Genome-material costs and functional trade-offs in the autopolyploid Solidago gigantea (giant goldenrod) series.

PREMISE: Increased genome-material costs of N and P atoms inherent to organisms with larger genomes have been proposed to limit growth under nutrient scarcities and to promote growth under nutrient enrichments. Such responsiveness may reflect a nutrient-dependent diploid versus polyploid advantage that could have vast ecological and evolutionary implications, but direct evidence that material costs increase with ploidy level and/or influence cytotype-dependent growth, metabolic, and/or resource-use trade-offs is limited. METHODS: We grew diploid, autotetraploid, and autohexaploid Solidago gigantea plants with one of four ambient or enriched N:P ratios and measured traits related to material costs, primary and secondary metabolism, and resource-use. RESULTS: Relative to diploids, polyploids invested more N and P into cells, and tetraploids grew more with N enrichments, suggesting that material costs increase with ploidy level. Polyploids also generally exhibited strategies that could minimize material-cost constraints over both long (reduced monoploid genome size) and short (more extreme transcriptome downsizing, reduced photosynthesis rates and terpene concentrations, enhanced N-use efficiencies) evolutionary time periods. Furthermore, polyploids had lower transpiration rates but higher water-use efficiencies than diploids, both of which were more pronounced under nutrient-limiting conditions. CONCLUSIONS: N and P material costs increase with ploidy level, but material-cost constraints might be lessened by resource allocation/investment mechanisms that can also alter ecological dynamics and selection. Our results enhance mechanistic understanding of how global increases in nutrients might provide a release from material-cost constraints in polyploids that could impact ploidy (or genome-size)-specific performances, cytogeographic patterning, and multispecies community structuring.

Genetic data improves niche model discrimination and alters the direction and magnitude of climate change forecasts.

Ecological niche models (ENMs) have classically operated under the simplifying assumptions that there are no barriers to gene flow, species are genetically homogeneous (i.e., no population-specific local adaptation), and all individuals share the same niche. Yet, these assumptions are violated for most broadly distributed species. Here, we incorporate genetic data from the widespread riparian tree species narrowleaf cottonwood (Populus angustifolia) to examine whether including intraspecific genetic variation can alter model performance and predictions of climate change impacts. We found that (1) P. angustifolia is differentiated into six genetic groups across its range from México to Canada and (2) different populations occupy distinct climate niches representing unique ecotypes. Comparing model discriminatory power, (3) all genetically informed ecological niche models (gENMs) outperformed the standard species-level ENM (3-14% increase in AUC; 1-23% increase in pROC). Furthermore, (4) gENMs predicted large differences among ecotypes in both the direction and magnitude of responses to climate change and (5) revealed evidence of niche divergence, particularly for the Eastern Rocky Mountain ecotype. (6) Models also predicted progressively increasing fragmentation and decreasing overlap between ecotypes. Contact zones are often hotspots of diversity that are critical for supporting species' capacity to respond to present and future climate change, thus predicted reductions in connectivity among ecotypes is of conservation concern. We further examined the generality of our findings by comparing our model developed for a higher elevation Rocky Mountain species with a related desert riparian cottonwood, P. fremontii. Together our results suggest that incorporating intraspecific genetic information can improve model performance by addressing this important source of variance. gENMs bring an evolutionary perspective to niche modeling and provide a truly "adaptive management" approach to support conservation genetic management of species facing global change.

Impacts of soil nitrogen and phosphorus levels on cytotype performance of the circumboreal herb Chamerion angustifolium: implications for polyploid establishment.

PREMISE: Although polyploidy commonly occurs in angiosperms, not all polyploidization events lead to successful lineages, and environmental conditions could influence cytotype dynamics and polyploid success. Low soil nitrogen and/or phosphorus concentrations often limit ecosystem primary productivity, and changes in these nutrients might differentially favor some cytotypes over others, thereby influencing polyploid establishment. METHODS: We grew diploid, established tetraploid, and neotetraploid Chamerion angustifolium (fireweed) in a greenhouse under low and high soil nitrogen and phosphorus conditions and different competition treatments and measured plant performance (height, biomass, flower production, and root bud production) and insect damage responses. By comparing neotetraploids to established tetraploids, we were able to examine traits and responses that might directly arise from polyploidization before they are modified by natural selection and/or genetic drift. RESULTS: We found that (1) neopolyploids were the least likely to survive and flower and experienced the most herbivore damage, regardless of nutrient conditions; (2) both neo- and established tetraploids had greater biomass and root bud production under nutrient-enriched conditions, whereas diploid biomass and root bud production was not significantly affected by nutrients; and (3) intra-cytotype competition more negatively affected diploids and established tetraploids than it did neotetraploids. CONCLUSIONS: Following polyploidization, biomass and clonal growth might be more immediately affected by environmental nutrient availabilities than plant survival, flowering, and/or responses to herbivory, which could influence competitive dynamics. Specifically, polyploids might have competitive and colonizing advantages over diploids under nutrient-enriched conditions favoring their establishment, although establishment may also depend upon the density and occurrences of other related cytotypes in a population.

