cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6h82k
title: Data from: Genetic covariance between components of male reproductive success: within-pair versus extra-pair paternity in song sparrows

description: The evolutionary trajectories of reproductive systems, including both male
 and female multiple mating and hence polygyny and polyandry, are expected
 to depend on the additive genetic variances and covariances in and among
 components of male reproductive success achieved through different
 reproductive tactics. However, genetic covariances among key components of
 male reproductive success have not been estimated in wild populations. We
 used comprehensive paternity data from socially monogamous but genetically
 polygynandrous song sparrows (Melospiza melodia) to estimate additive
 genetic variance and covariance in the total number of offspring a male
 sired per year outside his social pairings (i.e. his total extra-pair
 reproductive success achieved through multiple mating) and his liability
 to sire offspring produced by his socially paired female (i.e. his success
 in defending within-pair paternity). Both components of male fitness
 showed nonzero additive genetic variance, and the estimated genetic
 covariance was positive, implying that males with high additive genetic
 value for extra-pair reproduction also have high additive genetic
 propensity to sire their socially paired female's offspring. There
 was consequently no evidence of a genetic or phenotypic trade-off between
 male within-pair paternity success and extra-pair reproductive success.
 Such positive genetic covariance might be expected to facilitate ongoing
 evolution of polygyny and could also shape the ongoing evolution of
 polyandry through indirect selection.
description: male.cov.data.dryad.finalPhenotypic data for the quantitative genetic analysis of male within-pair paternity success and extra-pair reproductive success.male.cov.Ainv.dryad.finalInverse A matrix underpinning quantitative genetic analysis of male within-pair paternity success and extra-pair reproductive success.
DOI: 10.5061/dryad.1fh61
title: Data from: Forelimb indicators of prey-size preference in the Felidae

description: The forelimbs, along with the crania, are an essential part of the
 prey-killing apparatus in cats. Linear morphometrics of the forelimbs were
 used to determine the morphological differences between felids that
 specialize on large prey, small prey, or mixed prey. We also compared the
 scaling of felid forelimbs to those of canids to test whether prey capture
 strategies affect forelimb scaling. Results suggest that large prey
 specialists have relatively robust forelimbs when compared with smaller
 prey specialists. This includes relatively more robust humeri and radii,
 relatively larger distal ends of the humerus, and relatively larger
 articular areas of the humerus and radius. Large prey specialists also had
 relatively longer olecranon processes of the ulna and wider proximal paws.
 These characters are all important for subduing large prey while the cat
 positions itself for the killing bite. Small prey specialists have
 relatively longer distal limb elements for swift prey capture, and mixed
 prey specialists had intermediate values with relatively more robust
 metacarpals. Arboreal felids also had more robust limbs. They had
 relatively longer proximal phalanges for better grip while climbing, and a
 relatively short brachial index (radius to humerus ratio). Additionally,
 we found that felids and canids differ in forelimb scaling, which
 emphasizes the dual use of forelimbs for locomotion and prey capture in
 felids. This morphometric technique worked well to separate prey-size
 preference in felids, but did not work as well to separate locomotor
 groups, as scansorial and terrestrial felids were not clearly
 distinguished.
description: Felidae and Canidae
 postcranial database
DOI: 10.5061/dryad.d88d8
title: Data from: Breeding season length and nest mortality drive cryptic life history variation in Dark-eyed Juncos (Junco hyemalis) breeding across a montane elevation gradient

