cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5255n
title: Data from: Phylogenetic and biogeographical relationships of the Sander pikeperches (Percidae: Perciformes): patterns across North America and Eurasia

description: North America and Eurasia share several closely related taxa that diverged
 either from the breakup of the Laurasian supercontinent or later closures
 of land bridges. Their modern population structures were shaped in
 Pleistocene glacial refugia and via later expansion patterns, which are
 continuing. The pikeperch genus Sander contains five species – two in
 North America (S. canadensis and S. vitreus) and three in Eurasia
 (S. lucioperca, S. marinus, and S. volgensis) – whose evolutionary
 relationships and relative genetic diversities were previously unresolved,
 despite their fishery importance. This is the first analysis to include
 the enigmatic and rare sea pikeperch S. marinus, nuclear DNA sequences,
 and multiple mitochondrial DNA regions. Bayesian and maximum-likelihood
 trees from three mitochondrial and three nuclear gene regions support the
 hypothesis that Sander diverged from its sister group Romanichthys/Zingel
 ∼24.6 Mya. North American and Eurasian Sander then differentiated ∼20.8
 Mya, with the former diverging ∼15.4 Mya, congruent with North American
 fossils dating to ∼16.3–13.6 Mya. Modern Eurasian species date to ∼13.8
 Mya, with S. volgensis being basal and comprising the sister group to
 S. lucioperca and S. marinus, which diverged ∼9.1 Mya. Genetic diversities
 of the North American species are higher than those in Eurasia, suggesting
 fewer Pleistocene glaciation bottlenecks.
description: Sander_spp_crhaplos_wallout_aln_dryadsubmisMitochondrial control region DNA sequence alignment file for all species of Sander and outgroupsSanderspp_cytbhaplos_wouts_aln_dryadsubMitochondrial cytochrome b gene DNA sequence alignment with all members of the genus Sander and outgroupsSanderspp_coihaplos_wouts_aln_dryadsubMitochondrial cytochrome oxidase subunit 1 (COI) DNA sequence alignment with all members of the genus Sander and outgroupsSanderspp_rag1_wouts_aln_dryadsubNuclear RAG1 DNA sequence alignment with all members of the genus Sander and outgroupsSander_spp_s7_wallout_aln_dryadsubNuclear s7 intron 1 DNA sequence alignment for all members of the genus Sander and outgroupsSander_spp_LdhA6_wallouts_aln_dryadsubNuclear lactate dehydrogenase A intron 6 (LdhA6) DNA sequence alignment for all members of the genus Sander and outgroups
DOI: 10.5061/dryad.b5n38
title: Data from: Physiology at near-critical temperatures, but not critical limits, varies between two lizard species that partition the thermal environment

description: The mechanisms that mediate the interaction between the thermal
 environment and species’ ranges are generally uncertain. Thermal
 environments may directly restrict species when environments exceed
 tolerance limits (i.e. the fundamental niche). However, thermal
 environments might also differentially affect relative performance among
 species prior to fundamental tolerances being met (i.e. the realized
 niche). We examined stress physiology (plasma glucose and corticosterone),
 mitochondrial performance, and the muscle metabolome of congeneric lizards
 that naturally partition the thermal niche, Elgaria multicarinata
 (southern alligator lizards; SAL) and E. coerulea (northern alligator
 lizards; NAL), in response to a thermal challenge to quantify variation in
 physiological performance and tolerance. Both NAL and SAL displayed
 physiological stress in response to high temperature, but neither showed
 signs of irreversible damage. NAL displayed a higher baseline
 mitochondrial respiration rate than SAL. Moreover, NAL substantially
 adjusted their physiology in response to thermal challenge whereas SAL did
 not. For example, the metabolite profile of NAL shifted with changes in
 key energetic molecules, whereas these were unaffected in SAL. Our results
 indicate that near-critical high temperatures should incur greater
 energetic cost in NAL than SAL via an elevated metabolic rate and changes
 to the metabolome. Thus, SAL displace NAL in warm environments that are
 within NAL's fundamental thermal niche, but relatively costly. Our
 results suggest that sub-critical thermal events can contribute to
 biogeographic patterns via physiological differences that alter the
 relative costs of living in warm or cool environments.
description: TelemecoEtAl2017_JAnimEcol_PhysiologyDataData for all physiological analyses and plots presented (e.g. plasma CORT, plasma glucose, mitochondrial respiration rates)TelemecoEtAl2017_JAnimEcol_MetaboliteDataMetabolite concentrations for each individualTelemecoEtAl2017_JAnimEcol_MetaboliteSummarySummary of metabolites for each treatment and species with functional groupings
DOI: 10.5061/dryad.0nd4r91
title: Data from: Interactions between plant defence signalling pathways: evidence from bioassays with insect herbivores and plant pathogens

