cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b37h81h1
title: Data from: Use it or lose it: reproductive implications of ecological specialization in a haematophagous ectoparasite

description: Using experimentally induced disruptive selection, we tested two
 hypotheses regarding the evolution of specialization in parasites. The
 ‘trade-off’ hypothesis suggests that adaptation to a specific host may
 come at the expense of a reduced performance when exploiting another host.
 The alternative ‘relaxed selection’ hypothesis suggests that the ability
 to exploit a given host would deteriorate when becoming obsolete. Three
 replicate populations of a flea Xenopsylla ramesis were maintained on each
 of two rodent hosts, Meriones crassus and Dipodillus dasyurus, for nine
 generations. Fleas maintained on a specific host species for a few
 generations substantially decreased their reproductive performance when
 transferred to an alternative host species, whereas they generally did not
 increase their performance on their maintenance host. The results support
 the ‘relaxed selection’ hypothesis of the evolution of ecological
 specialization in haematophagous ectoparasites, while suggesting that
 trade-offs are unlikely drivers of specialization. Further work is needed
 to study the extent by which the observed specializations are based on
 epigenetic or genetic modifications.
description: Egg
 productionEach row represents eggs
 laid by a group of fleas fed simultaneously on the same
 host.Pupation
 successEach row represents a
 clutch of eggs laid at the same day by a group of females fed on the same
 host individualEmergence
 successEach row represents a
 group of papae from the same clutch of eggs laid at the same day by a
 group of females fed on the same host individual
DOI: 10.5061/dryad.sk2nd
title: Data from: Heterologous expression and transcript analysis of gibberellin biosynthetic genes of grasses reveals novel functionality in the GA3ox family.

description: Background: The gibberellin (GA) pathway plays a central role in the
 regulation of plant development, with the 2-oxoglutarate-dependent
 dioxygenases (2-ODDs: GA20ox, GA3ox, GA2ox) that catalyse the later steps
 in the biosynthetic pathway of particularly importance in regulating
 bioactive GA levels. Although GA has important impacts on crop yield and
 quality, our understanding of the regulation of GA biosynthesis during
 wheat and barley development remains limited. In this study we identified
 or assembled genes encoding the GA 2-ODDs of wheat, barley and
 Brachypodium distachyon and characterised the wheat genes by heterologous
 expression and transcript analysis. Results: The wheat, barley and
 Brachypodium genomes each contain orthologous copies of the GA20ox, GA3ox
 and GA2ox genes identified in rice, with the exception of OsGA3ox1 and
 OsGA2ox5 which are absent in these species. Some additional paralogs of
 2-ODD genes were identified: notably, a novel gene in the wheat B genome
 related to GA3ox2 was shown to encode a GA 1-oxidase, named as TaGA1ox-B1.
 This enzyme is likely to be responsible for the abundant 1β-hydroxylated
 GAs present in developing wheat grains. We also identified a related gene
 in barley, located in a syntenic position to TaGA1ox-B1, that encodes a GA
 3,18-dihydroxylase which similarly accounts for the accumulation of
 unusual GAs in barley grains. Transcript analysis showed that some
 paralogs of the different classes of 2-ODD were expressed mainly in a
 single tissue or at specific developmental stages. In particular,
 TaGA20ox3, TaGA1ox1, TaGA3ox3 and TaGA2ox7 were predominantly expressed in
 developing grain. More detailed analysis of grain-specific gene expression
 showed that while the transcripts of biosynthetic genes were most abundant
 in the endosperm, genes encoding inactivation and signalling components
 were more highly expressed in the seed coat and pericarp. Conclusions: The
 comprehensive expression and functional characterisation of the multigene
 families encoding the 2-ODD enzymes of the GA pathway in wheat and barley
 will provide the basis for a better understanding of GA-regulated
 development in these species. This analysis revealed the existence of a
 novel, endosperm-specific GA 1-oxidase in wheat and a related GA
 3,18-dihydroxylase enzyme in barley that may play important roles during
 grain expansion and development.
description: GA3ox_matrixTrimmed, aligned GA3ox protein sequencesGA3ox_treeRooted GA3ox tree in Nexus formatGA20ox_matrixTrimmed, aligned GA20ox protein sequencesGA20ox_treeRooted GA20ox tree in Nexus formatGA2ox_matrixTrimmed, aligned GA2ox protein sequencesGA2ox_treeRooted GA2ox tree in Nexus format
DOI: 10.5061/dryad.f8fk7
title: Data from: Melampyrum sylvaticum as a pre-diapause host plant of the scarce fritillary (Euphydryas maturna) in Finland

