cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1hg75
title: Data from: Nonspecific PCR amplification by high-fidelity polymerases: implications for next-generation sequencing of AFLP markers.

description: High-fidelity “proofreading” polymerases are often used in library
 construction for next-generation sequencing projects, in an effort to
 minimize errors in the resulting sequence data. The increased template
 fidelity of these polymerases can come at the cost of reduced template
 specificity, and library preparation methods based on the AFLP technique
 may be particularly susceptible. Here, we compare AFLP profiles generated
 with standard Taq and two versions of a high-fidelity polymerase. We find
 that Taq produces fewer and brighter peaks than high-fidelity polymerase,
 suggesting that Taq performs better at selectively amplifying templates
 that exactly match the primer sequences. Because the higher accuracy of
 proofreading polymerases remains important for sequencing applications, we
 suggest that it may be more effective to use alternative library
 preparation methods.
description: FishPeakAreaPeak area calculated by Genemapper from ABI sequencer chromatograms for European minnow samples. Each column labelled "Peak X bp" is an AFLP locus with a fragment length of X base pairs. In the column "Polymerase", "PHU" refers to Phusion, "HOT" to Phusion Hot Start II, and "TAQ" to standard Taq polymerase.FishPeakHeightPeak height in Relative Fluorescent Units (RFU) calculated by Genemapper from ABI sequencer chromatograms for European minnow samples. Each column labelled "Peak X bp" is an AFLP locus with a fragment length of X base pairs. In the column "Polymerase", "PHU" refers to Phusion, "HOT" to Phusion Hot Start II, and "TAQ" to standard Taq polymerase.RicePeakAreaPeak area calculated by Genemapper from ABI sequencer chromatograms for rice samples. Each column labelled "Peak X bp" is an AFLP locus with a fragment length of X base pairs. In the column "Polymerase", "PHU" refers to Phusion, "HOT" to Phusion Hot Start II, and "TAQ" to standard Taq polymerase.RicePeakHeightPeak height in Relative Fluorescent Units (RFU) calculated by Genemapper from ABI sequencer chromatograms for rice samples. Each column labelled "Peak X bp" is an AFLP locus with a fragment length of X base pairs. In the column "Polymerase", "PHU" refers to Phusion, "HOT" to Phusion Hot Start II, and "TAQ" to standard Taq polymerase.
DOI: 10.5061/dryad.2dp4q
title: Data from: Female responses to experimental removal of sexual selection in Drosophila melanogaster

description: Background: Despite the common assumption that multiple mating should in
 general be favored in males, but not in females, to date there is no
 consensus on the general impact of multiple mating on female fitness.
 Notably, very little is known about the genetic and physiological features
 underlying the female response to sexual selection pressures. By combining
 an experimental evolution approach with genomic techniques, we
 investigated the effects of single and multiple matings on female
 fecundity and gene expression. We experimentally manipulated the
 opportunity for mating in replicate populations of Drosophila melanogaster
 by removing components of sexual selection, with the aim of testing
 differences in short term post-mating effects of females evolved under
 different mating strategies. Results: We show that monogamous females
 suffer decreased fecundity, a decrease that was partially recovered by
 experimentally reversing the selection pressure back to the ancestral
 state. The post-mating gene expression profiles of monogamous females
 differ significantly from promiscuous females, involving 9% of the genes
 tested (approximately 6% of total genes in D. melanogaster). These
 transcripts are active in several tissues, mainly ovaries, neural tissues
 and midgut, and are involved in metabolic processes, reproduction and
 signaling pathways. Conclusions: Our results demonstrate how the female
 post-mating response can evolve under different mating systems, and
 provide novel insights into the genes targeted by sexual selection in
 females, by identifying a list of candidate genes responsible for the
 decrease in female fecundity in the absence of promiscuity.
description: monoprom_fecundity1_continuously_housed_with_males_1_timepointmonoprom_fecundity2_single_mating_1_timepointmonoprom_fecundity3_single_mating_timeseriesmonoprom_fecundity4_continuously_housed_with_males_timeseriesmonoprom_REVERSED_fecundity_continuously_housed_with_males_1_timepointmonoprom_wing_length
DOI: 10.5061/dryad.tf704
title: Data from: Rapid diversification associated with ecological specialization in Neotropical Adelpha butterflies

