cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.vn707
title: Data from: Transmission and temporal dynamics of anther-smut disease (Microbotryum) on alpine carnation (Dianthus pavonius)

description: 1. Theory has shown that sterilizing diseases with frequency-dependent
 transmission (characteristics shared by many sexually transmitted
 diseases) can drive host populations to extinction. 2. Anther-smut disease
 (caused by Microbotryum sp.) has become a model plant pathogen system for
 studying the dynamics of vector and sexually transmitted diseases:
 infected individuals are sterilized, producing spores instead of pollen,
 and the disease is spread between reproductive individuals by insect
 pollinators. We investigated anther-smut disease in a heavily infected
 population of Dianthus pavonius (alpine carnation) over an eight-year
 period to determine disease impacts on host population dynamics. 3. Over
 the eight years, disease prevalence remained consistently high
 (&gt;40%) while the host population numbers declined by over 50%. 4.
 The observed rate of vector transmission to reproductive, adult hosts was
 inadequate to explain the high disease prevalence. Additional
 density-dependent aerial transmission to highly susceptible juveniles,
 indicated from experimental field and greenhouse studies, is likely to
 play a key role in maintaining the high disease prevalence. 5.
 Epidemiological models that accounted for the mixed transmission mode
 predicted an eventual decline in disease. 6. Synthesis: Our results
 demonstrate that high prevalence of a sterilizing disease does not
 necessarily drive host populations towards extinction and also highlights
 the importance of demographic studies for establishing the presence of
 alternative transmission modes.
description: Marked plant and spore
 deposition dataExcel file with 5 data
 sheets: 1)All marked adults. This mark recapture data for each individual
 in the adult-plant demography study. Columns Qx, Qy, dx, dy, and coin are
 all identifying information on the location of the plants. Status codes:
 D=diseased, H= healthy, X=dead, V=vegetative, HH=healthy hermaphrodite, MS
 or HMS = healthy male-sterile. Columns marked ‘present’ indicate survival
 (1=surv, 0=dead). Columns marked ‘flwr’ indicate whether or not a plant
 flowered (1=flowered, 0=did not flower). Columns marked ‘infl’ indicate
 the number of inflorescences produced. 2) Subset used for aster. This is
 the subset of the marked plants used for aster analyses. Only individuals
 that were present in 2009, had complete data (e.g. no ‘lost’ or ‘missing’
 years) and did not change disease status were included. 3) Implant data.
 This the complete data for the transplanted 1-year old plants in the
 implant experiment. 4) Spores on sticky traps. Spore counts from sticky
 traps laid out around 4 diseased plants, with three strips (A,B, and C)
 per plant. 5) Spore on flowers. Spore counts from sampled healthy flowers
 in transect 1.For
 dryad.xlsx
DOI: 10.5061/dryad.1593
title: Data from: Microsatellites reveal origin and genetic diversity of Eurasian invasions by one of the world's most notorious marine invader, Mnemiopsis leidyi (Ctenophora)

description: Marine invasions take place at an increasing rate. When occurring in
 blooms, zooplanktivorous comb jellies of the genus Mnemiopsis are able to
 cause pelagic regime shifts in coastal areas, and may cause the collapse
 of commercially important fish populations. Using microsatellites,
 developed for the first time in the phylum Ctenophora, we show that
 Mnemiopsis leidyi has colonized Eurasia from two source regions. Our
 preliminary data set included 4 sites within the putative source region
 (US East Coast and Gulf of Mexico), and 10 invaded locations in Eurasian
 waters. Bayesian clustering and phylogeographic approaches revealed the
 origin of earlier invasions of the Black and Caspian Sea in the 1980s /
 1990s within or close to the Gulf of Mexico, while the 2006-invasion of
 the North and Baltic Seas can be directly traced to New England (pairwise
 FST = 0). We found no evidence for mixing among both gene pools in the
 invaded areas. While the genetic diversity (allelic richness) remained
 similar in the Baltic Sea compared to the source region New England, it
 was reduced in the North Sea, supporting the view of an initial invasion
 of Northern Europe to a Baltic Sea port. In Black / Caspian Sea samples,
 we found a gradual decline in allelic richness compared to the Gulf of
 Mexico-region, supporting a stepping-stone model of colonization with two
 sequential genetic founder events. Our data also suggest that current
 practises to reduce biological invasions via treatment of ballast water
 are insufficient to prevent repeated invasions of gelatinous zooplankton.
description: MnemiopsisMsatDataGENETIXDryad.xls
DOI: 10.5061/dryad.sn6tv
title: Data from: Windows of opportunity for germination of riparian species after restoring water level fluctuations: a field experiment with controlled seed banks

