cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2fk77
title: Data from: Baculovirus infection triggers a positive phototactic response in caterpillars (a response to Dobson et al. Biol Letters 2015).

description: We recently reported that baculovirus Spodoptera exigua multiple
 nucleopolyhedrovirus (SeMNPV) triggers positive phototaxis in Spodoptera
 exigua larvae, leading to death at elevated positions. Dobson et al. [1]
 (University of Stirling, Scotland) question our interpretation of the
 data. Unfortunately, Dobson et al. rely on unwarranted assumptions
 possibly reflecting a poor understanding of baculovirus–insect
 pathobiology, make invalid comparisons and fail to take relevant
 literature into account. Here, we recapitulate the context and
 interpretation of our experiments and highlight the misinterpretations by
 Dobson et al.
description: raw data Figure
 1CHeight (mm) at which
 each individual larva (n=16) was found at the indicated time points. At
 each time point survival was monitored (alive/dead
 =A/D).raw_data_Fig1C.xlsxraw data Figure 1BHeight (mm) at which each individual larva (n=16) was found at the indicated time points . At each time point survival was monitored (alive/dead =A/D).raw_data_Fig1B.xlsxraw_data_Fig1DHeight (mm) at which each individual larva (n=32) was found at the indicated time points. At each time point survival was monitored (alive/dead =A/D).
DOI: 10.5061/dryad.pb4p1
title: Data from: Precipitation alters interactions in a grassland ecological community

description: Climate change is transforming precipitation regimes world-wide. Changes
 in precipitation regimes are known to have powerful effects on plant
 productivity, but the consequences of these shifts for the dynamics of
 ecological communities are poorly understood. This knowledge gap hinders
 our ability to anticipate and mitigate the impacts of climate change on
 biodiversity. Precipitation may affect fauna through direct effects on
 physiology, behaviour or demography, through plant-mediated indirect
 effects, or by modifying interactions among species. In this paper, we
 examined the response of a semi-arid ecological community to a fivefold
 change in precipitation over 7 years. We examined the effects of
 precipitation on the dynamics of a grassland ecosystem in central
 California from 2007 to 2013. We conducted vegetation surveys, pitfall
 trapping of invertebrates, visual surveys of lizards and
 capture–mark–recapture surveys of rodents on 30 plots each year. We used
 structural equation modelling to evaluate the direct, indirect and
 modifying effects of precipitation on plants, ants, beetles, orthopterans,
 kangaroo rats, ground squirrels and lizards. We found pervasive effects of
 precipitation on the ecological community. Although precipitation
 increased plant biomass, direct effects on fauna were often stronger than
 plant-mediated effects. In addition, precipitation altered the sign or
 strength of consumer-resource and facilitative interactions among the
 faunal community such that negative or neutral interactions became
 positive or vice versa with increasing precipitation. These findings
 indicate that precipitation influences ecological communities in multiple
 ways beyond its recognized effects on primary productivity. Stochastic
 variation in precipitation may weaken the average strength of biotic
 interactions over time, thereby increasing ecosystem stability and
 resilience to climate change.
description: Deguines_etal_JAE_carrizoThe table "Deguines_etal_JAE_carrizo.csv" contains the abundance and density data from 2007 to 2013 for the groups considered in our study.Deguines_etal_JAE_linearregressionsThe table "Deguines_etal_JAE_linearregressions.csv" contains the standardized coefficient of each path along with their 95% bias-corrected confidence intervals estimated from the multi-group analysis using the software AMOS 22.0.0 (Arbuckle 2006).Deguines_etal_JAE_scriptFile "Deguines_etal_JAE_script.r" is a script for running analyses in our article with the software R.
DOI: 10.5061/dryad.b34s4
title: Data from: High throughput techniques to reveal the molecular physiology and evolution of digestion in spiders

