cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8792d
title: Data from: Molecular signatures of selection on reproductive character displacement of flower color in Phlox drummondii

description: Character displacement, which arises when species diverge in sympatry to
 decrease competition for resources or reproductive interference, has been
 observed in a wide variety of plants and animals. A classic example of
 reproductive character displacement, presumed to be caused by reinforcing
 selection, is flower-color variation in the native Texas wildflower Phlox
 drummondii. Here we use population genetic analyses to investigate
 molecular signatures of selection on flower-color variation in this
 species. First, we quantify patterns of neutral genetic variation across
 the range of P. drummondii to demonstrate that restricted gene flow and
 genetic drift cannot explain the pattern of flower color divergence in
 this species. There is evidence of extensive gene flow across populations
 with different flower colors, suggesting selection caused flower-color
 divergence. Second, analysis of sequence variation in the genes underlying
 this divergence reveals a signature of a selective sweep in one of the two
 genes, further indicating selection is responsible for divergence in
 sympatry. The lack of a signature of selection at the second locus does
 not necessarily indicate a lack of selection on this locus but instead
 brings attention to the uncertainty in depending on molecular signatures
 to identify selection.
description: microsat
 genotypesThis file contains the
 microsatellite lengths for each individual at each of the 9 loci.
 Population number and name are indicated in the left
 columns.microsatgeno.xls
DOI: 10.5061/dryad.4t0v127
title: Data from: Pearl millet and cowpea intercrop response to applied nutrients in West Africa

description: In the Sahel, crop production is dominated by pearl millet [Pennisetum
 glaucum (L.) R. Br.] cropping systems including intercropping with cowpea
 [Vigna unguiculata (L.) Walp]. The research objectives were to determine
 pearl millet sole crop (PMSC) and intercrop nutrient response functions,
 profit opportunities from fertilizer use, and a means of relating
 intercrop to PMSC response. Pearl millet–cowpea trials were conducted in
 Niger and Mali. The treatment structure was an incomplete factorial with
 five, four, and four levels of P, N, and K, respectively. Response
 functions were determined for intercropping with cowpea yield converted to
 a pearl millet grain yield equivalent for ratios of cowpea to pearl millet
 grain value (CpPm) ranging from 1 to 5 kg kg–1. Response functions were
 also determined in consideration of fodder value. A method of adjusting
 PMSC response coefficients with CpPm as the independent variable was
 developed for determination of intercrop response functions. Yields and
 responses to nutrients were low but adequate for profitable N and P use.
 Value of intercrop production ranged from 50 to 125% more compared with
 PMSC for CpPm of 2 and 4, and the respective response to 10 kg ha–1 P was
 28 and 135% more with intercrop. Consideration of fodder added 23% to the
 yield value. Application of N and P for intercrop compared with PMSC
 production has much more profit potential. The ability to apply PMSC
 functions in determination of pearl millet–cowpea responses to applied
 nutrients offers a means to improve fertilizer use for the intercrop.
description: West Africa Pearl Millet
 data setResearch was conducted
 in Burkina Faso, Mali and Niger for the Sahel and Sudan Savanna
 agroecological zones. Trials had similar basic treatment structures for
 determination of response functions for N, P, and K, and a diagnostic
 treatment for resposne to Mg, S, Zn and B. Most treatments in Niger were
 intercroped with cowpea and with 2.5 Mg ha-1 yr-1 manure applied but had
 additional treatments for determination of the effect of manure and/or
 intercropping on yield and response. Most treatments in Mali were sole
 crop pearl millet with added treatments determination of the effect of
 intercropping on yield and response, all with no manure applied. In
 Burkina Faso, trials were conducted at Dori in 2014-2015 and all
 treatments were with pearl millet sole crop with or without 5 Mg ha-1
 manure applied in 2014 and evaluating the residual effect of manure in
 2015.W
 Africa Pearl Millet data set.xlsx
DOI: 10.5061/dryad.c0r18
title: Data from: Cooperative investment in public goods is kin directed in communal nests of social birds

