cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.p49b1
title: Data from: Adaptive divergence in a defense symbiosis driven from the top down

description: Most studies of adaptive radiation in animals focus on resource
 competition as the primary driver of trait divergence. The roles of other
 ecological interactions in shaping divergent phenotypes during such
 radiations have received less attention. We evaluate natural enemies as
 primary agents of diversifying selection on the phenotypes of an actively
 diverging lineage of gall midges on tall goldenrod. In this system, the
 gall of the midge consists of a biotrophic fungal symbiont that develops
 on host-plant leaves and forms distinctly variable protective carapaces
 over midge larvae. Through field studies, we show that fungal gall
 morphology, which is induced by midges (i.e., it is an extended phenotype)
 is under directional and diversifying selection by parasitoid enemies.
 Overall, natural enemies disruptively select for either small or large
 galls, mainly along the axis of gall thickness. These results imply that
 predators are driving the evolution of phenotypic diversity in symbiotic
 defense traits in this system, and that divergence in defensive morphology
 may provide ecological opportunities that help to fuel the adaptive
 radiation of this genus of midges on goldenrods. This enemy-driven
 phenotypic divergence in a diversifying lineage illustrates the potential
 importance of consumer-resource and symbiotic species interactions in
 adaptive radiation.
description: WSU Common garden data
 for 2010 on A. carboniferaData associated with Am.
 Nat. publication: Adaptive divergence in a defense symbiosis driven from
 the top down. Includes the WSU Common Garden data for 2010 on Asteromyia
 carbonifera selection. See Readme.txt file for variable
 descriptions.WSU_plot_10_v3-1_edit.csv
DOI: 10.5061/dryad.426rq
title: Data from: The fitness consequences of kin-biased dispersal in a cooperatively breeding bird

description: Cooperative alliances among kin may not only lead to indirect fitness
 benefits for group-living species, but can also provide direct benefits
 through access to mates or higher social rank. However, the immigrant sex
 in most species loses any potential benefits of living with kin unless
 immigrants disperse together or recruit relatives into the group in
 subsequent years. To look for evidence of small subgroups of related
 immigrants within social groups (kin substructure), we used
 microsatellites to assess relatedness between immigrant females of the
 cooperatively breeding superb starling, Lamprotornis superbus. We
 determined how timing of immigration led to kin subgroup formation and if
 being part of one influenced female fitness. Although mean relatedness in
 groups was higher for males than females, 26% of immigrant females were
 part of a kin subgroup with a sister. These immigrant sibships formed
 through kin recruitment across years more often than through coalitions
 immigrating together in the same year. Furthermore, females were more
 likely to breed when part of a kin subgroup than when alone, suggesting
 that female siblings form alliances that may positively influence their
 fitness. Ultimately, kin substructure should be considered when
 determining the role of relatedness in the evolution of animal societies.
description: Site R Values
 DryadQueller and Goodnight R
 values from cooperatively breeding superb starlings (Lamprotornis
 superbus). Data are from nine sites at the Mpala Research Centre in
 central Kenya from birds present from 2001 through
 2013.
DOI: 10.5061/dryad.t40f2
title: Data from: Penalized likelihood methods improve parameter estimates in occupancy models

