cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.69f22
title: Data from: Systematics of the cosmopolitan aquatic genus Elatine

description: The cosmopolitan genus Elatine (Elatinaceae) includes about 25 aquatic
 species of mostly diminutive aquatic plants, whose relationships have not
 been evaluated using a phylogenetic approach. The taxonomic study of this
 group has been complicated by the small stature of the plants, their
 minute reproductive structures, and their cosmopolitan distribution.
 Consequently, much uncertainty exists with respect to species
 delimitations, their geographical distributions, and interspecific
 relationships. To clarify the infrageneric classification of Elatine and
 to provide insights on interspecific relationships within the genus, we
 conducted a phylogenetic study of nearly all (24) of the currently
 recognized species using both morphological and molecular data. The tree
 topology obtained based on morphological data (including vegetative and
 reproductive characters) was less-resolved than the trees based on
 molecular data, derived from either nuclear (ITS) or two plastid regions
 (matK/trnK and rbcL). However, the tree topology obtained from combined
 morphological and molecular data was well resolved and placed the
 morphologically distinctive E. alsinastrum as the sister group of the
 remaining species, which fell within two major clades: a clade of
 4-merous-flowered species and a clade of 3-merous species, within which
 was embedded a subclade of 2-merous species. Although a number of
 topological differences occurred between the ITS and plastid tree
 topologies, significant incongruence was observed only for the placements
 of E. americana and E. hexandra, possibly resulting from reticulate
 evolution. Bergia, the sister genus of Elatine, comprises larger species,
 which often are mostly helophytic but never truly aquatic. Ancestral state
 reconstructions based on the ITS tree indicated that a morphological
 reduction series (in stature and floral merosity) exists among Elatine
 species, which is best explained as a consequence of adaptation to their
 aquatic life. These phylogenetic analyses also have helped to clarify the
 infrageneric classification of the genus and to provide a better
 understanding of the natural and nonindigenous distributions of the
 species. The new monotypic section Elatine sect. Cymifera, including E.
 brochonii, is described.
description: ITS
 alignmentaligned ITS sequences
 from Elatine and Bergia speciesITS_alignment_Hamid_Razifard_22MAR16.nexmatK alignmentaligned matK sequences from Elatine and Bergia speciesmatK_alignment_Hamid_Razifard_22MAR16.nexrbcL alignmentaligned rbcL sequences from Elatine and Bergia speciesrbcL_alignment_Hamid_Razifard_22MAR16.nex
DOI: 10.5061/dryad.6rg07
title: Data from: Aposematism: balancing salience and camouflage

description: Aposematic signals are often characterized by high conspicuousness. Larger
 and brighter signals reinforce avoidance learning, distinguish defended
 from palatable prey and are more easily memorized by predators.
 Conspicuous signalling, however, has costs: encounter rates with naive,
 specialized or nutritionally stressed predators are likely to increase. It
 has been suggested that intermediate levels of aposematic conspicuousness
 can evolve to balance deterrence and detectability, especially for
 moderately defended species. The effectiveness of such signals, however,
 has not yet been experimentally tested under field conditions. We used
 dough caterpillar-like baits to test whether reduced levels of aposematic
 conspicuousness can have survival benefits when predated by wild birds in
 natural conditions. Our results suggest that, when controlling for the
 number and intensity of internal contrast boundaries (stripes), a
 reduced-conspicuousness aposematic pattern can have a survival advantage
 over more conspicuous signals, as well as cryptic colours. Furthermore, we
 find a survival benefit from the addition of internal contrast for both
 high and low levels of conspicuousness. This adds ecological validity to
 evolutionary models of aposematic saliency and the evolution of honest
 signalling.
description: Survival
 dataPredation rates on dough
 stimuli (see README.txt)survivaldata.txtColour dataAvian visual model responses (see README.txt)colourdata.txt
DOI: 10.5061/dryad.420k8
title: Data from: Defining the role of the MADS-box gene, Zea agamous like1, a target of selection during maize domestication

