cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q477f90
title: Data from: Climate-based seed transfer of a widespread shrub: population shifts, restoration strategies and the trailing edge

description: Genetic resources have to be managed appropriately to mitigate the impact
 of climate change. For many wildland plants, conservation will require
 knowledge of the climatic factors affecting intraspecific genetic
 variation to minimize maladaptation. Knowledge of the interaction between
 traits and climate can focus management resources on vulnerable
 populations, provide guidance for seed transfer and enhance fitness and
 resilience under changing climates. In this study, traits of big sagebrush
 (Artemisia tridentata) were examined among common gardens located in
 different climates. We focus on two subspecies, wyomingensis and
 tridentata, that occupy the most imperiled warm-dry spectrum of the
 sagebrush biome. Populations collected across the sagebrush biome were
 recorded for flower phenology and survival. Mixed-effects models examined
 each trait to evaluate genetic variation, environmental effects, and
 adaptive breadth of populations. Climate variables derived from population
 source locations were significantly associated with these traits (P
 &lt; 0.0001), explaining 31% and 11% of the flower phenology and
 survival variation, respectively. To illustrate our model and assess
 variability in prediction, we examine fixed and focal point seed transfer
 approaches to map contemporary and climate model ensemble projections in
 two different regions of the sagebrush biome. A comparison of seed
 transfer areas predicts that populations from warmer climates become more
 prevalent, replacing colder-adapted populations by mid-century. However,
 these warm-adapted populations are often located along the trailing edge,
 margins of the species range predicted to be lost due to a contraction of
 the climatic niche. Management efforts should focus on the collection and
 conservation of vulnerable populations and prudent seed transfer to colder
 regions where these populations are projected to occur by mid-century. Our
 models provide the foundation to develop an empirical, climate-based seed
 transfer system for current and future restoration of big sagebrush.
description: Survival, phenology and
 climate dataArtemisia tridentata
 common garden trait data and corresponding population-source climate
 variables. Information on column headers for climate variables can be
 found at: https://adaptwest.databasin.org/pages/adaptwest-climatena. Each
 sheet of the excel file will need to be saved as a .csv file and run with
 the R code found at:
 https://github.com/lchaney/Sagebrush_Synth.Richardson_dryad.xlsx
DOI: 10.5061/dryad.56n7v
title: Data from: Dry season survival of juvenile salmonids in an intermittent coastal stream

description: We estimated dry season survival of imperiled salmonids in an intermittent
 coastal stream in California across four years (2009-2012). Our study
 encompassed two dry and two wet winters allowing us to explore patterns of
 survival across and within dry seasons with different antecedent
 precipitation. Apparent survival of age-0+ steelhead trout (Oncorhynchus
 mykiss) was higher following wet winters compared to dry winters.
 Moreover, antecedent precipitation was positively correlated with
 cumulative survival of age-0+ steelhead. Within years, apparent survival
 of steelhead varied among weeks with a tendency to decrease in the late
 summer indicating that fish exhibited some resistance to seasonal drought.
 Additionally, we found a slight but significant survival advantage for
 age-0+ coho salmon (O. kisutch) compared to equal-aged steelhead. Our
 results emphasize the influence of antecedent precipitation in driving the
 survival of imperiled salmonids and highlight that these fishes are
 somewhat resistant to seasonal drought, at least to a point.
description: Age-0+ Steelhead
 Survival Input FileThis input file was used
 for the among-year detection/survival probability analysis of age-0+
 steelheadST_YOY.INPAge-0+ Steelhead and Coho Survival Input File (Year 2011)This input file was used for the within-year detection/survival probability analysis of age-0+ steelhead and coho2011.INPMark-Recapture SpreadsheetThis spreadsheet was used to create the INP files used for the among-year and within-year detection/survival probability analyses. Please view README file.JWF_MarkRecapture.xlsx
DOI: 10.5061/dryad.8984
title: Data from: Mitochondrial phylogeny of the Chrysis ignita (Hymenoptera: Chrysididae) species group based on simultaneous Bayesian alignment and phylogeny reconstruction

