cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.56894
title: Data from: Rapid and repeatable shifts in life-history timing of Rhagoletis pomonella (Diptera: Tephritidae) following colonization of novel host plants in the Pacific Northwestern United States

description: Host shifts of phytophagous insect specialists to novel plants can result
 in divergent ecological adaptation, generating reproductive isolation and
 potentially new species. Rhagoletis pomonella fruit flies in eastern North
 America underwent a host shift ~160 ya from native downy hawthorn
 (Crataegus mollis) to introduced, domesticated apple (Malus domestica).
 Divergent selection on diapause phenology related to the earlier fruiting
 time of apples versus downy hawthorns resulted in partial allochronic
 reproductive isolation between the fly races. Here, we test for how rapid
 and repeatable shifts in life-history timing are driving ecological
 divergence of R. pomonella in the Pacific Northwestern USA. The fly was
 introduced into the region via larval-infested apples 40–65 ya and now
 attacks native black hawthorn (Crataegus douglasii) and introduced
 ornamental hawthorn (Crataegus monogyna), in addition to early- and
 late-maturing apple varieties in the region. To investigate the
 life-history timing hypothesis, we used a field-based experiment to
 characterize the host-associated eclosion and flight activity patterns of
 adults, and the feeding times of larvae at a field site in Vancouver,
 Washington. We also assessed the degree to which differences in
 host-fruiting time generate allochronic isolation among apple-, black
 hawthorn-, and ornamental hawthorn-associated fly populations. We conclude
 that host-associated fly populations are temporally offset 24.4% to 92.6%
 in their seasonal distributions. Our results imply that R. pomonella
 possesses the capacity for rapid and repeatable shifts in diapause life
 history to match host-fruiting phenology, which can generate ecologically
 based reproductive isolation, and potentially biodiversity in the process.
description: Eclosion and Activity
 DataEclosion and flight
 activity data for each population (black hawthorn-, early apple-, late
 apple-, and ornamental hawthorn- associated flies) collected in 2013 in
 Vancouver, WA.Fruit
 DataSoftness (inverse of
 firmness) and diameter data for fruits from the four hosts analyzed in
 this study (black hawthorn, early-and late-ripening apple, and ornamental
 hawthorn.KVUO Airport Weather
 Data Vancouver WA_DRYADAbiotic data taken at a
 weather station (KVUO in Vancouver, WA) near the field site. Dates range
 from March to December 2013.Larval
 abundanceBoth numbers of fruit
 and numbers of larvae emerging from the fruit of each host to determine
 larval abundance on given dates.Soil
 TemperaturesSoil temperatures were
 recorded both inside and outside eclosion tents to determine if
 significant alterations in temperature resulted from the shading effects
 of the tents themselves.
DOI: 10.5061/dryad.73p72
title: Data from: Environmental fluctuations promote intraspecific diversity and population persistence via inflationary effects

description: The impact of temporal variation in the environment, specifically the
 amount of temporal autocorrelation, on population processes is of growing
 interest in ecology and evolutionary biology. It was recently discovered
 that temporal autocorrelation in the environment can significantly
 increase the abundance of populations that would otherwise have low, or
 even negative long-term growth rates (via so-called ‘inflationary
 effects’), provided that immigration from another source prevents
 extinction. Here we use a mathematical model to ask whether inflationary
 effects can also increase population persistence without immigration if
 different phenotypes within that population partition growth over time and
 buffer each other from extinction via mutation. Using a combination of
 analytical and numerical methods, we find that environmental
 autocorrelation can inflate the abundance of phenotypes that would
 otherwise be excluded from the population, provided that phenotypes are
 sufficiently different in their use of the environment. This inflation of
 abundance at the phenotypic level also generates an inflation of abundance
 at the population level. Remarkably, intraspecific inflationary effects
 can increase both phenotypic and whole population abundance even if one or
 all phenotypes are maladapted to the environment, as long as mutations
 prevent phenotypic extinction during periods of poor environmental
 conditions. Given the prevalence of temporally autocorrelated
 environmental variables in nature, intraspecific inflationary effects have
 the potential to be of widespread importance for population persistence as
 well as the maintenance of intraspecific diversity.
description: main data
 fileIIEdata.tar.gz is a zip
 file that contains all of the simulation data files.IIEdata.tar.gzIIEdataIIEdata.nb is a Mathematica notebook file containing the scripts for manipulating and graphing the raw data files contained in IIEdata.tar.gz.
DOI: 10.5281/zenodo.18386634
title: Design Patterns to Support the Usability and User Experience Evaluation of Dashboards for Decision Support Systems
DOI: 10.5281/zenodo.18386633
title: Design Patterns to Support the Usability and User Experience Evaluation of Dashboards for Decision Support Systems
DOI: 10.5061/dryad.012s5
title: Data from: Bottlenecks and selective sweeps during domestication have increased deleterious genetic variation in dogs