description: The manner in which individual life history traits respond to the
 environment and to each other, and how these traits combine to form
 overall patterns of life history variation, remains poorly characterized
 in wild populations. We monitored breeding Dark-eyed Juncos (Junco
 hyemalis) across a 700-m elevational range. We compared breeding season
 length, temporal patterns of breeding activity, adult body size, clutch
 size, brood size, nestling quality, and nest mortality among elevations.
 We also compared environmental measures across the studied elevations to
 determine whether abiotic factors explained life history trait variation.
 We used 12 microsatellite loci to test for genetic differentiation in
 populations at different elevations. Finally, we constructed a computer
 simulation to evaluate the combined effects of observed variation in life
 history traits. We found differences among elevations in breeding season
 length and in patterns of reproductive timing, which did not match each
 other and which were not explained solely by abiotic factors. We found no
 differences among elevations in adult body size, clutch size, brood size,
 or nestling quality. Nest mortality increased significantly with
 elevation. Genetic differentiation was too low to define distinct
 subpopulations. The simulation suggested that differences in mortality, in
 combination with differences in breeding season length, contributed to
 substantial differences in reproductive success among elevations. Thus,
 although individual life history traits showed little evidence of
 variation in response to the environment or to each other and little
 genetic differentiation, variation in breeding season length and in nest
 mortality were potential drivers of substantial elevational variation in
 overall life history in this system. These results demonstrate that
 individual life history traits may vary substantially in their patterns of
 variation, and that some life history traits may have disproportionate
 effects on overall life history.
description: dryad_genotypesThis file contains the microsatellite genotypes for adult Dark-eyed Juncos captured along the elevation gradient.dryad_individual_measurementsThis file contains the field measurements made of Dark-eyed Juncos.dryad_nest_survivalThis file contains data on monitored Dark-eyed Junco nests, from which survival probabilities were calculated.
DOI: 10.5061/dryad.575p1
title: Data from: Broad-scale genetic patterns of New Zealand abalone, Haliotis iris, across a distribution spanning 13° latitude and major oceanic water masses

description: The New Zealand black-foot abalone, Haliotis iris, or pāua, is endemic to
 the rocky reefs surrounding New Zealand, whose main land mass spans 13° of
 latitude and separates the Tasman Sea from the Pacific Ocean. In this
 study, we examined the population genetic structure of this important
 commercial, cultural and recreational species by genotyping nine
 microsatellite loci in 485 pāua from 27 locations distributed across
 mainland New Zealand and the Chatham Islands. We found low, but
 significant, levels of genetic differentiation. Key genetic breaks were
 identified among the Chatham Islands and mainland samples; patterns that
 are strongly corroborated by prior work employing mtDNA sequences. AMOVAs
 indicated that samples from the south of the North Island were more
 similar to the South Island samples than to other North Island samples,
 however multivariate analysis and Bayesian clustering could not identify a
 significant pattern. Differentiation between the Chatham Islands and the
 mainland is most likely due to isolation by distance, while
 differentiation of North Island samples corresponds with major components
 of New Zealand’s oceanography, Cook Strait and the East Cape. Despite
 intense fishing pressure, we detected no signature of genetic bottlenecks
 in any region suggesting that population sizes have remained relatively
 stable over recent time or that the census size of this species is much
 larger than its effective population size.
description: Sampling locations,
 dates, and coordinatesFile is a tab-delimited
 text file that contains sampling locations (abbreviations and geographic
 coordinates) and sample collection dates for abalone.Sampling_Information-2012-04-10.txtTotal Data GenepopFile contains genotypes for abalone from for 27 locations using 9 microsatellite loci (labeled as total data in the manuscript). File is a text file in Genepop format. See Sampling_Information-2012-04-10.txt for geographic coordinates and sampling dates.27pops-9loci-GENEPOP-2012-04-10.txt5-Loci Data GenepopFile contains genotypes for abalone from for 27 locations using 5 microsatellite loci (labeled as 5-loci data from the manuscript). Loci AB22, AB31, AB75, EDN91 were excluded due to null alleles. File is a text file in Genepop format. See Sampling locations, dates, and coordinates (Sampling_Information-2012-04-10.txt) for geographic coordinates and sampling dates.27pops-5loci-GENEPOP-2012-04-10.txt24-Locations Data GenepopFile contains genotypes for abalone from for 24 locations using 9 microsatellite loci (labeled as 24-locations data from the manuscript). Locations TSK, WAI, and WST were excluded due to null alleles. File is a text file in Genepop format. See Sampling locations, dates, and coordinates (Sampling_Information-2012-04-10.txt) for geographic coordinates and sampling dates.24pops-9loci-GENEPOP-2012-04-10.txt
DOI: 10.5061/dryad.32875
title: Data from: Prenatal alcohol exposure increases postnatal acceptability of nicotine odor and taste in adolescent rats

