The early impact of COVID-19 on local commerce: changes in spend across neighborhoods and online

We document a number of striking features about the initial impact of the pandemic on local commerce across 16 US cities. There are two novel contributions from this analysis: exploration of neighborhood-level effects and shifts between offline and online purchasing channels. In our analysis we use approximately 450 million credit card transactions per month from a rolling sample of 11 million anonymized customers between October 2019 and March 2020. Across the 16 cities we profile, consumers decreased spend on the set of goods and services we define as “local commerce” by 12.8% between March 2019 and March 2020. Growth in all 16 cities was negative. Consumers shifted a substantial share of local commerce spend online, such that year-over-year growth in online spend was small, but positive, at 1.5%. With respect to grocery and pharmacy purchases, online spend grew at least three times as fast as offline spend. Overall spend declines were uniform across neighborhoods of differing median household income, though lower-income neighborhoods experienced the highest proportion of extreme negative declines. We also find evidence that many low-income neighborhoods are increasing spend on online grocery slower than others, but increasing their use of online restaurants the fastest. Consumers in low-income neighborhoods also tend to live farther from the grocery stores at which they shop. Compared to their counterparts in higher-income neighborhoods, consumers in low-income neighborhoods have not been more likely to shop at grocery stores closer to where they live since the onset of the pandemic

Museomics of a rare taxon: placing Whalleyanidae in the Lepidoptera Tree of Life

https://doi.org/10.1111/syen.12503Museomics is a valuable approach that utilizes the diverse biobanks that are natural history museums. The ability to sequence genomes from old specimens has expanded not only the variety of interesting taxa available to study but also the scope of questions that can be investigated in order to further knowledge about biodiversity. Here, we present whole genome sequencing results from the enigmatic genus Whalleyana (comprising two species - occurring in drier biomes of Madagascar - previously placed in a monotypic superfamily, Whalleyanoidea), as well as from certain species of the families Callidulidae and Hyblaeidae (Calliduloidea and Hyblaeoidea, respectively). Library preparation was carried out on four museum specimens and one existing DNA extract and sequenced with Illumina short reads. De novo assembly resulted in highly fragmented genomes with the N50 ranging from 317 to 2078 bp. Mining of a manually curated gene set of 331 genes from these draft genomes had an overall gene recovery rate of 64-90%. Phylogenetic analysis places Whalleyana as sister to Callidulidae and Hyblaea as sister to Pyraloidea. Since the former sister-group relationship turns out to be also supported by ten morphological synapomorphies, we propose to formally assign the Whalleyanidae to the superfamily Calliduloidea. These results highlight the usefulness of not only museum specimens but also existing DNA extracts, for whole genome sequencing and gene mining for phylogenomic studies.Peer reviewe

Physiological differences between female limited, alternative life history strategies: the Alba phenotype in the butterfly Colias croceus

Across a wide range of taxa, individuals within populations exhibit alternative life history strategies (ALHS) where their phenotypes dramatically differ due to divergent investments in growth, reproduction and survivorship, with the resulting trade-offs directly impacting Darwinian fitness. Though the maintenance of ALHS within populations is fairly well understood, little is known regarding the physiological mechanisms that underlie ALHS and how environmental conditions can affect the evolution and expression of these phenotypes. One such ALHS, known as Alba, exists within females of many species in the butterfly genus Colias. Previous works in New World species not only found that female morphs differ in their wing color due to a reallocation of resources away from the synthesis of wing pigments to other areas of development, but also that temperature played an important role in these trade-offs. Here we build on previous work conducted in New World species by measuring life history traits and conducting lipidomics on individuals reared at hot and cold temperatures in the Old World species Colias croceus. Results suggest that the fitness of Alba and orange morphs likely varies with rearing temperature, where Alba females have higher fitness in cold conditions and orange in warm. Additionally shared traits between Old and New World species suggest the Alba mechanism is likely conserved across the genus. Finally, in the cold treatment we observe an intermediate yellow morph that may have decreased fitness due to slower larval development. This cost may manifest as disruptive selection in the field, thereby favoring the maintenance of the two discrete morphs. Taken together these results add insights into the evolution of, and the selection on, the Alba ALHS.Peer reviewe

