cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.146b6
title: Data from: Effects of macronutrient intake on the lifespan and fecundity of the marula fruit fly, Ceratitis cosyra (Tephritidae): extreme lifespan in a host specialist.

description: In insects, lifespan and reproduction are strongly associated with
 nutrition. The ratio and amount of nutrients individuals consume affects
 their life expectancy and reproductive investment. The geometric framework
 (GF) enables us to explore how animals regulate their intake of multiple
 nutrients simultaneously and determine how these nutrients interact to
 affect life history traits of interest. Studies using the GF on
 host-generalist tephritid flies have highlighted trade-offs between
 longevity and reproductive effort in females, mediated by the protein to
 carbohydrate (P:C) ratio that individuals consume. Here, we tested how P
 and C intake affect lifespan (LS) in both sexes, and female lifetime (LEP)
 and daily (DEP) egg production, in Ceratitis cosyra, a host-specialist
 tephritid fly. We then determined the P:C ratio that C. cosyra defends
 when offered a choice of foods. Female LS was optimised at a 0:1 P:C ratio
 whereas to maximise their fecundity females needed to consume a higher P:C
 ratio (LEP = 1:6 P:C; DEP = 1:2.5 P:C). In males, LS was also optimised at
 a low P:C ratio of 1:10. However, when given the opportunity to regulate
 their intake, both sexes actively defended a 1:3 P:C ratio, which is
 closer to the target for DEP than either LS or LEP. Our results show that
 female C. cosyra experienced a moderate trade-off between LS and
 fecundity. Moreover, the diets that maximised expression of LEP and DEP
 were of lower P:C ratio than those required for optimal expression of
 these traits in host-generalist tephritids or other generalist insects.
description: Consumption - No choice
 experimentNutrient consumption in
 the no choice experimentNoChoiceConso.xlsxEgg production - No choice experimentNoChoiceEggs.xlsxConsumption - Dietary choice experimentChoiceExperiment.xlsx
DOI: 10.5061/dryad.64pg3
title: Data from: Nomenclature for the nameless: a proposal for an integrative molecular taxonomy of cryptic diversity exemplified by planktonic foraminifera

description: Investigations of biodiversity, biogeography and ecological processes rely
 on the identification of “species” as biologically significant, natural
 units of evolution. In this context, morpho-taxonomy only provides an
 adequate level of resolution if reproductive isolation matches
 morphological divergence. In many groups of organisms, morphologically
 defined species often disguise considerable genetic diversity, which may
 be indicative of the existence of cryptic species. The diversity hidden by
 morphological species can be disentangled through genetic surveys, which
 also provide access to data on the ecological distribution of genetically
 circumscribed units. These units can be identified by unique DNA sequence
 motifs and allow studies of evolutionary and ecological processes at
 different levels of divergence. However, the nomenclature of genetically
 circumscribed units within morphological species is not regulated and
 lacks stability. This represents a major obstacle to efforts to synthesize
 and communicate data on genetic diversity for multiple stakeholders. We
 have been confronted with such an obstacle in our work on planktonic
 foraminifera, where the stakeholder community is particularly diverse,
 involving geochemists, paleoceanographers, paleontologists and biologists,
 and the lack of stable nomenclature beyond the level of formal
 morphospecies prevents effective transfer of knowledge. To circumvent this
 problem, we have designed a stable, reproducible and flexible nomenclature
 system for genetically circumscribed units, analogous to the principles of
 a formal nomenclature system. Our system is based on the definition of
 unique DNA sequence motifs collocated within an individual, their
 typification (in analogy with holotypes), utilization of their
 hierarchical phylogenetic structure to define levels of divergence below
 that of the morphospecies, and a set of nomenclature rules assuring
 stability. The resulting molecular operational taxonomic units (MOTUs)
 remain outside the domain of current nomenclature codes, but are linked to
 formal morphospecies as regulated by the codes. Subsequently we show how
 this system can be applied to classify genetically defined units using the
 SSU rDNA marker in planktonic foraminifera and we highlight its potential
 use for other groups of organisms where similarly high levels of
 connectivity between molecular and formal taxonomies can be achieved.
description: Supplementary material
 1Data
 used for the Implementation of the molecular nomenclature system for the
 Globigerinella plexus. The description of the fields is provided in the
 file.Supplementary
 material_1.xlsxSupplementary material
 2Data
 used for the Implementation of the molecular nomenclature system for
 Pulleniatina obliquiloculata. The description of the fields is provided in
 the file.Supplementary
 material_2.xlsx
DOI: 10.5061/dryad.4pf25
title: Data from: Spatial and temporal patterns of frugivorous Hornbill movements in Central Africa and their implications for rain forest conservation