description: Human studies indicate that alcohol exposure during gestation not only
 increases the chance for later alcohol abuse, but also nicotine
 dependence. The flavor attributes of both alcohol and nicotine can be
 important determinants of their initial acceptance and they both share the
 component chemosensory qualities of an aversive odor, bitter taste and
 oral irritation. There is a growing body of evidence demonstrating
 epigenetic chemosensory mechanisms through which fetal alcohol exposure
 increases adolescent alcohol acceptance, in part, by decreasing the
 aversion to alcohol's bitter and oral irritation qualities, as well
 as its odor. Given that alcohol and nicotine have noteworthy chemosensory
 qualities in common, we investigated whether fetal exposure to alcohol
 increased the acceptability of nicotine's odor and taste in
 adolescent rats. Study rats were alcohol-exposed during fetal development
 via the dams' liquid diet. Control animals received ad lib access to
 an iso-caloric, iso-nutritive diet throughout gestation. Odorant-induced
 innate behavioral responses to nicotine odor (Experiment 1) or
 orosensory-mediated responses to nicotine solutions (Experiment 2) were
 obtained, using whole-body plethysmography and brief access lick tests,
 respectively. Compared to controls, rats exposed to fetal alcohol showed
 an enhanced nicotine odor response that was paralleled by increased oral
 acceptability of nicotine. Given the common aversive component qualities
 imbued in the flavor profiles of both drugs, our findings demonstrate that
 like postnatal alcohol avidity, fetal alcohol exposure also influences
 nicotine acceptance, at a minimum, by decreasing the aversion of both its
 smell and taste. Moreover, they highlight potential chemosensory-based
 mechanism(s) by which fetal alcohol exposure increases the later initial
 risk for nicotine use, thereby contributing to the co-morbid expression
 with enhanced alcohol avidity. Where common chemosensory mechanisms are at
 play, our results suggest broader implications related to the consequence
 of fetal exposure with one substance of abuse and initial acceptability of
 others.
description: Brief Access Lick
 DataThis files provides
 brief-access lick data for sucrose and nicotine solution as a function of
 maternal alcohol exposure, weight of the animal at the time of testing and
 sex of the animal. The different sheets provide the mean lick data for
 each concentration as well as the mean latency to first lick at each
 concentration of tasting.Sniffing Behavior
 DataThe data represent the
 deconstruction of the sniffing patterns of adolescent rats into 14
 response variables in response to nicotine odor at different
 concentrations of odorant. The animals in the study received either
 prenatal alcohol or control exposure.
DOI: 10.5061/dryad.1t93v
title: Data from: Dietary macronutrients modulate the fatty acyl composition of rat liver mitochondrial cardiolipins