description: Background: Spiders are known for their predatory efficiency and for their
 high capacity of digesting relatively large prey. They do this by
 combining both extracorporeal and intracellular digestion. Whereas many
 high throughput (“-omics”) techniques focus on biomolecules in spider
 venom, so far this approach has not yet been applied to investigate the
 protein composition of spider midgut diverticula (MD) and digestive fluid
 (DF). Results: We here report on our investigations of both MD and DF of
 the spider Nephilingis (Nephilengys) cruentata through the use of next
 generation sequencing and shotgun proteomics. This shows that the DF is
 composed of a variety of hydrolases including peptidases, carbohydrases,
 lipases and nuclease, as well as of toxins and regulatory proteins. We
 detect 25 astacins in the DF. Phylogenetic analysis of the corresponding
 transcript(s) in Arachnida suggests that astacins have acquired an
 unprecedented role for extracorporeal digestion in Araneae, with different
 orthologs used by each family. The results of a comparative study of
 spiders in distinct physiological conditions allow us to propose some
 digestion mechanisms in this interesting animal taxon. Conclusion: All the
 high throughput data allowed the demonstration that DF is a secretion
 originating from the MD. We identified enzymes involved in the
 extracellular and intracellular phases of digestion. Besides that, data
 analyses show a large gene duplication event in Araneae digestive process
 evolution, mainly of astacin genes. We were also able to identify proteins
 expressed and translated in the digestive system, which until now had been
 exclusively associated to venom glands.
description: ML gene tree of astacins
 from Arachnida taxaNexus file including the
 DNA multiple alignment of astacins across 243 terminals, and the
 respective ML gene tree.MSA_and_TreeFile_Arachnida_Astacins_gene_tree_for_TreeBase.nex
DOI: 10.5061/dryad.f420m4q
title: Data from: The Phylogeny of the Diploporita: a polyphyletic assemblage of blastozoan echinoderms

description: The phylogenetic relationships of Paleozoic blastozoan echinoderms are
 poorly understood and many of the traditionally ascribed groups are likely
 polyphyletic. Diploporitans, those blastozoans with double pore
 (diplopore) respiratory structures, have never been placed within a
 rigorous phylogenetic framework and their highly variable morphologies
 suggest that they do not represent a natural clade. A maximum parsimony
 phylogenetic analysis, spanning a wide range of diploporitan and related
 taxa, indicates that diplopore-bearing blastozoans are a polyphyletic
 grouping and, consequently, that diplopore respiratory structures have
 evolved more than once within the echinoderms. A constraint analyses
 indicate that a single diplopore-bearing clade bearing the traditionally
 defined Glyptosphaeritida, Sphaeronitida, Asteroblastida is less
 parsimonious than multiple diplopore-bearing clades inferred by the
 unconstrained analysis.
description: Supplementary_SheffieldandSumrall_ExplanationofCharactersList of characters used in this analysis with explanations of character statesDataMatrix_SheffieldSumrall_DiploporitaCharacter codings for all specimens used in analysis. Explanations for each character can be found in .docx file within this Dryad repositorycomparision_Noconstraint_Family_templetonCoding for Templeton test comparing forced monophyletic groupings of families within Diploporita against no constraints.Comparison_noConstraint_Diploporita_TempletonCoding for Templeton test comparing forced monophyletic grouping of Diploporita versus no constraints
DOI: 10.5061/dryad.8394
title: Data from: Placentation and maternal investment in mammals

description: The mammalian placenta exhibits striking interspecific morphological
 variation, yet the implications of such diversity for reproductive
 strategies and fetal development remain obscure. More invasive hemochorial
 placentas, in which fetal tissues directly contact the maternal blood
 supply, are believed to facilitate nutrient transfer, resulting in higher
 fetal growth rates, and to be a state of relative fetal advantage in the
 evolution of maternal-offspring conflict. The extent of interdigitation
 between maternal and fetal tissues has received less attention than
 invasiveness but is also potentially important because it influences the
 surface area for exchange. We show that although increased placental
 invasiveness and interdigitation are both associated with shorter
 gestations, interdigitation is the key variable. Gestation times
 associated with highly interdigitated labyrinthine placentas are 44% of
 those associated with less interdigitated villous and trabecular
 placentas. There is, however, no relationship between placental traits and
 neonatal body and brain size. Hence, species with more interdigitated
 placentas produce neonates of similar body and brain size but in less than
 half the time. We suggest that the effects of placental interdigitation on
 growth rates and the way that these are traded off against gestation
 length may be promising avenues for understanding the evolutionary
 dynamics of parent-offspring conflict.
description: Capellini et
 al2011_AmNat_DataCapellini et
 alAmNat_Data.xls
DOI: 10.5061/dryad.876dn
title: Data from: Spatial and temporal drivers of phenotypic diversity in polymorphic snakes

