cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5bd66
title: Data from: The trophic vacuum and the evolution of complex life cycles in trophically-transmitted helminths

description: Parasitic worms (helminths) frequently have complex life cycles in which
 they are transmitted trophically between two or more successive hosts.
 Sexual reproduction often takes place in high trophic-level (TL)
 vertebrates, where parasites can grow to large sizes with high fecundity.
 Direct infection of high TL hosts, while advantageous, may be unachievable
 for parasites constrained to transmit trophically, because helminth
 propagules are unlikely to be ingested by large predators. Lack of niche
 overlap between propagule and definitive host (the trophic transmission
 vacuum) may explain the origin and/or maintenance of intermediate hosts,
 which overcome this transmission barrier. We show that nematodes infecting
 high TL definitive hosts tend to have more successive hosts in their life
 cycles. This relationship was modest, though, driven mainly by the minimum
 TL of hosts, suggesting that the shortest trophic chains leading to a host
 define the boundaries of the transmission vacuum. We also show that
 alternative modes of transmission, like host penetration, allow nematodes
 to reach high TLs without intermediate hosts. We suggest that widespread
 omnivory as well as parasite adaptations to increase transmission probably
 reduce, but do not eliminate, the barriers to the transmission of
 helminths through the food web.
description: Life cycle lengths and
 definitive host trophic levels for parasitic nematodesTV_dryad.csvLife cycle lengths and definitive host trophic levels for parasitic nematodes in OUCH formatOUCH_analysis_dryad.csvPhylogenetic tree for parasitic nematodes used for regression analysesTV_tree_phylo_regress.nexPhylogenetic tree for parasitic nematodes used to compare transmission strategiesReduced_phylo_BL_all_strat_ultra.nex
DOI: 10.5061/dryad.7g8cn
title: Data from: Adhesion force mapping on wood by atomic force microscopy: influence of surface roughness and tip geometry

description: This study attempts to address the interpretation of atomic force
 microscopy (AFM) adhesion force measurements conducted on the
 heterogeneous rough surface of wood and natural fibre materials. The
 influences of wood surface roughness, tip geometry and wear on the
 adhesion force distribution are examined by cyclic measurements conducted
 on wood surface under dry inert conditions. It was found that both the
 variation of tip and surface roughness of wood can widen the distribution
 of adhesion forces, which are essential for data interpretation. When a
 common Si AFM tip with nanometre size is used, the influence of tip wear
 can be significant. Therefore, control experiments should take the
 sequence of measurements into consideration, e.g. repeated experiments
 with used tip. In comparison, colloidal tips provide highly reproducible
 results. Similar average values but different distributions are shown for
 the adhesion measured on two major components of wood surface (cell wall
 and lumen). Evidence supports the hypothesis that the difference of the
 adhesion force distribution on these two locations was mainly induced by
 their surface roughness.
description: Supporting
 InformationThe file contains four
 figures and 1 table to provide details of the experiments and support the
 discussion in the paperadhesion force
 dataThe adhesion force data
 obtained from AFM measurements
DOI: 10.5061/dryad.0dn7s
title: Data from: Genetic estimates of population age in the water flea, Daphnia magna

description: Genetic datasets can be used to date evolutionary events, even on recent
 time scales if sufficient data are available. We used statistics
 calculated from multilocus microsatellite datasets to estimate population
 ages in data generated through coalescent simulations and in samples from
 populations of known age in a metapopulation of Daphnia magna in Finland.
 Our simulation results show that age estimates improve with additional
 loci and define a time frame over which these statistics are most useful.
 On the most recent time scales, assumptions regarding the model of
 mutation (infinite sites vs. stepwise mutation) have little influence on
 estimated ages. In older populations, size homoplasy among microsatellite
 alleles results in a downwards bias for estimates based on the infinite
 sites model. In the Finnish D. magna metapopulation, our genetically
 derived estimated ages were biased upwards. Potential sources of this bias
 include: the underlying model of mutation, gene flow, founder size, and
 the possibility of persistent source populations in the system. Our
 simulated data show that genetic age estimation is possible, even for very
 young populations, but our empirical data highlight the importance of
 factors such as migration and founding size when these statistics are
 applied in natural populations.
description: Raw Daphnia
 genotypesRaw (unbinned) genotypes
 at 14 microsatellite loci for each of 14 sampled populations of Daphnia
 magna.Raw-Storgrundet.csvRecoded Daphnia genotypesRecoded (binned) genotypes at 14 microsatellite loci for each of 14 sampled Daphnia magna populations.Recoded-Storgrundet.csvSample locationsGPS coordinates for each of the 14 sampled Daphnia magna populations from Storgrundet, a rocky island in the Tvarminne archipelago of Finland.SampleSites.xls
DOI: 10.5061/dryad.4mf63
title: Data from: Size matters: male and female mate choice leads to size-assortative pairing in a coral reef cardinalfish

