cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1sc1s
title: Data from: Competing for seed dispersal: evidence for the role of avian seed hoarders in mediating apparent predation among oaks

description: In communities of large-seeded tree species, generalist seed hoarders
 often link the temporally variable dynamics of various species in ways
 that can result in indirect ecological interactions. A special case of
 such interactions is ‘apparent predation’ – when variation in seed
 production of one tree species changes the outcome of the interaction
 between seed hoarders and another tree species from seed dispersal
 mutualism to predation. We investigated how two species of avian hoarders
 responded to differences in acorn availability among individual valley
 oaks (Quercus lobata) and across a landscape dominated by blue oaks (Q.
 douglasii) to determine whether seed dispersal and predation dynamics
 result in apparent predation between these oak species. California
 scrub-jays (Aphelocoma californica), high-quality seed dispersers with
 large spatial scales of resource perception, showed strong numerical and
 functional responses to individually large Q. lobata acorn crops when
 landscape-level acorn crops were low, but the numerical response was not
 observed when Q. douglasii produced a good acorn crop the subsequent year.
 In contrast, acorn woodpeckers (Melanerpes formicivorus), which are
 significant acorn predators, exhibited a consistent functional response to
 individual Q. lobata acorn crops independent of landscape-wide
 availability. Consequently, Q. lobata experienced increased predation and
 a near absence of high-quality seed dispersal when Q. douglasii acorns
 were abundant. Our results suggest that apparent predation among oak
 species can arise from contrasting responses of generalist seed predators
 and dispersers to acorn availability on different spatial scales. Thus,
 the spatial scale of resource perception, which can differ greatly among
 generalist seed hoarders, may provide a proximate mechanism underlying
 indirect, temporally variable ecological affects such as apparent
 predation among sympatric species of large-seeded trees.
description: Pesendorfer_Koenig_FE_2016: Focal Tree Watches60-minute observations of Quercus lobata trees. Number of dropped, eaten and transported acorns, number of birds attending tree, intra- and interspecific aggression and acorns handled by each species. Parameter code key in second tabPesendorfer_Koenig_FE_2016.xlsx
DOI: 10.5061/dryad.4b4rb
title: Data from: What is the primary function of the early teleost gill? Evidence for Na+/NH4+ exchange in developing rainbow trout (Oncorhynchus mykiss)

description: Post-hatch fishes lack a functional gill and use cutaneous surfaces for
 exchange with the surrounding environment. The ionoregulatory hypothesis
 posits that ionoregulation is the first physiological process to be
 limited by cutaneous exchange, necessitating its shift to the gills. We
 hypothesized that the ontogeny of branchial ammonia excretion (Jamm) is
 coupled to Na+ uptake (Graphic) in accordance with the current model for
 Graphic exchange in freshwater. Using divided chambers, branchial and
 cutaneous Jamm, Graphic and oxygen consumption (MO2) by larval rainbow
 trout were assessed. Following hatch, the skin accounted for 97% and 86%
 of total Jamm and Graphic, respectively. Jamm and Graphic shifted to the
 gills simultaneously at 15 days post-hatch (dph) and were highly
 correlated (R2 = 0.951) at the gills, but not the skin, over development.
 Contrastingly, MO2 shifted significantly later at 27 dph, in agreement
 with the ionoregulatory hypothesis. Moreover, the mRNA expression and/or
 enzymatic activity of Rhesus proteins, Na+/H+-exchanger, H+-ATPase,
 Na+/K+-ATPase and carbonic anhydrase, all key components of the
 Graphic-exchange system, increased in the gills over larval development.
 We propose that the ontogeny of branchial Graphic occurs as Graphic
 exchange and provide evidence for a novel element to the ionoregulatory
 hypothesis, the excretion of potentially lethal metabolic ammonia.
description: Data for Figures 1 and
 3Raw
 values for branchial, cutaneous, and total ammonia excretion, Na uptake,
 and oxygen consumption presented in figures 1 and 3.Figure 1 and
 3.xlsxData for Figure
 2Raw
 values for relative (% Total) branchial and cutaneous ammonia excretion,
 Na uptake, and oxygen consumption presented in figure
 2.Figure
 2.xlsxData for Figure
 4Relative quantities
 (delta Cq) values used to calculate gene expression in figure 4. Gene
 expression was normalized to B-Actin and EF1a and is expressed relative to
 the the gill at 3 days post-hatch for any given target gene. Expression
 was calculated using Bio-Rad CFX Manager 3.0 software.Figure
 4.xlsxData for Figure
 5Raw
 enzyme activity values for Na/K-ATPase, H-ATPase, and CA used in figure
 5.Figure
 5.xlsxData for Figure
 6Raw
 ammonia turnover time and whole-body total ammonia values presented in
 figure 6.Figure
 6.xlsx
DOI: 10.5061/dryad.23tp6
title: Data from: Adaptation and acclimation of aerobic exercise physiology in Lake Whitefish ecotypes (Coregonus clupeaformis)

