cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q4r60
title: Data from: Multifarious selection through environmental change: acidity and predator-mediated adaptive divergence in the moor frog (Rana arvalis)

description: Environmental change can simultaneously cause abiotic stress and alter
 biological communities, yet adaptation of natural populations to
 co-changing environmental factors is poorly understood. We studied
 adaptation to acid and predator stress in six moor frog (Rana arvalis)
 populations along an acidification gradient, where abundance of
 invertebrate predators increases with increasing acidity of R. arvalis
 breeding ponds. First, we quantified divergence among the populations in
 anti-predator traits (behaviour and morphology) at different rearing
 conditions in the laboratory (factorial combinations of acid or neutral pH
 and the presence or the absence of a caged predator). Second, we evaluated
 relative fitness (survival) of the populations by exposing tadpoles from
 the different rearing conditions to predation by free-ranging dragonfly
 larvae. We found that morphological defences (relative tail depth) as well
 as survival of tadpoles under predation increased with increasing pond
 acidity (under most experimental conditions). Tail depth and larval size
 mediated survival differences among populations, but the contribution of
 trait divergence to survival was strongly dependent on prior rearing
 conditions. Our results indicate that R. arvalis populations are adapted
 to the elevated predator pressure in acidified ponds and emphasize the
 importance of multifarious selection via both direct (here: pH) and
 indirect (here: predators) environmental changes.
description: larvaltraitsExp1_Egea-SerranoetalJan14Larval morphology divergence in the lab (Experiment 1)activityrepeated_Egea-SerranoetalJan14Larval activity analyses in the lab (Experiment 1, repeated measures)survivalexp2_Egea-SerranoetalJan14Survival under direct predation (Experiment 2)fielddata_Egea-Serranoetal21Jan14Larval trait divergence in the wild (Supplementary material)distancesEgea-SerranoetalJan14MRM data for among population trait divergence – survival difference associations (Supplementary material)
DOI: 10.5061/dryad.18n7k
title: Data from: Fine-scale refuges can buffer demographic and genetic processes against short-term climatic variation and disturbance: a 22 year case study of an arboreal marsupial

description: Ecological disturbance and climate are key drivers of temporal dynamics in
 the demography and genetic diversity of natural populations. Microscale
 refuges are known to buffer species’ persistence against environmental
 change, but the effects of such refuges on demographic and genetic
 patterns in response to short-term environmental variation are poorly
 understood. We quantified demographic and genetic responses of mountain
 brushtail possums (Trichosurus cunninghami) to rainfall variability
 (1992–2013) and to a major wildfire. We hypothesized that there would be
 underlying differences in demographic and genetic processes between an
 unburnt mesic refuge and a topographically exposed zone that was burnt in
 2009. Fire caused a 2-year decrease in survival in the burnt zone, but the
 population grew after the fire due to immigration, leading to increased
 expected heterozygosity. We documented a fire-related behavioural shift,
 where the rate of movement by individuals in the unburnt refuge to the
 burnt zone decreased after fire. Irrespective of the fire, there were
 long-term differences in demographic and genetic parameters between the
 mesic/unburnt refuge and the nonmesic/burnt zone. Survival was high and
 unaffected by rainfall in the refuge, but lower and rainfall-dependent in
 the nonmesic zone. Net movement of individuals was directional, from the
 mesic refuge to the nonmesic zone, suggesting fine-scale source–sink
 dynamics. There were higher expected heterozygosity (HE) and temporal
 genetic stability in the refuge, but lower HE and marked temporal genetic
 structure in the exposed habitat, consistent with reduced generational
 overlap caused by elevated mortality and immigration. Thus, fine-scale
 refuges can mediate the short-term demographic and genetic effects of
 climate and ecological disturbance.
description: Multistate CMR
 inputExcel file with
 multistate capture histories for male and female group of individuals in
 non-mesic.burnt (B) and mesic/unburnt (B) zones of the Cambarville study
 site. Columns can be concatenated to create MARK input file. Second
 worksheet includes dates of trapping sessions and temporal rainfall
 covriates.GenotypesMultilocus microsatellite genotypes of Trichosurus cunninghami in GenAlEx format. Individuals are grouped by trapping session, such that each individual appears mutliple times in the file. XY (UTM) coordinates are provided after the genotypes, followed by further information on trapping region and year of sampling, to allow for further data sorting.Data for GLMM of new capturesCapture records of individuals used for GLMM analysis of spatial and temporal variation in capture patterns and individual characteristicsData for analysis of female reproductive output
DOI: 10.5061/dryad.8f3bk
title: Data from: Molecular data and ploidal levels indicate several putative allopolyploidization events in the genus Potentilla (Rosaceae)

