cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p0v93
title: Data from: The tempo of trait divergence in geographic isolation: avian speciation across the Marañon valley of Peru

description: Geographic isolation is considered essential to most speciation events,
 but our understanding of what controls the pace and degree of phenotypic
 divergence among allopatric populations remains poor. Why do some taxa
 exhibit phenotypic differentiation across barriers to dispersal, whereas
 others do not? To test factors controlling phenotypic divergence in
 allopatry, we employed a comparative phylogeographic approach consisting
 of replicates of ecologically similar Andean bird species isolated across
 a major biogeographic barrier, the Marañon valley of Peru. Our study
 design leverages variation among co-distributed taxa in their degree of
 plumage, morphometric and vocal differentiation across the Marañon to
 examine the tempo of phenotypic evolution. We found that substantial
 plumage differences between populations required roughly two million years
 to evolve. In contrast, morphometric trait evolution showed greater
 idiosyncrasy and stasis. Our results demonstrate that despite a large
 degree of idiosyncrasy in the relationship between genetic and phenotypic
 divergence across taxa and environments, comparative studies within
 regions may reveal predictability in the pace of phenotypic divergence.
 Our results also suggest that social selection is important for driving
 differentiation of populations found in similar environments.
description: Morphometric
 measurementsMorphometric
 measurements taken from museum round skins with a digital calipers.
 Specimen locality information can be found in Supplementary Appendix 2 of
 the manuscript.Morph.adults.csvPlumage spectraPlumage reflectance spectra from 10 patches. The first column is the wavelength, and each additional column represents the mean of three readings for each patch. Specimen locality information can be found in Supplementary Appendix 2 of the manuscript.Plumage_spectra.zipVocal_Frequency_SelectionsVocal frequency tables. Each table was produced by drawing selection boxes around songs in Raven Pro v1.4 (Cornell Lab of Ornithology).
DOI: 10.5061/dryad.nn153
title: Data from: Resolving phylogenetic relationships of the recently radiated carnivorous plant genus Sarracenia using target enrichment

description: The North American carnivorous pitcher plant genus Sarracenia
 (Sarraceniaceae) is a relatively young clade (&lt;3 million years ago)
 displaying a wide range of morphological diversity in complex trapping
 structures. This recently radiated group is a promising system to examine
 the structural evolution and diversification of carnivorous plants;
 however, little is known regarding evolutionary relationships within the
 genus. Previous attempts at resolving the phylogeny have been
 unsuccessful, most likely due to few parsimony-informative sites
 compounded by incomplete lineage sorting. Here, we applied a target
 enrichment approach using multiple accessions to assess the relationships
 of Sarracenia species. This resulted in 199 nuclear genes from 75
 accessions covering the putative 8–11 species and 8 subspecies/varieties.
 In addition, we recovered 42 kb of plastome sequence from each accession
 to estimate a cpDNA-derived phylogeny. Unsurprisingly, the cpDNA had few
 parsimony-informative sites (0.5%) and provided little information on
 species relationships. In contrast, use of the targeted nuclear loci in
 concatenation and coalescent frameworks elucidated many relationships
 within Sarracenia even with high heterogeneity among gene trees. Results
 were largely consistent for both concatenation and coalescent approaches.
 The only major disagreement was with the placement of the purpurea
 complex. Moreover, results suggest an Appalachian massif biogeographic
 origin of the genus. Overall, this study highlights the utility of target
 enrichment using multiple accessions to resolve relationships in recently
 radiated taxa.
description: concatenation_RAxMLConcatenation tree for 75 accessions across Sarraceniaceaeconcatenation_SarraceniaConcatenation sequences of 75 accessions used for RAxML analysis in phylip formatChloroplast_Sarracenia42kb of chloroplast for 75 accessions of Sarraceniaceae in phylip format. Was analyzed in RAxML.chloroplast_RAxMLSarracenia chloroplast tree estimated using RAxML with 75 accessionsMPEST_199Sarracenia species tree estimated from 199 genes in MP-ESTMPEST_accessionAccession tree estimated using 199 genes in MP-ESTSarracenia_fasta_199Zip file containing the 199 genes in fasta formatgenetrees_nwkThe zip file contains all the bootstrap gene files. There are 199 files (one for each gene) with 500 bootstrapped gene trees within each file. These were all estimated from RAxML and used in MP-EST to estimate the species tree.
DOI: 10.5061/dryad.79d43
title: Data from: The extent and consequences of p-hacking in science

