cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2j05h
title: Data from: Subtle individual variation in indeterminate growth leads to major variation in survival and lifetime reproductive output in a long-lived reptile

description: 1. The consequences of individual variation in life-history traits have
 been well studied due to their importance in evolutionary ecology.
 However, a trait that has received little empirical attention is the rate
 of indeterminate growth. In long-lived ectotherms, subtle variation in
 growth after maturity could have major effects over the animals’
 lifetimes. 2. These effects are difficult to measure due to the challenges
 involved in reliably estimating individual variation in the face of
 environmental stochasticity, and the need to account for trade-offs among
 growth, reproduction and survival. However, modelling advances have made
 such analysis possible if long-term high-quality data sets are available.
 3. We used an integrated state-space modelling framework to reveal
 relationships between indeterminate growth, reproduction and survival in a
 population of North American snapping turtles (Chelydra serpentina) using
 a 41-year data set for 298 adult females. 4. A hierarchical version of the
 von Bertalanffy model fitted to data on carapace lengths showed
 substantial individual variation in growth trajectories, and hierarchical
 models fitted to clutch-mass data and recapture histories showed that
 reproductive output and survival probability increased with size.
 Integration of these models revealed no detectable trade-offs – i.e.,
 individual growth parameters were not correlated with size-specific
 survival or reproduction rates, and individual variation in reproductive
 output did not affect the size-specific survival rate. Consequently,
 individual variation in growth parameters was estimated to result in
 &gt; 2-fold variation in post-maturity life expectancy and &gt;
 4-fold variation in expected lifetime reproductive output. 5. These
 results illustrate that indeterminate growth can have major fitness
 consequences in long-lived species. We suggest that the individual
 variation in growth rates reflects variation in environments experienced
 during development or later life. An understanding of this variation may
 be essential for predicting the population dynamics of long-lived species
 under threat and identifying the most important environments to protect.
description: Data on growth,
 reproduction, and survival of adult female snapping turtles in Algonquin
 Park, CanadaThe file has a set of
 matrices showing encounter histories, carapace lengths, and clutch masses
 for 298 adult females over 41 years (1972-2012). These correspond exactly
 to the data used in the article, which are also provided in OpenBUGS
 format as Supporting Information.Snapper data for analysis
 1972-2012 for Dryad.xlsx
DOI: 10.5061/dryad.m21q0th
title: Data from: The most effective pollinator principle applies to new invasive pollinators

description: G.L. Stebbins’ most effective pollinator principle states that when
 pollinators are not limiting, plants are expected to specialize and adapt
 to the more abundant and effective pollinator species available. In this
 study, we quantify the effectiveness of bees, hummingbirds and hawkmoths
 in a Chilean population of Erythranthe lutea (Phrymaceae), and examine
 whether flower traits are subject to pollinator-mediated selection by the
 most effective pollinator species during two consecutive years. Unlike
 most species in the pollinator community, the visitation rate of the
 recently arrived Bombus terrestris did not change substantially between
 years, which together its high and stable pollen delivery to flower
 stigmas made this species the most important in the pollinator assemblage
 followed by the solitary bee Centris nigerrima. Flower traits were under
 significant selection in the direction expected for short-tongue bees,
 suggesting that E. lutea is in the initial steps of adaptation to the
 highly effective exotic bumblebee. Our results confirm the applicability
 of Stebbins' principle for new invasive pollinators, and stress their
 importance in driving flower adaptation of native plant species, a
 critical issue in the face of biotic exchange and homogenization.
description: Pollen
 DepositionThis file contains data
 on pollen deposition effectiveness per single visit (Dv), and a summary of
 Dv-values per species and year.Visitation
 RatesThis file contains data
 on the number of visits per pollinator species per observation period, and
 visitation rate estimates on a yearly basis. Empty cells indicate lack of
 observation for a given species (not zero value).selection16Data contains raw plant traits (tube length and corolla size) and seed production as a measure of individual female fitness during 2016. Every value is the average from three randomly chosen flowers and capsules from the same plant.selection17Data contains raw plant traits (tube length and corolla size) and seed production as a measure of individual female fitness during 2017. Every value is the average from three randomly chosen flowers and capsules from the same plant.Tongue lengthContains data on tongue length for Bombus terrestris and Centris nigerrima.Pollen LimitationContains data on seed production in control (not manipulated) flowers and experimental (pollen supplemented) flowers in 2016 and 2017.
DOI: 10.5061/dryad.3cp3t
title: Data from: Correlation between genetic diversity and environmental suitability: taking uncertainty from ecological niche models into account