description: Several naturally occurring hybrids in Potentilla (Rosaceae) have been
 reported, but no molecular evidence has so far been available to test
 these hypotheses of hybridization. We have compared a nuclear and a
 chloroplast gene tree to identify topological incongruences that may
 indicate hybridization events in the genus. Furthermore, the monophyly and
 phylogenetic position of the proposed segregated genera Argentina, Ivesia
 and Horkelia have been tested. The systematic signal from the two
 morphological characters, style- and anther shape, has also been
 investigated by ancestral state reconstruction, to elucidate how well
 these characters concur with the results of the molecular phylogenies. Six
 major clades, Anserina, Alba, Fragarioides, Reptans, ivesioid and
 Argentea, have been identified within genus Potentilla. Horkelia, Ivesia
 and Horkeliella (the ivesioid clade), form a monophyletic group nested
 within Potentilla. Furthermore, the origin of the proposed segregated
 genus Argentina (the Anserina clade) is uncertain but not in conflict with
 a new generic status of the group. We also found style morphology to be an
 informative character that reflects the phylogenetic relationships within
 Potentilla. Five well-supported incongruences were found between the
 nuclear and the chloroplast phylogenies, and three of these involved
 polyploid taxa. However, further investigations, using low copy molecular
 markers, are required to infer the phylogeny of these species and to test
 the hypothesis of hybrid origin.
description: ITS.ETS.alignment.fig_3Alignment of 1075 DNA characters and 136 gap-code characters from the nuclear ribosomal markers 'ITS1 (partial), 5.8S rRNA gene and ITS2 (partial)' and 'external transcribed spacer (partial) and 18S rRNA gene (partial)'. Gaps are indicated by "-". Also included in the file are the instructions to MrBayes used to analyze the data.ITS.ETS.trees.fig_3The resulting 50% majority rule consensus trees (with and without branch length data) from the analysis of the data in "ITS.ETS.alignment.fig_3.nex". The tree with branch lengths was used for figure 3.trnLF-trnSG.alignemnt.fig4Alignment of 2722 DNA characters and 239 gap-code characters from the plastid markers 'tRNA-Leu gene (partial), trnL-trnF IGS and tRNA-Phe gene (partial)' and 'trnS-trnG IGS parital tRNA-Gly gene'. Gaps are indicated by "-". Also included in the file are the instructions to MrBayes used to analyze the data.trnLF-trnSG.tree.fig4The resulting 50% majority rule consensus trees (with and without branch length data) from the analysis of the data in "trnLF-trnSG.alignemnt.fig4.nex". The tree with branch lengths was used for figure 4.
DOI: 10.5061/dryad.p2f7c
title: Data from: Defining conservation units in a stocking-induced genetic melting pot: unravelling native and multiple exotic genetic imprints of recent and historical secondary contact in Adriatic grayling

