cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9t3js
title: Data from: Experiencing El Niño conditions during early life reduces recruiting probabilities but not adult survival

description: In wild long-lived animals, analysis of impacts of stressful natal
 conditions on adult performance has rarely embraced the entire age-span,
 and the possibility that costs are expressed late in life has seldom been
 examined. Using 26 years of data from 8,541 fledglings and 1,310 adults of
 the blue-footed booby (Sula nebouxii), a marine bird that can live up to
 23 years, we tested whether experiencing the warm waters and food scarcity
 associated with El Niño in the natal year reduces recruitment or survival
 over the adult lifetime. Warm water in the natal year reduced the
 probability of recruiting; each additional degree (°C) of water
 temperature meant a reduction of roughly 50% in fledglings’ probability of
 returning to the natal colony as breeders. Warm water in the current year
 impacted adult survival, with greater effect at the oldest ages than
 during early adulthood. However, warm water in the natal year did not
 affect survival at any age over the adult lifespan. A previous study
 showed that early recruitment and widely spaced breeding allow boobies
 that experience warm waters in the natal year to achieve normal fledgling
 production over the first 10 years; our results now show that this
 reproductive effort incurs no survival penalty, not even late in life.
 This pattern is additional evidence of buffering against stressful natal
 conditions via life-history adjustments.
description: Ancona_et_al_Supp_Material_Appendix_1Capture-recapture histories of 1,310 fledglings (687 males and 623 females) that recruited at ages 2 – 6 years between 1988 and 2013 on Isla Isabel, Mexico.RecruitmentRecruiting probabilities of 8,541 blue-footed booby fledglings from 15 cohorts.
DOI: 10.5061/dryad.sk94j
title: Data from: Adaptive molecular evolution of a defence gene in sexual but not functionally asexual evening primroses

description: Theory predicts that sexual reproduction provides evolutionary advantages
 over asexual reproduction by reducing mutational load and increasing
 adaptive potential. Here, we test the latter prediction in the context of
 plant defences against pathogens because pathogens frequently reduce plant
 fitness and drive the evolution of plant defences. Specifically, we ask
 whether sexual evening primrose plant lineages (Onagraceae) have faster
 rates of adaptive molecular evolution and altered gene expression of a
 class I chitinase, a gene implicated in defence against pathogens, than
 functionally asexual evening primrose lineages. We found that the ratio of
 amino acid to silent substitutions (Ka/Ks = 0.19 vs. 0.11 for sexual and
 asexual lineages, respectively), the number of sites identified to be
 under positive selection (four vs. zero for sexual and asexual lineages,
 respectively) and the expression of chitinase were all higher in sexual
 than in asexual lineages. Our results are congruent with the conclusion
 that a loss of sexual recombination and segregation in the Onagraceae
 negatively affects adaptive structural and potentially regulatory
 evolution of a plant defence protein.
description: FASTA sequence files for
 the chiB coding regions of 32 Onagraceae species.Dryad_JEB2012_ChiB.docxDryad_JEB2012_ChiB.txt
DOI: 10.5061/dryad.j10r6
title: Data from: Hybridization during altitudinal range shifts: nuclear introgression leads to extensive cyto-nuclear discordance in the fire salamander