description: The hindcast of shifts in the geographical ranges of species as estimated
 by ecological niche modelling (ENM) has been coupled with
 phylogeographical patterns, allowing the inference of past processes that
 drove population differentiation and genetic variability. However, more
 recently, some studies have suggested that maps of environmental
 suitability estimated by ENM may be correlated to species' abundance,
 raising the possibility of using environmental suitability to infer
 processes related to population demographic dynamics and genetic
 variability. In both cases, one of the main problems is that there is a
 wide variation in ENM development methods and climatic models. In this
 study, we analyse the relationship between heterozygosity (He) and
 environmental suitability from multiple ENMs for 25 population estimates
 for Dipteryx alata, a widely distributed, endemic tree species of the
 Cerrado region of central Brazil. We propose a new approach for generating
 a statistical distribution of correlations under randomly generated ENM.
 The confidence intervals from these distributions indicate how model
 selection with different properties affects the ability to detect a
 correlation of interest (e.g. the correlation between He and suitability).
 Additionally, our approach allows us to explore which particular ensemble
 of ENMs produces the better result for finding an association between
 environmental suitability and He. Caution is necessary when choosing a
 method or a climatic data set for modelling geographical distributions,
 but the new approach proposed here provides a conservative way to evaluate
 the ability of ensembles to detect patterns of interest.
description: Diniz-Filho_etal_MER_2015The following data and achieves are available from DRYAD for Diniz-Filho et al. - Mol. Ecol. Res. 1) Sampling localities, codes, latitudes and longitudes, Heterozygosity for 25 populations of D. alata in Brazilian Cerrado (Baru25pops.xlsx); 2) Genotypes for 8 microsatellite loci for 642 individuals of D. alata from 25 populations (baru_FSTAT_8loci.dat); 3) R-script for the analyses shown in this paper, including generating heterozygosity by resampling and the random selection of ENMs for ensemble correlations (ENM_selection.R); 4) Vector of heterozygosity used in the analyses (he.txt); 5) Environmental suitabilities of ENMs in the 25 populations of D. alata (ENM.txt); 6) Occurrence records for D. alata in Brazilian Cerrado (D_alata_occurrence_records.txt); 7) Occurrence records in a Neotropical grid with resolution of 0.5o (D_alata_neotropic_grid.txt), used in BIOENSEMBLES; 8) One of the environmental data (CCSM climatic model for current time) in the Neotropical grid used in the modeling process with BIOENSEMBLES (be_biovar_CCSM_0k_neotropic.txt - other similar data sets are available at www.ecoclimate.org).
DOI: 10.5061/dryad.j4802
title: Data from: Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation

description: Several evolutionary theories predict that rates of morphological change
 should be positively associated with the rate at which new species arise.
 For example, the theory of punctuated equilibrium proposes that phenotypic
 change typically occurs in rapid bursts associated with speciation events.
 However, recent phylogenetic studies have found little evidence linking
 these processes in nature. Here we demonstrate that rates of species
 diversification are highly correlated with the rate of body size evolution
 across the 30,000+ living species of ray-finned fish that comprise the
 majority of vertebrate biological diversity. This coupling is a general
 feature of fish evolution and transcends vast differences in ecology and
 body-plan organization. Our results may reflect a widespread speciational
 mode of character change in living fishes. Alternatively, these findings
 are consistent with the hypothesis that phenotypic ‘evolvability’ – the
 capacity of organisms to evolve – shapes the dynamics of speciation
 through time at the largest phylogenetic scales.
description: rate-smoothed
 mega-phylogeny of actinopterygiiansPhylogeny based upon
 RAXML analysis of 13 gene concatenated data set assembled using phlawd
 pipeline and rate-smoothed using treePL. See methods and supplemental
 methods for details of tree construction.Rabosky_et_al_timetree.tre
DOI: 10.5061/dryad.n4120
title: Data from: Habitat heterogeneity induces rapid changes in the feeding behaviour of generalist arthropod predators

