cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.v5g0p
title: Data from: Complex phylogeographic patterns indicate Central American origin of two widespread Mesoamerican Quercus (Fagaceae) species

description: The northern Neotropical region is characterized by a heterogeneous
 geological and climatic history. Recent studies have shown contrasting
 patterns regarding the role of geographic elements as barriers that could
 have determined phylogeographic structure in various species. Recently,
 the phylogeography and biogeography of Quercus species have been studied
 intensively, and the patterns observed so far suggest contrasting
 evolutionary histories for Neotropical species in comparison with their
 Holarctic relatives. The goal of this study was to describe the
 phylogeographic structure of two Neotropical oak species (Quercus insignis
 and Quercus sapotifolia) in the context of the geological and
 palaeoclimatic history of the northern Neotropics. Populations through the
 distribution range of both species were collected and characterized using
 nine chloroplast DNA microsatellite loci. Both oak species showed high
 levels of genetic diversity and strong phylogeographic structure. The
 distribution of genetic variation in Q. insignis suggested an influence of
 two major barriers, the Isthmus of Tehuantepec and the Nicaraguan
 Depression, while Q. sapotifolia exhibited a genetic structure defined by
 the heterogeneity of the Chortis highlands. The haplotype networks of both
 species indicated complex histories, suggesting that colonization from the
 Sierra Madre de Chiapas to central Mexico and from the north of the
 Nicaraguan Depression to the Costa Rican mountains may have occurred
 during different stages, and apparently more than one time. In conclusion,
 the phylogeographic structure of Neotropical oak species seems to be
 defined by a combination of geological and climatic events.
description: Datos_RodriguezCorreaEtalTREEGentGenom2016CpSSR data for two Neotropical oak species (see manuscript for details)
DOI: 10.5061/dryad.7q18vk6
title: Data from: Pre-dispersal context and presence of opposite sex modulate density dependence and sex bias of dispersal

description: Density-dependent dispersal (DDD) has been observed across taxa, and is
 expected to affect phenomena such as population dynamics, biological
 invasions, range expansions, and community assembly. However, little is
 known about whether the patterns of DDD are robust to changes in the
 environment. For example, the pre-dispersal context could affect the
 physiology of organisms, which in turn could alter their DDD. Similarly,
 in sexually reproducing organisms, males and females might be
 differentially affected by the environment, with possible changes in their
 dispersal properties. To investigate some of these issues, we performed
 three independent experiments using laboratory populations of Drosophila
 melanogaster, which tested the effects of pre-dispersal context, sex of
 the dispersers and presence of mates on DDD. A two-patch dispersal setup
 was used to estimate the dispersal propensity and temporal dispersal
 profile of adult fruit flies. Comparing the data from two different
 pre-dispersal contexts (variable and uniform pre-dispersal adult
 densities), we found that longer pre-dispersal exposure to higher
 densities led to stronger negative DDD in both males and females.
 Surprisingly, this change in DDD strength was accompanied by a switch in
 the direction of sex-biased dispersal: from female-biased dispersal at a
 low density to male-biased dispersal at a high density. Moreover, we found
 that patterns of both density dependence and sex bias were contingent upon
 the interaction of males and females, as neither sex exhibited DDD in the
 absence of the other. Taken together, these results suggest that DDD and
 sex-biased dispersal can be labile and be driven by the environmental
 context. Finally, we discuss the potential implications of these findings
 in terms of various ecological and evolutionary processes.
description: Mishra et
 al_DryadData_OikosThe file contains data
 from three experiments. For each experiment, there is data for dispersal
 propensity and temporal distribution of dispersers. All columns are
 labelled and self-explanatory. SEM = Standard Error.
DOI: 10.5061/dryad.1gv31
title: Data from: Ecosystem nitrogen retention is regulated by plant community trait interactions with nutrient status in an alpine meadow

