cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3f5j9
title: Data from: Prevalence of transcription factors in ascomycete and basidiomycete fungi

description: Background: Gene regulation underlies fungal physiology and therefore is a
 major factor in fungal biodiversity. Analysis of genome sequences has
 revealed a large number of putative transcription factors in most fungal
 genomes. The presence of fungal orthologs for individual regulators has
 been analysed and appears to be highly variable with some regulators
 widely conserved and others showing narrow distribution. Although
 genome-scale transcription factor surveys have been performed before, no
 global study into the prevalence of specific regulators across the fungal
 kingdom has been presented. Results: In this study we have analysed the
 number of members for 37 regulator classes in 77 ascomycete and 31
 basidiomycete fungal genomes and revealed significant differences between
 ascomycetes and basidiomycetes. In addition, we determined the presence of
 64 regulators characterised in ascomycetes across these 108 genomes. This
 demonstrated that overall the highest presence of orthologs is in the
 filamentous ascomycetes. A significant number of regulators lacked
 orthologs in the ascomycete yeasts and the basidiomycetes. Conversely, of
 seven basidiomycete regulators included in the study, only one had
 orthologs in ascomycetes. Conclusions: This study demonstrates a
 significant difference in the regulatory repertoire of ascomycete and
 basidiomycete fungi, at the level of both regulator class and individual
 regulator. This suggests that the current regulatory systems of these
 fungi have been mainly developed after the two phyla diverged. Most
 regulators detected in both phyla are involved in central functions of
 fungal physiology and therefore were likely already present in the
 ancestor of the two phyla.
description: Neighbor-Joining tree of
 the AraR homologs using Aspergillus nidulans XlnR as an
 outgroupThe genes marked in
 yellow were maintained in the comparison. AN10550 was manually removed, as
 it clearly did not fall into the same cluster as the other genes. In fact,
 this gene is GalR, which is unique to A. nidulans.Figure3.pdf
DOI: 10.5061/dryad.3pq02
title: Data from: Among-strain consistency in the pace and shape of senescence in duckweed

description: 1.Comparative studies have demonstrated extensive variation in
 age-trajectories of mortality and fecundity, both within and among
 species, with many taxa exhibiting a general pattern of age-related
 demographic decline referred to as senescence. Whereas a considerable body
 of theory is devoted to explaining the origin and persistence of
 senescence, the evolutionary forces underlying variation in demographic
 trajectories more generally remain poorly understood. 2.Studying variation
 in demographic trajectories is complicated by the fact that different
 species (or even different populations of a given species) may live and
 reproduce on different time scales, which, for comparative purposes, can
 make it challenging to disentangle patterns of age-related demographic
 change (the shape of demographic age trajectories) from the time scale on
 which those changes happen (the pace of demographic age trajectories).
 3.Here we examine variation in the pace and shape of demographic
 trajectories among strains of the aquatic plant Lemna turionifera Landolt
 from 24 sites across Alberta, Canada. Our main objectives were to describe
 the shape of demographic trajectories in L. turionifera, and test for
 among-strain variation in pace and shape. We also tested whether potential
 variation in pace and shape is (i) constrained by tradeoffs with other
 life history traits, and (ii) consistent with local adaptation to
 environmental characteristics at the sites of strain origin. 4.The strains
 we examined were overwhelmingly subject to age-related increases in
 mortality and declines in fecundity, with increases in mortality tending
 to decelerate and plateau at advanced ages. Despite substantial
 among-strain variation in cumulative fecundity and plant size, measures of
 pace and shape did not in themselves vary significantly among strains.
 Both within and among strains, we observed a negative relationship between
 plant size and the shape of fecundity trajectories, but we found no other
 evidence for life history tradeoffs involving pace or shape, nor for local
 adaptation. 5.Synthesis. Angiosperms display remarkable demographic
 variation. Our results suggest that the pace and shape of demographic
 trajectories are highly conserved within one particular angiosperm species
 (L. turionifera), despite substantial among-strain variation in other life
 history traits.
description: Raw data and
 codeZip archive containing
 the raw data, R script, and associated materials required to reproduce our
 analyses.pace-shape-duckeed.zip
DOI: 10.5061/dryad.51mm0
title: Data from: Influence of introgression and geological processes on phylogenetic relationships of western North American mountain suckers (Pantosteus, Catostomidae)

