cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5683/sp2/xqwjum
title: Data from: Rapid adaptive evolution of colour vision in the threespine stickleback radiation

description: AbstractVision is a sensory modality of fundamental importance for many animals, aiding in foraging, detection of predators, and mate choice. Adaptation to local ambient light conditions is thought to be commonplace, and a match between spectral sensitivity and light spectrum is predicted. We use opsin gene expression to test for local adaptation and matching of spectral sensitivity in multiple independent lake populations of threespine stickleback populations derived since the last ice age from an ancestral marine form. We show that sensitivity across the visual spectrum is shifted repeatedly towards longer wavelengths in freshwater compared with the ancestral marine form. Laboratory rearing suggests this shift is largely genetically based. Using a new metric, we found that the magnitude of shift in spectral sensitivity in each population corresponds strongly to the transition in the availability of different wavelengths of light between the marine and lake environment. We also found evidence of local adaptation by sympatric benthic and limnetic ecotypes to different light environments within lakes. Our findings indicate rapid parallel evolution of the visual system to altered light conditions. The changes have not, however, yielded a close matching of spectrum-wide sensitivity to wavelength availability, for reasons we discuss.
DOI: 10.5683/sp2/0medxm
title: Data from: Rapid diversification of sexual signals in Hawaiian Nesosydne planthoppers (Hemiptera: Delphacidae): the relative role of neutral and selective forces

description: AbstractChanges in sexual signals have the potential to promote rapid divergence and reproductive isolation among populations of animals. Thus, identifying processes contributing to variation in signals is key to understanding the drivers of speciation. However, it is difficult to identify the processes initiating changes in signals in empirical systems because (1) the demographic history of populations under study is usually unclear, and (2) there is no unified hypothesis-testing framework for evaluating the simultaneous contribution of multiple processes. A unique system for study in the Hawaiian Islands, the planthopper species Nesosydne chambersi, offers a clear demographic context to disentangle these factors. By measuring variation in male vibratory sexual signals across different genetic populations on the island of Hawaii, we found that that multiple signal traits varied significantly between populations. We developed a mixed modelling framework to simultaneously test competing hypotheses about which processes contribute to changes in signal traits: genetic drift, sensory drive or reproductive character displacement. Our findings suggest that signal divergence proceeds along different axes for different signal traits under the influence of both neutral and selective processes. They are the first, to our knowledge, to document the relative importance of multiple processes on divergence in sexual signals.
DOI: 10.5683/sp2/ceezll
title: Data from: Rapid evolution accelerates plant population spread in fragmented experimental landscapes

description: AbstractPredicting the speed of biological invasions and native species migrations requires an understanding of the ecological and evolutionary dynamics of spreading populations. Theory predicts that evolution can accelerate species’ spread velocity, but how landscape patchiness—an important control over traits under selection—influences this process is unknown. We manipulated the response to selection in populations of a model plant species spreading through replicated experimental landscapes of varying patchiness. After six generations of change, evolving populations spread 11% farther than nonevolving populations in continuously favorable landscapes and 200% farther in the most fragmented landscapes. The greater effect of evolution on spread in patchier landscapes was consistent with the evolution of dispersal and competitive ability. Accounting for evolutionary change may be critical when predicting the velocity of range expansions.
DOI: 10.5683/sp2/xa6ng1
title: Data from: Rapid increases in forest understory diversity and productivity following a mountain pine beetle (Dendroctonus ponderosae) outbreak in pine forests

