounts for substantial diversity in animal form and considerable work
 has focused on identifying the factors accounting for this variation.
 Little is known, however, about how serial homologues originally become
 repeated, or about the relative timing of repeat individuation relative to
 repeat origin. Here, we show that the serially repeated eyespots on
 nymphalid butterfly wings most likely arose as a small cluster of units on
 the ventral hindwing that were later co-opted to the dorsal and anterior
 wing surfaces. Based on comparative analyses of over 400 species, we found
 support for a model of eyespot origin followed by redeployment, rather
 than by the conventional model, where eyespots arose as a complete row of
 undifferentiated units that later gained individuation. In addition,
 eyespots most likely evolved from simpler pattern elements,
 single-coloured spots, which were already individuated among different
 wing sectors. Finally, the late appearance of eyespots on the dorsal,
 hidden wing surface further suggests that these novel complex traits
 originally evolved for one function (thwarting predator attacks) and
 acquired a second function (sexual signalling) when moved to a different
 body location. This broad comparative analysis illustrates how serial
 homologues may initially evolve as a few units serving a particular
 function and subsequently become repeated in novel body locations with new
 functions.
description: Data and phylogenetic
 estimates for Oliver et al. 2014Each NEXUS-formatted
 file includes (1) a phylogenetic estimate of relationships among nymphalid
 butterfly families based on Wahlberg et al. (2009) and (2) a data matrix
 for wing pattern characters.MatricesAndTrees.zip
DOI: 10.5061/dryad.24r7q
title: Data from: Rapid evolution of asymmetric reproductive incompatibilities in stalk-eyed flies

description: The steps by which isolated populations acquire reproductive
 incompatibilities remain poorly understood. One potentially important
 process is postcopulatory sexual selection because it can generate
 divergence between populations in traits that influence fertilization
 success after copulation. Here we present a comprehensive analysis of this
 form of reproductive isolation by conducting reciprocal crosses between
 variably diverged populations of stalk-eyed flies (Teleopsis dalmanni).
 First, we measure seven types of reproductive incompatibility between
 copulation and fertilization. We then compare fertilization success to
 hatching success to quantify hybrid inviability. Finally, we determine if
 sperm competition acts to reinforce or counteract any incompatibilities.
 We find evidence for multiple incompatibilities in most crosses, including
 failure to store sperm after mating, failure of sperm to reach the site of
 fertilization, failure of sperm to fertilize eggs, and failure of embryos
 to develop. Local sperm have precedence over foreign sperm, but this
 effect is due mainly to differences in sperm transfer and reduced hatching
 success. Crosses between recently diverged populations are asymmetrical
 with regard to the degree and type of incompatibility. Because sexual
 conflict in these flies is low, postcopulatory sexual selection, rather
 than antagonistic coevolution, likely causes incompatibilities due to
 mismatches between male and female reproductive traits.
description: Measures of
 noncompetitive gametic isolationResults of paired
 matings between male and female stalk-eyed flies from 4 different
 populations, Gombak, Soraya, Lawang, and Cameron. Columns indicate
 relative divergence between populations (A = within population, B =
 between populations diverged 0.1 MYA, C = populations diverged 0.5 MYA,
 and D = populations diverged 1.0 MYA).Rose&Wilk_reproisoldata.xlsMeasures of competitive gametic isolationSecond male sperm precedence scored from microsatellite genotypes of 10-20 progeny produced by females of a population mated to two males from the same or different population. Populations used are Gombak, Soraya, and Lawang.Rose&Wilk_P2data.xls
DOI: 10.5061/dryad.7pd82
title: Data from: Coexistence and origin of trophic ecotypes of pygmy whitefish, Prosopium coulterii, in southwestern Alaskan lake

