cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.61t9h
title: Data from: Constraints on the evolution of function-valued traits: a study of growth in Tribolium castaneum

description: Growth trajectories often impact individual fitness. They are continuous
 by nature and so are amenable to analysis using a function-valued (FV)
 trait framework to reveal their underlying genetic architecture. Previous
 studies have found high levels of standing additive genetic (co)variance
 for growth trajectories despite the expectation that growth should be
 responding to frequent strong directional selection. In this study, the FV
 framework is used to estimate the additive genetic covariance function for
 growth trajectories in larval Tribolium castaneum to address questions
 about standing additive genetic (co)variance and possible evolutionary
 constraints on growth and to predict responses to four plausible selection
 regimes. Results show that additive genetic (co)variance is high at the
 early ages, but decreases towards later ages in the larval period. A
 selection gradient function of the same size and in the same direction of
 the first eigenfunction of the G-function should give the maximal
 response. However, evolutionary constraints may be acting to keep this
 maximal response from being realized, through either conflicting effects
 on survivability and fecundity of larger body size, few evolutionary
 directions having sufficient additive variance for a response, genetic
 trade-offs with other traits or physiological regulatory mechanisms. More
 light may be shed on these constraints through the development of more
 sophisticated statistical approaches and implementation of additional
 empirical studies to explicitly test for specific types of constraints.
description: Tribolium Larval Mass
 DataThe file gives mass
 measurements for individuals who are listed in rows. The first three
 columns list identifying information for each larva; the first column
 gives the ID number, the second gives the sire number, and the third gives
 the dam number. The fourth column gives the hatch date, from which each
 'age' is measured. From here, each data entry takes three
 columns: one for date of measurement, one for days since hatch (or, age at
 measurement), and one for the actual mass measurement (which is in grams).
 The numbers following the headings in this column represent the number of
 each measurement (i.e. 'mass5' indicates the fifth mass
 measure). Data concerning the pupal stage begin at the 44th column. The
 first three columns are the date of pupation, pupation age, and pupal
 mass. The 47th column indicates the sex of the individual, with 1
 representing a male and 0 representing a female. The last two columns
 indicate the date and age of eclosion to the adult stage, respectively.
 Any blank entries represent a lack of data points either for that
 measurement or for that identifying information.Trib2010data.xls
DOI: 10.5061/dryad.2jh157f
title: Data from: Quantification of motor speech impairment and its anatomic basis in primary progressive aphasia

description: Objective: To evaluate whether a quantitative speech measure is effective
 in identifying and monitoring motor speech impairment (MSI) in patients
 with primary progressive aphasia (PPA), and to investigate the
 neuroanatomical basis of MSI in PPA. Methods: Sixty-four patients with PPA
 were evaluated at baseline, with a subset (N=39) evaluated longitudinally.
 Articulation rate (AR), a quantitative measure derived from spontaneous
 speech, was measured at each timepoint. MRI was collected at baseline.
 Differences in baseline AR were assessed across PPA subtypes, separated by
 severity level. Linear mixed-effects models were conducted to assess
 groups differences across PPA subtypes in rate of decline in AR over a
 one-year period. Cortical thickness measured from baseline MRIs was used
 to test hypotheses about the relationship between cortical atrophy and
 MSI. Results: Baseline AR was reduced for patients with non-fluent variant
 PPA (nfvPPA), as compared to other PPA subtypes and controls, even in mild
 stages of disease. Longitudinal results showed a greater rate of decline
 in AR for the nfvPPA group over one year, as compared to logopenic and
 semantic variant subgroups. Reduced baseline AR was associated with
 cortical atrophy in left-hemisphere premotor and supplementary motor
 cortices. Conclusions: The AR measure is an effective quantitative index
 of MSI that detects MSI in mild disease stages and tracks decline in MSI
 longitudinally. The AR measure additionally demonstrates anatomic
 localization to motor-speech specific cortical regions. Our findings
 suggest that this quantitative measure of MSI might have utility in
 diagnostic evaluation and monitoring of motor speech impairments in PPA.
description: Table e-1. Baseline
 speech/language characteristics per patientTable
 e1.pdfTable e-2. Supplemental
 CDR language domain as defined by Knopman, Weintraub, and Pankratz
 (2011)Table
 e2_v2.pdfTable e-3. Operational
 guidelines for motor speech severity ratingsTable
 e3_v2.pdfTable e-4. Motor speech
 features and criteria for diagnosing AOS, DysarthriaTable
 e4_v2.pdfTable e-5. Motor speech
 characterizations (consensus ratings) per patientTable
 e5.pdfFigure e-1. Motor speech
 regions of interest labelled using SpeechLabel parcellation
 paradigmFigure
 e1_v2.pdf
DOI: 10.5061/dryad.gd0m3
title: Data from: Generation length for mammals