description: The physiological mechanisms underlying local adaptation in natural
 populations of animals, and whether the same mechanisms contribute to
 adaptation and acclimation, are largely unknown. Therefore, we tested for
 evolutionary divergence in aerobic exercise physiology in laboratory bred,
 size-matched crosses of ancestral, benthic, normal Lake Whitefish
 (Coregonus clupeaformis) and derived, limnetic, more actively-swimming
 ‘dwarf’ ecotypes. We acclimated fish to constant swimming (emulating
 limnetic foraging) and control conditions (emulating normal activity
 levels) to simultaneously study phenotypic plasticity. We found extensive
 divergence between ecotypes: dwarf fish generally had constitutively
 higher values of traits related to oxygen transport (ventricle size) and
 use by skeletal muscle (percent oxidative muscle, mitochondrial content),
 and also evolved differential plasticity of mitochondrial function
 (Complex I activity and flux through Complexes I-IV and IV). The effects
 of swim-training were less pronounced than differences among ecotypes and
 the traits which had a significant training effect (ventricle protein
 content, ventricle MDH activity and muscle Complex V activity) did not
 differ among ecotypes. Only one trait, ventricle mass, varied in a similar
 manner with acclimation and adaptation and followed a pattern consistent
 with genetic accommodation. Overall, the physiological and biochemical
 mechanisms underlying acclimation and adaptation to swimming activity in
 Lake Whitefish generally differ.
description: R code for nested,
 two-way ANOVAsR code for nested,
 two-way ANOVAs (example for Fig. 1A)Figs1-6_MixedEffectsModel_Code.RR_Code_for_DFAR_Code_for_DFA (Fig. 7)Fig7_DFA_Code.RFig1A_HematocritData for Figure 1AFig1B_VentricleMassData for Figure 1BFig2_HeartEnzymesData for Figure 2Fig3A_PercentRMData for Figure 3AFig3C,E_CapillaryDensityData for Figure 3C,EFig4_MuscleEnzymesData for Figure 4Fig5_MitoRespirationData for Figure 5Fig6_ETCenzymesData for Figure 6Fig7_DF(tank_means)Data for Figure 7 - tank means for all significant variables
DOI: 10.5061/dryad.211vn8m4
title: Data from: An evolutionary history of the selectin gene cluster in humans

description: Molecules involved in leukocyte trafficking have a central role in the
 development of inflammatory and immune responses. We performed FST
 analysis of the selectin cluster, as well as of SELPLG, ICAM1 and VCAM1.
 Peaks of significantly high population genetic differentiation were
 restricted to two regions in SELP and one in SELPLG. Resequencing data
 indicated that the region covering SELP exons 11–13 displays high
 nucleotide diversity in Africans and Europeans (CEU), and a high level of
 within-species diversity compared with inter-specific divergence. Analysis
 of inferred haplotypes revealed a complex phylogeny with two deeply
 separated clades that coalesce at ~3.5 million years (MY) plus a minor
 clade with a TMRCA (time to the most recent common ancestor) of ~2.2 MY. A
 splicing assay indicated no haplotype-specific effect on SELP exon 14
 inclusion. These data are consistent with a model of multiallelic
 balancing selection; single-nucleotide polymorphism analysis indicated
 that the Val640Leu variant represents a likely selection target. In
 populations of Asian ancestry a distinct haplotype, possibly carrying
 regulatory variants, has been driven to high frequency by positive
 selection. No deviation from neutrality was observed for the SELPLG
 region. Resequencing of SELP in chimpanzees revealed a haplotype phylogeny
 with extremely deep basal branches, suggesting either long-standing
 balancing selection or ancestral population structure. Thus, SELP has
 experienced a complex selective history, possibly as a result of local
 adaptation. Variants in the gene have been associated with autoimmune and
 cardiovascular diseases. Association studies would benefit from both
 taking the complex SELP haplotype structure into account and from analysis
 of possible regulatory variants in the gene.
description: Haplotype_tableList of haplotypes identified in 40 Asian chromosomesChimpanzee_variantsVariants identified in chimpanzees
DOI: 10.5061/dryad.bg6fn
title: Data from: Seed dispersal anachronisms: rethinking the fruits extinct megafauna ate

