cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5683/sp2/7qdler
title: Not a melting pot: plant species aggregate in their non-native range

description: AbstractAim: Plant species continue to be moved outside of their native range by human activities. Here, we aim at determining whether, once introduced, plants assimilate into native communities, or whether they aggregate, thus forming mosaics of native- and alien-rich communities. Alien species may aggregate in their non-native range due to shared habitat preferences, such as their tendency to establish in high-biomass, species-poor areas. Location: 22 herbaceous grasslands in 14 countries, mainly in the temperate zone. Time period: 2012 - 2016. Major taxa studied: Plants. Methods: We used a globally coordinated survey. Within this survey, we found 46 plant species, predominantly from Eurasia, for which we had co-occurrence data in their native and non-native range. We test for differences in co-occurrence patterns of 46 species, between their native (home) and non-native (away) range. We also tested whether species had similar habitat preferences, by testing for differences in total biomass and species richness of the patches species occupy in their native and non-native range. Results: We found the same species to show different patterns of association, depending on whether they were in their native or non-native range. Alien species were negatively associated with native species, and aggregated instead with other alien species in species-poor, high-biomass communities in their non-native, compared to their native range. Main conclusions: The strong differences between the native (home) and non-native (away) range in species co-occurrence patterns are evidence that how species associate with resident communities in their non-native range is not species-dependent, but rather a property of being away from their native range. These results thus highlight that species may undergo important ecological changes when introduced away from their native range. Overall, we show origin-dependent associations that result in novel communities in which alien-rich patches exist within a mosaic of native-dominated communities.
DOI: 10.5683/sp2/vkh3le
title: On the evolutionary epidemiology of SARS-CoV-2

description: AbstractThere is no doubt that the novel coronavirus SARS-CoV-2 that causes COVID-19 is mutating and thus has the potential to adapt during the current pandemic. Whether this evolution will lead to changes in the transmission, the duration, or the severity of the disease is not clear. This has led to considerable scientific and media debate, from raising alarms about evolutionary change to dismissing it. Here we review what little is currently known about the evolution of SARS-CoV-2 and extend existing evolutionary theory to consider how this disease might evolve during the COVID-19 pandemic. While there is currently no definitive evidence that SARS-CoV-2 is undergoing further adaptation, continued, evidence-based, analysis of evolutionary change is important so that public health measures can be adjusted in response to substantive changes in the infectivity or severity of COVID-19.
DOI: 10.5683/sp2/qrlrc9
title: Patterns, predictors, and consequence of dominance in hybrids

description: AbstractCompared to those of their parents, are the traits of first-generation (F1) hybrids typically intermediate, biased toward one parent, or mismatched for alternative parental phenotypes? And how does hybrid trait expression affect fitness? To address this empirical gap, we compiled data from 198 studies in which traits were measured in a common environment for two parent taxa and their F1 hybrids. We find that individual traits in F1s are, on average, halfway between the parental midpoint and one parental value (e.g., hybrid trait values are 0.75 if parents'values are 0 &1). When considering pairs of traits together, a hybrid's bivariate phenotype tends to resemble one parent (pairwise parent-bias) about 50 % more than the other while also exhibiting a similar magnitude of mismatch due to different traits having dominance in conflicting directions. We detect no phylogenetic signal nor an effect of parental genetic distance on dominance or mismatch. Using data from an experimental field planting of recombinant hybrid sunflowers, we illustrate that pairwise parent-bias improves fitness whereas pairwise mismatch reduces fitness. In sum, our study has three major conclusions. First, hybrids between ecologically divergent natural populations are not phenotypically intermediate but rather exhibit substantial mismatch while also resembling one parent more than the other. Second, dominance and mismatch do not seem to be governed by general rules but rather by the idiosyncratic evolutionary trajectories of individual traits in individual populations or species. Finally, selection against hybrids likely results from selection against both intermediate and mismatched phenotypes.
DOI: 10.5683/sp2/u6kcqd
title: Phylogenetic analysis of the distribution of deadly amatoxins among the little brown mushrooms of the genus Galerina

