cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.sp800
title: Data from: Predictability and irreversibility of genetic changes associated with flower color evolution in Penstemon barbatus

description: Two outstanding questions in evolutionary biology are whether, and how
 often, the genetic basis of phenotypic evolution is predictable; and
 whether genetic change constrains evolutionary reversibility. We address
 these questions by studying the genetic basis of red flower color in
 Penstemon barbatus. The production of red flowers often involves the
 inactivation of one or both of two anthocyanin pathway genes, Flavonoid
 3',5'-hydroxylase (F3'5'h) and Flavonoid
 3'-hydroxylase (F3'h). We used gene expression and enzyme
 function assays to determine that redundant inactivating mutations to
 F3'5'h underlie the evolution of red flowers in P. barbatus.
 Comparison of our results to previously characterized shifts from blue to
 red flowers suggests that the genetic change associated with the evolution
 of red flowers is predictable: when it involves elimination of
 F3'5'H activity, functional inactivation or deletion of this
 gene tends to occur; however, when it involves elimination of F3'H
 activity, tissue-specific regulatory substitutions occur and the gene is
 not functionally inactivated. This pattern is consistent with emerging
 data from physiological experiments indicating that F3'h may have
 pleiotropic effects and is thus subject to purifying selection. The
 multiple, redundant inactivating mutations to F3'5'h suggest
 that reversal to blue-purple flowers in this group would be unlikely.
description: allQPCRdataIncludes all relevant relative expression data from the paper. In particular, F3'h, F3'5'h, Dfr, and Fls expression data. All data is relative to a single Penstemon neomexicanus floral cDNA sample and has been relativized to expression of elongation factor alpha.DFRenzymeDataData from DFR in vitro enzyme assays - includes relative amounts of DHK, DHQ, and DHM converted by each species.F2sAlleleSpecificExprAllele specific expression at F3'5'h in selected F2 individuals. The gene was amplified and cloned from cDNA. Then individual colonies were subjected to PCR and CAPS marker genotyping to determine the relative abundance of the two alleles in the cDNA sample.F3'5'hInVitroAssayDataF3'5'h in vitro enzyme assay data for Penstemon neomexicanus, P. barbatus, and our experimental constructs. DHQ production is considered an intermediate reaction product and was included in our measurement of "amount of DHK converted".PyroseqDataAllele-specific expression data obtained through pyrosequencing. We compared differences in F3'5'h allelic expression in cDNA to gDNA for three F1 individuals
DOI: 10.5061/dryad.bq3k83n
title: Data from: Genetic variation in mutualistic and antagonistic interactions in an invasive legume

description: Mutualists may play an important role in invasion success. The ability to
 take advantage of novel mutualists or survive and reproduce despite a lack
 of mutualists may facilitate invasion by those individuals with such
 traits. Here, we used two greenhouse studies to examine how soil microbial
 communities in general and mutualistic rhizobia in particular affect the
 performance of a legume species (Medicago polymorpha) that has invaded
 five continents. We performed two plant growth experiments with Medicago
 polymorpha, inoculating them with soil slurries in one experiment or
 rhizobial cultures in another experiment. For both experiments, we
 compared the growth of Medicago in competition with conspecific or
 heterospecific plants and examined variation among plant genotypes
 collected from the native and introduced ranges. We found that all
 genotypes experienced similar increases in biomass and formed more nodules
 that house rhizobia bacteria when inoculated with soil from a previously
 invaded site, compared to uninoculated plants or plants inoculated with
 soil from uninvaded and low invasion sites. In a second experiment, plants
 inoculated with rhizobia generally produced more biomass, had greater
 tolerance to interspecific competition, and had greater effects on
 competitor biomass than uninoculated plants. However, plant genotypes
 collected from the native range benefited more from rhizobia and were less
 tolerant of competition relative to genotypes collected from the
 introduced range. In the introduced range, compatible mutualists may not
 be readily available but competition is intense, causing Medicago to
 evolve to benefit less from interactions with rhizobia mutualists, while
 simultaneously becoming more tolerant of competition.
description: Trait data from Expts 1
 and 2Data from experiments 1
 and 2, in separate spreadsheetsDryad
 submission.xlsx
DOI: 10.5061/dryad.kg66r
title: Data from: Reconstructing the invasion history of Heracleum persicum (Apiaceae) into Europe

