cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t1cc5
title: Data from: Evolutionary reconstruction supports the presence of a Pleistocene Arctic refugium for a large mammal species

description: Aim: The presence of refugia in the Canadian High Arctic has been subject
 to debate for decades. We investigated the potential existence of Arctic
 refugia during the Pleistocene for a large mammal species in the Canadian
 Archipelago because if these refugia were present, reconsideration of the
 evolutionary histories of North American fauna and flora beyond the major
 refugia of Beringia and south of the Laurentide and Cordilleran Ice Sheets
 would be required. Peary caribou (Rangifer tarandus pearyi), identified as
 a subspecies based on morphological characteristics, inhabits the Canadian
 Arctic Islands and Boothia Peninsula. Previous studies demonstrated
 incomplete lineage sorting of mitochondrial DNA interpreted as a Beringian
 origin but were based on small sample sizes. Location: Canadian Arctic.
 Major taxa studied: Mammals: caribou (Rangifer tarandus). Methods: We used
 two molecular markers (microsatellites and mitochondrial DNA) and
 approximate Bayesian computations (ABC) testing the hypotheses of
 colonization out of Beringia into the Arctic Islands following the Last
 Glacial Maximum (LGM) or a divergence from Beringia significantly before
 the end of the LGM within a different refugium. Results: The
 coalescent-based analyses rejected a recent Beringian origin with
 subsequent colonization, instead supporting a divergence of Peary caribou
 from Beringia ~100,000 years ago linking it to the last interglacial/early
 Wisconsin Glacial Stage (125,000–75,000 years ago). Admixture on Banks
 Island with Beringian-derived barren-ground caribou is indicative of
 post-Pleistocene secondary contact; further supporting a divergent history
 of Peary caribou within a separated Arctic refugium. Main conclusions: Our
 results offer support for the existence of an Arctic refugium for large
 mammal species and add to the increasing evidence of such refugia in North
 America. This has significant implications on understanding the evolution
 and conservation of Arctic species, particularly in light of sensitivities
 and adaptive potential to a rapidly changing climate.
description: Microsatellite data for:
 Evolutionary reconstruction supports the presence of a Pleistocene Arctic
 refugium for a large mammal speciesThis is the
 microsatellite data that was used in the paper with the title:
 Evolutionary reconstruction supports the presence of a Pleistocene Arctic
 refugium for a large mammal speciesRengifer_tarandus_microsatellites_2017-07-26.xlsx
DOI: 10.5061/dryad.bp479
title: Data from: Fresh frozen cortical strut allograft in two-level anterior cervical corpectomy and fusion

description: Anterior cervical corpectomy and fusion (ACCF) is one of the main surgical
 strategies for the management of multilevel cervical spondylotic
 myelopathy (MCSM). High complication rates of graft bone fracture,
 resorption, displacement, and fusion collapse or pseudarthrosis have been
 previously reported. The strategies to prevent the aforementioned
 complications include using fresh frozen cortical strut allograft (FFCSA)
 to keep most of the original bone quality and using additional anterior
 plate fixation to improve the fusion stability and union rate. In this
 study, we evaluated 4-year follow-ups for surgical outcomes and analyzed
 the risk factors of MCSM patients who received 2-level ACCF with FFCSA and
 titanium dynamic plate fixation. We retrospectively collected preoperative
 and postoperative radiographic and clinical data of patients from 2005 to
 2009; the inclusion criteria were having been diagnosed as MCSM and having
 received 2-level ACCF with an FFCSA fibular shaft and an anterior dynamic
 plate. The cervical curvature lordosis improved and the neurogenic
 function recovered well postoperatively. Visual analog scale for neck pain
 and neck disability index scores both decreased after 12 and 48 months
 following surgery. The Japanese Orthopaedic Association score recovery
 rate at postoperative 4 years was 87.5%. Fusion rates achieved 100% at 12
 months. The preoperative Nurick score seemed to be the only significant
 risk factor correlated with the functional recovery rate at 4 years after
 the surgery. In conclusion, based on a minimum 4-year follow-up of 2-level
 ACCF with FFCSA and dynamic titanium plates for patients with MCSM, the
 surgical results were satisfying and the complication rates were low.
description: ACCF Raw
 DataRaw data of surgical
 results of our ACCF patients series
DOI: 10.5061/dryad.16m3n
title: Data from: Peptides derived from cadherin juxtamembrane region inhibit platelet function

