cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4tg23
title: Data from: Node-based measures of connectivity in genetic networks

description: At-site environmental conditions can have strong influences on genetic
 connectivity, and in particular on the immigration and settlement phases
 of dispersal. However, at-site processes are rarely explored in landscape
 genetic analyses. Networks can facilitate the study of at-site processes,
 where network nodes are used to model site-level effects. We used
 simulated genetic networks to compare and contrast the performance of 7
 node-based (as opposed to edge-based) genetic connectivity metrics. We
 simulated increasing node connectivity by varying migration in two ways:
 we increased the number of migrants moving between a focal node and a set
 number of recipient nodes, and we increased the number of recipient nodes
 receiving a set number of migrants. We found that two metrics in
 particular, the average edge weight and the average inverse edge weight,
 varied linearly with simulated connectivity. Conversely, node degree was
 not a good measure of connectivity. We demonstrated the use of average
 inverse edge weight to describe the influence of at-site habitat
 characteristics on genetic connectivity of 653 American martens (Martes
 americana) in Ontario, Canada. We found that highly connected nodes had
 high habitat quality for marten (deep snow and high proportions of
 coniferous and mature forest) and were farther from the range edge. We
 recommend the use of node-based genetic connectivity metrics, in
 particular, average edge weight or average inverse edge weight, to model
 the influences of at-site habitat conditions on the immigration and
 settlement phases of dispersal.
description: Mean landcover in
 buffers around marten sample locationsThis file includes the
 mean and standard deviation of the climate and landcover variables within
 each 9-km radius buffer around American marten (Martes americana) sampling
 sites (n=29) in Ontario, Canada.koen_landcover_in_buffers.csvMicrosatellite genotypes of American marten in Ontario, CanadaThis file contains genotypes (12 microsatellite loci) for 653 martens sampled at 29 sites in Ontario, Canada. See also: Koen EL, J Bowman, CJ Garroway, SC Mills, and PJ Wilson (2012) Landscape resistance and American marten gene flow. Landscape Ecology 27(1): 29-43.koen_marten_genotypes.csvSimulated microsatellite data and summaries of simulated dataThese files represent network metrics for the focal node only, derived from 25 replicates of the simulated data. Also included are examples of our simulated microsatellite data. ReadMe files are within the zipped folder.koen_SimulatedData.zip
DOI: 10.5061/dryad.hj13q
title: Data from: Ecology of tern flight in relation to wind, topography and aerodynamic theory

description: Flight is an economic mode of locomotion, because it is both fast and
 relatively cheap per unit of distance, enabling birds to migrate long
 distances and obtain food over large areas. The power required to fly
 follows a U-shaped function in relation to airspeed, from which context
 dependent ‘optimal’ flight speeds can be derived. Crosswinds will displace
 birds away from their intended track unless they make compensatory
 adjustments of heading and airspeed.We report on flight track measurements
 in five geometrically similar tern species ranging one magnitude in body
 mass, from both migration and the breeding season at the island of O ¨
 land in the Baltic Sea. When leaving the southern point of O ¨ land,
 migrating Arctic and common terns made a 608 shift in track direction,
 probably guided by a distant landmark. Terns adjusted both airspeed and
 heading in relation to tail and sidewind, where coastlines facilitated
 compensation. Airspeed also depended on ecological context (searching
 versus not searching for food), and it increased with flock size.
 Species-specific maximum range speed agreed with predicted speeds from a
 new aerodynamic theory. Our study shows that the selection of airspeed is
 a behavioural trait that depended on a complex blend of internal and
 external factors.
description: Tern flight
 dataData on flight speed
 measurements of five species of terns.
DOI: 10.5061/dryad.447sq
title: Data from: Nutrition shapes life-history evolution across species