Detection of (1,3)-β-d-Glucan in Cerebrospinal Fluid in Histoplasma Meningitis

The diagnosis of central nervous system (CNS) histoplasmosis is often difficult. Although cerebrospinal fluid (CSF) (1,3)-β-d-glucan (BDG) is available as a biological marker for the diagnosis of fungal meningitis, there are limited data on its use for the diagnosis of Histoplasma meningitis. We evaluated CSF BDG detection, using the Fungitell assay, in patients with CNS histoplasmosis and controls. A total of 47 cases and 153 controls were identified. The control group included 13 patients with a CNS fungal infection other than histoplasmosis. Forty-nine percent of patients with CNS histoplasmosis and 43.8% of controls were immunocompromised. The median CSF BDG level was 85 pg/ml for cases, compared to <31 pg/ml for all controls (P < 0.05) and 82 pg/ml for controls with other causes of fungal meningitis (P = 0.27). The sensitivity for detection of BDG in CSF was 53.2%, whereas the specificity was 86.9% versus all controls and 46% versus other CNS fungal infections. CSF BDG levels of ≥80 pg/ml are neither sensitive nor specific to support a diagnosis of Histoplasma meningitis

Chromosome Level Assembly of the Comma Butterfly (Polygonia c-album)

The comma butterfly (Polygonia c-album, Nymphalidae, Lepidoptera) is a model insect species, most notably in the study of phenotypic plasticity and plant-insect coevolutionary interactions. In order to facilitate the integration of genomic tools with a diverse body of ecological and evolutionary research, we assembled the genome of a Swedish comma using 10X sequencing, scaffolding with matepair data, genome polishing, and assignment to linkage groups using a high-density linkage map. The resulting genome is 373 Mb in size, with a scaffold N50 of 11.7 Mb and contig N50 of 11,2Mb. The genome contained 90.1% of single-copy Lepidopteran orthologs in a BUSCO analysis of 5,286 genes. A total of 21,004 gene-models were annotated on the genome using RNA-Seq data from larval and adult tissue in combination with proteins from the Arthropoda database, resulting in a high-quality annotation for which functional annotations were generated. We further documented the quality of the chromosomal assembly via synteny assessment with Melitaea cinxia. The resulting annotated, chromosome-level genome will provide an important resource for investigating coevolutionary dynamics and comparative analyses in Lepidoptera.Peer reviewe

Risk assessment based on indirect predation cues: revisiting fine-grained variation

To adaptively express inducible defenses, prey must gauge risk based on indirect cues of predation. However, the information contained in indirect cues that enable prey to fine-tune their phenotypes to variation in risk is still unclear. In aquatic systems, research has focused on cue concentration as the key variable driving threat-sensitive responses to risk. However, while risk is measured as individuals killed per time, cue concentration may vary with either the number or biomass killed. Alternatively, fine-grained variation in cue, that is, frequency of cue pulses irrespective of concentration, may provide a more reliable signal of risk. Here, we present results from laboratory experiments that examine the relationship between red-eyed treefrog tadpole growth and total cue, cue per pulse, and cue pulse frequency. We also reanalyze an earlier study that examined the effect of fine-grained variation in predator cues on wood frog tadpole growth. Both studies show growth declines with increasing cue pulse frequency, even though individual pulses in high-frequency treatments contained very little cue. This result suggests that counter to earlier conclusions, tadpoles are using fine-grained variation in cue arising from the number of predation events to assess and respond to predation risk, as predicted by consumer–resource theory.ECU Open Access Publishing Support Fund; National Science Foundation Grant Numbers: 0716923, 071722

From inquilines to gall inducers:Genomic signature of a life-style transition in synergus gall wasps