description: Genomic scans for genes that show the signature of past selection have
 been widely applied to a number of species and have identified a large
 number of selection candidate genes. In cultivated maize (Zea mays ssp.
 mays) selection scans have identified several hundred candidate
 domestication genes by comparing nucleotide diversity and differentiation
 between maize and its progenitor, teosinte (Z. mays ssp. parviglumis). One
 of these is a gene called zea agamous-like1 (zagl1), a MADS-box
 transcription factor, that is known for its function in the control of
 flowering time. To determine the trait(s) controlled by zagl1 that was
 (were) the target(s) of selection during maize domestication, we created a
 set of recombinant chromosome isogenic lines that differ for the maize
 versus teosinte alleles of zagl1 and which carry cross-overs between zagl1
 and its neighbor genes. These lines were grown in a randomized trial and
 scored for flowering time and domestication related traits. The results
 indicated that the maize versus teosinte alleles of zagl1 affect flowering
 time as expected, as well as multiple traits related to ear size with the
 maize allele conferring larger ears with more kernels. Our results suggest
 that zagl1 may have been under selection during domestication to increase
 the size of the maize ear.
description: Zagl1_dataExcel file containing genotype, phenotype and genetic stock data.
DOI: 10.5061/dryad.cv791
title: Data from: Novel fine-scale aerial mapping approach quantifies grassland weed cover dynamics and response to management

description: Invasive weeds threaten the biodiversity and forage productivity of
 grasslands worldwide. However, management of these weeds is constrained by
 the practical difficulty of detecting small-scale infestations across
 large landscapes and by limits in understanding of landscape-scale
 invasion dynamics, including mechanisms that enable patches to expand,
 contract, or remain stable. While high-end hyperspectral remote sensing
 systems can effectively map vegetation cover, these systems are currently
 too costly and limited in availability for most land managers. We
 demonstrate application of a more accessible and cost-effective remote
 sensing approach, based on simple aerial imagery, for quantifying weed
 cover dynamics over time. In California annual grasslands, the target
 communities of interest include invasive weedy grasses (Aegilops
 triuncialis and Elymus caput-medusae) and desirable forage grass species
 (primarily Avena spp. and Bromus spp.). Detecting invasion of annual
 grasses into an annual-dominated community is particularly challenging,
 but we were able to consistently characterize these two communities based
 on their phenological differences in peak growth and senescence using
 maximum likelihood supervised classification of imagery acquired twice per
 year (in mid- and end-of season). This approach permitted us to map
 weed-dominated cover at a 1-m scale (correctly detecting 93% of weed
 patches across the landscape) and to evaluate weed cover change over time.
 We found that weed cover was more pervasive and persistent in management
 units that had no significant grazing for several years than in those that
 were grazed, whereas forage cover was more abundant and stable in the
 grazed units. This application demonstrates the power of this method for
 assessing fine-scale vegetation transitions across heterogeneous
 landscapes. It thus provides means for small-scale early detection of
 invasive species and for testing fundamental questions about landscape
 dynamics.
description: NDVI_Values_At_GroundTruth_PointsThis file provides NDVI values associated with forage and weedy vegetation, as derived from digitized imagery. These data are summarized in Figure 3 in the associated manuscript.NDVIValues.csvGroundTruthTestsThis file contains classification values (map categories) for ground-truth point values for each classification approach x input type combination examined. Please see associated article for details.Accuracy_MetricsThis file contains accuracy metrics for each classification approach x input type combination examined. These values are derived from ground-truth tests (see GroundTruthTests). Please see associated article for details.
DOI: 10.5061/dryad.2247c
title: Data from: Host-specialist lineages dominate the adaptive radiation of reef coral endosymbionts