description: Sparse, incomplete and inappropriate historical records of invasive
 species often hamper invasive species management interventions. Population
 genetic analyses of invaders might provide a suitable context for the
 identification of their source populations and possible introduction
 routes. Here, we describe the population genetics of Heracleum persicum
 Desf. ex Fisch and trace its route of introduction into Europe.
 Microsatellite markers revealed a significantly higher genetic diversity
 of H. persicum in its native range, and the loss of diversity in the
 introduced range may be attributed to a recent genetic bottleneck.
 Bayesian cluster analysis on regional levels identified three and two
 genetic clusters in the native and the introduced ranges, respectively. A
 global structure analysis revealed two worldwide distinct genetic groups:
 one primarily in Iran and Denmark, the other primarily in Norway. There
 were also varying degrees of admixture in England, Sweden, Finland and
 Latvia. Approximate Bayesian computation indicated two independent
 introductions of H. persicum from Iran to Europe: the first one in Denmark
 and the second one in England. Finland was subsequently colonized by
 English populations. In contrast to the contemporary hypothesis of English
 origin of Norwegian populations, we found Finland to be a more likely
 source for Norwegian populations, a scenario supported by higher estimated
 historical migration from Finland to Norway. Genetic diversity per se is
 not a primary determinant of invasiveness in H. persicum. Our results
 indicate that, due to either pre-adaptations or rapid local adaptations,
 introduced populations may have acquired invasiveness after subsequent
 introductions, once a suitable environment was encountered.
description: Rijal_et_al_Data_filesFile contains microsatellite genotype data for Heracleum persicum and various input files for structure, Approximate Bayesian Computation, Isolation with migration and basic genetic diversity analyses.
DOI: 10.5061/dryad.842r3
title: Data from: Maintaining animal assemblages through single-species management: the case of threatened caribou in boreal forest

description: With the intensification of human activities, preserving animal
 populations is a contemporary challenge of critical importance. In this
 context, the umbrella species concept is appealing because preserving a
 single species should result in the protection of multiple co-occurring
 species. Practitioners, though, face the task of having to find suitable
 umbrellas to develop single-species management guidelines. In North
 America, boreal forests must be managed to facilitate the recovery of the
 threatened boreal caribou (Rangifer tarandus). Yet, the effect of caribou
 conservation on co-occurring animal species remains poorly documented. We
 tested if boreal caribou can constitute an effective umbrella for boreal
 fauna. Birds, small mammals, and insects were sampled along gradients of
 post-harvest and post-fire forest succession. Predictive models of
 occupancy were developed from the responses of 95 species to
 characteristics of forest stands and their surroundings. We then assessed
 the similarity of species occupancy expected between simulated harvested
 landscapes and a 90 000-km2 uncut landscape. Managed landscapes were
 simulated based on three levels of disturbance, two timber-harvest
 rotation cycles, and dispersed or aggregated cut-blocks. We found that
 management guidelines that were more likely to maintain caribou
 populations should also better preserve animal assemblages. Relative to
 fragmentation or harvest cycle, we detected a stronger effect of habitat
 loss on species assemblages. Disturbing 22%, 35%, and 45% of the landscape
 should result, respectively, in 80%, 60%, and 40% probability for caribou
 populations to be sustainable; in turn, this should result in regional
 species assemblages with Jaccard similarity indices of 0.86, 0.79, and
 0.74, respectively, relative to the uncut landscape. Our study thus
 demonstrates the value of single-species management for animal
 conservation. Our quantitative approach allows for the evaluation of
 management guidelines prior to implementation, thereby providing a tool
 for establishing suitable compromises between economic and environmental
 sustainability of human activities.
description: PA_animal_data_Bichet_et_al_2015Raw presence/absence data for birds, ants, ground beetles, flying beetles and small mammals sampled in Eastern-Canada boreal forest, together with habitat variables identified from digital eco-forest maps.Species_occurrence_probability_Bichet_et_al_2015Mean species occurrence probability in each management scenario, calculated as the sum of species-specific occurrence probability in each pixel divided by the number of pixels in each simulated landscape.
DOI: 10.5061/dryad.7jd15
title: Data from: Limits of use of social media for monitoring biosecurity events

