cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.14288/1.0434199
title: Inferring the evolutionary model of community-structuring traits with convolutional kitchen sinks: Code and data

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;When communities are assembled through processes such as filtering or limiting similarity acting on phylogenetically conserved traits, the evolutionary signature of those traits may be reflected in patterns of community membership. We show how the model of trait evolution underlying community-structuring traits can be inferred from community membership data using both a variation of a traditional eco-phylogenetic metric--the mean pairwise distance (MPD) between taxa--and a recent machine learning tool, Convolutional Kitchen Sinks (CKS). Both methods perform well across a range of phylogenetically informative evolutionary models, but CKS outperforms MPD as tree size increases. We demonstrate CKS by inferring the evolutionary history of freeze tolerance in angiosperms. Our analysis is consistent with a late burst model of freeze tolerance, suggesting it evolved recently. We suggest that data ordered on phylogenies such as trait values, species interactions, or community presence/absence are good candidates for CKS modeling because the generative models produce structured differences between neighboring points that CKS is well-suited for. We introduce the R package &lt;em&gt;kitchen&lt;/em&gt; to perform CKS for generic application of the technique.&lt;/p&gt;
DOI: 10.14288/1.0447340
title: Data for “Aligning urban forest management actions with urban sustainability goals: A multi-city expert elicitation”

description: Data for “Aligning urban forest management actions with urban sustainability goals: A multi-city expert elicitation” by Bassett et al. Article abstract: City leaders are setting ambitious plans to achieve critical urban sustainability goals such as reducing urban heat, mitigate flooding during storms, and conserving biodiversity, and increasingly rely on urban forests as a key nature-based solution to such challenges. Current paradigms of urban forest management typically prioritize goals like increasing tree canopy cover that are often viewed as proxies for increased ecosystem service provision, in a general sense. However, urban foresters, the professionals with responsibility to manage urban forests, are increasingly faced with the complex challenge of managing for new goals related to ecosystem services, biodiversity, or people-nature relationships, as cities increasingly set goals centered on such outcomes, without robust guidelines to follow. We ask: How can urban foresters align their street tree management actions with specific urban sustainability goals? We conducted a structured expert elicitation of urban forest professionals in three cities: Vancouver, British Columbia, Canada; Honolulu, Hawaiʻi, US; and Washington, DC, US. Participants assessed the impacts of forty direct management actions on five goals (1) canopy cover increase and tree risk reduction, (2) urban heat reduction, (3) people-nature relationships, (4) wildlife habitat, and (5) stormwater interception and infiltration. While certain actions (e.g., in the mature tree maintenance phase) were selected as needed to advance every goal, experts identified numerous actions which aligned with one or several goals, but not all. Pre-planting actions, specifically site selection and species selection, presented the greatest opportunities to advance specific goals, suggesting that aligning this phase with city sustainability goals is critical. Participants were highly confident in being able to advance all goals through street tree management and were more confident in being able to advance the goals of increasing canopy cover while reducing tree risk and of mitigating urban heat, possibly because these goals more closely align with traditional canopy cover goal setting. This research underscores the necessity of considering site-level actions to advance strategic sustainability goals, while also revealing the complexity of the task that professionals are charged with in making site-level decisions. Our findings further motivate the need for further research and tools to help support professionals in their decision-making.
DOI: 10.14288/1.0443034
title: Data for: Sun, Ogushi, Tseng -Lepidoptera species richness and community composition in urban street trees

