cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5683/sp2/igvu3v
title: Data from: Whole plastome sequencing reveals deep plastid divergence and cytonuclear discordance between closely related balsam poplars, Populus balsamifera and P. trichocarpa (Salicaceae)

description: AbstractAs molecular phylogenetic analyses incorporate ever-greater numbers of loci, cases of cytonuclear discordance – the phenomenon in which nuclear gene trees deviate significantly from organellar gene trees – are being reported more frequently. Plant examples of topological discordance, caused by recent hybridization between extant species, are well known. However, examples of branch-length discordance are less reported in plants relative to animals. We use a combination of de novo assembly and reference-based mapping using short-read shotgun sequences to construct a robust phylogeny of the plastome for multiple individuals of all the common Populus species in North America. We demonstrate a case of strikingly high plastome divergence, in contrast to little nuclear genome divergence, in two closely related balsam poplars, Populus balsamifera and Populus trichocarpa (Populus balsamifera ssp. trichocarpa). Previous studies with nuclear loci indicate that the two species (or subspecies) diverged since the late Pleistocene, whereas their plastomes indicate deep divergence, dating to at least the Pliocene (6–7 Myr ago). Our finding is in marked contrast to the estimated Pleistocene divergence of the nuclear genomes, previously calculated at 75 000 yr ago, suggesting plastid capture from a ‘ghost lineage’ of a now-extinct North American poplar.
DOI: 10.5683/sp2/gasvct
title: Data from: Why less complexity produces better forecasts: an independent data evaluation of kelp habitat models

description: AbstractUnderstanding how species are distributed in the environment is increasingly important for natural resource management, particularly for keystone and habitat forming species, and those of conservation concern. Habitat suitability models are fundamental to developing this understanding; however their use in management continues to be limited due to often-vague model objectives and inadequate evaluation methods. Along the Northeast Pacific coast, canopy kelps (Macrocystis pyrifera and Nereocystis luetkeana) provide biogenic habitat and considerable primary production to nearshore ecosystems. We investigated the distribution of these species by examining a series of increasingly complex habitat suitability models ranging from process-based models based on species' ecology to complex Generalised Additive Models applied to purpose-collected survey data. Seeking limits on model complexity, we explored the relationship between model complexity and forecast skill, measured using both cross-validation and independent data evaluation. Our analysis confirmed the importance of predictors used in models of coastal kelp distributions developed elsewhere (i.e., depth, bottom type, bottom slope, and exposure); it also identified additional important factors including salinity, and interactions between exposure and salinity, and slope and tidal energy. Comparative results showed that cross-validation can lead to over-fitting, while independent data evaluation clearly identified the appropriate model complexity for generating habitat forecasts. Our results also illustrate that, depending on the evaluation data, predictions from simpler models can out-perform those from more complex models. Collectively, the insights from evaluating multiple models with multiple data sets contribute to the holistic assessment of model forecast skill. The continued development of methods and metrics for evaluating model forecasts with independent data, and the explicit consideration of model objectives and assumptions, promise to increase the utility of model forecasts to decision makers.
DOI: 10.5683/sp2/gjyw5w
title: Data from: Widespread genetic incompatibilities between first-step mutations during parallel adaptation of Saccharomyces cerevisiae to a common environment

description: AbstractIndependently evolving populations may adapt to similar selection pressures via different genetic changes. The interactions between such changes, such as in a hybrid individual, can inform us about what course adaptation may follow and allow us to determine whether gene flow would be facilitated or hampered following secondary contact. We used Saccharomyces cerevisiae to measure the genetic interactions between first-step mutations that independently evolved in the same biosynthetic pathway following exposure to the fungicide nystatin. We found that genetic interactions are prevalent and predominantly negative, with the majority of mutations causing lower growth when combined in a double mutant than when alone as a single mutant (sign epistasis). The prevalence of sign epistasis is surprising given the small number of mutations tested and runs counter to expectations for mutations arising in a single biosynthetic pathway in the face of a simple selective pressure. Furthermore, in one third of pairwise interactions, the double mutant grew less well than either single mutant (reciprocal sign epistasis). The observation of reciprocal sign epistasis among these first adaptive mutations arising in the same genetic background indicates that partial postzygotic reproductive isolation could evolve rapidly between populations under similar selective pressures, even with only a single genetic change in each. The nature of the epistatic relationships was sensitive, however, to the level of drug stress in the assay conditions, as many double mutants became fitter than the single mutants at higher concentrations of nystatin. We discuss the implications of these results both for our understanding of epistatic interactions among beneficial mutations in the same biochemical pathway and for speciation.
DOI: 10.5683/sp2/rdsps0
title: Worldwide evidence of a unimodal relationship between productivity and plant species richness