description: The definition of conservation units is crucial for the sustainable
 management of endangered species, though particularly challenging when
 recent and past anthropogenic and natural gene flow might have played a
 role. The conservation of the European grayling, Thymallus thymallus, is
 particularly complex in its southern distribution area, where the Adriatic
 evolutionary lineage is endangered by a long history of anthropogenic
 disturbance, intensive stocking and potentially widespread genetic
 introgression. We provide mtDNA sequence and microsatellite data of 683
 grayling from 30 sites of Adriatic as well as Danubian and Atlantic
 origin. We apply Bayesian clustering and Approximate Bayesian Computation
 (ABC) to detect microgeographic population structure and to infer the
 demographic history of the Adriatic populations, to define appropriate
 conservation units. Varying frequencies of indigenous genetic signatures
 of the Adriatic grayling were revealed, spanning from marginal genetic
 introgression to the collapse of native gene pools. Genetic introgression
 involved multiple exotic source populations of Danubian and Atlantic
 origin, thus evidencing the negative impact of few decades of stocking.
 Within the Adige River system, a contact zone of western Adriatic and
 eastern Danubian populations was detected, with ABC analyses suggesting a
 historical anthropogenic origin of eastern Adige populations, most likely
 founded by medieval translocations. Substantial river-specific population
 substructure within the Adriatic grayling Evolutionary Significant Unit
 points to the definition of different conservation units. We finally
 propose a catalog of management measures, including the legal prohibition
 of stocking exotic grayling and the use of molecular markers in
 supportive- and captive-breeding programs.
description: final-ALL_Thymallus_aligned-ins.phymtDNA control region sequence alignment used to generate the phylogenetic tree presented in Fig. S1. Nexus format.SSR_datasetMicrosatellite data set, with individual information about sampling location and GenBank reference for mtDNA control regionnABCtemolo_4pops_SSRS_IMicrosatellite data set analysed in ABC
DOI: 10.5061/dryad.q4f09sr3
title: Data from: Dynamic transmission, host quality and population structure in a multi-host parasite of bumble bees

description: The evolutionary ecology of multi-host parasites is predicted to depend
 upon patterns of host quality and the dynamics of transmission networks.
 Depending upon the differences in host quality and transmission
 asymmetries, as well as the balance between intra- and inter-specific
 transmission, the evolution of specialist or generalist strategies is
 predicted. Using a trypanosome parasite of bumble bees we ask how host
 quality and transmission networks relate to parasite population structure
 across host species, and thus the potential for the evolution of
 specialist strains adapted to different host species. Host species
 differed in quality, with parasite growth varying across host species.
 Highly asymmetric transmission networks, together with differences in host
 quality, likely explain local population structure of the parasite across
 host species. However, parasite population structure across years was
 highly dynamic, with parasite populations varying significantly from one
 year to the next within individual species at a given site. This suggests
 that, whilst host quality and transmission may provide the opportunity for
 short-term host specialisation by the parasite, repeated bottlenecking of
 the parasite, in combination with its own reproductive biology, overrides
 these smaller scale effects, resulting in the evolution of a generalist
 parasite.
description: DataThis file contains the
 data analysed in both experiments 1 and 2. Each experiment's data set
 has been saved in different sheets. Both sheets have a legend with the
 description of the contents of each column.SourceCodeRarefactorThis file contains the explanation and the source code of the software written in C++ that was used to produce the rarefaction curves for the samplings of alleles found in a population.bootstrapCritidia1
DOI: 10.5061/dryad.3t761
title: Data from: A falsification of the citation impediment in the taxonomic literature