description: Rapid diversification is often associated with morphological or ecological
 adaptations that allow organisms to radiate into novel niches. Neotropical
 Adelpha butterflies, which comprise over 200 species and subspecies, are
 characterized by extraordinary breadth in host plant use and wing colour
 patterns compared to their closest relatives. To examine the relationship
 between phenotypic and species diversification, we reconstructed the
 phylogenetic history of Adelpha and its temperate sister genus Limenitis
 using genomewide restriction-site-associated DNA (RAD) sequencing. Despite
 a declining fraction of shared markers with increasing evolutionary
 distance, the RAD-Seq data consistently generated well-supported trees
 using a variety of phylogenetic methods. These well-resolved phylogenies
 allow the identification of an ecologically important relationship with a
 toxic host plant family, as well as the confirmation of widespread,
 convergent wing pattern mimicry throughout the genus. Taken together, our
 results support the hypothesis that evolutionary innovations in both
 larvae and adults have permitted the colonization of novel host plants and
 fuelled adaptive diversification within this large butterfly radiation.
description: Haplotypes for all loci
 and individualsOutput of the final step
 of the pyRAD software pipeline (Eaton and Ree, 2013). File contains both
 haplotypes for 125 individuals at 144,699 loci. This is the
 "raw" data set subjected to additional filtering (see scripts)
 before phylogenetic analysis.all_haplotypes.txtPartitioning ScriptsThis folder contains a short pipeline (3 Python scripts) for partitioning loci haplotype data by the number of individuals without data. A README file explains how to use the scripts.Partitioning.zipPhylogenetic TreesReadable trees (.tre) corresponding to paper figures as follows: RAxML_concat--Figure 2; BEAST--Figure 3; RAxML_presabs, RAxML_SNP, and NJst--Figure S3; RAxML_PartitionX--Figure S4.Tree_files.zipRaw_Reads_AGTCAGRaw reads with index AGTCAG.AGTCAG.fastq.zipRaw_Reads_CTGAGARaw reads with index CTGAGA.CTGAGA.fastq.zipRaw_Reads_GACTTCRaw reads with index GACTTC.GACTTC.fastq.zipRaw_Reads_TCAGCTRaw reads with index TCAGCT.TCAGCT.fastq.zip
DOI: 10.5061/dryad.364j2
title: Data from: Molecular phylogenetics, species diversity, and biogeography of the Andean lizards Proctoporus (Squamata: Gymnophthalmidae)

description: The family Gymnophthalmidae comprises ca. 220 described species of
 Neotropical lizards distributed from southern Mexico to Argentina. It
 includes 36 genera, among them Proctoporus, which contains six currently
 recognized species occurring across the yungas forests and wet montane
 grasslands of the Amazonian versant of the Andes from central Peru to
 central Bolivia. Here, we investigate the phylogenetic relationships and
 species limits of Proctoporus and closely related taxa by analyzing 2121
 base pairs of mitochondrial (12S, 16S, and ND4) and nuclear (c-mos) genes.
 Our taxon sampling of 92 terminals includes all currently recognized
 species of Proctoporus and 15 additional species representing the most
 closely related groups to the genus. Maximum parsimony, maximum likelihood
 and Bayesian phylogenetic analyses recovered a congruent, fully resolved,
 and strongly supported hypothesis of relationships that challenges
 previous phylogenetic hypotheses and classifications, and biogeographic
 scenarios. Our main results are: (i) discovery of a strongly supported
 clade that includes all species of Proctoporus and within which are nested
 the monotypic Opipeuter xestus (a genus that we consider a junior synonym
 of Proctoporus), and two species of Euspondylus, that are therefore
 transferred to Proctoporus; (ii) the paraphyly of Proctoporus bolivianus
 with respect to P. subsolanus, which is proposed as a junior synonym of P.
 bolivianus; (iii) the detection of seven divergent and reciprocally
 monophyletic lineages (five of them previously assigned to P. bolivianus)
 that are considered confirmed candidate species, which implies that more
 candidate species are awaiting formal description and naming than
 currently recognized species in the genus; (iv) rejection of the
 hypothesis that Proctoporus diversified following a south to north pattern
 parallel to the elevation of the Andes; (v) species diversity in
 Proctoporus is the result of in situ diversification through vicariance in
 the grasslands of the high Andes, with at least five dispersals
 contributing to montane forest species.
description: Proctoporus_12SSequence alignment for the 12S rRNA mitochondrial gene region. Please refer to Table 1 of the associated manuscript for specimen information.Proctoporus_16SSequence alignment for the 16S rRNA mitochondrial gene region. Please refer to Table 1 of the associated manuscript for specimen information.Proctoporus_ND4Sequence alignment for the ND4 rRNA mitochondrial gene region. Please refer to Table 1 of the associated manuscript for specimen information.Proctoporus_CMOSSequence alignment for the C-mos gene region. Please refer to Table 1 of the associated manuscript for specimen information.
DOI: 10.5061/dryad.pj5sf05
title: Data from: High levels of polyandry, but limited evidence for multiple paternity, in wild populations of the western rock lobster (Panulirus cygnus)