description: The juxtamembrane domains (JMD) of transmembrane proteins are rich in
 critical peptide sequences that participate in dynamic cell signaling
 events. Synthetic JMD peptides derived from cadherin cell adhesion
 proteins have previously been shown to modulate platelet function. In this
 study, we aimed to develop functional bioactive agents from
 bioinformatically-identified critical peptide sequences. We synthesized
 overlapping 12-15 amino acids peptides from E- and N-cadherin JMD and
 assessed their effect on platelet aggregation and platelet ATP secretion.
 Peptides derived from close to the membrane proximal region inhibit
 platelet function. Sequential deletion of amino acids from the N- and
 C-termini of the inhibitory E-cadherin peptides identified the short
 K756EPLLP763 motif as a critical bioactive sequence. Alanine scanning
 studies further identified that the dileucine (LL) motif and positively
 charged lysine (K) are crucial for peptide activity. Moreover, scrambled
 peptides failed to show any effect on platelet activity. We conclude that
 peptides derived from JMD of E-cadherin provide potential lead peptides
 for the development of anti-thrombotic agents and to enable further
 understanding of the role of cadherins in platelet function.
description: Modified and updated
 data of Peptides derived from cadherin juxtamembrane region inhibit
 platelet functionThis includes raw data
 of used for this manuscript.Golla et
 al.xls
DOI: 10.5061/dryad.b191j
title: Data from: Pairing context determines condition-dependence of song rate in a monogamous passerine bird

description: Condition-dependence of male ornaments is thought to provide honest
 signals on which females can base their sexual choice for genetic quality.
 Recent studies show that condition-dependence patterns can vary within
 populations. Although long-term association is thought to promote honest
 signalling, no study has explored the influence of pairing context on the
 condition-dependence of male ornaments. In this study, we assessed the
 influence of natural variation in body condition on song rate in zebra
 finches (Taeniopygia guttata) in three different situations: during short
 and long encounters with an unfamiliar female, and within heterosexual
 mated pairs. We found consistent individual differences in male directed
 and undirected song rate. Moreover, body condition had a positive effect
 on song rate in paired males. However, male song rate was not influenced
 by body condition during short or long encounters with unfamiliar females.
 Song rate appears to be an unreliable signal of condition to prospective
 females as even poor-condition birds can cheat and sing at a high rate. By
 contrast, paired females can reliably use song rate to assess their
 mate's body condition, and possibly the genetic quality. We propose
 that species' characteristics, such as mating system, should be
 systematically taken into account to generate relevant hypotheses about
 the evolution of condition-dependent male ornaments.
description: Data
 fileData on song rate as a
 function of treatmentsdata_dryad.xls
DOI: 10.5061/dryad.86pg46n
title: Data from: Patterns of cross-resistance and collateral sensitivity between clinical antibiotics and natural antimicrobials

