cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5683/sp2/0fqs2u
title: Data from: Recurrent selection explains parallel evolution of genomic regions of high relative but low absolute differentiation in a ring species

description: AbstractRecent technological developments allow investigation of the repeatability of evolution at the genomic level. Such investigation is particularly powerful when applied to a ring species, in which spatial variation represents changes during the evolution of two species from one. We examined genomic variation among three subspecies of the greenish warbler ring species, using genotypes at 13 013 950 nucleotide sites along a new greenish warbler consensus genome assembly. Genomic regions of low within-group variation are remarkably consistent between the three populations. These regions show high relative differentiation but low absolute differentiation between populations. Comparisons with outgroup species show the locations of these peaks of relative differentiation are not well explained by phylogenetically conserved variation in recombination rates or selection. These patterns are consistent with a model in which selection in an ancestral form has reduced variation at some parts of the genome, and those same regions experience recurrent selection that subsequently reduces variation within each subspecies. The degree of heterogeneity in nucleotide diversity is greater than explained by models of background selection, but is consistent with selective sweeps. Given the evidence that greenish warblers have had both population differentiation for a long period of time and periods of gene flow between those populations, we propose that some genomic regions underwent selective sweeps over a broad geographic area followed by within-population selection-induced reductions in variation. An important implication of this ‘sweep-before-differentiation’ model is that genomic regions of high relative differentiation may have moved among populations more recently than other genomic regions.
DOI: 10.5683/sp2/bct62d
title: Data from: Reduced mycorrhizal responsiveness leads to increased competitive tolerance in an invasive exotic plant

description: AbstractArbuscular mycorrhizal (AM) fungi can exert a powerful influence on the outcome of plant–plant competition. Since some exotic plants interact differently with soil biota such as AM fungi in their new range, range-based shifts in AM responsiveness could shift competitive interactions between exotic and resident plants, although this remains poorly studied. We explored whether genotypes of the annual exotic Centaurea solstitialis (yellow starthistle), collected from populations across the native and non-native ranges, differed in responsiveness to AM fungi in the introduced range and whether range-based differences in mycorrhizal responsiveness affected how strongly C. solstitialis tolerated competition with the North American native bunchgrass, Stipa pulchra. Grown alone, C. solstitialis from both ranges derived only weak benefits from AM fungi. However, association with AM fungi was costly to plants when grown in competition with S. pulchra. The magnitude of the suppressive effect of AM fungi was greater for genotypes from native versus introduced populations. Synthesis. Many exotic invasive species are known to associate weakly with AM fungi, which may be beneficial in disturbed habitats where competition for resources is low. Our results indicate that reduced mycorrhizal associations may also benefit invaders in a competitive environment. Centaurea solstitialis were more strongly suppressed by established S. pulchra plants in the presence versus absence of AM fungi, but exotic genotypes were less suppressed than native genotypes. This suggests that AM fungi may contribute to invasion resistance in established native communities, but range-based shifts in the way exotic genotypes respond to AM fungal partners may counter such biotic resistance.
DOI: 10.5683/sp2/7tb3gj
title: Data from: Reductions in prolonged swimming capacity following freshwater colonization in multiple threespine stickleback populations.

description: AbstractWe compared ancestral anadromous-marine and nonmigratory, stream-resident threespine stickleback (Gasterosteus aculeatus) populations to examine the outcome of relaxed selection on prolonged swimming performance. We reared marine and stream-resident fish from two locations in a common environment and found that both stream-resident populations had lower critical swimming speeds (Ucrits) than marine populations. F1 hybrids from the two locations displayed significant differences in dominance, suggesting that the genetic basis for variation in Ucrit differs between locations. To determine which traits evolved in conjunction with, and may underlie, differences in performance capacity we measured a suite of traits known to affect prolonged swimming performance in fishes. While some candidate traits did not evolve (standard metabolic rate and two body shape traits), multiple morphological (pectoral fin size, shape and four body shape measures) and physiological (maximum metabolic rate; MMR) traits evolved in the predicted direction in both stream-resident populations. However, data from F1 hybrids suggested that only one of these traits (MMR) had dominance effects similar to those of Ucrit in both locations. Overall, our data suggest that reductions in prolonged swimming performance were selected for in non-migratory populations of threespine stickleback, and that decreases in MMR may mediate these reductions in performance.
DOI: 10.5683/sp2/t1vxbr
title: Data from: Refining the conditions for sympatric ecological speciation

