cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.14288/1.0397650
title: Data from: Using genetic relatedness to understand heterogeneous distributions of urban rat-associated pathogens

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Urban Norway rats (&lt;i&gt;Rattus norvegicus&lt;/i&gt;) carry several pathogens transmissible to people. However, pathogen prevalence can vary across fine spatial scales (i.e., by city block). Using a population genomics approach, we sought to describe rat movement patterns across an urban landscape, and to evaluate whether these patterns align with pathogen distributions. We genotyped 605 rats from a single neighborhood in Vancouver, Canada and used 1,495 genome-wide single nucleotide polymorphisms to identify parent-offspring and sibling relationships using pedigree analysis. We resolved 1,246 pairs of relatives, of which only 1% of pairs were captured in different city blocks. Relatives were primarily caught within 33 meters of each other leading to a highly leptokurtic distribution of dispersal distances. Using binomial generalized linear mixed models we evaluated whether family relationships influenced rat pathogen status with the bacterial pathogens &lt;i&gt;Leptospira interrogans&lt;/i&gt;, &lt;i&gt;Bartonella tribocorum&lt;/i&gt;, and &lt;i&gt;Clostridium difficile&lt;/i&gt;, and found that an individual’s pathogen status was not predicted any better by including disease status of related rats. The spatial clustering of related rats and their pathogens lends support to the hypothesis that spatially restricted movement promotes the heterogeneous patterns of pathogen prevalence evidenced in this population. &lt;span lang="EN-US" style="background:white;"&gt;Our findings also highlight the utility of evolutionary tools to understand movement and rat-associated health risks in urban landscapes.&lt;/span&gt;&lt;/p&gt;
DOI: 10.14288/1.0398032
title: Investigating morphological complexes using informational dissonance and bayes factors: A case study in corbiculate bees

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;It is widely recognized that different regions of a genome often have different evolutionary histories and that ignoring this variation when estimating phylogenies can be misleading. However, the extent to which this is also true for morphological data is still largely unknown. Discordance among morphological traits might plausibly arise due to either variable convergent selection pressures or else phenomena such as hemiplasy. Here we investigate patterns of discordance among 282 morphological characters, which we scored for 50 bee species particularly targeting corbiculate bees, a group that includes the well-known eusocial honeybees and bumblebees. As a starting point for selecting the most meaningful partitions in the data, we grouped characters as morphological modules, highly integrated trait complexes that as a result of developmental constraints or coordinated selection we expect to share an evolutionary history and trajectory. In order to assess conflict and coherence across and within these morphological modules, we used recently developed approaches for computing Bayesian phylogenetic information allied with model comparisons using Bayes factors. We found that despite considerable conflict among morphological complexes, accounting for among-character and among-partition rate variation with individual gamma distributions, rate multipliers, and linked branch lengths can lead to coherent phylogenetic inference using morphological data. We suggest that evaluating information content and dissonance among partitions is useful step in estimating phylogenies from morphological data, just as it is with molecular data. Furthermore, we argue that adopting emerging approaches for investigating dissonance in genomic datasets may provide new insights into the integration and evolution of anatomical complexes.&lt;/p&gt;
DOI: 10.14288/1.0398089
title: The genome of Draba nivalis shows signatures of adaptation to the extreme environmental stresses of the Arctic

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;The Arctic is one of the most extreme terrestrial environments on the planet. Here we present the first complete genome assembly of a plant adapted to the high Arctic, Draba nivalis (Brassicaceae), an attractive model species for studying plant adaptation to the stresses imposed by this harsh environment. We used an iterative scaffolding strategy with data from short-reads, single-molecule long reads, proximity ligation data, and a genetic map to produce a 302 Mb assembly that is highly contiguous with 91.6% assembled into eight chromosomes (the base chromosome number). To identify candidate genes and gene families that may have facilitated adaptation to Arctic environmental stresses, we performed comparative genomic analyses with nine non-Arctic Brassicaceae species. We show that the D. nivalis genome contains expanded suites of genes associated with drought and cold stress (e.g. related to the maintenance of oxidation-reduction homeostasis, meiosis, and signaling pathways). The expansions of gene families associated with these functions appear to be driven in part by the activity of transposable elements. Tests of positive selection identify suites of candidate genes associated with meiosis and photoperiodism, as well as cold, drought, and oxidative stress responses. Our results reveal a multifaceted landscape of stress adaptation in the D. nivalis genome, offering avenues for the continued development of this species as an Arctic model plant.
DOI: 10.14288/1.0397533
title: Beyond seedlings: ectomycorrhizal fungal networks and growth of mature Pseudotsuga menziesii

