cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5683/sp2/heu7bm
title: Data from: Spartina alterniflora genotypic identity affects plant and consumer responses in an experimental marsh community

description: Abstract1. Competition and herbivory are ubiquitous processes known to interactively shape plant performance, distribution and community assembly. Likewise, plant genetic variation and associated trait differences can impact both plant-plant and plant-herbivore interactions individually, yet few studies have explored these interactions simultaneously. 2. Salt marsh communities are an ideal system to study these questions, as they are dominated along the Atlantic and Gulf coasts of the United States by a foundation plant species, Spartina alterniflora, with high levels of genetically-based trait variation. Furthermore, consumer pressure and plant competitors are known to influence both the distribution and production of Spartina. We manipulated Spartina genetic identity, neighbor identity (needlerush, Juncus roemerianus), and consumer presence (snail, Littoraria irrorata) in a one-year field experiment in St. Joseph Bay, FL to test how the strength and direction of neighbor and consumer interactions vary by plant genotype. 3. Consumer effects on Spartina were generally stronger and more variable than those of the plant neighborhood, and these effects were generally consistent across Spartina genotypes. However, genotype-specific variation in morphology, phenology, and palatability significantly influenced both consumer and neighbor responses to Spartina: the consumer Littoraria was more likely to climb palatable Spartina genotypes, and neighboring Juncus had shorter stems in the presence of highly productive Spartina genotypes. 4. Synthesis. Our results add to the growing list of examples highlighting the role of intraspecific variation in species interactions, and suggest that variation in these interactions may promote the maintenance of plant genetic variation and community composition.
DOI: 10.5683/sp2/qeryvw
title: Data from: Spatial patterns and rarity of the white-phased ‘Spirit Bear’ allele reveals gaps in habitat protection

description: AbstractPreserving genetic and phenotypic diversity can help safeguard not only biodiversity but also cultural and economic values. Here, we present data that emerged from Indigenous-led research at the intersection of evolution and ecology to support conservation planning of a culturally salient, economically valuable, and rare phenotypic variant. We addressed three conservation objectives for the white-phased ‘Spirit bear’ polymorphism, a rare and endemic white-coated phenotype of black bear (Ursus americanus) in Kitasoo/Xai’xais and Gitga’at Territories and beyond in coastal British Columbia, Canada. First, we used non-invasively collected hair samples (n = 385 bears over ~18,000 km2) to assess the spatial variation in the frequency of the allele that controls the white-coloured morph (mc1r). Second, we compared our observed allele frequencies at mc1r with those expected under Hardy-Weinberg equilibrium. Finally, we examined how well current protected areas in the region aligned with spatial hotspots of Spirit bear alleles. We found that landscape-level allele frequency was lower than previously reported. For example, our systematic sampling estimated a frequency of 0.25 (95% CI 0.13-0.41) on Gribbell Island compared with the previously reported estimate of 0.56. Also, in contrast with previous reports, we failed to detect a statistically significant departure from Hardy-Weinberg equilibrium at mc1r, which calls into question the previously-posited role of homozygote gene flow, heterozygote disadvantage, and positive assortative mating in the maintenance of this polymorphism. Finally, we found a discrepancy between the placement of protected areas and the 90th percentile hotspots (upper 10% of all estimated values) of Spirit bear alleles, with ~50% of hotspots falling outside of protected areas. These results provide new insight into hypotheses related to the maintenance of this rare polymorphism, and directly relevant information to support evidence-based opportunities for Indigenous Nations of the area to attend to gaps in conservation planning.
DOI: 10.5683/sp2/txhrzs
title: Data from: Spatial variation in herbivory, climate and isolation predict plant height and fruit phenotype in Plectritis congesta island populations