description: Generation length (GL) is defined as the average age of parents of the
 current cohort, reflecting the turnover rate of breeding individuals in a
 population. GL is a fundamental piece of information for population
 ecologist as well as for measuring species threat status (e.g. in the IUCN
 Red List). Here we present a dataset including GL records for all extant
 mammal species (n=5426). We first reviewed all data on GL published in the
 IUCN Red List database. We then calculated a value for species with
 available reproductive parameters (reproductive life span and age at first
 reproduction). We assigned to missing-data species a mean GL value from
 congeneric or confamilial species (depending on data availability).
 Finally, for a few remaining species, we assigned mean GL values from
 species with similar body mass and belonging to the same order. Our work
 provides the first attempt to complete a database of GL for mammals; it
 will be an essential reference point for all conservation-related studies
 that need pragmatic information on species GL, such as population dynamics
 and applications of the IUCN Red List assessment.
description: Generation Lenght for
 Mammals
DOI: 10.15468/dl.2gbu9p
title: Occurrence Download

description: A dataset containing 6658 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON ((-101.3031 19.44734, -101.1508 19.44823, -101.1522 19.56503, -101.3041 19.56257, -101.3031 19.44734))",
 "HasCoordinate is true"
 ]
}

 The dataset includes 6658 records from 65 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000562-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.ff32k
title: Data from: Persistence and dispersal in a Southern Hemisphere glaciated landscape: the phylogeography of the spotted snow skink (Niveoscincus ocellatus) in Tasmania

description: Background: The aim of this research was to identify the effects of
 Pleistocene climate change on the distribution of fauna in Tasmania, and
 contrast this with biotic responses in other temperate regions in the
 Northern and Southern Hemisphere that experienced glacial activity during
 this epoch. This was achieved by examining the phylogeographic patterns in
 a widely distributed Tasmanian endemic reptile, Niveoscincus ocellatus.
 204 individuals from 29 populations across the distributional range of N.
 ocellatus were surveyed for variation at two mitochondrial genes (ND2,
 ND4), and two nuclear genes (β-globin, RPS8). Phylogenetic relationships
 were reconstructed using a range of methods (maximum parsimony, Bayesian
 inference and haplotype networks), and the demographic histories of
 populations were assessed (AMOVA, Tajima’s D, Fu’s Fs, mismatch
 distributions, extended Bayesian skyline plots, and relaxed random walk
 analyses). Results: There was a high degree of mitochondrial haplotype
 diversity (96 unique haplotypes) and phylogeographic structure, where
 spatially distinct groups were associated with Tasmania’s Northeast and a
 large area covering Southeast and Central Tasmania. Phylogeographic
 structure was also present within each major group, but the degree varied
 regionally, being highest in the Northeast. Only the Southeastern group
 had a signature of demographic expansion, occurring during the Pleistocene
 but post-dating the Last Glacial Maximum. In contrast, nuclear DNA had low
 levels of variation and a lack of phylogeographic structure, and further
 loci should be surveyed to corroborate the mitochondrial inferences.
 Conclusions: The phylogeographic patterns of N. ocellatus indicate
 Pleistocene range and demographic expansion in N. ocellatus, particularly
 in the Southeast and Central areas of Tasmania. Expansion in Central and
 Southeastern areas appears to have been more recent in both demographic
 and spatial contexts, than in Northeast Tasmania, which is consistent with
 inferences for other taxa of greater stability and persistence in
 Northeast Tasmania during the Last Glacial Maximum. These phylogeographic
 patterns indicate contrasting demographic histories of populations in
 close proximity to areas directly affected by glaciers in the Southern
 Hemisphere during the LGM.
description: mitochondrial DNA
 sequence dataSequences of ND2 and
 ND4mtDNA_data.nexBeta-globin sequence dataDNA sequences of the Beta-globin regionBglobin_data.nex
DOI: 10.5061/dryad.t01q1
title: Data from: Can differential nutrient extraction explain property variations in a predatory trap?