description: Background: The scarce fritillary Euphydryas (Hypodryas) maturna (L.) is
 included in the Habitats Directive's Annexes II and IV(a). Therefore,
 it is crucially important to be able to define the habitat and breeding
 places of E. maturna in a correct and unbiased way. New information: Data
 on a previously unknown pre-diapause main host plant, the small cow-wheat
 (Melampyrum sylvaticum L.), of Euphydryas maturna in Finland is presented.
description: Larval nest locations
 and host plants of Euphydryas maturna from Sipoo, S
 FinlandEmaturna_Sipoo_2014.csvLarval nest locations and host plants of Euphydryas maturna from Sipoo, S FinlandEmaturna_Sipoo_2014.xls
DOI: 10.5061/dryad.j3mp2
title: Data from: Segregation of a QTL cluster for home-cage activity using a new mapping method based on regression analysis of congenic mouse strains

description: Recent genetic studies have shown that genetic loci with significant
 effects in whole-genome quantitative trait loci (QTL) analyses were lost
 or weakened in congenic strains. Characterisation of the genetic basis of
 this attenuated QTL effect is important to our understanding of the
 genetic mechanisms of complex traits. We previously found that a consomic
 strain, B6-Chr6CMSM, which carries chromosome 6 of a wild-derived strain
 MSM/Ms on the genetic background of C57BL/6J, exhibited lower home-cage
 activity than C57BL/6J. In the present study, we conducted a composite
 interval QTL analysis using the F2 mice derived from a cross between
 C57BL/6J and B6-Chr6CMSM. We found one QTL peak that spans 17.6 Mbp of
 chromosome 6. A subconsomic strain that covers the entire QTL region also
 showed lower home-cage activity at the same level as the consomic strain.
 We developed 15 congenic strains, each of which carries a shorter
 MSM/Ms-derived chromosomal segment from the subconsomic strain. Given that
 the results of home-cage activity tests on the congenic strains cannot be
 explained by a simple single-gene model, we applied regression analysis to
 segregate the multiple genetic loci. The results revealed three loci (loci
 1–3) that have the effect of reducing home-cage activity and one locus
 (locus 4) that increases activity. We also found that the combination of
 loci 3 and 4 cancels out the effects of the congenic strains, which
 indicates the existence of a genetic mechanism related to the loss of
 QTLs.
description: Data for QTL analysis
 and regression analysisThree spread sheets
 showing data for the QTL analysis and the regression analysis condunted in
 this paper.Data_koide.xlsx
DOI: 10.5061/dryad.67r45
title: Data from: Population admixture and high larval viability among urban toads

description: In terms of evolutionary biology, a population admixture of more than two
 distinct lineages may lead to strengthened genetic variation through
 hybridization. However, a population admixture arising from artificial
 secondary contact poses significant problems in conservation biology. In
 urban Tokyo, a population admixture has emerged from two lineages of
 Japanese common toad: native Bufo japonicus formosus and nonnative B.
 japonicus japonicus, of which the latter was introduced in the early 20th
 century. To evaluate the degree of genetic disturbance in the admixed
 population of these two subspecies, we analyzed genotypes of toads
 distributed within and outside Tokyo by assessing mtDNA and seven
 microsatellite loci. We found that the introduced B. japonicus japonicus
 genotype dominates six local populations in the Tokyo admixture zone and
 was clearly derived from past introgressive hybridization between the two
 subspecies. These observations were supported by morphological
 assessments. Furthermore, the average larval survival rate in Tokyo was
 significantly higher than that outside Tokyo, suggesting that the
 temporary contribution of introduced toads occurred through introgression.
 The fitness of toads in urban Tokyo may thus be increasing with the
 assistance of nonnative individuals.
DOI: 10.15468/dl.9g4vb9
title: Occurrence Download

