cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5683/sp2/3ogt1v
title: Data from: Time scale matters: genetic analysis does not support adaptation-by-time as the mechanism for adaptive seasonal declines in kokanee reproductive lifespan

description: AbstractSeasonal declines of fitness-related traits are often attributed to environmental effects or individual-level decisions about reproductive timing and effort, but genetic variation may also play a role. In populations of Pacific salmon (Oncorhynchus spp.), seasonal declines in reproductive life span have been attributed to adaptation-by-time, in which divergent selection for different traits occurs among reproductively isolated temporal components of a population. We evaluated this hypothesis in kokanee (freshwater obligate Oncorhynchus nerka) by testing for temporal genetic structure in neutral and circadian-linked loci. We detected no genetic differences in presumably neutral loci among kokanee with different arrival and maturation dates within a spawning season. Similarly, we detected no temporal genetic structure in OtsClock1b, Omy1009uw, or OmyFbxw11, candidate loci associated with circadian function. The genetic evidence from this study and others indicates a lack of support for adaptation-by-time as an important evolutionary mechanism underlying seasonal declines in reproductive life span and a need for greater consideration of other mechanisms such as time-dependent, adaptive adjustment of reproductive effort.
DOI: 10.5683/sp2/bqbi7s
title: Data from: Time to get moving: assisted gene flow of forest trees

description: AbstractGeographic variation in trees has been investigated since the mid-18th century. Similar patterns of clinal variation have been observed along latitudinal and elevational gradients in common garden experiments for many temperate and boreal species. These studies convinced forest managers that a ‘local is best’ seed source policy was usually safest for reforestation. In recent decades, experimental design, phenotyping methods, climatic data and statistical analyses have improved greatly and refined but not radically changed knowledge of clines. The maintenance of local adaptation despite high gene flow suggests selection for local adaptation to climate is strong. Concerns over maladaptation resulting from climate change have motivated many new genecological and population genomics studies; however, few jurisdictions have implemented assisted gene flow (AGF), the translocation of pre-adapted individuals to facilitate adaptation of planted forests to climate change. Here, we provide evidence that temperate tree species show clines along climatic gradients sufficiently similar for average patterns or climate models to guide AGF in the absence of species-specific knowledge. Composite provenancing of multiple seed sources can be used to increase diversity and buffer against future climate uncertainty. New knowledge will continue to refine and improve AGF as climates warm further.
DOI: 10.5683/sp2/0djfr5
title: Data from: Tisaniba, a new genus of marpissoid jumping spiders from Borneo (Araneae: Salticidae)

description: AbstractSix new species of marpissoid jumping spiders from Sarawak, Borneo, are described in the new genus Tisaniba Zhang & Maddison. They are the type species, T. mulu Zhang & Maddison sp. nov., as well as the species T. bijibijan Zhang & Maddison sp. nov., T. dik Zhang & Maddison sp. nov., T. kubah Zhang & Maddison sp. nov., T. selan Zhang & Maddison sp. nov., and T. selasi Zhang & Maddison sp. nov. The spiders are small and brown to black, living in leaf litter in the tropical forest. Phylogenetic analyses based on 28s and 16sND1 genes indicate that they are a distinctive group within the marpissoids. Diagnostic illustrations and photographs of living spiders are provided for all species.
DOI: 10.5683/sp2/qaw6rz
title: Data from: Too much of a good thing: The unique and repeated paths toward copper adaptation

description: AbstractCopper is a micronutrient essential for growth due to its role as a co-factor in enzymes involved in respiration, defense against oxidative damage, and iron uptake. Yet too much of a good thing can be lethal, and yeast cells typically do not have tolerance to copper levels much beyond the concentration in their ancestral environment. Here, we report a short-term evolutionary study of Saccharomyces cerevisiae exposed to levels of copper sulfate that are inhibitory to the initial strain. We isolated and identified adaptive mutations soon after they arose, reducing the number of neutral mutations, to determine the first genetic steps that yeast take when adapting to copper. We analyzed 34 such strains through whole-genome sequencing and by assaying fitness within different environments; we also isolated a subset of mutations through tetrad analysis of four lines. We identified a multi-layered evolutionary response. In total, 57 single base-pair mutations were identified across the 34 lines. In addition, gene amplification of the copper metallothionein protein, CUP1, was rampant, as was chromosomal aneuploidy. Four other genes received multiple, independent mutations in different lines (the vacuolar transporter genes VTC1 and VTC4; the plasma membrane H+-ATPase PMA1; and MAM3, a protein required for normal mitochondrial morphology). Analyses indicated that mutations in all four genes, as well as CUP1 copy number, contributed significantly to explaining variation in copper tolerance. Our study thus finds that evolution takes both common and less trodden pathways toward evolving tolerance to an essential, but highly toxic, micronutrient.
DOI: 10.5683/sp2/snuidg
title: Data from: Topology of tree-mycorrhizal fungus interaction networks in xeric and mesic Douglas-fir forests