description: BACKGROUND: Some neotropical, fleshy-fruited plants have fruits
 structurally similar to paleotropical fruits dispersed by megafauna
 (mammals &gt;103 kg), yet these dispersers were extinct in South
 America 10–15 Kyr BP. Anachronic dispersal systems are best explained by
 interactions with extinct animals and show impaired dispersal resulting in
 altered seed dispersal dynamics. METHODOLOGY/PRINCIPAL FINDINGS: We
 introduce an operational definition of megafaunal fruits and perform a
 comparative analysis of 103 Neotropical fruit species fitting this
 dispersal mode. We define two megafaunal fruit types based on previous
 analyses of elephant fruits: fruits 4–10 cm in diameter with up to five
 large seeds, and fruits &gt;10 cm diameter with numerous small seeds.
 Megafaunal fruits are well represented in unrelated families such as
 Sapotaceae, Fabaceae, Solanaceae, Apocynaceae, Malvaceae, Caryocaraceae,
 and Arecaceae and combine an overbuilt design (large fruit mass and size)
 with either a single or few (&lt;3 seeds) extremely large seeds or
 many small seeds (usually &gt;100 seeds). Within-family and
 within-genus contrasts between megafaunal and non-megafaunal groups of
 species indicate a marked difference in fruit diameter and fruit mass but
 less so for individual seed mass, with a significant trend for megafaunal
 fruits to have larger seeds and seediness. CONCLUSIONS/SIGNIFICANCE:
 Megafaunal fruits allow plants to circumvent the trade-off between seed
 size and dispersal by relying on frugivores able to disperse enormous seed
 loads over long-distances. Present-day seed dispersal by scatter-hoarding
 rodents, introduced livestock, runoff, flooding, gravity, and
 human-mediated dispersal allowed survival of megafauna-dependent fruit
 species after extinction of the major seed dispersers. Megafauna
 extinction had several potential consequences, such as a scale shift
 reducing the seed dispersal distances, increasingly clumped spatial
 patterns, reduced geographic ranges and limited genetic variation and
 increased among-population structuring. These effects could be extended to
 other plant species dispersed by large vertebrates in present-day,
 defaunated communities.
description: Fruit characteristics of
 megafauna-dependent speciesDataset with fruit
 traits of megafauna-dependet plant species in Brazil. Description of the
 variables is included in the file.journal.pone.0001745.s001.xls
DOI: 10.5061/dryad.5b58j
title: Data from: Polylysogeny magnifies competitiveness of a bacterial pathogen in vivo

description: The rise of next generation sequencing is revealing a hidden diversity of
 temperate phages within the microbial community. While a handful of these
 phages have been well characterized, for the vast majority, the role of
 phage carriage, and especially multiple phage carriage, is poorly
 understood. The Liverpool Epidemic Strain of Pseudomonas aeruginosa is an
 aggressive pathogen in Cystic Fibrosis lung infections that has recently
 been found to contain several unique prophages within its genome. Here we
 experimentally investigate the role of two of these phages in vivo, using
 an insect model of infection. We find that while no benefit is conferred
 by phage carriage in single bacterial infections, phages confer a large
 fitness advantage during mixed infections by mediating bacteria-bacteria
 competition. Differences between the two phages appeared to be associated
 with the rate at which the competitor acquired the phage, and therefore
 resistance. However the advantage was greatest in the polylysogen,
 carrying both phages. These finding suggest that the LES phages may play
 an important role in host invasions and more generally show that the
 carriage of multiple phages may itself be beneficial by hindering the
 spread of resistance in rival bacterial populations.
description: growth rates and time to
 deathTotal bacterial and
 phage density measured over time to establish growth rates. Time to death
 was measured in the same experiment for the 24hr group.fitnessFitness estimates for each strain relative to the isogenic phage free strain. The proportion of lysogens identified among the originally phage free competitor strain is also estimated and total densities of each strain included.
DOI: 10.5061/dryad.m7d8m
title: Data from: Chronic anthropogenic disturbance drives the biological impoverishment of the Brazilian Caatinga vegetation

