cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1p80f
title: Data from: A method for analysis of phenotypic change for phenotypes described by high-dimensional data

description: The analysis of phenotypic change is important for several evolutionary
 biology disciplines, including phenotypic plasticity, evolutionary
 developmental biology, morphological evolution, physiological evolution,
 evolutionary ecology and behavioral evolution. It is common for
 researchers in these disciplines to work with multivariate phenotypic
 data. When phenotypic variables exceed the number of research
 subjects—data called ‘high-dimensional data’—researchers are confronted
 with analytical challenges. Parametric tests that require high observation
 to variable ratios present a paradox for researchers, as eliminating
 variables potentially reduces effect sizes for comparative analyses, yet
 test statistics require more observations than variables. This problem is
 exacerbated with data that describe ‘multidimensional’ phenotypes, whereby
 a description of phenotype requires high-dimensional data. For example,
 landmark-based geometric morphometric data use the Cartesian coordinates
 of (potentially) many anatomical landmarks to describe organismal shape.
 Collectively such shape variables describe organism shape, although the
 analysis of each variable, independently, offers little benefit for
 addressing biological questions. Here we present a nonparametric method of
 evaluating effect size that is not constrained by the number of phenotypic
 variables, and motivate its use with example analyses of phenotypic change
 using geometric morphometric data. Our examples contrast different
 characterizations of body shape for a desert fish species, associated with
 measuring and comparing sexual dimorphism between two populations. We
 demonstrate that using more phenotypic variables can increase effect
 sizes, and allow for stronger inferences.
description: pupfish
 shapeProcrustes residuals,
 source, sex, and centroid size data for 54 specimens of Cyprinodon
 pecosensis. Data were collected from collections from the Museum of
 Southwestern Biology, University of New Mexico. Accession numbers are as
 follows: Marsh sample: MSB 49238; Sinkhole sample: MSB
 43612.collyer.et.al.pupfish.data.csv
DOI: 10.5061/dryad.25v2429
title: Data from: Individual variation, population-specific behaviours, and stochastic processes shape marine migration phenologies

description: 1. The phenology of long distance migrations can influence individual
 fitness, moderate population dynamics, and regulate the availability of
 ecosystem services to other trophic levels. Phenology varies within and
 among populations, and can be influenced by conditions individuals
 experience both prior to departure and encounter en route. 2. Assessing
 how intrinsic and extrinsic factors (e.g. individual physical condition
 vs. environmental conditions) interact to influence variation in migratory
 phenologies across ecological scales is often limited due to logistical
 constraints associated with tracking large numbers of individuals from
 multiple populations simultaneously. 3. We used two natural tags, DNA and
 otolith microstructure analysis, to estimate the relative influence of
 individual traits (life history strategy, body size at departure, and
 growth during migration), population-specific strategies, and interannual
 variability on the phenology of marine migrations in juvenile sockeye
 salmon Oncorhynchus nerka. 4. We show that the timing and duration of
 juvenile sockeye salmon migrations were correlated with both life history
 strategy and body size, while migration duration was also correlated with
 departure timing and growth rates during migration. Even after accounting
 for the effect of individual traits, several populations exhibited
 distinct migration phenologies. Finally, we observed substantial
 interannual and residual variation, suggesting stochastic environmental
 conditions moderate the influence of carry-over effects that develop prior
 to departure, as well as population-specific strategies. 5. Migratory
 phenologies are shaped by complex interactions between drivers acting at
 multiple ecological and temporal scales. Given evidence that intraspecific
 diversity can stabilize ecological systems, conservation efforts should
 seek to maintain migratory variation among populations and preserve
 locally adapted phenotypes; however, variation within populations, which
 may buffer systems from environmental stochasticity, should also be
 regularly assessed and preserved.
description: individualPhenologyData.csvIndividual migration data from juvenile sockeye salmon estimated from field sampling program and otolith microstructure.individualOtolithData.csv
DOI: 10.5061/dryad.5j7m6
title: Data from: Complex sources of variance in female dominance rank in a nepotistic society