description: Many animals exhibit size-assortative mating, and matching theory predicts
 this occurs because both males and females prefer bigger mates. Monogamy
 and size-assortative pairing have been described for coral reef fishes,
 but the underlying behavioral mechanism has not been tested. Here, we took
 a long-term observational and experimental study to resolve the causes of
 size-based pairing in the paternal mouthbrooding coral reef cardinalfish
 Sphaeramia nematoptera. For 65 pairs observed over a 23-month period,
 there was a strong size-correlation between paired males and females. This
 size-assortative mating was not a consequence of pairing at a young age as
 re-pairing was common, with only 7% juvenile pairs still found together
 after 8 months. For adults that changed partners over this period, there
 was a strong correlation between the size of individuals and the size of
 their new partners. Following experimental removal of partners, both males
 and females quickly repaired with partners of similar or larger size.
 Together, these results suggest that size-assortative mating is explained
 by a mutual preference by both males and females for larger mates. We
 suggest that monogamous pairing occurs in cardinalfish because
 mouthbrooding restricts multiple mating by males. Size-assortative pairing
 follows as larger males likely prefer the more fecund larger females, and
 larger females prefer larger males because they can successfully brood all
 of their eggs. Mutual mate choice will likely explain size-assortative
 pairing in other fish species with paternal care.
description: FiguresThis is the sorted data for the figures in the associated publicationSizeAssortment24-7-15original data of observations and experimentsSizeAss 16-2-16data of experiments and observations, updated with new and old information re standard length and gender of individuals
DOI: 10.5061/dryad.bt739
title: Data from: Mandible allometry in extant and fossil Balaenopteridae (Cetacea: Mammalia): the largest vertebrate skeletal element and its role in rorqual lunge-feeding

description: Rorqual whales (crown Balaenopteridae) are unique among aquatic
 vertebrates in their ability to lunge-feed. During a single lunge,
 rorquals rapidly engulf a large volume of prey-laden water at high speed,
 which they then filter to capture suspended prey. Engulfment biomechanics
 are mostly governed by the coordinated opening and closing of the
 mandibles at large gape angles, which differentially exposes the floor of
 the oral cavity to oncoming flow. Mouth area in rorquals is delimited by
 unfused bony mandibles that form kinetic linkages to each other and with
 the skull. The relative scale and morphology of these skeletal elements
 have profound consequences for the energetic efficiency of foraging in
 these gigantic predators. Here we performed a morphometric study of
 rorqual mandibles using a dataset derived from a survey of museum
 specimens. Across adult specimens of extant balaenopterids, mandibles
 range in size from ~1-6 m in length, and at their upper limit they
 represent the single largest osteological element of any vertebrate,
 living or extinct. Our analyses determined that rorqual mandibles exhibit
 positive allometry, whereby the relative size of these mandibles becomes
 greater with increasing body size. These robust scaling relationships
 allowed us to predict mandible length for fragmentary remains (e.g.,
 incomplete and/or fossil specimens), as we demonstrated for two partial
 mandibles from the latest Miocene of California, U.S.A., and for mandibles
 from previously described fossil balaenopterids. Furthermore, we showed
 the allometry of mandible length to body size in extant mysticetes, which
 hints at fundamental developmental constraints in mysticetes despite their
 ecomorphologic differences in the feeding styles. Lastly, we outlined how
 our findings can be used to test hypotheses about the antiquity and
 evolution of lunge-feeding.
description: Fig5AC_mandibleThis file is a nexus file that uses log-transformed museum specimens from the first dataset (mature specimens only) to regress C-C against by Cu and Ch (mandible measurements) using PICs. See main text for details on tree source.Supplemental DataWord document that provides full institutional abbreviations in the morphometric dataset; results on PICs of extant morphometric data; and predictive equations for estimating complete mandibles and body size in extinct balaenopterids.Fig6_CHvTLThis file is a nexus file that uses log-transformed museum specimens from the second dataset (mature and immature specimens only) to regress Ch (mandible measurements) against TL using PICs for all extant Mysticeti. See main text for details on tree source.Mandibles MS dataset_R1_finalSpecimen-based morphometrics for both datasets (first and second) used in the analyses. See main text for details.
DOI: 10.5061/dryad.7825c
title: Data from: Coordination strategies of chimpanzees and human children in a stag hunt game

