cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1f090
title: Data from: Warming alters food web-driven changes in the CO2 flux of experimental pond ecosystems

description: Evidence shows the important role biota play in the carbon cycle, and
 strategic management of plant and animal populations could enhance CO2
 uptake in aquatic ecosystems. However, it is currently unknown how
 management-driven changes to community structure may interact with climate
 warming and other anthropogenic perturbations to alter CO2 fluxes. Here we
 showed that under ambient water temperatures, predators (three-spined
 stickleback) and nutrient enrichment synergistically increased primary
 producer biomass, resulting in increased CO2 uptake by mesocosms in early
 dawn. However, a 3°C increase in water temperatures counteracted positive
 effects of predators and nutrients, leading to reduced primary producer
 biomass and a switch from CO2 influx to efflux. This confounding effect of
 temperature demonstrates that climate scenarios must be accounted for when
 undertaking ecosystem management actions to increase biosequestration.
description: Effects of temperature,
 nutrients and predators on CO2 fluxes and communities in pond
 mesocosmsThis data represents the
 independent and combined effects of increased temperatures (3 C), nutrient
 additions, and addition of predators (Three-Spined Stickelback) to carbon
 dioxide fluxes, primary producers biomass (periphyton + phytoplankton) and
 consumer biomass in pond mesocosms. Responses were measure after 12 and 16
 months from initiation of perturbations. Study took place at the
 University of British Columbia's (Vancouver, Canada) experimental
 pond facility in 2010.Pond
 data.csv
DOI: 10.5061/dryad.dg367
title: Data from: Accuracy of background matching and prey detection: predation by blue tits (Cyanistes caeruleus) indicates intense selection for highly matching prey colour pattern

description: 1. Although background matching decreases prey detectability, resemblance
 between camouflaged prey and their visual background is seldom perfect.
 This could be because even a moderate resemblance might provide sufficient
 protection, and additional adjustment of colour pattern might give little
 benefit. Alternatively, close resemblance to background may not be
 attained due to trade-offs or constraints. To understand selection on
 colour patterns of camouflaged prey and the existence of inaccurate
 background matching, it is necessary to investigate how detectability of a
 colour pattern varies with its resemblance to the background. 2. We
 trained wild-caught blue tits (Cyanistes caeruleus) to search for
 artificial prey. We manipulated the resemblance of the artificial prey
 items to the visual backgrounds. 3. For the first half of the twelve
 repeated prey presentations we found a non-linear relationship between
 resemblance and detectability, such that for prey that had high background
 matching, a change in resemblance resulted in a larger change in
 detectability than an equal change in resemblance did for prey with lower
 background matching. However, for the second half of the presentations
 this relationship was linear. Moreover, in a two-patch-type habitat a prey
 pattern that was a compromise between the two different backgrounds did
 after few initial presentations equally well as the prey pattern that
 matched highly one of the backgrounds. 4. Our results indicate an intense
 selection for close matching in a single background. Yet, in the
 heterogeneous environment that consisted of two backgrounds the
 compromise, which only loosely resembled either background, provided good
 protection. Therefore, we conclude that cryptic colour patterns that bear
 only a loose resemblance to a given background, and thus represent
 inaccurate background matching, may be adaptive outcomes.
description: Search times for
 background-matching preyData on blue tits'
 (Cyanistes caeruleus) search times for artificial, cryptic prey items on
 two different backgrounds (a or b). The colour pattern of the prey
 consisted of 4 black shapes, but the prey differed with respect to how
 closely they resembled the patterning of the two backgrounds. The number
 of elements that match backgrounds a and b are used to describe prey
 appearance. Thus for example 3:1 means that the prey had 3 shapes that
 were found in background a and 1 shape that was found in background b.
 Each of the 70 birds received 12 subsequent presentations of one prey type
 and in one background type only. The data show the 12 search times (in
 seconds) for each individual (s1, s2,...s12).searchtimes.txt
DOI: 10.5061/dryad.vk25n
title: Data from: Sex in an uncertain world: environmental stochasticity helps restore competitive balance between sexually and asexually reproducing populations