description: Intense geological activity caused major topographic changes in Western
 North America over the past 15 million years. Major rivers here are
 composites of different ancient rivers, resulting in isolation and mixing
 episodes between river basins over time. This history influenced the
 diversification of most of the aquatic fauna. The genus Pantosteus is one
 of several clades centered in this tectonically active region. The eight
 recognized Pantosteus species are widespread and common across
 southwestern Canada, western USA and into northern Mexico. They are
 typically found in medium gradient, middle-elevation reaches of rivers
 over rocky substrates. This study (1) compares molecular data with
 morphological and paleontological data for proposed species of Pantosteus,
 (2) tests hypotheses of their monophyly, (3) uses these data for
 phylogenetic inferences of sister-group relationships, and (4) estimates
 timing of divergence events of identified lineages. Using 8055 base pairs
 from mitochondrial DNA protein coding genes, Pantosteus and Catostomus are
 reciprocally monophyletic, in contrast with morphological data. The only
 exception to a monophyletic Pantosteus is P. columbianus whose mtDNA is
 closely aligned with C. tahoensis because of introgression. Within
 Pantosteus, several species have deep genetic divergences among allopatric
 sister lineages, several of which are diagnosed and elevated to species,
 bringing the total diversity in the group to 11 species. Conflicting
 molecular and morphological data may be resolved when patterns of
 divergence are shown to be correlated with sympatry and evidence of
 introgression.
description: MtDNA sequence nexus
 file for Pantosteus and outgroupsInformation on
 partitions within the data file are in the readme file.pan.phylo.new.reordered.nonint.ml.nexBeast xml file for Pantosteuspan.new.cal.otu.edited.xmlMorphological data in nexus formatAnalysis was conducted with a heuristic Maximum Parsimony search for 1000 replicates which produced 63 trees which we presented the strict consensus of.smith catostomin 15 feb 13.nex
DOI: 10.5061/dryad.hp77gb5
title: Data from: Intra-specific relatedness, spatial clustering and reduced demographic performance in tropical rainforest trees

description: Intra-specific negative density dependence promotes species coexistence by
 regulating population sizes. Patterns consistent with such density
 dependence are frequently reported in diverse tropical tree communities.
 Empirical evidence demonstrating whether intra-specific variation is
 related to these patterns, however, is lacking. The present study
 addresses this important knowledge gap by genotyping all individuals of a
 tropical tree in a long-term forest dynamics plot in tropical China. We
 show that related individuals are often spatially clustered, but having
 closely related neighbors reduces the growth performance of focal trees.
 We infer from the evidence, that dispersal limitation and negative density
 dependence are operating simultaneously to impact the spatial
 distributions of genotypes in a natural population. Furthermore, dispersal
 limitation decreases local intra-specific genetic diversity and increases
 negative density dependence thereby promoting niche differences and
 species co-existence as predicted by theory.
description: Beilschmiedia
 roxburghiana microsatellitesSummarized
 characteristics of microsatellites of Beilschmiedia roxburghiana used in
 this article including the locus name, repeat motif, primer sequences,
 size range and annealing temperature (Ta).B. roxburghiana
 microsatellites.xlsxBeilschmiedia
 roxburghiana genetic dataThe genetic data of all
 363 individuals of Beilschmiedia roxburghiana including the individual
 tags in XSBN plot and allele size in each loci obtained from all
 individuals.B. roxburghiana genetic
 data.xlsxBeilschmiedia
 roxburghiana genetic distanceGenetic distance between
 all two individual pairs calculated based on all loci. The coordinates of
 363 individuals of Beilschmiedia roxburghiana in XSBN plot are also
 given.B.
 roxburghiana genetic
 distance.xlsxBeilschmiedia
 roxburghiana DBH dataThe DBH of 363
 individuals of Beilschmiedia roxburghiana at both 2007 census and 2017
 censusB.
 roxburghiana DBH data.xlsx
DOI: 10.5061/dryad.nc6bs
title: Data from: Not only for egg yolk - functional and evolutionary insights from expression, selection and structural analyses of Formica ant vitellogenins