description: Predators exhibit flexible foraging to facilitate taking prey that offer
 important nutrients. Because trap-building predators have limited control
 over the prey they encounter, differential nutrient extraction and trap
 architectural flexibility may be used as a means of prey selection. Here,
 we tested whether differential nutrient extraction induces flexibility in
 architecture and stickiness of a spider's web by feeding Nephila
 pilipes live crickets (CC), live flies (FF), dead crickets with the web
 stimulated by flies (CD) or dead flies with the web stimulated by crickets
 (FD). Spiders in the CD group consumed less protein per mass of lipid or
 carbohydrate, and spiders in the FF group consumed less carbohydrates per
 mass of protein. Spiders from the CD group built stickier webs that used
 less silk, whereas spiders in the FF group built webs with more radii,
 greater catching areas and more silk, compared with other treatments. Our
 results suggest that differential nutrient extraction is a likely
 explanation for prey-induced spider web architecture and stickiness
 variations.
description: Blamiresetal_droplet
 counts1Counts of glue droplets
 along single strands of spiral thread.Blamiresetal_droplet
 morphology1Measurements made on
 magnified glue droplets to calculate spiral droplet morphological
 parameters.Blamiresetal_Nutrients
 analysisNutrient analysis on all
 insect bodies collected throughout the study. Specimens are coded as to
 whether or not they were analysed whole (W), CRICKETS (C) or flies (F),
 fed live (L) or dead (D) or decoupled from their vibrations
 (V).Blamiresetal_nutrients
 overviewNutrient analyses
 compiled into nutrients analyzed and treatments
 segregated.Blamiresetal_prey
 consumptionApproximate masses of
 prey eaten across treatments. Provides mean whole prey masses compared to
 the masses of prey remains in enclosures after feeding.Blamiresetal_spiral
 stickinessOverview of spiral
 stickiness measurements. These data are accumulated from individual
 stickiness tests which comprise of over 20 individual xl files (&gt;200
 individual tests), which we can provide if requested.Blamiresetal_web
 geometry measurements2Provides an overview of
 all web architectural measurements made for all
 spiders.
DOI: 10.5061/dryad.561hm
title: Data from: Ploidy and domestication are associated with genome size variation in Palms

