cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sc1156g
title: Data from: Larval density mediates knockdown resistance to pyrethroid insecticides in adult Aedes aegypti

description: Background: Understanding mechanisms driving insecticide resistance in
 vector populations remains a public health priority. To date, most
 research has focused on the genetic mechanisms underpinning resistance,
 yet it is unclear what role environmental drivers may play in shaping
 phenotypic expression. One of the key environmental drivers of Aedes
 aegypti mosquito population dynamics is resource-driven intraspecific
 competition at the larval stage. We experimentally investigated the role
 of density-dependent larval competition in mediating resistance evolution
 in Ae. aegypti, using knockdown resistance (kdr) as a marker of genotypic
 resistance and CDC bottle bioassays to determine phenotype. We reared
 first-instar larvae from susceptible and pyrethroid-resistant
 field-derived populations of Ae. aegypti at high and low density and
 measured the resulting phenotypic resistance and population kdr allele
 frequencies. Results: At low density, only 48.2% of the resistant
 population was knocked down, yet at high density, the population was no
 longer phenotypically resistant - 93% were knocked down when exposed to
 permethrin, which is considered susceptible according to WHO guidelines.
 Furthermore, the frequency of the C1534 kdr allele in the resistant
 population at high density decreased from 0.98 ± 0.04 to 0.69 ± 0.04 in
 only one generation of selection. Conclusions: Our results indicate that
 larval conditions, specifically density, can impact both phenotype and
 genotype of pyrethroid-resistant populations. Furthermore, phenotypic
 susceptibility to pyrethroids may be re-established in a resistant
 population through a gene x environment interaction, a finding that can
 lead to the development of novel resistance management strategies that
 capitalize on density-induced costs.
description: Bottle bioassay Data -
 CDCThese are data from the
 CDC bioassays to assess phenotypic resistance. Each sheet is a different
 population. AS is the resistant population, FAS is the intermediate
 (mixture) population, and F is the susceptible population. 50 and 500 are
 the larval densities.BBA_Larval_exps.xlsxkdr genotypesThese are the kdr genotypes for ~30 individuals per population/treatment/replicate combination. AS = resistant population; F= susceptible; FAS=mixture. Cys is the genotype for F1534C and Ile is the genotype for V1016I.Larval_exps_genotypes.xlsxDevelopment timeThese are data on development time from 1st instar to adult. AS= resistant population, F=susceptible, and FAS= mixture. 50 and 500 represent the larval densities.Development_time.xlsx
DOI: 10.5061/dryad.d866h
title: Data from: Isotopic niches support the resource breadth hypothesis

description: Because a broad spectrum of resource use allows species to persist in a
 wide range of habitat types, and thus permits them to occupy large
 geographical areas, and because broadly distributed species have access to
 more diverse resource bases, the resource breadth hypothesis posits that
 the diversity of resources used by organisms should be positively related
 with the extent of their geographic ranges. We investigated isotopic niche
 width in a small radiation of South American birds in the genus Cinclodes.
 We analysed feathers of 12 species of Cinclodes to test the isotopic
 version of the resource breadth hypothesis and to examine the correlation
 between isotopic niche breadth and morphology. We found a positive
 correlation between the widths of hydrogen and oxygen isotopic niches
 (which estimate breadth of elevational range) and widths of the carbon and
 nitrogen isotopic niches (which estimates the diversity of resources
 consumed, and hence of habitats used). We also found a positive
 correlation between broad isotopic niches and wing morphology. Our study
 not only supports the resource breadth hypothesis but it also highlights
 the usefulness of stable isotope analyses as tools in the exploration of
 ecological niches. It is an example of a macroecological application of
 stable isotopes. It also illustrates the importance of scientific
 collections in ecological studies.
description: Rader et al.
 Supplemental DataThis data file contains
 morphological and stable isotope data from 13 species of Cinclodes
 ovenbirds, along with museum collections metadata for each
 specimen.SupplementalDataS2.csv
DOI: 10.5061/dryad.24s5j
title: Data from: Admixture mapping in a hybrid zone reveals loci associated with avian feather coloration

