cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g23j32s
title: Data from: Large‐scale molecular diet analysis in a generalist marine mammal reveals male preference for prey of conservation concern

description: Sex‐specific diet information is important in the determination of
 predator impacts on prey populations. Unfortunately, the diet of males and
 females can be difficult to describe, particularly when they are marine
 predators. We combined two molecular techniques to describe haul‐out use
 and prey preferences of male and female harbor seals (Phoca vitulina) from
 Comox and Cowichan Bay (Canada) during 2012–2013. DNA metabarcoding
 quantified the diet proportions comprised of prey species in harbor seal
 scat, and qPCR determined the sex of the individual that deposited each
 scat. Using 287 female and 260 male samples, we compared the monthly sex
 ratio with GLMs and analyzed prey consumption relative to sex, season,
 site, and year with PERMANOVA. The sex ratio between monthly samples
 differed widely in both years (range = 12%–79% males) and showed different
 patterns at each haul‐out site. Male and female diet differed across both
 years and sites: Females consumed a high proportion of demersal fish
 species while males consumed more salmonid species. Diet composition was
 related to both sex and season (PERMANOVA: R2 = 27%, p &lt; 0.001; R2
 = 24%, p &lt; 0.001, respectively) and their interaction (PERMANOVA:
 R2 = 11%, p &lt; 0.001). Diet differences between males and females
 were consistent across site and year, suggesting fundamental foraging
 differences, including that males may have a larger impact on salmonids
 than females. Our novel combination of techniques allowed for both prey
 taxonomic and spatiotemporal resolution unprecedented in marine predators.
description: Sex of depositor and
 diet proportions for individual scat samplesThe file lists the sex
 of the scat depositor, individual sample ID, sampling month, sampling
 season, sampling year, and sampling site, as well as the diet proportions
 of different prey species (in %) for each individual sample used in the
 study. Salmonid prey species proportions are listed separately for
 juvenile and adult salmon. The columns with prey species diet proportions
 are followed by columns showing diet proportions by order (for fish) or
 higher taxonomic level for invertebrates (Crustacea and
 Cephalopoda).Data accessibility file for
 Dryad.csv
DOI: 10.5061/dryad.1005
title: Data from: Nitrate reductase phylogeny of potato (Solanum sect. Petota) genomes with emphasis on the origins of the polyploid species

description: Solanum section Petota is taxonomically difficult, partly because of
 interspecific hybridization at both the diploid and polyploid levels.
 There is much disagreement regarding species boundaries and affiliation of
 species to series. Elucidating the phylogenetic relationships within the
 polyploids is crucial for an effective taxonomic treatment of the section
 and for the utilization of wild potato germplasm in breeding programs. We
 here infer relationships among the potato diploids and polyploids using
 nitrate reductase (NIA) sequence data in comparison to prior plastid
 phylogenies and: 1) examine genome types within section Petota, 2) show
 species in the polyploid series Conicibaccata, Longipedicellata, and in
 the Iopetalum group to be derived from allopolyploidization, 3) support an
 earlier hypothesis by confirming S. verrucosum as the maternal genome
 donor for the polyploid species S. demissum as well as species in the
 Iopetalum Group, 4) demonstrate that S. verrucosum is the closest relative
 to the maternal genome donor for species in ser. Longipedicellata, 5)
 support the close relationship between S. acaule and diploid species from
 series Megistacroloba and Tuberosa, and 6) show the North and Central
 American B genome species to be well distinguished from the A genome
 species of South America.
description: Supplementary Figures
 1-4SUPPLEMENTARY FIGURE 1.
 Maximum likelihood phylogram for diploid species. SUPPLEMENTARY FIGURE 2.
 Bayesian phylogram of diploid species. SUPPLEMENTARY FIGURE 3. Strict
 consensus of 9482 equal-length trees (L=712, CI=0.680, RI=0.846) of
 diploid and polyploid species. SUPPLEMENTARY FIGURE 4. Maximum likelihood
 phylogram of diploid and polyploid species.Rodriguez SystBot vol 34 p 207
 suppl figs. 1-4.pdf
DOI: 10.5061/dryad.558
title: Data from: More taxa or more characters revisited: combining data from nuclear protein-encoding genes for phylogenetic analyses of Noctuoidea (Insecta: Lepidoptera)

