cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4fd0k
title: Data from: Multilocus phylogeny and a new classification for Southeast Asian and Melanesian forest frogs (family Ceratobatrachidae)

description: We present a near comprehensive, densely sampled, multilocus phylogenetic
 estimate of species relationships within the anuran family
 Ceratobatrachidae, a morphologically and ecologically diverse group of
 frogs from the island archipelagos of Southeast Asia and the South-West
 Pacific. Ceratobatrachid frogs consist of three clades: a small clade of
 enigmatic, primarily high-elevation, semi-aquatic Sundaland species
 currently assigned to Ingerana (for which we erect a new genus), which is
 the sister taxon of two large, monophyletic radiations, each situated on
 islands on either side of Wallace's Line. One radiation is composed
 of Philippine species of Platymantis and the other contains all taxa from
 the eastern Indonesian, New Guinean, Solomon, Bismarck, and Fijian
 archipelagos. Several additional genera (Batrachylodes, Discodeles,
 Ceratobatrachus, and Palmatorappia) are nested within Platymantis, and of
 these Batrachylodes and Discodeles are nonmonophyletic. To address the
 widespread paraphyly of the genus Platymantis and several additional
 nomenclatural issues, we undertook a wholesale nomenclatural
 reorganization of the family. Given our partially unresolved phylogeny,
 and in order to impart a conservative, stable taxonomy, involving a
 minimal number of genus-species couplet changes, we propose a conservative
 classification representing a few compromises. These changes are designed
 to preserve maximally the presumed original intent of taxonomy (widely
 used group names associated with morphological and ecological diversity of
 particular species or groups of species) while implementing a hierarchical
 system that is consistent with the estimate of phylogeny based on new
 molecular data.
description: Concatenated Alignment
 FileThis is the concatenated
 alignment file, formatted as nexus. Locus positions within alignment are
 provided within a character block at the bottom of the alignment
 file.Brown.etal.2014_ConcatenatedAlignment.nexBayesian_MCCTThe maximum clade credibility topology resulting from partitioned Bayesian analyses in the program MrBayes.ML_BootstrapTopologyThe maximum likelihood bootstrap topology resulting from partitioned ML analyses.
DOI: 10.5061/dryad.61cf7
title: Data from: Sex-specific heterogeneity in fixed morphological traits influences individual fitness in a monogamous bird population

description: Theoretical work has emphasized the important role of individual traits on
 population dynamics, but empirical models are often based on average or
 stage-dependent demographic rates. In this study on a monogamous bird, the
 Eurasian hoopoe (Upupa epops), we show how the interactions between male
 and female fixed and dynamic heterogeneity influence demographic rates and
 population dynamics. We built an integral projection model including
 individual sex, age, condition (reflecting dynamic heterogeneity) and
 fixed morphology (reflecting fixed heterogeneity). Fixed morphology was
 derived from a principal component analysis of six morphological traits.
 Our results revealed that reproductive success and survival were linked to
 fixed heterogeneity whereas dynamic heterogeneity influenced mainly the
 timing of reproduction. Fixed heterogeneity had major consequences for the
 population growth rate, but interestingly, its effect on population
 dynamics differed between the sexes. Female fixed morphology was directly
 linked to annual reproductive success whereas male fixed morphology
 influenced also annual survival, being twice higher in large than in small
 males. Even in a monogamous bird with shared parental care, large males
 can reach 10\% higher fitness than females. Including the dynamics of male
 and female individual traits in population models refines our
 understanding of the individual mechanisms that influence demographic
 rates and population dynamics and can help identifying differences in
 sex-specific strategies.
description: Adult
 SurvivalData used to estimate
 adult survivalSurvival_adult.txtTransitionInheritanceReproductionBreeding ProbabilitiesBreeding_Proba.txtFirst-year SurvivalSurvival_firstyear.txt
DOI: 10.5061/dryad.d4977
title: Data from: Bayesian inference reveals positive but subtle effects of experimental fishery closures on marine predator demographics