description: Like many organisms, individuals of the freshwater ostracod species
 Eucypris virens can have either obligate sexual or asexual reproductive
 modes. Both types of individual routinely co-occur, including in the same
 temporary freshwater pond (their natural habitat in which they undergo
 seasonal diapause). Given the well-known two-fold cost of sex, this begs
 the question of how sexually reproducing individuals are able to co-exist
 with their asexual counterparts in spite of such overwhelming costs.
 Environmental stochasticity in the form of “false dawn” inundations (where
 the first hydration is ephemeral and causes loss of early hatching
 individuals) may provide an advantage to the sexual subpopulation, which
 exhibits greater variation in hatching times following inundation. We
 explore the potential role of environmental stochasticity in this system
 using life-history data analysis, climate data and matrix projection
 models. In the absence of environmental stochasticity, the population
 growth rate is significantly lower in sexual subpopulations. Climate data
 reveal that “false dawn” inundations are common. Using matrix projection
 modeling with and without environmental stochasticity, we demonstrate that
 this phenomenon can restore appreciable balance to the system, in terms of
 growth rates. This provides support for the role of environmental
 stochasticity in helping to explain the maintenance of sex and the
 occurrence of geographic parthenogenesis.
description: ostracod life
 historyOntogenetic survivorship
 and stage duration for Eucypris virens individuals as described in the
 associated article.ostracod.csv
DOI: 10.5061/dryad.727
title: Data from: Phylogenetic hypotheses of the relationships of arthropods to Precambrian and Cambrian problematic fossil taxa

description: A number of Vendian (latest Precambrian) body fossils have traditionally
 been considered arthropods or arthropodlike organisms. Several Cambrian
 "weird wonders" have also been linked with the arthropods.
 However, these relationships are difficult to express in traditional
 Linnean systematics. I present a morphological cladistic analysis of seven
 Vendian "arthropodlike" taxa compared with 21 representative
 Cambrian arthropods, lobopods, and weird wonders. Four arthropods from the
 later Phanerozoic (a pycnogonid, a monuran, and the problematic
 Cheloniellon and Arthropleura), five extant tardigrades, two extant
 kinorhynchs, and an extant priapulid, myriapod, pycnogonid, and
 onychophoran are also included. Monophyly of the Arthropoda is supported,
 but the anomalocarids and their relatives (Anomalopoda) fall out very
 close to the base of the traditional Arthropoda and should be included
 within it. The relationships among arthropods with uniramous appendages
 are not well resolved, but the group does not appear to be monophyletic.
 The biramous arthropods do form a clade and are divided into a
 crustaceanomorph clade and an arachnomorph clade that includes the
 trilobites. Most Vendian arthropodlike fossils form two clades, the
 Vendiamorpha and the Sprigginidae, in the arthropod stem group. The
 Lobopoda is a monophyletic clade with three branches: tardigrades,
 onychophorans, and marine lobopods. An unranked taxonomic scheme is
 proposed for the major clades identified here. There is no compelling
 reason to accept the hypothesis that the Vendian organisms included here
 are not metazoans.
description: Waggoner
 AppendixArthros.nex
DOI: 10.5061/dryad.jf715
title: Data from: The tetrapod fauna of the upper Permian Naobaogou Formation of China: a new species of Elginia (Parareptilia, Pareiasauria)

