cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.k40527n
title: Data from: Postglacial range expansion shaped the spatial genetic structure in a marine habitat-forming species: implications for conservation plans in the Eastern Adriatic Sea

description: Aim: Understanding how historical and contemporary processes shaped and
 maintain spatial patterns of genetic diversity is a major goal for
 conservation biologists. Here, we characterized the pattern of neutral
 genetic diversity and we inferred underlying processes in the
 habitat-forming octocoral Paramuricea clavata in the Adriatic Sea, a
 peculiar phylogeographic region of the Mediterranean Sea. Location:
 Eastern coast of the Adriatic Sea. Methods: We genotyped seven
 microsatellites in 454 individuals of P. clavata from 13 populations
 recolonized after the last glacial maximum (LGM). We estimated the levels
 of contemporary connectivity and genetic drift and we reconstructed the
 demographic history of these populations. Results: The pattern of spatial
 genetic structure resulted from the combination of hierarchical genetic
 clusters and isolation by distance (IBD). A significant decrease in
 genetic diversity and an increase of the frequencies of individual alleles
 likely due to allele surfing from the south to the north of the area were
 observed as expected after a postglacial sequential recolonization. Based
 on maximum likelihood analyses, the foundation of these populations was
 not linked to dramatic change in population size. Main conclusion:
 Oceanographic barriers to gene flow combined to the restricted dispersal
 of P. clavata likely maintain the hierarchical structure and the IBD
 pattern. We suggest that the latitudinal genetic gradient results from a
 northward ‘serial founder events’ recolonization. By integrating patterns
 and processes, we bridge the gap between the evolutionary and the
 conservation biology of P. clavata, providing management guidelines, which
 will benefit the associated coralligenous biodiversity.
description: Microsatellite dataset
 for Paramuricea clavata in the Eastern Adriatic SeaThis data file contains
 the genotypes at 7 microsatellites obtained for 454 individuals of
 Paramuricea clavata coming from 13 populations from the Eastern Adriatic
 Sea.Ledoux
 et al_Pclavata_Adriatic.txt
DOI: 10.5061/dryad.12q6c78
title: Data from: Early rehabilitation to prevent post-intensive care syndrome in critically ill patients: a systematic review and meta-analysis

description: Introduction: We examined the effectiveness of early rehabilitation for
 the prevention of post-intensive care syndrome (PICS), characterised by an
 impaired physical, cognitive, or mental health status, among survivors of
 critical illness. Methods: We performed a systematic literature search of
 several databases (Medline, Embase, and Cochrane Central Register of
 Controlled Trials) and a manual search to identify randomised controlled
 trials (RCTs) comparing the effectiveness of early rehabilitation versus
 no early rehabilitation or standard care for the prevention of PICS. The
 primary outcomes were short-term physical-, cognitive-, and mental
 health-related outcomes assessed during hospitalisation. The secondary
 outcomes were the standardised, long-term health-related quality of life
 scores (EuroQol 5 Dimension [EQ5D] and the Medical Outcomes Study 36-Item
 Short Form Health Survey Physical Function scale [SF-36 PF]). We used the
 Grading of Recommendations Assessment, Development and Evaluation (GRADE)
 approach to rate the quality of evidence (QoE). Results: Six RCTs selected
 from 5,105 screened abstracts were included. Early rehabilitation
 significantly improved short-term physical-related outcomes, as indicated
 by an increased Medical Research Council scale score (MRC score)
 [standardised mean difference (SMD): 0.38, 95% confidence interval (CI):
 0.10–0.66, p = 0.009] (QoE: low) and a decreased incidence of ICU-acquired
 weakness (ICU-AW) [odds ratio (OR) 0.42, 95% CI 0.22 to 0.82, p = 0.01]
 (QoE: low), compared to standard care or no early rehabilitation. However,
 the two groups did not differ in terms of cognitive-related delirium-free
 days (SMD: -0.02, 95% CI: -0.23–0.20) (QoE: low) and the mental
 health-related Hospital Anxiety and Depression Scale score (odds ratio:
 0.79, 95% CI: 0.29–2.12) (QoE: low). Early rehabilitation did not improve
 the long-term outcomes of PICS as characterised by EQ5D and SF-36PF.
 Conclusions: Early rehabilitation improved only short-term
 physical-related outcomes in critically ill patients. Additional large
 RCTs are needed.
description: Data
DOI: 10.5061/dryad.8gf34g5
title: Data from: Sex bias in ability to cope with cancer: Tasmanian devils and facial tumour disease.