description: Ecologically, morphologically, and genetically distinct populations within
 single taxa often co-exist in postglacial lakes and have provided
 important model systems with which to investigate ecological and
 evolutionary processes such as niche partitioning and ecological
 speciation. Within the Salmonidae, these species complexes have been well
 studied, particularly within the Coregonus clupeaformis-C. laveratus (lake
 and European whitefish, respectively) group, but the phenomenon has been
 less well documented in the other whitefish genera, Prosopium and
 Stenodus. Here, we examined the morphology, feeding biology, and genetic
 structure of three putative forms of the pygmy whitefish, Prosopium
 coulterii, that were first reported from Chignik Lake, southwestern
 Alaska, over 40 years ago. Field collections and morphological analyses
 resolved a shallow water (&lt; 5 m depth) low gill raker count form
 (&lt; 15 first arch gill rakers), a deepwater (&gt; 30 m), low
 gill raker form, and a deepwater, high gill raker count (&gt; 15 gill
 rakers) form. The two low gill raker count forms fed almost exclusively on
 benthic invertebrates (mostly chironomids), while the deepwater, high gill
 raker count form fed almost exclusively on zooplankton, differences in
 diet that were also reflected in differences both in δ13C and δ15N stable
 isotopes. All three forms were characterized by the same major
 mitochondrial DNA clade that has been associated with persistence in, and
 postglacial dispersal from, a Beringian glacial refugium. Analysis of
 variation at nine microsatellite DNA loci indicated low, but significant
 differentiation amongst forms, especially between the two low gill raker
 count forms and the high gill raker count form. The extent of
 differentiation along phenotypic (considerable) and genetic (subtle) axes
 amongst the Chignik Lake forms is similar to that found amongst distinct
 taxa of Prosopium found in pre-glacial Bear Lake (Utah-Idaho, USA) which
 is probably at least ten times older than Chignik Lake. Our analyses
 illustrate the potential for the postglacial differentiation in traits
 subject to divergent natural selection across variable environments.
description: microsatellite allele
 frequenciesMicrosatellite DNA
 allele frequencies in base pairsApril113Stomach contentsproportional diet contents (range from 0 - 1.0) for pygmy whitefishdryad.xlsStable isotope dataStable isotope (C, N) for Chignik Lake pygmy whitefish collected in 2008, 2009dryad.xlsdistancesfromlandmarks_dryadlinear distances from landmark data for pygmy whitefish collected 2008, 2009 from Chignik Lake
DOI: 10.25919/dxe8-jz09
title: A Standard Metadata Template For Representing Water Samples

description: This dataset provides a standardised template for representing metadata associated with water samples (including groundwater and surface water) within the CSIRO Mineral Resources Discovery program. The template captures core sample properties such as name, identifier, type, and location, along with related contextual metadata including project details, sampling point information, and key water measurements (e.g. pH and Eh).
The template is implemented within CMR Specify (CMR Discovery Sample Collection Management System) to support the systematic cataloguing of legacy and newly acquired mineral exploration samples. Adoption of this standard reduces redundant metadata entry, improves data integrity, and enhances the curation and discovery of physical samples across the program.
DOI: 10.5061/dryad.rr387
title: Data from: Structure of a mosaic hybrid zone between the field crickets Gryllus firmus and G. pennsylvanicus

description: Hybrid zones provide insight into the nature of species boundaries and the
 evolution of barriers to gene exchange. Characterizing multiple regions
 within hybrid zones is essential for understanding both their history and
 current dynamics. Here, we describe a previously uncharacterized region of
 a well-studied hybrid zone between two species of field crickets, Gryllus
 pennsylvanicus and G. firmus. We use a combination of mitochondrial DNA
 sequencing, morphological data, and modeling of environmental variables to
 identify the ecological factors structuring the hybrid zone and define
 patterns of hybridization and introgression. We find an association
 between species distribution and natural habitat; Gryllus pennsylvanicus
 occupies natural habitat along forest edges and natural clearings, whereas
 G. firmus occupies more disturbed areas in agricultural and suburban
 environments. Hybridization and introgression occur across patch
 boundaries; there is evidence of substantial admixture both in
 morphological characters and mtDNA, over a broad geographic area.
 Nonetheless, the distribution of morphological types is bimodal. Given
 that F1 hybrids are viable and fertile in the lab, this suggests that
 strong pre-zygotic barriers are operating in this portion of the hybrid
 zone.
description: Cricket morphological
 dataMorphological
 measurements for each individual cricket.Individualcricketdata.csvCollecting locality environmental variablesEnvironmental variables for each collecting locality in Pennsylvania.Environmental_Variables.xlsmtDNA SNP genotypesGenotype data for mtDNA SNPs for a subset of crickets from the Pennsylvania hybrid zonemtDNA_genotypes.xlsx
DOI: 10.5061/dryad.1pb6t
title: Data from: Patterns of pollen dispersal in a small population of the Canarian endemic palm (Phoenix canariensis)

