cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.435h5
title: Data from: Incomplete host immunity favors the evolution of virulence in an emergent pathogen

description: Immune memory evolved to protect hosts from reinfection, but incomplete
 responses that allow future reinfection might inadvertently select for
 more harmful pathogens. We present empirical and modeling evidence that
 incomplete immunity promotes the evolution of higher virulence in a
 natural host-pathogen system. We performed sequential infections of house
 finches with Mycoplasma gallisepticum strains of varying virulence.
 Virulent bacterial strains generated stronger host protection against
 reinfection than less virulent strains, and thus excluded less virulent
 strains from infecting previously-exposed hosts. In a two-strain model,
 the resulting fitness advantage selected for an almost two-fold increase
 in pathogen virulence. Thus, the same immune systems that protect hosts
 from infection can concomitantly drive the evolution of more harmful
 pathogens in nature.
description: Data from sequential
 exposure experimentsWild-caught house
 finches were individually housed and sequentially inoculated with pairs of
 Mycoplasma gallisepticum strains that were either identical or of
 differing virulence. Measures include pathogen load, clinical signs
 ("Eye Score"), and ELISA S/P data for primary and secondary
 exposures.Exposuredata_bothyears.xls
DOI: 10.5061/dryad.4bm536k
title: Data from: A selective fungal transport organ (mycangium) maintains coarse phylogenetic congruence between fungus-farming ambrosia beetles and their symbionts

description: Thousands of species of ambrosia beetles excavate tunnels in wood to farm
 fungi. They maintain associations with particular lineages of fungi, but
 the phylogenetic extent and mechanisms of fidelity are unknown. We test
 the hypothesis that selectivity of their mycangium enforces fidelity at
 coarse phylogenetic scales, while permitting promiscuity among closely
 related fungal mutualists. We confirm a single evolutionary origin of the
 Xylosandrus complex – a group of several xyleborine genera that farm fungi
 in the genus Ambrosiella. Multi-level co-phylogenetic analysis revealed
 frequent symbiont switching within major Ambrosiella clades, but not
 between clades. The loss of the mycangium in Diuncus, a genus of
 evolutionary cheaters, was commensurate with loss of fidelity to fungal
 clades, supporting the hypothesis that the mycangium reinforces fidelity.
 Finally, in-vivo experiments tracked symbiotic compatibility throughout
 the symbiotic life cycle of Xylosandrus compactus and demonstrated that
 closely related Ambrosiella symbionts are interchangeable, but the
 probability of fungal uptake in the mycangium was significantly lower in
 more phylogenetically distant species of symbionts. Symbiont loads in
 experimental subjects were similar to wild-caught beetles. We conclude
 that partner choice in ambrosia beetles is achieved biochemically in the
 mycangium, and co-phylogenetic inferences can be used to predict the
 likelihood of specific symbiont switches.
description: swapping_experiments_dataRaw data from symbiont swapping experiments involving ambrosia beetle Xylosandrus compactus and five species of ambrosiella fungi.Fungi_tree_and_alignmentAlignment and tree from Ambrosiella fungi in nexus format.Beetle_tree_and_alignmentAlignment and tree for for ambrosia Xyleborini ambrosia beetles in Nexus format.scripts_used_phylogenyScripts used to generate ambrosia beetle and fungus phylogenies.
DOI: 10.5061/dryad.h22n9
title: Data from: Nonrandom dispersal drives phenotypic divergence within a bird population

description: Gene flow through dispersal has traditionally been thought to function as
 a force opposing evolutionary differentiation. However, directional gene
 flow may actually reinforce divergence of populations in close proximity.
 This study documents the phenotypic differentiation over more than two
 decades in body size (tarsus length) at a very short spatial scale (1.1
 km) within a population of pied flycatchers Ficedula hypoleuca inhabiting
 deciduous and coniferous habitats. Unlike females, males breeding in the
 deciduous forest were consistently larger than those from the managed
 coniferous forest. This assortment by size is likely explained by preset
 habitat preferences leading to dominance of the largest males and
 exclusion of the smallest ones toward the nonpreferred coniferous forest
 coupled with directional dispersal. Movements of males between forests
 were nonrandom with respect to body size and flow rate, which might
 function to maintain the phenotypic variation in this heritable trait at
 such a small spatial scale. However, a deeply rooted preference for the
 deciduous habitat might not be in line with its quality due to the
 increased levels of breeding density of hole-nesting competitors therein.
 These results illustrate how eco-evolutionary scenarios can develop under
 directional gene flow over surprisingly small spatial scales. Our findings
 come on top of recent studies concerning new ways in which dispersal and
 gene flow can influence microevolution.
description: INDIV_DATANB OCCUPATION_DATA
DOI: 10.5061/dryad.mq8r2
title: Data from: Hunting, exotic carnivores, and habitat loss: anthropogenic effects on a native carnivore community, Madagascar