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;The triple threats of climate change, habitat loss, and environmental pollution have stimulated discussion on how urban areas can be modified to both mitigate heat increases and provide habitat for wildlife such as insects. The strategy of using trees to reduce temperatures has been adopted by numerous cities. However, the majority of street trees planted around the world are non-native. Studies conducted in non-urban areas have demonstrated in comparison to native plants, non-native plants are less likely to support native insect diversity. Here we use a database approach to quantify the number of native Lepidoptera species associated with 76 of the most common street tree species planted in Vancouver, Canada. We tested the prediction that compared to non-native trees, native street trees will support a higher diversity and unique community of native Lepidoptera. As predicted, native street trees were associated with five times as many native Lepidoptera species, and the Lepidoptera communities supported by native vs. non-native street trees were distinct. There was no difference in native Lepidoptera associations between broadleaf vs. coniferous street trees. These results are consistent with studies that have used active sampling techniques to investigate insect richness on a smaller subset of native and non-native tree species. Collectively, these data provide good evidence that the planting native instead of non-native trees will help stem the loss of insect diversity in urban areas.&lt;/p&gt;
DOI: 10.14288/1.0443033
title: Mitochondrial phylogenomics of liverworts

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;&lt;strong&gt;Premise: &lt;/strong&gt;Liverworts, with approximately 7,300 species worldwide, exhibit remarkable morphological diversity, in terms of growth form, ontogeny and architecture. Based on phylogenetic inferences drawn from DNA data, including recent genomic-scale data, the relationships among families and orders have been constantly revised and refined, although new topological incongruences have emerged. The liverwort mitochondrial genome exhibits lower average substitution rates compared to their nuclear and plastid genomes, and shows less structural variation, suggesting its suitability for inferring relationships at higher taxonomic levels.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Methods:&lt;/strong&gt; The mitochondrial genomes of 112 liverworts were sequenced, covering 105 species, 52 families and 18 orders. We analysed the structures of the liverwort mitogenomes using Mauve alignment. Maximum likelihood and Bayesian inference methods were used to infer a family-level phylogeny of liverworts.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;We assembled the complete mitochondrial genome for 23 species and identified four new structural variants. Phylogenetic inferences from mitochondrial genome sequences confirmed the monophyly of most suprafamilial taxa, with the expectations of Porellales, Ptilidiales, and Pelliidae. &lt;em&gt;Herzogianthus&lt;/em&gt; (Ptilidiales) was well-supported as a sister group to Jungermanniales sensu lato, rather than forming a monophyletic lineage with &lt;em&gt;Ptilidium &lt;/em&gt;(Ptilidiales). Given its distinct morphological traits, this genus should be singled out and elevated to a new order.&lt;/p&gt; &lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;The overall architecture of liverwort mitogenomes remains highly conserved, with taxa that diverged over 470 Mya still having co-linear mitogenomes. This study provides a genetic resource for future evolutionary research across the liverworts and highlights the utility of mitogenome across lineages diversifying for 470 Mya, including for family‐level classification.&lt;/p&gt;
DOI: 10.14288/1.0448161
title: Data for "Climate warming will test the limits of thermal plasticity in rainbow trout, a globally distributed fish"

description: This dataset contains all supplemental figures, tables, data files of physiological data and results of RNAseq analysis for the paper "Climate warming will test the limits of thermal plasticity in rainbow trout, a globally distributed fish". All raw sequencing data are available in NCBI under BioProject ID: PRJNA759286.
DOI: 10.14288/1.0443095
title: Replication Data for: Fundamental Learning Differences Across Five Dog Breed Clades: Breed-specific Predispositions, Individual Experiences, or a Fusion of Both?

description: Learning is crucial for shaping domestic dogs’ behaviour through life experiences, yet not all breeds exhibit the same learning aptitude towards a particular task. The current study's objective was to identify differences in fundamental learning features across and within five breed clades and elucidate the underlying factors contributing into these differences. Dogs (N=111) from five different breed clades (UK Rural, Retrievers, Asian Spitz, European Mastiff, and New World) participated in a virtual learning task with their owners. Owners completed validated questionnaires of Impulsivity and Reward Responsiveness. The learning task comprised of reinforcing an arbitrary behaviour (hand-touch) through multiple sessions of Acquisition (reinforcing the hand-touch), Discrimination (reinforcing the hand-touch on one of two hands) and Reversal Learning (reinforcing the hand-touch on the opposite hand), followed by a single session of Extinction (hand-touch not reinforced). Results showed notable differences across the studied breed clades in certain learning components. However, these disparities may not solely stem from inherent cognitive variations among breeds but rather potentially influenced by contextual factors such as the human-dog communication dynamics attributed to breeds’ cooperativity. Furthermore, breed clades differed in the contributing factors predicting individual learning performances, which also highlights the potential effect of breeds’ historical function.
DOI: 10.14288/1.0443770
title: R code for: Following regulation, imidacloprid persists and flupyradifurone increases in non-target wildlife

