cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j8qv9
title: Data from: The phylogeny and biogeography of Hakea (Proteaceae) reveals the role of biome shifts in a continental plant radiation

description: The frequency of evolutionary biome shifts during diversification has
 important implications for our ability to explain geographic patterns of
 plant diversity. Recent studies present several examples of biome shifts,
 but whether frequencies of biome shifts closely reflect geographic
 proximity or environmental similarity of biomes remains poorly known. We
 explore this question by using phylogenomic methods to estimate the
 phylogeny of Hakea, a diverse Australian genus occupying a wide range of
 biomes. Model-based estimation of ancestral regions indicates that Hakea
 began diversifying in the Mediterranean biome of southern Australia in the
 Middle Eocene – Early Oligocene, and dispersed repeatedly into other
 biomes across the continent. We infer around 47 shifts between biomes.
 Frequencies of shifts between pairs of biomes are usually similar to those
 expected from their geographic connectedness or climatic similarity, but
 in some cases are substantially higher or lower than expected, perhaps
 reflecting how readily key physiological traits can be modified to adapt
 lineages to new environments. The history of frequent biome-shifting is
 reflected in the structure of present-day assemblages, which tend to be
 more phylogenetically diverse than null-model expectations. The case of
 Hakea demonstrates that the radiation of large plant clades across wide
 geographic areas need not be constrained by dispersal limitation or
 conserved adaptations to particular environments.
description: mcmctree.phyChronogram of Hakea and outgroup taxa from anchored enrichment phylogenomic data. The topology is based on a species tree produced by ASTRAL-II. Node depths are median values of the posterior distribution of node depths from an mcmctree analysis, calibrated to an absolute timescale using three fossil-based outgroup calibrations.
DOI: 10.15468/dl.mnpszm
title: Occurrence Download

description: A dataset containing 329 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Sciadocladus kerrii"
 ]
}

 The dataset includes 329 records from 41 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001431-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.n4r23
title: Data from: Species patch size at seeding affects diversity and productivity responses in establishing grasslands

description: 1. Species interactions in diverse plant communities affect
 community-scale functions such as above-ground biomass production,
 diversity and invasion resistance. While the strength of these formative
 interactions can be affected by the balance of inter- and intraspecific
 interactions among the resident species, it is unclear over what distances
 individuals typically interact in grasslands and whether or not species
 interactions at seeding can be effectively manipulated to improve these
 responses. 2. In a three-year study, we tested whether manipulating the
 size of seeded species patches affected above-ground biomass, diversity
 and invasion resistance in experimentally restored grassland plots (16
 m2). Plots were divided into patches that were 1, 0.5, 0.25 or 0.125 m on
 a side, and the equivalent of 1 m2 in each plot was seeded with one of 16
 grassland species (1728 seeds/m2). A final treatment involved mixing and
 broadcasting all seeds into an undivided plot to mimic typical restoration
 approaches. 3. Using successively smaller initial seed patches resulted in
 plots that were less diverse and initially more productive (~25%
 difference in second-year biomass production) than larger patch
 counterparts. Smaller patch plots also had a greater selection effect and
 experienced increases in resident species connectivity, suggesting that
 diversity declines and productivity gains resulted from the enhanced
 establishment and spread of more productive seeded species. 4. Plots
 seeded with larger patches of the resident species were initially more
 invaded than those seeded with smaller patches, but this effect diminished
 over time. This likely reflects the ability of the non-seeded species to
 more effectively colonize larger patches with poor seeded species
 establishment. 5. Mixed seeding plots were most similar to the smallest
 patch plots in their metrics of resident species spatial pattern,
 diversity and invasion resistance. However, these plots were initially
 less productive and had a weaker selection effect, which reflects a
 different compositional outcome, than the structured seeding plots. 6.
 Synthesis: Species interact over sub-metre scales in establishing
 tallgrass prairie and, once established, their patterns may change over
 time. Given these dynamics, structured seeding approaches may be used over
 traditional mixed seeding approaches to control species dominance and
 preserve seeded species diversity within grassland systems.
description: Species pattern data
 2010 2011 2012Block, patch treatment,
 year, no. conspecific patches, no. interspecific edges, proportion of
 interspecific neighbourships (determined using QRULE,
 http://www.umces.edu/al/program/gardner/Qrule)species pattern data 2010 2011
 2012.csvHarvest data 2010 2011
 2012Block, patch treatment,
 year, invader biomass, total biomass, Simpson's diversity,
 complementarity & selection effectsharvest data 2010 2011
 2012.csv
DOI: 10.5061/dryad.5618c1m
title: Data from: Handling stress and sample storage are associated with weaker complement-mediated bactericidal ability in birds but not bats