description: The tragedy of the commons predicts social collapse when public goods are
 jointly exploited by individuals attempting to maximise their fitness at
 the expense of other social group members. However, animal societies have
 evolved many times despite this vulnerability to exploitation by selfish
 individuals. Kin selection offers a solution to this social dilemma, but
 in large social groups mean relatedness is often low. Sociable weavers
 (Philetairus socius) live in large colonies that share the benefits of a
 massive communal nest, which requires individual investment for
 construction and maintenance. Here, we show that despite low mean kinship
 within colonies, relatives are spatially and socially clustered and that
 nest-building males have higher local relatedness to other colony members
 than do non-building males. Alternative hypotheses received little
 support, so we conclude that the benefits of the public good are shared
 with kin and that cooperative investment is, despite the large size and
 low relatedness of these communities, kin-directed.
description: Individual network
 associationsMatrices of distance
 between nest chambersDistance
 Matrices.zipThatch building per
 individualThatch
 building.txt
DOI: 10.5061/dryad.d0k6q
title: Data from: Postcrania of juvenile Pinacosaurus grangeri (Ornithischia: Ankylosauria) from the Upper Cretaceous Alagteeg Formation, Alag Teeg, Mongolia: implications for ontogenetic allometry in ankylosaurs

description: The ankylosaurine Pinacosaurus is one of the best known ankylosaur to date
 in terms of the number and preservational quality of specimens. Juvenile
 to sub-adult postcrania collected by the Soviet-Mongolian Paleontological
 Expedition from the Upper Cretaceous Alagteeg Formation at Alag Teeg,
 Mongolia can be assigned to Pinacosaurus grangeri based on discrete
 cranial characters. One individual is significantly larger than the others
 and demonstrates delayed fusion of postcranial elements with the earliest
 occurring between dorsal ribs and vertebrae. The robustness of forelimb
 elements is positively allometric with respect to their length, indicating
 weight-bearing relationship. Such length-dependent correlations are not
 seen in the hind limbs. Finally, incipient cervical half rings suggest a
 developmental pathway of outgrowths from the underlying band combined with
 fusion of overlying osteoderms.
description: Supplemental_Data_1Measurement data (in mm) for all specimens used in regression and statistical analyses
DOI: 10.5061/dryad.t4313
title: Data from: The differential impact of a native and a non-native ragwort species (Senecioneae) on the first and second trophic level of the rhizosphere food web

description: Whereas the impact of exotic plant species on above-ground biota is
 relatively well-documented, far less is known about the effects of
 non-indigenous plants on the first and second trophic level of the
 rhizosphere food web. Here, rhizosphere communities of the invasive
 narrow-leaved ragwort Senecio inaequidens and the native tansy ragwort
 Jacobaea vulgaris, co-occurring in three semi-natural habitats are
 compared. For both species, two life stages were taken into consideration.
 Quantitative PCR assays for the analyses of bacterial and fungal
 communities at a high taxonomic level were optimized, and it was
 investigated whether changes in the primary decomposer community were
 translated in alterations in bacterivorous and fungivorous nematode
 communities. In contrast to J. vulgaris, small but significant reductions
 were observed for Actinobacteria and Bacteroidetes (both p &lt; 0.05)
 in case of the invasive S. inaequidens. More pronounced changes were
 detected for the overall nematode community density, and, more
 specifically, for the bacterivorous genus Anaplectus and the family
 Monhysteridae (both p &lt; 0.05), as well as the necromenic
 Pristionchus (p &lt; 0.001). At high taxonomic level, no differences
 were observed in fungal rhizosphere communities between native and
 non-native ragwort species. The impact of plant developmental stages on
 rhizosphere biota was prominent. The overall bacterial and fungal
 biomasses, as well as a remarkably consistent set of constituents
 (Actinobacteria, α- and β-Proteobacteria and Bacteroidetes) were
 negatively affected by plant stage for both ragwort species. Although
 later developmental stages of plants generally coincided with lower levels
 for individual nematode taxa, densities of the fungivorous genera
 Diphtherophora and Tylolaimophorus remain unaltered. Hence, even at a high
 taxonomic level, differential effects of native and non-native ragwort
 could be pinpointed. However, plant developmental stage has a more
 prominent impact and this impact was similar in nature for both native and
 non-native ragwort species.
description: Converted-qPCR-Data_nematodes_bacteria_fungiIn this data file you can find the data we used to execute our statistical tests. Converted Ct values are shown and the transformed data is shown in purple. (Making use of linear relationship between primary qPCR output, Ct values, and the number of individuals, nematode concentrations expressed as individuals per 100 g of soil were calculated. As both the resulting nematode densities and the concentrations of bacterial and fungal DNA (ng per 0.25 g soil) didn’t show a normal distribution, data were transformed. Primary counts were log transformed (ln(y+0.1)). A constant (0.1) was added to push data away from the lower bound zero.) A legend is added to explain the meaning of the first six rows.
DOI: 10.5061/dryad.6ss2t
title: Data from: Temporal population genetic instability in range edge Western Toads, Anaxyrus boreas