description: Knowledge of the ecological dynamics between hosts and pathogens during
 the initial stages of disease emergence is crucial to understanding the
 potential for evolution of new interspecific interactions. Tasmanian devil
 (Sarcophilus harrisii) populations have declined precipitously owing to
 infection by a transmissible cancer (devil facial tumour disease, DFTD)
 that emerged approximately 20 years ago. Since the emergence of DFTD, and
 as the disease spreads across Tasmania, the number of devil has dropped up
 to 90% across 80% of the species’ distributional range. As a result, the
 disease is expected to act as a strong selective force on hosts to develop
 mechanisms of tolerance and/or resistance to the infection. We assessed
 the ability of infected devils to cope with infection, which translates
 into host tolerance to the cancer, by using the reaction norm of the
 individual body condition by tumour burden. We found that body condition
 of infected hosts is negatively affected by cancer progression. Males and
 females presented significant differences in their tolerance levels to
 infection, with males suffering declines of up to 25% of their body
 condition, in contrast to &lt;5% in females. Sex-related differences
 in tolerance to cancer progression may select for changes in life history
 strategies of the host and could also alter the selective environment for
 the tumours.
description: Raw
 datasetRuiz_Aravena_et_al_raw_data.csvRuiz_Aravena_et_al_GAMM_codeR code to run the models presented in Table 1.
DOI: 10.15468/dl.rr2s57
title: Occurrence Download

description: A dataset containing 150 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-5000.0",
 "TaxonKey is Crateva religiosa"
 ]
}

 The dataset includes 150 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001165-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5rh14nc
title: Data from: The convergent evolution of snake-like forms by divergent evolutionary pathways in squamate reptiles

description: Convergent evolution of phenotypes is considered evidence that evolution
 is deterministic. Establishing if such convergent phenotypes arose through
 convergent evolutionary pathways is a stronger test of determinism. We
 studied the evolution of snake-like body shapes in six clades of lizards,
 each containing species ranging from short-bodied and pentadactyl to
 long-bodied and limbless. We tested whether body shapes that evolved in
 each clade were convergent, and whether clades evolved snake-like body
 shapes following convergent evolutionary pathways. Our analyses showed
 that indeed species with the same numbers of digits in each clade evolved
 convergent body shapes. We then compared evolutionary pathways among
 clades by considering patterns of evolutionary integration and shape of
 relationship among body parts, patterns of vertebral evolution, and models
 of digit evolution. We found that all clades elongated their bodies
 through the addition, not elongation, of vertebrae, and had similar
 patterns of integration. However, patterns of integration, the body parts
 that were related by a linear or a threshold model, and patterns of digit
 evolution differed among clades. These results showed that clades followed
 different evolutionary pathways. This suggests an important role of
 historical contingency as opposed to determinism in the convergent
 evolution of snake-like body shapes.
description: Bergmann and Morinaga
 Convergent Evolution DatasetA csv file that contains
 morphometric data for all species included in the manuscript. Description
 of the variables is provided above the table. Scientific names match those
 on the phylogeny included in another file.Bergmann and Morinaga
 Convergent Evolution PhylogenyPhylogeny used for data
 analysis. Derived from phylogenies by Pyron et al. (2013) and Siler &
 Brown (2011). See article for details. Species names match those in the
 dataset. Tree is ultrametric.
DOI: 10.15468/dl.9dwr94
title: Occurrence Download

description: A dataset containing 177 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-5000.0",
 "TaxonKey is Cratoxylum cochinchinense"
 ]
}