description: 1. Restoration activities aiming at increasing vegetation diversity often
 try to stimulate both dispersal and germination. In wetlands, dispersal
 and germination are coupled as water and water level fluctuations (WLF)
 simultaneously influence seed transport and germination conditions (soil
 moisture). Water regime shifts have been shown to affect vegetation
 composition. However, the interactions between WLF, dispersal and
 subsequent germination as drivers of such changes are still poorly
 understood, especially within the complexity of a field situation. 2. We
 tested the effect of soil moisture on ten riparian species in the
 greenhouse and sowed these species on 135 field locations in nine wetlands
 with recently restored WLF. We used quantile regressions to test the
 effects of WLF on the window of opportunity for germination from sown
 seeds and other seeds naturally dispersed to our plots, as well as on
 community diversity. 3. Soil moisture significantly affected germination
 both in the greenhouse and in the field. In the complexity of a field
 situation, a flooding depth just below the soil level, an intermediate
 flooding duration and a high flooding frequency provided the best
 opportunities for maximal germination. This was because these conditions
 enhanced germination from the seed bank as well as increasing germination
 from dispersed seeds. Seedling diversity showed identical patterns. 4.
 Other known (i.e., light conditions) and unknown factors played a role as
 we found low and variable germination, even under optimal conditions. We
 found evidence that WLF can affect vegetation zonation as flooded seedling
 communities contained more species with high moisture affinity. 5.
 Synthesis and applications. Water level fluctuations provide clear windows
 of opportunity for germination both from the seed bank and from dispersed
 seeds. Water regime changes are therefore likely to strongly affect
 recruitment opportunities and subsequent community assembly in riparian
 ecosystems, for instance through climate change or management. Water level
 fluctuations can be used as management tool to stimulate plant recruitment
 and seedling diversity in riparian wetlands.
description: field and greenhouse
 data on germination of 10 wetland speciesThe datafile consists of
 two tabs, one containing germination measurements in the field and one
 containing germination data of the same species under greenhouse
 conditionsdata_sarneeletal_2014_JoApE.xlsx
DOI: 10.5061/dryad.1sv2t4c
title: Data from: Indirect interactions shape selection in a multi-species foodweb

description: Species do not live, interact, or evolve in isolation, but are instead
 members of complex ecological communities. In ecological terms, complex
 multi-species interactions can be understood by considering indirect
 effects that are mediated by changes in traits and abundances of
 intermediate species. Interestingly, traits and abundances are also
 central to our understanding of phenotypic selection, suggesting that
 indirect effects may be extended to understand evolution in complex
 communities. Here, we explore indirect ecological effects and their
 evolutionary corollary in a well-understood foodweb comprising a plant,
 its herbivores, and enemies that select for opposite defensive phenotypes
 in one of the herbivores. We show that ecological indirect interactions
 are mediated by changes to both the traits and abundances of intermediate
 species, and that these changes ultimately reduce enemy attack and weaken
 selection. We discuss the generality of the link between indirect effects
 and selection. We go on to argue that local adaptation and
 eco-evolutionary feedback may be less likely in complex multi-species
 foodwebs than in simpler food chains (e.g. coevolution). Overall,
 considering selection in complex interaction networks can facilitate the
 rapprochement of community ecology and evolution.
description: indirecteffect_fordryad
DOI: 10.5061/dryad.bp95q
title: Data from: Outlier loci detect intraspecific biodiversity amongst spring and autumn spawning herring across local scales