description: The wide-ranging, cumulative, negative effects of anthropogenic
 disturbance, including habitat degradation, exotic species, and hunting,
 on native wildlife has been well documented across a range of habitats
 worldwide with carnivores potentially being the most vulnerable due to
 their more extinction prone characteristics. Investigating the effects of
 anthropogenic pressures on sympatric carnivores is needed to improve our
 ability to develop targeted, effective management plans for carnivore
 conservation worldwide. Utilizing photographic, line-transect, and habitat
 sampling, as well as landscape analyses and village-based bushmeat hunting
 surveys, we provide the first investigation of how multiple forms of
 habitat degradation (fragmentation, exotic carnivores, human encroachment,
 and hunting) affect carnivore occupancy across Madagascar’s largest
 protected area: the Masoala-Makira landscape. We found that as degradation
 increased, native carnivore occupancy and encounter rates decreased while
 exotic carnivore occupancy and encounter rates increased. Feral cats
 (Felis species) and domestic dogs (Canis familiaris) had higher occupancy
 than half of the native carnivore species across Madagascar’s largest
 protected landscape. Bird and small mammal encounter rates were negatively
 associated with exotic carnivore occupancy, but positively associated with
 the occupancy of four native carnivore species. Spotted fanaloka (Fossa
 fossana) occupancy was constrained by the presence of exotic feral cats
 and exotic small Indian civet (Viverricula indica). Hunting was intense
 across the four study sites where hunting was studied, with the highest
 rates for the small Indian civet ( individuals consumed/year), the
 ring-tailed vontsira (Galidia elegans) ( consumed/year), and the fosa
 (Cryptoprocta ferox) ( consumed/year). Our modeling results suggest
 hunters target intact forest where carnivore occupancy, abundance, and
 species richness, are highest. These various anthropogenic pressures and
 their effects on carnivore populations, especially increases in exotic
 carnivores and hunting, have wide-ranging, global implications and demand
 effective management plans to target the influx of exotic carnivores and
 unsustainable hunting that is affecting carnivore populations across
 Madagascar and worldwide.
description: Farris et al. Madagascar
 dataExcel data file
 containing the photographic captures of wildlife at seven sites, ranked by
 their varying degrees of degradation (S01-S07), across the Masoala-Makira
 landscape. Photographic capture data contains the common name, scientific
 name, number of photos, and number of individuals of each animal captured,
 as well as the date and time of the capture and the camera type the animal
 was photographed with and the type of human observed (researcher,
 non-researcher), where applicable.
DOI: 10.5061/dryad.5c6f6
title: Data from: Testing for multiple invasion routes and source populations for the invasive brown treesnake (Boiga irregularis) on Guam: implications for pest management

description: The brown treesnake (Boiga irregularis) population on the Pacific island
 of Guam has reached iconic status as one of the most destructive invasive
 species of modern times, yet no published works have used genetic data to
 identify a source population. We used DNA sequence data from multiple
 genetic markers and coalescent-based phylogenetic methods to place the
 Guam population within the broader phylogeographic context of B.
 irregularis across its native range and tested whether patterns of genetic
 variation on the island are consistent with one or multiple introductions
 from different source populations. We also modeled a series of demographic
 scenarios that differed in the effective size and duration of a population
 bottleneck immediately following the invasion on Guam, and measured the
 fit of these simulations to the observed data using approximate Bayesian
 computation. Our results exclude the possibility of serial introductions
 from different source populations, and instead verify a single origin from
 the Admiralty Archipelago off the north coast of Papua New Guinea. This
 finding is consistent with the hypothesis that B. irregularis was
 accidentally transported to Guam during military relocation efforts at the
 end of World War II. Demographic model comparisons suggest that multiple
 snakes were transported to Guam from the source locality, but that fewer
 than 10 individuals could be responsible for establishing the population.
 Our results also provide evidence that low genetic diversity stemming from
 the founder event has not been a hindrance to the ecological success of B.
 irregularis on Guam, and at the same time offers a unique ‘genetic
 opening’ to manage snake density using classical biological approaches.
description: mtDNA ND4, ND4L, and
 tRNAs nexus FileND4_ND4L_tRNAs.nexBi_TBP nexus fileTATA Box Binding proteinBi_TBP.nexRAG-1 nexus fileRecombination Activation Gene, subunit 1RAG-1.nexCmos nexus fileCmos proto-oncogeneCmos.nexMyHC-2 nexus fileMyosin Heavy Chain, type IIMyHC-2.nex
DOI: 10.34740/kaggle/dsv/14631439
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.5061/dryad.8518
title: Data from: Influence of Tertiary paleoenvironmental changes on the diversification of South American mammals: a relaxed molecular clock study within xenarthrans.