description: A dataset containing 14711 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Adinetidae, Brachionidae, Gastropodidae, Dicranophoridae, Asplanchnidae, Euchlanidae, Proalidae, Notommatidae, Philodinidae, Collothecidae, Lepadellidae, Conochilidae, Trichocercidae, Epiphanidae, Trochosphaeridae, Flosculariidae, Habrotrochidae, Hexarthridae, Ituridae, Lecanidae, Lindiidae, Mytilinidae, Trichotriidae, Microcodidae, Philodinavidae, Synchaetidae, Testudinellidae, Scaridiidae, Tetrasiphonidae, Centropagidae, Diaptomidae, Cyclopidae, Halicyclopidae, Lernaeidae, Canthocamptidae, Ameiridae, Laophontidae, Phyllognathopodidae, Miraciidae, Ergasilidae, Daphniidae, Moinidae, Bosminidae, Chydoridae, Macrothricidae, Ilyocryptidae, Neothricidae)",
 "Geometry POLYGON ((-181.131592 -37.12775, -187.78141 -33.078885, -189.068184 -33.987495, -186.411552 -37.925243, -192.774353 -44.251839, -195.387383 -46.345032, -192.379532 -48.31083, -188.062592 -45.989329, -183.377609 -41.69727, -180.416107 -38.542795, -181.131592 -37.12775))"
 ]
}

 The dataset includes 14711 records from 34 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001044-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.3q7c9
title: Data from: Bridge under troubled water: turbulence and niche partitioning in fish foraging

description: The coexistence of competing species relies on niche partitioning.
 Competitive exclusion is likely inevitable at high niche overlap, but such
 divide between competitors may be bridged if environmental circumstances
 displace competitor niches to enhance partitioning. Foraging-niche
 dimension can be influenced by environmental characteristics, and if
 competitors react differently to such conditions, coexistence can be
 facilitated. We here experimentally approach the partitioning effects of
 environmental conditions by evaluating the influence of water turbulence
 on foraging-niche responses in two competing fish species, Eurasian perch
 Perca fluviatilis and roach Rutilus rutilus, selecting from planktonic and
 benthic prey. In the absence of turbulence, both fish species showed high
 selectivity for benthic chironomid larvae. R. rutilus fed almost
 exclusively on zoobenthos, whereas P. fluviatilis complemented the benthic
 diet with zooplankton (mainly copepods). In turbulent water, on the other
 hand, the foraging-niche widths of both R. rutilus and P. fluviatilis
 increased, while their diet overlap simultaneously decreased, caused by
 20% of the R. rutilus individuals turning to planktonic (mainly bosminids)
 prey, and by P. fluviatilis increasing foraging on littoral/benthic food
 sources. We show that moderate physical disturbance of environments, such
 as turbulence, can enhance niche partitioning and thereby coexistence of
 competing foragers. Turbulence affects prey but not fish swimming
 capacities, with consequences for prey-specific distributions and
 encounter rates with fish of different foraging strategies (pause-travel
 P. fluviatilis and cruise R. rutilus). Water turbulence and prey community
 structure should hereby affect competitive interaction strengths among
 fish species, with consequences for coexistence probability as well as
 community and system compositions.
description: Water
 qualityPerch
 dietRoach
 diet
DOI: 10.5061/dryad.qv2g5
title: Data from: Beyond species recognition: somatic state affects long distance sex pheromone communication

description: Long-range sex pheromones have been subjected to substantial research with
 a particular focus on their biosynthesis, peripheral perception, central
 processing and the resulting orientation behaviour of perceivers.
 Fundamental to the research on sex attractants was the assumption that
 they primarily coordinate species recognition. However, especially when
 they are produced by the less limiting sex (usually males), the evolution
 of heightened condition dependence might be expected and long-range sex
 pheromones might, therefore, also inform about a signaller's quality.
 Here we provide, to our knowledge, the first comprehensive study of the
 role of a male's long-range pheromone in mate choice that combines
 chemical analyses, video observations and field experiments with a
 multifactorial manipulation of males' condition. We show that the
 emission of the long-distance sex pheromone of the burying beetle,
 Nicrophorus vespilloides is highly condition-dependent and reliably
 reflects nutritional state, age, body size and parasite load—key
 components of an individual's somatic state. Both, the quantity and
 ratio of the pheromone components were affected but the time invested in
 pheromone emission was largely unaffected by a male's condition.
 Moreover, the variation in pheromone emission caused by the variation in
 condition had a strong effect on the attractiveness of males in the field,
 with males in better nutritional condition, of older age, larger body size
 and bearing less parasites being more attractive. That a single pheromone
 is influenced by so many aspects of the somatic state and causes such
 variation in a male's attractiveness under field conditions was
 hitherto unknown and highlights the need to integrate indicator models of
 sexual selection into pheromone research.
description: Data Chemnitz et al Proc
 R SocExcel table contains lab
 and field data on long range sex pheromone communication. The first five
 sheets contain data collected in the lab, the last four sheets data
 collected in the field.Chemnitz et al ProcRSoc data
 dryad.xlsx
DOI: 10.5061/dryad.b6gp8
title: Data from: Outer bark thickness decreases more with height on stems of fire-resistant than fire-sensitive Floridian oaks (Quercus spp.; Fagaceae)