description: A central question concerning data collection strategy for molecular
 phylogenies has been, is it better to increase the number of characters or
 the number of taxa sampled to improve the robustness of a phylogeny
 estimate? A recent simulation study concluded that increasing the number
 of taxa sampled is preferable to increasing the number of nucleotide
 characters, if taxa are chosen specifically to break up long branches. We
 explore this hypothesis by using empirical data from noctuoid moths, one
 of the largest superfamilies of insects. Separate studies of two nuclear
 genes, elongation factor-1α (EF-1α) and dopa decarboxylase (DDC), have
 yielded similar gene trees and high concordance with morphological
 groupings for 49 exemplar species. However, support levels were quite low
 for nodes deeper than the subfamily level. We tested the effects on
 phylogenetic signal of (1) increasing the taxon sampling by nearly 60%, to
 77 species, and (2) combining data from the two genes in a single
 analysis. Surprisingly, the increased taxon sampling, although designed to
 break up long branches, generated greater disagreement between the two
 gene data sets and decreased support levels for deeper nodes. We appear to
 have inadvertently introduced new long branches, and breaking these up may
 require a yet larger taxon sample. Sampling additional characters
 (combining data) greatly increased the phylogenetic signal. To contrast
 the potential effect of combining data from independent genes with
 collection of the same total number of characters from a single gene, we
 simulated the latter by bootstrap augmentation of the single-gene data
 sets. Support levels for combined data were at least as high as those for
 the bootstrap-augmented data set for DDC and were much higher than those
 for the augmented EF-1α data set. This supports the view that in obtaining
 additional sequence data to solve a refractory systematic problem, it is
 prudent to take them from an independent gene.
description: Mitchell et al Data
 Setmitchell.nexus
DOI: 10.5061/dryad.f12d430
title: Data from: Evolutionary dynamics of specialisation in herbivorous stick insects

description: Understanding the evolutionary dynamics underlying herbivorous insect
 mega-diversity requires investigating the ability of insects to shift and
 adapt to different host plants. Feeding experiments with nine related
 stick insect species revealed that insects retain the ability to use
 ancestral host plants after shifting to novel hosts, with host plant
 shifts generating fundamental feeding niche expansions. These expansions
 were however not accompanied by expansions of the realized feeding niches,
 as species on novel hosts are generally ecologically specialized. For
 shifts from angiosperm to chemically challenging conifer hosts, generalist
 fundamental feeding niches even evolved jointly with strong host plant
 specialization, indicating that host plant specialization is not driven by
 constraints imposed by plant chemistry. By coupling analyses of plant
 chemical compounds, fundamental and ecological feeding niches in multiple
 insect species, we provide novel insights into the evolutionary dynamics
 of host range expansion and contraction in herbivorous insects.
description: Feeding experiment:
 Weight gain and survival data of Timema fed with different
 plantsWe performed a feeding
 experiment using 12 Timema populations from 9 Timema species. We measured
 weight gain and survival of multiple individuals from each of these
 populations, after feeding them during ten days in 7 different feeding
 treatments (i.e., 7 different host plants known to be used by some stick
 insects from the Timema genus under natural conditions)Larose2018_EcolLetters_feedingexp_data.xlsxSecondary feeding experiment: Survival data for 3 Timema population fed with 3 novel plantsWe performed a feeding experiment using 3 Timema populations from 3 different Timema species. We measured survival of multiple individuals from each of these populations, after feeding them during ten days with 3 plants (i.e., 3 feeding treatments: Rhus ovata (sumac), Baccharis pilularis (coyote), Artemisia californica (sage)) currently not used, to our knowledge, by stick insects of the Timema genus under natural conditions.Larose2018_EcolLetters_sidefeedingexp_data.xlsxPhenolic and terpenic chemical composition of 7 Timema host plantsWe extracted and quantified compounds in the phenolic and terpene classes of secondary metabolites from leaves of seven Timema stick insects host plant species included in a feeding experiments (i.e., Ceanothus thyrsiflorus (lil), Adenostoma fasciculatum (cha), Quercus agrifolia (oak), Arctostaphylos glauca (mz), Pseudotsuga menziesii (df), Abies concolor (wf), Sequoia sempervirens (rdw); see Table 1 of the related article), for terpenes and phenolics, respectively. For each plant species, we extracted compounds from five independent replicates for both phenols and terpenes (See the related article to know more about the used Methods).Larose2018_EcolLetters_Plantchemistry_data.xlsx
DOI: 10.5061/dryad.7956
title: Data from: Establishment success of introduced amphibians increases in the presence of congeneric species