description: Nutrition is a key component of life-history theory, yet we know little
 about how diet quality shapes life-history evolution across species. Here,
 we test whether quantitative measures of nutrition are linked to
 life-history evolution across 96 species of butterflies representing over
 50 independent diet shifts. We find that butterflies feeding on high
 nitrogen host plants as larvae are more fecund, but their eggs are smaller
 relative to their body size. Nitrogen and sodium content of host plants
 are also both positively related to eye size. Some of these relationships
 show pronounced lineage-specific effects. Testis size is not related to
 nutrition. Additionally, the evolutionary timing of diet shifts is not
 important, suggesting that nutrition affects life histories regardless of
 the length of time a species has been adapting to its diet. Our results
 suggest that, at least for some lineages, species with higher nutrient
 diets can invest in a range of fitness-related traits like fecundity and
 eye size while allocating less to each egg as offspring have access to a
 richer diet. These results have important implications for the evolution
 of life histories in the face of anthropogenic changes in nutrient
 availability.
description: individual_collection_dataHost plant nutrition and butterfly life history and morphological data for butterflies from museum collection. Each row represents an individual butterfly. Variables determined as described in associated manuscript. Average eye width measured in mm. Wing length measured in cm. Wing length was log transformed for analyses. Nutrient data is in units of % dry mass for host plant material, calculations described in manuscript.individual_field_dataHost plant nutrition, butterfly life history and morphological data from wild-collected butterflies. Each row represents an individual. Genitalia area was measured in mm^2, and wing length in cm. Wing length was log transformed for analysis. Nutrition data measured in % dry mass, calculated as described in the manuscript. This data is needed for the example code to work. Example code is located at: https://github.com/EMSwanson/Published-papers with filename "PGLS analyses for egg number and nitrogen females.R"butterfly_treeThis file contains the phylogeny used for the analyses in the associated paper. Example code for loading phylogeny, and running PGLS analysis for fecundity and nitrogen from the "individual_field_data.csv" located at: https://github.com/EMSwanson/Published-papers with filename "PGLS analyses for egg number and nitrogen females.R".
DOI: 10.5061/dryad.143r1
title: Data from: Interglacial microrefugia and diversification of a cactus species complex: phylogeography and palaeodistributional reconstructions for Pilosocereus aurisetus and allies

description: The role of Pleistocene climate changes in promoting evolutionary
 diversification in global biota is well documented, but the great majority
 of data regarding this subject come from North America and Europe, which
 were greatly affected by glaciation. The effects of Pleistocene changes on
 cold- and/or dry-adapted species in tropical areas where glaciers were not
 present remain sparsely investigated. Many such species are restricted to
 small areas surrounded by unfavourable habitats, which may represent
 potential interglacial microrefugia. Here, we analysed the phylogeographic
 structure and diversification history of seven cactus species in the
 Pilosocereus aurisetus complex that are restricted to rocky areas with
 high diversity and endemism within the Neotropical savannas of eastern
 South America. We combined palaeodistributional estimates with standard
 phylogeographic approaches based on two chloroplast DNA regions (trnT-trnL
 and trnS-trnG), exon 1 of the nuclear gene PhyC and 10 nuclear
 microsatellite loci. Our analyses revealed a phylogeographic history
 marked by multiple levels of distributional fragmentation, isolation
 leading to allopatric differentiation and secondary contact among
 divergent lineages within the complex. Diversification and demographic
 events appear to have been affected by the Quaternary climatic cycles as a
 result of isolation in multiple patches of xerophytic vegetation. These
 small patches presently harbouring P. aurisetus populations seem to
 operate as microrefugia, both at present and during Pleistocene
 interglacial periods; the role of such microrefugia should be explored and
 analysed in greater detail.
description: Bonatelli_etal_Pilosocereus_SSRdataSSR data from populations of six species of the Pilosocereus aurisetus group (Cactaceae)
DOI: 10.5061/dryad.07k4p
title: Data from: Tropical tree species traits drive soil cation dynamics via effects on pH: a proposed conceptual framework