description: A focus on novel, confirmatory, and statistically significant results
 leads to substantial bias in the scientific literature. One type of bias,
 known as “p-hacking,” occurs when researchers collect or select data or
 statistical analyses until nonsignificant results become significant.
 Here, we use text-mining to demonstrate that p-hacking is widespread
 throughout science. We then illustrate how one can test for p-hacking when
 performing a meta-analysis and show that, while p-hacking is probably
 common, its effect seems to be weak relative to the real effect sizes
 being measured. This result suggests that p-hacking probably does not
 drastically alter scientific consensuses drawn from meta-analyses.
description: Data from: The extent
 and consequences of p-hacking in scienceThis zip file consists
 of three parts. 1. Data obtained from text-mining and associated analysis
 files. 2. Data obtained from previously published meta-analyses and
 associated analysis files. 3. Analysis files used to conduct meta-analyses
 of the data. Read me files are contained within this zip
 file.FILES_FOR_DRYAD.zip
DOI: 10.5061/dryad.jf7b3
title: Data from: Quantifying MCMC exploration of phylogenetic tree space

description: In order to gain an understanding of the effectiveness of phylogenetic
 Markov chain Monte Carlo (MCMC), it is important to understand how quickly
 the empirical distribution of the MCMC converges to the posterior
 distribution. In this paper we investigate this problem on phylogenetic
 tree topologies with a metric that is especially well suited to the task:
 the subtree prune-and-regraft (SPR) metric. This metric directly
 corresponds to the minimum number of MCMC rearrangements required to move
 between trees in common phylogenetic MCMC implementations. We develop a
 novel graph-based approach to analyze tree posteriors and find that the
 SPR metric is much more informative than simpler metrics that are
 unrelated to MCMC moves. In doing so we show conclusively that topological
 peaks do occur in Bayesian phylogenetic posteriors from real data sets as
 sampled with standard MCMC approaches, investigate the efficiency of
 Metropolis-coupled MCMC (MCMCMC) in traversing the valleys between peaks,
 and show that conditional clade distribution (CCD) can have systematic
 problems when there are multiple peaks.
description: Supplementary
 InformationMethods for computing
 access time statistics as well as supplementary tables and
 figures.sprmix_supp.pdf
DOI: 10.5061/dryad.0262m
title: Data from: Lilac and honeysuckle phenology data 1956-2014

description: The dataset is comprised of leafing and flowering data collected across
 the continental United States from 1956 to 2014 for purple common lilac
 (Syringa vulgaris), a cloned lilac cultivar (S. x chinensis 'Red
 Rothomagensis') and two cloned honeysuckle cultivars (Lonicera
 tatarica 'Arnold Red' and L. korolkowii 'Zabeli').
 Applications of this observational dataset range from detecting regional
 weather patterns to understanding the impacts of global climate change on
 the onset of spring at the national scale. While minor changes in methods
 have occurred over time, and some documentation is lacking, outlier
 analyses identified fewer than 3% of records as unusually early or late.
 Lilac and honeysuckle phenology data have proven robust in both model
 development and climatic research.
description: Lilac Honeysuckle
 1956-2014 leafing and flowering phenology v13The dataset is comprised
 of leafing and flowering data collected across the continental United
 States from 1956 to 2014 for purple common lilac (Syringa vulgaris), a
 cloned lilac cultivar (S. x chinensis ‘Red Rothomagensis’) and two cloned
 honeysuckle cultivars (Lonicera tartarica ‘Arnold Red’ and L. korolkowii
 ‘Zabeli’). Applications of this observational dataset range from detecting
 regional weather patterns to understanding the impacts of global climate
 change on the onset of spring at the national scale. While minor changes
 in methods have occurred over time, and some documentation is lacking,
 outlier analyses identified fewer than 3% of records as unusually early or
 late. Lilac and honeysuckle phenology data have proven robust in both
 model development and climatic research.
DOI: 10.15468/vvqsya
title: Museo de Ictiología de la Universidad Tecnológica Indoamérica (MZUTI)