description: 1. In addition to acute transformations of ecosystems caused by
 deforestation, old-growth forests worldwide are being increasingly altered
 by low-intensity but chronic human disturbance. Overgrazing and the
 continuous extraction of forest products are important drivers of chronic
 disturbance, which can lead to the gradual local extinction of species and
 the alteration of vegetation structure. 2. We tested this hypothesis in
 the Brazilian Caatinga vegetation, one of the most species-rich and
 populated semi-arid regions of the world. Using a multi-model averaging
 approach we examined the impact of five recognized indicators of chronic
 disturbance (i.e. proximity to urban centre, houses, roads, density of
 people and livestock) on the diversity, abundance and evenness of 30 woody
 plant communities. We separately tested the response of seedlings,
 saplings, and adults to identify the ontogenetic stages that are most
 susceptible to chronic disturbance. 3. We recorded over 11 000 individuals
 belonging to 51 plant species. As expected, most indicators of chronic
 disturbance were negatively related to species diversity and stem
 abundance, with a variable effect on community evenness. The density of
 people and livestock were the main factors driving changes in plant
 communities, with a stronger negative impact on seedling and sapling
 diversities. Species composition also varied significantly with
 disturbance indicators, irrespective of ontogeny. 4. Our results show the
 potential negative impact that chronic disturbance can have on Caatinga
 plant assemblages and highlight the fact that disturbance resulting from
 an extractivism-based and subsistence economy are probably driving
 old-growth forest stands towards shrub-dominated secondary stands. 5.
 Synthesis and applications. These findings indicate that chronic
 disturbance should not continue to be neglected and we argue for (1)
 research and rural programs able to support better practices in terms of
 land use and sustainable exploitation of forest resources, (2) improved
 governance and law enforcement to shift extractivism towards sustainable
 standards, and (3) expanding the coverage and effective implementation of
 strictly protected areas.
description: Data from 30 plant
 communities sampled in distinct ontogenetic stages at Brazilian
 CaatingaTables with species
 abundance data of 30 plant communities surveyed in distinct ontogenetic
 stages (seedling, sapling and adult) and the chronic disturbance
 predictors measured in each plot. We also measured the soil type of each
 plot to control its effect.Data_Ribeiro et al
 2015_JPE.xls
DOI: 10.15468/dl.5z4692
title: Occurrence Download

description: A dataset containing 254 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Nicotiana rosulata",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 254 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000954-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.192f1
title: Data from: Extinctions, genetic erosion and conservation options for the black rhinoceros (Diceros bicornis)

description: The black rhinoceros is again on the verge of extinction due to
 unsustainable poaching in its native range. Despite a wide historic
 distribution, the black rhinoceros was traditionally thought of as
 depauperate in genetic variation, and with very little known about its
 evolutionary history. This knowledge gap has hampered conservation efforts
 because hunting has dramatically reduced the species’ once continuous
 distribution, leaving five surviving gene pools of unknown genetic
 affinity. Here we examined the range-wide genetic structure of historic
 and modern populations using the largest and most geographically
 representative sample of black rhinoceroses ever assembled. Using both
 mitochondrial and nuclear datasets, we described a staggering loss of 69%
 of the species’ mitochondrial genetic variation, including the most
 ancestral lineages that are now absent from modern populations.
 Genetically unique populations in countries such as Nigeria, Cameroon,
 Chad, Eritrea, Ethiopia, Somalia, Mozambique, Malawi and Angola no longer
 exist. We found that the historic range of the West African subspecies (D.
 b. longipes), declared extinct in 2011, extends into southern Kenya, where
 a handful of individuals survive in the Masai Mara. We also identify
 conservation units that will help maintain evolutionary potential. Our
 results suggest a complete re-evaluation of current conservation
 management paradigms for the black rhinoceros.
description: Microsatellite genotypes
 for the black rhinoceros (Diceros bicornis)Microsatellite dataset
 used in this study. This file includes the genotypes for 11 microsatellite
 loci for both historic and modern black rhinoceros samples. Individuals
 represent 12 populations and are numbered from 1-560.BlackRhinoMsats.xlsx
DOI: 10.5061/dryad.bj546
title: Data from: Shared phylogeographical breaks in a Caribbean coral reef sponge and its invertebrate commensals