description: Humid tropical forests are major players in the global carbon cycle,
 despite evidence that cations (rock-derived, positively charged ions) can
 limit or co-limit net primary productivity (NPP). In mature forests, tight
 cation cycling, i.e., without leaching losses, could maintain cation
 stocks on site. That mechanism does not explain how regenerating tropical
 secondary forest trees start from seeds and accrue large cation stocks in
 biomass, when growing on soils depleted in available cations. We propose a
 new mechanism that links tree species’ traits to soil cation availability
 via impacts on soil pH, a ‘master’ biogeochemical driver. We tested
 plot-level effects of tree species on soil pH, soil extractable cations,
 and cation accrual in biomass in a unique, 25-yr-old,
 randomized-complete-block experiment in which climate, soil, and previous
 land-use history were similar across four native tree species grown in
 mono-dominant plantations in Costa Rica. Surface-soil pH in this Oxisol,
 initially 4.52 (±0.02), declined to 4.14 (±0.02) under Pentaclethra
 macroloba, a nodulated legume, and increased to 4.71 (±0.08) under
 Vochysia guatemalensis, an aluminum (Al) accumulator. The range in pH
 corresponds to a five-fold difference in proton concentrations, which is
 sufficient to alter dispersion of organo-mineral colloids. Cation stocks
 in biomass differed across species by 1.7-, 1.9-, 2.8-, 2.9-, 3.1-, 3.5-,
 and 17.2-fold for iron (Fe), calcium (Ca), potassium (K), manganese (Mn),
 strontium (Sr), magnesium (Mg), and Al, respectively. Differential
 acquisition of available soil cations was an unlikely explanation for
 measured differences among species because changes in extractable soil
 cation stocks were unrelated to cation accrual in biomass. Soil pH and
 biomass cation stocks were highly correlated, however. By our proposed
 conceptual framework, species traits that strongly increase proton
 concentrations and decrease pH in soil, e.g., support of N fixation,
 increase colloid aggregation, reducing cation availability. Traits that
 reduce soil protons and increase pH, e.g., Al+3 accumulation, disperse
 colloids, thereby releasing cations occluded during pedogenesis. This
 highlights a novel biogeochemical role for the Al-accumulation trait,
 i.e., liberation of occluded soil cations. Further studies would clarify
 effects of soil pH on cation supply via colloid dispersion, and its
 importance for nutrient acquisition in cation-depleted soils.
description: Russell et al
 data_170724The field data were
 collected over the course of a 12-year field study at La Selva Biological
 Station, Costa Rica. The data file was created in Excel; this single file
 contains 10 sheets. Please see the first sheet in this file, labeled
 ‘Metadata’ for descriptions of the data.
DOI: 10.5061/dryad.1pj16
title: Data from: Sex-specific selection under environmental stress in seed beetles

description: Sexual selection can increase rates of adaptation by imposing stronger
 selection in males, thereby allowing efficient purging of the mutation
 load on population fitness at a low demographic cost. Indeed, sexual
 selection tends to be male-biased throughout the animal kingdom, but
 little empirical work has explored the ecological sensitivity of this sex
 difference. In this study, we generated theoretical predictions of
 sex-specific strengths of selection, environmental sensitivities and
 genotype-by-environment interactions, and tested them in seed beetles by
 manipulating either larval host plant or rearing temperature. Using
 fourteen isofemale lines, we measured sex-specific reductions in fitness
 components, genotype-by-environment interactions, and strength of
 selection (variance in fitness) in the juvenile and adult stage. As
 predicted, variance in fitness increased with stress, was consistently
 greater in males than females for adult reproductive success (implying
 strong sexual selection), but was similar in the sexes in terms of
 juvenile survival across all stress-levels. While genetic variance in
 fitness increased in magnitude under severe stress, heritability
 decreased, and particularly so in males. Moreover, genotype-by-environment
 interactions for fitness were common but specific to the type of stress
 and each sex and life stage, suggesting that new environments may change
 the relative alignment and strength of selection in males and females. Our
 study thus exemplifies how environmental stress can influence the relative
 forces of natural and sexual selection, as well as concomitant changes in
 genetic variance in fitness, which are predicted to have consequences for
 rates of adaptation in sexual populations.
description: Fitness
 dataJuvenile survival and
 adult reproductive success for isofemale lines of C. maculatus in 5
 different environments.
DOI: 10.5061/dryad.qn254
title: Data from: Hypothesised diprotomeric enzyme complex supported by stochastic modelling of Palytoxin-induced Na/K pump channels