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;After regulation of pesticides, determination of their persistence in the environment is an important indicator of effectiveness of these measures. We quantified concentrations of two types of systemic insecticides: neonicotinoids (imidacloprid, acetamiprid, clothianidin, thiacloprid, and thiamethoxam) and butenolides (flupyradifurone), in off-crop non-target media of hummingbird cloacal fluid, honey bee (&lt;em&gt;Apis mellifera&lt;/em&gt;) nectar and honey, and wildflowers before and after regulation of imidacloprid on highbush blueberries in Canada in April 2021. We found that mean total pesticide load increased in hummingbird cloacal fluid, nectar, and flower samples following imidacloprid regulation. On average, we did not find evidence of a decrease in imidacloprid concentrations after regulation. However, there were some decreases, some increases and other cases with no changes in imidacloprid levels depending on the specific media, time point of sampling and site type. At the same time, we found an overall increase in flupyradifurone, acetamiprid, thiamethoxam and thiacloprid, but no change in clothianidin concentrations. In particular, flupyradifurone concentrations observed in biota sampled near to agricultural areas increased by 2-fold in honey bee nectar, 7-fold in hummingbird cloacal fluid, and 8-fold in flowers after the 2021 imidacloprid regulation. The highest residue detected in this study was flupyradifurone at 665 ng/mL (PPB) in honey bee nectar. Mean total pesticide loads were highest in honey samples (84 ± 10 PPB) followed by nectar (56 ± 7 PPB), then hummingbird cloacal fluid (1.8 ± 0.5 PPB), and least, flowers (0.51 ± 0.06 PPB). Our results highlight that limited regulation of imidacloprid does not immediately reduce residue concentrations while other systemic insecticides, possibly replacement compounds, concurrently increase in wildlife.&lt;/p&gt;
DOI: 10.14288/1.0445252
title: R code for: Following regulation, imidacloprid persists and flupyradifurone increases in non-target wildlife

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;After regulation of pesticides, determination of their persistence in the environment is an important indicator of effectiveness of these measures. We quantified concentrations of two types of systemic insecticides: neonicotinoids (imidacloprid, acetamiprid, clothianidin, thiacloprid, and thiamethoxam) and butenolides (flupyradifurone), in off-crop non-target media of hummingbird cloacal fluid, honey bee (&lt;em&gt;Apis mellifera&lt;/em&gt;) nectar and honey, and wildflowers before and after regulation of imidacloprid on highbush blueberries in Canada in April 2021. We found that mean total pesticide load increased in hummingbird cloacal fluid, nectar, and flower samples following imidacloprid regulation. On average, we did not find evidence of a decrease in imidacloprid concentrations after regulation. However, there were some decreases, some increases and other cases with no changes in imidacloprid levels depending on the specific media, time point of sampling and site type. At the same time, we found an overall increase in flupyradifurone, acetamiprid, thiamethoxam and thiacloprid, but no change in clothianidin concentrations. In particular, flupyradifurone concentrations observed in biota sampled near to agricultural areas increased by 2-fold in honey bee nectar, 7-fold in hummingbird cloacal fluid, and 8-fold in flowers after the 2021 imidacloprid regulation. The highest residue detected in this study was flupyradifurone at 665 ng/mL (PPB) in honey bee nectar. Mean total pesticide loads were highest in honey samples (84 ± 10 PPB) followed by nectar (56 ± 7 PPB), then hummingbird cloacal fluid (1.8 ± 0.5 PPB), and least, flowers (0.51 ± 0.06 PPB). Our results highlight that limited regulation of imidacloprid does not immediately reduce residue concentrations while other systemic insecticides, possibly replacement compounds, concurrently increase in wildlife.&lt;/p&gt;
DOI: 10.14288/1.0443772
title: Moving in Pain - treadmill locomotion in response to experimental knee pain

description: This dataset comprises gait data collected during treadmill locomotion with and without experimental knee pain of varying intensities and delivery methods. The data include knee biomechanics, spatiotemporal outcomes, pain intensity, and electrical current magnitude. Scripts used to analyze the data are included and which export statistical results that were used in the final manuscript.
DOI: 10.14288/1.0443771
title: Data from: Investigation of heterotrophs reveals new insights in dinoflagellate evolution