description: Global forage-fish landings are increasing, with potentially grave
 consequences for marine ecosystems. Predators of forage fish may be
 influenced by this harvest, but the nature of these effects is
 contentious. Experimental fishery manipulations offer the best solution to
 quantify population-level impacts, but are rare. We used Bayesian
 inference to examine changes in chick survival, body condition and
 population growth rate of endangered African penguins Spheniscus demersus
 in response to eight years of alternating time-area closures around two
 pairs of colonies. Our results demonstrate that fishing closures improved
 chick survival and condition, after controlling for changing prey
 availability. However, this effect was inconsistent across sites and
 years, highlighting the difficultly of assessing management interventions
 in marine ecosystems. Nevertheless, modelled increases in population
 growth rates exceeded 1% at one colony; i.e. the threshold considered
 biologically meaningful by fisheries management in South Africa. Fishing
 closures evidently can improve the population trend of a forage-fish
 dependent predator – we therefore recommend they continue in South Africa
 and support their application elsewhere. However, detecting demographic
 gains for mobile marine predators from small no-take zones requires
 experimental time-frames and scales that will often exceed those desired
 by decision-makers.
description: Chick_SurvivalData used to estimate rates of chick survival to fledgingCondition_WCData used to estimate chick body condition for the Western Cape islands.Condition_ECData used to estimate chick condition for the Eastern Cape islands.
DOI: 10.5061/dryad.q3d2m
title: Data from: Genetic diversity and spatial genetic structure of the grassland perennial Saxifraga granulata along two river systems

description: Due to changes in land use, the natural habitats of an increasing number
 of plant species have become more and more fragmented. In landscapes that
 consist of patches of suitable habitat, the frequency and extent of
 long-distance seed dispersal can be expected to be an important factor
 determining local genetic diversity and regional population structure of
 the remaining populations. In plant species that are restricted to
 riparian habitats, rivers can be expected to have a strong impact on the
 dynamics and spatial genetic structure of populations as they may enable
 long-distance seed dispersal and thus maintain gene flow between
 fragmented populations. In this study, we used polymorphic microsatellite
 markers to investigate the genetic diversity and the spatial genetic
 structure of 28 populations of Saxifraga granulata along two rivers in
 central Belgium. We hypothesized that rivers might be essential for gene
 flow among increasingly isolated populations of this species. Genetic
 diversity was high (HS = 0.68), which to a certain extent can be explained
 by the octoploid nature of S. granulata in the study area. Populations
 along the Dijle and Demer rivers were also highly differentiated (G”ST =
 0.269 and 0.164 and DEST = 0.190 and 0.124, respectively) and showed
 significant isolation-by-distance, indicating moderate levels of gene flow
 primarily between populations that are geographically close to each other.
 Along the river Demer population genetic diversity was higher upstream
 than downstream, suggesting that seed dispersal via the water was not the
 primary mode of dispersal. Overall, these results indicate that despite
 increasing fragmentation populations along both rivers were highly
 genetically diverse. The high ploidy level and longevity of S. granulata
 have most likely buffered negative effects of fragmentation on genetic
 diversity and the spatial genetic structure of populations in riparian
 grasslands.
description: GeneMapper data of 560
 individuals of Saxifraga granulata collected along two rivers in
 BelgiumRaw GeneMapper data with
 four extra columns with information about the samples (i.e. Sort, River,
 Population, Individual). Without the first four columns data can be easily
 read via the r function read.GeneMapper() from the r-package
 'polysat'.Saxifraga_Rivers_GeneMapper.xlsx
DOI: 10.5061/dryad.4q6h2
title: Data from: How bird clades diversify in response to climatic and geographic factors