description: AbstractClimate and herbivory can each drive natural selection on plant traits, but may interact to give rise to different patterns in trait distributions when surveyed across island populations. These different patterns may arise because the occurrence of ungulate herbivores often varies across archipelagos, potentially leading to strong and abrupt spatial heterogeneity in the direction or intensity of natural selection. In contrast, climate tends to vary gradually and thus is more likely to lead to gradual clines in trait values. Population isolation may also affect trait values, given that random genetic drift may fix alleles or traits in the absence of gene flow, or because gene flow between populations with similar or opposing selection pressures may augment or swamp the effects of selection. Here, we estimate the independent and interactive effects of deer, climate and isolation on fruit phenotype and plant height in 285 Plectritis congesta populations at 77 island and 44 mainland sites in western North America. Plectritis congesta is a palatable winter annual with two fruit phenotypes based on a simple Mendelian locus with clear dominance, and heritable variation in height as a polygenic trait. Fruit phenotype and plant height were well-predicted by deer occurrence; plants in populations with resident deer were short (15.0 ± 1.1 cm) and mainly expressed wingless fruits (73.0 ± 4.0 %), whereas plants in populations without deer were 2.6 times taller (38.9 ± 5.3 cm) and only 9.0 ± 1.6 % expressed wingless fruits. Wingless fruits were less common in populations experiencing wetter conditions with more seasonal variability in temperatures, particularly in the absence of deer. In contrast, population isolation was unrelated to fruit phenotype, except in populations rarely exposed to deer, where plants expressed phenotypes more like those in populations without deer as isolation increased. Our results are consistent with the hypothesis that spatial variation in browsing by deer, or other factors correlated with it, contributes to population-level variation in fruit phenotype and plant height in P. congesta, and that climate leads to a modest spatial gradient in plant height.
DOI: 10.5683/sp2/qhp7ft
title: Data from: Specialization and generalization in the diversification of phytophagous insects: tests of the musical chairs and oscillation hypotheses

description: AbstractEvolutionary biologists have often assumed that ecological generalism comes at the expense of less intense exploitation of specific resources and that this trade-off will promote the evolution of ecologically specialized daughter species. Using a phylogenetic comparative approach with butterflies as a model system, we test hypotheses that incorporate changes in niche breadth and location into explanations of the taxonomic diversification of insect herbivores. Specifically, we compare the oscillation hypothesis, where speciation is driven by host-plant generalists giving rise to specialist daughter species, to the musical chairs hypothesis, where speciation is driven by host-plant switching, without changes in niche breadth. Contrary to the predictions of the oscillation hypothesis, we recover a negative relationship between host-plant breadth and diversification rate and find that changes in host breadth are seldom coupled to speciation events. By contrast, we present evidence for a positive relationship between rates of host switching and butterfly diversification, consonant with the musical chairs hypothesis. These results suggest that the costs of trophic generalism in plant-feeding insects may have been overvalued and that transitions from generalists to ecological specialists may not be an important driver of speciation in general.
DOI: 10.5683/sp2/btuysl
title: Data from: Species interactions mediate thermal evolution

description: AbstractUnderstanding whether populations and communities can evolve fast enough to keep up with ongoing climate change is one of the most pressing issues in biology today. A growing number of studies have documented rapid evolutionary responses to warming, suggesting that populations may be able to persist despite temperature increases. The challenge now is to better understand how species interactions, which are ubiquitous in nature, mediate these population responses to warming. Here we use laboratory natural selection experiments in a freshwater community to test hypotheses related to how thermal evolution of Daphnia pulex to two selection temperatures (12˚C, 18˚C) is mediated by rapid thermal evolution of its algal resource (Scenedesmus obliquus), or by the presence of the zooplankton predator Chaoborus americanus. We found that cold-evolved algae (a high-quality resource), facilitated the evolution of increased thermal plasticity in Daphnia populations selected at 12˚C, for both body size and per capita growth rates (r). Conversely, warm-evolved algae facilitated the evolution of increased r thermal plasticity for Daphnia at selected at 18˚C. Lastly, we found that the effect of selection temperature on evolved Daphnia body size was more pronounced when Daphnia were also reared with predators. These data demonstrate that trait evolution of a focal population to the thermal environment can be affected by both bottom-up and top-down species interactions, and that rapid temperature evolution of a resource can have cascading effects on consumer thermal evolution. Our study highlights the importance of incorporating species interactions when estimating ecological and evolutionary responses of populations and communities to ongoing temperature warming.
DOI: 10.5683/sp2/zdf9rp
title: Data from: Species richness change across spatial scales

description: AbstractHumans have elevated global extinction rates and thus lowered global-scale species richness. However, there is no a priori reason to expect that losses of global species richness should always, or even often, trickle down to losses of species richness at regional and local scales, even though this relationship is often assumed. Here, we show that scale can modulate our estimates of species richness change through time in the face of anthropogenic pressures, but not in a unidirectional way. Instead, the magnitude of species richness change through time can increase, decrease, reverse, or be unimodal across spatial scales. Using several case studies, we show different forms of scale-dependent richness change through time in the face of anthropogenic pressures. For example, Central American corals show a homogenization pattern, where small scale richness is largely unchanged through time, while larger scale richness change is highly negative. Alternatively, birds in North America showed a differentiation effect, where species richness was again largely unchanged through time at small scales, but was more positive at larger scales. Finally, we collated data from a heterogeneous set of studies of different taxa measured through time from sites ranging from small plots to entire continents, and found highly variable patterns that nevertheless imply complex scale-dependence in several taxa. In summary, understanding how biodiversity is changing in the Anthropocene requires an explicit recognition of the influence of spatial scale, and we conclude with some recommendations for how to better incorporate scale into our estimates of change.
DOI: 10.5683/sp2/dq34gv
title: Data from: Species turnover (β diversity) in ectomycorrhizal fungi linked to NH4+ uptake capacity