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Dinoflagellates are diverse and ecologically important protists characterized by many morphological and molecular traits that set them apart from other eukaryotes. These features include, but are not limited to, massive genomes organized using bacterially-derived histone-like proteins (HLPs) and dinoflagellate viral nucleoproteins (DVNP) rather than histones, and a complex history of photobiology with many independent losses of photosynthesis, numerous cases of serial secondary and tertiary plastid gains, and the presence of horizontally acquired bacterial rhodopsins and type II RuBisCo. Elucidating how this all evolved depends on knowing the phylogenetic relationships between dinoflagellate lineages. Half of these species are heterotrophic, but existing molecular data is strongly biased toward the photosynthetic dinoflagellates due to their amenability to cultivation and prevalence in culture collections. These biases make it impossible to interpret the evolution of photosynthesis, but may also affect phylogenetic inferences that impact our understanding of character evolution. Here, we address this problem by isolating individual cells from the Salish Sea and using single cell, culture-free transcriptomics to expand molecular data for dinoflagellates to include 27 more heterotrophic taxa, resulting in a roughly balanced representation. Using these data, we performed a comprehensive search for proteins involved in chromatin packaging, plastid function, and photoactivity across all dinoflagellates. These searches reveal that 1) photosynthesis was lost at least 21 times, 2) two known types of HLP were horizontally acquired around the same time rather than sequentially as previously thought; 3) multiple rhodopsins are present across the dinoflagellates, acquired multiple times from different donors; 4) kleptoplastic species have nucleus-encoded genes for proteins targeted to their temporary plastids and they are derived from multiple lineages, and 5) warnowiids are the only heterotrophs that retain a whole photosystem, although some photosynthesis-related electron transport genes are widely retained in heterotrophs, likely as part of the iron-sulfur cluster pathway that persists in non-photosynthetic plastids.&lt;/p&gt;
DOI: 10.14288/1.0444942
title: Data from: A multifaceted ecological assessment reveals the invasion of the freshwater red macroalga Montagnia macrospora (Batrachospermales, Rhodophyta) in Taiwan

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Invasive freshwater macroalgae are rarely described. &lt;em&gt;Montagnia macrospora&lt;/em&gt; is a freshwater red alga introduced from South America to East Asia via the global aquarium trade. The earliest occurrence record of this alga in Taiwan is dated 2005. To determine whether &lt;em&gt;M. macrospora &lt;/em&gt;has become invasive in Taiwan and to understand the traits that facilitated its invasion, we took a multifaceted approach that combines examination of ecological background and population genetic analysis. Our island-wide survey showed that &lt;em&gt;M. macrospora&lt;/em&gt; is widespread in the field across Taiwan, where the climate greatly differs from that of South America, and can self-sustain for nearly a decade. Our population genetic analysis revealed a lack of genetic diversity of &lt;em&gt;M. macrospora&lt;/em&gt; in Taiwan, consistent with the hypothesis that the alga expanded through asexual reproduction. Moreover, during our long-term ecological assessments and field surveys, we observed that&lt;em&gt;M. macrospora&lt;/em&gt; is an ecological generalist that can survive in a wide range of temperature, pH, illumination, and nutrient enrichment. Taken together, our data suggest that &lt;em&gt;M. macrospora&lt;/em&gt; has successfully invaded the freshwater ecosystems ofTaiwan, likely due to its ability to disperse asexually and to grow under broad environmental conditions. We hope that our study brings attention to invasive freshwater algae, which have been overlooked in conservation planning and management.&lt;/p&gt;
DOI: 10.14288/1.0444943
title: Data from: Investigation of heterotrophs reveals new insights in dinoflagellate evolution