description: The ignita species group within the genus Chrysis includes over 100 cuckoo
 wasp species, which all lead a parasitic lifestyle and exhibit very
 similar morphology. The lack of robust, diagnostic morphological
 characters has hindered phylogenetic reconstructions and contributed to
 frequent misidentification and inconsistent interpretations of species in
 this group. Therefore, molecular phylogenetic analysis is the most
 suitable approach for resolving the phylogeny and taxonomy of this group.
 We present a well-resolved phylogeny of the Chrysisignita species group
 based on mitochondrial sequence data from 41 ingroup and six outgroup
 taxa. Although our emphasis was on European taxa, we included samples from
 most of the distribution range of the C. ignita species group to test for
 monophyly. We used a continuous mitochondrial DNA sequence consisting of
 16S rRNA, tRNAVal, 12S rRNA and ND4. The location of the ND4 gene at the
 3′ end of this continuous sequence, following 12S rRNA, represents a novel
 mitochondrial gene arrangement for insects. Due to difficulties in
 aligning rRNA genes, two different Bayesian approaches were employed to
 reconstruct phylogeny: (1) using a reduced data matrix including only
 those positions that could be aligned with confidence; or (2) using the
 full sequence dataset while estimating alignment and phylogeny
 simultaneously. In addition maximum-parsimony and maximum-likelihood
 analyses were performed to test the robustness of the Bayesian approaches.
 Although all approaches yielded trees with similar topology, considerably
 more nodes were resolved with analyses using the full data matrix.
 Phylogenetic analysis supported the monophyly of the C. ignita species
 group and divided its species into well-supported clades. The resultant
 phylogeny was only partly in accordance with published subgroupings based
 on morphology. Our results suggest that several taxa currently treated as
 subspecies or names treated as synonyms may in fact constitute separate
 species. Our study provides a solid basis for further systematic
 investigations of this enigmatic insect group.
description: MAP_alignment_of_complete_datasethighly_supported_positions_only
DOI: 10.5061/dryad.p9r4k
title: Data from: How big is it really? Assessing the efficacy of indirect estimates of body size in Asian elephants

description: Information on an organism’s body size is pivotal in understanding its
 life history and fitness, as well as helping inform conservation measures.
 However, for many species, particularly large-bodied wild animals, taking
 accurate body size measurements can be a challenge. Various means to
 estimate body size have been employed, from more direct methods such as
 using photogrammetry to obtain height or length measurements, to indirect
 prediction of weight using other body morphometrics or even the size of
 dung boli. It is often unclear how accurate these measures are because
 they cannot be compared to objective measures. Here, we investigate how
 well existing estimation equations predict the actual body weight of Asian
 elephants Elephas maximus, using body measurements (height, chest girth,
 length, foot circumference and neck circumference) taken directly from a
 large population of semi-captive animals in Myanmar (n = 404). We then
 define new and better fitting formulas to predict body weight in Myanmar
 elephants from these readily available measures. We also investigate
 whether the important parameters height and chest girth can be estimated
 from photographs (n = 151). Our results show considerable variation in the
 ability of existing estimation equations to predict weight, and that the
 equations proposed in this paper predict weight better in almost all
 circumstances. We also find that measurements from standardised
 photographs reflect body height and chest girth after applying minor
 adjustments. Our results have implications for size estimation of large
 wild animals in the field, as well as for management in captive settings.
description: Photographic and
 measured body parameter data for Asian elephantsSheet 1: Elephant chest
 girth and height estimated from photographs by four measurers Sheet 2:
 Body parameter measurements for Asian elephantsPhotoDRYAD.xlsx
DOI: 10.5061/dryad.014v6
title: Data from: Impact of an ivermectin mass drug administration on scabies prevalence in a remote Australian Aboriginal community

