cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5683/sp2/f1lwec
title: Data from: Cryptic genetic variation shapes the adaptive evolutionary potential of enzymes

description: AbstractGenetic variation among orthologous proteins can cause cryptic phenotypic properties that only manifest in changing environments. Such variation may impact the evolvability of proteins, but the underlying molecular basis remains unclear. Here, we performed comparative directed evolution of four orthologous metallo-β-lactamases toward a new function and found that different starting genotypes evolved to distinct evolutionary outcomes. Despite a low initial fitness, one ortholog reached a significantly higher fitness plateau than its counterparts, via increasing catalytic activity. By contrast, the ortholog with the highest initial activity evolved to a less-optimal and phenotypically distinct outcome through changes in expression, oligomerization and activity. We show how cryptic molecular properties and conformational variation of active site residues in the initial genotypes cause epistasis, that could lead to distinct evolutionary outcomes. Our work highlights th e importance of understanding the molecular details that connect genetic variation to protein function to improve the prediction of protein evolution.
DOI: 10.5683/sp2/5jrz8j
title: Data from: Cultural isolation is greater than genetic isolation across an avian hybrid zone

description: AbstractElucidating the relationship between genetic and cultural evolution is important in understanding speciation, as learned premating barriers might be involved in maintaining species differences. Here we test this relationship by examining a widely recognized premating barrier, bird song, in a hybrid zone between black-throated green (Setophaga virens) and Townsend's warblers (S. townsendi). We use song analysis, genomic techniques and playback experiments to characterize the cultural and genetic backgrounds of individuals in this region, expecting that if song is an important reproductive barrier between these species, there should be a strong relationship between song and genotype. We show that songs in the hybrid zone correspond to the distinctly different songs found in allopatry but that song and genotype are not tightly coupled in sympatry. Allopatric individuals responded only to local songs, indicating that individuals may have learned to respond to songs they commonly hear. We observed discordance between song and genotype clines; a narrower cline suggests that cultural selection on song is stronger than natural selection on genotype. These findings indicate that song is unlikely to play a role in reproductive isolation between these species, and we suggest that spatial variation in song may nonetheless be maintained by frequency-dependent cultural selection. This decoupling of genes and culture may contribute to hybridization in this region.
DOI: 10.5683/sp2/omn3wb
title: Data from: Data archiving is a good investment

description: AbstractFunding agencies are reluctant to support data archiving, even though large research funders such as the National Science Foundation (NSF) and the National Institutes of Health acknowledge its importance for scientific progress. Our quantitative estimates of data reuse indicate that ongoing financial investment in data-archiving infrastructure provides a high scientific return.
DOI: 10.5683/sp2/bipgmp
title: Data from: Decomposing variation in male reproductive success: age-specific variances and covariances through extra-pair and within-pair reproduction

description: Abstract1. Age-specific variances and covariances in reproductive success shape the total variance in lifetime reproductive success (LRS), age-specific opportunities for selection, and population demographic variance and effective size. Age-specific (co)variances in reproductive success achieved through different reproductive routes must therefore be quantified to predict population, phenotypic and evolutionary dynamics in age-structured populations. 2. While numerous studies have quantified age-specific variation in mean reproductive success, age-specific variances and covariances in reproductive success, and the contributions of different reproductive routes to these (co)variances, have not been comprehensively quantified in natural populations. 3. We applied ‘additive’ and ‘independent’ methods of variance decomposition to complete data describing apparent (social) and realised (genetic) age-specific reproductive success across 11 cohorts of socially monogamous but genetically polygynandrous song sparrows (Melospiza melodia). We thereby quantified age-specific (co)variances in male within-pair and extra-pair reproductive success (WPRS and EPRS) and the contributions of these (co)variances to the total variances in age-specific reproductive success and LRS. 4. ‘Additive’ decomposition showed that within-age and among-age (co)variances in WPRS across males aged 2–4 years contributed most to the total variance in LRS. Age-specific (co)variances in EPRS contributed relatively little. However, extra-pair reproduction altered age-specific variances in reproductive success relative to the social mating system, and hence altered the relative contributions of age-specific reproductive success to the total variance in LRS. 5. ‘Independent’ decomposition showed that the (co)variances in age-specific WPRS, EPRS and total reproductive success, and the resulting opportunities for selection, varied substantially across males that survived to each age. Furthermore, extra-pair reproduction increased the variance in age-specific reproductive success relative to the social mating system to a degree that increased across successive age classes. 6. This comprehensive decomposition of the total variances in age-specific reproductive success and LRS into age-specific (co)variances attributable to two reproductive routes showed that within-age and among-age covariances contributed substantially to the total variance and that extra-pair reproduction can alter the (co)variance structure of age-specific reproductive success. Such covariances and impacts should consequently be integrated into theoretical assessments of demographic and evolutionary processes in age-structured populations.
DOI: 10.5683/sp2/ottcq7
title: Data from: Defining isoscapes in the Northeast Pacific as an index of ocean productivity