description: 1. Occupancy models are employed in species distribution modelling to
 account for imperfect detection during field surveys. While this approach
 is popular in the literature, problems can occur when estimating the model
 parameters. In particular, the maximum likelihood estimates can exhibit
 bias and large variance for data sets with small sample sizes, which can
 result in estimated occupancy probabilities near 0 and 1 (‘boundary
 estimates’). 2. In this paper, we explore strategies for estimating
 parameters based on maximizing a penalized likelihood. Penalized
 likelihood methods augment the usual likelihood with a penalty function
 that encodes information about what parameter values are undesirable. We
 introduce penalties for occupancy models that have analogues in ridge
 regression and Bayesian approaches, and we compare them to a penalty
 developed for occupancy models in prior work. 3. We examine the bias,
 variance and mean squared error of parameter estimates obtained from each
 method on synthetic data. Across all of the synthetic data sets, the
 penalized estimation methods had lower mean squared error than the maximum
 likelihood estimates. We also provide an example of the application of
 these methods to point counts of avian species. Penalized likelihood
 methods show similar improvements when tested using empirical bird point
 count data. 4. We discuss considerations for choosing among these methods
 when modelling occupancy. We conclude that penalized methods may be of
 practical utility for fitting occupancy models with small sample sizes,
 and we are releasing R code that implements these methods.
description: Hutchinson et al
 dataThis file contains the
 data used in the empirical case study of our manuscript. The first three
 tabs contain site occupancy, survey-specific covariates, and site-specific
 covariates for our full (656 sites, 3 surveys) survey effort. The last
 three tabs contain site occupancy, survey-specific covariates, and
 site-specific covariates for the first 2 surveys from 55 randomly-selected
 sites (the reduced data set in the paper). Further information is
 available in the attached "ReadMe" file.
DOI: 10.5061/dryad.63s8h
title: Data from: Defining the risk landscape in the context of pathogen pollution: Toxoplasma gondii in sea otters along the Pacific Rim

description: Pathogens entering the marine environment as pollutants exhibit a spatial
 signature driven by their transport mechanisms. The sea otter (Enhydra
 lutris), a marine animal that lives much of its life within sight of land,
 presents a unique opportunity to understand land-sea pathogen
 transmission. Using a dataset on Toxoplasma gondii prevalence across sea
 otter range from Alaska to California, we found that the dominant drivers
 of infection risk vary depending upon the spatial scale of analysis. At
 the population level, regions with high T. gondii prevalence had higher
 human population density and a greater proportion of human-dominated land
 uses suggesting a strong role for population density of the felid
 definitive host of this parasite. This relationship persisted when a
 subset of data were analysed at the individual level: large-scale patterns
 in sea otter T. gondii infection prevalence were largely explained by
 individual exposure to areas of high human housing unit density, and other
 landscape features associated with anthropogenic land use, such as
 impervious surfaces and cropping land. These results contrast with the
 small-scale, within-region analysis, in which age, sex and prey choice
 accounted for most of the variation in infection risk, and terrestrial
 environmental features provided little variation to help in explaining
 observed patterns. These results underscore the importance of spatial
 scale in study design when quantifying both individual-level risk factors
 and landscape-scale variation in infection risk.
description: Otter_tg_codeMain code for analyses. Run this file in R. Note: May require installation of additional R package dependencies.Otter_tg_FunctionsCustom functions used by Otter_tg_code. Keep this file in the same working directory.Data PrepData preparation and variable creation code needed for Otter_tg_code. Keep in the same working directory.otter_tg_datasetPrimary dataset.Predict_dataSynthetic data used for model-based predictions.WS_data_summaryWatershed data summary table.
DOI: 10.5061/dryad.683br42
title: Data from: Evolutionary rates of mid-Permian tetrapods from South Africa and the role of temporal resolution in turnover reconstruction