description: BACKGROUND: Comparative genomic data among organisms allow the
 reconstruction of their phylogenies and evolutionary time scales.
 Molecular timings have been recently used to suggest that environmental
 global change have shaped the evolutionary history of diverse terrestrial
 organisms. Living xenarthrans (armadillos, anteaters and sloths)
 constitute an ideal model for studying the influence of past environmental
 changes on species diversification. Indeed, extant xenarthran species are
 relicts from an evolutionary radiation enhanced by their isolation in
 South America during the Tertiary era, a period for which major climate
 variations and tectonic events are relatively well documented. RESULTS: We
 applied a Bayesian approach to three nuclear genes in order to relax the
 molecular clock assumption while accounting for differences in
 evolutionary dynamics among genes and incorporating paleontological
 uncertainties. We obtained a molecular time scale for the evolution of
 extant xenarthrans and other placental mammals. Divergence time estimates
 provide substantial evidence for contemporaneous diversification events
 among independent xenarthran lineages. This correlated pattern of
 diversification might possibly relate to major environmental changes that
 occurred in South America during the Cenozoic. CONCLUSIONS: The observed
 synchronicity between planetary and biological events suggests that global
 change played a crucial role in shaping the evolutionary history of extant
 xenarthrans. Our findings open ways to test this hypothesis further in
 other South American mammalian endemics like hystricognath rodents,
 platyrrhine primates, and didelphid marsupials.
description: Delsuc_BMCEvolBiol_2004_a2bv2Nucleotide alignment concatenation of codon positions 1+2 of ADRA2B and VWF plus all positions of BRCA1 for 50 mammalian taxa.Delsuc_BMCEvolBiol_2004_abv2Nucleotide alignment concatenation of codon positions 1+2 of ADRA2B, VWF and BRCA1 for 50 mammalian taxa.Delsuc_BMCEvolBiol_2004_abv3Nucleotide alignment concatenation of all codon positions of ADRA2B, BRCA1 and VWF for 50 mammalian taxa.Delsuc_BMCEvolBiol_2004_a2bv2Chronogram inferred from the a2bv2 dataset using Multidivtime.Delsuc_BMCEvolBiol_2004_abv2Chronogram inferred from the abv2 dataset using Multidivtime.Delsuc_BMCEvolBiol_2004_abv3Chronogram inferred from the abv3 dataset using Multidivtime.
DOI: 10.5061/dryad.3h46r
title: Data from: Having a lot of a good thing: multiple important group memberships as a source of self-esteem