description: Compared to applications that trigger massive information streams, like
 earthquakes and human disease epidemics, the data input for agricultural
 and environmental biosecurity events (ie. the introduction of unwanted
 exotic pests and pathogens), is expected to be sparse and less frequent.
 To investigate if Twitter data can be useful for the detection and
 monitoring of biosecurity events, we adopted a three-step process. First,
 we confirmed that sightings of two migratory species, the Bogong moth
 (Agrotis infusa) and the Common Koel (Eudynamys scolopaceus) are reported
 on Twitter. Second, we developed search queries to extract the relevant
 tweets for these species. The queries were based on either the taxonomic
 name, common name or keywords that are frequently used to describe the
 species (symptomatic or syndromic). Third, we validated the results using
 ground truth data. Our results indicate that the common name queries
 provided a reasonable number of tweets that were related to the ground
 truth data. The taxonomic query resulted in too small datasets, while the
 symptomatic queries resulted in large datasets, but with highly variable
 signal-to-noise ratios. No clear relationship was observed between the
 tweets from the symptomatic queries and the ground truth data. Comparing
 the results for the two species showed that the level of familiarity with
 the species plays a major role. The more familiar the species, the more
 stable and reliable the Twitter data. This clearly presents a problem for
 using social media to detect the arrival of an exotic organism of
 biosecurity concern for which public is unfamiliar.
description: Welvaert et al. Bogong
 moth and Common Koel surveillanceThe EXCEL datasheets
 "Common Moth", "Common Koel 1", "Common Koel
 2", Common Koel 3", "Symp Moth 1", "Symp
 Moth2", "Symp Koel 1", "Symp Koel 2", "Symp
 Koel 3", and "Symp Koel 4" are relevance summaries
 (0=non-relevant, 1=relevant) of de-identified tweets (from Twitter).
 Tweets were produced using the Commonwealth Scientific & Industrial
 Research Organisations Emergency Situation Awareness (ESA) system. They
 are derived by the searches defined within the associated manuscript. The
 survey data of Bogong Moth data are field data collected from the summit
 ridge of Mount Gingera, Brindabella Ranges, Australia. Please contact the
 correspondence author, Peter Caley (peter.caley@csiro.au), for further
 information.Welvaert_etal_Dryad_Data_Revised.xlsx
DOI: 10.5061/dryad.dc66k
title: Data from: Understanding the biological invasion risk posed by the global wildlife trade: propagule pressure drives the introduction and establishment of Nearctic turtles

description: Biological invasions are a key component of human-induced global change.
 The continuing increase in global wildlife trade has raised concerns about
 the parallel increase in the number of new invasive species. However, the
 factors that link the wildlife trade to the biological invasion process
 are still poorly understood. Moreover, there are analytical challenges in
 researching the role of global wildlife trade in biological invasions,
 particularly issues related to the under-reporting of introduced and
 established populations in areas with reduced sampling effort. In this
 work, we use high-quality data on the international trade in Nearctic
 turtles (1999–2009) coupled with a statistical modelling framework, which
 explicitly accounts for detection, to investigate the factors that
 influence the introduction (release, or escape into the wild) of globally
 traded Nearctic turtles and the establishment success (self-sustaining
 exotic populations) of slider turtles (Trachemys scripta), the most
 frequently traded turtle species. We found that the introduction of a
 species was influenced by the total number of turtles exported to a
 jurisdiction and the age at maturity of the species, while the
 establishment success of slider turtles was best associated with the
 propagule number (number of release events), and the number of native
 turtles in the jurisdiction of introduction. These results indicate both a
 direct and indirect association between the wildlife trade and the
 introduction of turtles and establishment success of slider turtles,
 respectively. Our results highlight the existence of gaps in the number of
 globally recorded introduction events and established populations of
 slider turtles, although the expected bias is low. We emphasize the
 importance of researching independently the factors that affect the
 different stages of the invasion pathway. Critically, we observe that the
 number of traded individuals might not always be an adequate proxy for
 propagule pressure and establishment success.
description: DataIntroductionNearcticTurtlesDataEstablishmentTrachemysDataSources
DOI: 10.5061/dryad.jr5fd
title: Data from: Impacts of dispersal on rapid adaptation and dynamic stability of Daphnia in fluctuating environments