 The dataset includes 177 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001166-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.cc8m5
title: Data from: A new western European Cretaceous bryozoan genus from the early Cenomanian radiation of neocheilostomes

description: Neocheilostomes possessing ovicells for larval brooding originated in the
 late Albian and radiated explosively in the Late Cretaceous. Our
 understanding of this radiation is hampered by poor knowledge of the
 taxonomy of the earliest neocheilostomes. Here we describe a new
 neocheilostome genus, Ehrhardina, from shallow-water sediments in the
 early Cenomanian of Western Europe. Two species (Ehrhardina voigti sp.
 nov. and E. pikeae sp. nov.) are referred to the new genus. Ehrhardina
 gen. nov. is an onychocellid characterized by large opesiae with
 proximolateral, symmetrical opesiular constrictions and proximolateral,
 long opesiular indentations, bilaterally symmetrical interzooidal
 avicularia and lacking spine bases, but with hyperstomial ovicells that
 have ectooecia formed of exterior wall calcification. Colonies are
 unusually large for encrusting onychocellids and multilaminar; ovicells
 are primitive in showing a median suture in the ectooecium. Similarities
 between Ehrhardina gen. nov. and Aechmella, Floridina, Floridinella, and
 Onychocella are discussed, and a key for the discrimination of these
 genera is provided. Ehrhardina gen. nov. is the oldest neocheilostome
 known to construct large, multilaminar colonies.
description: Morphological
 measurements on Ehrhardina voigti gen. nov.Summary of morphological
 measurements on Ehrhardina voigti gen. et sp. nov. SEM images were
 analysed using the image-processing program ImageJ.Summary_of_measurements_on_E_voigti.xlsxMorphological measurements on Ehrardina pikeae gen. et sp. nov.Summary of morphological measurements on Ehrhardina pikeae gen. et sp. nov. SEM images were analysed using the image-processing program ImageJ.Summary_of_measurements_on_E_pikeae.xlsx
DOI: 10.5061/dryad.9gn6n
title: Data from: Environmental drivers and phylogenetic constraints of growth phenologies across a large set of herbaceous species

description: 1. Because perennial herbs of temperate climates develop their aboveground
 parts every year anew, their success critically depends on the timing and
 speed of this growth (growth phenology). These parameters can play a role
 in species coexistence and may differ along environmental gradients.
 Still, we know little about them, as most phenological data come from
 observations of flowering and to a lesser degree leafing onset. 2. We
 collected data on growth phenology of about 400 perennial herbs in a
 botanical garden to make the results independent of local differences in
 climatic drivers as much as possible. Using these data, we determined
 species-specific parameters of Day of peak growth, Day of maturity, and
 two types of growth rates associated with the change in plant size.
 Environmental conditions in which these species occur in the field were
 assessed using Ellenberg indicator values, which express species'
 optima along gradients of moisture, nutrients and temperature. 3. Both
 timing and speed of growth estimated in the common garden were affected by
 light and moisture conditions of the habitats where the species typically
 occur. All parameters showed phylogenetic conservatism. 4. We identified
 two relationships among these parameters of growth phenology: (i) species
 with early peak growth had high relative growth rates in contrast to late
 species; (ii) tall species showed later peak growth than short species
 which more often grew early. The first relationship is associated with
 survival under forest canopy, where species are selected to grow early and
 fast before trees leaf out, which restricts their size. The latter is
 associated with (asymmetric) competition for light in open habitats, where
 the main selection factor is for tall stature, which cannot be attained
 early in the season. 5. Synthesis: We show that large differences in size
 growth dynamics among herbaceous species are constrained by a few key
 tradeoffs involving height at maturity, rate of growth, and time when
 maximum height is attained. These tradeoffs correspond to major selective
 forces acting on herbaceous plants in temperate climates.
description: Huang et al.
 JEcol-2017-0542.R1-growth phenology
DOI: 10.5061/dryad.1vh64
title: Data from: Taxonomic revision of the Malagasy Camponotus grandidieri and niveosetosus species groups (Hymenoptera, Formicidae) using qualitative and quantitative morphology