description: Background: Scabies is endemic in many Aboriginal and Torres Strait
 Islander communities, with 69% of infants infected in the first year of
 life. We report the outcomes against scabies of two oral ivermectin mass
 drug administrations (MDAs) delivered 12 months apart in a remote
 Australian Aboriginal community. Methods: Utilizing a before and after
 study design, we measured scabies prevalence through population census
 with sequential MDAs at baseline and month 12. Surveys at months 6 and 18
 determined disease acquisition and treatment failures. Scabies
 infestations were diagnosed clinically with additional laboratory
 investigations for crusted scabies. Non-pregnant participants weighing ≥15
 kg were administered a single 200 μg/kg ivermectin dose, repeated after
 2–3 weeks if scabies was diagnosed, others followed a standard alternative
 algorithm. Principal Findings: We saw &gt;1000 participants at each
 population census. Scabies prevalence fell from 4% at baseline to 1% at
 month 6. Prevalence rose to 9% at month 12 amongst the baseline cohort in
 association with an identified exposure to a presumptive crusted scabies
 case with a higher prevalence of 14% amongst new entries to the cohort. At
 month 18, scabies prevalence fell to 2%. Scabies acquisitions six months
 after each MDA were 1% and 2% whilst treatment failures were 6% and 5%
 respectively. Conclusion: Scabies prevalence reduced in the six months
 after each MDA with a low risk of acquisition (1–2%). However, in a
 setting where living conditions are conducive to high scabies
 transmissibility, exposure to presumptive crusted scabies and population
 mobility, a sustained reduction in prevalence was not achieved. Clinical
 Trial Registration: Australian New Zealand Clinical Trial Register
 (ACTRN—12609000654257).
description: Scabies_Repository_finalScabies infestation status of human participants from a remote Aboriginal community in Northern Australia.
DOI: 10.5061/dryad.ht348n1
title: Data from: Experimental herbivore exclusion, shrub introduction, and carbon sequestration in alpine plant communities

description: Background: Shrub cover in arctic and alpine ecosystems has increased in
 recent decades, and is predicted to further increase with climate change.
 Changes in shrub abundance may alter ecosystem carbon (C) sequestration
 and storage, with potential positive feedback on global C cycling. Small
 and large herbivores may reduce shrub expansion and thereby counteract the
 positive feedback on C cycling, but herbivore pressures have also changed
 in the alpine-arctic tundra; the increased shrub cover together with
 changes in herbivore pressure is leading to unpredictable changes in
 carbon sequestration and storage. In this study we investigate the
 importance of herbivory and shrub introduction for carbon sequestration in
 the short term. We measured standing biomass and daytime mid-growing
 season carbon fluxes in plots in a full factorial design where we excluded
 small and large mammalian herbivores and introduced Salix by planting
 Salix transplants. We used three study sites: one Empetrum-dominated
 heath, one herb- and cryptogam-dominated meadow, and one Salix-dominated
 shrub community in the low-alpine zone of the Dovre Mountains, Central
 Norway. Results: After 2 years, significant treatment effects were
 recorded in the heath community, but not in the meadow and shrub
 communities. In the heath community cessation of herbivory increased
 standing biomass due to increased biomass of dwarf shrubs. Cessation of
 herbivory also reduced biomass of bryophytes and ecosystem respiration
 (ER). Except for an increase in biomass of deciduous shrubs caused by the
 Salix introduction, the only effect of Salix introduction was an increase
 in biomass of graminoids in the heath. Conclusions: Our short-term study
 demonstrated that herbivore exclusion had small but still significant
 effects on heath vegetation, whereas such effects were not apparent in the
 herb-and cryptogam-dominated meadow and the Salix-dominated shrub
 community. Following the treatments over more years is needed to estimate
 the long-term effects on community structure and the consequences for C
 sequestration in the three plant communities. Such data are important for
 predicting the impact of shrub expansion on C budgets from alpine regions.
description: CO2 fluxes and biomass
 during experimental herbivore exclusion and shrub
 introductionField data of CO2 fluxes
 (including Net Ecosystem Exchange, Ecosystem Respiration and Gross
 Ecosystem Photosynthesis) and the environment (such as light, moisture,
 and air, surface, and soil temperature) during measurements and vegetation
 data (including absolute abundance and measured and estimated biomass of
 functional groups). Methods and experimental design is explained in
 publication. The data is processed in R core Team 2017.Data_fluxes_and_biomass_BMC_Ecology_Dryad.xlsx
DOI: 10.5061/dryad.b1q08
title: Data from: Assortative mating by colored ornaments in blue tits: space and time matter