description: AbstractThe search for predictions of species diversity across environmental gradients has challenged ecologists for decades. The humped-back model (HBM) suggests that plant diversity peaks at intermediate productivity; at low productivity few species can tolerate the environmental stresses, and at high productivity a few highly competitive species dominate. Over time the HBM has become increasingly controversial, and recent studies claim to have refuted it. Here, by using data from coordinated surveys conducted throughout grasslands worldwide and comprising a wide range of site productivities, we provide evidence in support of the HBM pattern at both global and regional extents. The relationships described here provide a foundation for further research into the local, landscape, and historical factors that maintain biodiversity.
DOI: 10.6084/m9.figshare.20138243
title: XYZ coordinates.zip

description: Xmol structure files of species optimized using B3LYP, B98, M06, M06-2X and G4 approaches.
DOI: 10.5683/sp2/nm3tb1
title: Disconnects between ecological theory and data in phenological mismatch research

description: AbstractClimate change may lead to phenological mismatches, where the timing of critical events between interacting species becomes de-synchronized, with potential negative consequences. Evidence documenting negative impacts on fitness is mixed. The Cushing match-mismatch hypothesis, the most common hypothesis underlying these studies, offers testable assumptions and predictions to determine consequences of phenological mismatch when combined with a pre-climate change baseline. Here, we highlight how improved approaches could rapidly advance mechanistic understanding. We find that currently no study has collected the data required to test this hypothesis well, and 71% of studies fail to define a baseline. Experiments that clearly link timing to fitness and test extremes, integration across approaches, and null models would aid robust predictions of shifts with climate change.
DOI: 10.5683/sp2/y2e644
title: Experimental hybridization studies suggest that pleiotropic alleles commonly underlie adaptive divergence between natural populations

description: AbstractThe alleles used for adaptation can pleiotropically affect traits under stabilizing selection. The fixation of alleles with deleterious pleiotropic effects causes compensatory alleles to be favoured by selection. Such compensatory alleles might segregate in interpopulation hybrids, resulting in segregation variance for traits where parents have indistinguishable phenotypes. If adaptation typically involves pleiotropy and compensation, then the segregation variance for traits under stabilizing selection is expected to increase with the magnitude of adaptive phenotypic divergence between parents. This prediction has not been tested empirically, and I gathered data from experimental hybridization studies to evaluate it. I found that pairs of parents which are more phenotypically divergent beget hybrids with more segregation variance in traits for which the parents are statistically indistinguishable. This result suggests that adaptive divergence between pairs of natural populations proceeds via pleiotropy and compensation, and that deleterious transgressive segregation variance accumulates systematically as populations diverge.
DOI: 10.5683/sp2/pucw5a
title: Fitness maps to a large-effect locus in introduced stickleback populations

description: AbstractMutations of small effect underlie most adaptation to new environments, but beneficial variants with large fitness effects are expected to contribute under certain conditions. Genes and genomic regions having large effects on phenotypic differences between populations are known from numerous taxa, but fitness effect sizes have rarely been estimated. We mapped fitness over a generation in an F2 intercross between a marine and a lake stickleback population introduced to a freshwater pond. A QTL map of the number of surviving offspring per F2 female detected a single, large-effect locus near Ectodysplasin (Eda), a gene having an ancient freshwater allele causing reduced bony armor and other changes. F2 females homozygous for the freshwater allele had twice the number of surviving offspring as homozygotes for the marine allele, producing a large selection coefficient, s = 0.50 ± 0.09 SE. Correspondingly, the frequency of the freshwater allele increased from 0.50 in F2 mothers to 0.58 in surviving offspring. We compare these results to observed allele frequency changes at the Eda gene in an Alaskan lake population colonized by marine stickleback in the 1980’s. The frequency of the freshwater Eda allele rose steadily over multiple generations and reached 95% within 20 years, yielding a similar estimate of selection, s = 0.49 ± 0.05. These findings are consistent with other studies suggesting strong selection on this gene (and/or linked genes) in fresh water. Selection on ancient genetic variants carried by colonizing ancestors is likely to increase the prevalence of large-effect fitness variants in adaptive evolution.
DOI: 10.5683/sp2/5ltcgl
title: Five-years of ocrelizumab in relapsing multiple sclerosis: OPERA studies open-label extension