description: Population bottlenecks, inbreeding, and artificial selection can all, in
 principle, influence levels of deleterious genetic variation. However, the
 relative importance of each of these effects on genome-wide patterns of
 deleterious variation remains controversial. Domestic and wild canids
 offer a powerful system to address the role of these factors in
 influencing deleterious variation because their history is dominated by
 known bottlenecks and intense artificial selection. Here, we assess
 genome-wide patterns of deleterious variation in 90 whole-genome sequences
 from breed dogs, village dogs, and gray wolves. We find that the ratio of
 amino acid changing heterozygosity to silent heterozygosity is higher in
 dogs than in wolves and, on average, dogs have 2–3% higher genetic load
 than gray wolves. Multiple lines of evidence indicate this pattern is
 driven by less efficient natural selection due to bottlenecks associated
 with domestication and breed formation, rather than recent inbreeding.
 Further, we find regions of the genome implicated in selective sweeps are
 enriched for amino acid changing variants and Mendelian disease genes. To
 our knowledge, these results provide the first quantitative estimates of
 the increased burden of deleterious variants directly associated with
 domestication and have important implications for selective breeding
 programs and the conservation of rare and endangered species.
 Specifically, they highlight the costs associated with selective breeding
 and question the practice favoring the breeding of individuals that best
 fit breed standards. Our results also suggest that maintaining a large
 population size, rather than just avoiding inbreeding, is a critical
 factor for preventing the accumulation of deleterious variants.
description: DOG_jackknife_on_sweep_nonsweep_dataWOLF_jackknife_on_sweep_nonsweep_dataDogwolf_vcf_Filtered_coding_region_with_Miyata_and_GerpScore_annotated.vcfGene_IDs_overlapping_sweep_regions.final
DOI: 10.5061/dryad.b3604
title: Data from: Evolutionary dynamics of a quantitative trait in a finite asexual population

description: In finite populations, mutation limitation and genetic drift can hinder
 evolutionary diversification. We consider the evolution of a quantitative
 trait in an asexual population whose size can vary and depends explicitly
 on the trait. Previous work showed that evolutionary branching is certain
 (“deterministic branching”) above a threshold population size, but
 uncertain (“stochastic branching”) below it. Using the stationary
 distribution of the population’s trait variance, we identify three
 qualitatively different sub-domains of “stochastic branching” and
 illustrate our results using a model of social evolution. We find that in
 very small populations, branching will almost never be observed; in
 intermediate populations, branching is intermittent, arising and
 disappearing over time; in larger populations, finally, branching is
 expected to occur and persist for substantial periods of time. Our study
 provides a clearer picture of the ecological conditions that facilitate
 the appearance and persistence of novel evolutionary lineages in the face
 of genetic drift.
description: Analysis and simulation
 codeZip file includes three
 directories. (1) Mathematica code to derive the main results. (2) R code
 to generate the figures. (3) C code to run the
 simulations.codes.zip
DOI: 10.5061/dryad.3j380
title: Data from: Directional selection for flowering time leads to adaptive evolution in Raphanus raphanistrum (Wild radish)