description: Premise of the study: In ecosystems maintained by low-intensity surface
 fires, tree bark thickness is a determinant of fire-survival because it
 protects underlying tissues from heat damage. However, it has been unclear
 whether relatively thick bark is maintained at all heights or only near
 the ground where damage is most likely. Methods: We studied six Quercus
 species from the red and white clades, with three species characteristic
 of fire-maintained savannas and three species characteristic of forests
 with infrequent fire. Inner and outer bark (secondary phloem and
 rhytidome, respectively) thicknesses were measured at intervals from 10 to
 300 cm above the ground. We used linear mixed-effects models to test for
 relationships among height, habitat, and clade on relative thickness (stem
 proportion) of total, inner, and outer bark. Bark moisture and tissue
 density were measured for each species at 10 cm. Key results: Absolute and
 relative total bark thickness declined with height, with no difference in
 height-related changes between habitat groups. Relative outer bark
 thickness showed a height-by-habitat interaction. There was a clade effect
 on relative thickness, but no interaction with height. Moisture contents
 were higher in inner than outer bark, and red oaks had denser bark than
 white oaks, but neither trait differed by habitat. Conclusions: Quercus
 species characteristic of fire-prone habitats invest more in outer bark
 near the ground where heat damage to outer tissues is most likely. Future
 investigations of bark should consider the height at which measurements
 are made and distinguish between inner and outer bark.
description: bark_thickness_dataThis file contains the full dataset of bark thickness measurements.bark_thickness_analysisThis R script produces summary statistics, model fits, and figures for the bark_thickness_data.csv file.
DOI: 10.5061/dryad.rr853
title: Data from: Historical baselines and the future of shell calcification for a foundation species in a changing ocean

description: Seawater pH and the availability of carbonate ions is decreasing due to
 anthropogenic carbon dioxide emissions, posing challenges for calcifying
 marine species. Marine mussels are of particular concern given their role
 as foundation species worldwide. Here, we document shell growth and
 calcification patterns in Mytilus californianus, the California mussel,
 over millennial and decadal scales. By comparing shell thickness across
 the largest modern shells, the largest mussels collected in the
 1960s-1970s and shells from two Native American midden sites (1000-2420
 years BP), we found that modern shells are thinner overall, thinner per
 age category, and thinner per unit length. Thus, the largest individuals
 of this species are calcifying less now than in the past. Comparisons of
 shell thickness in smaller individuals over the past 10-40 years, however,
 do not show significant shell thinning. Given our sampling strategy, these
 results are unlikely to simply reflect within-site variability or
 preservation effects. Review of environmental and biotic drivers known to
 affect shell calcification suggest declining ocean pH as a likely
 explanation for the observed shell thinning. Further future decreases in
 shell thickness could have significant negative impacts on M.
 californianus survival and, in turn, negatively impact the species rich
 complex that occupies mussel beds.
description: Modern_archival_midden_comparison_fig1Mytilus californianus data used in Fig 1 of the ms with measurements of shell dimensions, masses, age, thickness and radiocarbon data, where applicable.Tatoosh_Archival_Small_Myt_californianusMytilus californianus morphological data from Tatoosh Island for modern and archival mussels. These data were used in Figs 2 and 3 of the manuscript.
DOI: 10.5061/dryad.6gb3977
title: Data from: Determining social and population structures requires multiple approaches: a case study of the desert ant Cataglyphis israelensis