Conserving threatened riparian ecosystems in the American West: Precipitation gradients and river networks drive genetic connectivity and diversity in a foundation riparian tree (Populus angustifolia).

Gene flow is an evolutionary process that supports genetic connectivity and contributes to the capacity of species to adapt to environmental change. Yet, for most species, little is known about the specific environmental factors that influence genetic connectivity, or their effects on genetic diversity and differentiation. We used a landscape genetic approach to understand how geography and climate influence genetic connectivity in a foundation riparian tree (Populus angustifolia), and their relationships with specieswide patterns of genetic diversity and differentiation. Using multivariate restricted optimization in a reciprocal causal modelling framework, we quantified the relative contributions of riparian network connectivity, terrestrial upland resistance and climate gradients on genetic connectivity. We found that (i) all riparian corridors, regardless of river order, equally facilitated connectivity, while terrestrial uplands provided 2.5× more resistance to gene flow than riparian corridors. (ii) Cumulative differences in precipitation seasonality and precipitation of the warmest quarter were the primary climatic factors driving genetic differentiation; furthermore, maximum climate resistance was 45× greater than riparian resistance. (iii) Genetic diversity was positively correlated with connectivity (R2  = 0.3744, p = .0019), illustrating the utility of resistance models for identifying landscape conditions that can support a species' ability to adapt to environmental change. From these results, we present a map highlighting key genetic connectivity corridors across P. angustifolia's range that if disrupted could have long-term ecological and evolutionary consequences. Our findings provide recommendations for conservation and restoration management of threatened riparian ecosystems throughout the western USA and the high biodiversity they support.

Variations in how medical researchers report patient demographics: a retrospective analysis of published articles.

Background: The use of demographic variables in the medical literature has been a topic of much recent debate. Recent studies found that race and socioeconomic status (SES) are inconsistently reported. Best-practice use of sex and gender has been contentious. We aimed to characterise the state of medical demographic reporting in greater detail, especially regarding geography and specific terms used in articles. Methods: Original articles were included from issues of the New England Journal of Medicine (NEJM), JAMA, The Lancet, and the American Journal of Epidemiology (AJE) published from 1 January to 31 December 2020 (n = 640). Articles without human participants, case reports, or with only aggregate data were excluded, leaving 594 articles. Use of age, sex, gender, race, ethnicity, and SES were coded, as well as corresponding author and participant geography. Findings: 99.0% of articles reported age. While 92.9% reported sex alone, only 4.7% used the term gender and 1.0% transgender. 47.8% of articles reported race and 29.6% reported ethnicity. Studies with U.S. corresponding authors or participants were significantly more likely to report race (72.9% and 73.7% respectively) or ethnicity (47.3% and 45.3% respectively) than those without (25.9% and 25.6% for race, 14.2% and 16.3% for ethnicity), p < 0.01 for all. Of articles reporting race, 40.9% used only a Black-white binary; of those reporting ethnicity, 85.2% included two or fewer terms. Under 5.0% of all articles used Office of Management and Budget (OMB) categories. Across all articles, 33.0% reported SES, from 15.2% in NEJM to 80.2% in AJE. Interpretation: We found that while some factors (age, sex) are reported consistently, others (gender, race, ethnicity, SES) are not, despite recent attention. Authors often rely on binary or limited categories that inadequately capture human diversity. The presence of U.S. researchers or participants increased the reporting of race and/or ethnicity, highlighting wide variations that persist even as multinational collaborations become widespread. Researchers should reflect on their use of these terms, justify their decisions, and report results with care. Funding: None.

Polyploidy in Indian paintbrush (Castilleja; Orobanchaceae) species shapes but does not prevent gene flow across species boundaries.