description: Current science evaluation still relies on citation performance, despite
 criticisms of purely bibliometric research assessments. Biological
 taxonomy suffers from a drain of knowledge and manpower, with poor
 citation performance commonly held as one reason for this impediment. But
 is there really such a citation impediment in taxonomy? We compared the
 citation numbers of 306 taxonomic and 2291 non-taxonomic research articles
 (2009–2012) on mosses, orchids, ciliates, ants, and snakes, using Web of
 Science (WoS) and correcting for journal visibility. For three of the five
 taxa, significant differences were absent in citation numbers between
 taxonomic and non-taxonomic papers. This was also true for all taxa
 combined, although taxonomic papers received more citations than
 non-taxonomic ones. Our results show that, contrary to common belief,
 taxonomic contributions do not generally reduce a journal's citation
 performance and might even increase it. The scope of many journals rarely
 featuring taxonomy would allow editors to encourage a larger number of
 taxonomic submissions. Moreover, between 1993 and 2012, taxonomic
 publications accumulated faster than those from all biological fields.
 However, less than half of the taxonomic studies were published in
 journals in WoS. Thus, editors of highly visible journals inviting
 taxonomic contributions could benefit from taxonomy's strong
 momentum. The taxonomic output could increase even more than at its
 current growth rate if: (i) taxonomists currently publishing on other
 topics returned to taxonomy and (ii) non-taxonomists identifying the need
 for taxonomic acts started publishing these, possibly in collaboration
 with taxonomists. Finally, considering the high number of taxonomic papers
 attracted by the journal Zootaxa, we expect that the taxonomic community
 would indeed use increased chances of publishing in WoS indexed journals.
 We conclude that taxonomy's standing in the present citation-focused
 scientific landscape could easily improve—if the community becomes aware
 that there is no citation impediment in taxonomy.
description: Supplementary
 MaterialOnline Appendices
 1-5
DOI: 10.5061/dryad.418p5
title: Data from: The role of phenotypic plasticity on population differentiation

description: Several evolutionary processes shape the genetic and phenotypic
 differentiation of populations. Among them, the joint effects of gene
 flow, selection and phenotypic plasticity are poorly known, especially
 when trying to understand how maladaptive plasticity affects population
 divergence. We extended a quantitative genetic model of Hendry et al.
 (2001) to describe these joint effects on phenotypic and additive genetic
 divergence between two populations, and their phenotypic and genetic
 differentiation (PST and QST). With individual-based simulations, we
 tested our model predictions and further modeled allelic differentiation
 at neutral (FST) and adaptive (FSTQ) loci. While adaptive phenotypic
 plasticity allows for large phenotypic divergence and differentiation
 despite high gene flow, maladaptive plasticity promotes genetic divergence
 and generates countergradient variation, under extensive migration with
 phenotypic differences sometimes opposed to genetic differences.
 Maladaptive plasticity can also promote adaptive phenotypic divergence by
 reducing the effective gene flow. Overall, plasticity decouples genetic
 from phenotypic differences between populations, and blurs the correlation
 between phenotypic divergence and local adaptation. By deriving models of
 population differentiation for three different life cycles, we further
 describe the effect of a species’ ecology on evolution in structured
 populations.
description: ini_files.tar.gzsimulation_results.tar.gzReadMe.pdf
DOI: 10.5061/dryad.mk609
title: Data from: Dissecting the hydrological niche: soil moisture, space and lifespan

description: Questions: Are communities structured on a hydrological (soil moisture)
 gradient? Is there spatial segregation into hydrological niches? What is
 the shape of the hydrological niches of individual species? Controlling
 for spatial autocorrelation, how much of the spatial structure in the
 community is due to variation in hydrology? Do annuals and perennials
 behave alike with respect to the above questions? Locations: La Mina in
 Moscosa Farm, Salamanca, western Spain (dehesa community) and Laguna Larga
 in the Urbión Peaks, Soria, central-northern Spain (alpine grassland).
 Methods: The presence of plant species was sampled in two contrasting
 field sites, for which we also built hydrological models. First, we
 reduced the dimensionality of the plant distribution data (non-metric
 multidimensional scaling) and measured the correlation between the
 resulting ordination and the hydrological gradient. Then we defined
 hydrological niches and tested niche segregation of plant species against
 null models (Pianka metrics). Finally, we characterized the hydrological
 niche of each species using generalised additive mixed models and
 partitioned the species distribution variance into (1) a hydrological
 component, (2) a linear trend component and (3) and a spatial component,
 defined through sets of spatial variables (Moran's eigenvector maps).
 Results: Both plant communities were primarily structured along
 hydrological gradients, and spatial segregation into hydrological niches
 occurred among perennial species, although not among annuals in the dehesa
 community. Dehesa annuals were spatially aggregated in the driest niches.
 Hydrological variation shaped the responses of 60% of the annual and about
 70% of the perennial species in both the dehesa meadow and the alpine
 community. Most responses were either monotonic or hump-shaped. Finally,
 spatially structured hydrological variation proved to be the main driver
 of spatially structured species composition in all cases. Conclusions:
 Linearly (gradient of slope) and topographically (at a fine scale)
 structured variation in hydrology is the main driver of spatially
 structured species composition in both communities. Our results support
 the ecological hypothesis that spatial niche segregation on soil moisture
 gradients is an important mechanism of co-existence for perennials in both
 test communities, although not for the species-rich sub-community of
 annuals in the dehesa meadow.
description: MoscosaFarm
 datasetUrbiónPeaks
 dataset
DOI: 10.5061/dryad.kh588
title: Data from: Species mtDNA genetic diversity explained by infrapopulation size in a host-symbiont system