description: AbstractAim: We modeled isoscapes in the Northeast Pacific using satellite-based data with the main objective of testing if isoscapes defined by a few key parameters can be used as a proxy for secondary productivity. Location: Northeast (NE) Pacific; 46 – 60⁰N and 125 – 165⁰W. Time period: From 1998 to 2017 (ongoing). Major taxa studied: Zooplankton with a focus on large herbivores. Methods: Approximately 280 summer zooplankton samples were analyzed for Carbon (δ13C) and Nitrogen (δ15N) stable isotope (SI) ratios. Environmental conditions experienced by zooplankton organisms were extracted from satellite, in situ sensor and model databases. A generalized additive model approach was used to explain the spatial variability of δ13C and δ15N values and predict isoscapes. Results: Sea surface temperature (SST), sea level anomaly (SLA) and chlorophyll-a concentration emerged as the significant SI predictors. Modelled isoscapes reproduced patterns observed in δ13C and δ15N value distribution, such as a decrease from the coast to offshore. The contribution of eddies in enhancing local production in the open ocean was also well captured by the models. In the central part of the NE Pacific higher SI values were correlated with higher large copepod biomass measured by the North Pacific Continuous Plankton Recorder (CPR) survey. However, in the area off the coast of British Columbia (BC) high δ15N variability appeared to be associated with episodic intrusions of coastal waters demonstrating that caution is needed when interpreting sharp changes in SI ratios. Main conclusions: While the mechanisms driving SI ratio variability are complex, we demonstrated that a few parameters used as a proxy for some of these major mechanisms are able to successfully produce isoscape models. This approach was proven useful to provide a qualitative estimate of the secondary production, which can be particularly valuable in a region where few data are available.
DOI: 10.5683/sp2/qafge5
title: Data from: Demographic mechanisms of inbreeding adjustment through extra-pair reproduction

description: Abstract1. One hypothesis explaining extra-pair reproduction is that socially monogamous females mate with extra-pair males to adjust the coefficient of inbreeding (f) of extra-pair offspring (EPO) relative to that of within-pair offspring (WPO) they would produce with their socially paired male. Such adjustment of offspring f requires non-random extra-pair reproduction with respect to relatedness, which is in turn often assumed to require some mechanism of explicit pre-copulatory or post-copulatory kin discrimination. 2. We propose three demographic processes that could potentially cause mean f to differ between individual females' EPO and WPO given random extra-pair reproduction with available males without necessarily requiring explicit kin discrimination. Specifically, such a difference could arise if social pairings formed non-randomly with respect to relatedness or persisted non-randomly with respect to relatedness, or if the distribution of relatedness between females and their sets of potential mates changed during the period through which social pairings persisted. 3. We used comprehensive pedigree and pairing data from free-living song sparrows (Melospiza melodia) to quantify these three processes and hence investigate how individual females could adjust mean offspring f through instantaneously random extra-pair reproduction. 4. Female song sparrows tended to form social pairings with unrelated or distantly related males slightly less frequently than expected given random pairing within the defined set of available males. Furthermore, social pairings between more closely related mates tended to be more likely to persist across years than social pairings between less closely related mates. However, these effects were small and the mean relatedness between females and their sets of potential extra-pair males did not change substantially across the years through which social pairings persisted. 5. Our framework and analyses illustrate how demographic and social structuring within populations might allow females to adjust mean f of offspring through random extra-pair reproduction without necessarily requiring explicit kin discrimination, implying that adjustment of offspring f might be an inevitable consequence of extra-pair reproduction. New theoretical and empirical studies are required to explore the general magnitude of such effects and quantify the degree to which they could facilitate or constrain long-term evolution of extra-pair reproduction.
DOI: 10.5683/sp2/p8xkws
title: Data from: Density-dependent signaling: an alternative hypothesis on the function of chemical signaling in a non-territorial solitary carnivore

description: AbstractBrown bears are known to use rubbing behavior as a means of chemical communication, but the function of this signaling is unclear. One hypothesis that has gained support is that male bears rub to communicate dominance to other males. We tested the communication of dominance hypothesis in a low-density brown bear population in southeast British Columbia. We contrasted rubbing rates for male and female bears during and after the breeding season using ten years of DNA-mark-recapture data for 643 individuals. Here we demonstrate that male brown bears rub 60% more during the breeding than the non-breeding season, while female rubbing had no seasonal trends. Per capita rub rates by males were, on average, 2.7 times higher than females. Our results suggest that the function of rubbing in the Rocky Mountains may not only be to communicate dominance, but also to self-advertise for mate attraction. We propose that the role of chemical communication in this species may be density-dependent, where the need to self-advertise for mating is inversely related to population density and communicating for dominance increases with population density. We suggest that future endeavors to elucidate the function of rubbing should sample the behavior across a range of population densities using camera trap and genotypic data.
DOI: 10.5683/sp2/kiegtp
title: Data from: Density-dependent space use affects interpretation of camera trap detection rates