description: Many mammalian societies are structured by dominance hierarchies, and an
 individual's position within this hierarchy can influence
 reproduction, behaviour, physiology and health. In nepotistic hierarchies,
 which are common in cercopithecine primates and also seen in spotted
 hyaenas, Crocuta crocuta, adult daughters are expected to rank immediately
 below their mother, and in reverse age order (a phenomenon known as
 ‘youngest ascendancy’). This pattern is well described, but few studies
 have systematically examined the frequency or causes of departures from
 the expected pattern. Using a longitudinal data set from a natural
 population of yellow baboons, Papio cynocephalus, we measured the
 influence of maternal kin, paternal kin and group size on female rank
 positions at two life history milestones, menarche and first live birth.
 At menarche, most females (73%) ranked adjacent to their family members
 (i.e. the female held an ordinal rank in consecutive order with other
 members of her maternal family); however, only 33% of females showed
 youngest ascendancy within their matriline at menarche. By the time they
 experienced their first live birth, many females had improved their
 dominance rank: 78% ranked adjacent to their family members and 49% showed
 youngest ascendancy within their matriline. The presence of mothers and
 maternal sisters exerted a powerful influence on rank outcomes. However,
 the presence of fathers, brothers and paternal siblings did not produce a
 clear effect on female dominance rank in our analyses, perhaps because
 females in our data set co-resided with variable numbers and types of
 paternal and male relatives. Our results also raise the possibility that
 female body size or competitive ability may influence dominance rank, even
 in this classically nepotistic species. In total, our analyses reveal that
 the predictors of dominance rank in nepotistic rank systems are much more
 complex than previously thought.
description: Lea_et_al_2014_dataData used for analyses described in 'Complex sources of variance in female dominance rank in a nepotistic society'. See the README file for explanations of column headings.
DOI: 10.5061/dryad.fp17j
title: Data from: Kooiichthys jono n. gen. n. sp., a primitive catfish (Teleostei, Siluriformes) from the marine Miocene of southern South America

description: A specimen of a remarkable new catfish genus and species was collected in
 middle/late Miocene marine beds of the Puerto Madryn Formation at the base
 of the marine cliff of the sea lion colony area near Puerto Pirámide,
 southern coast of Península Valdés, northeastern Patagonia, Argentina.
 Siluriforms (catfishes) constitute a most important monophyletic
 ostariophysan group of mainly freshwater fishes that occurs in almost all
 continents but it is especially diverse in South America. Catfishes are
 presently distributed in tropical to temperate areas and a small number of
 species are marine or amphibiotic. The new catfish shows many primitive
 features for catfishes in the maxilla, autopalatine, hyal elements, and
 Weberian apparatus. The genus is clearly distinguished by four
 autapomorphies: sand clock—shaped autopalatine, posterior limb of
 autopalatine widening strongly, post-articular arm of autopalatine longer,
 and a metapterygoid longer than broad. One tree was obtained both under
 equal and implied weighting with the following topology: a basal polytomy
 in the Siluriformes formed by Diplomystidae, Bachmanniidae, Kooiichthys
 and the Siluroidei. The new species appears to have been a marine or
 amphibiotic taxon: it was collected in beds considered to represent the
 Maximum Flooding Horizon of the transgression that deposited the Puerto
 Madryn Formation. The coast at this moment was at approximately 90 km to
 the west. According to faunistic evidence, the sea was warm temperate.
description: Appendix2_CECharacter and Character State Descriptions for Phylogenetic AnalysisAppendix3_CEFormatted Data File Used in the Phylogenetic Analysis
DOI: 10.5061/dryad.7qp63
title: Data from: The loss of taste genes in cetaceans

description: [No abstract entered]
description: trees and sequences for
 taste receptor genestrees and
 sequences.rar
DOI: 10.5061/dryad.45ng8
title: Data from: When a male perceives a female: the effect of waxy components on the body surface on decision-making in the invasive pest weevil

description: Insects utilize various semiochemicals for sexual communication and mate
 recognition; these can therefore be used to govern the behaviours of
 harmful pest species, and several candidate chemicals have been explored
 for this purpose. For the West Indian sweet potato weevil, Euscepes
 postfasciatus, which is one of the most serious pests of sweet potato, no
 effective capture techniques, such as sex pheromone lures, exist. Toward
 exploring promising procedures for monitoring these weevils, we assessed
 the effect of secretions on the body surface on the recognition of
 congeners and on courtship behaviour in the weevils. Our study clearly
 demonstrated that weevils responded to extracts from the body surface, and
 the behaviour adopted by the weevils varied significantly depending on the
 condition of the extracts. Furthermore, we found a significantly prolonged
 retention time for males on glass beads covered with extracts of females
 based on survival analysis. These findings are, as far as we are aware,
 the first to show the effect of lipid components of the body surface on
 decision-making in these economically important pest weevils.
description: Data of behavioural
 assay to the hexane extractsData of behavioral
 experiment using alive weevils
DOI: 10.5061/dryad.1v87f
title: Data from: Post-fire changes in forest carbon storage over a 300-year chronosequence of Pinus contorta-dominated forests