description: Identifying the genetic bases for color patterns has provided important
 insights into the control and expression of pigmentation and how these
 characteristics influence fitness. However, much more is known about the
 genetic bases for traits based on melanin pigments than for traits based
 on another major class of pigments, carotenoids. Here we use natural
 admixture in a hybrid zone between Audubon’s and myrtle warblers
 (Setophaga coronata auduboni / S. c. coronata) to identify genomic regions
 associated with both types of pigmentation. Warblers are known for rapid
 speciation and dramatic differences in plumage. For each of five plumage
 coloration traits, we found highly significant associations with multiple
 SNPs across the genome and these were clustered in discrete regions.
 Regions near significantly associated SNPs were enriched for genes
 associated with keratin filaments, fibrils that makeup feathers. A
 carotenoid-based trait that differs between the taxa—throat color—had more
 than a dozen genomic regions of association. One cluster of SNPs for this
 trait overlaps the Scavenger Receptor Class F Member 2 (SCARF2) gene.
 Other scavenger receptors are presumed to be expressed at target tissues
 and involved in the selective movement of carotenoids into the target
 cells, making SCARF2 a plausible new candidate for carotenoid processing.
 In addition, two melanin-based plumage traits—colors of the eye line and
 eye spot—show very strong associations with a single genomic region
 mapping to chromosome 20 in the zebra finch. These findings indicate that
 only a subset of the genomic regions differentiated between these two
 warblers are associated with the plumage differences between them and
 demonstrate the utility of reduced-representation genomic scans in hybrid
 zones.
description: VCF file for SNPs used
 in GEMMA analysisVariant Call Format file
 (GZipped) for individuals used for genotype-phenotype associations. Sample
 ID information can be found in the electronic supplementary information on
 the publisher's website.plumage_yrwa.snp.variants.only.filter.removed.minGQ20.max.missing.2.maf.01.vcf.recode.vcf.gzPlumage association dataPhenotype data used for the GEMMA analysis. Columns indicate: Record#, a unique identifier, Site, with nearest city / notable location, whether this site was located in the hybrid zone or in allopatry (myrtle versus Audubon's), Lat, Long, and five plumage characters: throat, spot, line, wing, and auricular.Plumage_association_data.xlsx
DOI: 10.5061/dryad.m5105
title: Data from: Genetic inference of epiphytic orchid colonization; it may only take one

description: Colonization of vacant habitat is a fundamental ecological process that
 affects the ability of species to persist and undergo range modifications
 in continually shifting landscapes. Thus, understanding factors that
 affect and limit colonization has important ecological and conservation
 implications. Epiphytic orchids are increasingly threatened by various
 factors, including anthropogenic habitat disturbance. As cleared areas
 (e.g. pastures) are recolonized by suitable host trees, the establishment
 and genetic composition of epiphytic orchid populations are likely a
 function of their colonization patterns. We used genetic analyses to infer
 the prevailing colonization pattern of the epiphytic orchid, Brassavola
 nodosa. Samples from three populations (i.e. individuals within a tree)
 from each of five pastures in the dry forest of Costa Rica were genotyped
 with neutral nuclear and chloroplast markers. Spatial autocorrelation and
 hierarchical genetic structure analyses were used to assess the
 relatedness of individuals within populations, among populations within
 pastures and among populations in different pastures. The results showed
 significant relatedness within populations (mean r = 0.166) and
 significant but lower relatedness among populations within a pasture (mean
 r = 0.058). Our data suggest that colonization of available habitats is by
 few individuals with subsequent population expansion resulting from in
 situ reproduction, and that individuals within a tree are not a random
 sample of the regional seed pool. Furthermore, populations within a
 pasture were likely colonized by seeds produced by founders of a
 neighbouring population within that pasture. These results have important
 ramifications for understanding conservation measures needed for this
 species and other epiphytic orchids.
description: Brassavola nodosa -
 Locations of populationsGPS data collected in
 the field.1. Brassavola - Locations of
 populations.xlsBrassavola nodosa -
 Allozyme data - PVR & HEF pops & reference LIB
 popSamples were collected
 in the field and analyzed genetically in the lab at the University of
 Georgia.2.
 Brassavola - Allozyme data - PVR & HEF pops & reference LIB
 pop.xlsBrassavola nodosa -
 Chloroplast haplotype sequence data - PVR & HEF popsSamples were collected
 in the field and analyzed genetically in the lab at the University of
 Georgia.3.
 Brassavola - Chloroplast haplotype sequence data - PVR & HEF
 pops.xlsx
DOI: 10.5061/dryad.hb4jd
title: Data from: A Devonian predatory fish provides insights into the early evolution of modern sarcopterygians