description: AbstractThe current unprecedented outbreak of mountain pine beetle (Dendroctonus ponderosae) in lodgepole pine (Pinus contorta) forests of western Canada has resulted in a landscape consisting of a mosaic of forest stands at different stages of mortality. Within forest stands, understory communities are the reservoir of the majority of plant species diversity and influence the composition of future forests in response to disturbance. Although changes to stand composition following beetle outbreaks are well documented, information on immediate responses of forest understory plant communities is limited. The objective of this study was to examine the effects of D. ponderosae-induced tree mortality on initial changes in diversity and productivity of understory plant communities. We established a total of 110 1-m2 plots across eleven mature lodgepole pine forests to measure changes in understory diversity and productivity as a function of tree mortality and below ground resource availability across multiple years. Overall, understory community diversity and productivity increased across the gradient of increased tree mortality. Richness of herbaceous perennials increased with tree mortality as well as soil moisture and nutrient levels. In contrast, the diversity of woody perennials did not change across the gradient of tree mortality. Understory vegetation, namely herbaceous perennials, showed an immediate response to improved growing conditions caused by increases in tree mortality. How this increased pulse in understory richness and productivity affects future forest trajectories in a novel system is unknown.
DOI: 10.5683/sp2/inr0ab
title: Data from: RapidRat: development, validation and application of a genotyping-by-sequencing panel for rapid biosecurity and invasive species management

description: AbstractInvasive alien species (IAS) are among the main causes of global biodiversity loss. Invasive brown (Rattus norvegicus) and black (R. rattus) rats, in particular, are leading drivers of extinction on islands, especially in the case of seabirds where &gt;50% of all extinctions have been attributed to rat predation. Eradication is the primary form of invasive rat management, yet this strategy has resulted in a ~10-38% failure rate on islands globally. Genetic tools can help inform IAS management, but such applications to date have been largely reactive, time-consuming, and costly. Here, we developed a Genotyping-in-Thousands by sequencing (GT-seq) panel for rapid species identification and population assignment of invasive brown and black rats (RapidRat) in Haida Gwaii, an archipelago comprising ~150 islands off the central coast of British Columbia, Canada. We constructed an optimized panel of 443 single nucleotide polymorphisms (SNPs) using previously generated double-digest restriction-site associated DNA (ddRAD) genotypic data (27,686 SNPs) from brown (n=295) and black rats (n=241) sampled throughout Haida Gwaii. The informativeness of this panel for identifying individuals to species and island of origin was validated relative to the ddRAD results; in all comparisons, admixture coefficients and population assignments estimated using RapidRat were consistent. To demonstrate application, 20 individuals from novel invasions of three islands (Agglomerate, Hotspring, Ramsay) were genotyped using RapidRat, all of which were confidently assigned (&gt;98.5% probability) to Faraday and Murchison Islands as putative source populations. These results indicated that a previous eradication on Hotspring Island was conducted at an inappropriate geographic scale; future management should expand the eradication unit to include neighboring islands to prevent re-invasion. Overall, we demonstrated that RapidRat is an effective tool for managing invasive rat populations in Haida Gwaii and provided a clear framework for GT-seq panel development for informing biodiversity conservation in other systems.
DOI: 10.5683/sp2/gy6blz
title: Data from: Rat aversion to isoflurane versus carbon dioxide

description: AbstractSome experts suggest that sedation of laboratory rodents with isoflurane before euthanasia with carbon dioxide (CO2) is a humane alternative to euthanasia with CO2 alone, but little research has compared aversion to these agents. Albino rats were tested in a light/dark box where they had the choice between remaining in a dark compartment filling with isoflurane or CO2, or escaping to a lit compartment. Experiment 1 validated the procedure by confirming that rats responded to agent and light intensity. In Experiment 2, 9/16 and 0/16 rats remained in the dark compartment until recumbent when initially exposed to isoflurane and CO2, respectively. In Experiment 3, more rats remained in the dark compartment until recumbent during initial (10/16) versus re-exposure (1/16) to isoflurane. These results indicate that initial exposure to CO2 is more aversive than isoflurane, and that re-exposure to isoflurane is more aversive than initial exposure. We conclude that sedation with isoflurane is a refinement over euthanasia with CO2 alone for rats that have not been previously exposed to inhalant anaesthetics.
DOI: 10.5683/sp2/lutyat
title: Data from: Rates of hypoxia induction alter mechanisms of O2 uptake and the critical O2 tension of goldfish