description: AbstractObjective To assess over 3 years of follow-up, the effects of maintaining or switching to ocrelizumab (OCR) therapy on clinical and MRI outcomes and safety measures in the open-label extension (OLE) phase of the pooled OPERA studies in relapsing multiple sclerosis. Methods After 2 years of double-blind, controlled treatment, patients continued OCR (600 mg infusions every 24 weeks) or switched from interferon (IFN) β-1a (44 μg 3 times weekly) to OCR when entering the OLE phase (3 years). Adjusted annualized relapse rate, time to onset of 24-week confirmed disability progression/improvement (CDP/CDI), brain MRI activity (gadolinium-enhanced and new/enlarging T2 lesions), and percentage brain volume change were analyzed. Results Of patients entering the OLE phase, 88.6% completed Year 5. The cumulative proportion with 24-week CDP was lower in patients who initiated OCR earlier, vs patients initially receiving IFN β-1a (16.1% vs 21.3% at Year 5; p=0.014). Patients continuing OCR maintained, and those switching from IFN β-1a to OCR attained near complete and sustained suppression of new brain MRI lesion activity from Year 3 to 5. Over the OLE phase, patients continuing OCR exhibited less whole brain volume loss from double-blind study baseline vs those switching from IFN β-1a (–1.87% vs –2.15% at Year 5; p&lt;0.01). Adverse events were consistent with past reports and no new safety signals emerged with prolonged treatment. Conclusion Compared with patients switching from IFN β-1a, earlier and continuous OCR treatment up to 5 years provided sustained benefit on clinical and MRI measures of disease progression.
DOI: 10.5683/sp2/tjix04
title: Genome-wide shifts in climate-related variation underpin responses to selective breeding in a widespread conifer

description: AbstractLocally adapted temperate tree populations exhibit genetic trade-offs among climate-related traits that can be exacerbated by selective breeding, and are challenging to manage under climate change. To inform climatically adaptive forest management, we investigated the genetic architecture and impacts of selective breeding on four climate-related traits in 105 natural and 20 selectively bred lodgepole pine populations from western Canada. Growth, cold injury and growth initiation and growth cessation phenotypes were tested for associations with 18,600 SNPs in natural populations to identify ‘positive effect alleles’ (PEAs). The effects of artificial selection for faster growth on PEA frequencies for each trait were quantified in breeding populations from different climates. Substantial shifts in PEA proportions and frequencies were observed across many loci after two generations of selective breeding for height, and responses of phenology-associated PEAs differed strongly among climatic regions. Extensive genetic overlap was evident among traits. Alleles most strongly associated with greater height were often also associated with greater cold injury and delayed phenology, although it is unclear whether potential trade-offs arose directly from pleiotropy or indirectly via genetic linkage. Modest variation among populations in PEA frequencies across many loci was associated with large phenotypic differences and strong climatic gradients, providing support for assisted gene flow polices. Relationships among genotypes, phenotypes and climate in natural populations were maintained or strengthened by selective breeding. However, future adaptive phenotypes and assisted gene flow may be compromised if selective breeding further increases the PEA frequencies of SNPs involved in adaptive trade-offs among climate-related traits.
DOI: 10.5683/sp2/oyty3f
title: Genomic analyses of phenotypic differences between native and invasive populations of diffuse knapweed (Centaurea diffusa)

description: AbstractInvasive species represent excellent opportunities to study the evolutionary potential of traits important to success in novel environments. Although some ecologically-important traits have been identified in invasive species, little is typically known about the genetic mechanisms that underlie invasion success in non-model species. Here, we use a genome-wide association (GWAS) approach to identify the genetic basis of trait variation in the non-model, invasive, diffuse knapweed (Centaurea diffusa Lam. [Asteraceae]). To assist with this analysis, we have assembled the first draft genome reference and fully annotated plastome assembly for this species, and the one of the first from this large, weedy, genus, which is of major ecological and economic importance. We collected phenotype data from 372 individuals from four native and four invasive populations of C. diffusa grown in a common environment. Using these individuals, we produced reduced-representation genotype-by-sequencing (GBS) libraries and identified 7058 SNPs. We identify two SNPs associated with leaf width in these populations, a trait which significantly varies between native and invasive populations. In this rosette forming species, increased leaf width is a major component of increased biomass, a common trait in invasive plants correlated with increased fitness. Finally, we use annotations from Arabidopsis thaliana to identify 98 candidate genes that are near the associated SNPs and highlight several good candidates for leaf width variation.
DOI: 10.5683/sp2/vjh4c8
title: Genomic differentiation and local adaptation on a microgeographic scale in a resident songbird