description: AbstractCamera-traps (CTs) are an increasingly popular tool for wildlife survey and monitoring. Estimating relative abundance in unmarked species is often done using detection rate as an index of relative abundance, which assumes a positive linear relationship with true abundance. This assumption may be violated if movement behavior varies with density, but the degree to which movement is density-dependent across taxa is unclear. The potential confounding of population-level relative abundance indices by movement depends on how regularly, and by what magnitude, movement rate and home-range size vary with density. We conducted a systematic review and meta-analysis to quantify relationships between movement rate, home range size, and density, across terrestrial mammalian taxa. We then simulated animal movements and CT sampling to test the effect of contrasting movement scenarios on CT detection rates. Overall, movement rate and home range size were negatively correlated with density and positively correlated with one another. The strength of the relationships varied significantly between taxa and populations. In simulations, detection rates were related to true abundance but underestimated change, particularly for slower moving species with small home ranges. In situations where animal space use changes markedly with density, we estimate that up to thirty percent of a true change in abundance may be missed due to the confounding effect of movement, making trend estimation more difficult. The common assumption that movement remains constant across densities is therefore violated across a wide range of mammal species. When studying unmarked species using CT detection rates, researchers and managers should consider that such indices of relative abundance reflect both density and movement. Practitioners interpreting changes in detection rates should be aware that observed differences may be biased low relative to true changes in abundance, and that further information on animal movement may be required to make robust inferences on population trends.
DOI: 10.5683/sp2/oxalmz
title: Data from: Dental ontogeny in extinct synapsids reveals a complex evolutionary history of the mammalian tooth attachment system

description: AbstractThe mammalian dentition is uniquely characterized by a combination of precise occlusion, permanent adult teeth, and a unique tooth attachment system. Unlike the ankylosed teeth in most reptiles, mammal teeth are supported by a ligamentous tissue that suspends each tooth in its socket, providing flexible and compliant tooth attachment that prolongs the life of each tooth and maintains occlusal relationships. Here we investigate dental ontogeny through histological examination of a wide range of extinct synapsid lineages to assess whether the ligamentous tooth attachment system is unique to mammals and to determine how it evolved. This study shows for the first time that the ligamentous tooth attachment system is not unique to crown mammals within Synapsida, having arisen in several non-mammalian therapsid clades as a result of neoteny and progenesis in dental ontogeny. Mammalian tooth attachment is here re-interpreted as a paedomorphic condition relative to the ancestral synapsid form of tooth attachment.
DOI: 10.5683/sp2/jn1mst
title: Data from: Detecting small-scale genotype-environment interactions in apomictic dandelion (Taraxacum officinale) populations

description: AbstractStudies of genotype × environment interactions (G×E) and local adaptation provide critical tests of natural selection’s ability to counter opposing forces such as gene flow. Such studies may be greatly facilitated in asexual species, given the possibility for experimental replication at the level of true genotypes (rather than populations) and the possibility of using molecular markers to assess genotype-environment associations in the field (neither of which is possible for most sexual species). Here we tested for G×E in asexual dandelions (Taraxacum officinale) by subjecting six genotypes to experimental drought, mown, and benign (control) conditions, and subsequently using microsatellites to assess genotype-environment associations in the field. We found strong G×E, with genotypes that performed poorly under benign conditions showing the highest performance under stressful conditions (drought or mown). Our six focal genotypes comprise &gt;80% of plants in local populations. The most common genotype in the field showed its highest relative performance under mown conditions (the most common habitat in our study area), and almost all plants of this genotype in the field were found growing in mowed lawns. Genotypes performing best under benign experimental conditions were found most frequently in unmown conditions in the field. These results are strongly indicative of local adaptation at a very small scale, with unmown microsites of only a few square meters typically embedded within larger mown lawns. By studying an asexual species we were able to map genotypes with known ecological characteristics to environments with high spatial precision.
DOI: 10.5683/sp2/c3icam
title: Data from: Detection of outlier loci and their utility for fisheries management