description: A warming climate may increase the frequency and severity of
 stand-replacing wildfires, reducing carbon (C) storage in forest
 ecosystems. Understanding the variability of post-fire C cycling on
 heterogeneous landscapes is critical for predicting changes in C storage
 with more frequent disturbance. We measured C pools and fluxes for 77
 lodgepole pine (Pinus contorta Dougl. ex Loud var. latifolia Engelm.)
 stands in and around Yellowstone National Park (YNP) along a 300-year
 chronosequence to examine how quickly forest C pools recover after a
 stand-replacing fire, their variability through time across a complex
 landscape, and the role of stand structure in this variability. Carbon
 accumulation after fire was rapid relative to the historical mean fire
 interval of 150-300 years, recovering nearly 80% of pre-fire C in 50 years
 and 90% within 100 years. Net ecosystem carbon balance (NECB) declined
 monotonically from 160 g C m-2 yr-1 at age 12 to 5 g C m 2 yr-1 at age
 250, but was never negative after disturbance. Decomposition and
 accumulation of dead wood contributed little to NECB relative to live
 biomass in this system. Aboveground net primary productivity was
 correlated with leaf area for all stands, and the decline in aboveground
 net primary productivity with forest age was related to a decline in both
 leaf area and growth efficiency. Forest structure was an important driver
 of ecosystem C, with ecosystem C, live biomass C, and organic soil C
 varying with basal area or tree density in addition to forest age. Rather
 than identifying a single chronosequence, we found high variability in
 many components of ecosystem C stocks through time; a &gt; 50% random
 subsample of the sampled stands was necessary to reliably estimate the
 non-linear equation coefficients for ecosystem C. At the spatial scale of
 YNP, this variability suggests that landscape C develops via many pathways
 over decades and centuries, with prior stand structure, regeneration, and
 within-stand disturbance all important. With fire rotation projected to be
 &lt; 30 years by mid century in response to a changing climate,
 forests in YNP will store substantially less C (at least 4.8 kg C/m2 or
 30% less).
description: YNP Chronosequence
 Carbon DataThis data file includes
 field data collected between 2004 and 2007 in and around Yellowstone
 National Park. It includes data from 77 lodgepole pine stands ranging in
 age from 12 years to 335 years old. Data include stand structural data as
 well as carbon data for all carbon pools in each stand. It is an MS Excel
 file with a tab describing each data column and a tab with the data
 themselves.
DOI: 10.5061/dryad.7sc06
title: Data from: Nest survival modeling using a multi-species approach in forests managed for timber and biofuel feedstock

description: 1. Switchgrass (Panicum virgatum) intercropping is a novel forest
 management practice for biomass production intended to generate cellulosic
 feedstocks within intensively managed loblolly pine-dominated landscapes.
 These pine plantations are important for early-successional bird species,
 as short rotation times continually maintain early successional habitat.
 We tested the efficacy of using community models compared to individual
 surrogate species models in understanding influences on nest survival. We
 analysed nest data to test for differences in habitat use for 14 bird
 species in plots managed for switchgrass intercropping and controls within
 loblolly pine (Pinus taeda) plantations in Mississippi, USA. 2. We adapted
 hierarchical models using hyper-parameters to incorporate information from
 both common and rare species to understand community-level nest survival.
 This approach incorporates rare species that are often discarded due to
 low sample sizes, but can inform community-level demographic parameter
 estimates. We illustrate use of this approach in generating both
 species-level and community-wide estimates of daily survival rates for
 songbird nests. We were able to include rare species with low sample size
 (minimum n = 5) to inform a hyper-prior, allowing us to estimate effects
 of covariates on daily survival at the community level, then compare this
 with a single-species approach using surrogate species. Using single
 species models, we were unable to generate estimates below a sample size
 of 21 nests per species. 3. Community model species-level survival and
 parameter estimates were similar to those generated by five single species
 models, with improved precision in community model parameters. 4.
 Covariates of nest placement indicated that switchgrass at the nest site
 (&lt; 4 m) reduced daily nest survival, although intercropping at the
 forest stand level increased daily nest survival. 5. Synthesis and
 applications. Community models represent a viable method for estimating
 community nest survival rates and effects of covariates while
 incorporating limited data for rarely detected species. Intercropping
 switchgrass in loblolly pine plantations slightly increased daily nest
 survival at the research plot scale (0.1 km2), although at a local scale
 (50 m2) switchgrass negatively influenced nest survival. A likely
 explanation supported by previous research is intercropping shifted
 community composition, favouring species with greater disturbance
 tolerance.
description: encounter_histories_and_independent_variablesThis is an R workspace that includes independent varibles "indep_variables" and nest encounter histories "ehdata" for songbird nests found and monitored in switchgrass intercropping biofuel experimental plots and control plots in Scooba Mississippi, 2011-2013.
DOI: 10.5061/dryad.1272
title: Data from: Dispersal to or from an African biodiversity hotspot?