description: Prior ecological research has shown that spatial processes can enhance the
 temporal stability of populations in fluctuating environments. Less
 explored is the effect of dispersal on rapid adaptation and its
 concomitant impact on population dynamics. For asexually reproducing
 populations, theory predicts that dispersal in fluctuating environments
 can facilitate asynchrony among clones and enhance stability by reducing
 temporal variability of total population abundance. This effect is
 predicted when clones exhibit heritable variation in environmental optima
 and when fluctuations occur asynchronously among patches. We tested this
 in the field using artificial ponds and metapopulations composed of a
 diverse assemblage of Daphnia pulex clones. We directly manipulated
 dispersal presence/absence and environmental fluctuations in the form of
 nutrient pulses. Consistent with predictions, dispersal enhanced temporal
 asynchrony among clones in the presence of nutrient pulses; this in turn
 stabilized population dynamics. This effect only emerged when patches
 experienced spatially asynchronous nutrient pulses (dispersal had no
 effect when patches were synchronously pulsed). Clonal asynchrony was
 driven by strong positive selection for a single clone that exhibited a
 performance advantage under conditions of low resource availability. Our
 work highlights the importance of dispersal as a driver of
 eco-evolutionary dynamics and population stability in variable
 environments.
description: Time series of clonal
 composition and diversityTime series of Daphnia
 pulex clone frequencies, abundances, log (abundance), log growth rates,
 and diversityClonal_composition_time_series.csvDaphnia pulex and chlorophyll a time seriesTime series of Daphnia pulex population density, log D. pulex density, chlorophyll-a concentration and log chlorophyll-a concentrationDpulex_density_chla_time_series.csvTemporal variability and synchrony measuresCoefficient of variation of Daphnia pulex density and chlorophyll-a concentration over time; synchrony of D. pulex clonal abundances over timeCV_synchrony_measures.csv
DOI: 10.5061/dryad.76k4j
title: Data from: Discovery and characterization of single nucleotide polymorphisms in coho salmon, Oncorhynchus kisutch

description: Molecular population genetic analyses have become an integral part of
 ecological investigation and population monitoring for conservation and
 management. Microsatellites have been the molecular marker of choice for
 such applications over the last several decades, but single nucleotide
 polymorphism (SNP) markers are rapidly expanding beyond model organisms.
 Coho salmon (Oncorhynchus kisutch) is native to the north Pacific Ocean
 and its tributaries, where it is the focus of intensive fishery and
 conservation activities. As it is an anadromous species, coho salmon
 typically migrate across multiple jurisdictional boundaries, complicating
 management and requiring shared data collection methods. Here, we describe
 the discovery and validation of a suite of novel SNPs and associated
 genotyping assays which can be used in the genetic analyses of this
 species. These assays include 91 that are polymorphic in the species and
 one that discriminates it from a sister species, Chinook salmon. We
 demonstrate the utility of these SNPs for population assignment and
 phylogeographic analyses, and map them against the draft trout genome. The
 markers constitute a large majority of all SNP markers described for coho
 salmon and will enable both population- and pedigree-based analyses across
 the southern part of the species native range.
description: Genotypic data for the
 ten validation populations of coho salmonGenotypes for 91 novel
 SNPs from ten populations of coho salmon from the West Coast of North
 America in standard GENEPOP format (two-digit). Data were generated using
 TaqMan assays (Applied Biosystems) and a Fluidigm EP1.coho_snpval91_GP2.txtTree file for Supplemental Figure 1NEXML tree file for the ten validation populations genotyped with the 91 SNP markers described in the paper.snpval91_CSNJ.nexml
DOI: 10.5061/dryad.rp131
title: Data from: Maternal size and age shape offspring size in a live-bearing fish, Xiphophorus birchmanni

