cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.91v3n
title: Data from: Genetic variation and clonal diversity in introduced populations of Mimulus guttatus assessed by genotyping at 62 single nucleotide polymorphism loci

description: Background: Single nucleotide polymorphisms (SNPs) are increasingly being
 used to study non-native populations. SNPs are relatively information poor
 on a per locus basis, but allow genotyping more loci than others markers
 (e.g., microsatellites) and have the advantage of consistent allele calls
 between studies. Aims: We investigated the utility of a newly developed
 set of SNP markers, suitable for high throughput genotyping to
 characterise genotypic variation and population structure in non-native
 populations of the facultative clonal herb Mimulus guttatus in the United
 Kingdom (UK). Methods: We analysed 62 SNP markers and using a high
 throughput platform genotyped 383 individuals from 10 populations from the
 native range in North America and 14 populations in the UK. Results: We
 found wide variation in genotypic diversity within UK populations,
 indicating reproductive strategies that vary from mostly clonal to mostly
 sexual. All but one UK population were, on average, more closely related
 to each other than to North American populations, and the exceptional UK
 population showed strong affinity to native Alaskan plants. Conclusions: A
 small number of SNPs can detect patterns of clonality and broad-scale
 relationships between native and introduced populations. However,
 elucidating population structure at a finer scale will require genotyping
 individuals at greater depth.
description: SNP genotypes for native
 and introduced populations of Mimulus guttatus375 SNP genotypes at 62
 SNP loci for native (North America) and introduced (United Kingdom)
 populations.SNP_genotypes_Mimulus_guttatus.txt
DOI: 10.5061/dryad.24vm627
title: Data from: Assessing reliance on vector navigation in the long-distance oceanic migrations of green sea turtles

description: Vector navigation, i.e. maintaining a constant heading for a given amount
 of time, is hypothesized to provide a viable basis for the navigational
 feats of a number of long-distance animal migrants. Since animals
 following this strategy are subject to drift by wind or by ocean current,
 performing long migrations relying on vector navigation is particularly
 challenging. We tested whether vector navigation could be involved in the
 migrations of green turtles (Chelonia mydas) that migrate between the
 remote Ascension Island and Brazil. To this aim, a novel approach was
 followed using individual-based numerical models to simulate migratory
 trajectories of virtual turtles that were compared to actual routes
 reconstructed by satellite. Simulated post-nesting migrations from
 Ascension revealed that weak currents enabled modeled turtles to reach the
 Brazilian coast, but only for a limited range of headings around due West.
 This conclusion was corroborated by comparing modeled trajectories with
 the actual routes of previously tracked turtles, with a bee-line vector
 navigation strategy providing the best fit, although a true navigation
 strategy directed to the landfall site produced similar results. Finally,
 we tested if a vector navigational strategy was feasible for the
 pre-breeding migration from Brazil towards Ascension, but modeled routes
 mostly failed to reach the island or a larger area around it, with
 individuals drifting away under the influence of currents. We conclude
 that Ascension turtles can take advantage of vector navigation when
 migrating towards a wide target like the Brazilian coast, while the
 demanding prebreeding migration likely requires more complex navigational
 systems.
description: Modelled
 turtles_interpolated_locationsInterpolated location
 data used for phase 2 models.Foraging grounds
 locationsPosition of foraging
 grounds for the 6 turtles for which this information is available (used
 for phase 2 simulations)Starting points phase 3
 modelStarting points for
 phase 3 simulations
DOI: 10.5061/dryad.mh4240m
title: Data from: Ageing via perception costs of reproduction magnifies sexual selection