description: Much of human cooperation takes place in mutualistic contexts in which the
 main challenge for individuals is how to coordinate decisions. In the
 current studies, we compared the abilities of chimpanzees and young
 children to coordinate with a partner in two versions of a Stag Hunt game.
 When risks were low (the hare was of low value) and information was cheap
 (the partner's behaviour was readily observable), partners of both
 species were able to successfully coordinate on the higher value stag more
 than 90% of the time. By contrast, when the risks were raised and
 observing the partner was more difficult, the chimpanzees became less
 successful, whereas the children compensated, and so remained highly
 successful, by communicating more often and more specifically. This
 pattern of results is consistent with the hypothesis that humans evolved
 unique skills of coordination and communication in the context of
 especially risky coordination problems.
description: chimpanzee stag hunt
 dataStagHunt_data.xlsx
DOI: 10.5061/dryad.g8h42
title: Data from: Historical introgression and the persistence of ghost alleles in the intermediate horseshoe bat (Rhinolophus affinis)

description: Phylogenetic conflicts between genetic markers can help to disentangle
 complex histories of phylogeography and introgression among taxa. We
 previously proposed that the Chinese mainland subspecies of the
 intermediate horseshoe bat Rhinolophus affinis himalayanus colonized
 Hainan Island to form the subspecies R. a. hainanus. Subsequent
 recolonization of the mainland formed a third taxon, R. a macrurus, and a
 secondary contact zone with the ancestral himalayanus. To test for
 historical and recurrent genetic exchange between these mainland
 subspecies, we sampled populations of each from two parapatric zones and
 undertook analyses using one mtDNA marker, three nuclear genes and 14
 microsatellites. Nuclear DNA, echolocation call frequencies and
 morphological data all recovered two taxa; however, a mtDNA phylogeny
 revealed two himalayanus clades, of which one clustered with macrurus, as
 well as some shared or related mtDNA haplotypes in eastern populations.
 Isolation-with-migration (IM) models suggested some mtDNA gene flow from
 macrurus to himalayanus. However, strong population structure in
 himalayanus raises the possibility that macrurus captured mtDNA from a
 coastal population of himalayanus that has since become rare or extinct.
 To reconcile these two sets of results, we suggest that the IM estimates
 might reflect historical mtDNA gene flow among populations of himalayanus,
 before mtDNA was subsequently captured by macrurus. Finally,
 microsatellite-based ABC analyses supported the island origin of macrurus;
 however, mtDNA-based ABC analyses suggest this taxon might have evolved on
 the mainland. Our findings highlight the importance of understanding
 population history and structure for interpreting hybridization and
 introgression events.
description: Microsatellite data and
 sequence data of R.affinis-Morphology data of R.
 affinisDIY ABC-input file of
 R.affinisDIY ABC-input file of
 R.affinis-microsatellite
DOI: 10.5061/dryad.sr61r
title: Data from: How well do molecular and pedigree relatedness correspond, in populations with variable mating systems, and types and quantities of molecular and demographic data?