description: 1. The “habitat heterogeneity hypothesis” predicts positive effects of
 structural complexity on species coexistence. Increasing habitat
 heterogeneity can change the diversity (number of species, abundances) and
 the functional roles of communities. The latter, however, is not well
 understood as species and individuals may respond very differently and
 dynamically to a changing environment. 2. Here, we experimentally test how
 habitat heterogeneity affects generalist arthropod predators, including
 epigaeic spiders, carabid and staphylinid beetles, under natural
 conditions by assessing their diversity and directly measuring their
 trophic interactions (which provide a proxy for their functional roles).
 The experiment was conducted in spring barley fields in Southern Sweden
 where habitat heterogeneity was manipulated by increasing within-field
 plant diversity. 3. Increased habitat heterogeneity triggered rapid
 changes in the feeding behaviour of generalist predators characterized by
 lower trophic specialization at both network (H2’, degree of interaction
 specialization in the entire network) and species level (d’, degree of
 interaction specialization at the species level). We presume that this is
 because spatial separation resulted in relaxed competition and allowed an
 increased overlap in resources used among predator species. Predators
 collected from heterogenous habitats also showed greater individual-level
 dietary variability which might be ascribed to relaxed intraspecific
 competition. 4. Our results provide conclusive evidence that habitat
 heterogeneity can induce rapid behavioural responses independent of
 changes in diversity, potentially promoting the stability of ecosystem
 functions.
description: foodweb
 dataDryad_staudacher.xlsx
DOI: 10.5061/dryad.m810q41
title: Data from: Light stabilizers added to the shell of coextruded wood-high density polyethylene composites to improve mechanical and anti-UV aging properties

description: Weathering of wood-plastic composite (WPC) leads to discoloration and
 cracks, which greatly limits its outdoor application. In this study, light
 stabilizers (including UV-327, HS-944, and Nano-SiO2) were added to the
 shell of coextruded high-density polyethylene (HDPE) based WPC to improve
 its anti-ultraviolet (UV) aging property and simultaneously to maintain
 its good mechanical property. The obtained results showed that the UV-327
 was the most effective light stabilizer on improving the mechanical and
 anti-UV aging properties of the composites among the three stabilizers
 used. WPC samples added with 2% UV-327 had the highest retention rates in
 flexural strength and also had the smoothest surface after 2500h of UV
 aging. The samples added with 2% UV-327 had the best protection for the
 discoloration, showing the lowest values of ΔE (color difference) and ΔL
 (luminescence) in all samples after 2500h of UV aging. WPC added with 2%
 UV-327 was oxidized to the slightest extent after 2500h of UV aging. The
 results reported herein serve to enhance the understanding of the
 efficiency of light stabilizers in preventing WPCs from UV degradation,
 with a view toward developing co-extruded WPCs with low cost, high anti-UV
 aging property and good mechanical property for outdoor applications.
description: RSOS-data
 availability
DOI: 10.5061/dryad.k4q1q
title: Data from: DNA barcoding survey of anurans across the Eastern Cordillera of Colombia and the impact of the Andes on cryptic diversity

description: Colombia hosts the second highest amphibian species diversity on Earth,
 yet its fauna remains poorly studied, especially using molecular genetic
 techniques. We present the results of the first wide-scale DNA barcoding
 survey of anurans of Colombia, focusing on a transect across the Eastern
 Cordillera. We surveyed 10 sites between the Magdalena Valley to the west
 and the eastern foothills of the Eastern Cordillera, sequencing portions
 of the mitochondrial 16S ribosomal RNA and cytochrome oxidase subunit 1
 (CO1) genes for 235 individuals from 52 nominal species. We applied two
 barcode algorithms, Automatic Barcode Gap Discovery and Refined Single
 Linkage Analysis, to estimate the number of clusters or “unconfirmed
 candidate species” supported by DNA barcode data. Our survey included ~7%
 of the anuran species known from Colombia. While barcoding algorithms
 differed slightly in the number of clusters identified, between three and
 ten nominal species may be obscuring candidate species (in some cases,
 more than one cryptic species per nominal species). Our data suggest that
 the high elevations of the Eastern Cordillera and the low elevations of
 the Chicamocha canyon acted as geographic barriers in at least seven
 nominal species, promoting strong genetic divergences between populations
 associated with the Eastern Cordillera.
description: Aligned DNA sequences
 for CO1 and 16S genes from Colombian frogsNexus file of aligned
 DNA sequence data representing two mitochondrial gene fragments, 16S
 (bases 1-604) and CO1 (bases 605-1262) obtained for 235 frog specimens
 collected along the Eastern Cordillera of the Colombian Andes, South
 America. Alignments were accomplished using default settings in the
 software package, MUSCLE (Edgar, 2004).Combined_16S_CO1_alignment.nex
DOI: 10.5061/dryad.d12635v
title: Data from: The consequences of daily cyclic hypoxia on a European grass shrimp: from short-term responses to long-term effects