description: In this article, we address the temporal stability of population genetic
 structure in a range-edge population that is undergoing continual,
 short-distance colonization events. We sampled western toad, Anaxyrus
 boreas, breeding populations over 2 seasons near their northern range
 limit in southeast Alaska. We sampled 20 ponds each during the summers of
 2008 and 2009, with 14 ponds sampled in both summers. We found
 considerable turnover in the population genetic relationships among ponds
 in those 2 seasons, as well as biologically meaningful genetic
 differentiation between years within some ponds. We found relatively
 consistent relationships between major population centers, whereas the
 relationships between the central ponds and smaller, outlying populations
 differed year to year. This finding indicates that multiple years of
 genetic sampling may be important for understanding the genetic landscape
 of some populations.
description: Dryad_microsatsspreadsheet of the allele lengths for each 162 individual, with year and population information
DOI: 10.15468/dl.wjgxuf
title: Occurrence Download

description: A dataset containing 2648 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Alkekengi",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 2648 records from 187 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000804-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.4gv6t
title: Data from: The geomagnetic environment in which sea turtle eggs incubate affects subsequent magnetic navigation behavior of hatchlings

description: Loggerhead sea turtle hatchlings (Caretta caretta) use regional magnetic
 fields as open-ocean navigational markers during trans-oceanic migrations.
 Little is known, however, about the ontogeny of this behaviour. As a first
 step towards investigating whether the magnetic environment in which
 hatchlings develop affects subsequent magnetic orientation behaviour, eggs
 deposited by nesting female loggerheads were permitted to develop in situ
 either in the natural ambient magnetic field or in a magnetic field
 distorted by magnets placed around the nest. In orientation experiments,
 hatchlings that developed in the normal ambient field oriented
 approximately south when exposed to a field that exists near the northern
 coast of Portugal, a direction consistent with their migratory route in
 the northeastern Atlantic. By contrast, hatchlings that developed in a
 distorted magnetic field had orientation indistinguishable from random
 when tested in the same north Portugal field. No differences existed
 between the two groups in orientation assays involving responses to
 orbital movements of waves or sea-finding, neither of which involves
 magnetic field perception. These findings, to our knowledge, demonstrate
 for the first time that the magnetic environment present during early
 development can influence the magnetic orientation behaviour of a neonatal
 migratory animal.
description: Magnetic orientation
 dataWave simulator
 dataSea finding
 data
DOI: 10.5061/dryad.1dn50
title: Data from: Estimating Bayesian phylogenetic information content