description: The interaction of dietary fats and carbohydrates on liver mitochondria
 were examined in male FBNF1 rats fed 20 different low-fat, isocaloric
 diets. Animal growth rates and mitochondrial respiratory parameters were
 essentially unaffected, but mass spectrometry-based, mitochondrial
 lipidomics profiling revealed increased levels of cardiolipins (CLs), a
 family of phospholipids essential for mitochondrial structure and
 function, in rats fed saturated or trans fat-based diets with a high
 glycemic index. These mitochondria showed elevated monolysocardiolipins (a
 CL precursor/product of CL degradation), elevated ratio of trans PC
 (18:1/18:1) to cis PC (18:1/18:1) (a marker of thiyl radical stress), and
 decreased ubiquinone Q9 -- the latter two of which imply a low-grade
 mitochondrial redox abnormality. Extended analysis demonstrated: (i)
 dietary fats and, to a lesser extent, carbohydrates induce changes in the
 relative abundance of specific CL species; (ii) Fatty acid (FA)
 incorporation into mature CLs undergoes both positive (&gt;400-fold)
 and negative (2.5-fold) regulation; and, (iii) dietary lipid abundance and
 incorporation of FAs into both the CL pool and specific mature tetra-acyl
 CLs are inversely related, suggesting previously unobserved compensatory
 regulation. This study reveals previously unobserved complexity/regulation
 of the central lipid in mitochondrial metabolism.
description: Data & R Code from:
 Dietary macronutrients modulate the Fatty Acyl composition of rat liver
 mitochondrial cardiolipins.The zip file contains
 all data and R code used to analyze Cardiolipin and related data. Please
 refer to README within the zip file for instructions on how to run the R
 code to produce all figures, including those found in the supplement and
 statistical tables in the supplement.Cardiolipin.zip
DOI: 10.5061/dryad.4sb063bn
title: Data from: Panmixia supports divergence with gene flow in Darwin’s small ground finch, Geospiza fuliginosa, on Santa Cruz, Galápagos Islands

description: The divergence-with-gene-flow model of speciation has a strong theoretical
 basis with a growing number of plausible examples in nature, but remains
 hotly debated. Darwin’s finches of the Galápagos Archipelago have played
 an important role in our understanding of speciation processes. Recent
 studies suggest that this group may also provide insights into speciation
 via divergence with gene flow. On the island of Santa Cruz, recent studies
 found evidence for adaptive divergence in Darwin’s small ground finch,
 Geospiza fuliginosa, between ecologically contrasting arid and humid
 zones. Despite the short geographical distance between these zones, strong
 disruptive selection during low rainfall periods is expected to generate
 and maintain adaptive divergence. Conversely, during high rainfall
 periods, when disruptive selection is predicted to be weakened, population
 divergence in adaptive traits is expected to break down. Because periods
 of low and high rainfall irregularly alternate, the geographical pattern
 of adaptive divergence can be assumed to break down and, importantly,
 regenerate in situ. Here, we use microsatellite allele frequency data to
 assess the genetic population structure of G. fuliginosa on Santa Cruz. We
 sample 21 sites and four ecological zones across the island. We reject
 hypotheses of population substructure linked to ecological and
 geographical differences among sites in favour of a single panmictic
 population. Panmixia implies high levels of gene flow within Santa Cruz,
 which favours selection over genetic drift as a valid process generating
 phenotypic divergence in G. fuliginosa on Santa Cruz. We discuss how our
 findings may support classic adaptation, phenotypic plasticity, matching
 habitat choice or any combination of these three processes.
description: Galligan et
 al__Panmixia__dataAllele size data for 12
 microsatellites
DOI: 10.5061/dryad.2ng06
title: Data from: Bottom-up vs. top-down effects on terrestrial insect herbivores: a meta-analysis

description: Primary consumers are under strong selection from resource (“bottom-up”)
 and consumer (“top-down”) controls, but the relative importance of these
 selective forces is unknown. We performed a meta-analysis to compare the
 strength of top-down and bottom-up forces on consumer fitness, considering
 multiple predictors that can modulate these effects: diet breadth, feeding
 guild, habitat/environment, type of bottom-up effects, type of top-down
 effects and how consumer fitness effects are measured. We focused our
 analyses on the most diverse group of primary consumers, herbivorous
 insects, and found that in general top-down forces were stronger than
 bottom-up forces. Notably, chewing, sucking and gall-making herbivores
 were more affected by top-down than bottom-up forces, top-down forces were
 stronger than bottom-up in both natural and controlled (cultivated)
 environments, and parasitoids and predators had equally strong top-down
 effects on insect herbivores. Future studies should broaden the scope of
 focal consumers, particularly in understudied terrestrial systems, guilds,
 taxonomic groups and top-down controls (e.g. pathogens), and test for more
 complex indirect community interactions. Our results demonstrate the
 surprising strength of forces exerted by natural enemies on herbivorous
 insects, and thus the necessity of using of a tri-trophic approach when
 studying insect-plant interactions.
description: Bottom-up Top-down
 Meta-analysis dataData used in the
 meta-analysis.Vidal&Murphy_meta-analysis.xlsx
DOI: 10.5061/dryad.qv731
title: Data from: Genetic background alters dominance relationships between mat alleles in the ciliate Tetrahymena thermophila

