cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9042
title: Data from: Variable helper effects, ecological conditions, and the evolution of cooperative breeding in the acorn woodpecker

description: The ecological conditions leading to delayed dispersal and helping
 behavior are generally thought to follow one of two contrasting scenarios:
 that conditions are stable and predictable resulting in young being
 ecologically forced to remain as helpers (extrinsic constraints and the
 "habitat saturation" hypothesis), or that conditions are highly
 variable and unpredictable leading to the need for helpers to raise young,
 at least when conditions are poor (intrinsic constraints and the
 "hard life" hypothesis). We investigated how variability in
 ecological conditions influences the degree to which helpers augment
 breeder fitness in the cooperatively breeding acorn woodpecker (Melanerpes
 formicivorus), a species in which the acorn crop, territory quality, and
 prior breeding experience all vary in ways that have important effects on
 fitness. We found that the relationship between ecological conditions and
 the probability that birds would remain as helpers was variable, but that
 helpers generally yielded greater fitness benefits when ecological
 conditions were favorable, rather than unfavorable, for breeding. These
 results affirm the importance of extrinsic constraints to delayed
 dispersal and cooperative breeding in this species, despite this
 species' dependence on a highly variable and unpredictable acorn
 crop. Our findings also confirm that helpers can have very different
 fitness effects depending on conditions, but that those effects are not
 necessarily greater when breeding conditions are unfavorable.
description: Annual survivorship
 dataThis file contains
 annual survivorship data, and is derived from our records of group
 membership. The file was created from our records as of 3 April 2010, and
 includes individuals for years that we have data on the acorn crop, were
 present for at least two 3-month intervals, and were in groups with no
 more than two cobreeder femalesSurvivalData.txtAnnual group reproductive success dataThis file contains annual reproductive success data for individual groups.ReproData.txtDelayed dispersal of helpersThis file contains annual data on the relationship between the acorn crop and whether helpers delayed dispersal or notDelayedDispersal.txtNumber of territories vs. the acorn cropThis file contains annual data on the number of territories present in the 'core' population by year and as a function of the prior fall's acorn cropNTerritoryData.txt
DOI: 10.5061/dryad.4b2158p
title: Data from: Evolution of the exclusively human-pathogen Neisseria gonorrhoeae: human-specific engagement of immunoregulatory Siglecs

description: Neisseria gonorrhoeae causes the sexually transmitted disease gonorrhea
 exclusively in humans and uses multiple strategies to infect, including
 acquisition of host sialic acids that cap and mask lipooligosaccharide
 termini, while restricting complement activation. We hypothesized that
 gonococci selectively target human anti-inflammatory sialic
 acid-recognizing Siglec receptors on innate immune cells to blunt host
 responses, and that pro-inflammatory Siglecs and SIGLEC pseudogene
 polymorphisms represent host evolutionary adaptions to counteract this
 interaction. N. gonorrhoeae can indeed engage multiple human but not
 chimpanzee CD33rSiglecs expressed on innate immune cells and in the
 genitourinary tract––including Siglec-11 (inhibitory) and Siglec-16
 (activating), which we detected for the first time on human cervical
 epithelium. Surprisingly, in addition to LOS-sialic acid, we found that
 gonococcal porin (PorB) mediated binding to multiple Siglecs. PorB also
 bound preferentially to human Siglecs and not chimpanzee orthologs,
 modulating host immune reactions in a human-specific manner. Lastly, we
 studied the distribution of null SIGLEC polymorphisms in a Namibian cohort
 with a high prevalence of gonorrhea, and found that uninfected women
 preferentially harbor functional SIGLEC16 alleles encoding an activating
 immune receptor. These results contribute to the understanding of the
 human specificity of N. gonorrhoeae and how it evolved to evade the human
 immune defense.
description: Siglec-Fc Binding Assays
 - Data of Figure 2, 3B, S6BRaw data and statistical
 analysis of Siglec-Fc binding assays with Neisseria gonorrhoeae
 strains.Data Fig2A 2B 3B
 SupplFig6B.pzfxFlow cytometry assay
 with Siglec-Fcs and LOS mutants - Fig.3C-GRaw data and statistical
 analysis of Flow cytometry data with Siglec-Fcs and different LOS mutants
 of Neisseria gonorrhoeae.Data
 Fig3C-G.pzfxSiglec-Fc Binding Assays
 with gonococcal porins - Fig.4Raw data and statistical
 analysis of binding assay with Siglec-Fcs and gonococcal
 porins.Data
 Fig4A 4B.pzfxIL-6 secretion assay -
 Fig.5ARaw data and statistical
 analysis of IL-6 secretion ELISA assay of Neisseria gonorrhoeae challenged
 THP-1 cells expressing Siglec-5 or Siglec-14.Data
 Fig5A.pzfxPhagocytosis assay -
 Fig.5BRaw data of phagocytosis
 assay with THP-1 cells expressing Siglec-14 challenged with gonococcal
 porins.Data
 Fig5B.xlsx
DOI: 10.5061/dryad.2q9r7
title: Data from: Age-dependent and lineage-dependent speciation and extinction in the imbalance of phylogenetic trees