description: Measuring the phylogenetic information content of data has a long history
 in systematics. Here we explore a Bayesian approach to information content
 estimation. The entropy of the posterior distribution compared to the
 entropy of the prior distribution provides a natural way to measure
 information content. If the data have no information relevant to ranking
 tree topologies beyond the information supplied by the prior, the
 posterior and prior will be identical. Information in data discourages
 consideration of some hypotheses allowed by the prior, resulting in a
 posterior distribution that is more concentrated (has lower entropy) than
 the prior. We focus on measuring information about tree topology using
 marginal posterior distributions of tree topologies. We show that both the
 accuracy and the computational efficiency of topological information
 content estimation improve with use of the conditional clade distribution,
 which also allows topological information content to be partitioned by
 clade. We explore two important applications of our method: providing a
 compelling definition of saturation, and detecting conflict among data
 partitions that can negatively affect analyses of concatenated data.
description: Supplementary
 MaterialsContains instructions,
 scripts, and data files needed to recreate all analyses presented in the
 paper. Please look first at the top-level _readme.txt file, which explains
 which directories correspond to specific tables and figures in the
 paper.supplementary.zip
DOI: 10.5061/dryad.27fb8
title: Data from: Anthropogenic transport of species across native ranges: unpredictable genetic and evolutionary consequences

description: Human activities are responsible for the translocation of vast amounts of
 organisms, altering natural patterns of dispersal and gene flow. Most
 research to date has focused on the consequences of anthropogenic
 transportation of non-indigenous species within introduced ranges, with
 little research focusing on native species. Here, we compared genetic
 patterns of the sessile marine invertebrate, Ciona intestinalis, which has
 highly restricted dispersal capabilities. We collected individuals in a
 region of the species' native range where human activities that are
 known to facilitate the artificial spread of species are prevalent. Using
 microsatellite markers, we revealed highly dissimilar outcomes. First, we
 found low levels of genetic differentiation among sites separated by both
 short and large geographical distances, indicating the presence of
 anthropogenic transport of genotypes, and little influence of natural
 geographical barriers. Second, we found significant genetic
 differentiation in pairwise comparisons among certain sites, suggesting
 that other factors besides artificial transport (e.g. natural dispersal,
 premodern population structure) may be shaping genetic patterns. Taken
 together, we found dissimilar patterns of population structure in a highly
 urbanized region that could not be predicted by artificial transport
 alone. We conclude that anthropogenic activities alter genetic composition
 of native ranges, with unknown consequences for species' evolutionary
 trajectories.
description: Microsat.DataRaw-microsatellite-data-file2011-2015 Jersey Shipping Data
DOI: 10.5061/dryad.6v7j674
title: Data from: From hand to mouth: monkeys require greater effort in motor preparation for voluntary control of vocalization than for manual actions

description: Voluntary control of vocal production is an essential component of the
 language faculty, which is thought to distinguish humans from other
 primates. Recent experiments have begun to reveal the capability of
 nonhuman primates to perform vocal control; however, the mechanisms
 underlying this ability remain unclear. Here, we revealed that Japanese
 macaque monkeys can learn to vocalise voluntarily through a different
 mechanism than that used for manual actions. The monkeys rapidly learned
 to touch a computer monitor when a visual stimulus was presented, and
 showed a capacity for flexible adaptation, such that they reacted when the
 visual stimulus was shown at an unexpected time. In contrast, successful
 vocal training required additional time, and the monkeys exhibited
 difficulty with vocal execution when the visual stimulus appeared earlier
 than expected; this occurred regardless of extensive training. Thus, motor
 preparation before execution of an action may be a key factor in
 distinguishing vocalisation from manual actions in monkeys; they do not
 exhibit a similar ability to perform motor preparation in the vocal
 domains. By performing direct comparisons, this study provides novel
 evidence regarding differences in motor control abilities between vocal
 and manual actions. Our findings support the suggestion that the
 functional expansion from hand to mouth might be a critical evolutionary
 event for the acquisition of voluntary control of vocalisations.
description: supplementary_data_01_trainingTraining data for vocal conditioning.supplementary_data_02_probeall data set for probe trials.
DOI: 10.5061/dryad.vr588
title: Data from: Host-parasitoid evolution in a metacommunity

