cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5683/sp2/cmxxwj
title: Data from: Previously unknown evolutionary groups dominate the ssDNA gokushoviruses in oxic and anoxic waters of a coastal marine environment

description: AbstractMetagenomic studies have revealed that ssDNA phages from the family Microviridae subfamily Gokushovirinae are widespread in aquatic ecosystems. It is hypothesized that gokushoviruses occupy specialized niches, resulting in differences among genotypes traversing water column gradients. Here, we use degenerate primers that amplify a fragment of the gene encoding the major capsid protein to examine the diversity of gokushoviruses in Saanich Inlet, a seasonally anoxic fjord on the coast of Vancouver Island, British Columbia. Amplicon sequencing of samples from the mixed oxic surface (10 m) and deeper anoxic (200 m) layers indicated a diverse assemblage of gokushoviruses, with greater richness at 10 m than 200 m. A comparison of amplicon sequences with sequences selected on the basis of RFLP patterns from eight surface samples collected over a one-year period revealed that gokushovirus diversity was higher in spring and summer during stratification, and lower in fall and winter after deep-water renewal, consistent with seasonal variability within gokushovirus populations. Phylogenetic analysis of clustered amplicons revealed at least five new phylogenetic clades of previously unknown sequences, with the most abundant group associated with viruses that infect SUP05, a ubiquitous and abundant member of marine oxygen minimum zones. Our results provide persuasive evidence that, while specific gokushovirus genotypes may have a narrow host range, hosts for gokushoviruses in Saanich Inlet consist of a wide range of bacterial taxa, including SUP05, a taxonomic clade of gamma proteobacterial sulfur oxidizers. Members of SUP05 are abundant in Saanich Inlet and involved in carbon, nitrogen, and sulfur cycling along the redoxline; thus, gokushoviruses are likely important mortality agents of these bacteria and have consequent influences on biogeochemical cycling in this system.
DOI: 10.5683/sp2/djijp0
title: Data from: Prey availability and ambient temperature influence carrion persistence in the boreal forest

description: Abstract1. Scavenging by vertebrates can have important impacts on food web stability and persistence, and can alter the distribution of nutrients throughout the landscape. However, scavenging communities have been understudied in most regions around the globe, and we lack understanding of the biotic drivers of vertebrate scavenging dynamics. 2. In this paper, we examined how changes in prey density and carrion biomass caused by population cycles of a primary prey species, the snowshoe hare (Lepus americanus), influence scavenging communities in the northern boreal forest. We further examined the impact of habitat and temperature on scavenging dynamics. 3. We monitored the persistence time, time until first scavenger, and number of species scavenging experimentally-placed hare carcasses over four consecutive years in the southwestern Yukon. We simultaneously monitored hare density and carrion biomass to examine their influence relative to temperature, habitat, and seasonal effects. For the primary scavengers, we developed species-specific scavenging models to determine variation on the effects of these factors across species, and determine which species may be driving temporal patterns in the entire community. 4. We found that the efficiency of the scavenging community was affected by hare density, with carcass persistence decreasing when snowshoe hare densities declined, mainly due to increased scavenging rates by Canada lynx (Lynx canadensis). However, prey density did not influence the number of species scavenging a given carcass, suggesting prey abundance affects carrion recycling but not necessarily the number of connections in the food web. In addition, scavenging rates increased in warmer temperatures, and there were strong seasonal effects on the richness of the vertebrate scavenging community. 5. Our results demonstrate that vertebrate scavenging communities are sensitive to changes in species’ demography and environmental change, and that future assessments of food web dynamics should consider links established through scavenging.
DOI: 10.5683/sp2/8vomwc
title: Data from: Priorities and motivations of marine coastal restoration research

description: AbstractActive restoration is becoming an increasingly important conservation intervention to counteract the degradation of marine coastal ecosystems. Understanding what has motivated the scientific community to research the restoration of marine coastal ecosystems and how restoration research projects are funded is essential if we want to scale-up restoration interventions to meaningful extents.Here, we systematically review and synthesize data to understand the motivations for research on the restoration of coral reefs, seagrass, mangroves, saltmarsh, and oyster reefs. We base this analysis off a published database of marine restoration studies, originally designed to estimate the cost and feasibility of marine coastal restoration, derived from mostly scientific studies published in peer-reviewed and some grey literature. For the present study, the database was updated with fields aimed at assessing the motivations, outcomes, and funding sources for each project. We classify restoration motivations into five categories: biotic, experimental, idealistic, legislative, and pragmatic. Moreover, we evaluate the variables measured and outcomes reported by the researchers and evaluate whether projects adhered to the Society for Ecological Restoration’s (SER) standards for the practice of ecological restoration. The most common motivation of the scientific community to study restoration in marine coastal ecosystems was experimental i.e. to seek experimental data to answer ecological research questions or improve restoration approach, as expected since mostly peer-reviewed literature was evaluated here. There were differences in motivations among the five coastal ecosystems. For instance, biodiversity enhancement was the most common case for a biotic motivation in mangrove restoration projects. The most common metrics evaluated were growth/productivity, survivorship, habitat function, physical attributes and reproduction. For most ecosystems, ecological outcomes were frequently reported, with socio-economic implications of the restoration rarely mentioned, except for mangroves. Projects were largely funded by governmental grants with some investment from private donations, non-governmental organizations, and the involvement of volunteers. Our findings and database provide critical data to align future research of the scientific community with the real social, economic and policy needs required to scale-up marine coastal restoration projects.
DOI: 10.5683/sp2/u4i3wh
title: Data from: Purifying selection in the toll-like receptors of song sparrows Melospiza melodia

