cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j76c4k4
title: Data from: Genetic source-sink dynamics among naturally structured and anthropogenically fragmented puma populations

description: Fragmentation of wildlife populations is increasing on a global scale and
 understanding current population genetic structure, genetic diversity, and
 genetic connectivity is key to informing wildlife management and
 conservation. We genotyped 992 pumas (Puma concolor) at 42 previously
 developed microsatellite loci and identified 10 genetic populations
 throughout the states of California and Nevada, USA. Although some genetic
 populations had large effective population sizes, others were small and
 inbred. Genetic diversity was extremely variable (heterozygosity, uHe =
 0.33–0.53), with some populations nearly as low as an endangered
 subspecies, the Florida Panther (P. c. coryi, uHe = 0.24). Specifically,
 pumas in the Sierra Nevada were genetically diverse and formed the largest
 genetic source population in the region. In contrast, coastal and southern
 populations surrounded by urbanization had low genetic diversity,
 fragmented gene flow, and tended to be genetic sinks. The strong
 population genetic structuring of pumas across California (FST =
 0.05–0.39) is vastly different than other genetic studies in
 less-urbanized states, including our analysis in Nevada, where pumas had
 few barriers to gene flow and weak population differentiation. Our results
 have far-reaching conservation and management implications for pumas and
 indicate large-scale fragmentation in one of North America’s most
 biodiverse and rapidly-urbanizing regions.
description: Gustafson_etal_COGE
DOI: 10.5061/dryad.p515n265
title: Data from: Pyrosequencing of prey DNA in reptile faeces: analysis of earthworm consumption by slow worms

description: Little quantitative ecological information exists on the diets of most
 invertebrate feeding reptiles, particularly nocturnal or elusive species
 that are difficult to observe. In the UK and elsewhere, reptiles are
 legally required to be relocated before land development can proceed, but
 without knowledge of their dietary requirements the suitability of
 receptor sites cannot be known. Here we tested the ability of non-invasive
 DNA-based molecular diagnostics (454 pyrosequencing) to analyse reptile
 diets, with the specific aims of determining which earthworm species are
 exploited by slow worms (the legless lizard Anguis fragilis) and whether
 they feed on the deeper-living earthworm species which only come to the
 surface at night. Slow worm faecal samples from four different habitats
 were analysed using earthworm-specific PCR primers. We found that 86% of
 slow worms (N=80) had eaten earthworms. In lowland heath and marshy, acid
 grassland Lumbricus rubellus, a surface-dwelling epigeic species,
 dominated slow worm diet. In two other habitats, riverside pasture and
 calciferous coarse grassland, diet was dominated by deeper-living anecic
 and endogeic species. We conclude that all species of earthworm are
 exploited by these reptiles and lack of specialisation allows slow worms
 to thrive in a wide variety of habitats. Pyrosequencing of prey DNA in
 faeces showed promise as a practical, rapid and relatively inexpensive
 means of obtaining detailed and valuable ecological information on the
 diets of reptiles.
description: Caerphilly
 SiteEarthworm prey DNA from
 slow worms (Anguis fragilis) amplified in PCR with earthworm-specific 12S
 primers and sequenced using the GS-FLX (Roche) platform. The number of
 identical sequences returned is indicated by the "Count" heading
 before each sequence.region1.txtRingwood SiteEarthworm prey DNA from slow worms (Anguis fragilis) amplified in PCR with earthworm-specific 12S primers and sequenced using the GS-FLX (Roche) platform. The number of identical sequences returned is indicated by the "Count" heading before each sequence.region2.txtEast Cowes SiteEarthworm prey DNA from slow worms (Anguis fragilis) amplified in PCR with earthworm-specific 12S primers and sequenced using the GS-FLX (Roche) platform. The number of identical sequences returned is indicated by the "Count" heading before each sequence.region3.txtFlat Holm SiteEarthworm prey DNA from slow worms (Anguis fragilis) amplified in PCR with earthworm-specific 12S primers and sequenced using the GS-FLX (Roche) platform. The number of identical sequences returned is indicated by the "Count" heading before each sequence.region4.txt
DOI: 10.5061/dryad.8tg11
title: Data from: Effectiveness of continence promotion for older women via community organisations: a cluster randomised trial