description: Herbicides have been the primary tool for controlling large populations of
 yield depleting weeds from agro-ecosystems, resulting in the evolution of
 widespread herbicide resistance. In response, nonherbicidal techniques
 have been developed which intercept weed seeds at harvest before they
 enter the soil seed bank. However, the efficiency of these techniques
 allows an intense selection for any trait that enables weeds to evade
 collection, with early-flowering ecotypes considered likely to result in
 early seed shedding. Using a field-collected wild radish population, five
 recurrent generations were selected for early maturity and three
 generations for late maturity. Phenology associated with flowering time
 and growth traits were measured. Our results demonstrate the adaptive
 capacity of wild radish to halve its time to flowering following five
 generations of early-flowering selection. Early-maturing phenotypes had
 reduced height and biomass at maturity, leading to less competitive, more
 prostrate growth forms. Following three generations of late-flowering
 selection, wild radish doubled its time to flowering time leading to
 increased biomass and flowering height at maturity. This study
 demonstrates the potential for the rapid evolution in growth traits in
 response to highly effective seed collection techniques that imposed a
 selection on weed populations within agro-ecosystems at harvest.
description: Flowering time selection
 DryadFlowering time selection
 data
DOI: 10.5061/dryad.sm86q
title: Data from: Habitat monitoring and projections for threatened Canada lynx: linking the Landsat archive with carnivore occurrence and prey density

description: Habitat degradation is the leading threat to US federally listed species,
 but monitoring changes in habitat extent, fragmentation or quality is not
 generally included in species recovery plans. Consecutive satellite images
 of the same area through time are commonly used to assess landscape
 changes, and image data are increasingly used to generate predictor
 variables for species–habitat models. A time series of satellite images
 has, however, rarely been used in conjunction with a species–habitat model
 to map changes in habitat extent or to predict wildlife–habitat dynamics
 through time. We used a time series of forest disturbance encompassing 16
 530 km2 of forestland in Maine to map and quantify change in forest types
 that influence probability of occurrence (POC) of the threatened Canada
 lynx Lynx canadensis. Integration with a predictive occurrence model
 developed from landscape conditions c. 2004 allowed us to retrospectively
 (1973–2004) assess changes at 2- to 4-year intervals, update predictions
 (2004–2010) and project the spatial distribution and extent of lynx
 foraging habitat over the next decade. Between 1975 and 1991, 40% of
 mature conifer forest in our study area was removed by stand-replacing
 harvests, coincident with the last regional outbreak of eastern spruce
 budworm Choristoneura fumiferana (Clem.). As those areas regenerated
 between 1991 and 2010, POC increased dramatically as broad-scale habitat
 conditions for lynx's primary prey, snowshoe hare Lepus americanus,
 improved. Projections suggest that continued forest regrowth will provide
 new habitat over the next decade, but fragmentation will increase, and by
 2022 the habitat distribution will shift southwards into areas where
 climate change or interspecific competition may limit lynx population
 expansion. Synthesis and applications. Conservation planning for vagile
 species that depend on ephemeral forest types, such as the Canada lynx in
 the north-eastern USA, requires habitat monitoring strategies that can
 adapt to changing landscape conditions. Although Maine's lynx
 population has increased since the 1990s, we recommend that continued
 monitoring of lynx habitat and population status is critical given habitat
 and climate uncertainty. We also recommend that habitat management efforts
 be targeted not only at areas currently occupied by lynx but also where
 habitat loss is expected to occur near-term from succession or in
 anticipation of the next budworm outbreak.
description: JAPPL-2015-00665
 mapsForest and habitat data
 underlying Figure 3 in JAPPL-2015-00665.JAPPL-2015-00665 Figure
 2Forest and habitat
 change 1975-2010 (Figure 2 in JAPPL-2015-00665)
DOI: 10.5061/dryad.b58r0
title: Data from: Direct and indirect genetic effects in life history traits of flour beetles (Tribolium castaneum)