description: Crown or modern sarcopterygians (coelacanths, lungfishes, and tetrapods)
 differ substantially from stem sarcopterygians, such as Guiyu and
 Psarolepis, and a lack of transitional fossil taxa limits our
 understanding of the origin of the crown group. The Onychodontiformes, an
 enigmatic Devonian predatory fish group, seems to have characteristics of
 both stem and crown sarcopterygians but is difficult to place because of
 insufficient anatomical information. We describe the new skull material of
 Qingmenodus, a Pragian (~409-million-year-old) onychodont from China,
 using high-resolution computed tomography to image internal structures of
 the braincase. In addition to its remarkable similarities with stem
 sarcopterygians in the ethmosphenoid portion, Qingmenodus exhibits
 coelacanth-like neurocranial features in the otic region. A phylogenetic
 analysis based on a revised data set unambiguously assigns onychodonts to
 crown sarcopterygians as stem coelacanths. Qingmenodus thus bridges the
 morphological gap between stem sarcopterygians and coelacanths and helps
 to illuminate the early evolution and diversification of crown
 sarcopterygians.
description: Lu_et_al_datamatrixData matrix of Qingmenodus
DOI: 10.5061/dryad.ps816
title: Data from: Sexual selection and diversification: reexamining the correlation between dichromatism and speciation rate in birds

description: Theory predicts that sexual selection can serve as an important driver of
 speciation, but phylogenetic comparative analyses have failed to
 demonstrate a consistent effect of sexual selection on species richness at
 macroevolutionary scales. Sexual dichromatism in birds is an example of a
 phenotypic trait that is hypothesized to reflect the intensity of sexual
 selection, yet previous studies have reached ambiguous conclusions
 regarding its role in promoting species diversification. Here, we revisit
 this problem by pairing published spectrophotometer estimates of plumage
 dichromatism in the bird-visible range with a newly developed method for
 modeling speciation rates on phylogenetic trees that explicitly accounts
 for diversification rate variation through time and among clades. We find
 little evidence linking dichromatism to speciation across birds, using
 several measures of dichromatism and macroevolutionary diversification.
 These results suggest that sexual dichromatism plays a limited role in
 determining speciation rates at macroevolutionary scales in birds.
description: the checklist of family
 cladesList of species and
 their assigned family clades included in the family-level
 analysisDyrad_family_clade.txtBAMM parameter settingcontaining the basic parameter settings for running BAMMcontrol.txt
DOI: 10.5061/dryad.9898r
title: Data from: Programmed life span in the context of evolvability

description: Population turnover is necessary for progressive evolution. In the context
 of a niche with fixed carrying capacity, aging contributes to the rate of
 population turnover. Theoretically, a population in which death is
 programmed on a fixed schedule can evolve more rapidly than one in which
 population turnover is left to a random death rate. Could aging evolve on
 this basis? Quantitative realization of this idea is problematic, since
 the short-term individual fitness cost is likely to eliminate any
 hypothetical gene for programmed death before the long-term benefit can be
 realized. In 2011, one of us proposed the first quantitative model based
 on this mechanism that robustly evolves a finite, programmed life span.
 That model was based on a viscous population in a rapidly changing
 environment. Here, we strip this model to its essence and eliminate the
 assumption of environmental change. We conclude that there is no obvious
 way in which this model is unrealistic, and that it may indeed capture an
 important principle of nature’s workings. We suggest aging may be
 understood within the context of the emerging science of evolvability.
description: Programmed_LS_All-figuresExcel file with data from all figuresdosstuffMinSenMinSenDataMinSenGMinSenGraphics
DOI: 10.5061/dryad.qs1k6
title: Data from: The present and future effects of land use on ecological assemblages in tropical grasslands and savannas in Africa