description: Polyandry, where multiple mating by females results in the temporal and
 spatial overlap of ejaculates from two or more males, is taxonomically
 widespread and occurs in varying frequencies within and among species. In
 decapods (crabs, lobsters, crayfish and prawns), rates of polyandry are
 likely to be variable, but the extent to which patterns of multiple
 paternity reflect multiple mating, and thus are shaped by post-mating
 processes that bias fertilization towards one or a subset of mated males,
 is unclear. Here, we use microsatellite markers to examine the frequency
 of multiple mating (presence of spermatophores from two or more males) and
 patterns of paternity in wild populations of western rock lobster
 (Panulirus cygnus). Our data confirm that &gt;45% of females had
 attached spermatophores arising from at least two males (i.e. confirming
 polyandry), but we found very limited evidence for multiple paternity;
 among 24 clutches sampled in this study, only two arose from
 fertilisations by two or more males. Single inferred paternal genotypes
 accounted for all remaining progeny genotypes in each clutch, including
 several instances when the mother had been shown to mate with two or more
 males. These findings highlight the need for further work to understand
 whether polyandry is adaptive and to uncover the mechanisms underlying
 post-mating paternity biases in this system.
description: Microsatellite
 dataData file with male,
 female and clutch genotypes.DATA FILE FOR ARCHIVE
 Genotypes_WRL_FINAL_.xlsx
DOI: 10.5061/dryad.8h007
title: Data from: Interactions among symbionts operate across scales to influence parasite epidemics

description: Parasite epidemics may be influenced by interactions among symbionts,
 which can depend on past events at multiple spatial scales. Within host
 individuals, interactions can depend on the sequence in which symbionts
 infect a host, generating priority effects. Across host individuals,
 interactions can depend on parasite phenology. To test the roles of
 parasite interactions and phenology in epidemics, we embedded multiple
 cohorts of sentinel plants, grown from seeds with and without a vertically
 transmitted symbiont, into a wild host population, and tracked foliar
 infections caused by three common fungal parasites. Within hosts, parasite
 growth was influenced by coinfections, but coinfections were often
 prevented by priority effects among symbionts. Across hosts, parasite
 phenology altered host susceptibility to secondary infections, symbiont
 interactions and ultimately the magnitude of parasite epidemics. Together,
 these results indicate that parasite phenology can influence parasite
 epidemics by altering the sequence of infection and interactions among
 symbionts within host individuals.
description: 2015_Fescue_phenology_interactions_experimentThe dataset contains 11 columns, described below. date = date that the leaf was surveyed for infection Tiller = tiller number on the plant (for some plants, the original tiller had to be replaced) ID = Plant ID number. Endophyte = Infection status of the seed by the fungal endophyte, Epichloë coenophiala. Leaf = Leaf number, indicating the relative age of each leaf on a tiller, with lower numbers corresponding to older leaves. LeafID = a unique ID for each leaf (combination of ID, Tiller, and Leaf). cohort = The experimental cohort the plant ID belongs to. There were three cohorts. The first cohort was placed on 22 June 2015, during the Colletotrichum epidemic, but before other parasite epidemics began. The second cohort was placed on 27 July 2015, shortly after the start of the Rhizoctonia epidemic, but before the Puccinia epidemic began. The third cohort was placed on 21 September 2015, shortly after the start of the Puccinia epidemic, when all three parasites were present. leaf.emergence = the date that each leaf emerged. For leaves that emerged before the start of the experiment, this date was set to the date that the plant was placed in the field. Puccinia, Colletotrichum, Rhizoctonia = the percent leaf area damaged by Puccinia, Colletotrichum, and Rhizoctonia, respectively. This is a measurement of infection severity.
DOI: 10.5061/dryad.bb7gp
title: Data from: Environmental heterogeneity leads to higher plasticity in dry-edge populations of a semiarid Chilean shrub: insights into climate change responses