description: Darwin's naturalization hypothesis predicts that the success of alien
 invaders will decrease with increasing taxonomic similarity to the native
 community. Alternatively, shared traits between aliens and the native
 assemblage may preadapt aliens to their novel surroundings, thereby
 facilitating establishment (the preadaptation hypothesis). Here we examine
 successful versus failed introductions of amphibian species across the
 globe, and find that the probability of successful establishment is higher
 when congeneric species are present at introduction locations, and
 increases with increasing congener species richness. After accounting for
 positive effects of congeners, residence time, and propagule pressure, we
 also find that invader establishment success is higher on islands than on
 mainland areas, and is higher in areas with abiotic conditions similar to
 the native range. These findings represent the first example in which the
 preadaptation hypothesis is supported in organisms other than plants, and
 suggest that preadaptation has played a critical role in enabling
 introduced species to succeed in novel environments.
description: AmNat_52253_Online_Appendix_AIntroduction data were based on information contained in: Kraus, F. (2009) Alien reptiles and amphibians: a scientific compendium and analysis. Springer, Netherlands.
DOI: 10.5061/dryad.2bk07
title: Data from: Extreme polyandry aids the establishment of invasive populations of a social insect

description: Although monandry is believed to have facilitated the evolution of
 eusociality, many highly eusocial insects have since evolved extreme
 polyandry. The transition to extreme polyandry was likely driven by the
 benefits of within-colony genetic variance to task specialization and/or
 disease resistance, but the extent to which it confers secondary benefits,
 once evolved, is unclear. Here we investigate the consequences of extreme
 polyandry on the invasive potential of the Asian honey bee, Apis cerana.
 In honey bees and other Hymenoptera, small newly founded invasive
 populations must overcome the genetic constraint of their sex
 determination system that requires heterozygosity at a sex-determining
 locus to produce viable females. We find A. cerana queens in an invasive
 population mate with an average of 27 males (range 16–42) that would
 result in the founding queen/s carrying 75% of their source population’s
 sex alleles in stored sperm. This mating frequency is similar to
 native-range Chinese A. cerana (mean 29 males, range 19–46). Simulations
 reveal that extreme polyandry reduces the risk, relative to monandry or
 moderate polyandry, that colonies produce a high incidence of inviable
 brood in populations that have experienced a founder event, that is, when
 sex allele diversity is low and/or allele frequencies are unequal. Thus,
 extreme polyandry aids the invasiveness of A. cerana in two ways: (1) by
 increasing the sex locus allelic richness carried to new populations with
 each founder, thereby increasing sex locus heterozygosity; and (2) by
 reducing the population variance in colony fitness following a founder
 event.
description: Genotype data for
 workersgenotype
 data.xlsx
DOI: 10.5061/dryad.qd63nh7
title: Data from: Density-dependent disease, life history tradeoffs, and the effect of leaf pathogens on a suite of co-occurring close relatives