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;1. Mycorrhizal networks are conduits for the transfer of resources between hosts. While ectomycorrhizal networks (EMN) are known to influence seedlings, their effect on adult tree growth remains unknown and may have important implications for forest responses to future climates.&lt;/p&gt; &lt;p&gt;2. We used annual basal area increment of trees and previously described Rhizopogon vesiculosus and Rhizopogon vinicolor EMNs to examine an association between the number of connections between trees through an EMN and the growth of adult interior Douglas-fir. We compared this relationship for the year the networks were mapped, in 2008, with eight years previous and eight years afterward. We also compared the variation in standardized growth (2000–2016) to examine the association between growth variability and EMN variables.&lt;/p&gt; &lt;p&gt;3. Greater growth was positively associated with 1) the number of connections to other trees via a Rhizopogon vinicolor EMN, and 2) the number of genets of Rhizopogon vesiculosis by which a tree was colonized. Variation of growth (2000–2016) was negatively associated with increasing number of connections to other trees via Rhizopogon vinicolor. Synthesis. These findings, for the first time, indicate that EMNs may positively influence the growth of adult trees. The difference in tree growth response between the sister fungal species highlights a novel avenue to identify interspecific and intraspecific differences between species occurring at different depths in the soil. Our study has important implications when considering the role of EMNs in influencing forest health and mitigating stress from environmental conditions.&lt;/p&gt;
DOI: 10.14288/1.0397964
title: Genomic differentiation and local adaptation on a microgeographic scale in a resident songbird

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;Elucidating forces capable of driving species diversification in the face of gene flow remains a key goal in evolutionary biology. Song sparrows, Melospiza melodia, occur as 25 subspecies in diverse habitats across North America, are among the continent’s most widespread vertebrate species, and are exemplary of many highly variable species for which the conservation of locally adapted populations may be critical to their range-wide persistence. We focus here on six morphologically distinct subspecies resident in the San Francisco Bay region, including three salt-marsh endemics and three residents in upland and riparian habitats adjacent to the Bay. We used reduced-representation sequencing to generate 2,773 SNPs to explore genetic differentiation, spatial population structure, and demographic history. Clustering separated individuals from each of the six subspecies, indicating subtle differentiation at microgeographic scales. Evidence of limited gene flow and low nucleotide diversity across all six subspecies further supports a hypothesis of isolation among locally adapted populations. We suggest that natural selection for genotypes adapted to salt marsh environments and changes in demography over the past century have acted in concert to drive the patterns of diversification reported here. Our results offer evidence of microgeographic specialization in a highly polytypic bird species long discussed as a model of sympatric speciation and rapid adaptation, and they support the hypothesis that conserving locally adapted populations may be critical to the range-wide persistence of similarly highly variable species.&lt;/p&gt;
DOI: 10.14288/1.0394201
title: Standard Operating Procedures for Sepsis CoLab Members: Dataverse Navigation and Use

description: Step-by-step instructions for CoLab members on navigating the Sepsis CoLab's Dataverse, downloading existing assets, requesting a new Dataverse for your project, uploading or modifying files, and submitting project proposals to access or contribute de-identified clinical datasets.
DOI: 10.14288/1.0397545
title: Multivariate phenotypic divergence along an urbanization gradient

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;A growing body of evidence suggests that natural populations can evolve to better tolerate the novel environmental conditions associated with urban areas. Invariably, studies of adaptive divergence in urban areas examine only one or a few traits at a time from populations residing only at the most extreme urban and nonurban habitats. Thus, whether urbanization is driving divergence in many traits simultaneously in a manner that varies with the degree of urbanization remains unclear. To address this gap, we generated seed families of white clover (Trifolium repens) collected from 27 populations along an urbanization gradient in Toronto, Canada, and grew them in a common garden to measure 14 phenotypic traits. Overall, families from urban sites had evolved later phenology and germination, larger flowers, thinner stolons, reduced cyanogenesis, greater biomass, and greater seed set. Pollinator observations revealed near complete turnover of pollinator morphological groups between urban and nonurban sites, which may explain some of the observed divergence in floral traits and phenology. Our results suggest that adaptation to urban environments involves multiple organismal traits.
DOI: 10.14288/1.0397976
title: COVID-19 clinician moral injury survey