description: Objectives: The primary objective of this cluster randomised controlled
 trial was to compare the effectiveness of the three experimental
 continence promotion interventions against a control intervention on
 urinary symptom improvement in older women with untreated incontinence
 recruited from community organisations. Setting: 71 community
 organisations across the United Kingdom Participants: 259 women aged 60
 years and older with untreated incontinence entered the trial; 88%
 completed the 3-month follow-up. Interventions: The three active
 interventions consisted of a single 60-minute group workshop on 1)
 continence education (20 clusters, 64 women); 2) evidence-based
 self-management (17 clusters, 70 women); or 3) combined education and
 self-management (17 clusters, 61 women). The control intervention was a
 single 60-minute educational group workshop on memory loss, polypharmacy
 and osteoporosis (17 clusters, 64 women). Primary and secondary outcome
 measures: The primary outcome was self-reported improvement in
 incontinence 3 months post-intervention at the level of the individual.
 The secondary outcome was change in the International Consultation on
 Incontinence Questionnaire (ICIQ). Changes in incontinence-related
 knowledge and behaviours were also assessed. Results: The highest rate of
 urinary symptom improvement occurred in the combined intervention group
 (66% vs 11% of the control group, prevalence difference 55%, 95% CI
 43%-67%, intracluster correlation 0). Thirty percent versus 6% of
 participants reported significant improvement respectively (prevalence
 difference 23%, 95% CI 10%-36%, intracluster correlation 0). The
 number-needed-to-treat was 2 to achieve any improvement in incontinence
 symptoms, and 5 to attain significant improvement. Compared to controls,
 the combined group reported an adjusted mean 2.05 point (95% CI 0.87-3.24)
 greater improvement on the ICIQ. Changes in knowledge and self-reported
 risk-reduction behaviours paralleled rates of improvement in all
 intervention arms. Conclusion: Continence education combined with
 evidence-based self-management improves symptoms of incontinence among
 untreated older women. Community organisations represent an untapped
 vector for delivering effective continence promotion interventions.
description: Urinary incontinence
 datasetUK_PROJECT_final_March152013_MJ_corrASH.csv
DOI: 10.5061/dryad.m2661
title: Data from: Water level fluctuations and metapopulation dynamics as drivers of genetic diversity in populations of three Tanganyikan cichlid fish species

description: Understanding how genetic variation is generated and maintained in natural
 populations, and how this process unfolds in a changing environment,
 remains a central issue in biological research. In this work, we analyzed
 patterns of genetic diversity from several populations of three cichlid
 species from Lake Tanganyika in parallel, using the mitochondrial DNA
 control region. We sampled populations inhabiting the littoral rocky
 habitats in both very deep, and very shallow areas of the lake. We
 hypothesized that the former would constitute relatively older, more
 stable and genetically more diverse populations, because they should have
 been less severely affected by the well-documented episodes of dramatic
 water level fluctuations. In agreement with our predictions, populations
 of all three species sampled in very shallow shorelines showed traces of
 stronger population growth than populations of the same species inhabiting
 deep shorelines. However, contrary to our working hypothesis, we found a
 significant trend towards increased genetic diversity in the younger,
 demographically less stable populations inhabiting shallow areas, in
 comparison to the older and more stable populations inhabiting the deep
 shorelines. We interpret this finding as the result of the establishment
 of metapopulation dynamics in the former shorelines, by the frequent
 perturbation and reshuffling of individuals between populations due to the
 lake level fluctuations. The repeated succession of periods of allopatric
 separation and secondary contact is likely to have further increased the
 rapid pace of speciation in lacustrine cichlids.
description: V. moorii mtDNA
 DloopsSequences of V. morii,
 from all localities. Sequence names match isolate names in supplementary
 table S1.Varia.fasTropheus sp. mtDNA DloopsSequences of Tropheus sp. from all localities. Sequence names match isolate names in supplementary table S1.Tropheus.fasE. cyanostictus mtDNA DloopsSequences of E. cyanostictus, from all localities. Sequence names match isolate names in supplementary table S1.Eretmodus.fas
DOI: 10.5061/dryad.g8f18
title: Data from: C4 photosynthesis evolved in warm climates but promoted migration to cooler ones