description: The Main Karoo Basin of South Africa contains a near-continuous sequence
 of continental deposition spanning 45 million years from the middle
 Permian to the Early Jurassic. The terrestrial vertebrates of this
 sequence provide a high-resolution stratigraphic record of regional
 origination and extinction, especially for the middle–late Permian. Until
 now, data have only been surveyed at coarse stratigraphic resolution using
 methods that are biased by non-uniform sampling rates, limiting our
 understanding of the dynamics of diversification through this important
 time period. High-resolution data now cross the mid-to-late Permian
 transition; to these we apply robust methods (gap-filler and modified
 gap-filler rates) for the inference of patterns of species richness,
 origination rates and extinction rates to a subset of 1321
 securely-identified fossil occurrences resolved to approximately 50 metre
 stratigraphic intervals. This dataset provides an approximate time
 resolution of 0.3-0.6 million years and shows that extinction rates
 increased considerably in the upper 100 metres of the middle Permian
 Abrahamskraal Formation, corresponding to the latest part of the
 Tapinocephalus Assemblage Zone (AZ). Origination rates were weakly
 elevated in the same interval, and were not sufficient to compensate for
 these extinctions. Subsampled species richness estimates for the lower
 part of the overlying Teekloof Formation (corresponding to the
 Pristerognathus and Tropidostoma AZs) are low, and show that species
 richness remained low for at least 1.5–3 million years after the main
 extinction pulse. A high unevenness of the taxon abundance-frequency
 distribution, which is classically associated with trophically unstable
 post-extinction faunas, in fact developed shortly before the acme of
 elevated extinction rates due to the appearance and proliferation of the
 dicynodont Diictodon. Our findings provide strong support for a Capitanian
 (‘end-Guadalupian’) extinction event among terrestrial vertebrates and
 suggest that further high-resolution quantitative studies may help resolve
 the lack of consensus among palaeobiologists regarding this event.
description: Supplementary Data 1 - R
 output of occurrences used in final analysisR output of specimen
 occurrences used in the final analysis. This includes occurrences from the
 middle Permian remaining after pruning of specimens with unacceptably high
 uncertainty surrounding their stratigraphic provenance. It also includes
 occurrence data for the late Permian Tropidostoma AZ.Dayetal - Supplementary Data
 1.txtSupplementary Table 1 -
 Input data for analysisSupplementary Table 1.
 Excel sheet with occurrence data used in this study. Sheet 1 shows
 occurrences in the Eodicynodon, Tapinocephalus and Pristerognathus
 assemblage zones. Sheet 2 shows occurrences in the Tropidostoma Assemblage
 Zone. Explanation of data collection is in the Materials and
 Methods.Dayetal - Supplementary Table
 1.xlsx
DOI: 10.5061/dryad.s7ph4
title: Data from: Estimating population density and connectivity of American mink using spatial capture-recapture

description: Estimating the abundance or density of populations is fundamental to the
 conservation and management of species, and as landscapes become more
 fragmented, maintaining landscape connectivity has become one of the most
 important challenges for biodiversity conservation. Yet these two issues
 have never been formally integrated together in a model that
 simultaneously models abundance while accounting for connectivity of a
 landscape. We demonstrate an application of using capture-recapture to
 develop a model of animal density using a least-cost path model for
 individual encounter probability that accounts for non-Euclidean
 connectivity of a highly structured network. We utilized scat detection
 dogs (Canis lupus familiaris) as a means of collecting non-invasive
 genetic samples of American mink (Neovison vison) individuals, and used
 spatial capture-recapture models (SCR) to gain inferences about mink
 population density and connectivity. Density of mink was not constant
 across the landscape, but rather increased with increasing distance from
 city, town, or village centers, and mink activity was associated with
 water. The SCR model allowed us to estimate the density and spatial
 distribution of individuals across a 389 km2 area. The model was used to
 investigate patterns of space usage and to evaluate covariate effects on
 encounter probabilities, including differences between sexes. This study
 provides an application of capture-recapture models based on ecological
 distance, allowing us to directly estimate landscape connectivity. This
 approach should be widely applicable to provide simultaneous direct
 estimates of density, space usage, and landscape connectivity for a range
 of species.
description: Data files for American
 mink SCR studyMink data files (mink
 encounter histories, x,y coordinates of statespace, trap locations, and
 rivers)minkData.zip
DOI: 10.5061/dryad.870j3
title: Data from: A multivariate approach to infer locomotor modes in Mesozoic mammals