description: Herring, Clupea harengus, is one of the ecologically and commercially most
 important species in European northern seas, where two distinct ecotypes
 have been described based on spawning time; spring and autumn. To date, it
 is unknown if these spring and autumn spawning herring constitute
 genetically distinct units. We assessed levels of genetic divergence
 between spring and autumn spawning herring in the Baltic Sea using two
 types of DNA markers, microsatellites and Single Nucleotide Polymorphisms,
 and compared the results with data for autumn spawning North Sea herring.
 Temporally replicated analyses reveal clear genetic differences between
 ecotypes and hence support reproductive isolation. Loci showing
 non-neutral behaviour, so-called outlier loci, show convergence between
 autumn spawning herring from demographically disjoint populations,
 potentially reflecting selective processes associated with autumn spawning
 ecotypes. The abundance and exploitation of the two ecotypes have varied
 strongly over space and time in the Baltic Sea, where autumn spawners have
 faced strong depression for decades. The results therefore have practical
 implications by highlighting the need for specific management of these
 co-occurring ecotypes to meet requirements for sustainable exploitation
 and ensure optimal livelihood for coastal communities.
description: Clupea harengus
 genotypes_Gulf of RigaIndividual genotypes for
 six herring samples from the Gulf of Riga
DOI: 10.5061/dryad.6gs68
title: Data from: Delayed transmission selects for increased survival of vesicular stomatitis virus

description: Life-history theory predicts that traits for survival and reproduction
 cannot be simultaneous maximized in evolving populations. For this reason,
 in obligate parasites such as infectious viruses, selection for improved
 between-host survival during transmission may lead to evolution of
 decreased within-host reproduction. We tested this idea using experimental
 evolution of RNA virus populations, passaged under differing transmission
 times in the laboratory. A single ancestral genotype of Vesicular
 Stomatitis Virus (VSV), a negative-sense RNA Rhabdovirus, was used to
 found multiple virus lineages evolved in either ordinary 24-hour
 cell-culture passage, or in delayed passages of 48 hours. After 30
 passages (120 generations of viral evolution), we observed that delayed
 transmission selected for improved extracellular survival, which
 traded-off with lowered viral fecundity (slower exponential population
 growth, and smaller mean plaque size). To further examine the confirmed
 evolutionary trade-off, we obtained consensus whole-genome sequences of
 evolved virus populations, to infer phenotype-genotype associations.
 Results implied that increased virus survival did not occur via
 convergence; rather, improved virion stability was gained via independent
 mutations in various VSV structural proteins. Our study suggests that RNA
 viruses can evolve different molecular solutions for enhanced survival
 despite their limited genetic architecture, but suffer generalized
 reproductive trade-offs that limit overall fitness gains.
description: Viral fecundity - growth
 curve raw dataGrowth rates for the
 evolved viral strainsfecunditygrowthcurves.xlsxViral fecundity - plaque size raw dataThis compares the fecundity of the evolved virus strains by measuring the size of plaques formed after infectionplaquesizefecundity2.xlsViral extracellular survival - raw dataThis is the data on how well the evolved viruses survived for a given period of time across various temperaturestemperature data.xlsxViral xtracellular survival - cleanThis is a cleaner data set with the extracelluar survival data, organized by temperature and viral class.ProTrans_ECSdata.xlsxViral fecundity - cleanThis is the fecundity data, organized by virus strain and measurement type: both growth rate and plaque size data are included.ProTrans_FecundityData.xlsx
DOI: 10.5061/dryad.0pg63
title: Data from: Wolbachia do not live by reproductive manipulation alone: infection polymorphism in Drosophila suzukii and D. subpulchrella