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Dinoflagellates are diverse and ecologically important protists characterized by many morphological and molecular traits that set them apart from other eukaryotes. These features include, but are not limited to, massive genomes organized using bacterially-derived histone-like proteins (HLPs) and dinoflagellate viral nucleoproteins (DVNP) rather than histones, and a complex history of photobiology with many independent losses of photosynthesis, numerous cases of serial secondary and tertiary plastid gains, and the presence of horizontally acquired bacterial rhodopsins and type II RuBisCo. Elucidating how this all evolved depends on knowing the phylogenetic relationships between dinoflagellate lineages. Half of these species are heterotrophic, but existing molecular data is strongly biased toward the photosynthetic dinoflagellates due to their amenability to cultivation and prevalence in culture collections. These biases make it impossible to interpret the evolution of photosynthesis, but may also affect phylogenetic inferences that impact our understanding of character evolution. Here, we address this problem by isolating individual cells from the Salish Sea and using single cell, culture-free transcriptomics to expand molecular data for dinoflagellates to include 27 more heterotrophic taxa, resulting in a roughly balanced representation. Using these data, we performed a comprehensive search for proteins involved in chromatin packaging, plastid function, and photoactivity across all dinoflagellates. These searches reveal that 1) photosynthesis was lost at least 21 times, 2) two known types of HLP were horizontally acquired around the same time rather than sequentially as previously thought; 3) multiple rhodopsins are present across the dinoflagellates, acquired multiple times from different donors; 4) kleptoplastic species have nucleus-encoded genes for proteins targeted to their temporary plastids and they are derived from multiple lineages, and 5) warnowiids are the only heterotrophs that retain a whole photosystem, although some photosynthesis-related electron transport genes are widely retained in heterotrophs, likely as part of the iron-sulfur cluster pathway that persists in non-photosynthetic plastids.&lt;/p&gt;
DOI: 10.14288/1.0445207
title: Data from: Investigation of heterotrophs reveals new insights in dinoflagellate evolution

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Dinoflagellates are diverse and ecologically important protists characterized by many morphological and molecular traits that set them apart from other eukaryotes. These features include, but are not limited to, massive genomes organized using bacterially-derived histone-like proteins (HLPs) and dinoflagellate viral nucleoproteins (DVNP) rather than histones, and a complex history of photobiology with many independent losses of photosynthesis, numerous cases of serial secondary and tertiary plastid gains, and the presence of horizontally acquired bacterial rhodopsins and type II RuBisCo. Elucidating how this all evolved depends on knowing the phylogenetic relationships between dinoflagellate lineages. Half of these species are heterotrophic, but existing molecular data is strongly biased toward the photosynthetic dinoflagellates due to their amenability to cultivation and prevalence in culture collections. These biases make it impossible to interpret the evolution of photosynthesis, but may also affect phylogenetic inferences that impact our understanding of character evolution. Here, we address this problem by isolating individual cells from the Salish Sea and using single cell, culture-free transcriptomics to expand molecular data for dinoflagellates to include 27 more heterotrophic taxa, resulting in a roughly balanced representation. Using these data, we performed a comprehensive search for proteins involved in chromatin packaging, plastid function, and photoactivity across all dinoflagellates. These searches reveal that 1) photosynthesis was lost at least 21 times, 2) two known types of HLP were horizontally acquired around the same time rather than sequentially as previously thought; 3) multiple rhodopsins are present across the dinoflagellates, acquired multiple times from different donors; 4) kleptoplastic species have nucleus-encoded genes for proteins targeted to their temporary plastids and they are derived from multiple lineages, and 5) warnowiids are the only heterotrophs that retain a whole photosystem, although some photosynthesis-related electron transport genes are widely retained in heterotrophs, likely as part of the iron-sulfur cluster pathway that persists in non-photosynthetic plastids.&lt;/p&gt;