description: AbstractCan speciation occur in a single population when different types of resources are available, in the absence of any geographical isolation, or any spatial or temporal variation in selection? The controversial topics of sympatric speciation and ecological speciation have already stimulated many theoretical studies, most of them agreeing on the fact that mechanisms generating disruptive selection, some level of assortment, and enough heterogeneity in the available resources, are critical for sympatric speciation to occur. Few studies, however, have combined the three factors and investigated their interactions. In this article, I analytically derive conditions for sympatric speciation in a general model where the distribution of resources can be uni- or bimodal, and where a parameter controls the range of resources that an individual can exploit. This approach bridges the gap between models of a unimodal continuum of resources and Levene-type models with discrete resources. I then test these conditions against simulation results from a recently published article (Thibert-Plante and Hendry 2011) and confirm that sympatric ecological speciation is favoured when (i) selection is disruptive (ie, individuals with an intermediate trait are at a local fitness minimum), (ii) resources are differentiated enough, and (iii) mating is assortative. I also discuss the role of mating preference functions, and the need (or lack thereof) for bimodality in resource distributions for diversification.
DOI: 10.5683/sp2/ibkc70
title: Data from: Relative importance of competition and plant-soil feedback, their synergy, context dependency and implications for coexistence

description: AbstractPlants interact simultaneously with each other and with soil biota, yet the relative importance of competition versus plant soil feedback (PSF) on plant performance is poorly understood. Using a meta-analysis of 38 published studies and 150 plant species, we show that effects of interspecific competition (either growing plants with a competitor or singly, or comparing inter- vs. intraspecific competition) and PSF (comparing home vs. away soil, live vs. sterile soil, or control vs. fungicide-treated soil) depended on treatments but were predominantly negative, broadly comparable in magnitude, and additive or synergistic. Stronger competitors experienced more negative PSF than weaker competitors when controlling for density (inter- to intraspecific competition), suggesting that PSF could prevent competitive dominance and promote coexistence. When competition was measured against plants growing singly, the strength of competition overwhelmed PSF, indicating that the relative importance of PSF may depend not only on neighbor identity but also density. We evaluate how competition and PSFs might interact across resource gradients; PSF will likely strengthen competitive interactions in high resource environments and enhance facilitative interactions in low resource environments. Finally, we provide a framework for filling key knowledge gaps and advancing our understanding of how these biotic interactions influence community structure.
DOI: 10.5683/sp2/jfja4i
title: Data from: Remarkable life history polymorphism may be evolving under divergent selection in the silverleaf sunflower

description: AbstractSubstantial intraspecific variation in life history is rare and potentially a signal of incipient ecological speciation, if variation is driven by geographically heterogenous natural selection. We present the first report of extensive life history polymorphism in Helianthus argophyllus, the silverleaf sunflower, and examine evidence for its evolution by divergent selection. In 18 populations sampled from across the species range and grown in a common garden, most quantitative traits covaried such that individuals could be assigned to two distinct life history syndromes: tall and late flowering with small initial flowerheads, or short and early flowering with larger initial flowerheads. Helianthus argophyllus exhibits regional genetic structure, but this population structure does not closely correspond with patterns of phenotypic variation. The early-flowering syndrome is primarily observed in populations from coastal barrier islands, while populations from the nearby mainland coast, although geographically and genetically close, are primarily late flowering. Additionally, several traits are more differentiated among regions than expected based on neutral genetic divergence (QST &gt; FST), including the first principal component score corresponding with life history syndrome. This discordance between patterns of phenotypic and genetic variation suggests that divergent selection is driving genetic differences in life history across the species range. If so, the silverleaf sunflower may be in early stages of ecological speciation.
DOI: 10.5683/sp2/syquup
title: Data from: Remarkably divergent regions punctuate the genome assembly of the Caenorhabditis elegans Hawaiian strain CB4856

description: AbstractThe Hawaiian strain (CB4856) of Caenorhabditis elegans is one of the most divergent from the canonical laboratory strain N2 and has been widely used in developmental, population and evolutionary studies. To enhance the utility of the strain, we have generated a draft sequence of the CB4856 genome, exploiting a variety of resources and strategies. The CB4856 genome when compared against the N2 reference has 327,050 single nucleotide variants (SNVs) and 79,529 insertion-deletion events (indels) that result in a total of 3.3 megabasepairs (Mb) of N2 sequence missing from CB4856 and 1.4 Mb of sequence present in CB4856 not present in N2. As previously reported, the density of SNVs varies along the chromosomes, with the arms of chromosomes showing greater average variation than the centers. In addition, we find 61 regions totaling 2.8 Mb, distributed across all six chromosomes, that have a greatly elevated SNV density, ranging from 2% to 16% SNVs. A survey of other wild isolates show that the two alternative haplotypes for each region are widely distributed, suggesting they have been maintained by balancing selection over long evolutionary times. These divergent regions contain an abundance of genes from large rapidly evolving families encoding F-box, MATH, BATH, seven-transmembrane G-coupled receptors, and nuclear hormone receptors suggesting that they provide selective advantages in natural environments. The draft sequence makes available a comprehensive catalog of sequence differences between the CB4856 and N2 strains that will facilitate the molecular dissection of their phenotypic differences. Our work also emphasizes the importance of going beyond simple alignment of reads to a reference genome when assessing differences between genomes.
DOI: 10.5683/sp2/hny3iy
title: Data from: Replicate divergence between and within sounds in a marine fish: the copper rockfish (Sebastes caurinus)