description: Drosophila suzukii recently invaded North America and Europe. Populations
 in Hawaii, California, New York and Nova Scotia are polymorphic for
 Wolbachia, typically with &lt;20% infection frequency. The Wolbachia
 in D. suzukii, denoted wSuz, is closely related to wRi, the variant
 prevalent in continental populations of D. simulans. wSuz is also nearly
 identical to Wolbachia found in D. subpulchrella, plausibly D.
 suzukii's sister species. This suggests vertical Wolbachia
 transmission through cladogenesis (“cladogenic transmission”). The
 widespread occurrence of 7-20% infection frequencies indicates a stable
 polymorphism. wSuz is imperfectly maternally transmitted, with wild
 infected females producing on average 5-10% uninfected progeny. As
 expected from its low frequency, wSuz produces no cytoplasmic
 incompatibility (CI), i.e., no elevated embryo mortality when infected
 males mate with uninfected females, and no appreciable sex-ratio
 distortion. The persistence of wSuz despite imperfect maternal
 transmission suggests positive fitness effects. Assuming a balance between
 selection and imperfect transmission, we expect a fitness advantage on the
 order of 20%. Unexpectedly, Wolbachia-infected females produce fewer
 progeny than do uninfected females. We do not yet understand the
 maintenance of wSuz in D. suzukii. The absence of detectable CI in D.
 suzukii and D. subpulchrella makes it unlikely that CI-based mechanisms
 could be used to control this species without transinfection using novel
 Wolbachia. Contrary to their reputation as horizontally transmitted
 reproductive parasites, many Wolbachia infections are acquired through
 introgression or cladogenesis and many cause no appreciable reproductive
 manipulation. Such infections, likely to be mutualistic, may be central to
 understanding the pervasiveness of Wolbachia among arthropods.
description: R CodeThis R file contains all
 of the code necessary to reproduce the analyses presented in the paper
 (except the phylogenetics) and figs 1, 3, and 4.SWD_Wolbachia_code.RSWD_WolbachiaThis file contains all data needed to reproduce our results.SWD_phylo2This nexus file contains the alignment nDNA and mtDNA used in the paper, plus the MrBays block required to conduct the partitioned Bayesian analysis described in the paper. MrBayes v3.2.2 using mpi for faster processing. MrBayes was executed as follows: mpirun -n 5 mb SWD_phylo2.nex &gt; out.txtDros_COIaNexus file with aligned Drosophila COI data. To generate the neighbor joining tree I opened PAUP* , loaded the data , entered the command "nj" and then saved the tree output.SWD_COI_Accession_numbersGenBank accession numbers for DNA sequences generated for this paper
DOI: 10.5061/dryad.rg148qj4
title: Data from: Sibling competition arena: selfing and a competition arena can combine to constitute a barrier to gene flow in sympatry

description: Closely-related species coexisting in sympatry provide critical insight
 into the mechanisms underlying speciation and the maintenance of genetic
 divergence. Selfing may promote reproductive isolation by facilitating
 local adaptation, causing reduced hybrid fitness in parental environments.
 Here, we propose a novel mechanism by which selfing can further impair
 interspecific gene flow: selfing may act to ensure that non-hybrid progeny
 systematically co-occur whenever hybrid genotypes are produced. Under a
 competition arena, the fitness differentials between non-hybrid and hybrid
 progeny are then magnified, preventing development of interspecific
 hybrids. We investigate whether this “sibling competition arena” can
 explain the coexistence in sympatry of closely-related species of the
 plant fungal pathogens (Microbotryum) causing anther-smut disease. The
 probabilities of intra-promycelial mating (automixis), outcrossing, and
 sibling competition were manipulated in artificial inoculations to
 evaluate their contribution to reproductive isolation. We report that both
 intra-promycelial selfing and sibling competition significantly reduced
 rates of hybrid infection beyond that expected based solely upon selfing
 rates and non-competitive fitness differentials between hybrid and
 non-hybrid progeny. Our results thus suggest that selfing and a sibling
 competition arena can combine to constitute a barrier to gene flow and
 diminish selection for additional barriers to gene flow in sympatry.
description: Gibsonetal_Evolution_11-0823.R1_DataArchive
DOI: 10.5061/dryad.j01j0
title: Data from: Heterozygote advantage at MHC DRB may influence response to infectious disease epizootics