description: The world is currently experiencing a period of rapid, human-driven
 biodiversity loss. Over the past decade, numerous metrics for biodiversity
 have been used to create indicators to track change in biodiversity.
 However, our ability to predict future changes has been limited. In this
 study, we use two very different models to predict the status and possible
 futures for the composition and diversity of ecological assemblages in
 African tropical grasslands and savannas under land-use change. We show
 that ecological assemblages are affected more by land use in African
 grasslands and savannas than in other biomes. We estimate that average
 losses of assemblage composition and diversity are already between 9.7 and
 42.0%, depending on the model and measure used. If current socio-economic
 trajectories continue (‘business-as-usual’), the likely associated
 land-use changes are predicted to lead to a further 5.6–12.3% loss of
 assemblage composition and diversity. In contrast, a scenario that assumes
 more efficient use of agricultural areas (thus requiring a smaller total
 area) could be associated with a partial reversal ‒ of as much as 3.2% ‒
 of past losses. While the agriculture that causes the majority of land-use
 change is an important source of economic growth, projections of the
 effects of land use on ecological assemblages can allow for more informed
 decisions.
description: Site Data for
 statistical biodiversity modelsSiteData.tar.gz
DOI: 10.5061/dryad.mr16q
title: Data from: Crossing the (Wallace) line: local abundance and distribution of mammals across biogeographic barriers

description: Past and ongoing vertebrate introductions threaten to rearrange ecological
 communities in the Indo-Malay Archipelago, one of Earth's most
 biodiverse regions. But the consequences of these translocations are
 difficult to predict. We compared local abundance and distributions in
 four tropical mammal lineages that have crossed from Asia to Wallacea or
 New Guinea. The local abundance of macaques (Macaca spp.), which naturally
 crossed Wallace's Line, was higher in Sulawesi (east of the line;
 mean = 3.7 individuals per camera station, 95% CI = 2.2: 5.1) than in
 Borneo (west of the line; mean = 1.1, CI = 0.8: 1.4), but the local
 abundance of Malay civets (Viverra tangalunga), Rusa deer, and Sus pigs
 was similar in their native ranges and where they had been introduced by
 humans east of Wallace's Line. Proximity to rivers increased Malay
 Civet local abundance and decreased the local abundance of pigs in parts
 of their introduced ranges (Maluku and New Guinea, respectively), while
 having no effect on local abundance in their native ranges (Borneo) or
 other areas where they have been introduced (Sulawesi). That local
 abundance was higher east of Wallace's Line in just one of four
 mammal lineages is consistent with findings from plant invasions, where
 most species have similar abundance in their native and introduced ranges.
 However, species’ ecology may change as they enter new communities, for
 example, their patterns of abundance at local scales. This could make it
 difficult to predict community structure in the face of ongoing species
 introductions.
description: civet_widecivet detection datadeer_widedeer detection datamacaque_wideMacaque detection datapig_widepig detection datasampcovs_camhours_wideSampling covariate - camera hourssite_covsSite covariates
DOI: 10.5061/dryad.53t31
title: Data from: Exams disadvantage women in introductory biology

description: The gender gap in STEM fields has prompted a great deal of discussion, but
 what factors underlie performance deficits remain poorly understood. We
 show that female students underperformed on exams compared to their male
 counterparts across ten large introductory biology course sections in fall
 2016 (N &gt; 1500 students). Females also reported higher levels of
 test anxiety and course-relevant science interest. Results from
 mediation analyses revealed an intriguing pattern: for female students
 only, and regardless of their academic standing, test anxiety negatively
 impacted exam performance, while interest in the course-specific science
 topics increased exam performance. Thus, instructors seeking equitable
 classrooms can aim to decrease test anxiety and increase student interest
 in science course content. We provide strategies for mitigating test
 anxiety and suggestions for alignment of course content with student
 interest, with the hope of successfully reimagining the STEM
 pathway as one that is equally accessible to all.
description: Data for 'Exams
 Disadvantage Women in Introductory Biology'Data on fall 2016
 students across large intro biology classes at the University of
 Minnesota, along with Motivated Strategies for Learning Questionnaire
 (MSLQ) survey data on a subset of those students.PLoSOneData_ExamsDisWomen.csv
DOI: 10.5061/dryad.561
title: Data from: Phylogenetic relationships of Agaric fungi based on nuclear large subunit ribosomal DNA sequences