description: Understanding what factors modulate sexual selection intensity is crucial
 to a wide variety of evolutionary processes. Recent studies show that
 perception of sex pheromones can severely impact male mortality when it is
 not followed by mating (perception costs of reproduction). Here, we
 examine the idea that this may magnify sexual selection by further
 decreasing the fitness of males with inherently low mating success, hence
 increasing the opportunity for sexual selection. We use mathematical
 modelling to show that even modest mortality perception costs can
 significantly increase variability in male reproductive success under a
 wide range of demographic conditions. We then conduct a series of assays
 suggesting that, in D. melanogaster, failure to reproduce early in life
 may, via perception costs of reproduction, significantly reduce the
 subsequent fitness of males (ca. 25%), due mostly to increased
 reproductive ageing. Altogether, our results strongly suggest that
 perception costs of reproduction can magnify sexual selection in a
 biologically significant way. Finally, we estimate that around 29% of
 available studies quantify sexual selection based on short-term fitness
 estimates that may fail to capture these effects (if they were present in
 their subject species), and suggest addressing the existence and impact of
 perception costs of reproduction across taxa should thus be a priority.
description: dataLifespan and
 reproductive data for PC and NPC treatments
DOI: 10.5061/dryad.22hb2
title: Data from: Limits to future adaptation in the invasive plant Polygonum cespitosum: expression of functional and fitness traits at elevated CO2

description: For organisms to adapt to future environments, they must both evolve
 appropriate functional responses and phenotypically express those
 responses under future climatic and CO2 conditions. We examined these 2
 components of future adaptation in an invasive annual plant (Polygonum
 cespitosum) by performing a “resurrection” experiment under field
 conditions simulating a future environment. Resurrection experiments
 reveal recent evolution by comparing genotypes from natural populations
 sampled across a multigeneration interval. We collected genotypes from the
 same 3 North American populations in 1994 and 2005 and raised inbred lines
 from these collections under free air CO2 enrichment to examine functional
 and fitness traits expressed in hot, dry conditions at both ambient and
 elevated CO2 (N = 295 plants). The species has rapidly evolved in its
 introduced range to increase photosynthetic rate (collection year effect P
 ≤ 0.011) and delay senescence (P = 0.017) under full-sun, dry field
 conditions, but these adaptive changes were not expressed when the field
 environment included elevated CO2 (within-treatment year effect P ≥ 0.20
 for both traits). Populations showed different levels of reproductive
 output and its genetic variance in these novel, stressful conditions.
 These findings illustrate constraints on evolutionary adaptation to
 predicted future conditions at both the species and population levels.
description: Horgan-Kobelski et al
 2015 Supporting DataThis spreadsheet
 contains the data presented in the figures, tables, and results of
 "Limits to future adaptation in an invasive plant: expression of
 functional and fitness traits at elevated CO2."
DOI: 10.5061/dryad.8f0c8
title: Data from: Efficient detection of repeating sites to accelerate phylogenetic likelihood calculations

description: The phylogenetic likelihood function is the major computational bottleneck
 in several applications of evolutionary biology such as phylogenetic
 inference, species delimitation, model selection and divergence times
 estimation. Given the alignment, a tree and the evolutionary model
 parameters, the likelihood function computes the conditional likelihood
 vectors for every node of the tree. Vector entries for which all input
 data are identical result in redundant likelihood operations which, in
 turn, yield identical conditional values. Such operations can be omitted
 for improving run-time and, using appropriate data structures, reducing
 memory usage. We present a fast, novel method for identifying and omitting
 such redundant operations in phylogenetic likelihood calculations, and
 assess the performance improvement and memory savings attained by our
 method. Using empirical and simulated data sets, we show that a prototype
 implementation of our method yields up to 12-fold speedups and uses up to
 78% less memory than one of the fastest and most highly tuned
 implementations of the phylogenetic likelihood function currently
 available. Our method is generic and can seamlessly be integrated into any
 phylogenetic likelihood implementation.
description: Memory requirements for
 indexing all repeats for the used data sets.The presented table
 displays the memory requirements for indexing all site repeats for each of
 the 10 data sets we used to evaluate our method. We have exhaustively
 checked all possible rootings for each parsimony tree and present the
 minimum, maximum and average number of entries table M must consist
 of.suppl.pdf
DOI: 10.5061/dryad.k2p51
title: Data from: Spatial patterns of extra-pair paternity for spotted towhees (Pipilo maculatus) in urban parks