description: Ecomorphological diversity of Mesozoic mammals was presumably constrained
 by selective pressures imposed by contemporary vertebrates. In accordance,
 Mesozoic mammals for a long time had been viewed as generalized,
 terrestrial, small-bodied forms with limited locomotor specializations.
 Recent discoveries of Mesozoic mammal skeletons with distinctive
 postcranial morphologies have challenged this hypothesis. However,
 ecomorphological analyses of these new postcrania have focused on a single
 taxon, a limited region of the skeleton, or have been largely qualitative.
 For more comprehensive locomotor inference in Mesozoic mammals, we applied
 multivariate analyses to a morphometric data set of extant small-bodied
 mammals. We used 30 osteological indices derived from linear measurements
 of appendicular skeletons of 107 extant taxa that sample 15 orders and
 eight locomotor modes. Canonical variate analyses show that extant
 small-bodied mammals of different locomotor modes have detectable and
 predictable morphologies. The resulting morphospace occupation reveals a
 morphofunctional continuum that extends from terrestrial to scansorial,
 arboreal, and gliding modes, reflecting an increasingly slender
 postcranial skeleton with longer limb output levers adapted for speed and
 agility, and extends from terrestrial to semiaquatic/semifossorial and
 fossorial modes, reflecting an increasingly robust postcranial skeleton
 with shorter limb output levers adapted for powerful, propulsive strokes.
 We used this morphometric data set to predict locomotor mode in ten
 Mesozoic mammals within the Docodonta, Multituberculata, Eutriconodonta,
 “Symmetrodonta,” and Eutheria. Our results indicate that these fossil taxa
 represent five of eight locomotor modes used to classify extant taxa in
 this study, in some cases confirming and in other cases differing from
 prior ecomorphological assessments. Together with previous locomotor
 inferences of 19 additional taxa, these results show that by the Late
 Jurassic mammals had diversified into all but the saltatorial and active
 flight locomotor modes, and that this diversification was greatest in the
 Eutriconodonta and Multituberculata, although sampling of postcranial
 skeletons remains uneven across taxa and through time.
description: Supplementary
 Materials
DOI: 10.5061/dryad.7f912
title: Data from: The evolutionary stability of cross-sex, cross-trait genetic covariances

description: Although knowledge of the selective agents behind the evolution of sexual
 dimorphism has advanced considerably in recent years, we still lack a
 clear understanding of the evolutionary durability of cross-sex genetic
 covariances that often constrain its evolution. We tested the relative
 stability of cross-sex genetic covariances for a suite of homologous
 contact pheromones of the fruit fly Drosophila serrata, along a
 latitudinal gradient that these traits have diverged in mean. Using a
 Bayesian framework, which allowed us to account for uncertainty in all
 parameter estimates, we compared divergence in the total amounts and
 orientations of genetic variance across populations, finding divergence in
 orientation but not total variance. We then statistically compared
 orientation divergence of within-sex (G) to cross-sex (B) covariance
 matrices. In line with a previous theoretical prediction, we find that the
 cross-sex covariance matrix, B, is more variable than either male or
 female within-sex covariance matrix. Decomposition of B matrices into
 their symmetrical and non-symmetrical components revealed that instability
 is linked to the degree of asymmetry. We also find that the degree of
 asymmetry correlates with latitude suggesting a role for spatially varying
 natural selection in shaping genetic constraints on the evolution of
 sexual dimorphism.
description: CHC data for nine
 populations of D.serrataSix log contrast values
 from the CHC profiles of males and females from nine D.serrata
 populations, spanning the east coast of Australia. Lc1: 5,9-C24:2 Lc2:
 5,9-C25:2 Lc3: 9-C25:1 Lc5: 2-Me-C26 Lc7: 2-Me-C28 Lc8:
 5,9-C29:2stability_B_serrata.xls
DOI: 10.5061/dryad.4t13k
title: Data from: DNA barcoding of invasive plants in China: a resource for identifying invasive plants