description: Phylogenetic relationships of mushrooms and their relatives within the
 order Agaricales were addressed using nuclear large subunit ribosomal DNA
 sequences. Approximately 900 bases of the 5' end of the
 nucleus-encoded large subunit RNA gene (nLSU-rDNA) were sequenced for 154
 selected taxa representing most families within the Agaricales. Several
 phylogenetic methods were used, including weighted and equally weighted
 parsimony (MP), maximum likelihood (ML), and distance methods (NJ). The
 starting tree for branch swapping in the ML analyses was the tree with the
 highest ML score among previously produced MP and NJ trees. A high degree
 of consensus was observed between phylogenetic estimates obtained through
 MP and ML. NJ trees differed according to the distance model that was
 used, however, all NJ trees still supported most of the same terminal
 groupings as MP and ML trees. NJ trees were always significantly
 suboptimal when evaluated against the best MP and ML trees, using both
 parsimony and likelihood tests. Our analyses suggest that weighted
 parsimony and ML provide the best estimates of Agaricales phylogeny.
 Similar support was observed between bootstrapping and jackknifing methods
 for evaluation of tree robustness. Phylogenetic analyses revealed many
 groups of agaricoid fungi that are supported by moderate to high bootstrap
 or jackknife levels or are consistent with morphology-based classification
 schemes. Analyzes also support separate placement of the boletes and
 russules, which are basal to the main core group of gilled mushrooms (the
 Agaricineae of Singer). Examples of monophyletic groups include the
 families Amanitaceae, Coprinaceae (excluding Coprinus comatus and
 subfamily Panaeolideae), Agaricaceae (excluding the Cystodermateae), and
 Strophariaceae pro parte (Stropharia, Pholiota, and Hypholoma); the
 mycorrhizal species of Tricholoma (including Leucopaxillus, also
 mycorrhizal); Mycena and Resinomycena; Termitomyces, Podabrella, and
 Lyophyllum; and Pleurotus with Hohenbuehelia. Several nonmonophyletic
 groups revealed by these data include the families Tricholomataceae,
 Cortinariaceae, and Hygrophoraceae and the genera Clitocybe, Omphalina,
 and Marasmius. This study provides a framework for future systematics
 studies in the Agaricales and suggestions for analyzing large molecular
 data sets.
description: Moncalvo et al Data
 Setmoncalvo.nexus
DOI: 10.5061/dryad.68ff1
title: Data from: The expression of established cognitive brain states stabilizes with working memory development

description: We present results from a longitudinal study conducted over 10 years in a
 sample of 126 8-33 year olds demonstrating that adolescent development of
 working memory is supported by decreased variability in the amplitude of
 expression of whole brain states of task-related activity. fMRI analyses
 reveal that putative gain signals affecting maintenance and retrieval
 aspects of working memory processing stabilize during adolescence, while
 those affecting sensorimotor processes do not. We show that trial-to-trial
 variability in the reaction time and accuracy of eye-movements during a
 memory guided saccade task are related to fluctuations in the amplitude of
 expression of task-related brain states, or brain state variability, and
 also provide evidence that individual developmental trajectories of
 reaction time variability are related to individual trajectories of brain
 state variability. These observations demonstrate that underlying the
 maturation of cognition through adolescence is the stabilization of
 widespread gain signals affecting already available cognitive processes.
description: fMRI Task Timing
 InformationThis XLS file contains
 the event time information for the 3 runs of the memory-guided saccade
 task. See the Information worksheet for more.fMRI
 Timing.xlsxfMRI Raw Data (part 1 of
 4)anon_archive_01.tarFMRI_README.txtfMRI Raw Data (part 2 of 4)anon_archive_02.tarFMRI_README.txtfMRI Raw Data (part 3 of 4)anon_archive_03.tarFMRI_README.txtfMRI Raw Data (part 4 of 4)anon_archive_04.tarFMRI_README.txtAnonymized Eye DataThis compressed file contains the raw eye-movement data recorded in the fMRI scanner. Data from each session is provided in the native eye-tracker format (ASL) as well as a standard ASCII text file. The uppermost directories refer to individual subjects with a 5 digit code. Within each subject directory is one or more sub directories corresponding to different sessions that subject participated in. Theses directories are labeled with a randomized alphanumeric code which corresponds to the date that the data was collected. The age of a subject at each session can be determined by examining the Subject Information XLS file and matching up the Subject ID and the Code. Within each session director are three .EYD (ASL format) files and .TXT files (ASCII). Each session consisted of three fMRI/behavioral task runs,AnonEyeData.zipEyeMovementREADME.txtSubject InformationAn XLS file containg basic information used to determine a subject's age at each session.