description: The pattern of inheritance and mechanism of sex determination can have
 important evolutionary consequences. We studied probabilistic sex
 determination in the ciliate Tetrahymena thermophila, which was previously
 shown to cause evolution of skewed sex ratios. We find that the genetic
 background alters the sex determination patterns of mat alleles in
 heterozygotes and that allelic interaction can differentially influence
 the expression probability of the 7 sexes. We quantify the dominance
 relationships between several mat alleles and find that A-type alleles,
 which specify sex I, are indeed recessive to B-type alleles, which are
 unable to specify that sex. Our results provide additional support for the
 presence of modifier loci and raise implications for the dynamics of sex
 ratios in populations of T. thermophila.
description: Dryad_SDPcountDataThe table contains the number of progeny with a particular genotype (either homozygote or heterozygote) that showed the respective sex (leftmost column). These counts were used to calculate SDPs (relative frequencies of sexes) shown in Table 2.JOHDominanceEstimate.nbThis is a mathematica notebook used to estimate the dominance relationship between mat alleles. The files takes as inputs sex determination patterns (SDPS) of the alleles and total number of progeny used to determine SDP. The equation used for estimate dominance and its confidence intervals are described in the methods section of the article. The raw data are provided in an accompanying excel sheet and the SDPs in Table 2 in the published article. The dominance estimates are also provided in the published article.
DOI: 10.5061/dryad.qv437
title: Data from: The geometry of nutrient-space based life-history trade-offs: sex-specific effects of macronutrient intake on the trade-off between encapsulation ability and reproductive effort in decorated crickets

description: Life-history theory assumes that traits compete for limited resources
 resulting in trade-offs. The most commonly manipulated resource in
 empirical studies is the quantity or quality of diet. Recent studies using
 the Geometric Framework for nutrition, however, suggest that trade-offs
 are often regulated by the intake of specific nutrients but a formal
 approach to identify and quantify the strength of such trade-offs is
 lacking. We posit that trade-offs occur whenever life-history traits are
 maximised in different regions of nutrient space, as evidenced by
 non-overlapping 95% confidence regions of the global maximum for each
 trait, and large angles (θ) between linear nutritional vectors and
 Euclidean distances (d) between global maxima. We then examined the
 effects of protein and carbohydrate intake on the trade-off between
 reproduction and aspects of immune function in male and female Gryllodes
 sigillatus. Female encapsulation ability and egg production increased with
 the intake of both nutrients, whereas male encapsulation ability increased
 with protein intake but calling effort increased with carbohydrate intake.
 The trade-offs between traits was therefore larger in males than females,
 as demonstrated by non-overlapping 95% confidence regions and larger θ and
 d. Under dietary choice, the sexes had similar regulated intakes but
 neither optimally regulated nutrient intake for maximal trait expression.
 We highlight that greater consideration of specific nutrient intake is
 needed when examining nutrient-space based trade-offs.
description: LH
 TradeOffs_DataData for Rapkin et al
 (2017) "The geometry of nutrient-space based life-history trade-offs:
 sex-specific effects of macronutrient intake on the trade-off between
 encapsulation ability and reproductive effort in decorated crickets".
 Includes data for Experiment 1: No Choice Feeding and Experiment 2: Choice
 Feeding.