cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2bq8g
title: Data from: Fear mediates trophic cascades: nonconsumptive effects of predators drive aquatic ecosystem function

description: Predators control prey populations and influence communities and the
 functioning of ecosystems through a combination of consumptive and
 nonconsumptive effects. These effects can be locally confined to one
 ecosystem but can also be extended to neighboring ecosystems. In this
 study, we investigated the nonconsumptive effects of terrestrial avian
 predators on the communities of aquatic invertebrates inhabiting
 bromeliads and on the functioning of these natural ecosystems. Bromeliads
 with stuffed birds placed nearby showed a decrease in aquatic damselfly
 larvae abundance and biomass, and we can infer that these changes were
 caused by antipredator responses. These larvae, which are top predators in
 bromeliad ecosystems, changed the composition of the entire aquatic
 invertebrate community. While total species richness, mesopredator
 richness, and shredder abundance increased in the presence of birds,
 scraper biomass decreased, possibly as a consequence of the increase in
 mesopredator richness. High scraper biomass in the absence of birds may
 have accelerated detrital decomposition, making more nutrients available
 for bromeliads, which grew more. These results show that nonconsumptive
 effects triggered by terrestrial predators can cascade down to lower
 trophic levels and dramatically affect the functioning of aquatic
 ecosystems, which can in turn alter nutrient provision to terrestrial
 ecosystems.
description: Final_data_set
DOI: 10.5061/dryad.g4g11
title: Data from: Studies in Lichens and Lichenicolous Fungi – no. 18: resolution of three names introduced by Degelius and Magnusson based on material from the Great Smoky Mountains

description: Arthonia biseptata is shown to be a species of Mycoporum, likely narrowly
 endemic to high elevations of the southern Appalachian Mountains and the
 new combination M. biseptatum is proposed. Lecidea degelii is shown to
 apply to the sorediate morphotype of Porpidia albocaerulescens. The
 results of molecular phylogenetic analyses of nrITS and mtSSU sequence
 data of sorediate and esorediate populations of P. albocaerulescens are
 presented. These analyses recovered the sorediate and esorediate
 morophotypes together in a single clade as strongly-supported monophyletic
 entities. As a result the new combination Porpidia degelii is proposed,
 the species illustrated, and the North American distribution of P. degelii
 with respect to P. albocaerulescens is discussed. These data strongly
 refute the notion that “species pairs” do not exist in Porpidia. Lecidea
 subtilis is placed in synonymy with Pyrrhospora varians.
description: Lendemer_Harris_datapacketThis zipped folder contains the input files for molecular phylogenetic analyses performed on sequences of Porpidia albocaerulescens s.l. This includes the following: 1) inputs for maximum parsimony, maximum likelihood and Bayesian inference analyses of an nrITS dataset, 2) inputs for maximum parsimony, maximum likelihood and Bayesian inference analyses of an mtSSU dataset, and 3) inputs for supplemental analyses of the same dataset with an additional sequence from GenBank that was added after the initial submission of the manuscript.
DOI: 10.5061/dryad.21j7k3f
title: Data from: Fire-sensitive species dominate seed rain in a long unburned Cerrado: implications for plant community diversity and woody encroachment in savannas

description: Woody encroachment is becoming common in tropical savannas. Seed rain data
 and seed addition experiments in a long unburned Brazilian savanna
 indicate that abundant seed rain of fire-sensitive species can surpass
 limitations to recruitment and lead to woody encroachment. Thus, active
 fire management may be required to maintain savanna diversity.
description: Vegetation, seed rain
 and limitation dataThis file contains
 information on aboveground vegetation, seed rain, seed and establishment
 limitations, per capita seed germination, species traits, and regression
 results (influence of species traits on limitation values). This study was
 conducted in a neotropical savanna (Cerrado) in southeast
 Brazil.Mariano et al -
 Data.xlsx
DOI: 10.5061/dryad.gb4kh
title: Data from: Phylogeographic structure and outbreeding depression reveal early stages of reproductive isolation in the Neotropical orchid Epidendrum denticulatum