description: The Zoology Museum of the Universidad Tecnológica Indoamérica (MZUTI) aims to promote research and conservation of biodiversity through the study of preserved specimens. It also seeks to facilitate the dissemination of biological knowledge within scientific, educational, and general public spheres.Currently, the ichthyological collection at MZUTI contains over 890 cataloged and systematized records. Of the total preserved specimens, 88% have been taxonomically identified to the species level, and 12% to the genus level.This resource shares all records of freshwater fish held in the MZUTI collection.El Museo de Zoología de la Universidad Tecnológica Indoamérica (MZUTI) tiene como objetivo principal fomentar la investigación y conservación de la biodiversidad mediante el estudio de especímenes preservados. Asimismo, busca promover y facilitar la difusión del conocimiento biológico en los ámbitos científico, educativo y para el público en general.Actualmente, la colección ictiológica del MZUTI cuenta con más de 890 registros catalogados y sistematizados. Del total de especímenes preservados, el 88% ha sido identificado taxonómicamente hasta el nivel de especie y el 12% hasta el nivel de género.Este recurso comparte todos los registros de peces de agua dulce resguardados en la colección del MZUTI.
DOI: 10.5061/dryad.928fj
title: Data from: A comprehensive analysis of teleost MHC class I sequences

description: Background: MHC class I (MHCI) molecules are the key presenters of
 peptides generated through the intracellular pathway to CD8-positive
 T-cells. In fish, MHCI genes were first identified in the early 1990′s,
 but we still know little about their functional relevance. The expansion
 and presumed sub-functionalization of cod MHCI and access to many
 published fish genome sequences provide us with the incentive to undertake
 a comprehensive study of deduced teleost fish MHCI molecules. Results: We
 expand the known MHCI lineages in teleosts to five with identification of
 a new lineage defined as P. The two lineages U and Z, which both include
 presumed peptide binding classical/typical molecules besides more derived
 molecules, are present in all teleosts analyzed. The U lineage displays
 two modes of evolution, most pronouncedly observed in classical-type alpha
 1 domains; cod and stickleback have expanded on one of at least eight
 ancient alpha 1 domain lineages as opposed to many other teleosts that
 preserved a number of these ancient lineages. The Z lineage comes in a
 typical format present in all analyzed ray-finned fish species as well as
 lungfish. The typical Z format displays an unprecedented conservation of
 almost all 37 residues predicted to make up the peptide binding groove.
 However, also co-existing atypical Z sub-lineage molecules, which lost the
 presumed peptide binding motif, are found in some fish like carps and
 cavefish. The remaining three lineages, L, S and P, are not predicted to
 bind peptides and are lost in some species. Conclusions: Much like
 tetrapods, teleosts have polymorphic classical peptide binding MHCI
 molecules, a number of classical-similar non-classical MHCI molecules, and
 some members of more diverged MHCI lineages. Different from tetrapods,
 however, is that in some teleosts the classical MHCI polymorphism
 incorporates multiple ancient MHCI domain lineages. Also different from
 tetrapods is that teleosts have typical Z molecules, in which the residues
 that presumably form the peptide binding groove have been almost
 completely conserved for over 400 million years. The reasons for the
 uniquely teleost evolution modes of peptide binding MHCI molecules remain
 an enigma.
description: Genomic scaffold
 sequences with MHC class I sequences from Atlantic
 salmonSequences are from a
 final assembly using Sanger (~4X) and Illumina (~202X) data assembled with
 MaSuRCA {Zimin, 2013}ssal_MHCI_scaffold.fasta
DOI: 10.5061/dryad.th09b
title: Data from: Decrease in ribosomal RNA in Candida albicans induced by serum exposure