description: The extra-pair (EP) mating system of birds may be influenced by food
 resources, such that nutritionally stressed females are unable to pursue
 EP fertilizations (constrained female hypothesis; CFH), or that females on
 poor territories acquire EP fertilizations during extra-territorial forays
 in search of food (mating opportunity hypothesis; MOH). Edges of urban
 habitat fragments are sites of apparent high food abundance for spotted
 towhees (Pipilo maculatus), and we used distance to habitat edge in four
 urban parks in Portland, OR, USA (2004-2006), to test the CFH and MOH. EP
 paternity was independent of park identity and year; 44% of nests
 contained EP young and 26% of all young were EP. As predicted by the CFH,
 EP paternity was more common in nests of long-tailed (presumably) high
 quality females. However, independently of tail length, younger females
 had more EP young than older females, a finding consistent with the MOH.
 Contrary to predictions of both hypotheses, the probability that a nest
 contained EP young was highest both at the habitat edge and habitat
 interior while the proportion of young in nests of EP origin (for nests
 with EP young) was highest at intermediate distances from habitat edge. We
 propose that high frequency of EP paternity among females in the interior
 occurred because, as predicted by the MOH, they ranged more widely in
 search of food and often encountered EP males. High probability of EP
 paternity near edges was likely unrelated to female quality. Instead,
 anthropogenic food sources may have attracted individuals to edges and
 increased encounters between potential EP mates. Simple opportunity seems
 likely to account for patterns of EP paternity in spotted towhees,
 suggesting that human altered environments have the potential to
 substantially affect EP mating behavior.
description: SPTO EPP data all
 nestsSheet one includes each
 nest with park data, distance to edge data, and female and male ID, plus
 the extra-pair status of the nestlings. Sheet two includes all nesting
 attempts by each female per year, along with the extra-pair paternity
 data, and male and female morphological data for the "best" nest
 (the nest used in our analysis w/ the greatest number of nestlings
 typed).
DOI: 10.15468/dl.cru2by
title: Occurrence Download

description: A dataset containing 2666 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cestrum nocturnum",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 2666 records from 215 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000875-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.83n0t
title: Data from: Species introduction promotes hybridization and introgression in Coregonus: is there sign of selection against hybrids?

description: Species introductions are considered one of the major drivers of
 biodiversity loss via ecological interactions and genetic admixture with
 local fauna. We examined two well-recognized fish species, native
 whitefish (Coregonus lavaretus) and introduced vendace (C. albula), as
 well as their morphological hybrids in a single lake to test for selection
 against hybrids and backcrosses in the wild. A representative random
 subsample of 693 individuals (27.8%) was taken from the total catch of
 coregonids. This subsample was examined with the aim to select circa 50
 individuals of pure whitefish (n=52), pure vendace (n=55) and putative
 hybrid (n=19) for genetic analyses. The subsequent microsatellites and
 mitochondrial (mt) DNA analyses provided compelling evidence of
 hybridization and introgression. Of the 126 fish examined, four were found
 to be F1, 14 backcrosses to whitefish, and seven backcrosses to vendace.
 The estimates of historical gene flow suggested higher rates from
 introduced vendace into native whitefish than vice versa, whereas
 estimates of contemporary gene flow were equal. Mitochondrial
 introgression was skewed, with 18 backcrosses having vendace mtDNA and
 only three with whitefish mtDNA. Hybrids and backcrosses had intermediate
 morphology and niche utilization compared to parental species. No evidence
 of selection against hybrids or backcrosses was apparent, as both hybrid
 and backcross growth rates and fecundities were high. Hybrids (F1) were
 only detected in two year-classes, suggesting temporal variability in
 mating between vendace and whitefish. However, our data show that hybrids
 reached sexual maturity and reproduced actively, with backcrosses recorded
 from six consecutive year-classes, whereas no F2 individuals were found.
 The results indicate widespread introgression, as 10.8% of coregonids were
 estimated to be backcrosses.
description: Kahilainen_etal_MEC_dryad_raw_dataGenetic and ecomorphological dataset from Kahilainen et al. Species introduction promotes hybridization and introgression in Coregonus: is there sign of selection against hybrids? Molecular Ecology (online ISSN:1095-8312). Columns A-B give individual code and a priori classification followed by mtDNA (C) and microsatellite data (D-Q). Columns R-U give assignment results from genetic data and final posteriori grouping (WF=whitefish, V=vendace, F1=F1 hybrid, BCV=backcross to vendace and BCWF=backcross to whitefish). Body size and morphology is given in W-AA, niche utilization in AB-AP and life-history traits in AQ-AU. Sex is coded as 1=female, 2=male, 3=juvenile and sexual maturity as 1-3=immature and 4=mature.
DOI: 10.5061/dryad.29710
title: Data from: Offspring of older parents are smaller—but no less bilaterally symmetrical—than offspring of younger parents in the aquatic plant Lemna turionifera