description: AbstractElucidating forces capable of driving species diversification in the face of gene flow remains a key goal in evolutionary biology. Song sparrows, Melospiza melodia, occur as 25 subspecies in diverse habitats across North America, are among the continent’s most widespread vertebrate species, and are exemplary of many highly variable species for which the conservation of locally adapted populations may be critical to their range-wide persistence. We focus here on six morphologically distinct subspecies resident in the San Francisco Bay region, including three salt-marsh endemics and three residents in upland and riparian habitats adjacent to the Bay. We used reduced-representation sequencing to generate 2,773 SNPs to explore genetic differentiation, spatial population structure, and demographic history. Clustering separated individuals from each of the six subspecies, indicating subtle differentiation at microgeographic scales. Evidence of limited gene flow and low nucleotide diversity across all six subspecies further supports a hypothesis of isolation among locally adapted populations. We suggest that natural selection for genotypes adapted to salt marsh environments and changes in demography over the past century have acted in concert to drive the patterns of diversification reported here. Our results offer evidence of microgeographic specialization in a highly polytypic bird species long discussed as a model of sympatric speciation and rapid adaptation, and they support the hypothesis that conserving locally adapted populations may be critical to the range-wide persistence of similarly highly variable species.
DOI: 10.5683/sp2/ml6chp
title: Global gradients in intraspecific variation in vegetative and floral traits are partially associated with climate and species richness

description: AbstractAim Intraspecific trait variation (ITV) within natural plant communities can be large, influencing local ecological processes and dynamics. Here, we shed light on how ITV in vegetative and floral traits responds to large-scale abiotic and biotic gradients (i.e. climate and species richness). Specifically, we tested if associations of ITV with temperature, precipitation and species richness were consistent with any of from four hypotheses relating to stress-tolerance and competition. Furthermore, we estimated the degree of correlation between ITV in vegetative and floral traits and how they vary along the gradients. Location Global. Time period 1975-2016. Major taxa studied Herbaceous and woody plants. Methods We compiled a dataset of 18,112 measurements of the absolute extent of ITV (measured as coefficient of variation) in nine vegetative and seven floral traits from 2,774 herbaceous and woody species at 2,306 locations. Results Large-scale associations between ITV and climate were trait-specific and more prominent for vegetative traits, especially leaf morphology, than for floral traits. ITV showed pronounced associations with climate, with lower ITV values in colder areas and higher values in drier areas. The associations of ITV with species richness were inconsistent across traits. Species-specific associations across gradients were often idiosyncratic and covariation in ITV was weaker between vegetative and floral traits than within the two trait groups. Main conclusions Our results show that, depending on the traits considered, ITV either increased or decreased with climate stress and species richness, suggesting that both factors can constrain or enhance ITV, which might foster plant-population persistence under stressful conditions. Given the species-specific responses and covariation in ITV, associations can be hard to predict for traits and species not yet studied. We conclude that considering ITV can improve our understanding of how plants cope with stressful conditions and environmental change across spatial and biological scales.
DOI: 10.5683/sp2/8g0vz7
title: Growth, metabolism, anatomy, behaviour, invertebrate drift

description: Abstract Adaptive trade-offs are fundamental mechanisms underlying phenotypic diversity, but the presence of generalizable patterns in multivariate adaptation and their mapping onto environmental gradients remain unclear. To understand how life-history affects multivariate trait associations, we examined relationships among growth, metabolism, anatomy and behaviour in rainbow trout juveniles from piscivore vs. insectivore ecotypes along an experimental gradient of food availability. We hypothesized that i) selection for larger size in piscivorous adults would select for higher juvenile growth at the cost of lower active metabolism; ii) elevated growth of piscivores would be supported by a greater productivity of their natal stream and more proactive foraging behaviours; and iii) general patterns of multivariate trait associations would match the predictions of the Pace-Of-Life Syndrome. Relative to insectivores, piscivorous fry showed a pattern of higher growth (+63%), maximum food intake (+33%), growth efficiency (+41%), and standard metabolic rate (SMR; +47%), but lower active metabolic capacity (maximum metabolic rate (MMR; -17%), aerobic scope (AS; -48%)), suggesting that faster piscivore growth is supported by greater food intake and digestive capacity but is traded-off against lower scope for active metabolism. A similar trade-off appeared among organ systems, with piscivorous fry exhibiting an 83% greater investment in average mass of organs associated with food consumption and processing (i.e. stomach and intestine), but an apparently smaller relative investment in organs involved in cardio-vascular or cognitive activities (heart and brain, respectively). Higher invertebrate drift in their natal rearing habitat, quicker behavioural transition to a novel food source and lower anxiety after a frightening event in piscivorous fry suggest that faster growth requires both proactive foraging behaviours and higher prey availability in the environment. Finally, the sampling of replicate insectivore populations confirmed their lower juvenile growth (-73% on average) and reduced environmental productivity of their natal streams (-45% lower drift abundance) relative to the piscivore ecotype. Our results suggest that selection for large adult body size influences selection on high juvenile growth, high basal metabolism and proactive behaviours, and that the intense phenotypic divergence between piscivorous and insectivorous rainbow trout may be constrained by environmental productivity.