description: Candida albicans is an important polymorphic human pathogen. It can switch
 from a unicellular yeast form to germinating hypha, which may play a role
 in making it the successful pathogen it is. This hyphal transformation can
 be triggered by various extracellular stimuli, the most potent one being
 serum from any source. We have previously reported that Candida albicans
 transiently polyadenylates portions of both the large and small subunits
 of ribosomal RNA, shortly after serum exposure. Northern blots at the same
 time suggested that serum might induce a decrease in total ribosomal RNA.
 We have carried out a number of experiments to carefully assess this
 possibility and now report that serum significantly reduces ribosomal RNA
 in Candida albicans. Fluorometric measurements, Northern blotting and
 quantitative RT-PCR, have all confirmed this decrease. Timed experiments
 show that serum induces this decrease rapidly, as it was seen in as early
 as five minutes. Cell mass is not decreased as total cellular protein
 content remains the same and metabolic activity does not appear to slow,
 as assessed by XTT assay, and by the observation that cells form hyphal
 structures robustly. Another hyphal inducer, N-acetylglucosamine, also
 caused RNA decrease, but to a lesser extent. We also observed it in
 non-germinating yeast, such as Candida glabrata. The reason for this
 decrease is unknown and overall our data suggests that decrease in rRNA
 does not play a causal role in hyphal transformation. Rapid and
 significant decrease in a molecule so central to the yeast’s biology is of
 some importance, and further studies, such as its effect on protein
 metabolism, will be required to better understand its purpose.
description: S1_DatasetRNA and Protein raw dataS2_FigureYPD 39oC t=1hr
DOI: 10.5061/dryad.hv431
title: Data from: Using parentage analysis to estimate rates of straying and homing in Chinook salmon (Oncorhynchus tshawytscha)

description: We used parentage analysis based on microsatellite genotypes to measure
 rates of homing and straying of Chinook salmon (Oncorhynchus tshawytscha)
 among five major spawning tributaries within the Wenatchee River,
 Washington. Based on analysis of 2248 natural-origin and 11594
 hatchery-origin fish, we estimated that the rate of homing to natal
 tributaries by natural-origin fish ranged from 0% to 99% depending on the
 tributary. Hatchery-origin fish released in one of the five tributaries
 homed to that tributary at a far lower rate than the natural-origin fish
 (71% compared to 96%). For hatchery-released fish, stray rates based on
 parentage analysis were consistent with rates estimated using physical tag
 recoveries. Stray rates among major spawning tributaries were generally
 higher than stray rates of tagged fish to areas outside of the Wenatchee
 River watershed. Within the Wenatchee watershed, rates of straying by
 natural-origin fish were significantly affected by spawning tributary and
 by parental origin: progeny of naturally spawning hatchery-produced fish
 strayed at significantly higher rates than progeny whose parents were
 themselves of natural origin. Notably, none of the 170 offspring that were
 products of mating by two natural-origin fish strayed from their natal
 tributary. Indirect estimates of gene flow based on FST statistics were
 correlated with but higher than the estimates from the parentage data.
 Tributary-specific estimates of effective population size were also
 correlated with the number of spawners in each tributary.
description: Spawning location and
 phenotypic data for parents and offspringwen04-06adultparentagewithphenosJun112014.csvWenatchee River Chinook salmon genetic and phenotypic datawen04-10allspringspawnersJan2014_withTumData.csv
DOI: 10.5061/dryad.3t082
title: Data from: Evolutionary change in testes tissue competition among experimental populations of house mice

description: Theory assumes that postcopulatory sexual selection favours increased
 investment in testes size because greater numbers of sperm within the
 ejaculate increase the chance of success in sperm competition, and larger
 testes are able to produce more sperm. However, changes in the
 organization of the testes tissue may also affect sperm production rates.
 Indeed, recent comparative analyses suggest that sperm competition selects
 for greater proportions of sperm-producing tissue within the testes. Here,
 we explicitly test this hypothesis using the powerful technique of
 experimental evolution. We allowed house mice (Mus domesticus) to evolve
 via monogamy or polygamy in six replicate populations across 24
 generations. We then used histology and image analysis to quantify the
 proportion of sperm-producing tissue (seminiferous tubules) within the
 testes of males. Our results show that males that had evolved with sperm
 competition had testes with a higher proportion of seminiferous tubules
 compared with males that had evolved under monogamy. Previously, it had
 been shown that males from the polygamous populations produced greater
 numbers of sperm in the absence of changes in testes size. We thus provide
 evidence that sperm competition selects for an increase in the density of
 sperm-producing tissue, and consequently increased testicular efficiency.
description: Testis tissue
 data
DOI: 10.5061/dryad.f6c56
title: Data from: Adjustments in habitat selection to changing availability induce fitness costs for a threatened ungulate