description: Abstract1. From the phytocentric perspective, a mycorrhizal network (MN) is formed when the roots of two or more plants are colonized by the same fungal genet. MNs can be modelled as interaction networks with plants as nodes and fungal genets as links. The potential effects of MNs on facilitation or competition between plants are increasingly recognized, but their network topologies remain largely unknown. This information is needed to understand the ecological significance of MN functional traits. 2. The objectives of this study were to describe the interaction network topologies of MNs formed between two ectomycorrhizal fungal species, Rhizopogon vesiculosus and R. vinicolor, and interior Douglas-fir trees at the forest stand scale, identify factors leading to this structure and to contrast MN structures between forest plots with xeric versus mesic soil moisture regimes. 3. Tuberculate mycorrhizas were sampled in six 10 × 10 m plots with either xeric or mesic soil moisture regimes. Microsatellite DNA markers were used to identify tree and fungal genotypes isolated from mycorrhizas and for comparison with reference tree boles above-ground. 4. In all six plots, trees and fungal genets were highly interconnected. Size asymmetries between different tree cohorts led to non-random MN topologies, while differences in size and connectivity between Rhizopogon species-specific subnetwork components contributed towards MN nestedness. Large mature trees acted as network hubs with a significantly higher node degree compared to smaller trees. MNs representing trees linked by R. vinicolor genets were mostly nested within larger, more highly connected R. vesiculosus-linked MNs. 5. Attributes of network nodes showed that hub trees were more important to MN topology on xeric than mesic sites, but the emergent structures of MNs were similar in the two soil moisture regimes. 6. Synthesis. This study suggests MNs formed between interior Douglas-fir trees and R. vesiculosus and R. vinicolor genets are resilient to the random loss of participants, and to soil water stress, but may be susceptible to the loss of large trees or fungal genets. Our results regarding the topology of MNs contribute to the understanding of forest stand dynamics and the resilience of forests to stress or disturbance.
DOI: 10.5683/sp2/j382pz
title: Data from: Towards an integrated database on Canadian ocean resources: benefits, current states, and research gaps

description: AbstractOceanic ecosystem services support a range of human benefits, and Canada has extensive research networks producing growing data sets. We present a first effort to compile, link, and harmonize available information to provide new perspectives on the status of Canadian ocean ecosystems and corresponding research. The metadata database currently includes 1094 individual assessments and data sets from government (n = 716), nongovernment (n = 320), and academic sources (n = 58), comprising research on marine species, natural drivers and resources, human activities, ecosystem services, and governance, with data sets spanning 1979–2012 on average. Overall, research shows a strong prevalence towards single-species fishery studies, with an underrepresentation of economic and social aspects, and of the Arctic region in general. Nevertheless, the number of studies that are multispecies or ecosystem-based have increased since the 1960s. We present and discuss two illustrative case studies — marine protected area establishment in Canada and herring resource use by the Heiltsuk First Nation — highlighting the potential use of multidisciplinary data sets drawn from metadata records. Identifying knowledge gaps is key to achieving the comprehensive, accessible and interdisciplinary data sets and subsequent analyses necessary for new sustainability policies that meet both ecological and socioeconomic needs.
DOI: 10.5683/sp2/bngfao
title: Data from: Trait-mediated community assembly: distinguishing the signatures of biotic and abiotic filters

description: AbstractConflicting hypotheses predict how traits mediate species establishment and community assembly. Traits of newly establishing individuals are predicted to converge, or be more similar to the resident, preexisting community, when the biotic or abiotic environment favors a single best phenotype, but are predicted to diverge when trait differences reduce competitive interactions. We tested these competing hypotheses using transplant seedlings in an old-field environment, and assessed the contribution of inter- and intra-specific transplant trait variation to community-level patterns. Using a soil moisture gradient and resident plant removals, we determined when traits of newly-establishing plants converge or diverge from the resident community by calculating community weighted mean traits for transplant and resident communities. We saw evidence of environmentally- and competitively-driven trait shifts that resulted in both trait convergence and divergence from the resident community, whose traits reflect the combined effects of both drivers. Leaf dry matter content (LDMC) of transplants diverged in the presence of competition, whereas plant height and stem-specific density (SSD) showed the opposite pattern, converging with the resident community in their presence. Specific leaf area (SLA) shifted with competition but did not reflect resident community SLA. All transplant traits were influenced by soil moisture, often in an interaction with competition, indicating that the strength of convergence or divergence is contingent on the abiotic environment. Intraspecific differences in transplant traits among treatments were evident in three of four traits; intraspecific height and SLA trends mirrored transplant community-level trends, whereas intraspecific shifts in SSD were distinct from community-level trends. Our study shows competition between plant species may cause traits of newly establishing plants to converge with the resident community, as frequently as it selects for trait divergence. These opposing effects of competition suggest that it plays a pervasive role in both intraspecific and species-level trait differences among communities.
DOI: 10.5683/sp2/84yfar
title: Data from: Transcriptome analysis indicates considerable divergence in alternative splicing between duplicated genes in Arabidopsis thaliana