description: Kinship analyses are important pillars of ecological and conservation
 genetic studies with potentially far-reaching implications. There is a
 need for power analyses that address a range of possible relationships.
 Nevertheless, such analyses are rarely applied, and studies that use
 genetic-data-based-kinship inference often ignore the influence of
 intrinsic population characteristics. We investigated 11 questions
 regarding the correct classification rate of dyads to relatedness
 categories (relatedness category assignments; RCA) using an
 individual-based model with realistic life history parameters. We
 investigated the effects of the number of genetic markers; marker type
 (microsatellite, single nucleotide polymorphism SNP, or both); minor
 allele frequency; typing error; mating system; and the number of
 overlapping generations under different demographic conditions. We found
 that (i) an increasing number of genetic markers increased the correct
 classification rate of the RCA so that up to &gt;80% first cousins can
 be correctly assigned; (ii) the minimum number of genetic markers required
 for assignments with 80 and 95% correct classifications differed between
 relatedness categories, mating systems, and the number of overlapping
 generations; (iii) the correct classification rate was improved by adding
 additional relatedness categories and age and mitochondrial DNA data; and
 (iv) a combination of microsatellite and single-nucleotide polymorphism
 data increased the correct classification rate if &lt;800 SNP loci
 were available. This study shows how intrinsic population characteristics,
 such as mating system and the number of overlapping generations, life
 history traits, and genetic marker characteristics, can influence the
 correct classification rate of an RCA study. Therefore, species-specific
 power analyses are essential for empirical studies.
description: RCAsimulationRCAsimulation.zip contains the simulation code (MATLAB) used in Kopps et al. 2015 and a manual on how to run the simulation.
DOI: 10.5061/dryad.cr922
title: Data from: The influence of meal size on prey DNA detectability in piscivorous birds

description: Molecular methods allow non-invasive assessment of vertebrate
 predator-prey systems at high taxonomic resolution by examining dietary
 samples such as faeces and pellets. To facilitate the interpretation of
 field-derived data, feeding trials, investigating the impacts of
 biological, methodological, and environmental factors on prey DNA
 detection have been conducted. The effect of meal size, however, has not
 yet been explicitly considered for vertebrate consumers. Moreover,
 different non-invasively obtained sample types remain to be compared in
 such experiments. Here, we present a feeding trial on abundant piscivorous
 birds, Great Cormorants (Phalacrocorax carbo), to assess meal size effects
 on post-feeding prey DNA detection success. Faeces and pellets were
 sampled twice a day after the feed of large (350-540 g), medium (190-345
 g), and small (15-170 g) fish meals contributing either a large
 (&gt;79%) or small (&lt;38%) share to the daily consumption.
 Samples were examined for prey DNA and fish hard parts. Molecular analysis
 of faeces revealed that both large meal size and share had a significantly
 positive effect on prey DNA detection rate post-feeding. Furthermore,
 large meals were detectable for a significantly longer time span with a
 detection limit at ~76 h and a 50% detection probability at ~32 h
 post-feeding. In pellets, molecular methods reliably identified the meal
 consumed the previous day, which was not possible via morphological
 analysis or when examining individual faeces. The less reliable prey DNA
 detection of small meals or meal shares in faeces signifies the importance
 of large numbers of dietary samples to obtain reliable trophic data.
description: consumed
 fishAn excel table of all
 fish individuals consumed by the four cormorants during the three
 experimental runs including fish species, total length, mass and start/end
 of consumption per fish species and cormorant.faeces_molecular_prey_detectionThe excel table "faeces_molecular_prey_detection" shows the results of the molecular screening of cormorant faeces produced in the feeding trial.pellets_morphological_and_molecular_prey_detectionThe excel table "pellets_morphological_and_molecular_prey_detection" shows the results of the DNA-based and morphological analysis of cormorant pellets produced during the feeding trial.
DOI: 10.5061/dryad.8951
title: Data from: Efficient screening of transgenic plant lines for ecological research