description: The effect of MHC polymorphism on individual fitness variation in the wild
 remains equivocal; however, much evidence suggests that heterozygote
 advantage is a major determinant. To understand the contribution of MHC
 polymorphism to individual disease resistance or susceptibility in natural
 populations, we investigated two MHC class II B loci, DQB and DRB, in the
 New Zealand sea lion (NZSL, Phocarctos hookeri). The NZSL is a threatened
 species which is unusually susceptible to death by bacterial infection at
 an early age; it has suffered three bacterial induced epizootics resulting
 in high mortality levels of young pups since 1997. The MHC DQB and DRB
 haplotypes of dead NZSL pups with known cause of death (bacteria,
 enteritis or trauma) were sequenced and reconstructed, compared to pups
 that survived beyond 2 months of age, and distinct MHC DRB allele
 frequency and genotype differences were identified. Two findings were
 striking: (i) one DRB allele was present only in dead pups, and (ii) one
 heterozygous DRB genotype, common in live pups, was absent from dead pups.
 These results are consistent with some functional relationship with these
 variants and suggest heterozygote advantage is operating at DRB. We found
 no association between heterozygosity and fitness at 17 microsatellite
 loci, indicating that general heterozygosity is not responsible for the
 effect on fitness detected here. This result may be a consequence of
 recurrent selection by multiple pathogen assault over recent years and
 highlights the importance of heterozygote advantage at MHC as a potential
 mechanism for fitness differences in wild populations.
description: DQB alignment file
 NZSLAll NZSL individuals,
 MHC DQB loci/DNA sequencesDQB alignment
 file.clustalDRB alignment
 fileAll NZSLs, MHC DRB
 clustal omega alignment fileMicrosatellite
 genotypesNZSL microsatellite
 genotypes for pups used in MHC study
DOI: 10.5061/dryad.m5p42
title: Data from: Devonian tetrapod-like fish reveals substantial parallelism in stem tetrapod evolution

description: The fossils assigned to the tetrapod stem group document the evolution of
 terrestrial vertebrates from lobe-finned fishes. During the past 18 years
 the phylogenetic structure of this stem group has remained remarkably
 stable, even when accommodating new discoveries such as the earliest known
 stem tetrapod Tungsenia and the elpistostegid (fish–tetrapod intermediate)
 Tiktaalik. Here we present a large lobe-finned fish from the Late Devonian
 period of China that disrupts this stability. It combines characteristics
 of rhizodont fishes (supposedly a basal branch in the stem group, distant
 from tetrapods) with derived elpistostegid-like and tetrapod-like
 characters. This mélange of characters may reflect either detailed
 convergence between rhizodonts and elpistostegids plus tetrapods, under a
 phylogenetic scenario deduced from Bayesian inference analysis, or a
 previously unrecognized close relationship between these groups, as
 supported by maximum parsimony analysis. In either case, the overall
 result reveals a substantial increase in homoplasy in the tetrapod stem
 group. It also suggests that ecological diversity and biogeographical
 provinciality in the tetrapod stem group have been underestimated.
description: The Nexus format
 fileThe Nexus format file
 for the maximum parsimony analysisHongyu_matrix_final_2017.nexThe Nexus format fileThe Nexus format file for the Bayesian inference analysisHongyu_matrix_final_2017simplifiedbayes.nex
DOI: 10.5061/dryad.hf49c
title: Data from: Footprints of divergent selection in natural populations of Castanopsis fargesii (Fagaceae)

description: Given predicted rapid climate change, an understanding of how
 environmental factors affect genetic diversity in natural populations is
 important. Future selection pressures are inherently unpredictable, so
 forest management policies should maintain both overall diversity and
 identify genetic markers associated with the environmental factors
 expected to change most rapidly, like temperature and rainfall. In this
 study, we genotyped 648 individuals in 28 populations of Castanopsis
 fargesii (Fagaceae) using 32 expressed sequence tag (EST)-derived
 microsatellite markers. After removing six loci that departed from
 Hardy–Weinberg equilibrium, we measured genetic variation, population
 structure and identified candidate loci putatively under selection by
 temperature and precipitation. We found that C. fargesii populations
 possessed high genetic diversity and moderate differentiation among them,
 indicating predominant outcrossing and few restrictions to gene flow.
 These patterns reduce the possible impact of stochastic effects or the
 influence of genetic isolation. Clear footprints of divergent selection at
 four loci were discovered. Frequencies of five alleles at these loci were
 strongly correlated with environmental factors, particularly extremes in
 precipitation. These alleles varied from being near fixation at one end of
 the gradient to being completely absent at the other. Our study species is
 an important forest tree in the subtropical regions of China and could
 have a major role in future management and reforestation plans. Our
 results demonstrate that the gene flow is widespread and abundant in
 natural populations, maintaining high diversity, while diversifying
 selection is acting on specific genomic regions.
description: original
 data