description: It is known that phylogenetic trees are more imbalanced than expected from
 a birth–death model with constant rates of speciation and extinction, and
 also that imbalance can be better fit by allowing the rate of speciation
 to decrease as the age of the parent species increases. If imbalance is
 measured in more detail, at nodes within trees as a function of the number
 of species descended from the nodes, age-dependent models predict levels
 of imbalance comparable to real trees for small numbers of descendent
 species, but predicted imbalance approaches an asymptote not found in real
 trees as the number of descendent species becomes large. Age-dependence
 must therefore be complemented by another process such as inheritance of
 different rates along different lineages, which is known to predict
 insufficient imbalance at nodes with few descendent species, but can
 predict increasing imbalance with increasing numbers of descendent
 species.
description: Holman imbalance
 Appendix 1Proof that weighted mean
 imbalance approaches an asymptote less than 1 as number of species
 increases, for a large class of age-dependent modelsHolman imbalance
 Appendix 2Analysis of imbalance in
 simulated trees generated by the Weibull modelHolman imbalance Folder
 1Program source code with
 sample input and output for Appendix 2Holman imbalance Folder
 2Program source code with
 sample input and output for Appendix 3Holman imbalance
 Appendix 3Analysis of imbalance in
 an empirical tree of life
DOI: 10.5061/dryad.8429
title: Data from: Evidence of the accumulation of allele-specific non-synonymous substitutions in the young region of recombination suppression within the mating-type chromosomes of Neurospora tetrasperma

description: Currently, little is known about the origin and early evolution of sex
 chromosomes. This largely due to the fact that ancient non-recombining sex
 chromosomes are highly degenerated, and thus provide little information
 about the early genomic events in their evolution. The Neurospora
 tetrasperma mating-type (mat) chromosomes contain a young (&lt;6 Mya)
 and large region (&gt;6.6Mb) of suppressed recombination, thereby
 providing a model system to study early stages of sex chromosome
 evolution. Here, we examined alleles of 207 genes located on the N.
 tetrasperma mat a and mat A chromosomes to test for signs of genomic
 alterations at the protein level in the young region of recombination
 suppression. We report that the N. tetrasperma mat a and mat A chromosomes
 have each independently accumulated allele-specific non-synonymous codon
 substitutions in a time-dependent, and gene-specific manner in the
 recombinationally suppressed region. In addition, examination of the ratio
 (ω) of non-synonymous substitutions (dN) to synonymous substitutions (dS)
 using maximum likelihood analyses, indicates that such changes are
 associated with relaxed purifying selection, a finding consistent with
 genomic degeneration. We also reveal that sex specific biases in mutation
 rates or selection pressures are not necessary for genomic alterations in
 sex chromosomes, and that recombination suppression in itself is
 sufficient to explain these results. The present findings greatly extend
 our current understanding of genomic events associated within the young
 region of recombination suppression in these fungal sex regulating
 chromosomes.
description: DataFile1DNA sequence data for the 207 genes associated with the publication.
DOI: 10.5061/dryad.58dm217
title: Data from: Senescent declines in elite tennis players are similar across the sexes