description: Assortative mating is a potential outcome of sexual selection and
 estimating its level is important to better understand local adaptation
 and underlying trait evolution. However, assortative mating studies
 frequently base their conclusions on small numbers of individuals sampled
 over short periods of time and limited spatial scales even though
 spatiotemporal variation is common. Here, we characterized assortative
 mating patterns over 10 years in four populations of the blue tit
 (Cyanistes caeruleus), a passerine bird. We focused on two plumage
 ornaments—the blue crown and the yellow breast patch. Based on data for
 1,657 pairs of birds, we found large interannual variation: assortative
 mating varied from positive to negative. To determine whether there was
 nonetheless a general trend in the data, we ran a within-study
 meta-analysis. It revealed that assortative mating was moderately positive
 for both ornaments. It also showed that mating patterns differed among
 populations, and especially between two neighboring populations that
 displayed phenotypic divergence. Our results therefore underscore that
 long-term studies are needed to draw broad conclusions about mating
 patterns in natural populations. They also call for studying the potential
 role of assortative mating in local adaptation and evolution of ornaments
 in both sexes in blue tits.
description: ColorTraitValuesColor trait values for associated pairs of blue tits per year and population (column 'pop'). Columns 'mID' and 'fID' refer to metal ring identity for males (m) and females (f) respectively. For full names for columns 5 to 16 ('mBB' to 'fYC') see Table 2 of the article (DOI: 10.1002/ece3.2822).
DOI: 10.5061/dryad.s4h53
title: Data from: Simultaneous estimation of occupancy and detection probabilities an illustration using Cincinnatian brachiopods

description: Preservation in the fossil record is never perfect in the sense that we
 cannot sample all individuals of a given population in time and space.
 Incomplete detection (i.e., preservation and modern-day sampling of
 fossils) often affects estimates of other paleobiological parameters of
 interest, such as occupancy and turnover. Here, I simultaneously model the
 occupancy and detection probability of taxa, teasing apart the zeros in
 data that reflect true absences and those that imply non-detection of taxa
 that were actually present in the space and time of interest. Occupancy
 modeling, an approach first developed in population ecology, can easily
 incorporate covariates of interest, such as sampling effort and habitat
 variables. I use a data set of brachiopod taxa from the Paleozoic to
 illustrate the utility of this approach for paleontological questions. I
 demonstrate a range of models, including those that allow colonization
 between time intervals and those that incorporate facies as site
 covariates. I also suggest how future data collection can be improved so
 that process- and sampling-oriented approaches such as occupancy modeling
 can be applied with ease to paleobiological settings to answer important
 paleoecological and evolutionary questions.
description: Liow_Supplementary_TextSupplementary text for main articleS Table 1 LiowSupplementary Table 1S Table 2 LiowSupplementary Table 2S Table 3 LiowSupplementary Table 3Sample informationSamples from which Herbetella observed occurrences arose (see main text and supplementary text)S H Data Samples.xlsxHerbetella data for Single Season ModelFormatted data for Herbetella to be used in "single season" occupancy modelsS H Data Single.xlsxHerbetella data for Multiple Season ModelFormatted data for Herbetella to be used in "multiple season" occupancy modelsS H Data Multi.xlsxHerbetella Data TripledTriplicated data for HerbetellaS H Data Tripled.xlsx
DOI: 10.5061/dryad.pj032
title: Data from: A new method for statistical detection of directional and stabilizing mating preference