description: Bursts in species diversification are well documented among animals and
 plants, yet few studies have assessed recent adaptive radiations of
 eukaryotic microbes. Consequently, we examined the radiation of the most
 ecologically dominant group of endosymbiotic dinoflagellates found in
 reef-building corals, Symbiodinium Clade C, using nuclear ribosomal
 (ITS2), chloroplast (psbAncr), and multilocus microsatellite genotyping.
 Through a hierarchical analysis of high-resolution genetic data, we
 assessed whether ecologically distinct Symbiodinium, differentiated by
 seemingly equivocal rDNA sequence differences, are independent species
 lineages. We also considered the role of host specificity in Symbiodinium
 speciation and the correspondence between endosymbiont diversification and
 Caribbean paleo-history. According to phylogenetic, biological, and
 ecological species concepts, Symbiodinium Clade C comprises many distinct
 species. Although regional factors contributed to population-genetic
 structuring of these lineages, Symbiodinium diversification was mainly
 driven by host specialization. By combining patterns of the
 endosymbiont's host specificity, water depth distribution, and
 phylogeography with paleo-historical signals of climate change, we
 inferred that present-day species diversity on Atlantic coral reefs
 stemmed mostly from a post-Miocene adaptive radiation. Host-generalist
 progenitors spread, specialized, and diversified during the ensuing epochs
 of prolonged global cooling and change in reef-faunal assemblages. Our
 evolutionary reconstruction thus suggests that Symbiodinium undergoes
 “boom and bust” phases in diversification and extinction during major
 climate shifts.
description: 13-0270_Microsat_DataMultilocus genotypes (10 microsatellite loci) obtained from Symbiodinium associated with the Caribbean reef corals Orbicella (Montastraea) and Siderastrea siderea.13-0270_Multilocus_Data_complete.xls13-0270_Clade C_ITS2Nexus file of ITS2 and partial 5.8S sequence of closely related Symbiodinium from the Atlantic and Pacific Oceans investigated during this research.13-0270_C1_radiation_psbANexus file of alignments of partial sequences (approximately 450 to 550 bases) of the non coding region of the psbA minicircle (unique to dinoflagellates). This alignment composes Symbiodinium members of the C1-group.13-0270_C3_radiation_psbANexus file of alignments of partial sequences (approximately 450 to 550 bases) of the non coding region of the psbA minicircle (unique to dinoflagellates). This alignment composes Symbiodinium members of the C3-group.
DOI: 10.5061/dryad.gf46s
title: Data from: Testosterone activates sexual dimorphism including male-typical carotenoid but not melanin plumage pigmentation in a female bird

description: In males it is frequently testosterone (T) that activates the expression
 of sexually selected morphological and behavioral displays, but the role
 of T in regulating similar traits in females is less clear. Here we
 combine correlational data with results from T and gonadotropin-releasing
 hormone (GnRH) manipulations in both sexes to assess the role of T in
 mediating sexually dimorphic coloration and morphology in the red-backed
 fairy-wren (Malurus melanocephalus). We show that (1) natural variation in
 female expression of ornamental traits (darkened bills and red back
 feathers) are positively associated with age and circulating androgen
 titres, (2) females have the capacity to express most male-typical traits
 in response to exogenous T, including carotenoid-pigmented body plumage,
 shorter feathers, darkened bill, and enlarged cloacal protuberance, but
 (3) appear constrained in production of male-typical melanin-pigmented
 plumage, and (4) low androgen levels during the pre-nuptial molt, probably
 due to low ovarian capacity for steroid production (or LH-sensitivity),
 prevent females from developing male-like ornamentation. Thus, females
 appear to retain molecular mechanism for hormonally regulated male-typical
 ornamentation, although these are rarely activated because of insufficient
 production of the hormonal signal.
description: Female age androgens and
 morphologyLong term observational
 data used to show age related changes in female bill color, plumage color,
 and plasma androgen concentrationsMolting male and female
 androgensLong term observational
 data used to assess relative androgen concentrations of molting red/black
 and brown males and femalesPre T treatment
 reflectance spectraRaw reflectance spectra
 data collected from males and females prior to treatment with either
 testosterone or control implantsPre T treatment
 dimorphismMeasurements of
 morphology (body size, bill, and plumage color) taken on male and female
 birds prior to treatment with testosterone or control
 implantsMid T treatment molt
 scoreTestosterone and control
 implanted male and female molt scores assessed midway through the
 experimental phaseEnd T treatment
 dimorphismMeasurements of bill and
 plumage coloration and body morphology taken at the time of implant
 removal from testosterone and control treated males and females. This data
 was used to generate two informative principal
 components.GnRH
 challengeAndrogen concentrations
 and other informative factors and covariates used in assessment of the
 effects of GnRH treatment on male and female red-backed
 fairy-wrens.
DOI: 10.5061/dryad.7h66k
title: Data from: A branch-heterogeneous model of protein evolution for efficient inference of ancestral sequences