description: 1. Sequential damage by attackers is hypothesized to result in reciprocal
 antagonism (cross-talk) between jasmonic acid (JA) and salicylic acid (SA)
 defence signalling pathways in plants. However, evidence for this
 cross-talk is not universal and several studies have found positive
 (synergistic) or no interaction whatsoever between JA and SA pathways. 2.
 Here we conducted a meta-analysis of studies on plant-mediated effects of
 initial attackers on performance of subsequent attackers to test the
 hypothesis of cross-talk between plant hormonal signalling pathways.3. We
 found a significant negative mean effect size of JA-inducing initial
 attackers on both JA- and SA-inducing subsequent attackers, but a
 non-significant effect of SA-inducing initial attackers on both JA- and
 SA-inducing subsequent attackers. Effects on subsequent herbivores were
 contingent on the biology of the initial attacker, with negative effects
 of JA-inducing initial herbivores and no effect of SA-inducing initial
 herbivores, whereas pathogens on average did not influence subsequent
 herbivores. Further, negative effects of JA-inducing initial herbivores on
 JA- and SA-inducing subsequent herbivores held when both attacks occurred
 on the same plant part, but when attacks were on different plant parts the
 effect of JA-inducing herbivores on SA-inducing herbivores was
 non-significant. 4. Synthesis. These results indicate that reciprocal
 antagonism between JA and SA pathways is not universal, and suggest
 asymmetry and specificity in plant-mediated interactions.
description: Moreira et
 al_JECOL_2018_Dryad
DOI: 10.5061/dryad.cj3315s
title: Data from: Genotype-by-sex-by-diet interactions for nutritional preference, dietary consumption and lipid deposition in a field cricket

description: Changes in feeding behaviour, especially the over-consumption of calories,
 has led to a rise in the rates of obesity, diabetes and other associated
 disorders in humans and a range of animals inhabiting human-influenced
 environments. However, understanding the relative contribution of genes,
 the nutritional environment and their interaction to dietary intake and
 lipid deposition in the sexes still remains a major challenge. By
 combining nutritional geometry with quantitative genetics, we determined
 the effect of genes, the nutritional environment and their interaction on
 the total nutritional preference (TP), total diet eaten (TE) and lipid
 mass (LM) of male and female black field crickets (Teleogryllus commodus)
 fed one of four diet pairs (DPs) differing in the ratio of protein to
 carbohydrate and total nutritional content. We found abundant additive
 genetic variance for TP, TE and LM in both sexes and across all four DPs,
 with significant genetic correlations between TE and TP and between TP and
 LM in males. We also found significant genotype-by-DP and
 genotype-by-sex-by-DP interactions for each trait and significant
 genotype-by-sex interactions for TE and LM. Complex interactions between
 genes, sex and the nutritional environment, therefore, play an important
 role in nutrient regulation and lipid deposition in T. commodus. This
 finding may also help explain the increasing rate of obesity and the
 maintenance of sex differences in obesity observed across many animal
 species, including humans.
description: Data for Rapkin et al
 2018Genotype, feeding and
 lipid data for Rapkin et al 2018 "Genotype-by-sex-by-diet
 interactions for nutritional preference, dietary consumption and lipid
 deposition in a field cricket". Data includes Sire, Dam, Sex and Diet
 Pair. Cricket body size (mm), total eaten (mg), total preference
 (calculated as total protein/total carbohydrate) and lipid mass
 (mg).HDY-18-A0089R_Rapkin et
 al.xlsx
DOI: 10.5061/dryad.n238t
title: Data from: Evolution and systematics of polyploid Nigritella (Orchidaceae)