description: PREMISE OF THE STUDY: The genome size of a species (C-value) is associated
 with growth, development and adaptation to environmental changes.
 Angiosperm C-values range 1200-fold and frequently vary within species,
 although little is known about the impacts of domestication on genome
 size. Genome size variation among related species of palms is of
 evolutionary significance because changes characterize clades and may be
 associated with polyploidy, transposon amplifications, deletions, or
 rearrangements. Further knowledge of genome size will provide crucial
 information needed for planning of whole genome sequencing and accurate
 annotations. We studied the genome size of Cocos nucifera and its
 variation among cultivars, and compared it to values for related palms
 from the Attaleinae subtribe. METHODS: Flow cytometric analysis of
 isolated nuclei from young palm leaves was used to estimate genome sizes
 of 23 coconut cultivars (Talls, Dwarfs, and hybrids) worldwide and 17
 Cocoseae species. Ancestral genome size was reconstructed on a maximum
 likelihood phylogeny of Attaleinae from seven WRKY loci. KEY RESULTS: The
 coconut genome is large—averaging 5.966 pg—and shows intraspecific
 variation associated with domestication. Variation among Tall coconuts was
 significantly greater than among Dwarfs. Attaleinae genomes showed
 moderate size variation across genera, except polyploids Jubaeopsis
 caffra, Voanioala gerardii, Beccariophoenix alfredii, and Allagoptera
 caudescens, which had larger genomes. CONCLUSIONS: Our results contribute
 to the understanding of the relationship between domestication and genome
 size in long-lived tree crops and provide a basis for whole-genome
 sequencing of the coconut and other domesticated plants. Polyploidy
 evolved independently in two clades within Attaleinae.
description: Maximum likelihood
 phylogeny of the Attaleinae based on WRKY genesNexus file of alignment
 of 56 sequences for the maximum likelihood phylogeny of Attaleinae
 (Arecaceae) based on concatenation of seven nuclear WRKY genes (5.648 kb)
 analysed using PHYML software. The ML tree was applied to Mesquite
 software for optimization of genome sizes across the Attaleinae phylogeny
 for reconstruction of ancestral genome sizes.PHYML
 tree_Attaleinae_WRKY.nex
DOI: 10.5061/dryad.rn262
title: Data from: Gene flow from an adaptively divergent source causes rescue through genetic and demographic factors in two wild populations of Trinidadian guppies

description: Genetic rescue, an increase in population growth owing to the infusion of
 new alleles, can aid the persistence of small populations, but its use as
 a management tool is limited by a lack of empirical data geared towards
 predicting effects of gene flow on local adaptation and demography.
 Experimental translocations provide an ideal opportunity to monitor the
 demographic consequences of gene flow. In this study we take advantage of
 two experimental introductions of Trinidadian guppies to test the effects
 of gene flow on downstream native populations. We individually marked
 guppies from the native populations to monitor population dynamics for 3
 months before and 26 months after gene flow. We genotyped all individuals
 caught during the first 17 months at microsatellite loci to classify
 individuals by their genetic ancestry: native, immigrant, F1 hybrid, F2
 hybrid, or backcross. Our study documents a combination of demographic and
 genetic rescue over multiple generations under fully natural conditions.
 Within both recipient populations, we found substantial and long-term
 increases in population size that could be attributed to high survival and
 recruitment caused by immigration and gene flow from the introduction
 sites. Our results suggest that low levels of gene flow, even from a
 divergent ecotype, can provide a substantial demographic boost to small
 populations, which may allow them to withstand environmental
 stochasticity.
description: FocalSites_GenGroup_0901_1106Capture records from monthly Trinidadian guppy monitoring of two populations between January 2009 and June 2011. Individual capture histories are coded by stream (CA vs TY), sex (M vs F), and genetic classification (Native-N, Immigrant-I, F1 hybrid - F1, F2 hybrid - F2)CA_CMR_genepop_allMicrosatellite data in genepop format for Caigual population of Trinidadian guppiesTY_CMR_genepop_allMicrosatellite data in genepop format for Taylor population of Trinidadian guppies
DOI: 10.5061/dryad.hj6f109
title: Data from: Limited phenological and dietary overlap between bee communities in spring flowering crops and herbaceous enhancements.