description: AbstractGene and genome duplication events have created a large number of new genes in plants that can diverge by evolving new expression profiles and functions (neofunctionalization) or dividing extant ones (subfunctionalization). Alternative splicing (AS) generates multiple types of mRNA from a single type of pre-mRNA by differential intron splicing. It can result in new protein isoforms or down-regulation of gene expression by transcript decay. Using RNA-seq we investigated the degree to which alternative splicing patterns are conserved between duplicated genes in Arabidopsis thaliana. Our results revealed that 30% of AS events in alpha whole genome duplicates, and 33% of AS events in tandem duplicates, are qualitatively conserved within leaf tissue. Loss of ancestral splice forms, as well as asymmetric gain of new splice forms, may account for this divergence. Conserved events had different frequencies, as only 31% of shared AS events in alpha whole genome duplicates and 41% of shared AS events in tandem duplicates had similar frequencies in both paralogs, indicating considerable quantitative divergence. Analysis of published RNA-seq data from nonsense mediated decay (NMD) mutants indicated that 85% of alpha whole genome duplicates and 89% of tandem duplicates have diverged in their AS-induced NMD. Our results indicate that alternative splicing shows a high degree of divergence between paralogs such that qualitatively conserved alternative splicing events tend to have quantitative divergence. Divergence in AS patterns between duplicates may be a mechanism of regulating expression level divergence.
DOI: 10.5683/sp2/qeieo8
title: Data from: Transcriptome comparative analysis of two Camellia species reveals lipid metabolism during mature seed natural drying

description: AbstractCamellia seed oil has been used as high quality and healthy food for over two thousand years. Seed drying management effects oil quality and quantity. however, the molecular mechanisms of fatty acid biosynthesis and accumulation during the drying process remain unknown. In this study, the transcriptomes of Camellia meiocarpa and C. oleifera seed were characterized at five moisture content levels (10 - 50%) to identify the major processes and reveal genes affecting lipid metabolism in response to nature drying. We found a total of 111,156 unigenes by de novo assembled from RNA-Seq libraries of five moisture content levels during after-ripening of C. meiocarpa (74,016) and C. oleifera (76,374). Ten pathways were closely linked to changes in oil content and composition with 244 genes involved in fatty acid synthesis and accumulation. Gene Ontology enrichment of differentially expressed genes (DEGs) indicated that fatty acid synthesis and accumulation are essential in C. meiocarpa while fatty acid accumulation in C. oleifera during nature drying process. Comparative analyses of DEGs between any two consecutive moisture contents, identified six and three key unigenes in C. Meiocarpa and C. oleifera seeds, respectively, and one additional unigene responsible for the difference between the two species’ fatty acid synthesis and accumulation. Natural drying has improved the quality and quantity of the camellia seed oil. The study provided: a) global transcriptional profiles at five moisture content levels during seed nature drying, b) insights into highlighting transcripts putatively involved in the regulation of the gene expression program and in specific processes likely essential for lipid metabolism, and c) an opportunity to discovering genes associated with oil seed quantity and quality improvement for the studied two camellia species.
DOI: 10.5683/sp2/yp2tj5
title: Data from: "Transcriptome resources for three hybrid sunflower species (Helianthus anomalus, H. deserticola, H paradoxus)" in Genomic Resources Notes accepted 1 February 2013–31 March 2013

description: AbstractThis article documents the public availability of three transcriptome sequences. These genomic resources were developed for the following species: Helianthus anomalus, Helianthus deserticola and Helianthus paradoxus.
DOI: 10.5683/sp2/f7yudj
title: Data from: Understanding the spectacular failure of DNA barcoding in willows (Salix): Does this result from a trans-specific selective sweep?