description: AbstractSome but not all of the species of 'little brown mushrooms' in the genus Galerina contain deadly amatoxins at concentrations equaling those in the death cap, Amanita phalloides. However, Galerina's ~300 species are notoriously difficult to identify by morphology and the identity of toxin-containing specimens has not been verified with DNA barcode sequencing. This left open the question of which Galerina species contain toxins and which do not. We selected specimens for toxin analysis using a preliminary phylogeny of the fungal DNA barcode region, the ribosomal internal transcribed spacer (ITS) region. Using liquid chromatography/mass spectrometry, we analyzed amatoxins from 70 samples of Galerina and close relatives, collected in western British Columbia, Canada. To put the presence of toxins into a phylogenetic context, we included the 70 samples in maximum likelihood analyses of 438 taxa, using ITS, RNA polymerase II second largest subunit gene (RPB2), and nuclear large subunit ribosomal RNA (LSU) gene sequences. We sequenced barcode DNA from types where possible to aid with applications of names. We detected amatoxins only in the 24 samples of the G. marginata s.l. complex in the Naucoriopsis clade. We delimited 56 putative Galerina species using Automatic Barcode Gap Detection software. Phylogenetic analysis showed moderate to strong support for Galerina infrageneric clades Naucoriopsis, Galerina, Tubariopsis, and Sideroides. Mycenopsis appeared paraphyletic and included Gymnopilus. Amatoxins were not detected in 46 samples from Galerina clades outside of Naucoriopsis or from outgroups. Our data show significant quantities of toxin in all mushrooms tested from the G. marginata s.l. complex. DNA barcoding revealed consistent accuracy in morphology-based identification of specimens to G. marginata s.l. complex. Prompt and careful morphological identification of ingested G. marginata s.l. has the potential to improve patient outcomes by leading to fast and appropriate treatment.
DOI: 10.5683/sp2/vuv6jy
title: Phylogenomics reveals novel relationships among Neotropical crocodiles (Crocodylus spp.)

description: AbstractExtant species in the order Crocodylia are remnants of an ancient lineage of large-bodied archosaur reptiles. Despite decades of systematic studies, phylogenetic relationships among members of the genus Crocodylus (true crocodiles) in the Neotropics are poorly understood. Here we estimated phylogenomic relationships among the four extant Crocodylus species in the Americas. Species-tree reconstructions using genotypic data from 17,538 SNPs collected for 33 individuals spanning six Crocodylus species (four ingroup and two outgroup) revealed novel relationships for all Neotropical species. For the first time, C. acutus, the American crocodile, was recovered as monophyletic when individuals from Antillean and continental populations were analyzed together. Our results also contradict previous inferences based on mitochondrial DNA data and a limited number of nuclear markers by robustly grouping Morelet's crocodile (C. moreletii) as the sister species to C. acutus., suggesting a novel phylogeographic hypothesis for the group. The present study punctuates the importance of using nuclear genome-wide information and representative sampling for resolving phylogenetic relationships, especially in broadly distributed species and those with complex evolutionary histories.
DOI: 10.5683/sp2/vw22kf
title: Predators override rainfall effects on tropical food webs

description: AbstractPredators alter ecological communities by inducing changes in prey abundance and phenotypes, including elemental and isotopic composition. Climatic factors are known to often moderate predator effects on prey abundance, but few studies consider the combined effects of climate and predators on prey phenotype. We examined how altered precipitation moderates the effects of predators on the abundance and the chemical composition of prey, as well as the indirect effects on the basal resource: leaf litter coated in biofilm. Using an experiment with an invertebrate food web module from tank bromeliads, we manipulated the presence of an odonate predator under scenarios of 10-fold decreased, ambient, and 3-fold increased precipitation and measured responses of prey and their basal resource. Predators reduced prey abundance while precipitation did not. Both precipitation and predators, either singly or interactively, affected the elemental composition of prey. Predators increased C:N ratios of detritivorous beetles under high precipitation, but reduced the C:N ratio of the basal resource. Precipitation reduced the N content of filter feeding mosquitoes. The observed changes in chemical composition may reflect physiological or developmental responses to stress imposed by both predators and drought. This study demonstrates that the impact of predators and precipitation can vary substantially across a food web, including additive and synergistic effects, and numerical and phenotypic responses.
DOI: 10.5683/sp2/t3sflo
title: Predicting the strength of urban-rural clines in a Mendelian polymorphism along a latitudinal gradient