description: 1.Biotic nitrogen (N) retention is an important ecosystem function in the
 context of ongoing land use intensification, N deposition and global
 warming. However, a paucity of experimental evidence limits understanding
 of how different plant community components influence N retention in
 terrestrial ecosystems. 2.In this investigation we conducted a 15N
 labelling experiment to test how plant community properties, including
 plant species richness/diversity, dominance and functional traits,
 influence plant N uptake and retention under different nutrient
 availabilities. A three-year experiment examined the effects of adding N
 (10 g N m−2 year−1) and phosphorus (P) (5 g P m−2 year−1) to an alpine
 meadow on the Qinghai-Tibetan Plateau. 3.Results show that 15N retention
 increased with the addition of N and P; the addition of P produced the
 largest increase of 15N retention in plant and soil N pools. Changes in
 soil nutrient conditions also facilitated different plant community
 controls on ecosystem N retention. Ecosystem 15N retention was influenced
 by species richness and root biomass in the control plots; whereas the N
 addition treatment showed an important effect of community-weighted means
 (CWM) of specific leaf area (SLA), and plots with additional P recorded
 lower CWM of root nitrogen content (root N) and larger CWM root:shoot
 ratios (R/S) as important determinants. 4.Synthesis. Ecosystem N retention
 was influenced by conservative and exploitative plant species and/or their
 traits under N deficient and abundant conditions, respectively, whereas
 species richness and community plant biomass were most influential under
 control conditions. The discovery of an interaction between plant
 community traits and nutrient biogeochemistry as a mechanism for ecosystem
 N retention offers a means to predict how vegetation in alpine meadow
 ecosystems will respond to expected global change.
description: Data submit
 -2017.11.28The data collected site
 was located at HBAMERS (latitude 37°37' N and longitude 101°12'
 E). The research station lies at 3200 m a.s.l on the Qinghai-Tibet plateau
 and is subjected to a typical plateau continental climate, with short cool
 summers and long cold winters. Mean annual temperature is 2 ℃ and mean
 annual precipitation is 500 mm; with over 80% of precipitation falling
 during the summer months from June to August. The experiment was conducted
 in an alpine meadow dominated by Kobresia humilis, Festuca sinensis,
 Elymus nutans, Poa pratensis, Stipa purpurea, Carex tristachya, Gentiana
 straminea, Potentilla nivea and Gentiana farreri. Soil type is Gelic
 Cambisol with an average thickness of 0.65 m.
DOI: 10.5061/dryad.6581hh9
title: Data from: Intraspecific interactions affect the spatial pattern of a dominant shrub in a semi-arid scrubland: a prospective approach

description: Dispersal, physical conditions and biotic interactions contribute to
 determine the spatial distribution of individuals in plant populations.
 Much of what we know has been learned from studies that retrospectively
 posit mechanisms presumed to have generated the observed spatial patterns.
 Here we present a prospective approach. We start by measuring spatial
 demographic effects and evaluate if they can generate observed spatial
 patterns. We evaluated the influence of interactions among conspecifics on
 vital rates, demography and spatial distribution of Croton aff. wagneri, a
 dominant shrub in dry Andean ecosystems. Recruitment, survival and growth
 varied in relation with distance to conspecifics neighbors and with their
 summed cover. We built a spatial individual-based model and simulated its
 population dynamics in 30 × 30 m plots for a 30 year periods. We compared
 the predicted spatial pattern from these demographic models with that
 observed among plants in sixteen independent plots with the same area.
 Simulated populations mimicked observed spatial patterns, although in
 plots at high elevations the simulated populations did not reproduce the
 observed inhibition at small scales. Observed and simulated patterns
 indicated differences between elevations in maximum aggregation and
 location of the distances with higher aggregation. We discuss how
 consideration of critical seed and juvenile stages and interspecific
 interactions could further improve our understanding of spatial pattern
 and recommend that these factors be considered in future models.
description: Demographic data of
 CrotonIt contains the
 information on: the location of seedlings in relation to the closest
 reproductive plant, the size and location of reproductive plants
 samples.Archivos_para_dryad.zip
DOI: 10.5061/dryad.10b5v
title: Data from: Costs of deception and learned resistance in deceptive interactions

description: The costs that species suffer when deceived are expected to drive learned
 resistance, although this relationship has seldom been studied
 experimentally. Flowers that elicit mating behaviour from male insects by
 mimicking conspecific females provide an ideal system for such
 investigation. Here, we explore interactions between a sexually deceptive
 daisy with multiple floral forms that vary in deceptiveness, and the male
 flies that pollinate it. We show that male pollinators are negatively
 impacted by the interaction, suffering potential mating costs in terms of
 their ability and time taken to locate genuine females within deceptive
 inflorescences. The severity of these costs is determined by the amount of
 mating behaviour elicited by deceptive inflorescences. However,
 inexperienced male flies exhibit the ability to learn to discriminate the
 most deceptive inflorescences as female mimics and subsequently reduce the
 amount of mating behaviour they exhibit on them with increased exposure.
 Experienced males, which interact with sexually deceptive forms naturally,
 exhibit similar patterns of reduced mating behaviour on deceptive
 inflorescences in multiple populations, indicating that pollinator
 learning is widespread. As sexually deceptive plants are typically
 dependent on the elicitation of mating behaviour from male pollinators for
 pollination, this may result in antagonistic coevolution within these
 systems.
description: Final
 dataContains raw data from
 experiments described in article. The first spreadsheet contains data from
 experiments investigating the potential mating costs suffered by deceived
 males, including whether they found the genuine female in deceptive
 inflorescences, how many missed mating opportunities they experienced and
 how much time remained after they found the female. It also shows the ID
 of the male used, which floral form it was tested on and what order number
 that floral form was (i.e. 1 or 2 ect for males used on more than one
 floral form). It also shows the percentage of mating behaviour that the
 male exhibited on the spots of the form in question. The next spreadsheet
 comprises data from our learning experiments and shows the percentage
 mating behaviour exhibited by inexperienced males during their first and
 second exposure to sexually deceptive G. diffusa inflorescences. It also
 shows the percentage of specific mating behaviours (inspecting, changing,
 hopping and turning). The last spreadsheet includes data comparing the
 percentage of mating behaviour that inexperienced and experienced males
 exhibited on sexually deceptive inflorescences of G. diffusa. It also
 states whether these males were wild caught within natural populations, or
 whether they were experimental males used in our previously mentioned
 learning experiments. For these experimental males we also state whether
 the data is from their first or second exposure to sexually deceptive
 inflorescences.
DOI: 10.5061/dryad.cf16m
title: Data from: Sex drives intra-cellular conflict in yeast