description: AbstractEctomycorrhizal (EcM) fungal communities may be shaped by both deterministic and stochastic processes, potentially influencing ecosystem development and function. We evaluated community assembly processes for EcM fungi of Pseudotsuga menziesii among 12 sites up to 400 km apart in southwest British Columbia (Canada) by investigating species turnover (β diversity) in relation to soil nitrogen (N) availability and physical distance. We then examined functional traits for an N-related niche by quantifying net fluxes of NH4+, NO3- and protons on excised root tips from three contrasting sites using a microelectrode ion flux measurement system. EcM fungal communities were well aligned with soil N availability and pH, with no effect of site proximity (distance-decay curve) on species assemblages. Species turnover was significant (β1/2 = 1.48) along soil N gradients, with many more Tomentella species on high-N than low-N soils, in contrast to Cortinarius species. Ammonium uptake was greatest in the spring on the medium and rich sites, and averaged over 190 nmol m−2 s−1 for Tomentella species. The lowest uptake rates of NH4+ were by non-mycorrhizal roots of axenically grown seedlings (10 nmol m−2 s−1), followed by Cortinarius species (60 nmol m−2 s−1). EcM roots from all sites displayed only marginal uptake of nitrate (8.3 nmol m−2 s−1). These results suggest NH4+ uptake capacity is an important functional trait influencing the assembly of EcM fungal communities. The diversity of EcM fungal species across the region arguably provides critical belowground adaptations to organic and inorganic N supply that are integral to temperate rainforest ecology.
DOI: 10.5683/sp2/flgbar
title: Data from: Stabilizing selection, mutational bias and the evolution of sex

description: AbstractStabilizing selection around a fixed phenotypic optimum is expected to disfavor sexual reproduction, since asexually reproducing organisms can maintain a higher fitness at equilibrium, while sex disrupts combinations of compensatory mutations. This conclusion rests on the assumption that mutational effects on phenotypic traits are unbiased, that is, mutation does not tend to push phenotypes in any particular direction. In this paper, we consider a model of stabilizing selection acting on an arbitrary number of polygenic traits coded by bialellic loci, and show that mutational bias may greatly reduce the mean fitness of asexual populations compared with sexual ones in regimes where mutations have weak to moderate fitness effects. Indeed, mutation and drift tend to push the population mean phenotype away from the optimum, this effect being enhanced by the low effective population size of asexual populations. In a second part, we present results from individual-based simulations showing that positive rates of sex are favored when mutational bias is present, while the population evolves towards complete asexuality in the absence of bias. We also present analytical (QLE) approximations for the selective forces acting on sex in terms of the effect of sex on the mean and variance in fitness among offspring.
DOI: 10.5683/sp2/9c9gic
title: Data from: Stark sexual display divergence among jumping spider populations in the face of gene flow

description: AbstractGene flow can inhibit evolutionary divergence by eroding genetic differences between populations. A current aim in speciation research is to identify conditions in which selection overcomes this process. We focused on a state of limited differentiation, asking whether selection enables divergence with gene flow in a set of Habronattus americanus jumping spider populations that exhibit three distinct male sexual display morphs. We found that each population is at high frequency or fixed for a single morph. These strong phenotypic differences contrast with low divergence at 210 AFLP markers, suggesting selection has driven or maintains morph divergence. Coinciding patterns of isolation by distance and ‘isolation by phenotype’ (i.e. increased genetic divergence among phenotypically contrasting populations) across the study area support several alternative demographic hypotheses for display divergence, each of which entails gene flow. Display-associated structure appears broadly distributed across the genome and the markers producing this pattern do not stand out from background levels of differentiation. Overall, the results suggest selection can promote stark sexual display divergence in the face of gene flow among closely related populations.
DOI: 10.5683/sp2/xuoymt
title: Data from: Strong and consistent natural selection associated with armour reduction in sticklebacks