description: The sodium-potassium pump (Na+/K+ pump) is crucial for cell physiology.
 Despite great advances in the understanding of this ionic pumping system,
 its mechanism is not completely understood. We propose the use of the
 Statistical Model Checker to investigate palytoxin-induced Na+/K+ pump
 channels. We modelled a system of reactions representing transitions
 between the conformational substates of the channel with parameters,
 concentrations of the substates, and reaction rates extracted from
 simulations reported in the literature, based on electrophysiological
 recordings in a whole-cell configuration. The model was implemented using
 the UPPAAL-SMC platform. Comparing simulations and probabilistic queries
 from stochastic system semantics with experimental data, it was possible
 to propose additional reactions to reproduce the single channel dynamic.
 The probabilistic analyses and simulations suggest that the
 palytoxin-induced Na+/K+ pump channel functions as a diprotomeric complex
 in which protein-protein interactions increase the affinity of the Na+/K+
 pump affinity for palytoxin.
description: PTX_Induced_Channel_Monomer_Vilallongaetal_Fig_2_3Source code implemented in UPPAAL to simulate activities of the channel through the Na/K-pump induced by the palytoxin. In this implementation, the palytoxin effect on the Na/K-pump is described considering the induced channel as a monomer.PTX_Induced_Channel_Diprotomer_Vilallongaetal_Fig_5_6Source code implemented in UPPAAL to simulate activities of the channel through the Na/K-pump induced by the palytoxin. In this implementation, the palytoxin effect on the Na/K-pump is described considering the induced channel as a diprotomeric complex.PTX_Induced_Channel_Vilallongaetal_Fig_5_6.xml
DOI: 10.5061/dryad.td161
title: Data from: Pollen dispersal in fragmented populations of the dioecious wind-pollinated tree, Allocasuarina verticillata (drooping sheoak, drooping she-oak; Allocasuarinaceae)

description: Vegetation clearing, land modification and agricultural intensification
 have impacted on many ecological communities around the world.
 Understanding how species respond to fragmentation and the scales over
 which functionality is retained, can be critical for managing biodiversity
 in agricultural landscapes. Allocasuarina verticillata (drooping sheoak,
 drooping she-oak) is a dioecious, wind-pollinated and -dispersed species
 with key conservation values across southeastern Australia. But vegetation
 clearing associated with agricultural expansion has reduced the abundance
 and spatial distribution of this species in many regions. Spatial genetic
 structure, relatedness among trees, pollen dispersal and mating patterns
 were examined in fragmented A. verticillata populations selected to
 represent the types of remnants that now characterise this species. Short
 scale spatial genetic structure (5–25 m) and relatedness among trees were
 observed in most populations. Unexpectedly, the two male trees closest to
 each female did not have a reproductive advantage accounting for only
 4–15% of the seed produced in larger populations. Biparental inbreeding
 was also generally low (&lt;4%) with limited evidence of seed crop
 domination by some male trees. More male trees contributed to seed crops
 in linear remnants (mean 17) compared to those from patch remnants (mean
 11.3) which may reflect differences in pollen dispersal within the two
 remnant types. On average, pollen travels ~100 m irrespective of remnant
 type but was also detected to have dispersed as far as 1 km in open
 landscapes. Low biparental inbreeding, limited reproductive assurance for
 near-neighbour and probably related males and variability in the distances
 over which females sample pollen pools suggest that some mechanism to
 prevent matings between relatives exists in this species.
description: PLOS ONE
 data
DOI: 10.5061/dryad.571
title: Data from: A new method to localize and test the significance of incongruence: detecting domain shuffling in the nuclear receptor superfamily