description: Bacteria interact with a multitude of other organisms, many of which
 produce antimicrobials. Selection for resistance to these antimicrobials
 has the potential to result in resistance to clinical antibiotics when
 active compounds target the same bacterial pathways. The possibility of
 such cross-resistance between natural antimicrobials and antibiotics has
 to our knowledge received very little attention. The antimicrobial
 activity of extracts from seaweeds, known to be prolific producers of
 antimicrobials, is here tested against Staphylococcus aureus isolates with
 varied clinical antibiotic resistance profiles. An overall effect
 consistent with cross-resistance is demonstrated, with multi-drug
 resistant S. aureus strains being on average more resistant to seaweed
 extracts. This pattern could potentially indicate that evolution of
 resistance to antimicrobials in the natural environment could lead to
 resistance against clinical antibiotics. However, patterns of
 antimicrobial activity of individual seaweed extracts vary considerably
 and include collateral sensitivity, where increased resistance to a
 particular antibiotic is associated with decreased resistance to a
 particular seaweed extract. Our correlation-based methods allow the
 identification of antimicrobial extracts bearing most promise for
 downstream active compound identification and pharmacological testing
description: Raw data and calculation
 of seaweed/antibiotic resistance scoresContained here is the
 raw data for "Patterns of cross-resistance and collateral sensitivity
 between clinical antibiotics and natural antimicrobials" accepted for
 publication in Evolutionary ApplicationsRaw and simplified
 data_AC_16_10_18.xlsx
DOI: 10.5061/dryad.3634m
title: Data from: Infectious disease dynamics inferred from genetic data via sequential Monte Carlo

description: Genetic sequences from pathogens can provide information about infectious
 disease dynamics that may supplement or replace information from other
 epidemiological observations. Most currently available methods first
 estimate phylogenetic trees from sequence data, then estimate a
 transmission model conditional on these phylogenies. Outside limited
 classes of models, existing methods are unable to enforce logical
 consistency between the model of transmission and that underlying the
 phylogenetic reconstruction. Such conflicts in assumptions can lead to
 bias in the resulting inferences. Here, we develop a general,
 statistically efficient, plug-and-play method to jointly estimate both
 disease transmission and phylogeny using genetic data and, if desired,
 other epidemiological observations. This method explicitly connects the
 model of transmission and the model of phylogeny so as to avoid the
 aforementioned inconsistency. We demonstrate the feasibility of our
 approach through simulation and apply it to estimate stage-specific
 infectiousness in a subepidemic of HIV in Detroit, Michigan. In a
 supplement, we prove that our approach is a valid sequential Monte Carlo
 algorithm. While we focus on how these methods may be applied to
 population-level models of infectious disease, their scope is more
 general. These methods may be applied in other biological systems where
 one seeks to infer population dynamics from genetic sequences, and they
 may also find application for evolutionary models with phenotypic rather
 than genotypic data.
description: Simulation
 StudyThis set of files
 contains scripts and data for replicating results of the simulation study
 presented in Figure 4.simulation_study.tar.gz
DOI: 10.5061/dryad.8m68k
title: Data from: Transgenerational plasticity following a dual pathogen and stress challenge in fruit flies

description: Background: Phenotypic plasticity operates across generations, when the
 parental environment affects phenotypic expression in the offspring.
 Recent studies in invertebrates have reported transgenerational plasticity
 in phenotypic responses of offspring when the mothers had been previously
 exposed to either live or heat-killed pathogens. Understanding whether
 this plasticity is adaptive requires a factorial design in which both
 mothers and their offspring are subjected to either the pathogen challenge
 or a control, in experimentally matched and mismatched combinations. Most
 prior studies exploring the capacity for pathogen-mediated
 transgenerational plasticity have, however, failed to adopt such a design.
 Furthermore, it is currently poorly understood whether the magnitude or
 direction of pathogen-mediated transgenerational responses will be
 sensitive to environmental heterogeneity. Here, we explored the
 transgenerational consequences of a dual pathogen and stress challenge
 administered in the maternal generation in the fruit fly, Drosophila
 melanogaster. Prospective mothers were assigned to a non-infectious
 pathogen treatment consisting of an injection with heat-killed bacteria or
 a procedural control, and a stress treatment consisting of sleep
 deprivation or control. Their daughters and sons were similarly assigned
 to the same pathogen treatment, prior to measurement of their reproductive
 success. Results: We observed transgenerational interactions involving
 pathogen treatments of mothers and their offspring, on the reproductive
 success of daughters but not sons. These interactions were unaffected by
 sleep deprivation. Conclusions: The direction of the transgenerational
 effects was not consistent with that predicted under a scenario of
 adaptive transgenerational plasticity. Instead, they were indicative of
 expectations based on terminal investment.
description: Nystrand et al. 2016.
 Transgenerational plasticity in fruit fliesExcel file containing
 experimental data for females and males.Nystrand et al. 2016. Dryad
 data BMC.xlsx
DOI: 10.5061/dryad.kk94gp2
title: Data from: Environmental estrogens cause predation-induced population decline in a freshwater fish