description: Estimation of mating preferences is a prerequisite for understanding how
 sexual selection through mate choice shapes both mating systems and sexual
 dimorphisms. Most studies of mating preferences assay mate choice using
 either a no choice or a binary choice design. Binary choice trials
 typically employ either an artificial signal or some fixed difference
 (e.g. colour or size) between the signalling individuals. Although
 statistically more powerful than no choice designs, such experiments
 cannot be used to detect stabilizing preference. Further, the use of
 artificial signals is problematic because signal components tend to be
 varied in isolation, and hence do not reflect natural variation. Here, we
 present a new method that uses natural variation among individuals in
 choice trials to determine if mating preference is absent, directional,
 and/or stabilizing. The protocol is tested using simulation and shown to
 be robust to the preference function, to have the required statistical
 power, to be unbiased in almost all cases, and to give confidence regions
 that modestly overestimate the desired 95% criterion. We demonstrate the
 use of the method with data from mate choice trials of the sand cricket,
 Gryllus firmus. Software to apply this new approach is provided in Dryad.
description: File for test
 dataSee readme
 fileTest.Data.csvTest.Data01File for 01 dataMain.program.female.preferenceThis is the main program. It has lines that are changed by the userMAIN.PROGRAM.FEMALE.PREFERENCE.RFunctions.for.Female.preferenceSet of functions used.
DOI: 10.5061/dryad.24kp5
title: Data from: Disentangling the effects of geographic and ecological isolation on genetic differentiation

description: Populations can be genetically isolated by both geographic distance and by
 differences in their ecology or environment that decrease the rate of
 successful migration. Empirical studies often seek to investigate the
 relationship between genetic differentiation and some ecological
 variable(s) while accounting for geographic distance, but common
 approaches to this problem (such as the partial Mantel test) have a number
 of drawbacks. In this article, we present a Bayesian method that enables
 users to quantify the relative contributions of geographic distance and
 ecological distance to genetic differentiation between sampled populations
 or individuals. We model the allele frequencies in a set of populations at
 a set of unlinked loci as spatially correlated Gaussian processes, in
 which the covariance structure is a decreasing function of both geographic
 and ecological distance. Parameters of the model are estimated using a
 Markov chain Monte Carlo algorithm. We call this method Bayesian
 Estimation of Differentiation in Alleles by Spatial Structure and Local
 Ecology (BEDASSLE), and have implemented it in a user-friendly format in
 the statistical platform R. We demonstrate its utility with a simulation
 study and empirical applications to human and teosinte datasets.
description: Teosinte BEDASSLE
 datasetteosinte.bedasssle.RobjHuman BEDASSLE datasethgdp.himalaya.bedassle.Robj
DOI: 10.26027/datarcav1x
title: Marine mammal sightings NW of Boa Vista island, Cabo Verde, November 14th and 15th, 2000, with related cruise data

description: Between May 3rd, 2000, and August 4th, 2001, a 55’ long sailing vessel ‘Rosita’ undertook a cruise around the North Atlantic, as described in the
cruise report and log files archived here. This archive focuses on two days of marine mammal sightings in the waters of the Cape Verde Islands – November 14th and 15th 2000, with sighting details and images.
description: Visual shipboard sightings and photographs. Not corrected for effort.
DOI: 10.5061/dryad.1pf8t
title: Data from: Parallelism in adaptive radiations of experimental Escherichia coli populations

description: Adaptive radiations are major contributors to species diversity. While the
 underlying mechanisms of adaptive radiations, specialization and
 trade-offs, are relatively well understood, the tempo and repeatability of
 adaptive radiations remain elusive. Ecological specialization can occur
 through the expansion into novel niches or through partitioning of an
 existing niche. To test how the mode of resource specialization affects
 the tempo and repeatability of adaptive radiations, we selected replicate
 bacterial populations in environments that promoted the evolution of
 diversity either through niche expansion or through niche partitioning,
 and in a third low-quality single-resource environment, in which diversity
 was not expected to evolve. Colony size diversity evolved equally fast in
 environments that provided ecological opportunities regardless of the mode
 of resource specialization. In the low quality environments, diversity did
 not consistently evolve. We observed the largest fitness improvement in
 the low quality environment and the smallest the glucose-limited
 environment. We did not observe a change in the rate of evolutionary
 change in either trait or environment, suggesting that the pool of
 beneficial mutations was not exhausted. Overall, the mode of resource
 specialization did not affect the tempo or repeatability of adaptive
 radiations. These results demonstrate the limitations of eco-evolutionary
 feedbacks to affect evolutionary outcomes.
description: Density_and_colony(H)This file contains the colony counts over the course of the selection experiment. This data was used to calculate the population density and the population diversity, calculated as Shannon-Wiener index H.Diversity_and_FitnessThis file contains the relative fitness data and diversity data calculated as CV* for generations 500 and 100.