description: The pareiasaur fossil record in China is poor compared to that of Russia
 or South Africa. A new pareiasaur specimen is here reported from the upper
 Permian Naobaogou Formation of the Daqing Mountains, Nei Mongol, China. It
 is recognized as a new species of Elginia, a taxon otherwise known only
 from the upper Permian Cutties Hillock Sandstone of Scotland. Diagnostic
 features include a moderately developed cheek flange; prominent otic notch
 (formed between squamosal and quadratojugal at the posterior margin of the
 temporal plate); enlarged supraorbital bosses on prefrontal, postfrontal,
 and postorbital; a hypertrophied supratemporal horn, and squamosal horn
 prominently projecting posteriorly from caudal margin of temporal plate.
 The new taxon is differentiated from E. mirabilis by a well-developed and
 crescentic postfrontal boss, which is the largest among a series of
 circumorbital bosses; upper orbital border distinctly domed with a smooth
 rather than angled anterodorsal margin; lesser developed cranial bosses,
 basal confluence of the transverse process and postzygapophysis produces
 at horizontal flange in some dorsal vertebrae. The new discovery
 significantly extends the geographic distribution of Elginia and
 Elginiidae.
description: Revised data matrix used
 in the cladistic analysis of pareiasauromorph
 interrelationshipsThis matrix corresponds
 to the revised characters and character states in this study. ‘?’ denotes
 missing data. Abbreviations: Ba., Bashkyroleter; Br., Bradysaurus; P.,
 Pareiasuchus.LiuBever2018Elginia.tnt
DOI: 10.5061/dryad.sj862
title: Data from: Absence of strong signal of background selection affecting nucleotide diversity in Drosophila pseudoobscura

description: Nucleotide variation correlates positively with regional rates of
 recombination in the genomes of many species, and intensive effort has
 been devoted to deciphering the evolutionary forces driving this
 association. The effects of sweeps associated with the spread of
 advantageous mutations and background selection associated with the
 removal of detrimental mutations are exceedingly hard to decouple. Here,
 we examine patterns of nucleotide variation in a subset of Drosophila
 pseudoobscura genes that are unlikely to have been affected by one extreme
 class of selective sweeps, and test for residual signal that may be
 attributable to background selection. While our statistical power is low
 due to the number of genes fitting our criteria and small numbers of
 sequences, the proportion of variation explained by our tests is extremely
 low and sometimes opposite in direction of predictions of background
 selection. We tentatively conclude that most of the association of
 nucleotide variation with recombination rate in this species is probably
 not attributable to background selection.
description: Raw molecular
 evolutionary parameters used for statisticsMeasures of intron pi
 and Tajima's D from various genes in Drosophila pseudoobscura, used
 to test for associations with coding region Ka/Ks (relative to D.
 miranda), coding region dxy (relative to D. miranda), and recombination
 rate (measured empirically within D. pseudoobscura)BgS_SuppTable1.csvRegression statistics from studyTable indicating regression coefficients, r(2) value, p-value, and sample size for all associations tested in studyBgS_SuppTable2.csv
DOI: 10.5061/dryad.5sh35
title: Data from: A rare study from the wintering grounds provides insight into the costs of malaria infection for migratory birds

description: Malaria parasites can have strong effects on the population dynamics and
 evolution of migratory bird species. In many species, parasite
 transmission occurs on the wintering grounds, but studies to determine the
 consequences of infection have taken place during the breeding season,
 when malaria parasites circulate at chronic levels. We examined the
 predictors of malarial infections for great reed warblers during the
 northern winter in Africa, where active parasite transmission is thought
 to occur and naïve individuals experience acute infections. Counter to
 expectations, we found that winter infection intensities were lower than
 those encountered on the breeding grounds. One potential explanation is
 that reduced immune function during breeding allows parasites to persist
 at higher chronic intensities. We found no relationships between the
 incidence or intensity of infection on condition (as measured by scaled
 mass index, plasma metabolites, and feather corticosterone), spring
 migration departure dates, or home range sizes. We also tested a
 prediction of the Hamilton–Zuk hypothesis and found that male ornament
 (song) quality was unrelated to parasitic infection status. Overall, our
 results provide the first evidence that long-distance migrants captured on
 their wintering grounds are in the chronic stage of infection, and suggest
 that winter studies may fare no better than breeding studies at
 determining the costs of acute malarial infection for great reed warblers.
description: GRW winter malaria
 dataThis file consists of
 data collected from great reed warblers at a Zambian study site.
 Information includes malaria prevalence, lineage, infection intensity,
 individual sex, age (1 = juvenile, 2 = adult), scaled mass index, BUTY,
 TRIG, departure date, whether males sang in Zambia or not, syllable
 repertoire size, and winter territory size (minimum convex
 polygons).
DOI: 10.5061/dryad.cn72p
title: Data from: MHC variation is related to a sexually selected ornament, survival and parasite resistance in common yellowthroats