description: 1. Salt marshes are a key coastal environment for their important role as
 nursery habitats for marine and estuarine fish and crustaceans. Salt
 marshes are variable environments where species can experience daily
 cyclic hypoxic stress, characterized by profound variations in oxygen
 partial pressure (pO2) from supersaturated conditions (~42kPa) to
 extremely hypoxic conditions (~3kPa) in ~12-hours. 2. Here, under
 laboratory conditions, we assessed the physiological consequences of
 exposing the shrimp Palaemon varians, a species commonly found in the salt
 marshes of northern Europe, to the daily cyclic hypoxic regime currently
 experienced in its habitat in August (7.1±1.8 hours day-1 below 4.0kPa).
 In the laboratory adults were kept at water pO2 &lt;4.5kPa for 7-hours
 each night and in normoxic conditions for the rest of the time. 3. We
 recorded an acceleration of P. varians’ moult cycle, which was 15% shorter
 in animals kept in cyclic hypoxia compared to animals in normoxia.
 Similarly, the pattern of expression of two cuticular proteins over an
 entire moult cycle indicated an effect of cyclic hypoxia on moult
 stage-related genes. After 16 days, morphological changes to the gills
 were detected, with shrimps in cyclic hypoxia having a 13.6% larger
 lamellar surface area (measured in µm2/mg animal) than normoxic animals,
 which could improve gas exchange capacity. Overall, phenotypic and
 morphological data indicate that faster moulting is triggered in response
 to cyclic hypoxia, with the benefit that gill modifications can be
 prompted more rapidly in order to meet oxygen requirements of the body. 4.
 On the first experimental day, in cyclic hypoxic exposed animals, we
 recorded a 50% decrease in feeding rates (during hypoxic conditions) in
 comparison to normoxic animals. Similarly, ammonium excretion was reduced
 by 66-75% during the 1st and 21st experimental day. Body size was reduced
 by ~4% after 28 days. Females that reproduced in cyclic hypoxic conditions
 reduced the amount of yolk in each egg by ~24%. Overall, results underline
 how, in a decapod shrimp living in a key coastal environment, many
 physiological parameters are impaired by a cyclic hypoxic regime that is
 currently found in its natural habitat.
description: Peruzza_FE-2018-234_dataThis file contains all raw data used in the figures of the paper, organised by figurePeruzza_et_al_FE_2018_data.xlsx
DOI: 10.5061/dryad.9472104
title: Data from: New phylogenetic insights into Hydrocharitaceae

description: Hydrocharitaceae is an acquatic monocots family, it has enormous
 importance for the equilibrium among ecosystems and as biological
 resource. Previous phylogenetic studies,on the family, did not received
 strong nodes support and clear congruent resolution. This study revises
 Hydrocharitaceae based on the most comprehensive dataset possible. The
 dataset include all the genera accepted and it is composed by molecular
 characters retrieved by GeneBank resource. Furthermore, only congruent DNA
 regions were considered and the resulting combined matrix was analysed
 with three different phylogenetic methods originating congruent
 topologies. Consequently, a new Hydrocaritaceae phylogeny was advanced in
 resolving taxa nodes position with high confidence hence new genera
 combinations needed to be proposed. As result, a more reliable
 Hydrocharitaceae phylogeny would be essential in order to improve the
 evolutionary model assessment of this poor size family, which can allow a
 high quality taxa management. The importance of delivering reproducible
 research was also stressed as it enhance value of any analysis
 (investigation) and makes possible delivering answer to different issues
 with higher confidence.
description: combine
 matrixcombine matrix wiyh 56
 taxamio56mafft
 .nex
DOI: 10.5061/dryad.1723
title: Data from: Implications of isolation and low genetic diversity in peripheral populations of an amphi-Atlantic coral