description: AbstractVariation in immune gene sequences is known to influence resistance to infectious diseases and parasites, and hence survival and mate choice, across animal taxa. Toll-like receptors (TLRs) comprise one essential gene family in the vertebrate innate immune system, and recognize evolutionarily conserved structures from all major microorganism classes. However, the causes and consequences of TLR variation in passerine birds remain largely unexplored. We examined seven TLR genes in song sparrows (Melospiza melodia), a species that is studied across North America. We then examined sequences from four unduplicated TLRs (TLR1LB, TLR3, TLR4 and TLR15) from birds in two parts of the species’ range (N = 27, N = 6), tested for evidence of selection, and conducted pilot analyses of the role of TLR heterozygosity in survival. We identified 45 SNPs: 19 caused changes in amino acid sequences, and two of these were likely deleterious. We found no evidence of codon-level episodic positive selection, but detected purifying selection at codons in all TLRs. Contrary to expectations we found no strong correlation between heterozygosity at TLRs and inbreeding coefficient f (estimate ± se = -0.68 ± 0.37, Radj2 = 0.08, F1,25 = 3.38, p = 0.08). In addition, pilot analyses revealed no relationship between TLR heterozygosity and survival (β ± SE: 0.09 ± 2.00, p = 0.96), possibly due to small sample size. Further analyses of genetic diversity in TLRs are likely to advance understanding of the effects of innate immune gene diversity on the fitness and persistence of wild populations.
DOI: 10.5683/sp2/9pbqes
title: Data from: QST FST comparisons with unbalanced half-sib designs

description: AbstractQST, a measure of quantitative genetic differentiation among populations, is an index that can suggest local adaptation if QST for a trait is sufficiently larger than the mean FST of neutral genetic markers. A previous method by Whitlock and Guillaume derived a simulation resampling approach to statistically test for a difference between QST and FST, but that method is limited to balanced data sets with offspring related as half-sibs through shared fathers. We extend this approach to (1) allow for a model more suitable for some plant populations or breeding designs in which offspring are related through mothers (assuming independent fathers for each offspring; half-sibs by dam), and (2) by explicitly allowing for unbalanced data sets. The resulting approach is made available through the R package QstFstComp.
DOI: 10.5683/sp2/gfijz1
title: Data from: QTL mapping identifies candidate alleles involved in adaptive introgression and range expansion in a wild sunflower

description: AbstractThe wild North American sunflowers Helianthus annuus and H. debilis are participants in one of the earliest identified examples of adaptive trait introgression, and the exchange is hypothesized to have triggered a range expansion in H. annuus. However, the genetic basis of the adaptive exchange has not been examined. Here, we combine quantitative trait locus (QTL) mapping with field measurements of fitness to identify candidate H. debilis QTL alleles likely to have introgressed into H. annuus to form the natural hybrid lineage H. a. texanus. Two 500-individual BC1 mapping populations were grown in central Texas, genotyped for 384 single nucleotide polymorphism (SNP) markers and then phenotyped in the field for two fitness and 22 herbivore resistance, ecophysiological, phenological and architectural traits. We identified a total of 110 QTL, including at least one QTL for 22 of the 24 traits. Over 75% of traits exhibited at least one H. debilis QTL allele that would shift the trait in the direction of the wild hybrid H. a. texanus. We identified three chromosomal regions where H. debilis alleles increased both female and male components of fitness; these regions are expected to be strongly favoured in the wild. QTL for a number of other ecophysiological, phenological and architectural traits colocalized with these three regions and are candidates for the actual traits driving adaptive shifts. G × E interactions played a modest role, with 17% of the QTL showing potentially divergent phenotypic effects between the two field sites. The candidate adaptive chromosomal regions identified here serve as explicit hypotheses for how the genetic architecture of the hybrid lineage came into existence.
DOI: 10.5683/sp2/mfkzqh
title: Data from: Quantifying how constraints limit the diversity of viable routes to adaptation