description: AbstractMeasuring the strength of natural selection is tremendously important in evolutionary biology, but remains a challenging task. In this work, we analyse the characteristics of selection for a morphological change (lateral-plate reduction) in the threespine stickleback Gasterosteus aculeatus. Adaptation to freshwater, leading to the reduction or loss of the bony lateral armor, has indeed occurred in parallel on numerous occasions in this species. Completely-plated and low-plated sticklebacks were introduced into a pond, and the phenotypic changes were tracked for twenty years. Fish from the last generation were genotyped for the Ectodysplasin-A (Eda) locus, the major gene involved in armor development. We found a strong fitness advantage for the freshwater-type fish (in average, 20% for the freshwater morph, and 92% for the freshwater genotype). The trend is best explained by assuming that this fitness advantage is maximum at the beginning of the invasion and decreases with time. Such fitness differences provide a quantifiable example of rapid selection-driven phenotypic evolution associated to environmental change in a natural population.
DOI: 10.5683/sp2/vqvg4k
title: Data from: Sumakuru, a deeply-diverging new genus of lyssomanine jumping spiders from Ecuador (Araneae: Salticidae)

description: AbstractThe lyssomanine jumping spider genus Sumakuru gen. n. is here described for Sumakuru bigal sp. n., from the Bigal River Biological Reserve in Ecuador. Known from a single male, the embolus of the palp takes the form of a smoothly arching curve, and appears fully mobile, being connected to the tegulum by a thin sclerite and a twisted hematodocha. Data from four gene regions (28S, 16SND1, CO1, wingless) indicate that Sumakuru is the sister group to all other sampled lyssomanines, diverging deeply on the stem lineage of the clade of other known lyssomanines. Unlike previous molecular results, the sampled species of Lyssomanes Hentz, 1845 are supported as monophyletic, with Chinoscopus Simon, 1900 as the sister to Lyssomanes.
DOI: 10.5683/sp2/lbkuls
title: Data from: Survival is negatively related to basal metabolic rate in tropical Andean birds

description: Abstract1. Life history theory postulates that physiological traits, such as energy metabolism, can be understood in terms of allocation trade-offs between self-maintenance and reproduction over an organism’s lifespan, and data show that metabolic intensity and survival vary inversely with latitude, with tropical birds exhibiting a ‘slow’ pace of life relative to temperature species. However, tropical regions harbor strong environmental gradients of their own, and it remains to be shown whether similar life history trade-offs between metabolism and longevity are reflected among tropical birds of the same latitude. 2. We estimated apparent annual survival in 37 species of tropical passerine birds along an elevational gradient (400–3000 m) in Peru to test whether variation in survival was influenced by basal metabolic rate (BMR; estimated at the same sites), elevation or both factors. We used path analysis to test our prediction that survival would decline as BMR increased, while accounting for the potential direct effects of elevation on survival due to differences in predation pressure or environmental conditions as well as potential indirect effects of elevation on BMR via temperature and the costs of thermoregulation. 3. Higher BMR in tropical passerine birds predicted lower apparent survival, regardless of the elevation at which species occurred. In addition, elevation had a direct negative effect on apparent survival, perhaps due to harsher abiotic conditions, low site fidelity, or both at high elevations. 4. We provide evidence of a link between metabolic rate and longevity previously undescribed in populations of free-living birds. Our results illustrate that tropical montane species may be characterized by a unique suite of traits in their pace of life, in which BMR does not differ from lowland birds, but survival does.
DOI: 10.5683/sp2/vtzenl
title: Data from: Targeted sequence capture and resequencing implies a predominant role of regulatory regions in the divergence of a sympatric lake whitefish species pair (Coregonus clupeaformis)

description: AbstractLatest technological developments in evolutionary biology bring new challenges in documenting the intricate genetic architecture of species in the process of divergence. Sympatric populations of lake whitefish represent one of the key systems to investigate this issue. Despite the value of random genotype-by-sequencing methods and decreasing cost of sequencing technologies, it remains challenging to investigate variation in coding regions, especially in the case of recently duplicated genomes as in salmonids, as this greatly complicates whole genome resequencing. We thus designed a sequence capture array targeting 2773 annotated genes to document the nature and the extent of genomic divergence between sympatric dwarf and normal whitefish. Among the 2728 genes successfully captured, a total of 2182 coding and 10 415 noncoding putative single-nucleotide polymorphisms (SNPs) were identified after applying a first set of basic filters. A genome scan with a quality-refined selection of 2203 SNPs identified 267 outlier SNPs in 210 candidate genes located in genomic regions potentially involved in whitefish divergence and reproductive isolation. We found highly heterogeneous FST estimates among SNP loci. There was an overall low level of coding polymorphism, with a predominance of noncoding mutations among outliers. The heterogeneous patterns of divergence among loci confirm the porous nature of genomes during speciation with gene flow. Considering that few protein-coding mutations were identified as highly divergent, our results, along with previous transcriptomic studies, imply that changes in regulatory regions most likely had a greater role in the process of whitefish population divergence than protein-coding mutations. This study is the first to demonstrate the efficiency of large-scale targeted resequencing for a nonmodel species with such a large and unsequenced genome.