description: Variation in immune defense influences infectious disease dynamics within
 and among species. Understanding how variation in immunity drives pathogen
 transmission among species is especially important for animals that are
 reservoir hosts for zoonotic pathogens. Bats in particular have a
 propensity to host serious viral zoonoses without developing clinical
 disease themselves. The immunological adaptations that allow bats to host
 viruses without disease may be related to their adaptations for flight
 (e.g., in metabolism and mediation of oxidative stress). A number of
 analyses report greater richness of zoonotic pathogens in bats than in
 other taxa such as birds (i.e., mostly volant vertebrates) and rodents
 (i.e., non-volant, small mammals), but immunological comparisons between
 bats and these other taxa are rare. To examine interspecific differences
 in bacterial killing ability (BKA), a functional measure of overall
 constitutive innate immunity, we use a phylogenetic meta-analysis to
 compare how BKA responds to the acute stress of capture and to storage
 time of frozen samples across the orders Aves and Chiroptera. After
 adjusting for host phylogeny, sample size, and total microbe
 colony-forming units, we find preliminary evidence that constitutive
 innate immune defense of bats may be more resilient to handling stress and
 storage time than that of birds. This pattern was also similar when
 analyzing the proportion of non-negative and positive effect sizes per
 species using phylogenetic comparative methods. We discuss potential
 physiological and evolutionary mechanisms by which complement proteins may
 differ between species orders and suggest future avenues for comparative
 field studies of immunity between sympatric bats, birds, and rodents in
 particular.
description: Becker et al PBZ
 treePhylogenetic tree of bat
 and bird species included in the analyses derived from the Open Tree of
 Life (ott_id in CSV).Becker et al PBZ data
 CSVIndividual effect size
 records and metadata (e.g., species order, assay type, sample type, total
 CFU, BKA covariate assessed).Becker et al
 PBZ_data.csv
DOI: 10.5061/dryad.8hc64
title: Data from: Selfing can facilitate transitions between pollination syndromes

description: Pollinator-mediated selection on plants can favor transitions to a new
 pollinator depending on the relative abundances and efficiencies of
 pollinators present in the community. A frequently observed example is the
 transition from bee pollination to hummingbird pollination. We present a
 population genetic model that examines whether the ability to inbreed can
 influence evolutionary change in traits that underlie pollinator
 attraction. We find that a transition to a more efficient, but less
 abundant pollinator is favored under a broadened set of ecological
 conditions if plants are capable of delayed selfing rather than obligately
 outcrossing. Delayed selfing allows plants carrying an allele that
 attracts the novel pollinator to reproduce even when this pollinator is
 rare, providing reproductive assurance. In addition, delayed selfing
 weakens the effects of Haldane's sieve by increasing the fixation
 probability for recessive alleles that confer adaptation to the new
 pollinator. Our model provides novel insight into the paradoxical
 abundance of recessive mutations in adaptation to hummingbird attraction.
 It further predicts that transitions to efficient but less abundant
 pollinators (such as hummingbirds in certain communities) should
 disproportionately occur in self-compatible lineages. Currently available
 mating system datasets are consistent with this prediction and we suggest
 future areas of research that will enable a rigorous test of this theory.
description: Script used for the
 boundary analysisThis script demonstrates
 our approach to calculating threshold values of parameters where the
 dominant eigenvalue of the matrix in eq. 7 (main text) equals
 zero.boundary.pyScript used for branching processThis demonstrates our approach for solving the branching process equations. For a given set of conditions, this script solves the system of equations to find U1 and U2, the fixation probabilities for the allele attractive to hummingbirds when it is present as a single copy.branchingProcess.py
DOI: 10.5061/dryad.c6bf5
title: Data from: An ant–plant mutualism through the lens of cGMP-dependent kinase genes

description: In plant–animal mutualisms, how an animal forages often determines how
 much benefit its plant partner receives. In many animals, foraging
 behaviour changes in response to foraging gene expression or activation of
 the cGMP-dependent protein kinase (PKG) that foraging encodes. Here, we
 show that this highly conserved molecular mechanism affects the outcome of
 a plant–animal mutualism. We studied the two PKG genes of Allomerus
 octoarticulatus, an Amazonian ant that defends the ant–plant Cordia nodosa
 against herbivores. Some ant colonies are better ‘bodyguards’ than others.
 Working in the field in Peru, we found that colonies fed with a PKG
 activator recruited more workers to attack herbivores than control
 colonies. This resulted in less herbivore damage. PKG gene expression in
 ant workers correlated with whether an ant colony discovered an herbivore
 and how much damage herbivores inflicted on leaves in a complex way;
 natural variation in expression levels of the two genes had significant
 interaction effects on ant behaviour and herbivory. Our results suggest a
 molecular basis for ant protection of plants in this mutualism.
description: Script and data
 filesThis zip archive
 contains four files: the main data, the herbivory data, the R script and
 the README file describing the content of the three other
 files.data_and_script.zip
DOI: 10.5061/dryad.65n35
title: Data from: Cut your losses: self-amputation of injured limbs increases survival