description: While the environmental correlates of global patterns in standing species
 richness are well understood, it is poorly known which environmental
 factors promote diversification (speciation minus extinction) in clades.
 We tested several hypotheses for how geographic and climatic variables
 should affect diversification using a large dataset of bird sister genera
 endemic to the New World. We found support for the area, evolutionary
 speed, environmental predictability and climatic stability hypotheses, but
 productivity and topographic complexity were rejected as explanations.
 Genera that had accumulated more species tend to occupy wider niche space,
 manifested both as occurrence over wider areas and in more habitats.
 Genera with geographic ranges that have remained more stable in response
 to glacial-interglacial changes in climate were also more species rich.
 Since many relevant explanatory variables vary latitudinally, it is
 crucial to control for latitude when testing alternative mechanistic
 explanations for geographic variation in diversification among clades.
description: Sister group means and
 contrastsData on means and
 contrasts between sister groupssister group means and
 contrasts.xlsxData on bird species in
 the sister groupsData on species in the
 sister groups used in the studybird
 database2017.xls
DOI: 10.5061/dryad.sj4q1
title: Data from: Species richness-productivity relationships of tropical terrestrial ferns at regional and local scales

description: 1. The species richness-productivity relationship (SRPR), by which the
 species richness of habitats or ecosystems is related to the productivity
 of the ecosystem or the taxon, has been documented both on regional and
 local scales, but its generality, biological meaning, and underlying
 mechanisms remain debated. 2. We evaluated the SRPR and 3 mechanistic
 hypotheses using terrestrial ferns in 18 study plots along an elevational
 gradient (500-4000 m) in Ecuador. We measured annual increases in
 above-ground biomass of 6175 fern individuals from 91 species over 2
 years, and estimated plot-level tree productivity from increases in
 above-ground woody biomass of 560 trees. Analyses were conducted by (a)
 comparing plots along the elevational gradient (regional scale) and (b)
 comparing plots within each elevational belt (local scale). 3. Fern
 diversity was related to the productivity of the fern assemblages, but not
 to above-ground productivity of the trees. At the regional scale, we found
 a positive relationship of fern species richness to fern productivity that
 appeared to be determined by an increase in the number of fern individuals
 and niche availability. In contrast, at the local scale this relationship
 was negative and likely driven by interspecific competition. 4. Synthesis:
 Plot diversity of ferns appears to be limited by the number of available
 niches and competition to occupy these niches. At the local scale, this is
 reflected in a negative SRPR probably driven by competition, whereas with
 increasing scale the positive influence of productivity emerges. This
 represents the first evidence that productivity and competition affect the
 diversity of tropical herb assemblages at the plot scale.
description: Kessler Data
 TableRaw data, details
 provided in the ReadMe file
DOI: 10.5061/dryad.bt651
title: Data from: Deep time diversity of metatherian mammals: implications for evolutionary history and fossil-record quality

description: Despite a global fossil record, Metatheria are now largely restricted to
 Australasia and South America. Most metatherian palaeodiversity studies to
 date are limited to particular subclades, time intervals and/or regions,
 and few consider uneven sampling. Here, we present a comprehensive new
 dataset on metatherian fossil occurrences (Barremian to end-Pliocene).
 These data are analysed using standard rarefaction and Share-holder Quorum
 Subsampling (including a new protocol for handling ‘Lagerstätten’-like
 localities). Global metatherian diversity was lowest during the
 Cretaceous, and increased sharply in the Paleocene, where the South
 American record begins. Global and South American diversity rose in the
 early Eocene then fell in the late Eocene, contrasting the North American
 pattern. In the Oligocene diversity declined in the Americas but this was
 more than offset by Oligocene radiations in Australia. Diversity continued
 to decrease in Laurasia with final representatives in North America
 (excluding the later entry of Didelphis virginiana) and Europe in the
 early Miocene, and Asia in the middle Miocene. Global metatherian
 diversity appears to have peaked in the early Miocene, especially in
 Australia. Following a trough in the late Miocene, the Pliocene saw
 another increase in global diversity. By this time, metatherian
 biogeographic distribution had essentially contracted to that of today.
 Comparison of the raw and sampling-corrected diversity estimates, coupled
 with evaluation of ‘coverage’ and number of prolific sites, demonstrates
 that the metatherian fossil record is spatially and temporally extremely
 patchy. Therefore, assessments of macroevolutionary patterns based on the
 raw fossil record (as in most previous studies) are inadvisable.
description: Supplementary_Data_July_29_2017_T1 Metatherian fossil dataset T2 Bibliographical references for datasets T3 Correlations between time bin length, number of genera and number of sites T4 Preservation, Origination and Extinction Rates T5 Coverage and sampling target T6 Prolific sites list T7 South American diversity curve calculated by SQS method with target set to 0 0.3Supplementary_Text_1R code for Metatheria Diversity Curves using Classic RarefactionSupplementary_Text_2R code for Metatheria Diversity Curves using SQS
DOI: 10.5061/dryad.86137tk6
title: Data from: Taxon Influence Index: assessing taxon-induced incongruities in phylogenetic inference