description: Aging is characterized by rising mortality, declining fertility and
 declines in physiological function with age (functional senescence).
 Sex-differences in the tempo and severity of survival and fertility
 declines are widespread, but it is less clear how often, and how much
 trajectories of functional senescence diverge between the sexes. We tested
 how physiological function changed with age in male and female elite
 tennis players using first-serve speed (power) and first-serve accuracy as
 performance measures. We found absolute differences between the sexes with
 men serving more quickly, but less accurately than women. Both power and
 accuracy showed senescent declines but these began earlier for power.
 There were signals of trait-compensation, where players with pronounced
 power declines showed increases in accuracy, which might partially buffer
 against power deterioration. However, there were no sex differences in how
 either trait changed with age, contrasting with other sports. Sex
 differences in functional senescence are probably shaped by interactions
 between natural and sexual selection, the proximate costs of trait
 expression and a trait’s genetic architecture, and so are highly
 trait-specific. We discuss the strengths and potential pitfalls of using
 elite athletes to disentangle these complex interactions.
description: Sutter_Barton_et_al_Behav_Ecol_DataData on serve speed and accuracy and the outcome of games (win / lose). Information that could identify individual players has been removed, in keeping with archiving guidelines.
DOI: 10.5061/dryad.7vs2r
title: Data from: Microclimatic differentiation of gene pools in the Lobaria pulmonaria symbiosis in a primeval forest landscape

description: Population genetics of the tree-colonizing lichen Lobaria pulmonaria were
 studied in the largest primeval beech forest of Europe, covering 10 000
 ha. During an intensive survey of the area, we collected 1522 thallus
 fragments originating from 483 trees, which were genotyped with 8 myco-
 and 14 photobiont-specific microsatellite markers. The mycobiont and
 photobiont of L. pulmonaria were found to consist of two distinct gene
 pools, which are co-existing within small areas of 3–180 ha in a
 homogeneous beech forest. The small-scale distribution pattern of the
 symbiotic gene pools was linked to altitude, and show habitat partitioning
 of lineages associated with either floodplains or mountain forests. Using
 Approximate Bayesian Computation (ABC), we dated the divergence of the two
 fungal gene pools of L. pulmonaria as the Early Pleistocene. Both fungal
 gene pools survived the Pleistocene glacial cycles in the Carpathians,
 though possibly in climatically different refugia. Fungal diversification
 prior to these cycles and the selection of photobionts with different
 altitudinal distributions explain the current sympatric, but ecologically
 differentiated habitat partitioning of L. pulmonaria. In addition, the
 habitat preferences of the mycobiont are determined by other factors and
 are rather independent of those of the photobiont at the landscape level.
 The distinct gene pools should be considered evolutionarily significant
 units, and deserve specific conservation priorities in the future, e.g.
 gene pool A, which is an Pliocene relict.
description: microsatellite &
 environmental data
DOI: 10.5061/dryad.qk26v
title: Data from: Cruzipain activates latent TGF-β from host cells during T. cruzi invasion