description: Understanding population-level effects of environmental stressors on
 aquatic biota requires knowledge of the direct adverse effects of
 pollutants on individuals and species interactions that relate to survival
 and reproduction. Here, we connect behavioral assays with survival trials
 and a modeling approach to quantify changes in antipredator escape
 performance of a larval freshwater fish following exposure to an
 environmental estrogen, and predict changes in population abundance. We
 quantified the effects of short-term (21 d) exposure to 17-β estradiol
 (E2) on the antipredator escape performance of larval fathead minnows
 (Pimephales promelas) and the probability of predation by a natural
 predator, the bluegill sunfish (Lepomis macrochirus). Compared with
 unexposed minnows, minnows exposed to environmentally relevant
 concentrations of E2 that approach total estrogenic activity of
 waste-water dominated environments (38 and 103 ng/L) had delayed response
 times and slower escape speeds, and were more susceptible to predation.
 Incorporating these data into a stage-structured population model
 demonstrated that enhanced predation mortality at the larval stage is
 sufficient to generate marked population declines. These results indicate
 that subtle, sub-lethal shifts in the behavior of individuals due to
 human-mediated environmental change can impact species interactions with
 measurable population-level effects. Such changes have the potential to
 alter higher-order trophic interactions and disrupt aquatic communities.
description: Performance_Predation_DataRaw behavioral datamodel_codeCode for the model.
DOI: 10.5061/dryad.pq84q
title: Data from: Early stages of sea-level rise lead to decreased salt marsh plant diversity through stronger competition in Mediterranean-climate marshes

description: Climate change shuffles species ranges and creates novel interactions that
 may either buffer communities against climate change or exacerbate its
 effect. For instance, facilitation can become more prevalent in salt
 marshes under stressful conditions while competition is stronger in benign
 environments. Sea-level rise (SLR) is a consequence of climate change that
 affects the distribution of stress from inundation and salinity. To
 determine how interactions early in SLR are affected by changes in these
 two stressors in Mediterranean-climate marshes, we transplanted marsh
 turfs to lower elevations to simulate SLR and manipulated cover of the
 dominant plant species, Salicornia pacifica (formerly Salicornia
 virginica). We found that both S. pacifica and the subordinate species
 were affected by inundation treatments, and that subordinate species cover
 and diversity were lower at low elevations in the presence of S. pacifica
 than when it was removed. These results suggest that the competitive
 effect of S. pacifica on other plants is stronger at lower tidal
 elevations where we also found that salinity is reduced. As sea levels
 rise, stronger competition by the dominant plant will likely reduce
 diversity and cover of subordinate species, suggesting that stronger
 species interactions will exacerbate the effects of climate change on the
 plant community.
description: Sea-level rise
 experiment plant cover dataRaw plant cover data
 collected from experimental sea-level rise plots from spring 2013 through
 fall 2015. Readme has description of species and other data
 codes.plant
 cover.csvSalinity
 dataSalinity data for
 experimental sea-level rise plots from spring 2013 through fall 2015.
 Column names described in Readme file.Env all
 times.csv
DOI: 10.15468/dl.ubkj2t
title: Occurrence Download

description: A dataset containing 32 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Physochlaina orientalis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 32 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000975-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.0p1f5
title: Data from: Testing the CREA ‘rule’ in Galliformes