description: When a data set is partitioned, the resulting subsets may contain
 phylogenetically conflicting signals if they have different evolutionary
 histories. In a data set with many taxa, a single taxon that contains
 multiple phylogenetic histories may result in significant global
 incongruence, but no methods are available in a parsimony framework to
 localize incongruence to specific clades in a phylogeny and test the
 significance of incongruence on a local scale. Here we present a new
 method to quantify the conflict between data partitions for any clade in a
 phylogeny and to test the statistical significance of that conflict using
 a metric called the local incongruence length difference. We apply this
 method to the evolutionary history of the nuclear receptor superfamily, a
 large group of transcriptional regulators that play essential roles in
 metazoan development and physiology. All nuclear receptors are composed of
 several discrete domains, including one that binds to DNA response
 elements on specific target genes and another that binds to the
 appropriate ligand. We have performed combined and separate phylogenetic
 analyses of these two domains and have tested the hypothesis that nuclear
 receptors have evolved by a simple process of lineage splitting and
 divergence, without domain shuffling or other forms of sequence transfer
 between proteins. Our analysis indicates that significant conflict exists
 between the partitioned domains at a limited number of nodes on the tree,
 suggesting that several groups of receptors are "hybrid
 proteins" formed by domain shuffling or other forms of sequence
 transfer between more ancient nuclear receptors.
description: Thornton and Desalle
 Data Setthornton_desalle.nexus
DOI: 10.5061/dryad.km83c
title: Data from: Museum DNA reveals the demographic history of the endangered Seychelles warbler

description: The importance of evolutionary conservation – how understanding
 evolutionary forces can help guide conservation decisions – is widely
 recognized. However, the historical demography of many endangered species
 is unknown, despite the fact that this can have important implications for
 contemporary ecological processes and for extinction risk. Here, we
 reconstruct the population history of the Seychelles warbler (Acrocephalus
 sechellensis) – an ecological model species. By the 1960s, this species
 was on the brink of extinction, but its previous history is unknown. We
 used DNA samples from contemporary and museum specimens spanning 140 years
 to reconstruct bottleneck history. We found a 25% reduction in genetic
 diversity between museum and contemporary populations, and strong genetic
 structure. Simulations indicate that the Seychelles warbler was
 bottlenecked from a large population, with an ancestral Ne of several
 thousands falling to &lt;50 within the last century. Such a rapid
 decline, due to anthropogenic factors, has important implications for
 extinction risk in the Seychelles warbler, and our results will inform
 conservation practices. Reconstructing the population history of this
 species also allows us to better understand patterns of genetic diversity,
 inbreeding and promiscuity in the contemporary populations. Our approaches
 can be applied across species to test ecological hypotheses and inform
 conservation.
description: Spurgin et al 2014 Evol
 Apps FINALThis folder contains
 data and R scripts for the paper Spurgin et al. (2014) 'Museum DNA
 reveals the demographic history of the endangered Seychelles warbler'
 There are 2 files in the 'Data' folder - raw microsatellite
 genotypes for each individual in genepop format, and heterozygosity for
 each locus and population in csv format.
DOI: 10.5061/dryad.1kv04
title: Data from: Environmental effects on the detection of adaptation

description: Detecting adaptation involves comparing the performance of populations
 evolving in different environments. This detection may be confounded by
 effects due to the environment experienced by organisms prior to the test.
 We tested whether such confounding effects occur, using spider-mite
 selection lines on two novel hosts and one ancestral host, after 15
 generations of selection. Mites were either sampled directly from the
 selection lines, or subjected to a common juvenile or to a common maternal
 environment, mimicking the most frequent environmental manipulations.
 These environments strongly affected all life-history traits. Moreover,
 the detection of adaptation and of correlated responses on the ancestral
 host was inconsistent among environments in almost 20% of the cases.
 Indeed, we did not detect responses unambiguously for any life-history
 trait. This inconsistency was due to differential environmental effects on
 lines from different selection regimes. Therefore the detection of
 adaptation requires a careful control of these environmental effects.
description: datadryadraw data all life history traits