description: AbstractWillows (Salix: Salicaceae) form a major ecological component of Holarctic floras, and consequently are an obvious target for a DNA-based identification system. We surveyed two to seven plastid genome regions (~3.8 kb; ~3% of the genome) from 71 Salix species across all five subgenera, to assess their performance as DNA barcode markers. Although Salix has a relatively high level of interspecific hybridization, this may not sufficiently explain the near complete failure of barcoding that we observed: only one species had a unique barcode. We recovered 39 unique haplotypes, from more than 500 specimens, that could be partitioned into six major haplotype groups. A unique variant of group I (haplotype 1*) was shared by 53 species in three of five Salix subgenera. This unusual pattern of haplotype sharing across infrageneric taxa is suggestive of either a massive non-random coalescence failure (incomplete lineage sorting), or of repeated plastid capture events, possibly including a historical selective sweep of haplotype 1* across taxonomic sections. The former is unlikely as molecular dating indicates that haplotype 1* originated recently, and is nested in the oldest major haplotype group in the genus. Further, we detected significant non-neutrality in the frequency spectrum of mutations in group I, but not outside group I, and demonstrated a striking absence of geographic structure to the haplotype distributions in this group. The most likely explanation for the patterns we observed involves recent repeated plastid capture events, aided by widespread hybridization and long-range seed dispersal, but primarily propelled by one or more trans-species selective sweeps.
DOI: 10.5683/sp2/wbkeab
title: Data from: Untangling the early diversification of eukaryotes: a phylogenomic study of the evolutionary origins of Centrohelida, Haptophyta, and Cryptista

description: AbstractAssembling the global eukaryotic tree of life has long been a major effort of Biology. In recent years, pushed by the new availability of genome-scale data for microbial eukaryotes, it has become possible to revisit many evolutionary enigmas. However, some of the most ancient nodes, which are essential for inferring a stable tree, have remained highly controversial. Among other reasons, the lack of adequate genomic datasets for key taxa has prevented the robust reconstruction of early diversification events. In this context, the centrohelid heliozoans are particularly relevant for reconstructing the tree of eukaryotes because they represent one of the last substantial groups that was missing large and diverse genomic data. Here, we filled this gap by sequencing high-quality transcriptomes for four centrohelid lineages, each corresponding to a different family. Combining these new data with a broad eukaryotic sampling, we produced a gene-rich taxon-rich phylogenomic dataset that enabled us to refine the structure of the tree. Specifically, we show that (i) centrohelids relate to haptophytes, confirming Haptista; (ii) Haptista relates to SAR; (iii) Cryptista share strong affinity with Archaeplastida; and (iv) Haptista + SAR is sister to Cryptista + Archaeplastida. The implications of this topology are discussed in the broader context of plastid evolution.
DOI: 10.5683/sp2/87kfcw
title: Data from: Urban rat races: spatial population genomics of brown rats (Rattus norvegicus) compared across multiple cities

description: AbstractUrbanization often substantially influences animal movement and gene flow. However, few studies to date have examined gene flow of the same species across multiple cities. In this study, we examine brown rats (Rattus norvegicus) to test hypotheses about the repeatability of neutral evolution across four cities: Salvador, Brazil; New Orleans, USA; Vancouver, Canada; New York City, USA. At least 150 rats were sampled from each city and genotyped for a minimum of 15,000 genome-wide SNPs. Levels of genome-wide diversity were similar across cities, but varied across neighborhoods within cities. All four populations exhibited high spatial autocorrelation at the shortest distance classes (&lt; 500 m) due to limited dispersal. Coancestry and evolutionary clustering analyses identified genetic discontinuities within each city that coincided with a resource desert in New York City, major waterways in New Orleans, and roads in Salvador and Vancouver. Such replicated studies are crucial to assessing the generality of predictions from urban evolution, and have practical applications for pest management and public health. Future studies should include a range of global cities in different biomes, incorporate multiple species, and examine the impact of specific characteristics of the built environment and human socioeconomics on gene flow.
DOI: 10.5683/sp2/uddvil
title: Data from: Urbanization drives the evolution of parallel clines in plant populations

description: AbstractUrban ecosystems are an increasingly dominant feature of terrestrial landscapes. While evidence that species can adapt to urban environments is accumulating, the mechanisms through which urbanization imposes natural selection on populations are poorly understood. The identification of adaptive phenotypic changes (i.e. clines) along urbanization gradients would facilitate our understanding of the selective factors driving adaptation in cities. Here, we test for phenotypic clines in urban ecosystems by sampling the frequency of a Mendelian-inherited trait—cyanogenesis—in white clover (Trifolium repens L.) populations along urbanization gradients in four cities. Cyanogenesis protects plants from herbivores, but reduces tolerance to freezing temperatures. We found that the frequency of cyanogenic plants within populations decreased towards the urban centre in three of four cities. A field experiment indicated that spatial variation in herbivory is unlikely to explain these clines. Rather, colder minimum winter ground temperatures in urban areas compared with non-urban areas, caused by reduced snow cover in cities, may select against cyanogenesis. In the city with no cline, high snow cover might protect plants from freezing damage in the city centre. Our study suggests that populations are adapting to urbanization gradients, but regional climatic patterns may ultimately determine whether adaptation occurs.