description: Members of the orchid genus Nigritella are widespread in European
 mountains, but species circumscriptions and evolutionary patterns in the
 genus are subjects to conflicting opinions. We analyzed a representative
 material of Nigritella for differentiation at nuclear and plastid marker
 loci. In agreement with predictions from embryological studies, diploid
 members of Nigritella are sexual and mostly out-crossing, whereas
 triploid, tetraploid and pentaploid members are apomicts. The diploid taxa
 were poorly differentiated in the investigated molecular markers, except
 for the western N. gabasiana, which was separated in plastid haplotypes.
 Polyploid Nigritella aggregate into three groups and within each of these
 groups apomictic polyploids have given rise to new species. Within the N.
 nigra group, the tetraploid N. nigra ssp. austriaca is somewhat
 differentiated from the triploid ssp. nigra at nuclear as well as plastid
 loci. Fusion of an unreduced egg cell from ssp. nigra with a haploid
 microgamete from Gymnadenia conopsea gave rise to Gymnigritella runei.
 Within the N. widderi group, N. archiducis-joannis is poorly separated
 from N. widderi in molecular markers, and the pentaploid N. buschmanniae
 has evolved by fusion of an unreduced egg cell from N. widderi with a
 haploid microgamete from a diploid Nigritella. Within the N. miniata
 group, N. stiriaca is somewhat differentiated from N. miniata at nuclear
 loci, but no other segregates of N. miniata are supported at species
 level. Polyploid Nigritella species accumulate genetic diversity by
 somatic mutations. In the widespread N. nigra ssp. austriaca and N.
 miniata this diversity is correlated to geography. Although some
 polyploids may be of recent origins, each polyploid contain genetic
 markers no longer encountered in diploid members of the genus. According
 to plastid marker data, Nigritella and Gymnadenia may constitute
 monophyletic sister genera.
description: Appendix 1 Nigritella
 data inds ver 3All genetic data for
 individual accessions of Nigritella, including nuclear microsatellite
 data, plastid haplotype data and ITS type
DOI: 10.5061/dryad.v63g0
title: Data from: Understanding the spatial scale of genetic connectivity at sea: unique insights from a land fish and a meta-analysis

description: Quantifying the spatial scale of population connectivity is important for
 understanding the evolutionary potential of ecologically divergent
 populations and for designing conservation strategies to preserve those
 populations. For marine organisms like fish, the spatial scale of
 connectivity is generally set by a pelagic larval phase. This has
 complicated past estimates of connectivity because detailed information on
 larval movements are difficult to obtain. Genetic approaches provide a
 tractable alternative and have the added benefit of estimating directly
 the reproductive isolation of populations. In this study, we leveraged
 empirical estimates of genetic differentiation among populations with
 simulations and a meta-analysis to provide a general estimate of the
 spatial scale of genetic connectivity in marine environments. We used
 neutral genetic markers to first quantify the genetic differentiation of
 ecologically-isolated adult populations of a land dwelling fish, the
 Pacific leaping blenny (Alticus arnoldorum), where marine larval dispersal
 is the only probable means of connectivity among populations. We then
 compared these estimates to simulations of a range of marine dispersal
 scenarios and to collated FST and distance data from the literature for
 marine fish across diverse spatial scales. We found genetic connectivity
 at sea was extensive among marine populations and in the case of A.
 arnoldorum, apparently little affected by the presence of ecological
 barriers. We estimated that ~5000 km (with broad confidence intervals
 ranging from 810 - 11,692 km) was the spatial scale at which
 evolutionarily meaningful barriers to gene flow start to occur at sea,
 although substantially shorter distances are also possible for some taxa.
 In general, however, such a large estimate of connectivity has important
 implications for the evolutionary and conservation potential of many
 marine fish communities.
description: Microsatsatellite
 DataThe total scored data
 set for all 17 microsatellite loci for Alticus arnoldorum, including
 sample site, latitude and LongitudeMeta-analysis
 DataThis is the data
 collected from each study used in the meta-analysis portion of the above
 publication. For each species data includes; Species, Oder (taxonomy),
 Spatial Pattern (as identified by authors), Number of populations (per
 study), Mean population size (calculated from the number of populations),
 Max Distance (the distance between the two farthest populations), FST for
 Max distance (the corresponding FST score for the two farthest
 populations), Min Distance (the distance between the two closest
 populations), FST for Min Distance (the corresponding, FST score for the
 two closest populations), FST slope (calculated as the the change in FST
 divided by the change in distance), IBD Present/Absent (as identified by
 authors), explanation of spatial pattern (as identified by authors) and
 reference
DOI: 10.5061/dryad.v94n6
title: Data from: Filter-dispersal assembly of lowland Neotropical rainforests across the Andes