description: Phylogeographic studies provide an important framework for investigating
 the mechanisms operating during the earliest stages of speciation, as
 reproductive barriers can be examined among divergent lineages in a
 geographic context. We investigated the evolution of early stages of
 intrinsic postmating isolation among different populations and lineages of
 Epidendrum denticulatum, a Neotropical orchid distributed across different
 biomes in South America. We estimated genetic diversity and structure for
 both nuclear and plastid markers, using a haplotype network,
 differentiation tests, Bayesian assignment analysis, and divergence time
 estimates of the main lineages. Reproductive barriers among divergent
 lineages were examined by analyzing seed viability following reciprocal
 crossing experiments. Strong plastid phylogeographic structure was found,
 indicating that E. denticulatum was restricted to multiple refuges during
 South American forest expansion events. In contrast, significant
 phylogeographic structure was not found for nuclear markers, suggesting
 higher gene flow by pollen than by seeds. Large asymmetries in seed set
 were observed among different plastid genetic groups, suggesting the
 presence of polymorphic genic incompatibilities associated with
 cytonuclear interactions. Our results confirm the importance of
 phylogeographic studies associated with reproductive isolation experiments
 and suggest an important role for outbreeding depression during the early
 stages of lineage diversification.
description: inputdata_nuclear_microsatsArlequin inputfile of nuclear microsatellitesinputdata_plastid_microsatsArlequin inputfile of plastid microsatellitesplastid_haplotype_listPlastid haplotype list for use in Arlequin software
DOI: 10.5061/dryad.81884
title: Data from: Differentiation at the MHCIIα and Cath2 loci in sympatric Salvelinus alpinus resource morphs in Lake Thingvallavatn

description: Northern freshwater fish may be suitable for the genetic dissection of
 ecological traits because they invaded new habitats after the last ice age
 (~10.000 years ago). Arctic charr (Salvelinus alpinus) colonizing streams
 and lakes in Iceland gave rise to multiple populations of small benthic
 morphotypes, often in sympatry with a pelagic morphotype. Earlier studies
 have revealed significant, but subtle, genetic differentiation between the
 three most common morphs in Lake Thingvallavatn. We conducted a population
 genetic screen on four immunological candidate genes Cathelicidin 2
 (Cath2), Hepcidin (Hamp), Liver expressed antimicrobial peptide 2a
 (Leap-2a), and Major Histocompatibility Complex IIα (MHCIIα) and a
 mitochondrial marker (D-loop) among the three most common Lake
 Thingvallavatn charr morphs. Significant differences in allele frequencies
 were found between morphs at the Cath2 and MHCIIα loci. No such signal was
 detected in the D-loop nor in the other two immunological genes. In Cath2
 the small benthic morph deviated from the other two (FST = 0.13), one of
 the substitutions detected constituting an amino acid replacement
 polymorphism in the antimicrobial peptide. A more striking difference was
 found in the MHCIIα. Two haplotypes were very common in the lake, and
 their frequency differed greatly between the morphotypes (from 22% to
 93.5%, FST = 0.67). We then expanded our study by surveying the variation
 in Cath2 and MHCIIα in 9 Arctic charr populations from around Iceland. The
 populations varied greatly in terms of allele frequencies at Cath2, but
 the variation did not correlate with morphotype. At the MHCIIα locus, the
 variation was nearly identical to the variation in the two benthic morphs
 of Lake Thingvallavatn. The results are consistent with a scenario where
 parts of the immune systems have diverged substantially among Arctic charr
 populations in Iceland, after colonizing the island ~10.000 years ago.
description: Kapralova2013_Charr2005Dataset 1 – Arctic Charr from Lake Thingvallavatn, collected in 2005. Collected in the field, phenotype and genotype of MHCIIalpha described in the lab.Kapralova2013_Charr2010Dataset 1 – Arctic Charr from Lake Thingvallavatn, collected in 2010. Captured in the wild, phenotyped and genotyped in the laboratory.
DOI: 10.5061/dryad.8d2f6
title: Data from: Two-phase importance sampling for inference about transmission trees