description: AbstractCities are emerging as models for addressing the fundamental question of whether populations evolve in parallel to similar environments. Here, we examine the environmental factors that drive the evolution of parallel urban-rural clines in a Mendelian trait—the cyanogenic antiherbivore defense of white clover (Trifolium repens). Previous work suggested urban-rural gradients in frost and snow depth could drive the evolution of reduced hydrogen cyanide (HCN) frequencies in urban populations. Here, we sampled over 700 urban and rural clover populations across 16 cities along a latitudinal transect in eastern North America. In each population, we quantified changes in the frequency of genotypes that produce HCN, and in a subset of the cities we estimated the frequency of the alleles at the two genes (CYP79D15 and Li) that epistatically interact to produce HCN. We then tested the hypothesis that cold climatic conditions are necessary for the evolution of cyanogenesis clines by comparing the strength of clines among cities located along a gradient of winter temperatures and frost exposure. Overall, half of the cities exhibited urban-rural clines in the frequency of HCN, whereby urban populations evolved lower HCN frequencies. Clines did not evolve in cities with the lowest temperatures and greatest snowfall, supporting the hypothesis that snow buffers plants against winter frost and constrains the formation of clines. By contrast, the strongest clines occurred in the warmest cities where snow and frost are rare, suggesting that alternative selective agents are maintaining clines in warmer cities. Some clines were driven by evolution at only CYP79D15, consistent with stronger and more consistent selection on this locus than on Li. Together, our results demonstrate that urban environments often select for similar phenotypes, but different selective agents and targets underlie the evolutionary response in different cities.
DOI: 10.5683/sp2/r8uwjx
title: Rainfall and nest site competition delay Mountain Bluebird and Tree Swallow breeding but do not impact productivity

description: AbstractOptimizing breeding phenology, an important aspect of fitness, is complex for migratory species as they must make key timing decisions early, and remotely, from breeding sites. We examined the role of weather (locally and cross-seasonally), cavity availability, and competitive exclusion in determining among-year variation in breeding phenology over 17 years for two migratory, cavity-nesting birds: Mountain Bluebirds (Sialia currucoides; n = 462 nests) and Tree Swallows (Tachycineta bicolor; n = 572) using natural tree cavities in British Columbia, Canada. We assessed weather effects within the winter and migratory range and at our study sites. We quantified competition as the proportion of cavities occupied by European Starlings (Sturnus vulgaris) (for both species) and Mountain Bluebird (for Tree Swallow only) in each year. For 229 bluebird and 177 swallow nests with known fates, we tested whether late years resulted in reduced productivity. Although the effects were small, heavy rainfall and strong diurnal westerly winds during migration were associated with breeding delays for Mountain Bluebirds. However, cavity availability (earlier breeding with increases) had a 5-8X greater effect on timing than migratory conditions. There was no evidence that starling competition delayed bluebirds. In Tree Swallows, greater local daily rainfall was associated with delayed breeding, as was starling abundance (the effect of starlings was 1.4X times smaller than that of rainfall). Neither bluebird abundance nor cavity availability changed swallow phenology. Neither species showed reduced productivity in late breeding years. In both species, individuals that bred late relative to conspecifics within-year had smaller clutches and greater probability of nest failure. We conclude that breeding ground conditions, particularly cavity limitation and local rainfall (for swallows), are important drivers of breeding phenology for our focal species, but that the productivity cost of late years, at least for Tree Swallows, is minimal.
DOI: 10.5683/sp2/paih92
title: Scientific shortcomings in environmental impact statements internationally

description: Abstract1. Governments around the world rely on environmental impact assessment to understand the environmental risks of proposed developments. 2. To examine the basis for these appraisals, we examine the output of environmental impact assessment processes in jurisdictions within seven countries, focusing on scope (spatial and temporal), mitigation actions, and whether impacts were identified as ‘significant’. 3. We find that the number of impacts characterized as significant is generally low. While this finding may indicate that environmental impact assessment is successful at promoting environmentally sustainable development, it may also indicate that the methods used to assess impact are biased against findings of significance. To explore the methods used, we investigate the environmental impact assessment process leading to significance determination. 4. We find that environmental Impact assessment reports could be more transparent with regards to the spatial scale they use to assess impacts to wildlife. We also find that few reports on mining projects consider temporal scales that are precautionary with regards to the effects of mines on water resources. Across our sample of reports, we find that few environmental impact assessments meaningfully consider the different ways that cumulative impacts can interact. 5. Across countries, we find that proposed mitigation measures are often characterized as effective without transparent justification, and sometimes are described in ways that render the mitigation measure proposal ambiguous. 6. Across the reports in our sample, professional judgement is overwhelmingly the determinant of impact significance, with little transparency around the reasoning process involved or input by stakeholders. 7. We argue that the credibility and accuracy of the environmental impact assessment process could be improved by adopting more rigorous assessment methodologies and empowering regulators to enforce their use.
DOI: 10.5683/sp2/tqh4cb
title: Selection on a small genomic region underpins differentiation in multiple color traits between two warbler species