description: Hamilton and Zuk (1982) proposed that females choose mates based on
 ornaments whose expression is dependent on their genetically based
 resistance to parasites. The Major Histocompatibility Complex (MHC) plays
 an important role in pathogen recognition and is a good candidate for
 testing the relationships between immune genes and both ornament
 expression and parasite resistance. We tested the hypothesis that female
 common yellowthroats prefer to mate with more ornamented males, because it
 is a signal of their MHC-based resistance to parasites and likelihood of
 survival. In this species, females prefer males that have larger black
 facial masks as extra-pair mates. Using pyrosequencing, we found that mask
 size was positively related to the number of different MHC class II
 alleles, as predicted if greater variation at the MHC allows for the
 recognition of a greater variety of pathogens. Furthermore, males with
 more MHC class II alleles had greater apparent survival, and resistance to
 malaria infection was associated with the presence of a particular MHC
 class II allele. Thus, extra-pair mating may provide female warblers with
 immunity genes that are related to parasite resistance, survival and the
 expression of a male ornament, consistent with good genes models of sexual
 selection.
description: Dunn_etal_dataField and molecular data used for analysis. Variable names are described in the ReadMe.txt file.
DOI: 10.5061/dryad.sh8b4
title: Data from: Phylogenetic stability, tree shape, and character compatibility: a case study using early tetrapods

description: Phylogenetic tree shape varies as the evolutionary processes affecting a
 clade change over time. In this study, we examined an empirical phylogeny
 of fossil tetrapods during several time intervals, and studied how
 temporal constraints manifested in patterns of tree imbalance and
 character change. The results indicate that the impact of temporal
 constraints on tree shape is minimal and highlights the stability through
 time of the reference tetrapod phylogeny. Unexpected values of imbalance
 for Mississippian and Pennsylvanian time slices strongly support the
 hypothesis that the Carboniferous was a period of explosive tetrapod
 radiation. Several significant diversification shifts take place in the
 Mississippian and underpin increased terrestrialization among the earliest
 limbed vertebrates. Character incompatibility is relatively high at the
 beginning of tetrapod history, but quickly decreases to a relatively
 stable lower level, relative to a null distribution based on constant
 rates of character change. This implies that basal tetrapods had high, but
 declining, rates of homoplasy early in their evolutionary history,
 although the origin of Lissamphibia is an exception to this trend. The
 time slice approach is a powerful method of phylogenetic analysis and a
 useful tool for assessing the impact of combining extinct and extant taxa
 in phylogenetic analyses of large and speciose clades.
description: characterCompatR script compiled for compatibility test
DOI: 10.5061/dryad.4rt17
title: Data from: Human-caused habitat fragmentation can drive rapid divergence of male genitalia