description: There has been growing interest in the statistics community to develop
 methods for inferring transmission pathways of infectious pathogens from
 molecular sequence data. For many datasets, the computational challenge
 lies in the huge dimension of the missing data. Here, we introduce an
 importance sampling scheme in which the transmission trees and phylogenies
 of pathogens are both sampled from reasonable importance distributions,
 alleviating the inference. Using this approach, arbitrary models of
 transmission could be considered, contrary to many earlier proposed
 methods. We illustrate the scheme by analysing transmissions of
 Streptococcus pneumoniae from household to household within a refugee
 camp, using data in which only a fraction of hosts is observed, but which
 is still rich enough to unravel the within-household transmission dynamics
 and pairs of households between whom transmission is plausible. We observe
 that while probability of direct transmission is low even for the most
 prominent cases of transmission, still those pairs of households are
 geographically much closer to each other than expected under random
 proximity.
description: Parsimony SNP trees for
 bacterial isolatesThis file contains
 parsimonious SNP trees for Streptococcus Pneumoniae isolates. Trees are
 constructed for serotypes NT, 23F, 23AF, 19F, 15BC, 14 and 6B, that were
 the most common serotypes in the original cohort study. This study
 assessed pneumococcal colonization in infants and their mothers, who lived
 in a refugee camp in Northwestern Thailand. The trees contain the
 following information for each isolate: MLST genotypes, household labels,
 mother/infant designation and sampling dates.data from Two phase importance
 sampling for inference about transmission
 trees.zip
DOI: 10.5061/dryad.kt845
title: Data from: The cost of migration: spoonbills suffer higher mortality during trans-Saharan spring migrations only

description: Explanations for the wide variety of seasonal migration patterns of
 animals all carry the assumption that migration is costly and that this
 cost increases with migration distance. Although in some studies, the
 relationships between migration distance and breeding success or annual
 survival are established, none has investigated whether mortality during
 the actual migration increases with migration distance. Here, we compared
 seasonal survival between Eurasian spoonbills (Platalea leucorodia
 leucorodia) that breed in The Netherlands and migrate different distances
 (ca 1000, 2000 and 4500 km) to winter in France, Iberia and Mauritania,
 respectively. On the basis of resightings of individually marked birds
 throughout the year between 2005 and 2012, we show that summer, autumn and
 winter survival were very high and independent of migration distance,
 whereas mortality during spring migration was much higher (18%) for the
 birds that wintered in Mauritania, compared with those flying only as far
 as France (5%) or Iberia (6%). As such, this study is the first to show
 empirical evidence for increased mortality during some long migrations,
 likely driven by the presence of a physical barrier (the Sahara desert) in
 combination with suboptimal fuelling and unfavourable weather conditions
 en route.
description: Seasonal resighting
 histories of adult Eurasian spoonbillsThe datafile contains
 seasonal resighting histories of 538 adult Eurasian spoonbills that breed
 in the Netherlands or Germany and winter in France, Iberia or Mauritania,
 resighted between October 2005 and September 2012. Resighting periods are
 defined as October-December and January-March in an individual's
 wintering area and April-June and July-September in the breeding areas in
 The Netherlands and Germany. The resighting history of an individual
 starts with the first resighting as an adult (3rd winter or older) in its
 wintering region, being France, Iberia or Mauritania (and indicated in the
 column "group" of the datafile). Further details can be found in
 the Supplementary Material associated with the
 manuscript.Seasonal_resighting_histories_spoonbills_2005_2012.txt
DOI: 10.15468/dl.hrfq53
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leptomicrurus collaris"
 ]
}

 The dataset includes 14 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001273-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.t7t54
title: Data from: Bacterial motility confers fitness advantage in the presence of phages