description: Ecological models predict that, in the face of climate change, taxa
 occupying steep altitudinal gradients will shift their distributions,
 leading to the contraction or extinction of the high-elevation
 (cold-adapted) taxa. However, hybridization between eco-morphologically
 divergent taxa commonly occurs in nature and may lead to alternative
 evolutionary outcomes, such as genetic merger or gene flow at specific
 genes. We evaluate this hypothesis by studying patterns of divergence and
 gene flow across three replicate contact zones between high- and
 low-elevation ecomorphs of the fire salamander (Salamandra salamandra)
 that have experienced altitudinal range shifts over the current
 postglacial period. Strong population structure with high genetic
 divergence in mitochondrial DNA suggests that vicariant evolution has
 occurred over several glacial-interglacial cycles, and that it has led to
 cryptic differentiation within ecomorphs. In current parapatric boundaries
 we do not find evidence for local extinction and replacement upon
 postglacial expansion. Instead parapatric taxa recurrently show
 discordance between mitochondrial and nuclear markers, suggesting nuclear
 mediated gene flow across contact zones. Isolation with migration models
 support this hypothesis by showing significant gene flow across all five
 parapatric boundaries. Together, our results suggest that, while some
 genomic regions, such as the mitochondria, may follow morphologic species
 traits and retreat to isolated mountain tops, other genomic regions, such
 as nuclear markers, may flow across parapatric boundaries, sometimes
 leading to a complete genetic merger. We show that despite high ecologic
 and morphologic divergence over prolonged periods of time, hybridization
 allows for evolutionary outcomes alternative to extinction and replacement
 of taxa in response to climate change.
description: 1.gene_alignmentsThis package contains: 1) alignments for mtDNA (Dloop, and cytb concatenated with Dloop), 2) unphased alignments for the five nuclear markers (1 sequence per individual), and 3) phased alignments for the five nuclear markers (2 sequences per individual).2.tree_filesThis package contains tree and xml files used in: 1) *BEAST, and 2) mtDNA phylogeny.3.IMa2_filesThis package contains input files for the IMa analyses concerning the five contact zones, and a summary of the replicated output files from each analysis.
DOI: 10.5061/dryad.b22430s2
title: Data from: NEMBASE4: the nematode transcriptome resource

description: Nematode parasites are of major importance in human health and
 agriculture, and free-living species deliver essential ecosystem services.
 The genomics revolution has resulted in the production of many datasets of
 expressed sequence tags (ESTs) from a phylogenetically wide range of
 nematode species, but these are not easily compared. NEMBASE4 presents a
 single portal onto extensively functionally annotated, EST-derived
 transcriptomes from over sixty species of nematodes, including plant and
 animal parasites and free-living taxa. Using the PartiGene suite of tools,
 we have assembled the ESTs publicly available for each species into a
 high-quality set of putative transcripts. These transcripts have been
 translated to produce a protein sequence resource, and each annotated with
 functional information derived from comparison to well-studied nematode
 species such as Caenorhabditis elegans and also other non-nematode
 resources. By cross-comparing the sequences within NEMBASE4, we have also
 generated a protein family assignment for each translation. The data are
 presented in an openly-accessible, interactive database. To demonstrate
 the utility of NEMBASE4, we have used the database to examine the
 uniqueness of the transcriptomes of major clades of parasitic nematodes,
 identifying lineage-restricted genes that may underpin particular
 parasitic phenotypes, possible viral pathogens of nematodes, and
 nematode-unique protein families that may be developed as drug targets.
description: Supplementary_InformationSupplementary information (alignments) for analyses reported in the manuscript
DOI: 10.5061/dryad.45623
title: Data from: Tempo and mode of performance evolution across multiple independent origins of adhesive toe pads in lizards