description: Tropical forest conservation and restoration require an understanding of
 the movements and habitat preferences of important seed dispersers. With
 forests now being altered at an unprecedented rate, avian frugivores are
 becoming increasingly vital for forest regeneration. Seed movement,
 however, is highly dependent on the behavioral characteristics of their
 dispersers. Here, we examined the movements, habitat preferences, and
 range sizes of two African frugivores: the Black-casqued (Ceratogymna
 atrata) and the White-thighed (Bycanistes albotibialis) Hornbill, in the
 lowland rain forests of southern Cameroon. Using satellite transmitters,
 we tracked eight hornbills for 3 yr to characterize their movements and
 relate them to environmental landscape features. Hornbill movements
 differed significantly, with B. albotibialis ranging over larger areas
 (mean = 20,274 ha) than C. atrata (mean = 5604 ha), and females of both
 species covering over 15 times the area of males. Evidence suggests that
 movements are irruptive during particular periods, perhaps driven by low
 resource availability. In addition, hornbills often returned to the same
 localities within a year, although movements were not characterized as
 migratory. Both species displayed significant differences in habitat
 preference, with B. albotibialis utilizing disturbed habitat more
 frequently than C. atrata (t = −22.04, P = 2.2 × 10−16). Major roads were
 found to act as barriers for C. atrata, but not for B. albotibialis. The
 ability of both hornbill species to move large distances suggests
 hornbills will play a vital role in the maintenance and regeneration of
 rain forests in Central Africa as forest fragmentation increases and
 terrestrial vertebrates decline in numbers.
description: HornbillmovementsrawdataTab-delimited raw text data file, with data recovered from satellite transmitters, before filtering for quality of satellite read.
DOI: 10.5061/dryad.jr0d5h7
title: Data from: Are there general laws for digit evolution in squamates? The loss and re-evolution of digits in a clade of fossorial lizards (Brachymeles, Scincinae)

description: Evolutionary simplification of autopodial structures is a major theme in
 studies of body‐form evolution. Previous studies on amniotes have
 supported Morse's law, that is, that the first digit reduced is Digit
 I, followed by Digit V. Furthermore, the question of reversibility for
 evolutionary digit loss and its implications for “Dollo's law”
 remains controversial. Here, we provide an analysis of limb and digit
 evolution for the skink genus Brachymeles. Employing phylogenetic,
 morphological, osteological, and myological data, we (a) test the
 hypothesis that digits have re‐evolved, (b) describe patterns of
 morphological evolution, and (c) investigate whether patterns of digit
 loss are generalizable across taxa. We found strong statistical support
 for digit, but not limb re‐evolution. The feet of pentadactyl species of
 Brachymeles are very similar to those of outgroup species, while the hands
 of these lineages are modified (2‐3‐3‐3‐2) and a have a reduced set of
 intrinsic hand muscles. Digit number variation suggests a more labile
 Digit V than Digit I, contrary to Morse's law. The observed pattern
 of digit variation is different from that of other scincid lizards
 (Lerista, Hemiergis, Carlia). Our results present the first evidence of
 clade‐specific modes of digit reduction.
description: Chronogram in Newick
 FormatNewick formatted
 chronogram file resulting from fossil-calibrated BEAST
 analyses.BrachChrono.newickChronogram in Nexus File FormatNexus file formatted chronograph resulting from fossil-calibrated analysis in BEASTBrachymeles_chronogram.treConcatenated Nexus Alignment FileNexus sequence alignment file with concatenated sequence data for the four loci employed in the study (ND1, BDNF, PTGER4, R35). Character block presented at the bottom of the file showing coding regions.ConcatenatedNexus.nexMorphological DataMorphological character data used for ancestral state reconstructions showing finger, toe and limb states for all taxa included in analyses, along with associated specimen voucher numbers.Morphology.xlsx
DOI: 10.5061/dryad.4f1r5vg8
title: Data from: Plant dispersal in the sub-Antarctic inferred from anisotropic genetic structure