description: Numerous Neotropical rainforest species are distributed in both Amazonia
 and Central America, reflecting a rich history of biotic interchange
 between regions. However, some plant lineages are endemic to one region,
 due in part to the dispersal barrier posed by the northern Andean
 cordilleras and adjacent savannas. To investigate the role of
 biogeographic filtering across the northern Andes in regional community
 assembly, we examined environmental tolerances, functional traits, and
 biogeographic distributions of &gt;1000 woody plant species (trees,
 shrubs, lianas) locally co-occurring in forest plots in lowland Panama
 (542 species) and Amazonian Ecuador (667 species). High regional abundance
 was strongly predictive of the probability of being geographically
 widespread (i.e., present on both sides of the Andes). However, we also
 found that species with broad environmental tolerances (those that are
 able to inhabit high elevations and areas of low mean annual
 precipitation) were more likely to have a cross-Andean distribution even
 after accounting for regional abundance, suggesting that biogeographic
 filtering for these traits has mediated cross-Andean dispersal. Regional
 abundance and environmental tolerances were additionally associated with a
 suite of life-history traits related to high dispersal-colonization
 ability, but most traits reflecting dispersal-colonization ability were
 not predictive of biogeographic distribution. Our results highlight how
 the process of biogeographic filtering, based primarily on environmental
 tolerances, has mediated regional-scale floristic assembly of Neotropical
 rainforests. The impacts of this process, which we term filter-dispersal
 assembly, are likely to be especially important to forests in Central
 America, where biotic interchange with Amazonia has heavily influenced
 regional community composition.
description: Species lists and traits
 for Yasuní and BCISpecies lists,
 biogeographic distributions, and environmental traits for woody plant
 species from Yasuní, Ecuador and Barro Colorado Island (BCI), Panama.
 Species lists were derived from 50-ha plots maintained by the Pontificia
 Universidad Católica del Ecuador and the Smithsonian Tropical Research
 Institute Center for Tropical Forest Science. Biogeographic distributions
 and environmental traits (i.e., elevational range, drought tolerance) were
 computed for each species using curated occurrence records from the Global
 Biodiversity Information Facility (GBIF). Trait metadata are provided in
 the first tab of the Excel file.species_lists_and_traits_Bemmels_et_al.xlsx
DOI: 10.5061/dryad.8764
title: Data from: Exploitation of the same trophic link favors convergence of larval life-history strategies in complex life cycle helminths

description: Switching from one host to the next is a critical life history transition
 in parasites with complex life cycles. Growth and mortality rates are
 thought to influence the optimal time and size at transmission, but these
 rates are difficult to measure in parasites. The parasite life cycle, in
 particular the trophic link along which transmission occurs, may be a
 reasonable proxy for these rates, leading to the hypothesis that life
 cycle should shape life history strategy. We compiled data on the size and
 age at infectivity for trophically-transmitted helminths (i.e.
 acanthocephalans, cestodes, and nematodes), and then categorized species
 into trophic links (e.g. planktonic crustaceans to fish, insects to
 terrestrial vertebrates, etc.). Comparative analyses that explicitly
 included stabilizing selection within trophic links fit the data
 significantly better than random walk models, indicating that parasites
 with different life cycles have different optimal times/sizes for host
 switching. The major helminth groups have often independently evolved
 similar life cycles, and we show that this has frequently led to
 convergent and/or parallel evolution of size and age at infectivity. This
 suggests that for particular life cycles there are universal optimal
 transmission strategies, applicable to widely divergent taxa, although the
 cases of parallelism might indicate that lineage-specific constraints
 sometimes prevent evolution to a single adaptive peak.
description: Benesh_etal_dryad_full_datasetBenesh_etal_dryad_species_avgs
DOI: 10.5061/dryad.8dh2m474
title: Data from: Tolerance requires the right smell: first evidence for interspecific selection on chemical recognition cues