description: Indirect genetic effects (IGEs) are the basis of social interactions among
 conspecifics, and can affect genetic variation of non-social as well as
 social traits. We used flour beetles (Tribolium castaneum) of two
 phenotypically distinguishable populations to estimate genetic
 (co)variances and the effect of IGEs on three life-history traits:
 development time (DT), growth rate (GR), and pupal body mass (BM). We
 found that GR was strongly affected by social environment with IGEs
 accounting for 18% of the heritable variation. We also discovered a
 sex-specific social effect: male ratio in a group significantly affected
 both GR and BM. That is, beetles grew larger and faster in male-biased
 social environments. Such sex-specific IGEs have not previously been
 demonstrated in a non-social insect. Our results show that beetles that
 achieve a higher BM do so via a slower GR in response to social
 environment. Existing models of evolution in age-structured or
 stage-structured populations do not account for IGEs of social cohorts. It
 is likely that such IGEs have played a key role in the evolution of
 developmental plasticity shown by Tenebrionid larvae in response to
 density. Our results document an important source of genetic variation for
 GR, often overlooked in life-history theory.
description: Dataset with raw
 phenotypesDataset with raw data,
 no data cleaning has been donedataset flour
 beetles.csvcorrected
 dataDataset with corrected
 data, used for the genetic analysispedigree
 fileDataset with the
 pedigree informationpedigree.txt
DOI: 10.5061/dryad.6g181
title: Data from: Limited dispersal in an ectoparasitic mite, Laelaps giganteus, contributes to significant phylogeographic congruence with their rodent hosts, Rhabdomys

description: To explore how biogeography, parasite life history and host vagility
 influences evolutionary codivergences, we followed a comparative
 phylogeography approach using a host specific non-permanent mite, Laelaps
 giganteus that occurs on four rodent species within the genus Rhabdomys. A
 mtDNA COI haplotype network derived for 278 parasite specimens showed
 marked phylogeographic congruence with host distributions. Analysis of the
 less variable nuclear intron Tropomyosin was in part consistent with these
 results. Although distance-based cophylogenetic analyses in AXPARAFIT
 failed to support significant mtDNA codivergences (P ≥ 0.02), event-based
 analyses revealed significant cophylogeny between sampling localities of
 Rhabdomys and Laelaps using CORE-PA (P = 0.046) and JANE (P = 0.026; P =
 0.00). These findings, in conjunction with the weak congruence previously
 reported among the permanent ectoparasitic lice Polyplax and Rhabdomys,
 suggest that host-parasite intimacy is not the most important driver of
 significant codivergence in our study system. Instead the more restricted
 dispersal ability of L. giganteus, when compared to Polyplax, resulted in
 stronger spatial structuring and this could have resulted in significant
 codivergence. Host switching occurred predominantly on the edges of host
 distributions and was probably facilitated by climate-induced range
 shifts. When host ranges shift, the phylogeographic structure of L.
 giganteus is not reflecting the host movements since most of the nest
 bound parasites do not disperse with the host (they miss the boat) and the
 genetic contribution of the few dispersing mite individuals is often
 overwhelmed by the large number of individuals already present in nests
 within the new environment (causing them to drown on arrival).
description: Dryad
 filesAll Bayesian analysis,
 TCS files and coevolution analysis files for both gene fragments are
 included.
DOI: 10.5061/dryad.52t20
title: Data from: Allelic variation of BnaC.TT2.a and its association with seed coat color and fatty acids in rapeseed (Brassica napus L.)