description: Climatic conditions and landscape features often strongly affect species’
 local distribution patterns, dispersal, reproduction and survival, and may
 therefore have considerable impacts on species' fine-scale spatial
 genetic structure (SGS). In this paper we demonstrate the efficacy of
 combining fine-scale SGS analyses with isotropic and anisotropic spatial
 autocorrelation techniques to infer the impact of wind patterns on plant
 dispersal processes. We genotyped 1304 Azorella selago (Apiaceae)
 specimens, a wind-pollinated and wind-dispersed plant, from four
 populations distributed across sub-Antarctic Marion Island. SGS was
 variable with Sp values ranging from 0.001 to 0.014, suggesting notable
 variability in dispersal distance and wind velocities between sites.
 Nonetheless, the data supported previous hypotheses of a strong NW – SE
 gradient in wind strength across the island. Anisotropic autocorrelation
 analyses further suggested that dispersal is strongly directional, but
 varying between sites depending on the local prevailing winds. Despite the
 high frequency of gale-force winds on Marion Island, gene dispersal
 distance estimates (σ) were surprisingly low (&lt; 10 m), most likely
 because of a low pollen dispersal efficiency. An SGS approach in
 association with isotropic and anisotropic analyses provides a powerful
 means to assess the relative influence of abiotic factors on dispersal,
 and allow inferences that would not be possible without this combined
 approach.
description: MEC-11-0847 Born
 CThis
 file is an excel spreadsheet giving details about individuals'
 locations (in decimal degree) and genotypes (6 microsatellites markers)
 for the four study sites presented in the study.
DOI: 10.5061/dryad.2d218
title: Data from: The continuum between semelparity and iteroparity: plastic expression of parity in response to season length manipulation in Lobelia inflata.

description: Background: Semelparity and iteroparity are considered to be distinct and
 alternative life-history strategies, where semelparity is characterized by
 a single, fatal reproductive episode, and iteroparity by repeated
 reproduction throughout life. However, semelparous organisms do not
 reproduce instantaneously; typically reproduction occurs over an extended
 time period. If variation in reproductive allocation exists within such a
 prolonged reproductive episode, semelparity may be considered iteroparity
 over a shorter time scale.This continuity hypothesis predicts that
 “semelparous” organisms with relatively low probability of survival after
 age at first reproduction will exhibit more extreme semelparity than those
 with high probability of adult survival. This contrasts with the
 conception of semelparity as a distinct reproductive strategy expressing a
 discrete, single, bout of reproduction, where reproductive phenotype is
 expected to be relatively invariant. Here, we manipulate expected season
 length—and thus expected adult survival—to ask whether Lobelia inflata, a
 classic “semelparous” plant, exhibits plasticity along a
 semelparous-iteroparous continuum. Results: Groups of replicated genotypes
 were manipulated to initiate reproduction at different points in the
 growing season in each of three years. In lab and field populations alike,
 the norm of reaction in parity across a season was as predicted by the
 continuity hypothesis: as individuals bolted later, they showed shorter
 time to, and smaller size at first reproduction, and multiplied their
 reproductive organs through branching, thus producing offspring more
 simultaneously. Conclusions: This work demonstrates that reproductive
 effort occurs along a semelparous-iteroparous continuum within a
 “semelparous” organism, and that variation in parity occurs within
 populations as a result of phenotypic plasticity.
description: Reproductive traits of
 Lobelia inflataThis dataset includes
 measurements of seven reproductive characteristics for 1,509 Lobelia
 inflata (Campanulaceae) individuals. Plants were grown in the lab or at a
 field site, but were originally sourced from a population in the Petawawa
 Research Forest (Ontario, Canada).BMC EB Data - Hughes and Simons
 2014.xls
DOI: 10.5061/dryad.07nj3
title: Data from: Genetic divergence between the sympatric queen morphs of the ant Myrmica rubra