description: Invasive plants have aroused attention globally for causing ecological
 damage and having a negative impact on the economy and human health.
 However, it can be extremely challenging to rapidly and accurately
 identify invasive plants based on morphology because they are an
 assemblage of many different families and many plant materials lack
 sufficient diagnostic characteristics during border inspections. It is
 therefore urgent to evaluate candidate loci and build a reliable genetic
 library to prevent invasive plants from entering China. In this study,
 five common single markers (ITS, ITS2, matK, rbcL and trnH-psbA) were
 evaluated using 634 species (including 469 invasive plant species in
 China, 10 new records to China, 16 potentially invasive plant species
 around the world but not introduced into China yet and 139 plant species
 native to China) based on three different methods. Our results indicated
 that ITS2 displayed largest intra- and interspecific divergence (1.72% and
 91.46%). Based on NJ tree method, ITS2, ITS, matK, rbcL and trnH-psbA
 provided 76.84%, 76.5%, 63.21%, 52.86% and 50.68% discrimination rates,
 respectively. The combination of ITS+matK performed best and provided
 91.03% discriminatory power, followed by ITS2+matK (85.78%). For
 identifying unknown individuals, ITS+matK had 100% correct identification
 rate based on our database, followed by ITS/ITS2 (both 93.33%) and
 ITS2+matK (91.67%). Thus, we propose ITS/ITS2+matK as the most suitable
 barcode for invasive plants in China. This study also demonstrated that
 DNA barcoding is an efficient tool for identifying invasive species.
description: all
 sequencesDNA Barcoding, invasive
 plants, ITS, ITS2, matKall_sequences.rartree files
DOI: 10.5061/dryad.67t23
title: Data from: Severe recent decrease of adult body mass in a declining insectivorous bird population

description: Migratory bird species that feed on air-borne insects are experiencing
 widespread regional declines, but these remain poorly understood.
 Agricultural intensification in the breeding range is often regarded as
 one of the main drivers of these declines. Here, we tested the hypothesis
 that body mass in breeding individuals should reflect habitat quality in
 an aerial insectivore, the tree swallow (Tachycineta bicolor), along a
 gradient of agricultural intensity. Our dataset was collected over 7 years
 (2005–2011) and included 2918 swallow captures and 1483 broods. Analyses
 revealed a substantial decline of the population over the course of the
 study (−19% occupancy rate), mirrored by decreasing body mass. This trend
 was especially severe in females, representing a total loss of 8% of their
 mass. Reproductive success was negatively influenced by intensive
 agriculture, but did not decrease over time. Interestingly, variation in
 body mass was independent of breeding habitat quality, leading us to
 suggest that this decline in body mass may result from carry-over effects
 from non-breeding areas and affect population dynamics through reduced
 survival. This work contributes to the growing body of evidence suggesting
 that declines in migratory aerial insectivores are driven by multiple,
 complex factors requiring better knowledge of year-round habitat use.
description: Female
 dataDataset comprising all
 captures of female tree swallows used in the study between 2005-2011. This
 dataset was used for analyses of body mass in females and a subset (only
 females captured at least in two different years) was used for analyses of
 within- vs between-individual change in body mass across
 years.femaledata.xlsMale dataDataset comprising all captures of male tree swallows used in the study between 2005-2011. This dataset was used for analyses of body mass in males.maledata.xlsBreeding success dataThis dataset comprises data on all clutches monitored between 2005-2011 and was used for analyses of breeding success (number of hatchlings and fledglings).clutchdata.xls
DOI: 10.5061/dryad.74tg7
title: Data from: Evolutionarily stable sex ratios and mutation load

description: Frequency-dependent selection should drive dioecious populations toward a
 1:1 sex ratio, but biased sex ratios are widespread, especially among
 plants with sex chromosomes. Here, we develop population genetic models to
 investigate the relationships between evolutionarily stable sex ratios,
 haploid selection, and deleterious mutation load. We confirm that when
 haploid selection acts only on the relative fitness of X and Y-bearing
 pollen and the sex ratio is controlled by the maternal genotype, seed sex
 ratios evolve toward 1:1. When we also consider haploid selection acting
 on deleterious mutations, however, we find that biased sex ratios can be
 stably maintained, reflecting a balance between the advantages of purging
 deleterious mutations via haploid selection, and the disadvantages of
 haploid selection on the sex ratio. Our results provide a plausible
 evolutionary explanation for biased sex ratios in dioecious plants, given
 the extensive gene expression that occurs across plant genomes at the
 haploid stage.
description: Hough et al. (2013).
 SupMat - Jan14