description: Wild bee populations have undergone declines in recent years across much
 of the Western world, and these declines have the potential to limit yield
 in pollination-dependent crops. Highbush blueberry, Vaccinium corymbosum,
 and tart cherry, Prunus cerasus, are spring-blooming crops that rely on
 the movement of pollen by bees and other insects for pollination. Wild bee
 populations can be increased on farmland by providing floral resources,
 but whether the addition of these plants translates into increased
 pollinator density on crop flowers has not been documented in most
 cropping systems. To determine the importance of providing additional
 floral resources for wild bee pollinator communities, we selected
 blueberry fields and tart cherry orchards with and without herbaceous
 floral enhancements in western Michigan, USA. The bee communities visiting
 crop flowers, enhancements and control grassy field margins were sampled
 over a five-year period. In addition, the pollen diets of the most
 abundant wild bee crop pollinators were quantified across Michigan to
 better understand their foraging niches and to identify potentially
 important alternative host plants. The presence of floral enhancements did
 not increase the abundance of wild bees on either blueberry or cherry
 flowers during bloom. The bee community visiting blueberry was evenly
 composed of short-season bees that fly only during the spring and
 long-season bees that fly in both spring and summer. In contrast, the bee
 community visiting cherry was dominated by short-season spring bees. The
 majority of pollen collected by the wild bee communities visiting
 blueberry and cherry was from spring-flowering woody plants, with limited
 use of the herbaceous enhancements. Enhancements attracted greater
 abundance and species richness of bees compared to control areas,
 including twice as many floral specialists. Conserving summer-flying,
 grassland associated bees is an appropriate goal for pollinator
 conservation programs. However, herbaceous enhancements may not provide
 adequate resources for the wild bees that pollinate spring-flowering
 crops. This study demonstrates that an examination of the pollen collected
 by wild bees across their flight periods can identify plant species to
 help them persist in intensively managed landscapes.
description: Blueberry_data_combinedOn-crop specimen data and observations and herbaceous enhancement floral and specimen data for blueberry sites.Cherry_data_combinedOn-crop specimen and observation and herbaceous enhancement floral and specimen data for cherry sites.Pollen_diet_dataPollen dietary data for important wild bee pollinator species for blueberry and cherry in Michigan.
DOI: 10.5061/dryad.p0h2678
title: Data from: Without management interventions, endemic wet-sclerophyll forest is transitioning to rainforest in World Heritage listed K’gari (Fraser Island), Australia

description: Wet-sclerophyll forests are unique ecosystems that can transition to
 dry-sclerophyll forests or to rainforests. Understanding of the dynamics
 of these forests for conservation is limited. We evaluated the long-term
 succession of wet-sclerophyll forest on World Heritage listed K’gari
 (Fraser Island)the world’s largest sand island. We recorded the presence
 and growth of tree species in three 0.4 hectare plots that had been
 subjected to selective logging, fire, and cyclone disturbance over 65
 years, from 1952 to 2017. Irrespective of disturbance regimes, which
 varied between plots, rainforest trees recruited at much faster rates than
 the dominant wet-sclerophyll forest trees, narrowly endemic species
 Syncarpia hillii and more common Lophostemon confertus. Syncarpia hillii
 did not recruit at the plot with the least disturbance and recruited only
 in low numbers at plots with more prominent disturbance regimes in the 
 10 cm at breast height size. Lophostemon confertus recruited at all plots
 but in much lower numbers than rainforest trees. Only five L. confertus
 were detected in the smallest size class (&lt; 10 cm diameter) in the
 2017 survey. Overall, we find evidence that more pronounced disturbance
 regimes than those that have occurred over the past 65 years may be
 required to conserve this wet-sclerophyll forest, as without intervention,
 transition to rainforest is a likely trajectory. Fire and other management
 tools should therefore be explored, in collaboration with Indigenous
 landowners, to ensure conservation of this wet-sclerophyll forest.
description: Raw data all plots
 1952-2017Contains raw information
 on trees &gt;10 cm DBH for each plot (i.e DYP 9) including Tree ID, tree
 species, measurement year, diameter at breast height (1.3m), calculated
 basal area, DBH size class, X and Y coordinates within plots (40m x
 100m).Raw_data_all_plots_1952-2017.xlsxRaw data all plots understory 2017Contains raw information on trees &lt;10 cm DBH for each plot including: Tree ID, tree species, DBH &lt;10cm, plot number, measurement year.Raw_data_all_plots_understory_2017.xlsxlinear mixed effects model datasetContains data on Shannons index, simpsons, evenness, year of measurement, plot ID, and section within plot for running linear mixed effects model on R.linear_mixed_effects_model_dataset .csvlinear mixed effects model codeContains R codes for running diversity indices and linear mixed effects modellinear_mixed_effects_model_code.Rmultivariate analyses codesContains R codes for running nMDS, betadisper, PERMANOVA, and pairwise adonis analyses.multivariate_analyses_codes.R