description: Color polymorphism in natural populations presents an ideal opportunity to
 study the evolutionary drivers of phenotypic diversity. Systems with
 striking spatial, temporal, and qualitative variation in color can be
 leveraged to study the mechanisms promoting the distribution of different
 types of variation in nature. We used the highly polymorphic ground snake
 (Sonora semiannulata), a putative coral snake mimic with both cryptic and
 conspicuous morphs, to compare patterns of neutral genetic variation and
 variation over space and time in color polymorphism to investigate the
 mechanistic drivers of phenotypic variation across scales. We found that
 strong selection promotes color polymorphism across spatial and temporal
 scales, with morph frequencies differing markedly between juvenile and
 adult age classes within a single population, oscillating over time within
 multiple populations, and varying drastically over the landscape despite
 minimal population genetic structure. However, we found no evidence that
 conspicuousness of morphs was related to which color pattern was favored
 by selection or to any geographic factors, including sympatry with coral
 snakes. We suggest that complex patterns of phenotypic variation in
 polymorphic systems may be a fundamental outcome of the conspicuousness of
 morphs and that explicit tests of temporal and geographic variation are
 critical to the interpretation of conspicuousness and mimicry.
description: AFLP and phenotypic
 trait allele tableAllele table for 106
 AFLP loci and two phenotypic traits (bands and stripes) for 224 ground
 snakes from central North America. Column headings are locus/trait names
 and rows labels are individual specimens. Datfile created and saved as
 .csv file in Microsoft Excel.CPALFPFINAL.csvAge-class, color pattern, and geographic locationSpecimen information (Specimen number,Year Collected,Country,State,County,Morph,Age Class) for 2380 ground snakes (Sonora semiannulata) from across central and western North America. In the Specimen number column, the letters that begin each specimen number indicate the natural history collection that the snake is from : Arizona State University (ASU), California Academy of Sciences (CAS), Museum of Southwestern Biology at the University of New Mexico (MSB), Museum of Vertebrate Zoology at the University of California (MVZ), New Mexico State University (NMSU), Sam Noble Museum at the University of Oklahoma (OMNH), San Diego Natural History Museum (SDNHM), University of Arizona (UAZ), University of Kansas (KU), , University of Texas – Arlington (UTA), the University of Texas - El Paso (UTEP), and the North American Field Herping Association (NAFHA). All other acronyms represent individual collector numbers for specimens that are not housed in natural history collections. In the Morph column, B=black-banded, M= red-striped and black-banded or mimetic, S=striped and U=uniform. In the Age-class column, J=juvenile and A=adult.Morph Table.csv
DOI: 10.5061/dryad.01ph1
title: Data from: Offspring social network structure predicts fitness in families

description: Social structures such as families emerge as outcomes of behavioural
 interactions among individuals, and can evolve over time if families with
 particular types of social structures tend to leave more individuals in
 subsequent generations. The social behaviour of interacting individuals is
 typically analysed as a series of multiple dyadic (pair-wise)
 interactions, rather than a network of interactions among multiple
 individuals. However, in species where parents feed dependent young,
 interactions within families nearly always involve more than two
 individuals simultaneously. Such social networks of interactions at least
 partly reflect conflicts of interest over the provision of costly parental
 investment. Consequently, variation in family network structure reflects
 variation in how conflicts of interest are resolved among family members.
 Despite its importance in understanding the evolution of emergent
 properties of social organization such as family life and cooperation,
 nothing is currently known about how selection acts on the structure of
 social networks. Here we show that the social network structure of broods
 of begging nestling great tits Parus major predicts fitness in families.
 Although selection at the level of the individual favours large nestlings,
 selection at the level of the kin-group primarily favours families that
 resolve conflicts most effectively.
description: GTs_Individual level
 data_Royle et al_Proc BIndividual level data
 fileGTs_Survival_Future
 RS_Brood Recruitment_Royle et al_Proc BData file on survival
 and future reproductive success of parents and recruitment success of
 broodsGTs_Begging_Feeding_Royle et al_Proc BData file on social network structure, begging behaviour of nestlings in broods and feeding behaviour of parents
DOI: 10.5061/dryad.m78fk
title: Data from: Loss of reproductive parasitism following transfer of male-killing Wolbachia to Drosophila melanogaster and Drosophila simulans