description: 1. Plant pathogens reduce the performance of their hosts and therefore may
 contribute to ecological mechanisms of coexistence. In Chesson’s
 framework, pathogens contribute to stabilizing mechanisms when they
 intensify negative intraspecific interactions, such as density-dependent
 disease. Additionally, pathogens contribute to equalizing mechanisms when
 they reduce differences in performance among species. Life history
 tradeoffs predict higher susceptibility to pathogens in rapidly growing
 species, which could equalize performance among fast- and slow-growing
 species in the presence of pathogens. 2. In a coastal prairie in
 California, we studied the impact of leaf diseases on the performance of
 seventeen coexisting species of Trifolium and Medicago (“clovers”). We
 transplanted clovers in randomized arrays into the natural prairie
 community in three years of common garden experiments. We quantified
 infection rates by isolating fungi from leaves, and we measured disease
 severity as percent leaf area damaged. In a fungicide experiment, we
 measured the impact of infection on biomass and survival. We assessed
 whether disease on transplants was positively related to natural abundance
 of that species in the surrounding community, which we monitored over 5
 years. We assessed life history tradeoffs by testing whether more rapidly
 growing species were more susceptible to pathogens. 3. Rank abundance of
 clover species was stable over five years despite marked environmental
 fluctuations. Across hosts, fungal infection was not linearly related to
 density, although transplants of species that were locally absent showed
 lower and more variable infection. Disease severity was greater for more
 abundant species in only one of three years, and response to fungicide was
 not stronger in more abundant species. Faster-growing species experienced
 greater fungal infection. Consistent with predictions of the leaf economic
 spectrum, the impact of infection on faster-growing species was less
 negative than for slower-growing species. 4. Our results suggest that life
 history tradeoffs in plant-pathogen interactions may contribute to
 equalizing mechanisms among species in this guild, but that the combined
 effects of greater infection with greater tolerance may limit rather than
 promote coexistence. We also found modest evidence that density-dependent
 disease may contribute to stabilizing mechanisms. Lack of host
 specificity, rapid evolution of host use, and temporal variation in
 climatic conditions may all influence the role that pathogens play in
 coexistence of these closely related plants.
description: DataS1_ParkerGilbert_JEcol2018 Clover and Fungal DataData on plant species abundance, fungal pathogens, foliar disease, and above ground biomass from multi-year study of diseases of 18 species of clovers at the Bodega Marine Reserve, Bodega Bay, California, USA.DataS1_ParkerGilbert_JEcol2018.zip
DOI: 10.5061/dryad.fj429
title: Data from: Canine length in wild male baboons: maturation, aging and social dominance rank

description: Canines represent an essential component of the dentition for any
 heterodont mammal. In primates, like many other mammals, canines are
 frequently used as weapons. Hence, tooth size and wear may have
 significant implications for fighting ability, and consequently for social
 dominance rank, reproductive success, and fitness. We evaluated sources of
 variance in canine growth and length in a well-studied wild primate
 population because of the potential importance of canines for male
 reproductive success in many primates. Specifically, we measured maxillary
 canine length in 80 wild male baboons (aged 5.04–20.45 years) from the
 Amboseli ecosystem in southern Kenya, and examined its relationship with
 maturation, age, and social dominance rank. In our analysis of maturation,
 we compared food-enhanced baboons (those that fed part time at a refuse
 pit associated with a tourist lodge) with wild-feeding males, and found
 that food-enhanced males achieved long canines earlier than wild-feeding
 males. Among adult males, canine length decreased with age because of
 tooth wear. We found some evidence that, after controlling for age, longer
 canines were associated with higher adult dominance rank (accounting for
 9% of the variance in rank), but only among relatively high-ranking males.
 This result supports the idea that social rank, and thus reproductive
 success and fitness, may depend in part on fighting ability mediated by
 canine size.
description: Study subjects,
 including feeding condition, age, maturation status, social rank, and
 canine lengthStudy subjects (N=5
 food-enhanced and 75 wild-feeding male baboons), including feeding
 condition, age, maturation status, social rank, and canine length.
 *Birthdate status indicates whether the birthdate is known or estimated,
 and what the error interval around the estimate is. 0 indicates an age
 known to within a few days; 1 indicates an estimate to within ± 1 year, 2
 indicates within ± 2 years, and so on. ** ‘Researcher’ indicates who
 measured the canines: JA: Jeanne Altmann, and JG: Jordi
 Galbany.Galbany et al Table 1 Canine
 Length in Wild Male Baboons.doc
DOI: 10.5061/dryad.976qm
title: Data from: Visible persistence of single-transient random dot patterns: spatial parameters affect the duration of fading percepts