description: The integument of insects is generally covered with cuticular hydrocarbons
 (CHC). They serve multiple functions, most prominent among them
 waterproofing and – especially among social insects – as communication
 signal. CHC profiles are incredibly diverse within and across species.
 However, the causes for CHC variation between species, and potential
 selection pressures that may shape CHC profiles, are hardly understood.
 Here, we investigated potential selection pressures on ant CHC. We tested
 the hypotheses that living in association with another species (e.g.,
 parabiosis), and the climate of the ant’s habitat, affect CHC composition.
 We conducted a large-scale comparison of 37 Camponotus species from five
 continents. Our results demonstrate that closely associated ant species
 possess significantly longer hydrocarbons and higher proportions of
 methylbranched alkenes and alkadienes than non- or loosely associated
 species. In contrast, climatic factors had no effects. This study shows
 that the need to be tolerated by another species greatly affects CHC
 profiles.
description: Proportion of substance
 classes in Camponotus speciesProportion of
 hydrocarbon substance classes and hydrocarbon chain length of cuticular
 profiles of Camponotus species. The data set is created using gas
 chromatography/mass spectrometry. Column headings: A - Camponotus species
 names; B - chain length of the hydrocarbons; C - identified substance
 class; D - proportion of the substance class and chain
 length.Raw
 data for Evolution.xls
DOI: 10.5061/dryad.jv7n7
title: Data from: The highs and lows of dispersal: how connectivity and initial population size jointly shape establishment dynamics in discrete landscapes

description: Identifying the main factors driving introduced populations to
 establishment is a major challenge of invasion biology. Due to their small
 initial size, introduced populations are most vulnerable to extinction
 because of demographic stochasticity or Allee effects. While an increase
 in initial population size is known to increase establishment success,
 much remains to be understood regarding its interplay with connectivity in
 spatially structured environments. In order to better understand how
 demographic mechanisms interact at such spatial scale, we developed a
 stochastic model of population dynamics in discrete space to investigate
 the effect of connectivity and initial population size on establishment.
 The predictions derived from the model were then tested using experimental
 introductions of an insect parasitoid (Trichogramma chilonis) in spatially
 structured laboratory microcosms. Both theoretical and experimental
 results demonstrated that the connectivity of the introduction site had 1)
 a deleterious effect in the first generation when the introduced
 population was small and 2) a beneficial impact brought about by
 metapopulation effects in the subsequent generations. Interestingly,
 populations displayed a weakly pushed invasion pattern promoting early
 establishment, which was mainly underpinned by dispersal stochasticity and
 the discrete nature of the landscape. These results shed light on the
 critical influence of landscape connectivity on establishment dynamics.
description: Experimental
 dataExperimental invasion
 dynamics recorded from gen0 (date of introduction) to gen9 (nine
 generations later). The experimental design includes the strain of
 Trichogramma chilonis used (T or R), the initial population size
 (propagule : high or low) and the connectivity level (high or
 low).experimental_data.xlsR simulation scriptScript (in R language) used to perform the simulations described in the article.script.R
DOI: 10.5061/dryad.72n14
title: Data from: Infection of the fittest: devil facial tumour disease has greatest effect on individuals with highest reproductive output

description: Emerging infectious diseases rarely affect all members of a population
 equally and determining how individuals’ susceptibility to infection is
 related to other components of their fitness is critical to understanding
 disease impacts at a population level and for predicting evolutionary
 trajectories. We introduce a novel state-space model framework to
 investigate survival and fecundity of Tasmanian devils (Sarcophilus
 harrisii) affected by a transmissible cancer, devil facial tumour disease.
 We show that those devils that become host to tumours have otherwise
 greater fitness, with higher survival and fecundity rates prior to
 disease-induced death than non-host individuals that do not become
 infected, although high tumour loads lead to high mortality. Our finding
 that individuals with the greatest reproductive value are those most
 affected by the cancer demonstrates the need to quantify both survival and
 fecundity in context of disease progression for understanding the impact
 of disease on wildlife populations.
description: Capture-recapture data
 Tasmanian devils, West Pencil Pine, 2006-2015Capture-recapture data
 from individually marked Tasmanian devils (Sarcophilus harrisii) collected
 between July 2006 and November 2015 from a population in western Tasmania
 (West Pencil Pine, 41°31 S, 145°46 E). Records inlcude information on
 pouch appearance, litter size and tumour load.CaptureData_TasmanianDevil_EcolLett2017.xlsx