description: Autotomy, self-induced limb loss, is an extreme trait observed throughout
 the animal kingdom; lizards drop their tails, crickets release their legs,
 and crabs drop their claws. These repeated evolutionary origins suggest
 that autotomy is adaptive. Yet, we do not have a firm understanding of the
 selective pressures that promote and maintain this extreme trait. Although
 multiple adaptive hypotheses exist, research has generally focused on
 autotomy’s adaptive value as a form of predator escape. However, autotomy
 could also be selected to reduce the cost of an injured limb, which we
 investigate here. Previously, this alternative hypothesis has been
 challenging to directly test because when an injury occurs on an
 autotomizable limb, that limb is almost always dropped (i.e., autotomy is
 behaviorally fixed within populations). Recently, however, we have
 identified a species, Narnia femorata (Insecta: Hemiptera: Coreidae),
 where some individuals autotomize limbs in response to injury, but some do
 not. This natural variation allowed us to investigate both the survival
 costs of retaining an injured limb and the benefits of autotomizing it. In
 this study, we find a positive association between autotomizing injured
 limbs and survival, thereby quantifying a new and likely widespread
 benefit of autotomy—reducing the cost of injury.
description: Experiment 1
 dataExperiment 2
 data
DOI: 10.5061/dryad.qb3sq2s
title: Data from: A wood-warbler produced through both interspecific and intergeneric hybridization

description: Hybridization between divergent taxa can provide insight into the
 breakdown of characters used in mate choice, as well as reproductive
 compatibility across deep evolutionary timescales. Hybridization can also
 occur more frequently in declining populations, as there is a smaller pool
 of conspecific mates from which to choose. Here we report an unusual
 combination of factors that has resulted in a rare, three-species
 hybridization event amongst two genera of warblers, one of which is
 experiencing significant population declines. We use bioacoustic,
 morphometric, and genetic data, to demonstrate that an early generation
 female hybrid between a golden-winged warbler (Vermivora chrysoptera) and
 a blue-winged warbler (V. cyanoptera) went on to mate and successfully
 reproduce with a chestnut-sided warbler (Setophaga pensylvanica). We
 studied the product of this event—a putative chrysoptera x cyanoptera x
 pensylvanica hybrid—and show that this male offspring sang songs like S.
 pensylvanica, but had morphometric traits similar to Vermivora warblers.
 The hybrid’s maternal parent had V. chrysoptera mitochondrial DNA and,
 with six plumage-associated loci, we predicted the maternal parent’s
 phenotype to show that it was likely an early generation Vermivora hybrid.
 That this hybridization event occurred within a population of Vermivora
 warblers in significant decline suggests that females may be making the
 best of a bad situation, and that wood-warblers in general have remained
 genetically compatible long after they evolved major phenotypic
 differences.
description: Culmen and Wing
 MeasurementsMeasurements of wing
 length and culmen length from 35 museum specimens from the Cornell Museum
 of Vertebrates as well as from the live putative hybrid individual.
 Abbreviations: GWWA, golden-winged warbler, BWWA, blue-winged warbler,
 CSWA, chestnut-sided warbler. Measurements for wing are from an
 unflattened wing to the nearest 0.5 mm. Measurements for culmen are from
 the tip of the nares to the end of the bill, to the nearest
 0.1mm.culmen_wing_measurements.csvFive nuclear alignment filesNucleotide alignments in "FASTA" format from five regions that differ between golden-winged and blue-winged warblers obtained from Sanger sequencing. Each file contains a short sequence for four individuals, two with sequence from chestnut-sided warblers (with associated Cornell University Museum of Vertebrates [CUMV] tissue numbers), one sequence from the putative hybrid, and one from Vermivora warblers. The Vermivora warbler sequence is a consensus sequence from the 24 resequenced genomes presented in Toews et al. 2016 (Current Biology) using the "mpileup" command in SAMTOOLS.nuclear alignments.zip
DOI: 10.5061/dryad.s2878
title: Data from: Systematics and evolution of inflorescence structure in the Tradescantia alliance (Commelinaceae)