description: Theory predicts that sex can drive the evolution of conflict within the
 cell. During asexual reproduction genetic material within the cell is
 inherited as a single unit, selecting for cooperation both within the
 genome as well as between the extra-genomic elements within the cell (e.g.
 plasmids and endosymbionts). Under sexual reproduction this unity is
 broken down as parental genomes are distributed between meiotic progeny.
 Genetic elements able to transmit to more than 50% of meiotic progeny have
 a transmission advantage over the rest of the genome and are able to
 spread, even where they reduce the fitness of the individual as a whole.
 Sexual reproduction is therefore expected to drive the evolution of
 selfish genetic elements (SGEs). Here we directly test this hypothesis by
 studying the evolution of two independent SGEs, the 2µm plasmid and
 selfish mitochondria, in populations of Saccharomyces cerevisiae.
 Following 22 rounds of sexual reproduction 2µm copy number increased by
 ~13.2 (+/-5.6) copies/cell, whereas in asexual populations copy number
 decreased by ~5.1 (+/-1.5) copies/cell. Given that the burden imposed by
 this parasite increases with copy number, these results support the idea
 that sex drives the evolution of increased SGE virulence. Moreover, we
 found that mitochondria that are respiratory-deficient rapidly invaded
 sexual but not asexual populations, demonstrating that frequent outcrossed
 sex can drive the de novo evolution of genetic parasites. Our study
 highlights the genomic perils of sex and suggests that SGEs may play a key
 role in driving major evolutionary transitions, such as uniparental
 inheritance.
description: data1_copy number and
 growth rateCopy number
 (plasmids/cell) and growth rate (mOD600/min) data collected from the same
 clones isolated from transfers 0 and 20 of the long term selection
 experiment.data2_respiratory
 deficinet countsCounts of aerobic
 respiratory deficient colonies (i.e. colonies unable to grow when
 transferred on to non-fermentable glycerol media) isolated from the long
 term selection experiment at 5 transfer intervals. Number of mutants,
 total colonies screened, and the resulting proportions are
 shown.
DOI: 10.5061/dryad.3547c
title: Data from: Balancing ecological costs and benefits of fire for population viability of disturbance-dependent butterflies

description: Disturbance is a fundamental ecological process and driver of population
 dynamics. Ecologists seek to understand the effects of disturbance on
 ecological systems and to use disturbance to modify habitats degraded by
 anthropogenic change. Demographic responses by plants to disturbance are
 often well described, but demographic responses by animals are less
 understood. This limits development of applied strategies that leverage
 disturbance to augment animal populations. We estimated demographic and
 behavioural responses of an endangered butterfly, Fender's blue,
 Plebejus icarioides fenderi, to experimental burning in Oregon, USA. We
 monitored butterfly vital rates for four years post-fire. Prescribed fire
 killed Fender's blue larvae. However, fecundity was higher relative
 to reference/unburned areas for two years after the burn and overwinter
 larval survivorship was higher for a year after the burn. Fire treatments
 did not influence adult movement behaviour. We used matrix models to
 project butterfly population dynamics in fire-driven successional
 landscapes. We compared optimal burn strategies given targeted burns, such
 as prescribed fire, to undirected burns, such as wildfires. Disturbance
 enhances population growth rate under both strategies, and the optimal
 proportion of landscape burned is similar in both cases. However, targeted
 burning leads to substantially higher population growth rates. Synthesis
 and applications. Demographic models allow planning of long-term and
 large-scale disturbance by balancing initial costs of disturbance with
 subsequent benefits. We use matrix models to project population growth in
 fire-driven successional landscapes and contrast prescribed burns with
 undirected burns (wildfires). We also use these models to evaluate the
 influence of local vs. non-local dispersal. Because random (non-local)
 dispersal allows individuals to disperse into areas that were just burned,
 non-local dispersal always increases population growth rates in this
 system. This contrasts with source-sink dynamics in stationary
 environments, in which local dispersal leads to higher population growth
 rates. Our matrix modelling approach has broad application to other
 disturbance-dependent taxa surviving in anthropogenically modified
 landscapes, and could be more widely applied to animal populations.
description: Warchola et al JapEcol
 2017 egg countFender's blue
 butterfly eggs in experimental plots.Warchola et al JApEcol
 2017 overwinter survivalSurvival of
 Fender's blue from eggs in June of one season to post-diapause larvae
 in April of the following season. "Damage" refers to the number
 of lupine leaves with larval damage in each plot
DOI: 10.5061/dryad.vt41c78j
title: Data from: Rates of morphological evolution are correlated with species richness in salamanders