description: AbstractThe rate of hypoxia induction (RHI) is an important but overlooked dimension of environmental hypoxia that may affect an organism’s survival. We hypothesized that, compared with rapid RHI, gradual RHI will afford an organism more time to alter plastic phenotypes associated with O2 uptake and subsequently reduce the critical O2 tension (Pcrit) of O2 uptake rate (ṀO2). We investigated this by determining Pcrit values for goldfish exposed to short (∼24 min), typical (∼84 min) and long (∼480 min) duration Pcrit trials to represent different RHIs. Consistent with our predictions, long duration Pcrit trials yielded significantly lower Pcrit values (1.0-1.4 kPa) than short and typical duration trials, which did not differ (2.6±0.3 and 2.5±0.2 kPa, respectively). Parallel experiments revealed these time-related shifts in Pcrit were associated with changes in aspects of the O2 transport cascade: gill surface areas and haemoglobin-O2 binding affinities were significantly higher in fish exposed to gradual RHIs over 480 min than fish exposed to rapid RHIs over 60 min. Our results also revealed that the choice of respirometric technique (i.e., closed versus intermittent) does not affect Pcrit or routine ṀO2, despite the significantly reduced water pH and elevated CO2 and ammonia levels measured following closed-circuit Pcrit trials of ∼90 min. Together, our results demonstrate that gradual RHIs result in alterations to physiological parameters that enhance O2 uptake in hypoxic environments. An organism’s innate Pcrit is therefore most accurately determined using rapid RHIs (&lt;90 min) so as to avoid the confounding effects of hypoxic acclimation.
DOI: 10.5683/sp2/muzoyz
title: Data from: Rattus population genomics across the Haida Gwaii archipelago provides a framework for guiding invasive species management

description: AbstractInvasive species have led to precipitous declines in biodiversity, especially in island systems. Brown (Rattus norvegicus) and black rats (R. rattus) are among the most invasive animals on the planet, with eradication being the primary tool for established island populations. The need for increased research for defining eradication units and monitoring outcomes has been highlighted as a means to maximize success. Haida Gwaii is an archipelago ~100 km off the northern coast of British Columbia, Canada that hosts globally significant breeding populations of seabirds that are at risk due to invasive rats. Here, we paired sampling of brown (n=287) and black (n=291) rats across the Haida Gwaii archipelago (British Columbia, Canada) with genotyping-by-sequencing (10,770-27,686 SNPs) to investigate patterns of population connectivity and infer levels/direction of gene flow among invasive rat populations in Haida Gwaii. We reconstructed three regional clusters for both species (north, central, south), with proximate populations within regions being largely more related than those that were more distant, consistent with predictions from island biogeography theory. Population assignment of recently detected individuals post-eradication on Faraday, Murchison, and the Bischof Islands revealed all were re-invaders from Lyell Island, rather than being on-island survivors. Based on these results, we identified six eradication units constituting single or clusters of islands that would limit the potential for re-invasion, some of which will need to be combined with biosecurity measures. Overall, our results highlight the importance of targeted research prior to conducting eradications and demonstrates a framework for applying population genomics for guiding invasive species management in island systems.
DOI: 10.5683/sp2/9rsuof
title: Data from: Recent non-hybrid origin of sunflower ecotypes in a novel habitat