description: AbstractConvergent adaptation can occur at the genome scale when independently evolving lineages use the same genes to respond to similar selection pressures. These patterns provide insights into the factors that facilitate or constrain the diversity of genetic responses that contribute to adaptive evolution. A first step in studying such factors is to quantify the observed amount of repeatability relative to expectations under a null hypothesis. Here, we formulate a novel metric to quantify the constraints driving the observed amount of repeated adaptation in pairwise contrasts based on the hypergeometric distribution, and then generalize this for simultaneous analysis of multiple lineages. This metric is explicitly based on the probability of observing a given amount of repeatability by chance under an arbitrary null hypothesis, and is readily compared among different species and types of trait. We also formulate a metric to quantify the effective proportion of genes in the genome that have the potential to contribute to adaptation. As an example of how these metrics can be used to draw inferences, we assess the amount of repeatability observed in existing datasets on adaptation to antibiotics in yeast and climate in conifers. This approach provides a method to test a wide range of hypotheses about how different kinds of factors can facilitate or constrain the diversity of genetic responses observed during adaptive evolution.
DOI: 10.5683/sp2/sx5q8o
title: Data from: Quantifying inbreeding avoidance through extra-pair reproduction

description: AbstractExtra-pair reproduction is widely hypothesised to allow females to avoid inbreeding with related socially-paired males. Consequently, numerous field studies have tested the key predictions that extra-pair offspring are less inbred than females’ alternative within-pair offspring, and that the probability of extra-pair reproduction increases with a female's relatedness to her socially-paired male. However such studies rarely measure inbreeding or relatedness sufficiently precisely to detect subtle effects, or consider biases stemming from failure to observe inbred offspring that die during early development. Analyses of multi-generational song sparrow (Melospiza melodia) pedigree data showed that most females had opportunity to increase or decrease the coefficient of inbreeding of their offspring through extra-pair reproduction with neighbouring males. In practice, observed extra-pair offspring had lower inbreeding coefficients than females’ within-pair offspring on average, while the probability of extra-pair reproduction increased substantially with the coefficient of kinship between a female and her socially-paired male. However, simulations showed that such effects could simply reflect bias stemming from inbreeding depression in early offspring survival. The null hypothesis that extra-pair reproduction is random with respect to kinship therefore cannot be definitively rejected in song sparrows, and existing general evidence that females avoid inbreeding through extra-pair reproduction requires re-evaluation given such biases.
DOI: 10.5683/sp2/kazyic
title: Data from: Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count?

description: AbstractA goal of many environmental DNA barcoding studies is to infer quantitative information about relative abundances of different taxa based on sequence read proportions generated by high-throughput sequencing. However, potential biases associated with this approach are only beginning to be examined. We sequenced DNA amplified from faeces (scats) of captive harbour seals (Phoca vitulina) to investigate whether sequence counts could be used to quantify the seals’ diet. Seals were fed fish in fixed proportions, a chordate-specific mitochondrial 16S marker was amplified from scat DNA and amplicons sequenced using an Ion Torrent PGM™. For a given set of bioinformatic parameters, there was generally low variability between scat samples in proportions of prey species sequences recovered. However, proportions varied substantially depending on sequencing direction, level of quality filtering (due to differences in sequence quality between species) and minimum read length considered. Short primer tags used to identify individual samples also influenced species proportions. In addition, there were complex interactions between factors; for example, the effect of quality filtering was influenced by the primer tag and sequencing direction. Resequencing of a subset of samples revealed some, but not all, biases were consistent between runs. Less stringent data filtering (based on quality scores or read length) generally produced more consistent proportional data, but overall proportions of sequences were very different than dietary mass proportions, indicating additional technical or biological biases are present. Our findings highlight that quantitative interpretations of sequence proportions generated via high-throughput sequencing will require careful experimental design and thoughtful data analysis.
DOI: 10.5683/sp2/q5nclp
title: Data from: Quantifying the effects of migration and mutation on adaptation and demography in spatially heterogeneous environments