description: Understanding the evolutionary history of species is at the core of
 molecular evolution and is done using several inference methods. The
 critical issue is to quantify the uncertainty of the inference. The
 posterior probabilities in Bayesian phylogenetic inference and the
 bootstrap values in frequentist approaches measure the variability of the
 estimates due to the sampling of sites from genes and the sampling of
 genes from genomes. However, they do not measure the uncertainty due to
 taxon sampling. Taxa that experienced molecular homoplasy, recent
 selection, a spur of evolution and so forth may disrupt the inference and
 cause incongruences in the estimated phylogeny. We define a Taxon
 Influence Index to assess the influence of each taxon on the phylogeny. We
 found that although most taxa have a weak influence on the phylogeny, a
 small fraction of influential taxa strongly alter it, even in clades only
 loosely related to them. We conclude that highly influential taxa should
 be given special attention and sampling them more thoroughly can lead to
 more dependable phylogenies.
description: Mariadassou_et_al_02Dec2011_DataFile_1Mariadassou_et_al_02Dec2011_DataFile_2
DOI: 10.5061/dryad.6cg6j
title: Data from: Is fasting safe? A chart review of adverse events during medically supervised, water-only fasting

description: Background: Evidence suggests that fasting, during which only water is
 consumed, results in potentially health promoting physiological effects.
 However, peer-reviewed research assessing the safety of water-only fasting
 is lacking. To address this, we conducted a chart review to describe
 adverse events (AEs) that occurred during medically supervised, water-only
 fasting. Methods: Electronic charts from patient visits to a residential
 medical facility from 2006 to 2011 were reviewed. Patients who were at
 least 21 years of age and water-only fasted for ≥2 consecutive days with a
 refeeding period equal to half of the fast length were included. Out of
 2539 charts, 768 visits met our inclusion and exclusion criteria. AEs were
 abstracted from chart notes and classified according to CTCAE (v4.03) and
 MedDRA (v12.1) terminology. Descriptive analysis of AEs is reported.
 Results: During the protocol period, the highest grade AE (HGAE) in 555
 visits was a grade 2 event or lower, in 212 visits it was a grade 3 event,
 in 1 visit it was a grade 4 event, and there were no grade 5 events. There
 were 2 (0.002%) visits with a serious adverse event (SAE). The majority of
 AEs identified were mild (n = 4490, 75%) in nature and known reactions to
 fasting. Conclusions: To our knowledge, this is the most comprehensive
 analysis of AEs experienced during medically supervised, water-only
 fasting conducted to date. Overall, our data indicate that the majority of
 AEs experienced were mild to moderate and known reactions to fasting. This
 suggests that the protocol used in this study can be safely implemented in
 a medical setting with minimal risk of a SAE.
description: fast_ae_protocol_r1.0fast_complaint_protocol_r1.0fast_daily_protocol_r1.0fast_disp_r1.0fast_visit_protocol_r1.0
DOI: 10.5061/dryad.nd76c
title: Data from: Phylogenetic relationships and the evolution of BMP4 in triggerfishes and filefishes (Balistoidea)