description: 1.Interannual variability in climatic conditions should be taken into
 account in climate change studies in semiarid ecosystems. It may determine
 differentiation in phenotypic plasticity among populations, with
 populations experiencing higher environmental heterogeneity showing higher
 levels of plasticity. 2.The ability of populations to evolve key
 functional traits and plasticity may determine the survival of plant
 populations under the drier and more variable climate expected for
 semiarid ecosystems. 3.Working with populations of the semiarid Chilean
 shrub Senna candolleana along its entire distribution range, we assessed
 inter- and intra-population variation in functional traits as well as in
 their plasticity in response to water availability. We measured
 morphological and physiological traits related to drought resistance in
 both field conditions and in a greenhouse experiment, where drought
 response was evaluated under two water availability treatments. 4.All
 populations responded plastically, but higher precipitation heterogeneity
 in dry-edge populations seemed to have selected for more plastic genotypes
 compared to populations growing at mesic sites and with more homogeneous
 environmental conditions. 5.Synthesis: Our results suggest adaptive
 plasticity since higher levels of phenotypic plasticity were positively
 associated with plant performance. However, we did not find evidence for
 genetic variation for plasticity within populations. To the extent that
 phenotypic plasticity may play a key role in future persistence,
 populations at mesic sites may be more vulnerable to climate change due to
 their lower plasticity and their current limitations to evolve novel norms
 of reaction. Conversely, although Senna candolleana populations at the
 dry-edge are exposed to higher levels of stress, they may be less
 susceptible to climate change in view of their greater plasticity. We
 highlight the need to consider population differentiation in both mean
 traits and their plasticity to model realistic scenarios of species
 distribution under climate change.
description: data
 base_LazaroNogal_JEcol-2014-0400.R1Common garden data base:
 Population differences in functional traits of Senna candolleana under two
 water availability levels (moist and drought) measured in common garden
 conditions in four populations and 10 families per population, along an
 aridity and precipitation heterogeneity gradient of Central Chile. Field
 measurements data base: functional traits related to drought resistance
 measured in the field in January 2011 along an aridity and precipitation
 heterogeneity gradient.
DOI: 10.5061/dryad.6qg43
title: Data from: Community-level flammability declines over 25 years of plant invasion in grasslands

description: 1. Exotic plant invasions can alter fire regimes in plant communities.
 Invaders often possess traits that differ from native plants in the
 community, resulting in increases or declines in community-level
 flammability, changing fire regimes, and potentially causing long-term
 modifications to plant community composition. Although considering traits
 of multiple invaders and native species together is useful to better
 understand how invasions change community-level flammability, few studies
 have done this. 2 Measured morphological and flammability traits of 51
 native and exotic plant species common in tussock grasslands in New
 Zealand’s south-eastern South Island to examine relationships between
 morphology and whole-plant and shoot-level flammability. Plant community
 data from 103 permanent transects in this region measured over a 25 year
 period (c. 1982-2007) were used to determine how flammability changed with
 increasing levels of plant invasion. 3. Invasion by exotic plants has led
 to reduced community-level flammability due to shifts from native tussock
 grasses with high flammability and high fuel loads to mat-forming exotic
 forbs with low flammability and little fuel. These changes will likely
 lead to considerable alterations to the fire regime, resulting in lower
 intensity fires that burn more patchily and for shorter amounts of time,
 potentially causing further changes in floristic composition. We found
 considerable differences in flammability across the wide range of species
 and growth forms that we studied, emphasising the importance of
 quantifying species-level flammability and the need to avoid treating
 grasslands as homogenous in terms of their flammability. Total biomass,
 leaf length and leaf area were the traits most positively correlated with
 flammability in these tussock grasslands. 4. SYNTHESIS. We show how plant
 invasions over decadal timescales have reduced the community-level
 flammability of tussock grasslands and, for the first time, demonstrate
 how this can be driven by exotic forbs. The total biomass of constituent
 species is a useful surrogate for community flammability across a wide
 range of species and growth forms in both temperate grasslands and savanna
 ecosystems and should be used in dynamic global vegetation models to
 assess how flammability varies under various global change scenarios.
description: Morphological and
 flammability traits of NZ tussock grasslandsThis dataset contains 3
 files: 1) Morphological and flammability traits measured at the shoot
 level for each sample. 2) Morphological traits measured at the leaf level
 for each subsample. 3) Morphological traits related to moisture content
 measured for each subsample.Data_community_flammability.zip
DOI: 10.5061/dryad.d9r3321
title: Data from: Impact of sexually antagonistic genital morphologies on female reproduction and wild population demography