description: C4 photosynthesis is considered an adaptation to warm climates, where its
 functional benefits are greatest and C4 plants achieve their highest
 diversity and dominance. However, whether inherent physiological barriers
 impede the persistence of C4 species in cool environments remains debated.
 Here, we use large grass phylogenetic and geographic distribution datasets
 to test whether (i) temperature influences the rate of C4 origins, (ii)
 photosynthetic types affect the rate of migration among climatic zones,
 and (iii) C4 evolution changes the breadth of the temperature niche. Our
 analyses show that C4 photosynthesis in grasses originated in tropical
 climates, and that C3 grasses were more likely to colonize cold climates.
 However, migration rates among tropical and temperate climates were higher
 in C4 grasses. Therefore, while the origins of C4 photosynthesis were
 concentrated in tropical climates, its physiological benefits across a
 broad temperature range expanded the niche into warmer and enabled
 diversification into cooler environments.
description: grass_temp_dataSee README file.data.frame.csv
DOI: 10.5061/dryad.p89m3
title: Data from: Evolutionary history of the angiosperm flora of China

description: High species diversity may result from recent rapid speciation in a
 ‘cradle’ and/or the gradual accumulation and preservation of species over
 time in a ‘museum’1,2. China harbours nearly 10% of angiosperm species
 worldwide and has long been considered as both a museum, owing to the
 presence of many species with hypothesized ancient origins3,4, and a
 cradle, as many lineages have originated as recent topographic changes and
 climatic shifts—such as the formation of the Qinghai–Tibetan Plateau and
 the development of the monsoon—provided new habitats that promoted
 remarkable radiation5. However, no detailed phylogenetic study has
 addressed when and how the major components of the Chinese angiosperm
 flora assembled to form the present-day vegetation. Here we investigate
 the spatio-temporal divergence patterns of the Chinese flora using a dated
 phylogeny of 92% of the angiosperm genera for the region, a nearly
 complete species-level tree comprising 26,978 species and detailed spatial
 distribution data. We found that 66% of the angiosperm genera in China did
 not originate until early in the Miocene epoch (23 million years ago
 (Mya)). The flora of eastern China bears a signature of older divergence
 (mean divergence times of 22.04–25.39 Mya), phylogenetic overdispersion
 (spatial co-occurrence of distant relatives) and higher phylogenetic
 diversity. In western China, the flora shows more recent divergence (mean
 divergence times of 15.29–18.86 Mya), pronounced phylogenetic clustering
 (co-occurrence of close relatives) and lower phylogenetic diversity.
 Analyses of species-level phylogenetic diversity using simulated branch
 lengths yielded results similar to genus-level patterns. Our analyses
 indicate that eastern China represents a floristic museum, and western
 China an evolutionary cradle, for herbaceous genera; eastern China has
 served as both a museum and a cradle for woody genera. These results
 identify areas of high species richness and phylogenetic diversity, and
 provide a foundation on which to build conservation efforts in China.
description: R code – Function to
 recognize recent diversification centers and ancient preserving
 centersThe R script contains a
 function to recognize recent diversification centers and ancient
 preserving centers.R_code –
 Function_to_recognize_recent_diversification_centers_and_ancient_preserving_centers.pdfDated_phylogeny_for_Chinese_angiospermsThe tree file is a dated phylogeny for Chinese angiosperms calculated in treePL. The data set includes 5,864 species representing 2,665 genera native to China (ca. 92% of angiosperm genera in China).
DOI: 10.5061/dryad.4f6fd
title: Data from: The relationship between poverty and healthcare seeking among patients hospitalized with acute febrile illnesses in Chittagong, Bangladesh