description: The triggerfishes (family Balistidae) and filefishes (family
 Monacanthidae) comprise a charismatic superfamily (Balistoidea) within the
 diverse order Tetraodontiformes. This group of largely marine fishes
 occupies an impressive ecological range across the world’s oceans, and is
 well known for its locomotor and feeding diversity, unusual body shapes,
 small genome size, and ecological and economic importance. In order to
 investigate the evolutionary history of these important fish families, we
 used multiple phylogenetic methods to analyze molecular data from 86
 species spanning the extant biodiversity of Balistidae and Monacanthidae.
 In addition to three gene regions that have been used extensively in
 phylogenetic analyses, we include sequence data for two mitochondrial
 regions, two nuclear markers, and the growth factor gene bmp4, which is
 involved with cranial development. Phylogenetic analyses strongly support
 the monophyly of the superfamily Balistoidea, the sister-family
 relationship of Balistidae and Monacanthidae, as well as three triggerfish
 and four filefish clades that are well resolved. A new classification for
 the Balistidae is proposed based on phylogenetic groups. Bayesian
 topology, as well as the timing of major cladogenesis events, is largely
 congruent with previous hypotheses of balistid phylogeny. However, we
 present a novel topology for major clades in the filefish family that
 illustrate the genera Aluterus and Stephanolepis are more closely related
 than previously posited. Molecular rates suggest a Miocene and Oligocene
 origin for the families Balistidae and Monacanthidae, respectively, and
 significant divergence of species in both families within the past 5
 million years. A second key finding of this study is that, relative to the
 other protein-coding gene regions in our DNA supermatrix, bmp4 shows a
 rapid accumulation of both synonymous and non-synonymous substitutions,
 especially within the family Monacanthidae. Overall substitution patterns
 in bmp4 support the hypothesis of stabilizing selection during the
 evolutionary history of regulatory genes, with a small number of isolated
 examples of accelerated non-synonymous changes detected in our phylogeny.
description: Balistoid Bayesian
 consensus treeBalistoid Bayesian
 consensus tree based upon the supermatrix also included in this data
 packageBalistoid_consensus_tree.treBalistoid aligned supermatrix for 9 gene regions from the mitochondrial and nuclear genome12S = 1-796 16S = 797-1340 4c4 = 1341-1851 rag2 = 1852-2653 bmp4 = 2654-3135 rhod = 3136-3445 cytB = 3446-4517 rag1 = 4518-5894 COI = 5895-6529Balistoid_supermatrix.nexBalistoid BEAST-derived divergence time treeBalistoid_divtimetree.tre
DOI: 10.5061/dryad.4b2g5
title: Data from: Expanding the understanding of local community assembly in adaptive radiations

description: Communities are thought to be assembled by two types of filters: by the
 environment relating to the fundamental niche and by biotic interactions
 relating to the realized niche. Both filters include parameters related to
 functional traits, and their variation along environmental gradients. Here
 we infer the general importance of environmental filtering of a functional
 trait determining local community assembly within insular adaptive
 radiations on the example of Caribbean Anolis lizards. We constructed maps
 for the probability of presence of Anolis ecomorphs
 (ecology-morphology-behavior specialists) on the Greater Antilles and
 overlaid these to estimate ecomorph community completeness (ECC) over the
 landscape. We then tested for differences in environmental parameter
 spaces among islands for real and cross-fitted ECC values to see whether
 the underlying assembly filters are deterministic (i.e., similar among
 islands). We then compared information-theoretic models of climatic and
 landscape parameters among Greater Antillean islands and inferred whether
 body mass as functional trait determines ECC. We found areas with high ECC
 to be strongly correlated to environmental filters, partly related to
 elevation. The environmental parameters influencing high ECC differed
 among islands. With the exception of the Jamaican twig ecomorph (which we
 suspect to be misclassified), smaller ecomorphs were more restricted to
 higher elevations than larger ones which might reflect filtering on the
 basis of differential physiological restrictions of ecomorphs. Our results
 in Anolis show that local community assembly within adaptive island
 radiations of animals can be determined by environmental filtering of
 functional traits, independently from species composition and realized
 environmental niche space.
description: Anolis coordinate data
 and Environmental Niche modelsCoordinate data for all
 Greater Antillean Anolis ecomorphs, and their Environmental Niche models
 computed with MAXENT. Each ENM was computed on the background of the
 Greater Antilles, so that the ENMs contain both sutability scores for the
 ecomorph's own island, as also values fitted on each other
 island.Anolis coordinates and
 ENMs.zip