description: The Camponotus grandidieri species group and Camponotus niveosetosus
 species group of the Malagasy region are revised. Species delimitation was
 inferred from the evidence of both qualitative morphological analysis and
 multivariate morphometry. The multivariate method combined the Nest
 Centroid (NC)-clustering method and Partitioning Algorithm based on
 Recursive Thresholding (PART) function to generate hypotheses about
 species boundaries (clusters) based on 19 continuous morphological traits
 of minor workers. The proposed species hypotheses were tested by
 cumulative cross-validated Linear Discriminant Analysis (LOOCV-LDA) and
 Principal Component Analysis in a shape space (shape PCA). Morphometric
 ratios for the subsets of minor and major workers were used in species
 descriptions and redefinitions. Here, eight species are recognized, of
 which three are newly described and five are redescribed. Four species
 belong to the Camponotus grandidieri species group: auropubens Forel,
 efitra n. sp., grandidieri Forel, and maintikibo n. sp.; and four species
 belong to the Camponotus niveosetosus species group: descarpentriesi
 Santschi, madagascarensis Forel stat. rev., mita n. sp., and voeltzkowii
 Forel. Camponotus auropubens aldabrensis Forel and C. olivieri freyeri
 Santschi are synonymized under C. auropubens. Camponotus grandidieri
 atrabilis Santschi and C. grandidieri comorensis Santschi are synonymized
 under C. grandidieri. Illustrated species identification keys for both
 minor and major castes, taxonomic discussions, images, and distribution
 maps for each species superimposed on the ecoregions of Madagascar are
 also provided.
description: Malagasy Camponotus
 grandidieri and niveosetosus species groups measurementsBasic measurements of
 individual specimens of the Malagasy Camponotus grandidieri and
 niveosetosus species groups arranged by species code, collection code, and
 specimen code (unique identification number). See text for
 abbreviationsSupple-material_Myrmotrema
 Measurements v1.xlsx
DOI: 10.5061/dryad.rh05d
title: Data from: A new mountain lizard from Montes de León (NW Iberian Peninsula): Iberolacerta monticola astur ssp. nov. (Squamata: Lacertidae)

description: Iberolacerta populations from the Northern Montes de León (NML) were
 studied by means of external morphology (scalation and biometry),
 osteology and genetics (mtDNA and microsatellites), searching for their
 homogeneity (“intrazonal analysis”) and, once verified, comparing them
 with Iberolacerta monticola s. str. (from Central Cantabrian Mountains)
 and I. galani (from Southern Montes de León) (“extrazonal analysis”) from
 neighboring areas.
description: genepop_input_HNF_sinC113Microsatellite data input for Genepopfinal_cytb_DLMitochondrial input data (cytb and Control Region) for Metapiga
DOI: 10.5061/dryad.7m0797t0
title: Data from: Evidence for structure and variable recombination rates among Dutch populations of the opportunistic human pathogen Aspergillus fumigatus

description: As the frequency of antifungal drug resistance continues to increase,
 understanding the genetic structure of fungal populations, where resistant
 isolates have emerged and spread, is of major importance. Aspergillus
 fumigatus is an ubiquitously distributed fungus and the primary causative
 agent of invasive aspergillosis (IA), a potentially lethal infection in
 immunocompromised individuals. In the last few years, an increasing number
 of A. fumigatus isolates has evolved resistance to triazoles, the primary
 drugs for treating IA infections. In most isolates, this
 multiple-triazole-resistance (MTR) phenotype is caused by mutations in the
 cyp51A gene, which encodes the protein targeted by the triazoles. We
 investigated the genetic differentiation and reproductive mode of A.
 fumigatus in the Netherlands, the country where the MTR phenotype probably
 originated, to determine their role in facilitating the emergence and
 distribution of resistance genotypes. Using 20 genome-wide neutral
 markers, we genotyped 255 Dutch isolates including 25 isolates with the
 MTR phenotype. In contrast to previous reports, our results show that
 Dutch A. fumigatus genotypes are genetically differentiated into five
 distinct populations. Four of the five populations show significant
 linkage disequilibrium, indicative of an asexual reproductive mode,
 whereas the fifth population is in linkage equilibrium, indicative of a
 sexual reproductive mode. Notably, the observed genetic differentiation
 among Dutch isolates does not correlate with geography, although all
 isolates with the MTR phenotype nest within a single, predominantly
 asexual, population. These results suggest that both reproductive mode and
 genetic differentiation contribute to the structure of Dutch A. fumigatus
 populations and are probably shaping the evolutionary dynamics of drug
 resistance in this potentially deadly pathogen.
description: A. fumigatus population
 geneticsKlaassen et al. Dryad
 entry.txt
DOI: 10.5061/dryad.hp08t
title: Data from: Parasite and host elemental content and parasite effects on host nutrient excretion and metabolic rate