description: Understanding macroevolutionary dynamics of trait evolution is an
 important endeavor in evolutionary biology. Ecological opportunity can
 liberate a trait as it diversifies through trait space, while genetic and
 selective constraints can limit diversification. While many studies have
 examined the dynamics of morphological traits, diverse morphological
 traits may yield the same or similar performance and as performance is
 often more proximately the target of selection, examining only morphology
 may give an incomplete understanding of evolutionary dynamics. Here we ask
 whether convergent evolution of pad-bearing lizards have followed similar
 evolutionary dynamics, or whether independent origins are accompanied by
 unique constraints and selective pressures over macroevolutionary time. We
 hypothesized that geckos and anoles each have unique evolutionary tempos
 and modes. Using performance data from 59 species, we modified Brownian
 Motion (BM) and Ornstein-Uhlenbeck (OU) models to account for repeated
 origins estimated using Bayesian ancestral state reconstructions. We
 discovered that adhesive performance in geckos evolved in a fashion
 consistent with Brownian Motion with a trend, whereas anoles evolved in
 bounded performance space consistent with more constrained evolution (an
 Ornstein-Uhlenbeck model). Our results suggest that convergent phenotypes
 can have quite distinctive evolutionary patterns, likely as a result of
 idiosyncratic constraints or ecological opportunities.
description: toe detachment angle
 trialsOur observed
 measurements of toe pad performance (toe detachment angle). These data
 include all of our observed trials, covering multiple individuals. The
 "individual" column represents the "names" of the
 individual animals tested and span multiple studies, hence there is no
 universal naming theme. Unique names relate to each individual. Note that
 some Anolis species are assigned a name of "NA" indicating that
 individual was not recored for that species. Following Hagey it al Journal
 of Experimental Biology 2016 219: 1603-1607; doi: 10.1242/jeb.129940, we
 fit each individual's set of trials to the weibull distribution,
 estimating a scale parameter with error for each individual. We then
 calculated a weighted species average using each individuals estimated
 scale parameter, weighted by the inverse of their
 error.toe pad presence
 absenceList of species and
 their toe pad assignment (presence or absence) used in our ancestral state
 reconstruciton
DOI: 10.5061/dryad.5rv40
title: Data from: Negative epistasis between beneficial mutations in an evolving bacterial population

description: Epistatic interactions between mutations play a prominent role in
 evolutionary theories. Many studies have found that epistasis is
 widespread, but they have rarely considered beneficial mutations. We
 analyzed the effects of epistasis on fitness for the first five mutations
 to fix in an experimental population of Escherichia coli. Epistasis
 depended on the effects of the combined mutations—the larger the expected
 benefit, the more negative the epistatic effect. Epistasis thus tended to
 produce diminishing returns with genotype fitness, although interactions
 involving one particular mutation had the opposite effect. These data
 support models in which negative epistasis contributes to declining rates
 of adaptation over time. Sign epistasis was rare in this genome-wide
 study, in contrast to its prevalence in an earlier study of mutations in a
 single gene.
description: Khan_etal_analysisR script used to: estimate beneficial mutation effects and epistasis parameters, perform statistical tests and generate all figures presented in Khan et al. (2011), except figures 1 and 4. Takes as input the file: genotype_fitness.txt.Khan_etal_Fig1R script to generate figure 1 of Khan et al. (2011). Takes as input the file: genotype_fitness.txt.Khan_etal_Fig4R script to generate figure 4 of Khan et al. (2011). Takes as input the file: genotype_fitness.txt.genotype_fitnessText file containing all replicate fitness measurements of each constructed genotype. Includes columns: strain, strain number; genotype, beneficial mutations present where r = rbs, t = topA, s = spoT, g = glmUS and p = pykF; mutations, number of beneficial mutations in the genotype; w, fitness estimate; block, experimental block; Plate, physical container used for the competition. This file is the input file for all analyses presented in Khan et al. (2011) Negative epistasis between beneficial mutations in an evolving bacterial population.raw_competition_dataText file containing raw data from all competition experiments. All competitions were performed over 2 transfer cycles. Fitness values from this file are summarized in 'genotype_fitness.txt', which is the input file for all analyses presented in Khan et al. (2011) Negative epistasis between beneficial mutations in an evolving bacterial population.
DOI: 10.5061/dryad.7ff11
title: Data from: Re-evaluating the geological evidence for Late Holocene marine incursion events along the Guerrero Seismic Gap on the Pacific Coast of Mexico