description: The genetic diversity of small populations is greatly influenced by local
 dispersal patterns and genetic connectivity among populations, with pollen
 dispersal being the major component of gene flow in many plants species.
 Patterns of pollen dispersal, mating system parameters and spatial genetic
 structure were investigated in a small isolated population of the
 emblematic palm Phoenix canariensis in Gran Canaria island (Canary
 Islands). All adult palms present in the study population (n=182), as well
 as 616 seeds collected from 22 female palms, were mapped and genotyped at
 8 microsatellite loci. Mating system analysis revealed an average of 5.8
 effective pollen donors (Nep) per female. There was strong variation in
 correlated paternity rates across maternal progenies (ranging from null to
 0.9) that could not be explained by the location and density of local
 males around focal females. Paternity analysis revealed a mean effective
 pollen dispersal distance of ~71 m, with ~70% of effective pollen
 originating from a distance of &lt;75 m, and 90% from &lt;200 m. A
 spatially explicit mating model indicated a leptokurtic pollen dispersal
 kernel, significant pollen immigration (12%) from external palm groves and
 a directional pollen dispersal pattern that seems consistent with local
 altitudinal air movement. No evidence of inbreeding or genetic diversity
 erosion was found, but spatial genetic structure was detected in the small
 palm population. Overall, the results suggest substantial pollen dispersal
 over the studied population, genetic connectivity among different palm
 groves and some resilience to neutral genetic erosion and subsequently to
 fragmentation.
description: Genotype data set of
 adults and offspringGenotype_Phoenix_Acusa.xls
DOI: 10.5061/dryad.nj0v4
title: Data from: Contrasting patterns of population structure and gene flow facilitate exploration of connectivity in two widely distributed temperate octocorals

description: Connectivity is an important component of metapopulation dynamics in
 marine systems and can influence population persistence, migration rates
 and conservation decisions associated with Marine Protected Areas (MPAs).
 In this study, we compared the genetic diversity, gene flow and population
 structure of two octocoral species, Eunicella verrucosa and Alcyonium
 digitatum, in the northeast Atlantic (ranging from the northwest of
 Ireland and the southern North Sea, to southern Portugal), using two
 panels of 13 and 8 microsatellite loci, respectively. Our results
 identified regional genetic structure in E. verrucosa partitioned between
 populations from southern Portugal, northwest Ireland and Britain/France;
 subsequent hierarchical analysis of population structure also indicated
 reduced gene flow between southwest Britain and northwest France. However,
 over a similar geographical area, A. digitatum showed little evidence of
 population structure, suggesting high gene flow and/or a large effective
 population size; indeed, the only significant genetic differentiation
 detected in A. digitatum occurred between North Sea samples and those from
 the English Channel/northeast Atlantic. In both species the vast majority
 of gene flow originated from sample sites within regions, with populations
 in southwest Britain being the predominant source of contemporary
 exogenous genetic variants for the populations studied. Overall,
 historical patterns of gene flow appeared more complex, though again
 southwest Britain appeared to be an important source of genetic variation
 for both species. Our findings have major conservation implications,
 particularly for E. verrucosa, a protected species in UK waters and listed
 by the IUCN as ‘Vulnerable’, and for the designation and management of
 European MPAs.
description: Alcyonium digitatum
 microsatellite dataAlcyonium digitatum
 microsatellite data. Excel file. Data for 8 loci in 2 column format, 648
 individuals, 20 sites.Alcyonium_digitatum_Genalex_Heredity.xlsxEunicella verrucosa microsatellite dataEunicella verrucosa microsatellite data. Excel file. Data for 13 loci in 2 column format, 905 individuals, 27 sites.Eunicella_verrucosa_Genalex_Heredity.xlsx