description: AbstractHow do mutation and gene flow influence population persistence, niche expansion, and local adaptation in spatially heterogeneous environments? In this article, we analyse a demographic and evolutionary model of adaptation to an environment containing two habitats in equal frequencies, and we bridge the gap between different theoretical frameworks. Qualitatively, our model yields four qualitative types of outcomes: (i) global extinction of the population (ii) adaptation to one habitat only, but also adaptation to both habitats with (iii) specialized phenotypes, or (iv) with generalized phenotypes; and we determine the conditions under which each equilibrium is reached. We derive new analytical approximations for the local densities and the distributions of traits in each habitat under a migration--selection--mutation balance, compute the equilibrium values of the means, variances and asymmetries of the local distributions of phenotypes, and contrast the effects of migration and mutation on the evolutionary outcome. We then check our analytical results by solving our model numerically, and also assess their robustness in the presence of demographic stochasticity. While increased migration results in a decrease in local adaptation, mutation in our model does not influence the values of the local mean traits. Yet, both migration and mutation can have dramatic effects on population size and even lead to metapopulation extinction when selection is strong. Niche expansion, the ability for the population to adapt to both habitats, can also be prevented by small migration rates and a reduced evolutionary potential characterised by rare mutation events of small effects; but niche expansion is otherwise the most likely outcome. Although our results are derived under the assumption of clonal reproduction, we finally show and discuss the links between our model and previous quantitative genetics models.
DOI: 10.5683/sp2/l3d0ru
title: Data from: Quantitative DNA metabarcoding: improved estimates of species proportional biomass using correction factors derived from control material

description: AbstractDNA metabarcoding is a powerful new tool allowing characterization of species assemblages using high-throughput amplicon sequencing. The utility of DNA metabarcoding for quantifying relative species abundances is currently limited by both biological and technical biases which influence sequence read counts. We tested the idea of sequencing 50/50 mixtures of target species and a control species in order to generate relative correction factors (RCFs) that account for multiple sources of bias and are applicable to field studies. RCFs will be most effective if they are not affected by input mass ratio or co-occurring species. In a model experiment involving three target fish species and a fixed control, we found RCFs did vary with input ratio but in a consistent fashion, and that 50/50 RCFs applied to DNA sequence counts from various mixtures of the target species still greatly improved relative abundance estimates (e.g. average per species error of 19 ± 8% for uncorrected vs. 3 ± 1% for corrected estimates). To demonstrate the use of correction factors in a field setting, we calculated 50/50 RCFs for 18 harbour seal (Phoca vitulina) prey species (RCFs ranging from 0.68 to 3.68). Applying these corrections to field-collected seal scats affected species percentages from individual samples (Δ 6.7 ± 6.6%) more than population-level species estimates (Δ 1.7 ± 1.2%). Our results indicate that the 50/50 RCF approach is an effective tool for evaluating and correcting biases in DNA metabarcoding studies. The decision to apply correction factors will be influenced by the feasibility of creating tissue mixtures for the target species, and the level of accuracy needed to meet research objectives.
DOI: 10.5683/sp2/rc9kwq
title: Data from: Quantitative genetic analysis indicates natural selection on leaf phenotypes across wild tomato species (Solanum sect. Lycopersicon; Solanaceae)

description: AbstractAdaptive evolution requires both raw genetic material and an accessible path of high fitness from one fitness peak to another. In this study, we used an introgression line (IL) population to map quantitative trait loci (QTL) for leaf traits thought to be associated with adaptation to precipitation in wild tomatoes (Solanum sect. Lycopersicon; Solanaceae). A QTL Sign Test showed that several traits likely evolved under directional natural selection. Leaf traits correlated across species do not share a common genetic basis, consistent with a scenario in which selection maintains trait covariation unconstrained by pleiotropy or linkage disequilibrium. Two large effect QTL for stomatal distribution colocalized with key genes in the stomatal development pathway, suggesting promising candidates for the molecular bases of adaptation in these species. Furthermore, macroevolutionary transitions between vastly different stomatal distributions may not be constrained when such large effect mutations are available. Finally, genetic correlations between stomatal traits measured in this study and data on carbon isotope discrimination from the same ILs, support a functional hypothesis that the distribution of stomata affects the resistance to CO2 diffusion inside the leaf, a trait implicated in climatic adaptation in wild tomatoes. Along with evidence from previous comparative and experimental studies, this analysis indicates that leaf traits are an important component of climatic niche adaptation in wild tomatoes, and demonstrates that some trait transitions between species could have involved few, large effect genetic changes, allowing rapid responses to new environmental conditions.
DOI: 10.5683/sp2/d9coji
title: Data from: Rain, predators, and spider sociality: a manipulative experiment

description: AbstractGroup-living organisms offer a unique perspective on how environmental gradients influence geographic distributions, as not only the properties of individuals, but also those of their groups interact with the environment to determine a species range. In turn, the ranges of group-living organisms should provide insights on the conditions that favor group versus solitary living. Here we show that rain intensity and predation by ants, factors postulated to exclude subsocial Anelosimus spiders from the lowland tropical rainforest, are greater in this habitat than at higher elevations. We further show that experimentally excluding these factors increases the survival of subsocial Anelosimus colonies when transplanted to the lowland rainforest, but not at their native higher elevation range. While providing a rare experimental test of the simultaneous importance of abiotic and biotic gradients on species range limits, these results provide direct evidence that adverse environmental factors may prevent solitary living and require group living in certain environments.