description: Several studies indicate that the activity of cruzipain, the main
 lysosomal cysteine peptidase of Trypanosoma cruzi, contributes to parasite
 infectivity. In addition, the parasitic invasion process of mammalian host
 cells is described to be dependent on the activation of the host TGF-β
 signaling pathway by T. cruzi. Here, we tested the hypothesis that
 cruzipain could be an important activator of latent TGF-β and thereby
 trigger TGF-β-mediated events crucial for the development of Chagas
 disease. We found that live epimastigotes of T. cruzi, parasite lysates
 and purified cruzipain were able to activate latent TGF-β in vitro. This
 activation could be inhibited by the cysteine peptidase inhibitor
 Z-Phe-Ala-FMK. Moreover, transfected parasites overexpressing chagasin, a
 potent endogenous cruzipain inhibitor, prevented latent TGF-β activation.
 We also observed that T. cruzi invasion, as well as parasite intracellular
 growth, were inhibited by the administration of Z-Phe-Ala-FMK or
 anti-TGF-β neutralizing antibody to Vero cell cultures. We further
 demonstrated that addition of purified cruzipain enhanced the invasive
 activity of trypomastigotes and that this effect could be completely
 inhibited by addition of a neutralizing anti-TGF-β antibody. Taken
 together, these results demonstrate that the activities of cruzipain and
 TGF-β in the process of cell invasion are functionally linked. Our data
 suggest that cruzipain inhibition is an interesting chemotherapeutic
 approach for Chagas disease not only because of its trypanocidal activity,
 but also due to the inhibitory effect on TGF-β activation.
description: Western Blot
 CZPWestern blot assay for
 cruzipain observationELISARaw data form TGF-b
 activation performed by ELISA assaysin
 vitroRaw data from T. cruzi
 infection assays
DOI: 10.5061/dryad.693b3f4
title: Data from: Distance and size matters: a comparison of six wildlife camera traps and their usefulness for wild birds

description: Camera traps are increasingly used in ecological research. However, tests
 of their performance are scarce. It is already known from previous work
 that camera traps frequently fail to capture visits by animals. This can
 lead to a misinterpretation of ecological results such as density
 estimates or predation events. While previous work is mainly based on
 mammals, for birds, no data about if and how camera traps can be
 successfully used to estimate species diversity or density are available.
 Hence, the goal of our study was an empirical validation of six different
 camera traps in the field. We observed a total number of N=4567 events
 (independent visits of a bird) in 100 different sessions from March 2017
 until January 2018, while camera traps were deployed. In addition, N=641
 events are based on a comparison of the two close-up camera traps
 especially designed for birds. These events were all directly observed by
 the authors. Thus, the cameras can be compared against the human observer.
 To give an overall assessment and a more generalizable result, we combined
 the data from the six camera traps and showed that bird size category
 (effect size = 0.207) and distance (effect size = 0.132) are the most
 important predictors for a successful trigger. Also, temperature had a
 small effect, and flock size had an impact with larger flocks being
 captured more often. The approach of the bird, whether it approached the
 camera frontally or laterally had no influence. In Table 8 we give some
 recommendations, based on our results, at which distances camera traps
 should be placed to get a 25%/50% and 70% capture rate for a given bird
 size.
description: Methods_Test_Cameras_close_up_DryadData for the close-up comaprison of the two camerasMethods_Test_Cameras_DryadData for the comparison of the six different camera traps
DOI: 10.5061/dryad.54q3f36
title: Data from: Phylogeny and evolutionary history of diplobathrid crinoids (Echinodermata)