description: Efficient molecular markers for the selection of rapeseed genetic
 materials with high seed oil content and ideal fatty acid (FA) composition
 are preferred by rapeseed breeders. Recently, we reported the molecular
 mechanism of TRANSPARENT TESTA 2 (TT2) in inhibiting seed FA biosynthesis
 in Arabidopsis. However, evidence showing the association of rapeseed TT2
 homologs and seed FA production are still insufficient. In this study, we
 collected 83 rapeseed (Brassica napus L.) landraces from different
 geographical backgrounds to conduct association mapping of BnaC.TT2.a in
 relation to seed coat color and FA biosynthesis. Population background was
 corrected by 84 pairs of SSR markers that were uniformly distributed among
 the linkage groups of the Tapidor-Ningyou-7 DH population. A single copy
 of BnaC.TT2.a for single nucleotide polymorphism (SNP) assay was cloned by
 a pair of previously reported specific primers. From the analysis of
 BnaC.TT2.a allelic variations using GLM+Q model, four SNPs on intron 1 of
 BnaC.TT2.a that were associated with seed FA were discovered. Moreover, an
 InDel at position 738 on exon 3 of BnaC.TT2.a indicated a change of
 protein function that was significantly associated with seed coat color,
 linoleic acid (C18:2), and total FA content. These findings revealed the
 role of BnaC.TT2.a in regulating the seed color formation and seed FA
 biosynthesis in rapeseed, thereby suggesting effective molecular markers
 for rapeseed breeding.
description: Zhou et al. PLOS ONE
 MS-data files (Tables)There are six tables in
 this file describing the results of traits as per our research objectives.
 Results could be studied from our manuscript submitted to PLOS ONE
 journal.Zhou et al.
 MS-Data.rtfZhou et al. PLOS ONE
 MS-FiguresThis file contains seven
 figures as a part of research findings in Zhou et al. manuscript submitted
 to PLOS ONE journal. Each figure is well defined with title and legends.
 Moreover, all the figures are well described in the text of our
 manuscript.Zhou et al.
 MS-Figures.pdf
DOI: 10.5061/dryad.v5r86
title: Data from: Microform-scale variations in peatland permeability and their ecohydrological implications

description: 1. The acrotelm-catotelm model of peatland hydrological and biogeochemical
 processes posits that the permeability of raised bogs is largely
 homogenous laterally but varies strongly with depth through the soil
 profile; uppermost peat layers are highly permeable while deeper layers
 are, effectively, impermeable. 2. We measured down-core changes in peat
 permeability, plant macrofossil assemblages, dry bulk density and degree
 of humification beneath two types of characteristic peatland microform –
 ridges and hollows – at a raised bog in Wales. Six 14C dates were also
 collected for one hollow and an adjacent ridge. 3. Contrary to the
 acrotelm-catotelm model, we found that deeper peat can be as highly
 permeable as near-surface peat and that its permeability can vary by more
 than an order of magnitude between microforms over horizontal distances of
 1-5 metres. 4. Our palaeo-ecological data paint a complicated picture of
 microform persistence. Some microforms can remain in the same position on
 a bog for millennia, growing vertically upwards as the bog grows. However,
 adjacent areas on the bog (&lt; 10 m distant) show switches between
 microform type over time, indicating a lack of persistence. 5. Synthesis.
 We suggest that the acrotelm-catotelm model should be used cautiously;
 spatial variations in peatland permeability do not fit the simple patterns
 suggested by the model. To understand how peatlands as a whole function
 both hydrologically and ecologically it is necessary to understand how
 patterns of peat physical properties and peatland vegetation develop and
 persist.
description: Baird_J_Ecol_K_summaryThis file contains the hydraulic conductivity values estimated from the piezometer tests.Baird_J_Ecol_K_raw_data_0.5_mThis file contains the raw hydraulic conductivity test data for the 0.5-m deep piezometers.Baird_J_Ecol_K_raw_data_0.9_mThis file contains the raw hydraulic conductivity test data for the 0.9-m deep piezometers.Baird_J_Ecol_plant_macsThis file contains the plant macrofossil data.Baird_J_Ecol_humThis file contains the peat humification data (on the von Post scale).Baird_J_Ecol_DBDThis file contains the peat dry bulk density data.