PREMISE OF STUDY: A difference in chromosome numbers (ploidy variation) between species is usually considered a major barrier to gene flow. Therefore, it is surprising that little is known about whether ploidy variation, both within and among species, influences spatial patterns of interspecific hybridization. The role that polyploidy plays in structuring gene flow patterns between three co-occurring Indian paintbrush (Castilleja) species is investigated. • METHODS: Reciprocal hand pollinations were performed in populations where the three species co-occur with and without variable plants (previous data tested the ancestral "hybrid" history of these variable plants). I measured fruit set, seed production, seed germination, and the DNA content of parent plants and 26 synthesized F(1) hybrids. Data were combined with pollinator fidelity data to estimate the contribution of individual barriers to reproductive isolation. • KEY RESULTS: Interspecific gene flow could occur in all directions, but barriers were weaker for conspecific vs. heterospecific crosses. Species were nearly fixed for different ploidy levels, but some deviations occurred, primarily in populations with variable plants. Interspecific gene flow could occur across ploidy levels, but it was more likely when species had the same number of chromosomes or when resulting F(1) hybrids had even numbers of chromosomes. Postzygotic reproductive barriers were generally weaker than pollinator fidelity. • CONCLUSIONS: Polyploidy likely plays a large role in shaping contemporary and historical patterns of gene flow among these species. This study suggests that differences in chromosome numbers among closely related, compatible species might help structure spatial patterns of hybridization.

Violations of Suicide-Prevention Guidelines in US Media Coverage of Physician's Suicide Death During the COVID-19 Pandemic.

Background: Healthcare workers are at elevated risk for suicide; though it has yet to be studied, this risk may be exacerbated by the COVID-19 pandemic. News media coverage of high-profile suicide is associated with an increased risk of subsequent suicides. No analysis has yet been published of US media practices for reporting on healthcare worker suicides during the pandemic. Aims: The researchers aimed to evaluate pandemic-era media practices by investigating adherence to best-practice suicide reporting guidelines in coverage of Dr. Lorna Breen's death. Methods: The researchers conducted a content analysis of all unique articles by top outlets reporting Dr. Breen's death between April 26 and 29, 2020, and scored them based on their adherence to the 15 best-practice suicide reporting guidelines. Results: Every media outlet violated an average of at least 5 of 15 suicide guidelines in reporting on Dr. Breen's death; some abided by as few as 2 of 15 recommended guidelines. Seven of 15 guidelines were adhered to by fewer than one third of articles. The National Suicide Prevention Lifeline number, notably easy to include, appeared in only 75% of articles. Limitations: The researchers were limited to reviewing media coverage of one specific instance of COVID-era healthcare worker suicide, making these findings applicable as a prominent case study rather than forming a generalizable claim about suicide reporting during the pandemic or about reporting on healthcare suicides. Conclusion: These violations highlight a range of opportunities to improve suicide prevention in the media, which has a responsibility to ensure reporting does not exacerbate the risk of suicide. Improved adherence to these guidelines could reduce harm for healthcare workers during the pandemic.

Exploring environmental selection on genome size in angiosperms.

Angiosperms show a remarkable range in genome size (GS), yet most species have small genomes, despite the frequency of polyploidy and repeat amplification in the ancestries of most lineages. It has been suggested that larger genomes incur costs that have driven selection for GS reduction, although the nature of these costs and how they might impact selection remain unclear. We explore potential costs of increased GS encompassing impacts on minimum cell size with consequences for photosynthesis and water-use efficiency and effects of greater nitrogen and phosphorus demands of the nucleus leading to more severe trade-offs with photosynthesis. We suggest that nutrient-, water-, and/or CO2-stressed conditions might favour species with smaller genomes, with implications for species' ecological and evolutionary dynamics.

Hospital outcomes in non-surgical patients identified at risk for OSA.

BACKGROUND: In-hospital respiratory outcomes of non-surgical patients with undiagnosed obstructive sleep apnea (OSA), particularly those with significant comorbidities are not well defined. Undiagnosed and untreated OSA may be associated with increased cardiopulmonary morbidity. STUDY OBJECTIVES: Evaluate respiratory failure outcomes in patients identified as at-risk for OSA by the Berlin Questionnaire (BQ). METHODS: This was a retrospective study conducted using electronic health records at a large health system. The BQ was administered at admission to screen for OSA to medical-service patients under the age of 80 years old meeting the following health system criteria: (1) BMI greater than 30; (2) any of the following comorbid diagnoses: hypertension, heart failure, acute coronary syndrome, pulmonary hypertension, arrhythmia, cerebrovascular event/stroke, or diabetes. Patients with known OSA or undergoing surgery were excluded. Patients were classified as high-risk or low-risk for OSA based on the BQ score as follows: low-risk (0 or 1 category with a positive score on the BQ); high-risk (2 or more categories with a positive score on BQ). The primary outcome was respiratory failure during index hospital stay defined by any of the following: orders for conventional ventilation or intubation; at least two instances of oxygen saturation less than 88% by pulse oximetry; at least two instances of respiratory rate over 30 breaths per minute; and any orders placed for non-invasive mechanical ventilation without a previous diagnosis of sleep apnea. Propensity scores were used to control for patient characteristics. RESULTS: Records of 15,253 patients were assessed. There were no significant differences in the composite outcome of respiratory failure by risk of OSA (high risk: 11%, low risk: 10%, p = 0.55). When respiratory failure was defined as need for ventilation, more patients in the low-risk group experienced invasive mechanical ventilation (high-risk: 1.8% vs. low-risk: 2.3%, p = 0.041). Mortality was decreased in patients at high-risk for OSA (0.86%) vs. low risk for OSA (1.53%, p < 0.001). CONCLUSIONS: Further prospective studies are needed to understand the contribution of undiagnosed OSA to in-hospital respiratory outcomes.