description: Delays in seeking appropriate healthcare can increase the case fatality of
 acute febrile illnesses, and circuitous routes of care-seeking can have a
 catastrophic financial impact upon patients in low-income settings. To
 investigate the relationship between poverty and pre-hospital delays for
 patients with acute febrile illnesses, we recruited a cross-sectional,
 convenience sample of 527 acutely ill adults and children aged over 6
 months, with a documented fever ≥38.0°C and symptoms of up to 14 days’
 duration, presenting to a tertiary referral hospital in Chittagong,
 Bangladesh, over the course of one year from September 2011 to September
 2012. Participants were classified according to the socioeconomic status
 of their households, defined by the Oxford Poverty and Human Development
 Initiative’s multidimensional poverty index (MPI). 51% of participants
 were classified as multidimensionally poor (MPI&gt;0.33). Median time
 from onset of any symptoms to arrival at hospital was 22 hours longer for
 MPI poor adults compared to non-poor adults (123 vs. 101 hours) rising to
 a difference of 26 hours with adjustment in a multivariate regression
 model (95% confidence interval 7 to 46 hours; P = 0.009). There was no
 difference in delays for children from poor and non-poor households (97
 vs. 119 hours; P = 0.394). Case fatality was 5.9% vs. 0.8% in poor and
 non-poor individuals respectively (P = 0.001)—5.1% vs. 0.0% for poor and
 non-poor adults (P = 0.010) and 6.4% vs. 1.8% for poor and non-poor
 children (P = 0.083). Deaths were attributed to central nervous system
 infection (11), malaria (3), urinary tract infection (2), gastrointestinal
 infection (1) and undifferentiated sepsis (1). Both poor and non-poor
 households relied predominantly upon the (often informal) private sector
 for medical advice before reaching the referral hospital, but MPI poor
 participants were less likely to have consulted a qualified doctor. Poor
 participants were more likely to attribute delays in decision-making and
 travel to a lack of money (P&lt;0.001), and more likely to face
 catastrophic expenditure of more than 25% of monthly household income
 (P&lt;0.001). We conclude that multidimensional poverty is associated
 with greater pre-hospital delays and expenditure in this setting. Closer
 links between health and development agendas could address these
 consequences of poverty and streamline access to adequate healthcare.
description: Poverty and AFI
 DatasetData underlying the
 publication titled, "The relationship between poverty and healthcare
 seeking among patients hospitalized with acute febrile illnesses in
 Chittagong, Bangladesh."Poverty and AFI Anon Dataset
 3-5-16.dta
DOI: 10.5061/dryad.145g7
title: Data from: Using genetic tools to estimate the prevalence of non-native red deer (Cervus elaphus) in a Western European population

description: Game species like the red deer have been subjected to anthropogenic
 impacts for centuries. Translocations are often carried out—sometimes
 illegally—not only for sporting purposes, but also to increase trophy
 quality, reduce inbreeding, or mitigate bottlenecks after excessive
 persecution. Apart from the blurring of large-scale genetic structure,
 translocations without adequate quarantine measure risk introducing
 pathogens into potentially immunologically naïve populations. It is
 therefore important to understand the frequency of clandestine
 translocations. Identification of non-autochthonous animals and their
 potential origin is often difficult and, in red deer, has been hampered by
 the lack of large-scale genotypic datasets for comparison. In the present
 study, we make use of a recently published European-wide microsatellite
 dataset to detect and quantify the presence of non-autochthonous red deer
 in a large population sample (n = 1,780) from Central Europe (Belgium).
 Using factorial correspondence analysis, assignment tests and Bayesian
 clustering algorithms we arrive at an estimate of 3.7% non-autochthonous
 animals (or their descendants). Some of these animals were assigned to a
 nearby French population and may have immigrated into Belgium naturally,
 but the large majority must have been introduced by humans. Our analysis
 pointed to the British Isles and Germany/Poland as the potential origin of
 many introduced deer, regions known to have been source populations for
 translocations in Europe and beyond. We found evidence for recreational
 hunters using carcasses from farmed deer to fulfill mandatory hunting
 quotas. Our study is the first to quantify the extent of human-mediated
 introductions in a European game species at such a large scale with large
 and representative sample sizes.
description: Genotype
 fileFile containing the
 genetic profile as well as the geographic origin of each Belgian and
 European deerprepare.data.xlsx
DOI: 10.5061/dryad.8422
title: Data from: Disentangling the formation of contrasting tree-line physiognomies combining model selection and Bayesian parameterization for simulation models