description: AbstractThe genomics of local adaptation is an increasingly active field, providing insights into the forces driving ecological speciation and the repeatability of evolution. Demography and gene flow play an important role in determining the paths by which parallel evolution occurs and the genomic signatures of adaptation. In the annual sunflowers, hybridization between species has repeatedly led to the colonization of extreme habitats, such as sand dunes. In a new case of adaptation to sand dunes that occurs in populations of H. petiolaris growing at Great Sand Dunes National Park and Preserve (Colorado), we wished to determine the age and long-term migration patterns of the system, as well as its ancestry. We addressed these questions with restriction-associated DNA (RAD) sequence data, aligned to a reference transcriptome. In an isolation with migration model using RAD sequences, coalescent analysis showed that the dune ecotype originated since the last ice age, which is very recent compared with the hybrid dune species, H. anomalus. Large effective population sizes and substantial numbers of gene migrants per generation between dune and nondune ecotypes explained the highly heterogeneous divergence observed among loci. Analysis of RAD-derived SNPs identified heterogeneous divergence between the dune and nondune ecotypes, as well as identifying its nearest relative. Our results did not support the hypothesis that the dune ecotype has hybrid ancestry, suggesting that adaptation of sunflowers to dunes has occurred by multiple mechanisms. The ancestry and long-term history of gene flow between incipient sunflower species provides valuable context for our understanding of ecological speciation and parallel adaptation.
DOI: 10.5683/sp2/wqy6ny
title: Data from: Recent Y chromosome divergence despite ancient origin of dioecy in poplars (Populus)

description: AbstractAll species of the genus Populus (poplar, aspen) are dioecious, suggesting an ancient origin of this trait. Despite some empirical counter examples, theory suggests that nonrecombining sex-linked regions should quickly spread, eventually becoming heteromorphic chromosomes. In contrast, we show using whole-genome scans that the sex-associated region in Populus trichocarpa is small and much younger than the age of the genus. This indicates that sex determination is highly labile in poplar, consistent with recent evidence of ‘turnover’ of sex-determination regions in animals. We performed whole-genome resequencing of 52 P. trichocarpa (black cottonwood) and 34 Populus balsamifera (balsam poplar) individuals of known sex. Genomewide association studies in these unstructured populations identified 650 SNPs significantly associated with sex. We estimate the size of the sex-linked region to be ~100 kbp. All SNPs significantly associated with sex were in strong linkage disequilibrium despite the fact that they were mapped to six different chromosomes (plus 3 unmapped scaffolds) in version 2.2 of the reference genome. We show that this is likely due to genome misassembly. The segregation pattern of sex-associated SNPs revealed this to be an XY sex-determining system. Estimated divergence times of X and Y haplotype sequences (6–7 Ma) are much more recent than the divergence of P. trichocarpa (poplar) and Populus tremuloides (aspen). Consistent with this, in P. tremuloides, we found no XY haplotype divergence within the P. trichocarpa sex-determining region. These two species therefore have a different genomic architecture of sex, suggestive of at least one turnover event in the recent past.
DOI: 10.5683/sp2/nqjtjh
title: Data from: Recently-formed polyploid plants diversify at lower rates

description: AbstractPolyploidy, the doubling of genomic content, is a widespread feature, especially among plants, yet its macro-evolutionary impacts are contentious. Traditionally, polyploidy has been considered an evolutionary dead-end, whereas recent genomic studies suggest that polyploidy has been a key driver of macro-evolutionary success. Here we examine the consequences of polyploidy on the time scale of genera across a diverse set of vascular plants, encompassing hundreds of inferred polyploidization events. Likelihood-based analyses indicate that polyploids generally exhibit lower speciation rates and higher extinction rates than diploids, providing the first quantitative corroboration of the dead-end hypothesis. The increased speciation rates of diploids can, in part, be ascribed to their capacity to speciate via polyploidy. Only particularly “fit” lineages of polyploids may persist to enjoy longer term evolutionary success.
DOI: 10.5683/sp2/ygshu6
title: Data from: Reciprocal abundance shifts of the intertidal sea stars, Evasterias troschelii and Pisaster ochraceus, following sea star wasting disease