description: 1. Functional responses in habitat selection occur when individuals adjust
 their selection of habitat features as a function of the availability of
 those features. Functional responses in habitat selection are generally
 assumed to be fitness-rewarding tactics and are used to guide conservation
 actions. Fitness consequences of functional responses, however, have
 rarely been evaluated. 2. Eighty-three caribou were followed with GPS
 collars to establish the link between functional responses in habitat
 selection and adult female survival, a strong fitness correlate for
 caribou. We measured how caribou avoidance of mixed/deciduous stands and
 6–20-year-old clearcuts varied with the proportion of 6–20-year-old
 clearcuts within their 100% minimal convex polygon (MCP), and if these
 functional responses were linked to survival. Mixed/deciduous stands and
 6–20-year-old clearcuts are risky for caribou because they are selected by
 moose, thereby attracting wolves and increasing predation risk for
 caribou. 3. Caribou avoided mixed/deciduous stands, especially when
 6–20-year-old clearcuts comprised a large proportion of their MCP, but
 this functional response did not differ between caribou that died and
 those that survived. When the proportion of 6–20-year-old clearcuts in the
 MCP was low, caribou generally had low odds of occurring near
 6–20-year-old clearcuts. However, when the proportion of clearcuts in the
 MCP was relatively high, caribou that strongly increased their odds of
 being near 6–20-year-old clearcuts were generally those that died. 4.
 Synthesis and applications. Assessing the fitness consequences of how
 animals respond to habitat disturbances is central to wildlife
 conservation. We demonstrate that distinct functional responses in habitat
 selection involve different mortality risks and that population dynamics
 should depend on the frequency of the different tactics observed within
 populations. Individuals that persistently select riskier areas should be
 important drivers of population decline. Caribou mortality could be
 reduced by decreasing the appeal of 6–20-year-old clearcuts for moose by
 removing deciduous vegetation through cleaning, which should reduce the
 selection of wolves for these stands. Removing deciduous vegetation should
 be especially effective in areas where those clearcuts comprise a large
 proportion of the landscape, because this is where a subset of the caribou
 population experiences high mortality rates by selecting 6–20-year-old
 clearcuts.
description: Data_Losier_et_al_JAPPL
DOI: 10.5061/dryad.7881
title: Data from: Genome-scale phylogenetics: inferring the plant tree of life from 18,896 gene trees

description: Phylogenetic analyses using genome-scale data sets must confront
 incongruence among gene trees, which in plants is exacerbated by frequent
 gene duplications and losses. Gene tree parsimony is a phylogenetic
 optimization criterion in which a species tree is selected that minimizes
 the number of gene duplications induced among a set of gene trees. The run
 time performance of previous implementations has limited its use on
 large-scale data sets. We used new software that incorporates recent
 algorithmic advances to examine the performance of gene tree parsimony on
 a plant data set consisting of 18,896 gene trees containing 510,922
 protein sequences from 136 plant taxa (giving a combined alignment length
 of &gt;2.9 million characters). The relationships inferred from the
 gene tree parsimony analysis were largely consistent with previous
 large-scale studies of backbone plant phylogeny and resolved some
 controversial nodes. The placement of taxa that were present in few gene
 trees generally varied the most among gene tree parsimony bootstrap
 replicates. Excluding these taxa either before or after the gene tree
 parsimony analysis revealed high levels of phylogenetic support across
 plants. The analyses supported magnoliids sister to a eudicot + monocot
 clade, and did not support the eurosid I and II clades. This study
 presents a nuclear genomic perspective on the broad scale phylogenic
 relationships among plants, and it demonstrates that nuclear genes with a
 history of duplication and loss can be phylogenetically informative for
 resolving the plant tree of life.
description: UnigeneAlignments