description: AbstractThe evolution of population structure in marine organisms and its relevance to conservation has recently received increasing attention. We tested the degree of genetic subdivision among ten populations of copper rockfish (Sebastes caurinus) representing paired samples of outer coast and the heads of five replicate sounds on the west coast of Vancouver Island, British Columbia using 17 microsatellite DNA loci. Overall, subdivision (FST) was low (FST = 0.031), but consistently higher between paired coast and head of inlet sites (mean FST = 0.047) compared to among five coast sites (mean FST = -0.001) or among the five head of inlet sites (mean FST = 0.026). Heterozygosity, allelic richness, and estimates of effective population size were also consistently lower in head of inlet sites than in coast sites. Bayesian analysis of population structure identified two genetic groups across all samples, a single genetic group amongst only coast samples, two genetic groups amongst head of inlet samples, and two genetic groups within each sound analysed separately. Head of inlet copper rockfish were also consistently shorter with lower condition factors, and grew more slowly than fish collected from coast sites. Our results implicate coast- head of inlet habitat transitions in driving the evolution of population structure, likely resulting from reduced physical connectivity and selection against immigrants in contrasting environments. Coast sites appear to be well served by existing marine protected areas. By contrast, head of inlet sites may require more specific local conservation measures as they appear to be less well connected to adjacent coast sites as well as to each other.
DOI: 10.5683/sp2/5crgas
title: Data from: Reproduction as a bottleneck to treeline advance across the circumarctic forest tundra ecotone

description: AbstractThe fundamental niche of many species is shifting with climate change, especially in sub-arctic ecosystems with pronounced recent warming. Ongoing warming in sub-arctic regions should lessen environmental constraints on tree growth and reproduction, leading to increased success of trees colonising tundra. Nevertheless, variable responses of treeline ecotones have been documented in association with warming temperatures. One explanation for time lags between increasingly favourable environmental conditions and treeline ecotone movement is reproductive limitations caused by low seed availability. Our objective was to assess the reproductive constraints of the dominant tree species at the treeline ecotone in the circumpolar north. We sampled reproductive structures of trees (cones and catkins) and stand attributes across circumarctic treeline ecotones. We used generalized linear mixed models to estimate the sensitivity of seed production and the availability of viable seed to regional climate, stand structure, and species-specific characteristics. Both seed production and viability of available seed were strongly driven by specific, sequential seasonal climatic conditions, but in different ways. Seed production was greatest when growing seasons with more growing degree days coincided with years with high precipitation. Two consecutive years with more growing degree days and low precipitation resulted in low seed production. Seasonal climate effects on the viability of available seed depended on the physical characteristics of the reproductive structures. Large-coned and -seeded species take more time to develop mature embryos and were therefore more sensitive to increases in growing degree days in the year of flowering and embryo development. Our findings suggest that both moisture stress and abbreviated growing seasons can have a notable negative influence on the production and viability of available seed at treeline. Our synthesis revealed that constraints on predispersal reproduction within the treeline ecotone might create a considerable time lag for range expansion of tree populations into tundra ecosystems.
DOI: 10.5683/sp2/zzhllc
title: Data from: Reproductive losses due to climate change-induced earlier flowering are not the primary threat to plant population viability in a perennial herb

description: Abstract1. Despite a global footprint of shifts in flowering phenology in response to climate change, the reproductive consequences of these shifts are poorly understood. Furthermore, it is unknown whether altered flowering times affect plant population viability. 2. We examine whether climate change-induced earlier flowering has consequences for population persistence by incorporating reproductive losses from frost damage (a risk of early flowering) in population models of a subalpine sunflower (Helianthella quinquenervis). Using long-term demographic data for three populations that span the species’ elevation range (8–15 years, depending on the population), we first examine how snowmelt date affects plant vital rates. To verify vital rate responses to snowmelt date experimentally, we manipulate snowmelt date with a snow removal experiment at one population. Finally, we construct stochastic population projection models and Life Table Response Experiments for each population. 3. We find that populations decline (λs &lt; 1) as snowmelt dates become earlier. Frost damage to flower buds, a consequence of climate change-induced earlier flowering, does not contribute strongly to population declines. Instead, we find evidence that negative effects on survival, likely due to increased drought risk during longer growing seasons, drive projected population declines under earlier snowmelt dates. 4. Synthesis. Shifts in flowering phenology are a conspicuous and important aspect of biological responses to climate change, but here we show that the phenology of reproductive events can be unreliable measures of threats to population persistence, even when earlier flowering is associated with substantial reproductive losses. Evidence for shifts in reproductive phenology, along with scarcer evidence that these shifts actually influence reproductive success, are valuable but can paint an incomplete and even misleading picture of plant population responses to climate change.
DOI: 10.5683/sp2/ioqjau
title: Data from: Reproductive success is energetically linked to foraging efficiency in Antarctic fur seals