description: AbstractDisease emergence occurs within the context of ecological communities, and disease driven declines in host populations can lead to complex direct and indirect ecological effects. Varying effects of a single disease among multiple susceptible hosts could benefit relatively resistant species. Beginning in 2013, an outbreak of sea star wasting disease (SSWD) led to population declines of many sea star species along the west coast of North America. Through field surveys and laboratory experiments, we investigated how and why the relative abundances of two co-occurring sea star species, Evasterias troschelii and Pisaster ochraceus, shifted during the ongoing wasting epidemic in Burrard Inlet, British Columbia, Canada. We hypothesized that Evasterias is competitively inferior to Pisaster but more resistant to SSWD. Thus, we predicted that SSWD-induced declines of Pisaster could mitigate the negative effects of SSWD on Evasterias, as the latter would experience competitive release. We document shifts in sea star abundance from 2007-2017: Pisaster abundance and mean size declined during the outbreak, while Evasterias abundance increased from relatively rare to numerically dominant within the intertidal. When exposed to symptomatic sea stars, Pisaster and Evasterias both showed signs of SSWD, but transmission and susceptibility was lower in Evasterias. Despite diet overlap documented in our field surveys, Evasterias was not outcompeted by Pisaster in laboratory trails conducted with the relatively small Pisaster available after the outbreak. Interference competition with larger Pisaster, or prey exploitation by Pisaster during summer when Evasterias is primarily subtidal, may explain the rarity of Evasterias prior to Pisaster declines. Our results suggest that indirect effects mediated by competition can mask some of the direct effects of disease outbreaks, and the combination of direct and indirect effects will determine the restructuring of a community after disturbance.
DOI: 10.5683/sp2/nb2klf
title: Data from: Recombination and hitchhiking of deleterious alleles

description: AbstractWhen new advantageous alleles arise and spread within a population, deleterious alleles at neighbouring loci can hitchhike alongside them and spread to ﬁxation in areas of low recombination, introducing a ﬁxed mutation load. We use branching processes and diffusion equations to calculate the probability that a deleterious allele hitchhikes and ﬁxes alongside an advantageous mutant. As expected, the probability of ﬁxation of a deleterious hitchhiker rises with the selective advantage of the sweeping allele and declines with the selective disadvantage of the deleterious hitchhiker. We then use computer simulations of a genome with an inﬁnite number of loci to investigate the increase in load after an advantageous mutant is introduced. We show that the appearance of advantageous alleles on genetic backgrounds loaded with deleterious alleles has two potential effects: it can ﬁx deleterious alleles and also facilitate the persistence of recombinant lineages that happen to occur. The latter is expected to reduce the signals of selection in the surrounding region. We consider these results in light of human genetic data to infer how likely it is that such deleterious hitchhikers have occurred in our recent evolutionary past.
DOI: 10.5683/sp2/4ibvsb
title: Data from: Reconciling extremely strong barriers with high levels of gene exchange in annual sunflowers

description: AbstractIn several cases, estimates of gene flow between species appears to be higher than predicted given the strength of interspecific barriers. However, as far as we are aware, detailed measurements of reproductive isolation have not previously been compared with a coalescent-based assessment of gene flow. Here, we contrast these two measures in two species of sunflower, Helianthus annuus and Helianthus petiolaris. We quantified the total reproductive barrier strength between these species by compounding the contributions of the following prezygotic and postzygotic barriers: ecogeographic isolation, reproductive asynchrony, immigrant inviability, pollen competition, hybrid seed formation, hybrid seed germination, hybrid pollen fertility, and hybrid seed set. The estimated probabilities that a reproductively successful hybrid is produced: range from 10^-4 to 10^-6 depending on the direction of the cross and the degree of independence among reproductive barriers. Population genetic estimates of gene flow estimated between these sunflower species (N_e m = 0.34-0.76) are due mainly to their large effective population sizes (N_e &gt;10^6). The interspecific migration rate (m) is very small (&lt;10^-7) and an order of magnitude lower than that expected based on our reproductive barrier strength estimates. Thus, even high levels of reproductive isolation (&gt; 0.999) may produce genomic mosaics.