description: Ecological stoichiometry uses the mass balance of elements to predict
 energy and elemental fluxes across different levels of ecological
 organization. A specific prediction of ecological stoichiometry is the
 growth rate hypothesis (GRH), which states that organisms with faster
 growth or reproductive rates will require higher phosphorus content for
 nucleic acid and protein synthesis. Although parasites are found
 ubiquitously throughout ecosystems, little is understood about how they
 affect nutrient imbalances in ecosystems. We (1) tested the GRH by
 determining the carbon (C), nitrogen (N), and phosphorus (P) content of
 parasitic trematodes and their intermediate host, the freshwater snail
 Elimia livescens, and (2) used this framework to determine the trematode
 effects on host nutrient excretion and metabolism. Snail and parasite
 tissues were analyzed for elemental content using a CHN analyzer and
 soluble reactive phosphorus (SRP) methods. Ammonium and SRP assays were
 used to estimate N and P excretion rates. A respirometer was used to
 calculate individual snail metabolism. Trematode tissues contained lower
 C:P and N:P (more P per unit C and N) than the snail tissues. Snail
 gonadal tissues more closely resembled the elemental content of parasite
 tissues, although P content was 13% higher in the gonad than the trematode
 tissues. Despite differences in elemental content, N and P excretion rates
 of snails were not affected by the presence of parasites. Parasitized
 snails maintained faster metabolic rates than nonparasitized snails.
 However, the species of parasite did not affect metabolic rate. Together,
 this elemental imbalance between parasite and host, and the altered
 metabolic rate of infected snails may lead to broader parasite effects in
 stream ecosystems.
description: Chodkowski_EE_elemental
DOI: 10.5061/dryad.07s9f96
title: Data from: Thorson’s rule, life history evolution and diversification of benthic octopuses (Cephalopoda: Octopodoidea)

description: Here we evaluate the so-called Thorson’s rule, which posits that
 direct-development and larger eggs are favored towards the poles in marine
 organisms and whose validity been the subject of considerable debate in
 the literature, combining an expanded phenotypic dataset encompassing 60
 species of benthic octopuses with a new molecular phylogeny. Phylogenetic
 reconstruction shows two clades: clade 1 including species of the families
 Eledonidae, Megaleledonidae, Bathypolypodidae and Enteroctopodidae, and
 clade 2 including species of Octopodidae. Egg size, development mode and
 all environmental variables exhibited phylogenetic signal, partly due to
 differences between the two clades: whereas most species in clade 1
 inhabit cold and deep waters, exhibit large eggs and hatchling with
 holobenthic development, species from clade 2 inhabit tropical-temperate
 and shallow waters, evolved small eggs and generally exhibit merobenthic
 development. Phylogenetic regressions show that egg size exhibits a
 conspicuous latitudinal cline, and that both egg size and development mode
 vary with water temperature. Additionally, analyses suggest that egg size
 is constrained by body size in lineages with holobenthic development.
 Taken together, results suggest that the variation in egg size and
 development mode across benthic octopuses is adaptive and associated with
 water temperature, supporting Thorson’s rule in these organisms.
description: Octopodoidea
 phylogenyThe Octopodoidea
 phylogeny was inferred using three mitochondrial genes – 16S rRNA (16S),
 Cytochrome Oxidase I (COI) and Cytochrome Oxidase III (COIII) – and one
 nuclear gene – Rhodopsin (RHO) – for a total of 61 species. The
 phylogenetic trees based on a Bayesian framework using Mr. Bayes v3.2
 (Ronquist et al. 2012) were performed by means of MCMCMC (Metropolis
 Coupling Monte Carlo Markov Chains), four chains were run using
 10,000,000. The trees were rooted using Vampyroteuthis infernalis as an
 outgroup. The phylogeny from the partitioned data set is consistent with
 the current octopus taxonomy. The consensus of 9,000 phylogenetic trees
 from MrBayes showed high posterior probability values (&gt; 0.95) for most
 of the nodes. The first group (‘clade 1’) includes primarily cold water
 and deep-sea species from the families Bathypolypodidae, Eledonidae,
 Enteroctopodidae, Megaleledonidae. The second group (‘clade 2’)
 encompasses tropical-temperate and shallow water species from the family
 Octopodidae.octopodoideaPart.nex.con.tre