description: Wolbachia manipulates insect host biology through a variety of means that
 result in elevated fitness of infected females, enhancing its own
 transmission. A Wolbachia strain (wInn) naturally infecting D. innubila
 induces male-killing, while native strains of D. melanogaster and D.
 simulans usually induce cytoplasmic incompatibility (CI). In this study,
 we transferred wInn to D. melanogaster and D. simulans by embryonic
 microinjection, expecting conservation of the male-killing phenotype to
 the novel hosts, which are more suitable for genetic analysis. In contrast
 to our expectations, there was no effect on offspring sex ratio.
 Furthermore, no CI was observed in the transinfected flies. Overall,
 transinfected D. melanogaster lines displayed lower transmission rate and
 lower densities of Wolbachia than transinfected D. simulans lines, in
 which established infections were transmitted with near-perfect fidelity.
 In D. simulans, strain wInn had no effect on fecundity and egg to adult
 development. Surprisingly, one of the two transinfected lines tested
 showed increased longevity. We discuss our results in the context of
 host-symbiont co-evolution and the potential of symbionts to invade novel
 host species.
description: Veneti et
 al_Heredity_raw data_30may2012Raw data associated with
 all tables presented in the manuscript
DOI: 10.5061/dryad.sd7vh
title: Data from: On the occurrence of three non-native cichlid species including the first record of a feral population of Pelmatolapia (Tilapia) mariae (Boulenger, 1899) in Europe

description: Thermally influenced freshwater systems provide suitable conditions for
 non-native species of tropical and subtropical origin to survive and form
 proliferating populations beyond their native ranges. In Germany,
 non-native convict cichlids (Amatitlania nigrofasciata) and tilapia
 (Oreochromis sp.) have established populations in the Gillbach, a small
 stream that receives warm water discharge from a local power plant. Here,
 we report on the discovery of spotted tilapia (Pelmatolapia mariae) in the
 Gillbach, the first record of a reproducing population of this species in
 Europe. It has been hypothesized that Oreochromis sp. in the Gillbach are
 descendants of aquaculture escapees and our mtDNA analysis found both O.
 mossambicus and O. niloticus maternal lineages, which are commonly used
 for hybrids in aquaculture. Convict cichlids and spotted tilapia were most
 probably introduced into the Gillbach by aquarium hobbyists. Despite their
 high invasiveness worldwide, we argue that all three cichlid species are
 unlikely to spread and persist permanently beyond the thermally influenced
 range of the Gillbach river system. However, convict cichlids from the
 Gillbach are known to host both native and non-native fish parasites and
 thus, non-native cichlids may constitute threats to the native fish fauna.
 We therefore strongly recommend continuous monitoring of the Gillbach and
 similar systems.
description: Lukas_et_al_tilapia_Gillbach_temperature_dataThis file contains the water temperature data collected at the Gillbach (NRW, Germany) in 2016 and 2017.
DOI: 10.5061/dryad.825ff
title: Data from: Post-metamorphic allometry in the earliest acrotretoid brachiopods from the lower Cambrian (Series 2) of South China, and its implications