description: Membership in important social groups can promote a positive identity. We
 propose and test an identity resource model in which personal self-esteem
 is boosted by membership in additional important social groups. Belonging
 to multiple important group memberships predicts personal self-esteem in
 children (Study 1a), older adults (Study 1b), and former residents of a
 homeless shelter (Study 1c). Study 2 shows that the effects of multiple
 important group memberships on personal self-esteem are not reducible to
 number of interpersonal ties. Studies 3a and 3b provide longitudinal
 evidence that multiple important group memberships predict personal
 self-esteem over time. Studies 4 and 5 show that collective self-esteem
 mediates this effect, suggesting that membership in multiple important
 groups boosts personal self-esteem because people take pride in, and
 derive meaning from, important group memberships. Discussion focuses on
 when and why important group memberships act as a social resource that
 fuels personal self-esteem.
description: Study 1a: Multiple group
 membership and self-esteem in childrenData is collected
 through surveys and compiled with the software package SPSS. Datafile
 contains items pertaining to multiple group membership (snoofgrps = number
 of groups children belong to, sgrp1name=group 1 name, sgrp1imp= importance
 of group 1, sgrp1fit = degree of fit).STUDY
 1A.children.savStudy 1b: Multiple group
 membership and self-esteem in older adultsData collected in the
 field, compiled using the software package SPSS.STUDY1B- older adults in
 China.savStudy 1c: Multiple group
 membership and self-esteem among homeless peopleSTUDY1C homeless
 sample.savStudy 2: Number of
 important groups versus number of friendsSTUDY2 school
 boys.savStudy 3a: University
 students in ChinaSTUDY3A-chinese university
 students.savStudy 3b: University
 students in AustraliaSTUDY3B-longformat W1-3 MGM and
 SE.savStudy
 4STUDY4-3groups.savStudy 5STUDY5- 7 groups-1.sav
DOI: 10.5061/dryad.7mj61
title: Data from: Elaborate visual and acoustic signals evolve independently in a large, phenotypically diverse radiation of songbirds

description: The concept of a macroevolutionary trade-off among sexual signals has a
 storied history in evolutionary biology. Theory predicts that if multiple
 sexual signals are costly for males to produce or maintain and females
 prefer a single, sexually selected trait, then an inverse correlation
 between sexual signal elaborations is expected among species. However,
 empirical evidence for what has been termed the ‘transfer hypothesis’ is
 mixed, which may reflect different selective pressures among lineages,
 evolutionary covariates or methodological differences among studies. Here,
 we examine interspecific correlations between song and plumage elaboration
 in a phenotypically diverse, widespread radiation of songbirds, the
 tanagers. The tanagers (Thraupidae) are the largest family of songbirds,
 representing nearly 10% of all songbirds. We assess variation in song and
 plumage elaboration across 301 species, representing the largest scale
 comparative study of multimodal sexual signalling to date. We consider
 whether evolutionary covariates, including habitat, structural and
 carotenoid-based coloration, and subfamily groupings influence the
 relationship between song and plumage elaboration. We find that song and
 plumage elaboration are uncorrelated when considering all tanagers,
 although the relationship between song and plumage complexity varies among
 subfamilies. Taken together, we find that elaborate visual and vocal
 sexual signals evolve independently among tanagers.
description: Appendix
 2Comma-separated values
 including data for each song and plumage complexity index for every
 species included in this study. Also includes categorizations in terms of
 presence and absence of structural and carotenoid coloration, habitat
 designation, and subfamily groupings.TipData.csvAppendix 1Raw data from 20 song characters for 321 species of tanagers.Appendix1.csvPosteriorTreesPosterior distribution of 50 phylogenies used in comparative analyses.
DOI: 10.5061/dryad.p0kj9
title: Data from: Life history traits and phenotypic selection among sunflower crop-wild hybrids and their wild counterpart: implications for crop allele introgression

description: Hybridization produces strong evolutionary forces. In hybrid zones,
 selection can differentially occur on traits and selection intensities may
 differ among hybrid generations. Understanding these dynamics in crop-wild
 hybrid zones can clarify crop-like traits likely to introgress into wild
 populations and the particular hybrid generations through which
 introgression proceeds. In a field experiment with four crop-wild hybrid
 Helianthus annuus (sunflower) cross types, we measured growth and life
 history traits and performed phenotypic selection analysis on early season
 traits to ascertain the likelihood, and routes, of crop allele
 introgression into wild sunflower populations. All cross types
 overwintered, emerged in the spring, and survived until flowering,
 indicating no early life history barriers to crop allele introgression.
 While selection indirectly favored earlier seedling emergence and taller
 early season seedlings, direct selection only favored greater early season
 leaf length. Further, there was cross type variation in the intensity of
 selection operating on leaf length. Thus, introgression of multiple early
 season crop-like traits, due to direct selection for greater early season
 leaf length, should not be impeded by any cross type and may proceed at
 different rates among generations. In sum, alleles underlying early season
 sunflower crop-like traits are likely to introgress into wild sunflower
 populations.
description: Kost_et_al_Dryad_1This data set has two tabs that will enable the analyses of percent spring emergence and probability that a planted seed flowered in the first year.Kost_et_al_Dryad_2This data set has two tabs that will enable the analyses of: 1) emergence date 2) census 1-3 height; 3) census 1-3 length of longest leaf; 4) survival to anthesis; and 5) the Pearson correlations presented in Table S1.Kost_et_al_Dryad_3This data set has two tabs that will enable the analyses of overall, cross type specific and density specific phenotypic selection analyses.
DOI: 10.5061/dryad.bv3c8b5
title: Data from: Parameters that remain consistent independent of pausing before gait-initiation during normal rise-to-walk behaviour delineated by sit-to-walk and sit-to-stand-and-walk