description: AbstractThe efficiency with which individuals extract energy from their environment defines their survival and reproductive success, and thus their selective contribution to the population. Individuals that forage more efficiently (i.e., when energy gained exceeds energy expended) are likely to be more successful at raising viable offspring than individuals that forage less efficiently. Our goal was to test this prediction in large long-lived mammals under free-ranging conditions. To do so, we equipped 20 lactating Antarctic fur seals (Arctocephalus gazella) breeding on the Kerguelen Island in the Southern Ocean with tags that recorded GPS locations, depth and tri-axial acceleration to determine at-sea behaviours and detailed time-activity budgets during their foraging trips. We also simultaneously measured energy spent at sea using the doubly-labeled water (DLW) method, and estimated the energy acquired while foraging from 1) type and energy content of prey species present in scat remains, and 2) numbers of prey capture attempts determined from head acceleration. Finally, we followed the growth of 36 pups from birth until weaning (of which 20 were the offspring of our 20 tracked mothers), and used the relative differences in body mass of pups at weaning as an index of first year survival and thus the reproductive success of their mothers. Our results show that females with greater foraging efficiencies produced relatively bigger pups at weaning. These mothers achieved greater foraging efficiency by extracting more energy per minute of diving rather than by reducing energy expenditure. This strategy also resulted in the females spending less time diving and less time overall at sea, which allowed them to deliver higher quality milk to their pups, or allowed their pups to suckle more frequently, or both. The linkage we demonstrate between reproductive success and the quality of individuals as foragers provides an individual-based quantitative framework to investigate how changes in the availability and accessibility of prey can affect fitness of animals.
DOI: 10.5683/sp2/87gau5
title: Data from: Resistance of soil biota and plant growth to disturbance increases with plant diversity

description: AbstractPlant diversity is critical to the functioning of ecosystems, potentially mediated in part by interactions with soil biota. Here, we characterized multiple groups of soil biota across a plant diversity gradient in a long-term experiment. We then subjected soil samples taken along this gradient to drought, freezing, and a mechanical disturbance to test how plant diversity affects the responses of soil biota and growth of a focal plant to these disturbances. High plant diversity resulted in soils that were dominated by fungi and associated soil biota, including increased arbuscular mycorrhizal fungi and reduced plant-feeding nematodes. Disturbance effects on the soil biota were reduced when plant diversity was high, resulting in higher growth of the focal plant in all but the frozen soils. These results highlight the importance of plant diversity for soil communities and their resistance to disturbance, with potential feedback effects on plant productivity.
DOI: 10.5683/sp2/jk2hoy
title: Data from: Resolving the conundrum of inbreeding depression but no inbreeding avoidance: estimating sex-specific selection on inbreeding by song sparrows (Melospiza melodia)

description: AbstractInbreeding avoidance among interacting females and males is not always observed despite inbreeding depression in offspring fitness, creating an apparent ‘inbreeding paradox’. This paradox could be resolved if selection against inbreeding was in fact weak, despite inbreeding depression. However, the net magnitude and direction of selection on the degree to which females and males inbreed by pairing with relatives has not been explicitly estimated. We used long-term pedigree data to estimate phenotypic selection gradients on the degree of inbreeding that female and male song sparrows (Melospiza melodia) expressed by forming socially-persistent breeding pairs with relatives. Fitness was measured as the total numbers of offspring and grand-offspring contributed to the population, and as corresponding expected numbers of identical-by-descent allele copies, thereby accounting for variation in offspring survival, reproduction and relatedness associated with variation in parental inbreeding. Estimated selection gradients on the degree to which individuals paired with relatives were weakly positive in females, but negative in males that formed at least one socially-persistent pairing. However, males that paired had higher mean fitness than males that remained socially unpaired. These analyses suggest that net selection against inbreeding may be weak in both sexes despite strong inbreeding depression, thereby resolving the ‘inbreeding paradox’.