description: Visible persistence refers to the continuation of visual perception after
 the physical termination of a stimulus. We studied an extreme case of
 visible persistence by presenting two matrices of randomly distributed
 black and white pixels in succession. On the transition from one matrix to
 the second, the luminance polarity of all pixels within a disk- or
 annulus-shaped area reversed, physically creating a single second-order
 transient signal. This transient signal produces the percept of a disk or
 an annulus with an abrupt onset and a gradual offset. To study the nature
 of this fading percept we varied spatial parameters, such as the inner and
 the outer diameter of annuli (Experiment I) and the radius and
 eccentricity of disks (Experiment III), and measured the duration of
 visible persistence by having subjects adjust the synchrony of the onset
 of a reference stimulus with the onset or the offset of the fading
 percept. We validated this method by comparing two modalities of the
 reference stimuli (Experiment I) and by comparing the judgments of fading
 percepts with the judgments of stimuli that actually fade in luminance
 contrast (Experiment II). The results show that (i) irrespective of the
 reference modality, participants are able to precisely judge the on- and
 the offsets of the fading percepts, (ii) auditory reference stimuli lead
 to higher visible persistence durations than visual ones, (iii) visible
 persistence duration increases with the thickness of annuli and the
 diameter of disks, but decreases with the diameter of annuli, irrespective
 of stimulus eccentricity. These effects cannot be explained by stimulus
 energy, which suggests that more complex processing mechanisms are
 involved. Seemingly contradictory effects of disk and annulus diameter can
 be unified by assuming an abstract filling-in mechanism that speeds up
 with the strength of the edge signal and takes more time the larger the
 stimulus area is.
description: Data Exp I -
 IIIAll data in Matlab
 format. A data description file is included in the zipped
 archive.Data.zip
DOI: 10.5061/dryad.cg389
title: Data from: Nurse species and indirect facilitation through grazing drive plant community functional traits in tropical alpine peatlands

description: Facilitation among plants mediated by grazers occurs when an unpalatable
 plant extends its protection against grazing to another plant. This type
 of indirect facilitation impacts species coexistence and ecosystem
 functioning in a large array of ecosystems worldwide. It has nonetheless
 generally been understudied so far in comparison with the role played by
 direct facilitation among plants. We aimed at providing original data on
 indirect facilitation at the community scale to determine the extent to
 which indirect facilitation mediated by grazers can shape plant
 communities. Such experimental data are expected to contribute to refining
 the conceptual framework on plant–plant–herbivore interactions in
 stressful environments. We set up a 2-year grazing exclusion experiment in
 tropical alpine peatlands in Bolivia. Those ecosystems depend entirely on
 a few, structuring cushion-forming plants (hereafter referred to as
 “nurse” species), in which associated plant communities develop. Fences
 have been set over two nurse species with different strategies to cope
 with grazing (direct vs. indirect defenses), which are expected to lead to
 different intensities of indirect facilitation for the associated
 communities. We collected functional traits which are known to vary
 according to grazing pressure (LDMC, leaf thickness, and maximum height),
 on both the nurse and their associated plant communities in grazed (and
 therefore indirect facilitation as well) and ungrazed conditions. We found
 that the effect of indirectly facilitated on the associated plant
 communities depended on the functional trait considered. Indirect
 facilitation decreased the effects of grazing on species relative
 abundance, mean LDMC, and the convergence of the maximum height
 distribution of the associated communities, but did not affect mean height
 or cover. The identity of the nurse species and grazing jointly affected
 the structure of the associated plant community through indirect
 facilitation. Our results together with the existing literature suggest
 that the “grazer–nurse–beneficiary” interaction module can be more complex
 than expected when evaluated in the field.
description: functional traits
 dataFunctional trait data
 for nurse and beneficiary species.data_ok.csvCover of benefiary speciesRelative cover of the beneficiary species in each plotdata_cover_ok.csv