Effects of soil nitrogen on diploid advantage in fireweed, Chamerion angustifolium (Onagraceae).

In many ecosystems, plant growth and reproduction are nitrogen limited. Current and predicted increases of global reactive nitrogen could alter the ecological and evolutionary trajectories of plant populations. Nitrogen is a major component of nucleic acids and cell structures, and it has been predicted that organisms with larger genomes should require more nitrogen for growth and reproduction and be more negatively affected by nitrogen scarcities than organisms with smaller genomes. In a greenhouse experiment, we tested this hypothesis by examining whether the amount of soil nitrogen supplied differentially influenced the performance (fitness, growth, and resource allocation strategies) of diploid and autotetraploid fireweed (Chamerion angustifolium). We found that soil nitrogen levels differentially impacted cytotype performance, and in general, diploids were favored under low nitrogen conditions, but this diploid advantage disappeared under nitrogen enrichment. Specifically, when nitrogen was scarce, diploids produced more seeds and allocated more biomass toward seed production relative to investment in plant biomass or total plant nitrogen than did tetraploids. As nitrogen supplied increased, such discrepancies between cytotypes disappeared. We also found that cytotype resource allocation strategies were differentially dependent on soil nitrogen, and that whereas diploids adopted resource allocation strategies that favored current season reproduction when nitrogen was limiting and future reproduction when nitrogen was more plentiful, tetraploids adopted resource allocation strategies that favored current season reproduction under nitrogen enrichment. Together these results suggest nitrogen enrichment could differentially affect cytotype performance, which could have implications for cytotypes' ecological and evolutionary dynamics under a globally changing climate.

Community genetics: what have we accomplished and where should we be going?

Research in community genetics seeks to understand how the dynamic interplay between ecology and evolution shapes simple and complex communities and ecosystems. A community genetics perspective, however, may not be necessary or informative for all studies and systems. To better understand when and how intraspecific genetic variation and microevolution are important in community and ecosystem ecology, we suggest future research should focus on three areas: (i) determining the relative importance of intraspecific genetic variation compared with other ecological factors in mediating community and ecosystem properties; (ii) understanding the importance of microevolution in shaping ecological dynamics in multi-trophic communities; and (iii) deciphering the phenotypic and associated genetic mechanisms that drive community and ecosystem processes. Here, we identify key areas of research that will increase our understanding of the ecology and evolution of complex communities but that are currently missing in community genetics. We then suggest experiments designed to meet these current gaps.

Tangled trios?: Characterizing a hybrid zone in Castilleja (Orobanchaceae).

Hybridization and polyploidization are exceedingly important processes because both influence the ecological envelope and evolutionary trajectory of land plants. These processes are frequently invoked for Castilleja (Indian paintbrushes) as contributors to morphological and genetic novelty and as complicating factors in species delimitations. Here, we provide a detailed analysis of morphological and genetic evidence for hybridization in a well-characterized hybrid swarm involving three broadly sympatric species (C. miniata, C. rhexiifolia, C. sulphurea) in western Colorado. Field-classified hybrids are present at high frequencies at these sites and show morphological intermediacy to and segregate for chloroplast DNA haplotypes with C. rhexiifolia and C. sulphurea. Contrarily, DNA content and AFLP variation show that field-classified hybrids are not recent hybrids but a distinctive fourth taxon. Actual hybrids (plants showing admixture ≥10% for two genotypic groups) comprised 13% of our sample, with most admixture involving C. rhexiifolia, C. sulphurea, and the unknown taxon. The identity of the field-classified "hybrids" remains unknown; they either represent a stabilized hybrid species or a species with uncharacteristically high diversity for color alleles. This study highlights the importance of examining concordance and discordance between morphology, cytology, and genetic criteria to understand the complex evolutionary history of diverse groups such as Castilleja.