description: Patch size and isolation are predicted to alter both species diversity and
 evolution; yet, there are few empirical examples of eco-evolutionary
 feedback in metacommunities. We tested three hypotheses about
 eco-evolutionary feedback in a gall-forming fly, Eurosta solidaginis and
 two of its natural enemies that select for opposite traits: (i)
 specialization and poor dispersal ability constrain a subset of natural
 enemies from occupying small and isolated patches, (ii) this constraint
 alters selection on the gall fly, causing phenotypic shifts towards traits
 resistant to generalist and dispersive enemies in small and isolated
 patches, and (iii) reduced dispersal evolves in small, isolated
 populations. We sampled patches in a natural metacommunity and found
 support for all hypotheses; Eurosta's specialist wasp parasitoid
 attacked fewer galls in small and isolated patches, generating a selection
 gradient that favoured small galls resistant to predation by a dispersive
 and generalist bird predator. Phenotype distributions matched this
 selection gradient, and these phenotypic differences were maintained in a
 common garden experiment. Finally, we found lower dispersal abilities in
 small and isolated patches, a phenotypic shift that aids in the
 maintenance of local adaptation. We suggest that the trophic rank and the
 species traits of consumers are central to evolution in metacommunities.
description: eurosta.dispersal.data.Start&Gilbert2016Sheet 1 represents data on gall size and attack rates of natural enemies. Patch is a unique number for each patch of goldenrod. Distance is the distance in meter from the largest patch to the focal patch. Stems is the number of ramets of goldenrod in the focal patch. Gall is the number of galls in a particular patch. Fly is binary where 0 represents Eurosta having died for any reason whereas 1 represents Eurosta which survived. Larvae is the same as fly but replaces zeros with NAs when there is no gall present in the line. Bird is binary where 0=no and 1=yes bird attack. Mordellistena, eury.obs, and eury.gig represent attack by different parasitoid species and are coded identically to bird attack. Diameter is the maximum horizontal diameter of the gall in mm. Sheet 2 shows data on dispersal data for individual eurosta. Individual is a unique identifier for each individual Eurosta. Patch is the natal patch of the focal Eurosta. Stems and distance are as described above. Gall refers to the gall number in sheet 1. Time represents when the data on each individual was collect where 1,2,3, and 4 represent 2,4,6, and 24 hours after release respectively. Dispersal is the cumulative distance moved by that fly in meters.gall.attack.data.Start&Gilbert2016.xlsx
DOI: 10.5061/dryad.md416
title: Data from: A dynamic state model of migratory behavior and physiology to assess the consequences of environmental variation and anthropogenic disturbance on marine vertebrates

description: Integrating behavior and physiology is critical to formulating new
 hypotheses on the evolution of animal life-history strategies. Migratory
 capital breeders acquire most of the energy they need to sustain
 migration, gestation and lactation before parturition. Therefore, when
 predicting the impact of environmental variation on such species, a
 mechanistic understanding of the physiology of their migratory behavior is
 required. Using baleen whales as a model system, we developed a dynamic
 state variable model that captures the interplay among behavioral
 decisions, energy, reproductive needs and the environment. We applied the
 framework to blue whales (Balaenoptera musculus) in the Eastern North
 Pacific Ocean, and explored the effects of environmental and anthropogenic
 perturbations on female reproductive success. We demonstrate the emergence
 of migration to track prey resources, enabling us to quantify the
 trade-offs among capital breeding, body condition, and metabolic expenses.
 We predict that periodic climatic oscillations affect reproductive success
 less than unprecedented environmental changes do. The effect of localized,
 acute anthropogenic impacts depended on whales' behavioral response
 to the disturbance; chronic, but weaker, disturbances had little effect on
 reproductive success. Because we link behavior and vital rates by modeling
 individuals' energetic budgets, we provide a general framework to
 investigate the ecology of migration and assess the population
 consequences of disturbance, while identifying critical knowledge gaps.
description: Rcpp model code and
 associated filesThe archive includes the
 Rcpp code to run the Stochastic Dynamic Programming model, forward Monte
 Carlo simulations and sensitivity analysis. The data files required to run
 the model are also attached. These include the coordinates of model
 locations (file locs_100 km), the number of hours available to feed at
 different locations over time (file twilight_times_byLoc_forModel) and the
 upwelling index per location over time (file UpwellingIndex1). The details
 of how these data were generated are reported in the
 manuscript.Rcpp code +
 files.zip