description: Order Diplobathrida is a major clade of camerate crinoids spanning the
 Ordovician–Mississippian, yet phylogenetic relationships have only been
 inferred for Ordovician taxa. This has hampered efforts to construct a
 comprehensive tree of life for crinoids and develop a classification
 scheme that adequately reflects diplobathrid evolutionary history. Here, I
 apply maximum parsimony and Bayesian phylogenetic approaches to the fossil
 record of diplobathrids to infer the largest tree of fossil crinoids to
 date, with over 100 genera included. Recovered trees provide a framework
 for evaluating the current classification of diplobathrids. Notably,
 previous suborder divisions are not supported, and superfamily divisions
 will require significant modification. Although numerous revisions are
 required for families, most can be retained through reassignment of
 genera. In addition, recovered trees were used to produce phylogeny‐based
 estimates of diplobathrid lineage diversity. By accounting for ghost
 lineages, phylogeny‐based richness estimates offer greater insight into
 diversification and extinction dynamics than traditional taxonomy‐based
 approaches alone and provide a detailed summary of the ~150 million‐year
 evolutionary history of Diplobathrida. This study constitutes a major step
 toward producing a phylogeny of the Crinoidea and documenting crinoid
 diversity dynamics. In addition, it will serve as a framework for
 subsequent phylogeny‐based investigations of macroevolutionary questions.
description: Supplemental Data 1 -
 Tables and FiguresSupplemental tables and
 figures to accompany "Phylogeny and evolutionary history of
 diplobathrid crinoids (Echinodermata)." Supplemental Table 1: Taxa
 coded; Supplemental Table 2: Characters and character states; Supplemental
 Table 3: Morphological characters shared among ≥75% of genera within major
 groups recovered; Supplemental Figure 1: Constraint tree used;
 Supplemental Figure 2: strict consensus tree recovered with Cleiocrinus
 included.Supplemental
 Data1.pdfSupplemental Data 2 -
 Parsimony matrixSuppmental Data 2:
 Diplobathrid character matrix and constraint for parsimony
 analysis.SupplementalData2.txtSupplemental Data 3 - recovered trees, Cleiocrinus excludedSupplemental Data 3: Trees recovered from parsimony analysis of Diplobathrids with Cleiocrinus excluded.SupplementalData3.txtSupplemental Data 4 - Recovered trees, Cleiocrinus includedSupplemental Data 4: Trees recovered from parsimony analysis of Diplobathrids with Cleiocrinus included.SupplementalData4.txtSupplemental Data 5 - Bayesian character matrix and commandsSupplemental Data 5: Diplobathrid character matrix and commands for Bayesian AnalysisSupplementalData5.txt
DOI: 10.5061/dryad.7nb71
title: Data from: The interaction between the spatial distribution of resource patches and population density: consequences for intra-specific growth and morphology

description: 1. How individuals within a population distribute themselves across
 resource patches of varying quality has been an important focus of
 ecological theory. The ideal free distribution predicts equal fitness
 amongst individuals in a 1 : 1 ratio with resources, whereas resource
 defence theory predicts different degrees of monopolization (fitness
 variance) as a function of temporal and spatial resource clumping and
 population density. 2. One overlooked landscape characteristic is the
 spatial distribution of resource patches, altering the equitability of
 resource accessibility and thereby the effective number of competitors.
 While much work has investigated the influence of morphology on
 competitive ability for different resource types, less is known regarding
 the phenotypic characteristics conferring relative ability for a single
 resource type, particularly when exploitative competition predominates. 3.
 Here we used young-of-the-year rainbow trout (Oncorhynchus mykiss) to test
 whether and how the spatial distribution of resource patches and
 population density interact to influence the level and variance of
 individual growth, as well as if functional morphology relates to
 competitive ability. Feeding trials were conducted within stream channels
 under three spatial distributions of nine resource patches (distributed,
 semi-clumped and clumped) at two density levels (9 and 27 individuals). 4.
 Average trial growth was greater in high-density treatments with no effect
 of resource distribution. Within-trial growth variance had opposite
 patterns across resource distributions. Here, variance decreased at
 low-population, but increased at high-population densities as patches
 became increasingly clumped as the result of changes in the levels of
 interference vs. exploitative competition. Within-trial growth was related
 to both pre- and post-trial morphology where competitive individuals were
 those with traits associated with swimming capacity and efficiency: larger
 heads/bodies/caudal fins and less angled pectoral fins. 5. The different
 degrees of within-population growth variance at the same density level
 found here, as a function of spatial resource distribution, provide an
 explanation for the inconsistencies in within-site growth variance and
 population regulation often noted with regard to density dependence in
 natural landscapes.
description: DataJacobsonetal2015This file contains the mass and growth metrics as well as length and size variables and pre- and post-trial partial warps for all individuals, with the treatment, week and channel in which they participated indicated. Also present is the information garnered from feeding videos, spatial resource patch use and number of observed chases.