description: Dispersal provides the opportunity to escape harm and colonize new
 patches, enabling populations to expand and persist. However, the benefits
 of dispersal associated with escaping harm will be dependent on the
 structure of the environment and the likelihood of escape. Here, we
 empirically investigate how the spatial distribution of a parasite
 influences the evolution of host dispersal. Bacteriophages are a strong
 and common threat for bacteria in natural environments and offer a good
 system with which to explore parasite-mediated selection on host
 dispersal. We used two transposon mutants of the opportunistic bacteria,
 Pseudomonas aeruginosa, which varied in their motility (a disperser and a
 nondisperser), and the lytic bacteriophage ФKZ. The phage was distributed
 either in the central point of colony inoculation only, thus offering an
 escape route for the dispersing bacteria; or, present throughout the agar,
 where benefits of dispersal might be lost. Surprisingly, we found
 dispersal to be equally advantageous under both phage conditions relative
 to when phages were absent. A general explanation is that dispersal
 decreased the spatial structuring of host population, reducing
 opportunities for parasite transmission, but other more idiosyncratic
 mechanisms may also have contributed. This study highlights the crucial
 role the parasites can play on the evolution of dispersal and, more
 specifically, that bacteriophages, which are ubiquitous, are likely to
 select for bacterial motility.
description: Figure 2a and b Area
 DispersedData shows the colony
 area of Pseudomonas aeruginosa after 48 hours growth and dispersal under
 different phage treatments (no phage, local phage and global phage), and
 different agar types (hard and soft). Data was collected in vitro and
 excel was used to create data file.Figure 3 Relative
 fitnessData shows the relative
 fitness of dispersers to non-dispersers (i.e. CFU disperser/ CFU
 non-disperser) in Pseudomonas aeruginosa after 48 hours growth and
 dispersal. Motility variants were tested across three treatment groups: No
 Phage, Local Phage and Global Phage. Excel was used to create the data
 file.
DOI: 10.5061/dryad.h768p
title: Data from: Frequent coinfection reduces RNA virus population genetic diversity

description: The masking of deleterious mutations by complementation and the
 reassortment of virus segments (virus sex) are expected to increase
 population genetic diversity among coinfecting viruses. Conversely,
 clonally reproducing or noncoinfecting virus populations may experience
 clonal interference where viral clones compete with one another,
 preventing selective sweeps. This dynamic reduces the efficiency of
 selection and increases the genetic diversity. To determine the relative
 influences of these forces on population genetic diversity, we evolved 6
 populations of bacteriophage φ6 under conditions promoting or preventing
 coinfection. Following 300 generations, we isolated and partially
 sequenced 10 clones from each population. We found greater diversity among
 asexual populations than sexual populations. Moreover, sexual populations
 did not show greater relative fitnesses than asexual populations, implying
 that reduced genetic variation did not result from purifying selection.
 However, sexual populations were less genetically robust than asexual
 populations and likely more prone to the deleterious epistatic effects of
 mutations. As such, a neutral mutation on the asexually evolved (robust)
 background could be profoundly deleterious on the sexually evolved
 (brittle) background. This could facilitate sexual populations undergoing
 greater purifying selection to remove deleterious mutations, but this
 selection is not reflected by increases in average population fitness. Our
 results bolster a growing literature suggesting that RNA virus
 segmentation is probably not a mechanism that evolved because it provides
 a generalized benefit of sex.
description: Dennehy et al. 2013
 JHered fitness dataFitness data of clones
 obtained from phage phi6 populations evolved at high and low MOI. Each
 clone's fitness was estimated 3x. Fitness estimated using equation: W
 = log(Nf/Ni) where Nf is the final population titer (pfus) after overnight
 growth on Pseudomonas phaseolicola and Ni is the initial inoculum
 size.
DOI: 10.5061/dryad.7fj38
title: Data from: Phenotypic divergence of the common toad (Bufo bufo) along an altitudinal gradient: evidence for local adaptation

description: Variation in the environment can induce different patterns of genetic and
 phenotypic differentiation among populations. Both neutral processes and
 selection can influence phenotypic differentiation. Altitudinal phenotypic
 variation is of particular interest in disentangling the interplay between
 neutral processes and selection in the dynamics of local adaptation
 processes but remains little explored. We conducted a common garden
 experiment to study the phenotypic divergence in larval life-history
 traits among nine populations of the common toad (Bufo bufo) along an
 altitudinal gradient in France. We further used correlation among
 population pairwise estimates of quantitative trait (QST) and neutral
 genetic divergence (FST from neutral microsatellite markers), as well as
 altitudinal difference, to estimate the relative role of divergent
 selection and neutral genetic processes in phenotypic divergence. We
 provided evidence for a neutral genetic differentiation resulting from
 both isolation by distance and difference in altitude. We found evidence
 for phenotypic divergence along the altitudinal gradient (faster
 development, lower growth rate and smaller metamorphic size). The
 correlation between pairwise QSTs–FSTs and altitude differences suggested
 that this phenotypic differentiation was most likely driven by
 altitude-mediated selection rather than by neutral genetic processes.
 Moreover, we found different divergence patterns for larval traits,
 suggesting that different selective agents may act on these traits and/or
 selection on one trait may constrain the evolution on another through
 genetic correlation. Our study highlighted the need to design more
 integrative studies on the common toad to unravel the underlying processes
 of phenotypic divergence and its selective agents in the context of
 environmental clines.
description: DryadData_Heredity_Bufo_altitudePhenotypic variation (larval period, mass at Gosner stage 42 and growth rate) of populations located along an altitudinal garden. Phenotypic traits have been measured in a common garden experiment.
DOI: 10.15468/dl.bx7vbr
title: Occurrence Download