description: AbstractGenetics-based approaches have informed fisheries management for decades, yet remain challenging to implement within systems involving recently diverged stocks or where gene flow persists. In such cases, genetic markers exhibiting locus-specific (“outlier”) effects associated with divergent selection may provide promising alternatives to loci that reflect genome-wide (“neutral”) effects for guiding fisheries management. Okanagan Lake kokanee (Oncorhynchus nerka), a fishery of conservation concern, exhibits two sympatric ecotypes adapted to different reproductive environments, however, previous research demonstrated the limited utility of neutral microsatellites for assigning individuals. Here, we investigated the efficacy of an outlier-based approach to fisheries management by screening &gt;11,000 expressed sequence tags for linked microsatellites and conducting genomic scans for kokanee sampled across seven spawning sites. We identified eight outliers among 52 polymorphic loci that detected ecotype-level divergence, whereas there was no evidence of divergence at neutral loci. Outlier loci exhibited the highest self-assignment accuracy to ecotype (92.1%), substantially outperforming 44 neutral loci (71.8%). Results were robust among-sampling years, with assignment and mixed composition estimates for individuals sampled in 2010 mirroring baseline results. Overall, outlier loci constitute promising alternatives for informing fisheries management involving recently diverged stocks, with potential applications for designating management units across a broad range of taxa.
DOI: 10.5683/sp2/dzjlgx
title: Data from: Development of an ultra-dense genetic map of the sunflower genome

description: AbstractThe development of ultra-dense genetic maps has the potential to facilitate detailed comparative genomic analyses and whole genome sequence assemblies. Here we describe the use of a custom Affymetrix GeneChip containing nearly 2.4 million features (25 bp sequences) targeting 86,023 unigenes from sunflower (Helianthus annuus L.) and related species to test for single-feature polymorphisms (SFPs) in a recombinant inbred line (RIL) mapping population derived from a cross between confectionery and oilseed sunflower lines (RHA280 x RHA801). We then employed an existing genetic map derived from this same population to rigorously filter out low quality data and place 67,486 features corresponding to 22,481 unigenes on the sunflower genetic map. The resulting map contains a substantial fraction of all sunflower genes and will thus facilitate a number of downstream applications, including genome assembly and the identification of candidate genes underlying QTL or traits of interest.
DOI: 10.5683/sp2/ihmqnm
title: Data from: Dietary stress does not strengthen selection against single deleterious mutations in Drosophila melanogaster

description: AbstractStress is generally thought to increase the strength of selection, although empirical results are mixed and general conclusions are difficult because data are limited. Here we compare the fitness effects of nine independent recessive mutations in Drosophila melanogaster in a high- and low-dietary-stress environment, estimating the strength of selection on these mutations arising from both a competitive measure of male reproductive success and productivity (female fecundity and the subsequent survival to adulthood of her offspring). The effect of stress on male reproductive success has not been addressed previously for individual loci and is of particular interest with respect to the alignment of natural and sexual selection. Our results do not support the hypothesis that stress increases the efficacy of selection arising from either fitness component. Results concerning the alignment of natural and sexual selection were mixed, although data are limited. In the low-stress environment, selection on mating success and productivity were concordant for five of nine mutations (four out of four when restricted to those with significant or near-significant productivity effects), whereas in the high-stress environment, selection aligned for seven of nine mutations (two out of two when restricted to those having significant productivity effects). General conclusions as to the effects of stress on the strength of selection and the alignment of natural and sexual selection await data from additional mutations, fitness components and stressors.
DOI: 10.5683/sp2/vbewry
title: Data from: Differential migratory timing of western populations of Wilson’s Warblers revealed by mitochondrial DNA and stable isotopes

description: AbstractMolecular markers and stable isotopes have provided important insights into the migratory connectivity of small landbirds. Research integrating these two methods has primarily focused on linking breeding and wintering sites, rather than focusing on timing of migratory movement of different breeding populations. We used mitochondrial DNA and isotopic markers to infer the timing of various breeding populations of migrating Wilson's Warblers (Cardellina pusilla) moving through a migratory stopover site, demonstrating the value of multiple sources of information in estimating the origin of migrants. Using mixed-stock analysis, we found that early spring migrants sampled in southwestern Arizona were dominated by warblers migrating to the West Coast of the contiguous United States, whereas later migrants included a large pulse of birds migrating to Alaska and western Canadian provinces. Stable hydrogen isotope data from individual birds showed the same timing pattern as genetic data. Had we used stable isotopes alone, we would not have been able to infer whether birds later in the migration season were most likely migrating to Alaska or the Interior West, given the large overlap in isotope values between those regions. The lack of mitochondrial group 2, common in the Interior West, in late-season migrants strongly suggests that these birds were migrating to breeding areas in Alaska or other northern regions. Studies that reveal the timing of migration of different breeding populations through stopover sites lay the foundation for more in-depth examination of seasonal interactions between migration and the stationary phases of the annual cycle.