description: Background: Rising-to-walk is an everyday transitional movement task
 rarely employed in gait rehabilitation. Sit-to-walk (STW) and
 sit-to-stand-and-walk (STSW), where a pause separates sit-to-stand and
 gait-initiation (GI) represent extremes of rising-to-walk behaviour.
 Delayed GI can indicate pathological impairment but is also observed in
 healthy individuals. We hypothesise that healthy subjects express
 consistent biomechanical parameters, among others that differ, during
 successful rising-to-walk task performance regardless of behaviour. This
 study therefore sought to identify if any parameters are consistent
 between STW and STSW in health because they represent normal rise-to-walk
 performance independent of pause, and also because they represent
 candidate parameters sensitive enough to monitor change in pathology.
 Methods: Ten healthy volunteers performed 5 trials of STW and STSW. Event
 timing, ground-reaction-forces (GRFs), whole-body-centre-of-mass (BCoM)
 displacement, and centre-of-pressure (CoP) to extrapolated BCoM (xCoM)
 distance (indicator of positional stability) up to the 3rd step were
 compared between-tasks with paired t-tests. For consistent parameters;
 agreement between-tasks was assessed using Bland-Altman analyses and
 minimal-detectable-change (MDC) calculations. Results: Mean vertical GRFs,
 peak forward momentum and fluidity during rising; CoP-xCoM separation at
 seat-off, upright, GI-onset, and steps1-2; and forward BCoM velocity were
 all significantly greater in STW. In contrast, peak BCoM vertical
 momentum, flexion-momentum time, and 3rd step stability were consistent
 between tasks and yielded acceptable reliability. Conclusion: STW is a
 more challenging task due to the merging of rising with GI reflected by
 greater CoP-xCoM separation compared to STSW indicative of more positional
 instability. However, BCoM vertical momentum, flexion-momentum time, and
 step3 stability remained consistent in healthy individuals and are
 therefore candidates with which to monitor change in gait rehabilitation
 following pathology. Future studies should impose typical pause-durations
 observed in pathology upon healthy subjects to determine if the parameters
 we have identified remain consistent.
description: Sit-to-walk and
 sit-to-stand-and-walk in young healthy adultsData.xlsx
DOI: 10.5061/dryad.km170
title: Data from: A quantum Samaritan’s dilemma cellular automaton

description: The dynamics of a spatial quantum formulation of the iterated Samaritan’s
 dilemma game with variable entangling is studied in this work. The game is
 played in the cellular automata manner, i.e. with local and synchronous
 interaction. The game is assessed in fair and unfair contests, in
 noiseless scenarios and with disrupting quantum noise.
description: qsdgca-dataThe zip file contains all the source date presented in the graphs of the article.
DOI: 10.5061/dryad.4b7k408g
title: Data from: An account of the taxonomy and distribution of Syllidae (Annelida, Polychaetes) in the eastern Mediterranean, with notes on the genus Prosphaerosyllis San Martín, 1984 in the Mediterranean

description: The syllid fauna of three locations in Crete and Israel (Eastern
 Mediterranean Sea) was studied, yielding 82 syllid species, many of which
 were found for the first time in the respective areas: Seventeen species
 were recorded for the first time on the Israeli coasts and 20 in Greek
 waters. Perkinsyllis augeneri (Hartmann-Schröder, 1979) and
 Prosphaerosyllis chauseyensis Olivier et al., 2011 are new records for the
 Mediterranean Sea. Detailed information are given on the morphology,
 ecology and distribution of the species recorded for the first time in the
 studied areas. In addition, an update on the distribution of the genus
 Prosphaerosyllis San Martín, 1984 in the Mediterranean is given and an
 identification key is provided.
description: Eastern Mediterranean
 Syllidae (Polychaeta)EasternMedSyllidsOccurrence.csv