description: A dataset listing the 1233 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((2.10798 45.11425,2.11208 45.10407,2.1204 45.10457,2.12987 45.09671,2.13877 45.08256,2.13885 45.0852,2.14072 45.08746,2.14212 45.08739,2.14368 45.08629,2.14422 45.08575,2.1457 45.08614,2.14781 45.08591,2.1489 45.08489,2.14874 45.08349,2.15123 45.0845,2.15248 45.08528,2.15497 45.08567,2.15575 45.08692,2.15731 45.08707,2.15957 45.08559,2.16066 45.08513,2.16339 45.08552,2.1658 45.08396,2.1658 45.08193,2.16666 45.08139,2.16814 45.08123,2.16938 45.08178,2.17375 45.08178,2.18216 45.1018,2.18173 45.10237,2.18183 45.10344,2.18125 45.10557,2.18115 45.10954,2.18202 45.11603,2.18029 45.11763,2.18074 45.12455,2.17938 45.12909,2.17961 45.1317,2.17836 45.13341,2.17541 45.13602,2.172 45.13817,2.16996 45.14771,2.16922 45.15701,2.1615 45.16415,2.15493 45.16903,2.1513 45.17055,2.14699 45.1711,2.12938 45.15076,2.1024 45.13275,2.09929 45.1289,2.10227 45.11947,2.10798 45.11425))",
 "OccurrenceStatus is Present"
 ]
}

 The dataset's 1233 records were derived from 73 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001265-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.548c1p1
title: Data from: A new Cathaysiorthis (Brachiopoda) fauna from the lower Llandovery of eastern Qinling, China

description: Following the end Ordovician mass extinction, brachiopod faunas were
 commonly of low diversity, generally rare in abundance, and restricted to
 shallow‐water environments in many places. The Cathaysiorthis fauna, first
 described from South East China, is the most diverse brachiopod fauna in
 the world succeeding the Hirnantia fauna, and has modified our previous
 views on the recovery of shelly benthos after the extinctions. Here, we
 report a newly‐discovered fauna with abundant Cathaysiorthis from the
 lower Zhangwan Formation (lower–middle Rhuddanian, lower Llandovery) in
 Qinling, Xichuan County, Henan Province, China. This fauna is slightly
 younger than that previously documented from South East China, and the
 evolution of Cathaysiorthis fauna, in terms of its composition, is
 discussed. The Qinling Cathaysiorthis fauna has a narrower bathymetric
 range (Benthic Assemblage Zone 3) than that of the fauna from South East
 China (BA 2–5) and occurred on the Qinling–Dabie Microplate located on the
 northwest margin of the South China Plate. The migration of the
 Cathaysiorthis fauna from the South China plate to Qinling–Dabie was
 achieved by larvae that used ambient ocean currents and possibly drifted
 from the Jiangnan Region of South East China to Qinling. The Qinling
 Cathaysiorthis fauna includes 13 species belonging to 12 genera. Two new
 species, Cathaysiorthis xichuanensis sp. nov. and Aegiria apta sp. nov.
 are established and described herein, and ten other species are discussed.
description: Measurements for new
 species of AegiriaMeasurements (in mm) for
 complete specimens of Aegiria apta sp. nov. Abbreviations L. Mus. and W.
 Mus. represent length and width of ventral muscle fields
 respectively.Measurements for new
 species of CathaysiorthisMeasurements (in mm) for
 complete specimens of Cathaysiorthis xichuanensis sp. nov. Abbreviations
 L. Mus. and W. Mus., L. Car. and W. Car. represent length and width of
 ventral muscle field and cardinalia respectively.