description: Plants stably transformed to manipulate the expression of genes mediating
 ecological performance have profoundly altered research in plant ecology.
 Agrobacterium-mediated transformation remains the most effective method of
 creating plants harboring a limited number of transgene integrations of
 low complexity. For ecological/physiological research, the following
 requirements must be met: 1) the regenerated plants should have the same
 ploidy level as the corresponding wild type plant and 2) contain a single
 transgene copy in a homozygous state; 3) the T-DNA must be completely
 inserted without vector backbone sequence and all its elements functional;
 and 4) the integration should not change the phenotype of the plant by
 interrupting chromosomal genes or by mutations occurring during the
 regeneration procedure. The screening process to obtain transformed plants
 that meet the above criteria is costly and time consuming and an optimized
 screening procedure is presented. We developed a flow chart that optimizes
 the screening process to efficiently select transformed plants for
 ecological research. It consists of segregational analyses, which select
 transgenic T1 and T2 generation plants with single T-DNA copies that are
 homozygous. Indispensable molecular genetic tests (flow cytometry,
 diagnostic PCRs and Southern blotting) are performed at the earliest and
 most effective times in the screening process. qPCR to quantify changes in
 transcript accumulation to confirm gene silencing or over-expression, are
 the last steps in the selection process. Since we routinely transform the
 wild tobacco, Nicotiana attenuata, with constructs that silence or
 ectopically over-express ecologically relevant genes, the proposed
 protocol is supported by examples from this system.
description: Supplemental Table
 S1Sequences of the primers
 used for diagnostic PCRs, Southern blotting, and qPCR.Supplemental Table
 S2Results of diagnostic
 PCRs with 44 different transgenic N. attenuata lines.
DOI: 10.5061/dryad.8gj1c
title: Data from: Diverse pollinator communities enhance plant reproductive success

description: Understanding the functional consequences of biodiversity loss is a major
 goal of ecology. Animal-mediated pollination is an essential ecosystem
 function and service provided to mankind. However, little is known how
 pollinator diversity could affect pollination services. Using a
 substitutive design, we experimentally manipulated functional group (FG)
 and species richness of pollinator communities to investigate their
 consequences on the reproductive success of an obligate out-crossing model
 plant species, Raphanus sativus. Both fruit and seed set increased with
 pollinator FG richness. Furthermore, seed set increased with species
 richness in pollinator communities composed of a single FG. However, in
 multiple-FG communities, highest species richness resulted in slightly
 reduced pollination services compared with intermediate species richness.
 Our analysis indicates that the presence of social bees, which showed
 roughly four times higher visitation rates than solitary bees or
 hoverflies, was an important factor contributing to the positive
 pollinator diversity–pollination service relationship, in particular, for
 fruit set. Visitation rate at different daytimes, and less so among flower
 heights, varied among social bees, solitary bees and hoverflies,
 indicating a niche complementarity among these pollinator groups. Our
 study demonstrates enhanced pollination services of diverse pollinator
 communities at the plant population level and suggests that both the niche
 complementarity and the presence of specific taxa in a pollinator
 community drive this positive relationship.
description: AlbrechtEtAl_DataTable1AlbrechtEtAl_DataTable2AlbrechtEtAl_DataTable3
DOI: 10.5061/dryad.n53d0
title: Data from: Bees eavesdrop upon informative and persistent signal compounds in alarm pheromones

description: Pollinators such as bees provide a critical ecosystem service that can be
 impaired by information about predation. We provide the first evidence for
 olfactory eavesdropping and avoidance of heterospecific alarm signals,
 alarm pheromones, at food sources in bees. We predicted that foragers
 would eavesdrop upon heterospecific alarm pheromones, and would detect and
 avoid conspicuous individual pheromone compounds, defined by abundance and
 how long they can linger to provide warning information (volatility). We
 show that Apis cerana foragers avoid the distinctive alarm pheromones of
 A. dorsata and A. mellifera, species that share the same floral resources
 and predators. We next examined responses to individual alarm pheromone
 compounds. Apis cerana foragers avoided isopentyl acetate (IPA), which is
 found in all three species and is the most abundant and volatile of the
 tested compounds. Interestingly, A. cerana also avoided two odor
 components, gamma-octanoic lactone (GOL) and (E)-2-decen-1-yl-acetate
 (DA), which are only present in A. dorsata alarm pheromone and are
 &gt;150-fold less volatile than IPA. Neural recordings (EAG) revealed
 that A. cerana antennae are 10-fold more sensitive to GOL and DA than to
 other tested compounds. Thus, the eavesdropping strategy is shaped by
 signal conspicuousness (abundance and commonality) and signal persistence
 (volatility).
description: AceranaEavesDataDryad3Eavesdropping behavioral and electrophysiological data