description: Vitellogenin, a storage protein, has been extensively studied for its
 egg-yolk precursor role, and it has been suggested to be fundamentally
 involved in caste differences in social insects. More than one
 vitellogenin copy has been reported in several oviparous species,
 including ants. However, the number and function of different
 vitellogenins, their phylogenetic relatedness and their role in
 reproductive queens and non-reproductive workers has been studied in few
 species only. We studied caste biased expression of vitellogenins in seven
 Formica ant species. Only one copy of conventional vitellogenin was
 identified in Formica species, and three vitellogenin homologues, derived
 from ancient duplications, which represent yet undiscovered
 vitellogenin-like genes. We show that each of these vitellogenin-like
 genes is present in all studied Hymenoptera and some of them in other
 insects as well. We show that after each major duplication event at least
 one of the vitellogenin-like genes has experienced a period of positive
 selection. This, combined with the observation that the vitellogenin-like
 genes have acquired or lost specific protein domains suggests sub- or
 neofunctionalization between vitellogenin and the duplicated genes. In
 contrast to earlier studies, vitellogenin was not consistently queen
 biased in its expression, and the caste bias of the three
 vitellogenin-like genes was highly variable among species. Furthermore, a
 truncated and Hymenoptera-specific vitellogenin-like gene, Vg-like-C, was
 consistently worker biased. Multispecies comparisons are essential for
 vitellogenin expression studies, and for gene expression studies in
 general, as we show that expression and also, putative functions cannot be
 generalized even among closely related species.
description: Morandin et al. Vg
 sequencesThis file contains
 Vitellogenin and Vitellogenin-like sequences (amino acid and predicted
 protein) used for the phylogenetic tree (Figure 1), annotated in insect
 species for Morandin et al. 2014.Morandin et al. Vg
 alignmentThis file contains the
 alignment of Vitellogenin and Vitellogenin-like sequences used for the
 phylogenetic tree (figure 1) presented in Morandin et al.
 2014.Morandin et al. FexsVgs
 alignmentThis file contains
 alignment generated via ClustalX of Vitellogenin and Vitellogenin-like
 sequences of Formica exsecta.
DOI: 10.5061/dryad.0vk58cn
title: Data from: Ecological and evolutionary drivers of the elevational gradient of diversity

description: Ecological, evolutionary, spatial and neutral theories make distinct
 predictions and provide distinct explanations for the mechanisms that
 control the relationship between diversity and the environment. Here, we
 test predictions of the elevational diversity gradient focusing on Iberian
 bumblebees, grasshoppers and birds. Processes mediated by local abundance
 and regional diversity concur in explaining local diversity patterns along
 elevation. Effects expressed through variation in abundance were similar
 among taxa and point to the overriding role of a physical factor,
 temperature. This determines how energy is distributed among individuals
 and ultimately how the resulting pattern of abundance affects species
 incidence. Effects expressed through variation in regional species pools
 depended instead on taxon-specific evolutionary history, and lead to
 diverging responses under similar environmental pressures. Local filters
 and regional variation also explain functional diversity gradients, in
 line with results from species richness that indicate an (local)
 ecological and (regional) historical unfolding of diversity–elevation
 relationships.
description: SurveyData_LaioloetalSite x species matrix of bird, grasshopper and bumblebee abundances in the Cantabrian Mountains, NW Spain. Data were collected by the authors of the study. Average annual temperature (0.1 ºC), accumulated precipitation (0.1 mm) elevation (m a.s.l.), habitat heterogeneity (Simpson's diversity Index) are also provided.DATASET_Laioloetal.txt
DOI: 10.5061/dryad.qc1nc
title: Data from: The effect of neighborhood size on effective population size in theory and in practice