description: Pairs of obligate social parasites and their hosts, where some of the
 parasites have recently diverged from their host through intraspecific
 social parasitism, provide intriguing systems for studying the modes and
 processes of speciation. Such speciation, probably in sympatry, has also
 been propounded in the ant Myrmica rubra and its intraspecific social
 parasite. In this species, parasitism is associated with queen size
 dimorphism, and the small microgyne has become a social parasite of the
 large macrogyne. Here, we investigated the genetic divergence of the host
 and the parasite queen morphs in 11 localities in southern Finland, using
 nuclear and mitochondrial markers of queens and workers. We formulated and
 tested four speciation-related hypotheses that differed in the degree of
 genetic divergence between the morphs. The queen morphs were genetically
 distinct from each other with little hybridization. In the nuclear data,
 when localities were nested within queen morphs in the hierarchical amova,
 39% of the genetic variation was explained by the queen morph
 (standardized F'CT = 0.63, uncorrected FCT = 0.39), whereas 18% was
 explained by the locality (F'SC = 0.39, FSC = 0.29). This result
 corroborated the hypothesis of advanced sympatric speciation. In contrast,
 the mitochondrial DNA could not settle between the hierarchical levels of
 locality and queen morph, thus substantiating equally the hypotheses of
 incipient and advanced sympatric speciation. Together, our results support
 the view that the microgynous parasite has genetically diverged from its
 macrogynous host to the level of a nascent species.
description: The microsatellite
 genotypes and mitochondrial DNA sequencesThe file contains tables
 of the microsatellite genotypes, mitochondrial DNA sequences and their
 references, and information about the localities of the samples used in
 this study.DRYAD_Leppanen et
 al_.xls
DOI: 10.5061/dryad.7vn28
title: Data from: Upregulation of NLRP3 inflammasome in the tears and ocular surface of dry eye patients

description: Purpose: To evaluate the mRNA and protein expressions of NLRP3
 inflammasome and its downstream inflammatory factors in human dry eye.
 Methods: We recruited 54 patients with Sjögren’s syndrome dry eye (SSDE),
 50 patients with non-Sjögren’s syndrome dry eye (NSSDE), and 46 healthy
 controls. Tear film breakup time (TBUT), Schirmer I test, and fluorescein
 staining (FL) were performed on all subjects. Tear samples were obtained
 to analyze the inflammatory cytokine levels of IL-1β and IL-18 via
 enzyme-linked immunosorbent (ELISA). Conjunctival impression cytology
 (CIC) specimens were collected to detect the mRNA expression of NLRP3,
 caspase-1, IL-1β, and IL-18 using quantitative RT-PCR, and the protein
 expression of NLRP3 and caspase-1 by Western blotting. Results: NLRP3 mRNA
 expression showed higher levels in both dry eye groups compared with
 controls, with a comparably significant elevation in the SSDE group
 (relative 2.47-fold upregulation, p&lt;0.05). NLRP3 protein expression
 was also increased in SSDE group (relative1.94-fold upregulation) compared
 with the controls. mRNA expression of caspase-1 was significantly
 upregulated in both SSDE (relative 1.44-fold upregulation, p&lt;0.05)
 and NSSDE (relative 1.32-fold upregulation, p&lt;0.05). Procaspase-1
 protein level was increased in SSDE (relative 1.84-fold upregulation) and
 NSSDE (relative 1.12-fold upregulation) versus controls; and caspase-1
 protein expression was also increased in SSDE (relative 1.49-fold
 upregulation) and NSSDE (relative 1.17-fold upregulation) compared with
 the controls. The patients with SSDE and NSSDE had higher IL-1β and IL-18
 mRNA values and protein expressions than the controls did. The relative
 mRNA expression of IL-1β upregulated 3.59-fold (p&lt;0.001) in SSDE
 and 2.13-fold (p&lt;0.01) in NSSDE compared with the controls. IL-1β
 protein level also showed significant upregulation in SSDE (p=0.01; vs.
 controls groups). IL-18 mRNA expression levels were significantly
 upregulated in the SSDE (relative 2.97-fold upregulation, p=0.001) and
 NSSDE (relative 2.05-fold upregulation, p=0.001) groups compared with the
 controls; tear IL-18 concentrations were also significantly increased in
 the SSDE (p&lt;0.001) and NSSDE (p&lt;0.05) groups. Conclusions:
 In the current study, we found that mRNA and protein expressions of NLRP3
 inflammasome were upregulated in human dry eyes, especially in SSDE; the
 downstream inflammatory factors caspase-1, IL-1β, and IL-18 were also
 elevated in dry eye patients. These observations suggest the involvement
 of NLRP3 inflammasome in the onset and development of the inflammation in
 dry eye.
description: Niu et al.plos one raw
 dataWe uploaded the clinical
 examination results,mRNA and protein expressions of NLRP3,caspase-1,IL-18
 and IL-1β. Also we uploaded Table 1 and Table 2
DOI: 10.5061/dryad.hm064
title: Data from: Above-ground and below-ground responses to long-term nutrient addition across a retrogressive chronosequence