description: The earliest growth of post-metamorphic (post-larval) shells in two
 species of Eohadrotreta is described from the Cambrian Shuijingtuo
 Formation of South China. Two different growth patterns can be observed by
 quantifying developmental variations in size and shape of successive
 stages of post-metamorphic shell growth (including the pedicle foramen
 forming stage, pedicle foramen enclosing stage and intertrough increasing
 stage) of Eohadrotreta zhenbaensis and Eohadrotreta? zhujiahensis. The
 pedicle foramen is never enclosed within the metamorphic shell of E.
 zhenbaensis, while the enclosed pedicle foramen of E.? zhujiahensis is
 located directly outside the metamorphic shell after the pedicle foramen
 enclosing stage. A strongly allometric growth pattern of E. zhenbaensis is
 demonstrated by the early enclosure of the pedicle foramen; an accelerated
 lengthening of the ventral intertrough is associated with the development
 of a more complex dorsal median septum during the intertrough increasing
 stage. By contrast, E.? zhujiahensis demonstrates possible paedomorphic
 development by delayed enclosure of pedicle foramen and an associated
 decreased lengthening of ventral intertrough during the intertrough
 increasing stage. This ontogenetic developmental sequence represents the
 marginal accretionary formation and growth of the pedicle foramen, which
 resembles that of linguloid brachiopods. Furthermore, the developmental
 process of the pedicle foramen of Eohadrotreta seems to recapitulate the
 likely evolutionary transition from the Botsfordiidae, with open
 delthyrium, to the Acrotheloidea, with an enclosed foramen. This study
 provides a unique opportunity to obtain a complete understanding of the
 ontogenetic development of the earliest acrotretoids, and casts new light
 on the phylogeny of lingulate brachiopods.
description: Appendix
 S1Average dimensions and
 ratios of ventral valve of Eohadrotreta zhenbaensis from the Cambrian
 (Series 2) Shuijingtuo Formation of the Three Gorges area, South China,
 demonstrating the three ontogenetic development stages
 respectively.Appendix
 S2Average dimensions and
 ratios of ventral and dorsal valves of Eohadrotreta zhenbaensis from the
 Cambrian (Series 2) Shuijingtuo Formation of the Three Gorges area, South
 China, demonstrating the three ontogenetic development stages
 respectively, including the whole ontogenetic development
 stages.Appendix
 S3Average dimensions and
 ratios of ventral valve of Eohadrotreta? zhujiahensis from the Cambrian
 (Series 2) Shuijingtuo Formation of the Three Gorges area, South China,
 demonstrating the three ontogenetic development stages
 respectively.Appendix
 S4Average dimensions and
 ratios of ventral and dorsal valves of Eohadrotreta? zhujiahensis from the
 Cambrian (Series 2) Shuijingtuo Formation of the Three Gorges area, South
 China, including the whole ontogenetic development
 stages.
DOI: 10.5061/dryad.p3378c3
title: Data from: Microscale trait-environment associations in two closely-related South African shrubs

description: Premise of the study: Plant traits are often associated with the
 environments in which they occur, but these associations often differ
 across spatial and phylogenetic scales. Here we study the relationship
 between microenvironment, microgeographical location, and traits within
 populations using co-occurring populations of two closely related
 evergreen shrubs in the genus Protea. Methods: We measured a suite of
 functional traits on 147 plants along a single steep mountainside where
 both species occur, and we used data-loggers and soil analyses to
 characterize the environment at 10 microsites spanning the elevational
 gradient. We used Bayesian path analyses to detect trait-environment
 relationships in the field for each species. We used complementary data
 from greenhouse grown seedlings derived from wild collected seed to
 determine whether associations detected in the field are the result of
 genetic differentiation. Key results: Microenvironmental variables
 differed substantially across our study site. We found strong evidence for
 six trait-environment associations, although these differed between
 species. We were unable to detect similar associations in greenhouse-grown
 seedlings. Conclusions: Several leaf traits were associated with
 temperature and soil variation in the field, but the inability to detect
 these in the greenhouse suggests that differences in the field are not the
 result of genetic differentiation. In compliance with data protection
 regulations, please contact the publication office if you would like to
 have your personal information removed from the database.
description: READMEREADME
 fileHybrid_Trait_DataField-based trait dataHybrid_Envi_DataField environmental dataGreenhouse_DataGreenhouse trait datasrczip folder containing R code and JAGS model files