description: Most models of nucleotide or amino acid substitution used in phylogenetic
 studies assume that the evolutionary process has been homogeneous across
 lineages and that composition of nucleotides or amino acids has remained
 the same throughout the tree. These oversimplified assumptions are refuted
 by the observation that compositional variability characterizes extant
 biological sequences. Branch-heterogeneous models of protein evolution
 that account for compositional variability have been developed, but are
 not yet in common use because of the large number of parameters required,
 leading to high computational costs and potential overparameterization.
 Here, we present a new branch-nonhomogeneous and nonstationary model of
 protein evolution that captures more accurately the high complexity of
 sequence evolution. This model, henceforth called Correspondence and
 likelihood analysis (COaLA), makes use of a correspondence analysis to
 reduce the number of parameters to be optimized through maximum
 likelihood, focusing on most of the compositional variation observed in
 the data. The model was thoroughly tested on both simulated and biological
 data sets to show its high performance in terms of data fitting and CPU
 time. COaLA efficiently estimates ancestral amino acid frequencies and
 sequences, making it relevant for studies aiming at reconstructing and
 resurrecting ancestral amino acid sequences. Finally, we applied COaLA on
 a concatenate of universal amino acid sequences to confirm previous
 results obtained with a nonhomogeneous Bayesian model regarding the early
 pattern of adaptation to optimal growth temperature, supporting the
 mesophilic nature of the Last Universal Common Ancestor.
description: Groussin_COaLA_SuppMatSupplementary Material of "A Branch-Heterogeneous Model of Protein Evolution for Efficient Inference of Ancestral"
DOI: 10.5061/dryad.km2s0
title: Data from: State transitions: a major mortality risk for seasonal species

description: Ageing results from the accumulation of multifactorial damage over time.
 However, the temporal distribution of this damage remains unknown. In
 seasonal species, transitions between seasons are critical periods of
 massive physiological remodelling. We hypothesised that these recurrent
 peaks of physiological remodelling are costly in terms of survival. We
 tested whether captive small primates exposed to an experimentally
 increased frequency of seasonal transitions die sooner than individuals
 living under natural seasonality. The results show that experiencing one
 additional season per year increases the mortality hazard by a factor of 3
 to 4, whereas the expected number of seasons lived is only slightly
 impacted by the seasonal rhythm. These results demonstrate that
 physiological transitions between periods of high and low metabolic
 activity represent a major mortality risk for seasonal organisms, which
 has been ignored until now.
description: Individual information
 and mortality/survival data for control and accelerated captive grey mouse
 lemursData_Microcebus_murinus.csv contains individuals’ characteristics and the dates each individual enters and exits each season, from birth to death or censoring time, collected on captive grey mouse lemurs living under a control versus accelerated seasonal rhythm.Mortality_individual_information_data_Microcebus_murinus.csvFemale_Reproduction_data_Microcebus murinusFemales_Reproduction.csv contains the dates each female gave birth and the number of offspring weaned after each birth.
DOI: 10.5061/dryad.f8c4f
title: Data from: Combining niche-shift and population genetic analyses predicts rapid phenotypic evolution during invasion