description: The distinction between the effective size of a population (Ne) and the
 effective size of its neighborhoods (Nn) has sometimes become blurred. Ne
 reflects the effect of random sampling on the genetic composition of a
 population of size N, whereas Nn is a measure of within-population spatial
 genetic structure and depends strongly on the dispersal characteristics of
 a species. Although Nn is independent of Ne, the reverse is not true.
 Using simulations of a population of annual plants, it was found that the
 effect of Nn on Ne was well approximated by Ne=N/(1−FIS), where FIS
 (determined by Nn) was evaluated population wide. Nn only had a notable
 influence of increasing Ne as it became smaller (less than or equal to16).
 In contrast, the effect of Nn on genetic estimates of Ne was substantial.
 Using the temporal method (a standard two-sample approach) based on 1000
 single-nucleotide polymorphisms (SNPs), and varying sampling method,
 sample size (2–25% of N) and interval between samples (T=1–32
 generations), estimates of Ne ranged from infinity to &lt;0.1% of the
 true value (defined as Ne based on 100% sampling). Estimates were never
 accurate unless Nn and T were large. Three sampling techniques were
 tested: same-site resampling, different-site resampling and random
 sampling. Random sampling was the least biased method. Extremely low
 estimates often resulted when different-site resampling was used,
 especially when the population was large and the sample fraction was
 small, raising the possibility that this estimation bias could be a factor
 determining some very low Ne/N that have been published.
description: Simulation
 codeSimulates an
 isolation-by-distance plant population and estimates the effective
 population size using the temporal method.PlantSimulation.txtSimulation ResultsResults of all simulations used to create figure and tables.SimulationResults.xlsx
DOI: 10.5061/dryad.519d0
title: Data from: Captive ancestry upwardly biases estimates of relative reproductive success

description: Supplementation programs, which release captive-born individuals into the
 wild, are commonly used to demographically bolster declining populations.
 In order to evaluate the effectiveness of these programs, the reproductive
 success of captive-born individuals released into the wild is often
 compared to the reproductive success of wild-born individuals in the
 recipient population (relative reproductive success, RRS). However, if
 there are heritable reductions in fitness associated with captive
 breeding, gene flow from captive-born individuals into the wild population
 can reduce the fitness of the wild population. Here, we show that when
 captive ancestry in the wild population reduces mean population fitness,
 estimates of RRS are upwardly biased, meaning that the relative fitness of
 captive-born individuals is over-estimated. Furthermore, the magnitude of
 this bias increases with the length of time that a supplementation program
 has been releasing captive-born individuals. This phenomenon has long-term
 conservation impacts since management decisions regarding the design of a
 supplementation program and the number of individuals to release can be
 based, at least in part, on RRS estimates. Therefore, we urge caution in
 the interpretation of relative fitness measures when the captive ancestry
 of the wild population cannot be precisely measured.
description: model2.8BScripts can be run by modifying RRSmodel.R to set the working directory. Parameters used in the manuscript have been entered into RRSmodel.R. However, the values can be modified to test other parameter values as desired. The script will write files to a directory called 'output' that must be in the working directory. The 'source' directory and its contents must also be in the working directory.
DOI: 10.5061/dryad.7944
title: Data from: Comparative phylogeography, genetic differentiation, and contrasting reproductive modes in three fungal symbionts of a multipartite bark beetle symbiosis

description: Multipartite symbioses are complex symbiotic relationships involving
 multiple interacting partners. These types of partnerships provide
 excellent opportunities in which to apply a comparative approach to
 identify common historical patterns of population differentiation and
 species-specific life history traits. Using three symbiotic blue stain
 fungal species (Ophiostomatacea) associated with outbreaking populations
 of the mountain pine beetle (Dendroctonus ponderosae Hopkins) in western
 Canada, we applied phylogenetic, population genetic, and demographic
 approaches to clarify phylogeographic patterns among the three fungal
 species. Broadly, the three species showed significant population
 differentiation, forming northern and southern populations, despite
 dramatic differences in haplotype diversity. Finer scale structuring and
 population demographic patterns were less consistent, showing some
 interspecific incongruence. By contrasting these species simultaneously,
 we were able to identify differences in recombination rate and ecological
 traits that can explain the observed patterns of incongruence among the
 fungal species. By applying a comparative approach to partners of a
 multipartite symbiosis we were able to distinguish congruent population
 structuring and species-specific differences that help us to understand
 the complexity and evolution of this symbiotic system.
description: TreeBASE S10954 -
 Concatenated matrix of four molecular loci for Ophiostoma
 montiumTreebase file containing
 a concatenated matrix of four nuclear loci for Ophiostoma montium: beta
 tubulin, elongation factor 1 alpha, actin, and ITS2+28S. Data is provided
 in a NEXUS format with character blocks representing each
 locus.TreeBase S11004 -
 Concatenated matrix of five loci from six closely related ophiostomatoid
 fungiThis data is based on an
 earlier publication (Roe et al. 2010 - Molecular Ecology Resources) and
 only data for Leptographium longiclavatum and Grosmannia clavigera are
 applicable to this study.Appendix1_CultureListSpecimen list, including GenBank and University of Alberta Microfungus Collection and Herbarium accession numbers.Appendix2_SingleLocusNetworksSingle locus parsimony networks for G. clavigera, L. longiclavatum, and O. montium.
DOI: 10.5061/dryad.ft922
title: Data from: Revisiting Santa Rosalia to unfold a degeneracy of classic models of speciation