description: AbstractSpeciation is one of the most important processes in biology, yet the study of the genomic changes underlying this process is in its infancy. North American warbler species Setophaga townsendi and S. occidentalis hybridize in a stable hybrid zone, following a period of geographic separation. Genomic differentiation accumulated during geographic isolation can be homogenized by introgression at secondary contact, while genetic regions that cause low hybrid fitness can be shielded from such introgression. Here we examined the genomic underpinning of speciation by investigating: (1) the genetic basis of divergent pigmentation traits between species, (2) variation in differentiation across the genome, and (3) the evidence for selection maintaining differentiation in the pigmentation genes. Using tens of thousands of single nucleotide polymorphisms (SNPs) genotyped in hundreds of individuals within and near the hybrid zone, genome-wide association mapping revealed a single SNP associated with cheek, crown, breast coloration, and flank streaking, reflecting pleiotropy (one gene affecting multiple traits) or close physical linkage of different genes affecting different traits. This SNP is within an intron of the RALY gene, hence we refer to it as the RALY SNP. We then examined between-species genomic differentiation, using both genotyping-by-sequencing and whole genome sequencing. We found that the RALY SNP is within one of the highest peaks of differentiation, which contains three genes known to influence pigmentation: ASIP, EIF2S2, and RALY (the ASIP-RALY gene block). Heterozygotes at this gene block are likely of reduced fitness, as the geographic cline of the RALY SNP has been narrow over two decades. Together, these results reflect at least one barrier to gene flow within this narrow (~200kb) genomic region that modulates plumage difference between species. Despite extensive gene flow between species across the genome, this study provides evidence that selection on a phenotype-associated genomic region maintains a stable species boundary.
DOI: 10.5683/sp2/ffufg1
title: Sequence alignments of Corallicolids, apicomplexan symbionts of coral

description: AbstractCorals (Metazoa; Cnidaria; Anthozoa) have recently been shown to play host to a widespread and diverse group of intracellular symbionts of the phylum Apicomplexa. These symbionts, colloquially called ‘corallicolids’, are mostly known through molecular analyses, and no formal taxonomy has been proposed. Another apicomplexan, Gemmocystis cylindrus (described from the coral Dendrogyra cylindrus), may be related to corallicolids, but lacks molecular data. Here, we isolate and describe motile trophozoite (feeding) corallicolids cells using microscopic (light, SEM, and TEM) and molecular phylogenetic analysis to provide the basis for a formal description. Phylogenetic analyses using nuclear and plastid rRNA operons, and three mitochondrial protein sequences derived from single-cell transcriptomes, all confirm that these organisms fall into a discrete deep-branching clade within the Apicomplexa not closely related to any known species or major subgroup. As a result, we assign this clade to a new order, Corallicolida ord. nov., and family, Corallicolidae fam. nov. We describe a type species, Corallicola aquarius gen. nov. sp. nov. from its Rhodactis sp. host, and also describe a second species, Anthozoaphila gnarlus gen. nov. sp. nov., from the coral host Madracis mirabilis. Finally, we propose reassigning the incertae sedis taxon G. cylindrus from the order Agamococcidiorida to the Corallicolida, based on similarities in morphology and host localization to that of the corallicolids.
DOI: 10.5683/sp2/h42zxk
title: Single cell transcriptomics of of Abedinium reveals a new early-branching dinoflagellate lineage

description: AbstractDinoflagellates possess many unique cellular characteristics with unresolved evolutionary histories including nuclei with greatly expanded genomes and chromatin packaged using histone-like proteins and dinoflagellate-viral nucleoproteins instead of histones, highly reduced mitochondrial genomes with extensive RNA editing, a mix of photosynthetic and cryptic secondary plastids, and tertiary plastids. Resolving the evolutionary origin of these traits requires understanding their ancestral states and early intermediates. Several deep-branching dinoflagellate lineages are good candidates for such reconstruction, however they tend to be delicate and environmentally sparse, so such analyses are not always simple. Here, we employ transcriptome sequencing from manually-isolated and microscopically documented cells to resolve the placement of two cells of one such genus, Abedinium, collected by ROV in deep waters off the coast of Monterey Bay. One cell corresponds to the only described species, A. dasypus, while the second cell is distinct and formally described as Abedinium folium, sp. nov. Abedinium has classically been assigned to the deep-branching dinoflagellates subgroup Noctilucea, which is weakly supported by phylogenetic analyses of the single characterized gene from any member of the genus, small subunit ribosomal RNA (SSU rRNA). However, a phylogenetic analysis based on 221 proteins from the transcriptome places Abedinium in a distinct lineage, separate from and basal to the Noctilucea and the rest of the core dinoflagellates. The transcriptome also contains evidence of a cryptic plastid functioning in the biosynthesis of isoprenoids, iron-sulfur clusters, and heme, a mitochondrial genome with all three expected protein-coding genes (cob, cox1, and cox3), and the presence of some but not all dinoflagellate-specific chromatin packaging proteins.