description: Rapid evolution of non-native species can facilitate invasion success, but
 recent reviews indicate that such microevolution rarely yields expansion
 of the climatic niche in the introduced habitats. However, because some
 invasions originate from a geographically restricted portion of the native
 species range and its climatic niche, it is possible that the frequency,
 direction and magnitude of phenotypic evolution during invasion has been
 underestimated. We explored the utility of niche-shift analyses in the red
 seaweed Gracilaria vermiculophylla, which expanded from the northeastern
 coastline of Japan to North America, Europe and northwestern Africa within
 the last 100 years. A genetically-informed climatic niche shift analysis
 indicates that native source populations occur in colder and highly
 seasonal habitats, while most non-native populations typically occur in
 warmer, less seasonal habitats. This climatic niche expansion predicts
 that non-native populations evolved greater tolerance for elevated heat
 conditions relative to native source populations. We assayed 935
 field-collected and 325 common-garden thalli from 40 locations and as
 predicted, non-native populations had greater tolerance for
 ecologically-relevant extreme heat (40ºC) than did Japanese source
 populations. Non-native populations also had greater tolerance for cold
 and low-salinity stresses relative to source populations. The importance
 of local adaptation to warm temperatures during invasion was reinforced by
 evolution of parallel clines: populations from warmer, lower-latitude
 estuaries had greater heat tolerance than did populations from colder,
 higher-latitude estuaries in both Japan and eastern North America. We
 conclude that rapid evolution plays an important role in facilitating the
 invasion success of this and perhaps other non-native marine species.
 Genetically-informed ecological niche analyses readily generate clear
 predictions of phenotypic shifts during invasions, and may help to resolve
 debate over the frequency of niche conservatism versus rapid adaptation
 during invasion.
description: MicrosatPloidyDataTable of individuals with ploidy information Individual_ID Population ID with individual numbers. See Appendix A for more information Life.history Morphological identification of life-history state msatploidy Microsatellite-based identification of ploidy mlg.id the multilocus ID for each diploid per population pgen probability that the thallus was a unique multi-locus genotype psex probability that the thallus represents a separate sexual reproductive event (i.e. a separate genet)PhenotypeDataPhenotype dataset assay Assay type (40deg, minus20deg, salinity) ind.type field vs common garden ind individual ID trt levels within each assay type SBS standardized bleaching code (-2 to 2)
DOI: 10.5061/dryad.bn796qq
title: Data from: Archosauromorph extinction selectivity during the Triassic-Jurassic mass extinction

description: Many traits have been linked to extinction risk among modern vertebrates,
 including mode of life and body size. However, previous work has indicated
 there is little evidence that body size, or any other trait, was selective
 during past mass extinctions. Here, we investigate the impact of the
 Triassic–Jurassic mass extinction on early Archosauromorpha (basal
 dinosaurs, crocodylomorphs and their relatives) by focusing on body size
 and other life history traits. We built several new archosauromorph
 maximum‐likelihood supertrees, incorporating uncertainty in phylogenetic
 relationships. These supertrees were then employed as a framework to test
 whether extinction had a phylogenetic signal during the Triassic–Jurassic
 mass extinction, and whether species with certain traits were more or less
 likely to go extinct. We find evidence for phylogenetic signal in
 extinction, in that taxa were more likely to become extinct if a close
 relative also did. However, there is no correlation between extinction and
 body size, or any other tested trait. These conclusions add to previous
 findings that body size, and other traits, were not subject to selection
 during mass extinctions in closely‐related clades, although the
 phylogenetic signal in extinction indicates that selection may have acted
 on traits not investigated here.
description: AppendicesA. Summary table of archosauromorphs, median femur lengths and ages B. KH and SH test outputs C. Phylo-D outputs for supertrees C, D and E D. PGLS outputs for supertrees C, D and EArchosaur femur dataAll collected femur data with notesArchosaur mode of life dataTable of modes of life for each archosauromorph speciesOcc_dataOccurrence data in an R-suitable formatOcc_data_femursOcc_data with femur length column includedAndresNexus file suitable for IQTREECabreiraNexus file suitable for IQTREEEzcurraNexus file suitable for IQTREEKammererNexus file suitable for IQTREENesbittNexus file suitable for IQTREEParkerNexus file suitable for IQTREE1_Equal_MBL_scalingR code for Equal and MBL scaling2a_Excel_to_timelistR code for converting occurrence data to a timelist object2b_cal3_ratesR code for calculating cal3 input rates2c_cal3_scalingR code for cal3 scaling3_Hedman_scalingR code for Hedman scaling4_pgls_phylo_d_codeR code for running Phylo-D and PGLS tests2015 Cohen datesText file of dates used for time periodsML taxa-matched treesIQTREE output phylogenies with synonymous taxa matched, suitable for R analysisProposed supertreesEight proposed supertree topologies, suitable for R analysisreadmeSummary of appendices and supplementary data contents