description: Limited dispersal and connectivity in marine organisms can have negative
 fitness effects in populations that are small and isolated, but reduced
 genetic exchange may also promote the potential for local adaptation.
 Here, we compare the levels of genetic diversity and connectivity in the
 coral Montastraea cavernosa among both central and peripheral populations
 throughout its range in the Atlantic. Genetic data from one mitochondrial
 and two nuclear loci in 191 individuals show that M. cavernosa is
 subdivided into three genetically distinct regions in the Atlantic:
 Caribbean-North Atlantic, Western South Atlantic (Brazil) and Eastern
 Tropical Atlantic (West Africa). Within each region, populations have
 similar allele frequencies and levels of genetic diversity; indeed, no
 significant differentiation was found between populations separated by as
 much as 3,000 km, suggesting that this coral species has the ability to
 disperse over large distances. Gene flow within regions does not, however,
 translate into connectivity across the entire Atlantic. Instead,
 substantial differences in allele frequencies across regions suggest that
 genetic exchange is infrequent between the Caribbean, Brazil and West
 Africa. Furthermore, markedly lower levels of genetic diversity are
 observed in the Brazilian and West African populations. Genetic diversity
 and connectivity may contribute to the resilience of a coral population to
 disturbance. Isolated peripheral populations may be more vulnerable to
 human impacts, disease or climate change relative to those in the
 genetically diverse Caribbean-North Atlantic region.
description: Sequences for b-tubulin
 2Sequences submitted to
 Genbank for beta-tubulin 2Btub1McavIndcExc.TXTSequences for cox1-trnM IGRDNA Sequences submitted to Genbank for cox1-trnM intergenic regionMNCMcavHap.nxsHaplotype Frequencies per populationHaplotype frequencies per locus for each population. Loci studied: beta-tubulin 1, beta-tubulin 2 and cox1-trnM IGR. Populations: Belize, Panama, Puerto Rico, Bermuda, Abrolhos (Brazil), Joao Pessoa (Brazil), Fortaleza (Brazil), Sao Tome.SuppTable1.xlsSequences for b-tubulin 2Sequences submitted to Genbank for beta-tubulin 2YtubMcavHap.nxsGenotypesGenotype over all loci for each sampled individual.SuppTable2.xls
DOI: 10.5061/dryad.5qm51
title: Data from: Occasional males in parthenogenetic populations of Asobara japonica (Hymenoptera: Braconidae): low Wolbachia titer or incomplete co-adaptation?

description: Wolbachia are endosymbiotic bacteria known to manipulate the reproduction
 of their hosts. Some populations of the parasitoid wasp Asobara japonica
 are infected with Wolbachia and reproduce parthenogenetically, while other
 populations are not infected and reproduce sexually. Wolbachia infected A.
 japonica females regularly produce small numbers of male offspring.
 Because all females in the field are infected and infected females are not
 capable of sexual reproduction, male production seems to be maladaptive.
 We investigated why these females nevertheless produce males. We tested
 three hypotheses: high rearing temperatures could result in higher
 offspring sex ratios (more males), low Wolbachia titer of the mother could
 lead to higher offspring sex ratios and/or the Wolbachia infection is of
 relatively recent origin and not enough time has passed to allow complete
 co-adaptation between Wolbachia and host. Thirty-three percent of the
 Wolbachia infected females produced males and 56% of these males were also
 infected with Wolbachia. Neither offspring sex ratio nor male infection
 frequency were significantly affected by rearing temperature or Wolbachia
 concentration of the mother. The mitochondrial DNA sequence of one of the
 uninfected populations was identical to that of two of the infected
 populations. Therefore, the initial Wolbachia infection of A. japonica
 must have occurred recently. Mitochondrial sequence variation among
 infected populations suggests that the spread of Wolbachia through the
 host populations involved horizontal transmission. We conclude that the
 occasional male production by Wolbachia infected females is most likely a
 maladaptive side-effect of incomplete co-evolution between symbiont and
 host in this relatively young infection.
description: Data Temperature
 Experiment (Sex Ratio & Male Infection Frequency)Data qPCR Experiment
 (Wolbachia Concentration)