description: The tempo and mode of species diversification and phenotypic evolution
 vary widely across the tree of life, yet the relationship between these
 processes is poorly known. Previous tests of the relationship between
 rates of phenotypic evolution and rates of species diversification have
 assumed that species richness increases continuously through time. If this
 assumption is violated, simple phylogenetic estimates of net
 diversification rate may bear no relationship to processes that influence
 the distribution of species richness among clades. Here we demonstrate
 that the variation in species richness among plethodontid salamander
 clades is unlikely to have resulted from simple time-dependent processes,
 leading to fundamentally different conclusions about the relationship
 between rates of phenotypic evolution and species diversification.
 Morphological evolutionary rates of both size and shape evolution are
 correlated with clade species richness, but are uncorrelated with simple
 estimators of net diversification that assume constancy of rates through
 time. This coupling between species diversification and phenotypic
 evolution is consistent with the hypothesis that clades with high rates of
 morphological trait evolution may diversify more than clades with low
 rates. Our results indicate that assumptions about underlying processes of
 diversity regulation have important consequences for interpreting
 macroevolutionary patterns.
description: Archivesee ReadMe file for description of data files.
DOI: 10.5061/dryad.r3r60
title: Data from: Likelihood-based inference of population history from low coverage de novo genome assemblies

description: Short-read sequencing technologies have in principle made it feasible to
 draw detailed inferences about the recent history of any organism. In
 practice, however, this remains challenging due to the difficulty of
 genome assembly in most organisms and the lack of statistical methods
 powerful enough to discriminate among recent, non-equilibrium histories.
 We address both the assembly and inference challenges. We develop a
 bioinformatic pipeline for generating outgroup-rooted alignments of
 orthologous sequence blocks from de novo low-coverage short-read data for
 a small number of genomes, and show how such sequence blocks can be used
 to fit explicit models of population divergence and admixture in a
 likelihood framework. To illustrate our approach, we reconstruct the
 Pleistocene history of an oak-feeding insect (the oak gallwasp Biorhiza
 pallida) which, in common with many other taxa, was restricted during
 Pleistocene ice ages to a longitudinal series of southern refugia spanning
 theWestern Palaearctic. Our analysis of sequence blocks sampled from a
 single genome from each of three major glacial refugia reveals support for
 an unexpected history dominated by recent admixture. Despite the fact that
 80% of the genome is affected by admixture during the last glacial cycle,
 we are able to infer the deeper divergence history of these populations.
 These inferences are robust to variation in block length, mutation model,
 and the sampling location of individual genomes within refugia. This
 combination of de novo assembly and numerical likelihood calculation
 provides a powerful framework for estimating recent population history
 that can be applied to any organism without the need for prior genetic
 resources.
description: Biorhiza pallida
 transcriptome built using TrinityThis transcriptome is
 assembled from larval B. pallida collected in Dorset, United Kingdom for
 another project. Headers are in the Trinity assembler
 formatBiorhiza_pallida_transcriptome.Trinity.fasta.gzBiorhiza_pallida.meta-assembly.faBiorhiza pallida combined assembly using clc bio v4.0.3Belizinella_gibbera.meta-assembly.faBelizinella gibbera combined assembly assembled by clc bio v4.0.3tar archive of 2kb alignmentstar archive containing all 4 combinations of 2kb alignments2kb.tgztar archive of alignment summaries for mathematicaContains 4 files each summarizing one of the 2kb alignments used as mathematica inputcounts.tgzscripts_for_Hearn_et_alTar archive of custom scripts referred to in Hearn et al 2013. Includes a document summarising each scriptBpal.BLAST_and_Coverage_filtered_noINDELS_2609.vcfVCF file for Biorhiza pallida ingroup individuals created using samtools. Contaminant and high coverage sequences have been removed from this file. The VCF_haploif_parser.pl script was run on this file.Bgib.BLAST_and_Coverage_filtered_noINDELS_2609.vcfVCF file of the outgroup Belizinella gibbera, contaminant and high coverage contigs removed. Produced using samtools mpileup.