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;&lt;b&gt;Background&lt;/b&gt;&lt;/p&gt; &lt;p&gt;Moral injury is an emerging explanation of burnout and suicidality, but remains poorly quantified in at-risk practitioners. We hypothesized that COVID-19 pandemic-related moral injury differs between frontline clinicians, genders, age, and country of practice.&lt;br&gt;  &lt;/p&gt; &lt;p&gt;&lt;b&gt;Methods&lt;/b&gt;&lt;/p&gt; &lt;p&gt;We conducted an online cross-sectional survey of international physicians, nurses, nurse practitioners, paramedics and respiratory therapists between April and June 2020.  We included the adapted version of the Expressions of Moral Injury Scale (EMIS). The primary outcome was differences in moral injury scores between clinician roles.&lt;/p&gt; &lt;p&gt;&lt;b&gt;Results&lt;/b&gt;&lt;/p&gt; &lt;p&gt;Three hundred and two clinicians participated, including physicians (61% [n=184]), nurses (28% [n=85]), and nurse practitioners (5% [n=14]). The median age was 39 (IQR 32-76), females comprised 54% of the respondents, and the majority resided in Canada (n =183 [61%]) or the United States (US; n = 106 [35%]). Emergency medicine (88% [n=265]), and intensive care (6% [n=17]) were the main specialties responding. Median moral injury scores across multiple domains were higher for nurses compared to physicians, as well as for younger, and female respondents. Moral injury scores were also significantly higher for respondents from the United States, the United Kingdom and Australia, compared to Canada.&lt;/p&gt; &lt;p&gt;&lt;b&gt;Conclusions&lt;/b&gt;&lt;/p&gt; &lt;p&gt;Our research suggests that during COVID-19, measures of moral injury differ across roles, gender and place of work. Future research is warranted to better understand the impact of moral injury on clinicians’ psychological well-being during the COVID-19 pandemic.&lt;/p&gt;
DOI: 10.14288/1.0397531
title: The sunflower (Helianthus annuusL.) genome reflects a recent history of biased accumulation of transposable elements

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;section data-lang="en" id="section-1-en" lang="en"&gt; &lt;p&gt;Aside from polyploidy, transposable elements are the major drivers of genome size increases in plants. Thus, understanding the diversity and evolutionary dynamics of transposable elements in sunflower (&lt;i&gt;Helianthus annuus&lt;/i&gt; L.), especially given its large genome size (∼3.5 Gb) and the well‐documented cases of amplification of certain transposons within the genus, is of considerable importance for understanding the evolutionary history of this emerging model species. By analyzing approximately 25% of the sunflower genome from random sequence reads and assembled bacterial artificial chromosome (BAC) clones, we show that it is composed of over 81% transposable elements, 77% of which are long terminal repeat (LTR) retrotransposons. Moreover, the LTR retrotransposon fraction in BAC clones harboring genes is disproportionately composed of chromodomain‐containing &lt;i&gt;Gypsy&lt;/i&gt; LTR retrotransposons (‘chromoviruses’), and the majority of the intact chromoviruses contain tandem chromodomain duplications. We show that there is a bias in the efficacy of homologous recombination in removing LTR retrotransposon DNA, thereby providing insight into the mechanisms associated with transposable element (TE) composition in the sunflower genome. We also show that the vast majority of observed LTR retrotransposon insertions have likely occurred since the origin of this species, providing further evidence that biased LTR retrotransposon activity has played a major role in shaping the chromatin and DNA landscape of the sunflower genome. Although our findings on LTR retrotransposon age and structure could be influenced by the selection of the BAC clones analyzed, a global analysis of random sequence reads indicates that the evolutionary patterns described herein apply to the sunflower genome as a whole.&lt;/p&gt; &lt;/section&gt;
DOI: 10.14288/1.0397896
title: Interspecific competition slows range expansion and shapes range boundaries

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p class="western" style="margin-top:16px;margin-bottom:4px;text-align:left;"&gt;&lt;span style="background:transparent none 0% 0%;"&gt;&lt;span style="page-break-after:avoid;"&gt;&lt;font color="#000000"&gt;&lt;font&gt;&lt;font&gt;Species expanding into new habitats as a result of climate change or human introductions will frequently encounter resident competitors. Theoretical models suggest that such interspecific competition can alter the speed of expansion and the shape of expanding range boundaries. However, competitive interactions are rarely considered when forecasting the success or speed of expansion, in part because there has been no direct experimental evidence that competition affects either expansion speed or boundary shape. Here we demonstrate that interspecific competition alters both expansion speed and range boundary shape. Using a two-species experimental system of the flour beetles &lt;/font&gt;&lt;/font&gt;&lt;/font&gt;&lt;font color="#000000"&gt;&lt;font&gt;&lt;font&gt;&lt;i&gt;Tribolium castaneum&lt;/i&gt;&lt;/font&gt;&lt;/font&gt;&lt;/font&gt;&lt;font color="#000000"&gt;&lt;font&gt;&lt;font&gt; and &lt;/font&gt;&lt;/font&gt;&lt;/font&gt;&lt;font color="#000000"&gt;&lt;font&gt;&lt;font&gt;&lt;i&gt;Tribolium&lt;/i&gt;&lt;/font&gt;&lt;/font&gt;&lt;/font&gt;&lt;font color="#000000"&gt;&lt;font&gt; &lt;/font&gt;&lt;/font&gt;&lt;font color="#000000"&gt;&lt;font&gt;&lt;font&gt;&lt;i&gt;confusum&lt;/i&gt;&lt;/font&gt;&lt;/font&gt;&lt;/font&gt;&lt;font color="#000000"&gt;&lt;font&gt;&lt;font&gt;, we show that interspecific competition dramatically slows expansion across a landscape over multiple generations. Using a parameterized stochastic model of expansion, we find that this slowdown can persist over the long-term. We also find that the shape of the moving range boundary changes continuously over many generations of expansion, first steepening and then becoming shallower, due to the competitive effect of the resident and density-dependent dispersal of the invader. This dynamic boundary shape suggests that current forecasting approaches assuming a constant shape could be misleading. More broadly, our results demonstrate that interactions between competing species can play a large role during range expansions and thus should be included in models and studies that monitor, forecast, or manage expansions in natural systems.&lt;/font&gt;&lt;/font&gt;&lt;/font&gt;&lt;/span&gt;&lt;/span&gt;&lt;/p&gt;
DOI: 10.14288/1.0397907
title: A study of tactical and sexual dimorphism in cognition with insights for sexual conflict