description: Alpine tree-line ecotones are characterized by marked changes at small
 spatial scales that may result in a variety of physiognomies. A set of
 alternative individual-based models was tested with data from four
 contrasting Pinus uncinata ecotones in the central Spanish Pyrenees to
 reveal the minimal subset of processes required for tree-line formation. A
 Bayesian approach combined with Markov chain Monte Carlo methods was
 employed to obtain the posterior distribution of model parameters,
 allowing the use of model selection procedures. The main features of real
 tree lines emerged only in models considering nonlinear responses in
 individual rates of growth or mortality with respect to the altitudinal
 gradient. Variation in tree-line physiognomy reflected mainly changes in
 the relative importance of these nonlinear responses, while other
 processes, such as dispersal limitation and facilitation, played a
 secondary role. Different nonlinear responses also determined the presence
 or absence of krummholz, in agreement with recent findings highlighting a
 different response of diffuse and abrupt or krummholz tree lines to
 climate change. The method presented here can be widely applied in
 individual-based simulation models and will turn model selection and
 evaluation in this type of models into a more transparent, effective, and
 efficient exercise.
description: Puncinata
 treeline
DOI: 10.5061/dryad.2g257
title: Data from: Effective size of a wild salmonid population is greatly reduced by hatchery supplementation

description: Many declining and commercially important populations are supplemented
 with captive-born individuals that are intentionally released into the
 wild. These supplementation programs often create large numbers of
 offspring from relatively few breeding adults, which can have substantial
 population-level effects. We examined the genetic effects of
 supplementation on a wild population of steelhead trout (Oncorhynchus
 mykiss) from the Hood River, Oregon, by matching 12 run-years of hatchery
 steelhead back to their broodstock parents. We show that the effective
 number of breeders producing the hatchery fish (broodstock parents; Nb)
 was quite small (harmonic mean Nb=25 fish per brood-year vs. 373 for wild
 fish), and was exacerbated by a high variance in broodstock reproductive
 success among individuals within years. The low Nb caused hatchery fish to
 have decreased allelic richness, increased average relatedness, more loci
 in linkage disequilibrium, and substantial leve ls of genetic drift in
 comparison to their wild-born counterparts. We also documented a
 substantial Ryman-Laikre effect whereby the additional hatchery fish
 doubled the total number of adult fish on the spawning grounds each year,
 but cut the effective population size of the total population (wild and
 hatchery fish combined) by two thirds. We demonstrate that, in this
 system, the Ryman-Laikre effect is most severe when (1) more than 10% of
 fish allowed onto spawning grounds are from hatcheries and (2) hatchery
 fish have high reproductive success in the wild. These results emphasize
 the tradeoffs that arise when supplementation programs attempt to balance
 disparate goals (increasing production while maintaining genetic diversity
 and fitness).
description: Winter_run steelhead
 hatchery genotypesGenotype data from
 winter-run hatchery steelhead.Winter_run_Steelhead.txt
DOI: 10.5061/dryad.6sv75
title: Data from: Climate-mediated changes in predator–prey interactions in the fossil record: a case study using shell-drilling gastropods from the Pleistocene Japan Sea

description: Paleoecological studies enhance our understanding of biotic responses to
 climate change because they consider long timescales not accessible
 through observational and experimental studies. Using predatory drillholes
 produced on fossil bivalve shells by carnivorous gastropods, we provide an
 example of how climate change affected predator–prey interactions. We
 quantitatively examine temporal changes in fossil molluscan assemblages
 and predation patterns from the Pleistocene Japan Sea, which experienced
 drastic environmental changes in relation to glacial–interglacial climate
 cycles. We found significant changes in predation patterns associated with
 a decline in the abundance of warm-water molluscan species.
 Climate-mediated fluctuations in the eustatic sea level and resultant
 weakening of the Tsushima Warm Current caused a decline in a warm-water
 shell-drilling predator, which moderated the predation pressure and size
 relationship between the predators and the bivalve prey. Our results
 indicate that climate-mediated range shifts of species in present-day and
 future marine ecosystems can likewise increase altered predator–prey
 interactions.
description: Supplementary Table
 1Supplementary Table 1 -
 Number of molluscan shells obtained from six stratigraphic horizons of the
 Wakimoto-2 section in the Oga Peninsula, northern Japan. Source data for
 Figure 2A–C.Supplementary Table
 2Supplementary Table 2 -
 Number of Glycymeris yessoensis shells obtained from six stratigraphic
 horizons of the Wakimoto-2 section in the Oga Peninsula, northern Japan.
 Source data for Figure 2D and Table 1.Supplementary Table
 3Supplementary Table 3 -
 Characteristics of Glycymeris yessoensis shells obtained from six
 stratigraphic horizons of the Wakimoto-2 section in the Oga Peninsula,
 northern Japan. Source data for Figures 4–5 and Table
 1.