description: Many studies of offspring size focus on differences in maternal investment
 that arise from ecological factors such as predation or competition.
 Classic theory predicts that these ecological factors will select for an
 optimal offspring size, and therefore that variation in a given
 environment will be minimized. Yet recent evidence suggests maternal
 traits such as size or age could also drive meaningful variation in
 offspring size. The generality of this pattern is unclear, as some studies
 suggest that it may represent non-adaptive variation or be an artifact of
 temporal or spatial differences in maternal environments. To clarify this
 pattern, we asked how maternal size, age and condition are related to each
 other in several populations of the swordtail Xiphophorus birchmanni. We
 then determined how these traits are related to offspring size, and
 whether they could resolve unexplained intra-population variation in this
 trait. We found that female size, age, and condition are correlated within
 populations; at some of these sites, older, larger females produce larger
 offspring than do younger females. The pattern was robust to differences
 among most, but not all, sites. Our results document a pattern that is
 consistent with recent theory predicting adaptive age- and size-dependence
 in maternal investment. Further work is needed to rule out non-adaptive
 explanations for this variation. Our results suggest that female size and
 age could play an under-appreciated role in population growth and
 evolution.
description: X. birchmanni life
 history dataLife history data from
 samples collected from wild populations of sheepshead swordtail, X.
 birchmanni, in Hidalgo, Mexico. NAs indicate missing data. Embryo staging
 was based on the methods described in Reznick DN, Endler JA. (1982)
 Evolution 86: 160-177, which in turn were based on the PhD thesis of SC
 Stearns. The embryo stage codes are as follows: VEE: Very early eyed EE:
 Early eyed LE: Late eyed VLE: Very late eye VY: Vitellogenic
 yolk
DOI: 10.5061/dryad.k086v
title: Data from: Influence of ecological and geological features on rangewide patterns of genetic structure in a widespread passerine.

description: Geological and ecological features restrict dispersal and gene flow,
 leading to isolated populations. Dispersal barriers can be obvious
 physical structures in the landscape; however microgeographic differences
 can also lead to genetic isolation. Our study examined dispersal barriers
 at both macro- and micro-geographical scales in the black-capped
 chickadee, a resident North American songbird. Although birds have high
 dispersal potential, evidence suggests dispersal is restricted by
 barriers. The chickadee’s range encompasses a number of physiological
 features which may impede movement and lead to divergence. Analyses of 913
 individuals from 34 sampling sites across the entire range using 11
 microsatellite loci revealed as many as 13 genetic clusters. Populations
 in the east were largely panmictic whereas populations in the western
 portion of the range showed significant genetic structure, which often
 coincided with large mountain ranges, such as the Cascade and Rocky
 Mountains, as well as areas of unsuitable habitat. Unlike populations in
 the central and southern Rockies, populations on either side of the
 northern Rockies were not genetically distinct. Furthermore, Northeast
 Oregon represents a forested island within the Great Basin; genetically
 isolated from all other populations. Substructuring at the
 microgeographical scale was also evident within the Fraser Plateau of
 central British Columbia, and in the southeast Rockies where no obvious
 physical barriers are present, suggesting additional factors may be
 impeding dispersal and gene flow. Dispersal barriers are therefore not
 restricted to large physical structures, although mountain ranges and
 large water bodies do play a large role in structuring populations in this
 study.
description: GenotypeData_DRYAD_Adams&Burg2014Genotype data for 913 individuals screened for 11 microsatellite loci.