description: Despite the large number of tsunamis that impact Mexico's Pacific
 coast, stratigraphic studies focusing on geological impacts are scanty,
 making it difficult to assess the long-term risks for this vulnerable
 region. Surface samples and six cores were taken from Laguna Mitla near
 Acapulco to examine sedimentological and geochemical evidence for marine
 incursion events. Sediment cores collected from behind the beach barrier
 are dominated by intercalated layers of peat and inorganic sediments,
 mostly silt and clay, with little or no sand. Sand- and shell-rich clastic
 layers with high levels of sulfur, calcium, and strontium only occur
 adjacent to the relict beach ridge remnants near the center of the lagoon.
 With the exception of one thin fine sand layer, the absence of sand in the
 near-shore cores and the predominance of the terrigenous element titanium
 in the inorganic layers, evidently eroded from the surrounding hillslopes,
 suggests that these large-grained intervals do not represent episodic
 marine incursions, but rather were likely formed by the erosion and
 redeposition of older marine deposits derived from the beach ridge
 remnants when water levels were high. These results do not support the
 occurrence of a large tsunami event at Laguna Mitla during the Late
 Holocene.
description: core 1Core 1 LOI,
 XRFcore 2Core 2 LOI,
 XRFcore 3Core 3 LOI,
 XRFcore 4Core 4 LOI,
 XRFcore 5Core 5 LOI,
 XRFcore 6Core 6 LOI,
 XRFSurface
 samplesSurface sample
 XRFsurface
 samples.xlsx
DOI: 10.5061/dryad.j2bb9
title: Data from: Molecular evolution patterns reveal life history features of mycoplasma-related endobacteria associated with arbuscular mycorrhizal fungi

description: The mycoplasma-related endobacteria (MRE), representing a recently
 discovered lineage of Mollicutes, are widely distributed across arbuscular
 mycorrhizal fungi (AMF, Glomeromycota). AMF colonize roots of most
 terrestrial plants and improve plant mineral nutrient uptake in return for
 plant-assimilated carbon. The role of MRE in the biology of their fungal
 hosts is unknown. To start characterizing this association, we assessed
 partitioning of MRE genetic diversity within AMF individuals and across
 the AMF phylogeographic range. We further used molecular evolution
 patterns to make inferences about MRE codivergence with AMF, their
 lifestyle and antiquity of the Glomeromycota–MRE association. While we did
 not detect differentiation between MRE derived from different continents,
 high levels of diversity were apparent in MRE populations within AMF host
 individuals. MRE exhibited significant codiversification with AMF over
 ecological time and the absence of codivergence over evolutionary time.
 Moreover, genetic recombination was evident in MRE. These patterns
 indicate that, while MRE transmission is predominantly vertical, their
 complex intrahost populations are likely generated by horizontal
 transmission and recombination. Based on predictions of evolutionary
 theory, we interpreted these observations as a suggestion that MRE may be
 antagonists of AMF. Finally, we detected a marginally significant
 signature of codivergence of MRE with Glomeromycota and the Endogone
 lineage of Mucoromycotina, implying that the symbiosis between MRE and
 fungi may predate the divergence between these two groups of fungi.
description: 16S_rRNA_MRENexus file of 16S rRNA gene sequences from MRE.MBLFP_MRENexus file of MBLFP gene sequences from MRE.
DOI: 10.5061/dryad.rg800
title: Data from: A reliable technique to quantify the individual variability of iridescent coloration in birds

description: The study of iridescent coloration in birds emerged only recently, mainly
 due to the difficulty inherent in quantifying its directionality.
 Directionality restrains color perception to a limited angle and thereby
 causes drastic changes in brightness when an animal is in motion. Although
 a versatile goniometer for quantifying iridescent coloration has been
 developed recently, so far, it has only been applied to measuring the
 highly directional iridescent coloration in a hummingbird species. Thus,
 the reliability of the goniometer for species displaying more common and
 less directional iridescent coloration has yet to be evaluated.
 Additionally, two important methodological aspects remain to be assessed
 before this apparatus can be used confidently: 1) whether directionality,
 which could be subject to sexual selection, can be quantified in a
 repeatable way; and 2) whether the apparatus gives more precise and
 accurate measurements than a less complex traditional method. Using
 feathers collected from 271 male tree swallows Tachycineta bicolor over
 two years, we found that the goniometer provided repeatable measurements
 of directionality across individuals and across three body regions, namely
 the crown, mantle and rump. The apparatus was also more repeatable than a
 traditional method involving a bifurcated probe and reduced a brightness
 bias associated with individual differences in barbule tilt. We strongly
 encourage researchers to invest in this methodological change considering
 the multiple advantages demonstrated and to quantify the directionality of
 iridescent coloration as to unveil its role in signaling and sexual
 selection.
description: data_JAB_J00750Spectral measurements of iridescent feathers from male tree swallows captured in 2013-2014 in southern Québec, Canada. A detailed description is available in the last sheet of the excel document.
DOI: 10.5061/dryad.24f64
title: Data from: Temperature can shape a cline in polyandry, but only genetic variation can sustain it over time