description: Offspring quality decreases with parental age in many taxa, with offspring
 of older parents exhibiting reduced lifespan, reproductive capacity, and
 fitness, compared to offspring of younger parents. These ‘parental age
 effects’, whose consequences arise in the next generation, can be
 considered as manifestations of parental senescence, in addition to the
 more familiar age-related declines in parent-generation survival and
 reproduction. Parental age effects are important because they may have
 feedback effects on the evolution of demographic trajectories and
 longevity. In addition to altering the timing of offspring life-history
 milestones, parental age effects can also have a negative impact on
 offspring size, with offspring of older parents being smaller than
 offspring of younger parents. Here, we consider the effects of advancing
 parental age on a different aspect of offspring morphology, body symmetry.
 In this study, we followed all 403 offspring of 30 parents of a
 bilaterally symmetrical, clonally reproducing aquatic plant species, Lemna
 turionifera, to test the hypothesis that successive offspring become less
 symmetrical as their parent ages, using the ‘Continuous Symmetry Measure’
 as an index. Although successive offspring of aging parents older than one
 week became smaller and smaller, we found scant evidence for any reduction
 in bilateral symmetry.
description: Ankutowicz_and_Laird_dataData from Ankutowicz and Laird, "Offspring of older parents are smaller—but no less bilaterally symmetrical—than offspring of younger parents in the aquatic plant Lemna turionifera"; see associated README file for column-header details.Ankutowicz_and_Laird_R_scriptsR scripts accompanying Ankutowicz and Laird, "Offspring of older parents are smaller—but no less bilaterally symmetrical—than offspring of younger parents in the aquatic plant Lemna turionifera"otsuMatlab function for image thresholding.segMatlab function for image segmentation.filtMatlab function for image filtering.floodfillMatlab function for flood-filling an image.boundMatlab function for boundary detection of an image.csm_mirrorMatlab function for finding the continuous symmetry measure (CSM) associated with bilateral (/mirror) symmetry in an image.
DOI: 10.5061/dryad.q0pv7
title: Data from: A controlled quasi-experimental study of an educational intervention to reduce the unnecessary use of antimicrobials for asymptomatic bacteriuria

description: Background: Asymptomatic bacteriuria (ABU) should only be treated in cases
 of pregnancy or in-patients undergoing urologic procedures; however,
 unnecessary treatment of ABU is common in clinical practice. Objective: To
 identify risk factors for unnecessary treatment and to assess the impact
 of an educational intervention focused on these risk factors on treatment
 of ABU. Design: Quasi-experimental study with a control group. Setting:
 Two tertiary teaching adult care hospitals. Participants: Consecutive
 patients with positive urine cultures between January 30th and April 17th,
 2012 (baseline) and January 30th and April 30th, 2013 (intervention).
 Intervention: In January 2013, a multifaceted educational intervention
 based on risk factors identified during the baseline period was provided
 to medical residents (monthly) on one clinical teaching unit (CTU) at one
 hospital site, with the CTU of the other hospital serving as the control.
 Results: During the baseline period, 160/341 (46.9%) positive urine
 cultures were obtained from asymptomatic patients at the two hospitals,
 and 94/160 (58.8%) were inappropriately treated with antibiotics. Risk
 factors for inappropriate use included: female gender (OR 2.1, 95% CI
 1.1-4.3), absence of a catheter (OR 2.5, 1.2-5), bacteriuria versus
 candiduria (OR 10.6, 3.8-29.4), pyuria (OR 2.0, 1.1-3.8), and positive
 nitrites (OR 2.2, 1.1-4.5). In 2013, only 2/24 (8%) of ABU patients were
 inappropriately treated on the intervention CTU as compared to 14/29 (52%)
 on the control CTU (OR 0.10; 95% CI 0.02-0.49). A reduction was also
 observed as compared to baseline on the intervention CTU (OR 0.1,
 0.02-0.7) with no significant change noted on the control CTU (OR 0.47,
 0.13-1.7). Conclusions: A multifaceted educational intervention geared
 towards medical residents with a focus on identified risk factors for
 inappropriate management of ABU was effective in reducing unnecessary
 antibiotic use.
description: ABU
 baselineData of
 baseline/pre-intervention periodABU
 interventionComparison baseline to
 intervention
DOI: 10.5061/dryad.1g7ns
title: Data from: Phase III of Wright's Shifting Balance Process and the variance among demes in migration rate