description: Understanding what shapes variation in genetic diversity among species
 remains a major challenge in evolutionary ecology, and it has been seldom
 studied in parasites and other host-symbiont systems. Here, we studied
 mtDNA variation in a host-symbiont non-model system: 418 individual
 feather mites from 17 feather mite species living on 17 different
 passerine bird species. We explored how a surrogate of census size, the
 median infrapopulation size (i.e., the median number of individual
 parasites per infected host individual), explains mtDNA genetic diversity.
 Feather mite species genetic diversity was positively correlated with mean
 infrapopulation size, explaining 34% of the variation. As expected from
 the biology of feather mites, we found bottleneck signatures for most of
 the species studied but, in particular, three species presented extremely
 low mtDNA diversity values given their infrapopulation size. Their
 star-like haplotype networks (in contrast with more reticulated networks
 for the other species) suggested that their low genetic diversity was the
 consequence of severe bottlenecks or selective sweeps. Our study shows for
 the first time that mtDNA diversity can be explained by infrapopulation
 sizes, and suggests that departures from this relationship could be
 informative of underlying ecological and evolutionary processes.
description: Alignment of all species
 and all individualsalignment.fastaSampling detailsTable_S1_2.xlsSimulation dataTable_S2.csv
DOI: 10.5061/dryad.kf251
title: Data from: Systems and complexity thinking in the general practice literature: an integrative, historical narrative review

description: PURPOSE: Over the past 7 decades, theories in the systems and complexity
 sciences have had a major influence on academic thinking and research. We
 assessed the impact of complexity science on general practice/family
 medicine. METHODS: We performed a historical integrative review using the
 following systematic search strategy: medical subject heading [humans]
 combined in turn with the terms complex adaptive systems, nonlinear
 dynamics, systems biology, and systems theory, limited to general
 practice/family medicine and published before December 2010. A total of
 16,242 articles were retrieved, of which 49 were published in general
 practice/family medicine journals. Hand searches and snowballing retrieved
 another 35. After a full-text review, we included 56 articles dealing
 specifically with systems sciences and general/family practice. RESULTS:
 General practice/family medicine engaged with the emerging systems and
 complexity theories in 4 stages. Before 1995, articles tended to explore
 common phenomenologic general practice/family medicine experiences.
 Between 1995 and 2000, articles described the complex adaptive nature of
 this discipline. Those published between 2000 and 2005 focused on
 describing the system dynamics of medical practice. After 2005, articles
 increasingly applied the breadth of complex science theories to health
 care, health care reform, and the future of medicine. CONCLUSIONS: This
 historical review describes the development of general practice/family
 medicine in relation to complex adaptive systems theories, and shows how
 systems sciences more accurately reflect the discipline’s philosophy and
 identity. Analysis suggests that general practice/family medicine first
 embraced systems theories through conscious reorganization of its
 boundaries and scope, before applying empirical tools. Future research
 should concentrate on applying nonlinear dynamics and empirical modeling
 to patient care, and to organizing and developing local practices,
 engaging in community development, and influencing health care reform.
description: Supplementary Figures
 and Tables