description: Many classic models of speciation incorporate assortative mating based on
 mating groups, such as plants with different flowering times, and they
 investigate whether an ecological trait under disruptive natural selection
 becomes genetically associated with the selectively neutral mating trait.
 It is well known that this genetic association is potently destroyed by
 recombination. In this note, we point out a more fundamental difficulty:
 if a “knife-edge” symmetry assumption of previous models is violated, then
 the mating trait is no longer neutral and sexual selection eliminates the
 polymorphism in the mating locus. This result strengthens the growing
 consensus that magic traits are the more likely route to nonallopatric
 speciation. We expand the model assuming also ecological selection on the
 mating trait and investigate the conditions for natural selection to
 overcome sexual selection and maintain mating polymorphism; we find that
 the combination of natural and sexual selection can cause also bistability
 of allele frequencies.
description: Norvaisas_Kisdi_MathematicaThe zip file contains three Mathematica notebooks, which were used to produce the figures as indicated in the file names. The notebooks are briefly annotated and are based on the equations given in the paper.
DOI: 10.5061/dryad.h5r77
title: Data from: Genome-wide SNPs identify limits to connectivity in the extreme freshwater disperser, spangled perch Leiopotherapon unicolor (Terapontidae)

description: The utility of restriction-site associated DNA sequencing (RADseq) to
 resolve fine-scale population structure was tested on an abundant and
 vagile fish species in a tropical river. Australia’s most widespread
 freshwater fish, the “extreme disperser” Leiopotherapon unicolor was
 sampled from six locations in an unregulated system, the Daly River in
 Australia’s Northern Territory. Despite an expectation of high
 connectivity based on life history knowledge of this species derived from
 arid zone habitats, L. unicolor was not a panmictic population in the
 tropical lower Daly. Using ~14,000 polymorphic RADseq loci, we found a
 pattern of upstream versus downstream population subdivision and evidence
 for differentiation among tributary populations. The magnitude of
 population structure was low with narrow confidence intervals (global FST
 = 0.014; 95% CI = 0.012, 0.016). Confidence intervals around pairwise FST
 estimates were all non-zero and consistent with the results of clustering
 analyses. This population structure was not explained by spatially
 heterogeneous selection acting on a subset of loci, or by sampling groups
 of closely related individuals (average within-site relatedness ≈ 0). One
 implication of the low but significant structure observed in the tropics
 is the possibility that L. unicolor may exhibit contrasting patterns of
 migratory biology in tropical versus arid zone habitats. We conclude that
 the RADseq revolution holds promise for delineating subtle patterns of
 population subdivision in species characterized by high within-population
 variation and low among-population differentiation.
description: RADseq-derived SNP
 genotype data: 14,031 loci, 48 individuals, species = Leiopotherapon
 unicolor.Data is R S4 class
 ‘genind’ object (adegenet R package): “unicolor_data.RData”. The data are
 RADseq-derived SNP genotypes scored for 14,031 loci in 48 individuals.
 Individual sample codes in this file include population identifier and
 individual identifier. Please see Readme.txt file.unicolor_data.RData