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;The sexes may have different optima in cognitive traits due to differences in life history strategies and the expense of investing in metabolically costly brain tissue. However, given genetic correlations, each sex could be constrained from reaching its cognitive optimum due to intralocus sexual conflict. We compared learning performance of two male alternative reproductive tactics and females from known genotypes (both sire and dam) in the livebearing fish &lt;i&gt;Xiphophorus multilineatus&lt;/i&gt;. We predicted that females’ learning performance would align with the learning performance of their sire’s genotype due to genetic correlation of cognitive traits. Using a classical conditioning assessment (associating a flashing light with a food reward), we detected mating tactic dimorphism in learning performance, with the behaviourally plastic sneaker males outperforming the behaviourally fixed &lt;a&gt;courter &lt;/a&gt;males. Unexpectedly, females sired by the faster-learning sneaker males performed significantly worse than sneaker males. We also detected an influence of brain size on female learning performance. Previous studies have found that females invest more in offspring sired by courter males, and we therefore hypothesize that maternal effects could potentially mitigate the influence of sexual conflict on a cognitive trait.&lt;/p&gt;
DOI: 10.14288/1.0394730
title: Salish Sea surface drifter dataset (2015-2018)

description: This dataset contains quality-controlled data from GPS-tracked expendable surface drifters in the Salish Sea, deployed over the years 2015-2018.
DOI: 10.14288/1.0395783
title: Data used in the figures of 'Wintertime variability of currents in the southwestern Taiwan Strait'

description: Analytical data in support of the manuscript "Wintertime Variability of Surface Currents on West Southern Taiwan Strait", which is submitted to Journal of Geophysical Research: Oceans. One could use the data to generate any figure in the manuscript.
DOI: 10.14288/1.0397657
title: Data from: Prey availability and ambient temperature influence carrion persistence in the boreal forest

description: &lt;b&gt;Abstract&lt;/b&gt;&lt;br/&gt;&lt;p&gt;1. Scavenging by vertebrates can have important impacts on food web stability and persistence, and can alter the distribution of nutrients throughout the landscape. However, scavenging communities have been understudied in most regions around the globe, and we lack understanding of the biotic drivers of vertebrate scavenging dynamics.&lt;/p&gt; &lt;p&gt;2. In this paper, we examined how changes in prey density and carrion biomass caused by population cycles of a primary prey species, the snowshoe hare (&lt;i&gt;Lepus americanus&lt;/i&gt;), influence scavenging communities in the northern boreal forest. We further examined the impact of habitat and temperature on scavenging dynamics.&lt;/p&gt; &lt;p&gt;3. We monitored the persistence time, time until first scavenger, and number of species scavenging experimentally-placed hare carcasses over four consecutive years in the southwestern Yukon. We simultaneously monitored hare density and carrion biomass to examine their influence relative to temperature, habitat, and seasonal effects. For the primary scavengers, we developed species-specific scavenging models to determine variation on the effects of these factors across species, and determine which species may be driving temporal patterns in the entire community.&lt;/p&gt; &lt;p&gt;4. We found that the efficiency of the scavenging community was affected by hare density, with carcass persistence decreasing when snowshoe hare densities declined, mainly due to increased scavenging rates by Canada lynx (&lt;i&gt;Lynx canadensis&lt;/i&gt;). However, prey density did not influence the number of species scavenging a given carcass, suggesting prey abundance affects carrion recycling but not necessarily the number of connections in the food web. In addition, scavenging rates increased in warmer temperatures, and there were strong seasonal effects on the richness of the vertebrate scavenging community.&lt;/p&gt; &lt;p&gt;5. Our results demonstrate that vertebrate scavenging communities are sensitive to changes in species’ demography and environmental change, and that future assessments of food web dynamics should consider links established through scavenging.&lt;/p&gt;