description: Aim: To test whether phylogeographical barriers in the brooding sponge
 Callyspongia vaginalis match breaks previously identified in the
 Caribbean. We also compared patterns of subdivision in the sponge to those
 of three of its commensals, the broadcast spawning brittle star Ophiothrix
 suensonii and the brooding amphipods Leucothoe ashleyae and L. kensleyi,
 and tested whether any shared breaks arose simultaneously. Location:
 Florida, Bahamas and the Caribbean. Methods: Subdivision of C. vaginalis
 populations was inferred from one mitochondrial (COI) and six nuclear loci
 using clustering analyses. We identified phylogeographical breaks in the
 sponge and its invertebrate commensals by determining geographical
 patterns of genetic variation and tested simultaneous population
 divergence across barriers shared among taxa using hierarchical
 approximate Bayesian computation. Results: Sponge populations were
 partitioned into western and eastern groups across the Caribbean, with
 hierarchical subdivision within regions. The sponge and its commensals
 shared barriers across their ranges despite differences in dispersal
 strategy: C. vaginalis, L. ashleyae and O. suensonii populations in
 Central America were isolated from the remainder of the Caribbean, and all
 four taxa shared a break between Florida and the Bahamas, although
 simultaneous population divergence could not be inferred with statistical
 certainty. Our results also suggest cryptic speciation within C.
 vaginalis. Main conclusions: Phylogeographical patterns in C. vaginalis
 largely matched barriers previously identified at the Florida Straits,
 Mona Passage and Bay of Honduras in other Caribbean taxa. Oceanographic
 features such as deep water between locations, strong currents, and eddies
 are likely mechanisms responsible for these breaks.
description: GPS_PhiST_DeBiasse_et_al_Journal_of_BiogeographyThis file contains the sampling site GPS coordinates and PhiST values for Callyspongia vaginalis, Leucothoe ashelyae, Leucothoe kensleyi, and Ophiothrix suensonii required for the Barrier analyses associated with the Journal of Biogeography manuscript "Shared phylogeographical breaks in a Caribbean coral reef sponge and its invertebrate commensals" by Melissa B. DeBiasse, Vincent P. Richards, Mahmood S. Shivji, and Michael E. Hellberg.
DOI: 10.5061/dryad.sk5sv1q
title: Data from: Introgression across hybrid zones is not mediated by Large X-effects in green toads with undifferentiated sex chromosomes

description: Divergence between incipient species remains an incompletely understood
 process. Hybrid zones provide great research potential, reflecting natural
 organismal genomic interactions and gene evolution in a variety of
 recombinants over generations. While sex chromosomes are known
 evolutionary drivers of reproductive isolation, empirical population
 genetics mostly examined species with heteromorphic sex chromosomes. We
 recently reported restricted introgression at sex-linked markers in an
 amphibian system with homomorphic sex chromosomes (Hyla), consistent with
 a Large X-effect, designating a greater role of sex chromosomes in driving
 hybrid incompatibilities. Here, using a similar approach, we examined two
 hybrid zones of Palearctic green toads (Bufo viridis subgroup), involving
 several lineages that arose at different times and form secondary
 contacts. We find no evidence for differential introgression of sex-linked
 vs. autosomal markers across both zones. This absence of Large X-effects
 in Bufo indicates that, unlike in Hyla, hybrid incompatibilities may not
 result from faster-heterogametic sex and faster-male aspects of Haldane’s
 rule. The recent suppression of XY recombination in Hyla, but not in Bufo,
 may have driven greater divergence between Hyla sex chromosomes, causing
 stronger reproductive isolation. Alternatively, stronger linkage among
 Hyla’s sex-linked markers could restrict introgression. We hypothesize
 that the degree of sex-specific recombination may condition the importance
 of homomorphic sex chromosomes in speciation.
description: GerchenEtAl_AmNatGenotyping data of green toads of the North-Italian and the Sicilian hybrid zone