description: The remarkable diversity of ant social organization is reflected in both
 their life history and population kin structure. Different species
 demonstrate a high variation with respect to both social structure and
 mating strategies: from the ancestral colony type that is composed of a
 single queen (monogyny), singly inseminated (monoandry), to the more
 derived states of colonies headed by a multiply inseminated queen
 (polyandry), to colonies composed of multiple queens (polygyny) that are
 either singly or multiply inseminated. Moreover, the population structure
 of an ant species can range from multicoloniality to polydomy to
 supercoloniality, and Cataglyphis is considered to be a model genus in
 regard to such diversity. The present study sought to determine the social
 and population structure of the recently described C. israelensis species
 in Israel. For this purpose we employed a multidisciplinary approach,
 rather than the commonly used single approach that is mostly based on
 genetics. Our study encompassed behavior (nest insularity/openness),
 chemistry (composition of nestmate recognition signals, cuticular
 hydrocarbons), and genetics (microsatellite polymorphism). Each approach
 has been shown to possess both advantages and disadvantages, depending on
 the studied species. Our findings reveal that C. israelensis colonies are
 headed by a single, multiply-inseminated queen and that the population
 structure is polydomous, with each colony comprising one main nest and
 several additional satellite nests. Moreover, our findings demonstrate
 that none of the above-noted approaches, when employed individually, is
 suitable or sufficient in itself for delineating population structure,
 thus emphasizing the importance of using multiple approaches when
 assessing such complex systems.
description: C. israelensis genotypes
 from Atlit and HabonimMicrosatellite genotypes
 of all the nests in Atlit and Habonim populations of Cataglyphis
 israelensisall atlit and habonim for
 genepop.txtC_israelensis CHC
 profilesCuticular
 hydrocarbons' composition for samples in Atlit and Habonim;
 Cataglyphis israelensisatlit and habonim nest
 locationsGPS positioning for
 nests of C. israelensis in Atlit and Habonim
DOI: 10.5061/dryad.tf8g2
title: Data from: Effects of microstimulation in the anterior intraparietal area during three-dimensional shape categorization

description: The anterior intraparietal area (AIP) of rhesus monkeys is part of the
 dorsal visual stream and contains neurons whose visual response properties
 are commensurate with a role in three-dimensional (3D) shape perception.
 Neuronal responses in AIP signal the depth structure of disparity-defined
 3D shapes, reflect the choices of monkeys while they categorize 3D shapes,
 and mirror the behavioral variability across different stimulus conditions
 during 3D-shape categorization. However, direct evidence for a role of AIP
 in 3D-shape perception has been lacking. We trained rhesus monkeys to
 categorize disparity-defined 3D shapes and examined AIP's
 contribution to 3D-shape categorization by microstimulating in clusters of
 3D-shape selective AIP neurons during task performance. We find that
 microstimulation effects on choices (monkey M1) and reaction times (monkey
 M1 and M2) depend on the 3D-shape preference of the stimulated site.
 Moreover, electrical stimulation of the same cells, during either the
 3D-shape-categorization task or a saccade task, could affect behavior
 differently. Interestingly, in one monkey we observed a strong correlation
 between the strength of choice-related AIP activity (choice probabilities)
 and the influence of microstimulation on 3D-shape-categorization behavior
 (choices and reaction time). These findings propose AIP as part of the
 network responsible for 3D-shape perception. The results also show that
 the anterior intraparietal cortex contains cells with different tuning
 properties, i.e. 3D-shape- or saccade-related, that can be dynamically
 read out depending on the requirements of the task at hand.
description: Proportion Preferred
 choices Per Coherence for Non-Stimulated trials of
 Monkey1ProportionPreferredResponsePerCoherence_NonStimulated_Monkey1.matProportionPreferredResponsePerCoherence_NonStimulated_Monkey2ProportionPreferredResponsePerCoherence_Stimulated_Monkey1ProportionPreferredResponsePerCoherence_Stimulated_Monkey2Reaction time (RT) for NonPreferred choices Per Coherence for non-Stimulated trials of Monkey1RTNonPreferredResponsePerCoherence_nonStimulated_Monkey1.matRTNonPreferredResponsePerCoherence_nonStimulated_Monkey2RTNonPreferredResponsePerCoherence_Stimulated_Monkey1RTNonPreferredResponsePerCoherence_Stimulated_Monkey2RTPreferredResponsePerCoherence_nonStimulated_Monkey1RTPreferredResponsePerCoherence_nonStimulated_Monkey2RTPreferredResponsePerCoherence_Stimulated_Monkey1RTPreferredResponsePerCoherence_Stimulated_Monkey2Read me