description: Biodiversity hotspots are centers of endemism and thus contain many
 range-restricted species. In addition, within these hotspots are often
 widespread species that might have originated within a hotspot before
 dispersing to neighboring or distant regions. We test this hypothesis
 through a phylogeographic analysis of a miniature leaf litter frog,
 Arthroleptis xenodactyloides, that has a large distribution throughout the
 Eastern Arc, a biodiversity hotspot, and other regions in East Africa.
 Maximum likelihood and Bayesian estimates of the mitochondrial gene
 phylogeny are used as a proxy for understanding the evolutionary history
 of diversification and the historical relationships between populations.
 The north-south range of this species extends for approximately 1900 km;
 our sampling covers approximately 85% of this range. Using phylogenetic
 comparative methods, we estimate the region of origin and direction of
 dispersal within A. xenodactyloides. We compare contrasting hypotheses of
 latitudinal range expansion using bayes factors. The ancestral region of
 origin of A. xenodactyloides is reconstructed as having occurred within
 the Eastern Arc before dispersing southwards into the Southern Rift
 mountains, probably in the Pleistocene. The phylogeographic structure
 within this leaf litter frog is surprisingly similar to that of forest
 birds, revealing that similar geographic features might have had a driving
 role in diversification of these very dissimilar taxa. Latitudinal
 expansion occurred early in the evolutionary history of A. xenodactyloides
 and may indicate that physiological adaptation facilitated its wide
 geographic distribution.
description: Aligned DNA sequences of
 Arthroleptis xenodactyloidesA nexus file containing
 aligned mitochondrial DNA sequences of Arthroleptis xenodactyloides and
 related species. Sequences aligned using ClustalX and then
 trimmed.xenodactyloides.nex
DOI: 10.5061/dryad.qk6d9
title: Data from: Recent speciation and secondary contact in endemic ants

description: Gene flow is the main force opposing divergent selection, and its effects
 are greater in populations in close proximity. Thus, complete reproductive
 isolation between parapatric populations is not expected, particularly in
 the absence of ecological adaptation and sharp environmental differences.
 Here, we explore the biogeographical patterns of an endemic ant species,
 Cataglyphis floricola, for which two colour morphs (black and bicolour)
 coexist in parapatry throughout continuous sandy habitat in southern
 Spain. Discriminant analyses of six biometric measurements of male
 genitalia and 27 cuticular hydrocarbons reveal high differentiation
 between morphs. Furthermore, the low number of shared alleles derived from
 nuclear markers (microsatellites) between the morphs at their contact zone
 suggests the absence of recent gene flow. Mitochondrial DNA (COI)
 phylogenetic analysis and median-joining networks show that the black
 morph is basal to the bicolour morph, with unique haplotypes recovered for
 each morph. Mismatch distribution analysis and Bayesian skyline plots
 suggest that they are undergoing different demographic changes, with the
 bicolour and black morphs at demographic equilibrium and expansion,
 respectively. Thus, our results show complete reproductive isolation
 between the two colour morphs as evidenced from genetic, chemical and
 morphological data. We suggest that these divergence events could be
 explained by historical vicariance during the Pleistocene, in which
 reproductive traits experienced strong divergent selection between the
 morphs initiating or culminating speciation.
description: Raw data used in: Recent
 speciation and secondary contact in endemic ants.This package contains
 the data used in the Manuscript Recent speciation and secondary contact in
 endemic ants, by Jowers et al. The files included are: 1) A table
 containing all sampling locations and GIS coordinates. 2) An by-indvidual
 sequence alignment of the mtDNA data in FASTA format, as well as the
 phylogenetic tree block in Newick format. 3) The microsatellite genotypes.
 4) The raw morphological data (copulatory pieces) measurements and, 5) the
 raw cuticular hydrocarbon data. For each of these, a ReadMe file is
 included, giving specific details of the contents and author's
 contact information.Jowers_et_al_Dryad.zip
DOI: 10.15468/dl.77mjc3
title: Occurrence Download

description: A dataset containing 2781985 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 IF(ISNULL(kingdomkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY kingdomkey, "year")) kingdomcount,
 IF(ISNULL(phylumkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY phylumkey, "year")) phylumcount,
 IF(ISNULL(classkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY classkey, "year")) classcount,
 IF(ISNULL(orderkey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY orderkey, "year")) ordercount,
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, "year")) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, "year")) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.datasetkey = '50c9509d-22c7-4a22-a47d-8c48425ef4a7'
 AND occurrence.hasgeospatialissues = FALSE
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND NOT occurrence.basisofrecord IN ('FOSSIL_SPECIMEN', 'LIVING_SPECIMEN')
 AND occurrence.occurrencestatus = 'PRESENT'
 AND (occurrence.classificationdetails['d7dddbf4-2cf0-4f39-9b2a-bb099caae36c']['specieskey'] &lt;&gt; '' AND occurrence."year" IS NOT NULL)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year"

 The dataset's 2781985 records were derived from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000943-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.