description: The aim of this study rests on three premises: 1) humans are altering
 ecosystems worldwide, 2) environmental variation often influences the
 strength and nature of sexual selection, and 3) sexual selection is
 largely responsible for rapid and divergent evolution of male genitalia.
 While each of these assertions has strong empirical support, no study has
 yet investigated their logical conclusion that human impacts on the
 environment might commonly drive rapid diversification of male genital
 morphology. We tested whether anthropogenic habitat fragmentation has
 resulted in rapid changes in the size, allometry, shape, and meristics of
 male genitalia in three native species of livebearing fishes (genus:
 Gambusia) inhabiting tidal creeks across six Bahamian islands. We found
 that genital shape and allometry consistently and repeatedly diverged in
 fragmented systems across all species and islands. Using a model selection
 framework, we identified three ecological consequences of fragmentation
 that apparently underlie observed morphological patterns: decreased
 predatory fish density, increased conspecific density, and reduced
 salinity. Our results demonstrate that human modifications to the
 environment can drive rapid and predictable divergence in male genitalia.
 Given the ubiquity of anthropogenic impacts on the environment, future
 research should evaluate the generality of our findings and potential
 consequences for reproductive isolation.
description: Environmental and
 morphological data for all 43 populationsSite means for all
 relevant environmental and morphological variables examined in the
 study.Heinen-Kay et al Evol App all
 site mean data.csv
DOI: 10.5061/dryad.04d0d
title: Data from: MSAP markers and global cytosine methylation in plants: a literature survey and comparative analysis for a wild growing species

description: Methylation of DNA cytosines affects whether transposons are silenced and
 genes are expressed, and is a major epigenetic mechanism whereby plants
 respond to environmental change. Analyses of methylation-sensitive
 amplification polymorphism (MS-AFLP or MSAP) have been often used to
 assess methyl-cytosine changes in response to stress treatments and, more
 recently, in ecological studies of wild plant populations. MSAP technique
 does not require a sequenced reference genome and provides many anonymous
 loci randomly distributed over the genome for which the methylation status
 can be ascertained. Scoring of MSAP data, however, is not straightforward,
 and efforts are still required to standardize this step to make use of the
 potential to distinguish between methylation at different nucleotide
 contexts. Furthermore, it is not known how accurately MSAP infers
 genome-wide cytosine methylation levels in plants. Here, we analyse the
 relationship between MSAP results and the percentage of global cytosine
 methylation in genomic DNA obtained by HPLC analysis. A screening of
 literature revealed that methylation of cytosines at cleavage sites
 assayed by MSAP was greater than genome-wide estimates obtained by HPLC,
 and percentages of methylation at different nucleotide contexts varied
 within and across species. Concurrent HPLC and MSAP analyses of DNA from
 200 individuals of the perennial herb Helleborus foetidus confirmed that
 methyl-cytosine was more frequent in CCGG contexts than in the genome as a
 whole. In this species, global methylation was unrelated to methylation at
 the inner CG site. We suggest that global HPLC and context-specific MSAP
 methylation estimates provide complementary information whose combination
 can improve our current understanding of methylation-based epigenetic
 processes in nonmodel plants.
description: Genome-wide cytosine
 methylation estimates of 200 plants of Helleborus foetidus obtained by
 HPLC and Methylation Scoring of MSAP dataGenome-wide cytosine
 methylation estimates in young leaves of 200 plants of Helleborus foetidus
 obtained using HPLC and the percentage of cytosine methylation in CCGG
 sites obtained by Methylation Scoring of MSAP data. Methylation scoring
 (MS50) was calculated as the percentage of MSAP loci scored as methylated
 (condition II + III).HPLC_MS_data_doi_10.5061_dryad.04d0d.txt
DOI: 10.5061/dryad.8n45g
title: Data from: Song discrimination by nestling collared flycatchers during early development

description: Pre-zygotic isolation is often maintained by species-specific signals and
 preferences. However, in species where signals are learnt, as in
 songbirds, learning errors can lead to costly hybridization. Song
 discrimination expressed during early developmental stages may ensure
 selective learning later in life but can be difficult to demonstrate
 before behavioural responses are obvious. Here, we use a novel method,
 measuring changes in metabolic rate, to detect song perception and
 discrimination in collared flycatcher embryos and nestlings. We found that
 nestlings as early as 7 days old respond to song with increased metabolic
 rate, and, by 9 days old, have increased metabolic rate when listening to
 conspecific when compared with heterospecific song. This early
 discrimination between songs probably leads to fewer heterospecific
 matings, and thus higher fitness of collared flycatchers living in
 sympatry with closely related species.
description: McFarlane_songrecognition_data