description: Interdemic selection by the differential migration of individuals out from
 demes of high fitness and into demes of low fitness (Phase III) is one of
 the most controversial aspects of Wright's Shifting Balance Theory. I
 derive a relationship between Phase III migration and the interdemic
 selection differential, S, and show its potential effect on FST. The
 relationship reveals a diversifying effect of interdemic selection by
 Phase III migration on the genetic structure of a metapopulation. Using
 experimental metapopulations, I explored the effect of Phase III migration
 on FST by comparing the genetic variance among demes for two different
 patterns of migration: (1) island model migration and (2) Wright's
 Phase III migration. Although mean migration rates were the same, I found
 that the variance among demes in migration rate was significantly higher
 with Phase III than with island model migration. As a result, FST for the
 frequency of a neutral marker locus was higher with Phase III than it was
 with island model migration. By increasing FST, Phase III enhanced the
 genetic differentiation among demes for traits not subject to interdemic
 selection. This feature makes Wright's process different from
 individual selection which, by reducing effective population size,
 decreases the genetic variance within demes for all other traits. I
 discussed this finding in relation to the efficacy of Phase III and random
 migration for effecting peak shifts, and the contribution of genes with
 indirect effects to among-deme variation.
description: WADE EVOLUTION SBT
 Migration Data to Gen 13These are the data from
 which the two tables in "Phase III of Wright's Shifting Balance
 Process and the variance among demes in migration rate" by M. J. Wade
 were assembled. They were collected during the course of the Wade and
 Goodnight (1991) Science paper on Wright's Shifting Balance
 Theory
DOI: 10.5061/dryad.r58r0
title: Data from: Sexual dimorphism, phenotypic integration, and the evolution of head structure in casque-headed lizards

description: Sexes can differ in features associated with differential reproduction,
 which can be used during courtship or aggressive encounters. Some traits
 tend to evolve independently between sexes and emerge as sexually
 dimorphic within the organismal phenotype. We characterize such a
 relationship by estimating the phenotypic integration of the head
 morphology and modularity of the crest in the casque-headed lizards
 (Corytophanidae). In this clade, some species show extreme sexual
 dimorphism (e.g., head crests in the genus Basiliscus) while in others,
 both sexes are monomorphic. To characterize these patterns, we define
 phenotypic integration at the interspecific level as a pattern or network
 of traits evidenced by phylogenetically adjusted correlations that persist
 among species. At this level, modularity is an increased connectedness
 (e.g., higher correlation) among sections of these networks that persist
 in a lineage during the evolution of complex phenotypes. To test both
 concepts, we used phylogenetic geomorphometrics to characterize the head
 structure of corytophanid lizards, based on a time-calibrated phylogeny
 that includes candidate fossil ancestors. We found evidence of an older
 diversification of corytophanids than previously reported (~67 vs. ~23.5
 MYA) and show that this clade includes two morphological head
 architectures: (1) Sexually dimorphic crests present in males that are
 evolving independently from the rest of the head structure, and (2) full
 integration of the head morphology in monomorphic species. We propose that
 both architectures are optimal evolutionary trajectories of the parietal
 crest bones in the head of these lizards. In sexually dimorphic species,
 these bones are elongated and thinner, and gave rise to the extended crest
 used in male courtship displays. In monomorphic species, the parietal
 crest grew thicker in both sexes to allow for a better insertion of
 muscles associated with a stronger bite.
description: Corytophanidae: data,
 trees, R code, TPS filesdata, trees, R code, TPS
 filesCorytophanidae_E&E_appendix.zip