description: The Tradescantia alliance (subtribes Tradescantiinae and Thyrsantheminae
 of tribe Tradescantieae, family Commelinaceae) comprises a group of
 closely related New World genera exhibiting considerable variation in
 morphological, life history, and genomic traits. Despite ecological and
 cytogenetic significance, phylogenetic relationships among genera and
 species remain uncertain. In particular, variation in inflorescence
 morphology has confounded classification and taxonomy. The presence of
 self compatible and incompatible species allowed us to test the hypothesis
 that self compatible species will have condensed inflorescences. We
 inferred phylogenetic relationships using two plastid loci (rpL16,
 trnL-trnF) for 85 taxa in Commelinaceae, with sampling focused in the
 Tradescantia alliance. Constraint tests supported only subtribe
 Tradescantiinae, Tripogandra and Tinantia as monophyletic, with
 Tripogandra nested within Callisia. We estimated ancestral states for both
 breeding system and inflorescence condensation and tested for a
 correlation. Inflorescence morphology, an important character for generic
 identification, is more labile than previously expected, with condensed
 inflorescences evolving twice with three subsequent reversals. Breeding
 system evolution is more complex, with many more switches between self
 compatibility and self incompatibility and more uncertainty in ancestral
 state estimates. While we did not find a correlation between self
 compatibility and inflorescence condensation, we propose additional floral
 and inflorescence characteristics that may have contributed to variation
 in breeding system.
description: 12595Commelinaceae DataTrait data compiled from primary literature regarding breeding system and inflorescence condensation for the Tradescantia allianceNWCommData.csv
DOI: 10.5061/dryad.hd4q3
title: Data from: Evolution of reproductive isolation in stickleback fish

description: To understand how new species form and what causes their collapse, we
 examined how reproductive isolation evolves during the speciation process,
 considering species pairs with little to extensive divergence, including a
 recently collapsed pair. We estimated many reproductive barriers in each
 of five sets of stickleback fish species pairs using our own data and
 decades of previous work. We found that the types of barriers important
 early in the speciation process differ from those important late. Two
 premating barriers—habitat and sexual isolation—evolve early in divergence
 and remain two of the strongest barriers throughout speciation. Premating
 isolation evolves before postmating isolation, and extrinsic isolation is
 far stronger than intrinsic. Completing speciation, however, may require
 postmating intrinsic incompatibilities. Reverse speciation in one species
 pair was characterized by significant loss of sexual isolation. We present
 estimates of barrier strengths before and after collapse of a species
 pair; such detail regarding the loss of isolation has never before been
 documented. Additionally, despite significant asymmetries in individual
 barriers, which can limit speciation, total isolation was essentially
 symmetric between species. Our study provides important insight into the
 order of barrier evolution and the relative importance of isolating
 barriers during speciation and tests fundamental predictions of ecological
 speciation.
description: Total and Shared
 RIFor
 each of the 5 species pair systems, point estimates and strongest and
 weakest estimates of total reproductive isolation from all available
 barriers and total reproductive isolation from four shared barriers that
 were measured in all 5 systems. Data presented in Figure 1 and Table
 S3.Total
 & Shared RI.csvTypes of Isolation:
 Premating, Postmating, Intrinsic, ExtrinsicFor each of the 5
 species pair systems, point estimates and strongest and weakest estimates
 of four types of isolation: premating, postmating, postmating intrinsic,
 and postmating extrinsic. Data presented in Figure 3.Pre,Post,Intrinsic,Extrinsic.csvIndividual Barrier AsymmetriesFor each of the 5 species pair systems, weighted mean or single estimates 95%CIs for individual barrier strengths for each species, which allowed us to test for asymmetries between species. Data presented in Figure 5.Total Isolation AsymmetriesFor each of the 5 species pair systems, point estimates and strongest and weakest estimates for total isolation of each species, which allowed us to test for asymmetries between species. Data presented in Figure 6.
DOI: 10.5061/dryad.j7g4p
title: Data from: Plumage colour and the expression of stress-related genes in gull chicks

description: In many bird populations, individuals show remarkable differences in
 feather colouration, which are often linked to individual differences in
 physiological traits, but the mechanisms maintaining this covariation are
 still unclear. Here, we investigate the variability of the melanic
 colouration in yellow-legged gull Larus michahellis chicks. In this
 species, hatchlings show high variability in the number and colour
 intensity of black spots in their plumage. In gulls, last-laid eggs
 receive less antioxidants but higher levels of androgens than first eggs.
 We first explored whether these remarkable differences within the clutch
 affect the feather melanisation during embryo development. Melanic
 colouration was not related to laying order, but nestling males were
 darker and had a larger spotted area than nestling females. In chicks
 hatching from first-laid eggs, the spot size and spot lightness were
 negatively correlated. We also explored the effect of the developmental
 environment, through a cross-fostering experiment, on the expression of
 five stress-related genes (SOD2, ALKBH3, HSPA8, NLRC5 and TRIAP1) and
 their link with melanic colouration. Post-hatching hierarchy did not
 affect the expression of any of the tested genes, but paler chicks showed
 reduced expression in some studied genes (SOD2, ALKBH3 and HSPA8) in
 comparison to darker chicks. Our results suggest that melanic chicks
 suffer less stress during development.
description: PlumageColour_GeneExpression