description: Recent comparative studies have indicated the existence of a common
 cranial evolutionary allometric (CREA) pattern in mammals and birds, in
 which smaller species have relatively smaller faces and bigger braincases
 than larger species. In these studies, cranial allometry was tested using
 a multivariate regression between shape (described using landmarks
 coordinates) and size (i.e. centroid size), after accounting for
 phylogenetic relatedness. Alternatively, cranial allometry can be
 determined by comparing the sizes of two anatomical parts using a
 bivariate regression analysis. In this analysis, a slope higher or lower
 than 1 indicates the existence of positive or negative allometry,
 respectively. Thus, in those species that support the CREA
 'rule', positive allometry is expected for the association
 between face size and braincase size, which would indicate that larger
 species have disproportionally larger faces. In the present study, I
 applied these two approaches to explore cranial allometry in 83
 Galliformes (Aves, Galloanserae), ranging in body weight from 30 g to 2.5
 kg. The multivariate regression between shape and centroid size revealed
 the existence of a significant allometric pattern resembling CREA, whereas
 the second analysis revealed a negative allometry for beak size and
 braincase size (i.e. contrary to the CREA 'rule', larger
 galliform species have disproportionally shorter beaks than smaller
 galliform species). This study suggests that the presence of CREA may be
 overestimated when using cranium size as the standard measurement.
description: GalliformesCraniumData set of 3D coordinates of 26 landmarks describing cranium shape of Galliformes (Aves, Galloanserae).
DOI: 10.5061/dryad.pt38f8s
title: Data from: Estimating range expansion of wildlife in heterogeneous landscapes: a spatially explicit state-space matrix model coupled with an improved numerical integration technique

description: Dispersal as well as population growth is a key demographic process that
 determines population dynamics. However, determining the effects of
 environmental covariates on dispersal from spatial-temporal abundance
 proxy data is challenging owing to the complexity of model specification
 for directional dispersal permeability and the extremely high
 computational loads for numerical integration. In this paper, we present a
 case study estimating how environmental covariates affect the dispersal of
 Japanese sika deer by developing a spatially explicit state-space matrix
 model coupled with an improved numerical integration technique (Markov
 chain Monte Carlo with particle filters). In particular, we explored the
 environmental drivers of inhomogeneous range expansion, characteristic of
 animals with short dispersal. Our model framework successfully reproduced
 the complex population dynamics of sika deer, including rapid changes in
 densely populated areas and distribution fronts within a decade.
 Furthermore, our results revealed that the inhomogeneous range expansion
 of sika deer seemed to be primarily caused by the dispersal process (i.e.,
 movement barriers in fragmented forests) rather than population growth.
 Our state-space matrix model enables the inference of population dynamics
 for a broad range of organisms, even those with low dispersal ability, in
 heterogeneous landscapes, and could address many pressing issues in
 conservation biology and ecosystem management.
description: data
DOI: 10.5061/dryad.5vr86
title: Data from: Specificity of oral immune priming in the red flour beetle Tribolium castaneum

description: Immune specificity is the degree to which a host’s immune system
 discriminates among various pathogens or antigenic variants. Vertebrate
 immune memory is highly specific due to antibody responses. On the other
 hand, some invertebrates show immune priming, i.e. improved survival after
 secondary exposure to a previously encountered pathogen. Until now,
 specificity of priming has only been demonstrated via the septic infection
 route or when live pathogens were used for priming. Therefore, we tested
 for specificity in the oral priming route in the red flour beetle,
 Tribolium castaneum. For priming, we used pathogen-free supernatants
 derived from three different strains of the entomopathogen, Bacillus
 thuringiensis, which express different Cry toxin variants known for their
 toxicity against this beetle. Subsequent exposure to the infective spores
 showed that oral priming was specific for two naturally occurring strains,
 while a third engineered strain did not induce any priming effect. Our
 data demonstrate that oral immune priming with a non-infectious bacterial
 agent can be specific, but the priming effect is not universal across all
 bacterial strains.
description: Raw data associated with
 Futo et al Biology LettersSurvival data after
 priming-challengeFuto et al Biolett
 data.xlsx