description: 1. There is much interest in understanding ecosystem responses to
 local-scale soil fertility variation, which has often been studied using
 retrogressive chronosequences that span thousands of years and show
 declining fertility and plant productivity over time. There have been few
 attempts to experimentally test how plant nutrient limitation changes
 during retrogression. 2. We studied a well-characterized system of 30
 forested lake islands in northern Sweden that collectively represent a
 5350-year post-fire retrogressive chronosequence, with fertility and
 productivity decreasing as time since fire increases. For each island we
 set up four plots on understorey vegetation, each subjected to a different
 fertilizer treatment over six years: no additions, nitrogen (N) only,
 phosphorus (P) only, and N + P. 3. We found that both N and P additions
 reduced feather moss and thus total plant biomass. Meanwhile the three
 dominant vascular plant species showed contrasting biomass responses, but
 similar responses of foliar nutrient concentrations to nutrient additions.
 Fertilization reduced most microbial groups and altered CO2 fluxes, most
 likely through feather moss reduction. Against expectations, the majority
 of interactive effects of N and P were antagonistic. 4. Changes in effects
 of nutrient additions during retrogression were usually modest. Empetrum
 hermaphroditum biomass was increasingly promoted by P and N + P addition
 while vascular plant N to P ratios were increasingly reduced by P
 addition, indicating increasing plant limitation by nutrients (notably P)
 during retrogression. Below-ground, positive effects of N addition on soil
 mineral N increased while negative effects of N addition on soil fungi
 decreased during retrogression; no other below-ground effects of
 fertilization changed along the gradient. 5. Synthesis. Our results show
 that forest understorey communities on islands of different fire history
 and thus stages of retrogression show relatively modest differences in how
 they respond to nutrient addition despite large changes in ecosystem
 productivity and soil fertility, probably because of high species turnover
 and adaptation of communities to infertile conditions. While increased
 nutrient availability (as expected through global change) may have
 important ecological consequences, these effects are likely, especially
 below-ground, to be rather similar across ecosystems that differ greatly
 in nutrient availability and productivity.
description: Raw data for island
 fertilization paperAll raw data for plants,
 soil microbes, and ecosystem properties for island fertilization
 paper.islands-fertilizer-data-for-dryad.xlsx
DOI: 10.15468/dl.xum7rk
title: Occurrence Download

description: A dataset containing 219 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is The InBIO Barcoding Initiative Database: Diptera 03 - Further records on Portuguese Limoniidae, Pediciidae and Tipulidae"
 ]
}

 The dataset includes 219 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000647-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.389
title: Data from: Mammalian evolution: timing and implications from using the LogDeterminant transform for proteins of differing amino acid composition

description: We explore the tree of mammalian mtDNA sequences, using particularly the
 LogDet transform on amino acid sequences, the distance Hadamard transform,
 and the Closest Tree selection criterion. The amino acid composition of
 different species show significant differences, even within mammals. After
 compensating for these differences, nearest-neighbor bootstrap results
 suggest that the tree is locally stable, though a few groups show slightly
 greater rearrangements when a large proportion of the constant sites are
 removed. Many parts of the trees we obtain agree with those on published
 protein ML trees. Interesting results include a preference for rodent
 monophyly. The detection of a few alternative signals to those on the
 optimal tree were obtained using the distance Hadamard transform (with
 results expressed as a Lento plot). One rearrangement suggested was the
 interchange of the position of primates and rodents on the optimal tree.
 The basic stability of the tree, combined with two calibration points
 (whale/cow and horse/rhinoceros), together with a distant secondary
 calibration from the mammal/bird divergence, allows inferences of the
 times of divergence of putative clades. Allowing for sampling variances
 due to finite sequence length, most major divergences amongst lineages
 leading to modern orders, appear to occur well before the
 Cretaceous/Tertiary (K/T) boundary. Implications arising from these early
 divergences are discussed, particularly the possibility of competition
 between the small dinosaurs and the new mammal clades.
description: Penny et al Data
 SetPenny.htm