description: Sexual conflict is a strong driver of evolution. The evolutionary outcomes
 of sexual conflict can, in turn, influence ecological processes within
 populations, e.g., demography. However, evidence for the latter hypothesis
 is scarce, especially in the wild. Here, we show that sexual conflict is
 associated with demographic processes determining population size in the
 ground beetle Carabus insulicola with elaborate male and female genitalia,
 based on individual- and population-level analyses. We found that sexually
 antagonistic selection can operate on the genitalia: longer male genitalia
 can be beneficial in sperm competition but decrease female reproductive
 success with increased egg dumping, while longer female genitalia are
 resistant to this male harassment via decreased egg dumping and increased
 fertilization rate. As expected from sexually antagonistic coevolution due
 to sexual conflict, we detected coevolutionary divergence between male and
 female genital sizes among populations. In parallel with decrease in
 female reproductive success, more harmful males with longer genitalia and
 less resistant females with shorter genitalia were related to small
 effective population sizes. Thus, sexual conflict may promote
 coevolutionary diversification between sexual traits, and this was
 associated with a demographic process. Our findings provide an insight
 into sex-driven eco-evolutionary dynamics in the wild.
description: Morphology data from 9
 populationsBody and genital sizes
 of males and females in 9 study populations of Carabus insulicola. MBL,
 male body length; CPL, copulatory piece length; FBL, female body length;
 VAL, vaginal appendix length.morphology_9pops.xlsGenetic data from 9 populationsMicrosatellite genotypes of individuals in 9 study populations of Carabus insulicola. Analyzed 6 loci are based on Takami and Katada (2001) Mol Ecol Notes. Data are arranged in GenAlEx format.microsatellites_9pops.xlsExperimental data from 2 populationsMorphological and behavioral data of individuals from 2 study populations (Aobayama and Ohshima) of Carabus insulicola.experiment_2pops.xlsx
DOI: 10.5061/dryad.9410t
title: Data from: The effect of top-predator presence and phenotype on aquatic microbial communities

description: The presence of predators can impact a variety of organisms within the
 ecosystem, including microorganisms. Because the effects of fish predators
 and their phenotypic differences on microbial communities have not
 received much attention, we tested how the presence/absence, genotype, and
 plasticity of the predatory three-spine stickleback (Gasterosteus
 aculeatus) influence aquatic microbes in outdoor mesocosms. We reared lake
 and stream stickleback genotypes on contrasting food resources to
 adulthood, and then added them to aquatic mesocosm ecosystems to assess
 their impact on the planktonic bacterial community. We also investigated
 whether the effects of fish persisted following the removal of adults, and
 the subsequent addition of a homogenous juvenile fish population. The
 presence of adult stickleback increased the number of bacterial OTUs and
 altered the size structure of the microbial community, whereas their
 phenotype affected bacterial community composition. Some of these effects
 were detectable after adult fish were removed from the mesocosms, and
 after juvenile fish were placed in the tanks, most of these effects
 disappeared. Our results suggest that fish can have strong short-term
 effects on microbial communities that are partially mediated by phenotypic
 variation of fish.
description: FCM_ARISA_data_2016