Gall wasps (Hymenoptera: Cynipidae) induce complex galls on oaks, roses and other plants, but the mechanism of gall induction is still unknown. Here we take a comparative genomic approach to revealing the genetic basis of gall induction. We focus on Synergus itoensis, a species that induces galls inside oak acorns. Previous studies suggested that this species evolved the ability to initiate gall formation recently, as it is deeply nested within the genus Synergus, whose members are mostly inquilines that develop inside the galls of other species. We compared the genome of S. itoensis to that of three related Synergus inquilines to identify genomic changes associated with the origin of gall induction. We used a novel Bayesian selection analysis, which accounts for branch-specific and gene-specific selection effects, to search for signatures of selection in 7,600 single-copy orthologous genes shared by the four Synergus species. We found that the terminal branch leading to S. itoensis had more genes with a significantly elevated dN/dS ratio (Positive Signature Genes, PSGs) than the other terminal branches in the tree; the S. itoensis branch also had more genes with a significantly decreased dN/dS ratio. Gene set enrichment analysis showed that the PSG set of S. itoensis, unlike those of the inquiline species, is enriched in several biological process Gene Ontology terms, the most prominent of which is “Ovarian Follicle Cell Development”. Our results indicate that the origin of gall induction is associated with distinct genomic changes, and provide a good starting point for further characterization of the genes involved

Plants, people and health: Three disciplines at work in Namaqualand

In Paulshoek, Namaqualand, three research projects focusing on medicinal plants were developed concurrently. The projects were based in the disciplines of anthropology, botany and chemistry. In this paper, we explore how these projects related to one another and describe the conversations that occurred in the process of searching for transdisciplinary knowledge. The projects ostensibly shared a common object of knowledge, but it was through working together that the medicinal plants constituted us as a community of scholars. As our insight into our respective disciplinary relationships with the plants grew, so did our understanding of the limitations of our respective disciplinary positions. The process made possible a &lsquo;reimagination&rsquo; of both the object of study and our relationships to it and to one another. The research project, conceptualised in 2009, engaged current debates on indigenous knowledge and its historical erasures, and offered an approach that has potential to produce new knowledges while respecting the integrity of the disciplines. This approach requires a non-competitive attitude to research and one that acknowledges the contributions that can be made by multiple approaches

Value of individual surgeon performance metrics as quality assurance measures in oesophagogastric cancer surgery

Background Surgeon‐level operative mortality is widely seen as a measure of quality after gastric and oesophageal resection. This study aimed to evaluate this alongside a compound‐level outcome analysis. Methods Consecutive patients who underwent treatment including surgery delivered by a multidisciplinary team, which included seven specialist surgeons, were studied. The primary outcome was death within 30 days of surgery; secondary outcomes were anastomotic leak, Clavien–Dindo morbidity score, lymph node harvest, circumferential resection margin (CRM) status, disease‐free (DFS), and overall (OS) survival. Results The median number of annual resections per surgeon was 10 (range 5–25), compared with 14 (5–25) for joint consultant teams (P = 0·855). The median annual surgeon‐level mortality rate was 0 (0–9) per cent versus an overall network annual operative mortality rate of 1·8 (0–3·7) per cent. Joint consultant team procedures were associated with fewer operative deaths (0·5 per cent versus 3·4 per cent at surgeon level; P = 0·027). The median surgeon anastomotic leak rate was 12·4 (range 9–20) per cent (P = 0·625 versus the whole surgical range), overall morbidity 46·5 (31–60) per cent (P = 0·066), lymph node harvest 16 (9–29) (P < 0·001), CRM positivity 32·0 (16–46) per cent (P = 0·003), 5‐year DFS rate 44·8 (29–60) per cent and OS rate 46·5 (35–53) per cent. No designated metrics were independently associated with DFS or OS in multivariable analysis. Conclusion Annual surgeon‐level metrics demonstrated wide variations (fivefold), but these performance metrics were not associated with survival