description: Multiple mating by females (polyandry) is a widespread behavior occurring
 in diverse taxa, species, and populations. Polyandry can also vary widely
 within species, and individual populations, so that both monandrous and
 polyandrous females occur together. Genetic differences can explain some
 of this intraspecific variation in polyandry, but environmental factors
 are also likely to play a role. One environmental factor that influences
 many fundamental biological processes is temperature. Higher temperatures
 have been shown to directly increase remating in laboratory studies of
 insects. In the longer term, high temperature could also help to drive the
 evolution of larger-scale patterns of behavior by changing the
 context-dependent balance of costs and benefits of polyandry across
 environments. We examined the relative influence of rearing and mating
 temperatures on female remating in populations of Drosophila pseudoobscura
 that show a latitudinal cline in polyandry in nature, using a range of
 ecologically relevant temperatures. We found that females of all genotypes
 remated more at cooler temperatures, which fits with the observation of
 higher average frequencies of polyandry at higher latitudes in this
 species. However, the impact of temperature was outweighed by the strong
 genetic control of remating in females in this species. It is likely that
 genetic factors provide the primary explanation for the latitudinal cline
 in polyandry in this species.
description: DRYAD Taylor et al. 2015
 Behav EcolData on female remating
 behaviour in D. pseudoobscura from North America that were raised and
 mated and different temperatures.
DOI: 10.5061/dryad.724mk
title: Data from: Network analyses reveal intra- and interspecific differences in behaviour when passing a complex migration obstacle

description: 1. Network theory offers new perspective on movement data by evaluating
 the relationships between animal movements (links) and detection locations
 (nodes) in spatially complex systems, including human-altered landscapes.
 2. We applied network analyses to intra- and interspecific movement
 patterns in the migration behaviour and dam passage success of two
 anadromous fish species, Pacific lamprey Entosphenus tridentatus Gairdner
 and Chinook salmon Oncorhynchus tshawytscha Walbaum, when moving through a
 large multi-fishway hydroelectric project (Bonneville Dam, USA). 3.
 Network analyses revealed greater variation in movement for Pacific
 lamprey compared with Chinook salmon. Salmon that passed the dam had
 networks consisting of more direct passage routes with fewer overall
 movements compared with lamprey that passed the dam. Lamprey that did not
 pass the dam exhibited a wide range of behaviours, from approaching only
 one fishway site to testing all possible passage routes. Accounting for
 the time spent in the network improved the ability to detect biological
 differences in network structure for lamprey that did and did not pass the
 dam. 4. The movement patterns likely resulted from different behavioural
 responses to complex environmental and internal factors affecting a
 philopatric species (Chinook salmon) versus a non-philopatric species
 (Pacific lamprey) when moving through an engineered environment designed
 primarily for salmon. 5. Synthesis and applications. Our case study
 highlights the potential for network analyses to link questions of basic
 movement ecology with monitoring of movement and behaviour in
 human-altered landscapes. Network analyses can thus serve as a valuable
 tool for describing movement and behaviour in the face of environmental
 change and assessing the effectiveness of mitigation efforts at spatially
 complex obstacles to animal movement.
description: 240 Chinook Salmon
 traits and network propertiesBiological traits and
 network properties for all 240 Chinook salmon analyzed in this
 study240
 Salmon traits and network
 properties.xls255 Lamprey traits and
 network propertiesBiological traits and
 network properties for all 255 Pacific lamprey analyzed in this
 study