Specimen collection is essential for modern science.

Natural history museums are vital repositories of specimens, samples and data that inform about the natural world; this Formal Comment revisits a Perspective that advocated for the adoption of compassionate collection practices, querying whether it will ever be possible to completely do away with whole animal specimen collection.

A set of principles and practical suggestions for equitable fieldwork in biology.

Field biology is an area of research that involves working directly with living organisms in situ through a practice known as "fieldwork." Conducting fieldwork often requires complex logistical planning within multiregional or multinational teams, interacting with local communities at field sites, and collaborative research led by one or a few of the core team members. However, existing power imbalances stemming from geopolitical history, discrimination, and professional position, among other factors, perpetuate inequities when conducting these research endeavors. After reflecting on our own research programs, we propose four general principles to guide equitable, inclusive, ethical, and safe practices in field biology: be collaborative, be respectful, be legal, and be safe. Although many biologists already structure their field programs around these principles or similar values, executing equitable research practices can prove challenging and requires careful consideration, especially by those in positions with relatively greater privilege. Based on experiences and input from a diverse group of global collaborators, we provide suggestions for action-oriented approaches to make field biology more equitable, with particular attention to how those with greater privilege can contribute. While we acknowledge that not all suggestions will be applicable to every institution or program, we hope that they will generate discussions and provide a baseline for training in proactive, equitable fieldwork practices.

Plumage Balances Camouflage and Thermoregulation in Horned Larks (Eremophila alpestris).

AbstractAnimal coloration serves many biological functions and must therefore balance potentially competing selective pressures. For example, many animals have camouflage in which coloration matches the visual background that predators scan for prey. However, different colors reflect different amounts of solar radiation and may therefore have thermoregulatory implications as well. In this study, we examined geographic variation in dorsal patterning, coloration, and solar reflectance among horned larks (Eremophila alpestris) of the western United States. We found that plumage brightness was positively associated with soil granularity, aridity, and temperature. Plumage redness-both in terms of saturation (i.e., chroma) and hue-was positively associated with soil redness and temperature, while plumage patterning was positively associated with soil granularity. Together, these plumage-environment associations support both background matching and Gloger's rule, a widespread ecogeographic pattern in animal coloration. We also constructed thermoregulatory models that estimated cooling benefits provided by solar reflectance profiles of the dorsal plumage of each specimen based on the collection site. We found increased cooling benefits in hotter, more arid environments. Finally, cooling benefits were positively associated with residual brightness, such that individuals that were brighter than expected based on environmental conditions also had higher cooling benefits, suggesting a trade-off between camouflage and thermoregulation. Together, these data suggest that natural selection has balanced camouflage and thermoregulation in horned larks, and they illustrate how multiple competing evolutionary pressures may interact to shape geographic variation in adaptive phenotypes.

A highly contiguous genome assembly for the California quail (Callipepla californica).

The California quail (Callipepla californica) is an iconic native bird of scrub and oak woodlands in California and the Baja Peninsula of Mexico. Here, we report a draft reference assembly for the species generated from PacBio HiFi long read and Omni-C chromatin-proximity sequencing data as part of the California Conservation Genomics Project (CCGP). Sequenced reads were assembled into 321 scaffolds totaling 1.08 Gb in length. Assembly metrics indicate a highly contiguous and complete assembly with a contig N50 of 5.5 Mb, scaffold N50 of 19.4 Mb, and BUSCO completeness score of 96.5%. Transposable elements (TEs) occupy 16.5% of the genome, more than previous Odontophoridae quail assemblies but in line with estimates of TE content for recent long-read assemblies of chicken and Peking duck. Together these metrics indicate that the present assembly is more complete than prior reference assemblies generated for Odontophoridae quail. This reference will serve as an essential resource for studies on local adaptation, phylogeography, and conservation genetics in this species of significant biological and recreational interest.

A highly contiguous reference genome for the Steller's jay (Cyanocitta stelleri).

The Steller's jay is a familiar bird of western forests from Alaska south to Nicaragua. Here, we report a draft reference assembly for the species generated from PacBio HiFi long-read and Omni-C chromatin-proximity sequencing data as part of the California Conservation Genomics Project (CCGP). Sequenced reads were assembled into 352 scaffolds totaling 1.16 Gb in length. Assembly metrics indicate a highly contiguous and complete assembly with a contig N50 of 7.8 Mb, scaffold N50 of 25.8 Mb, and BUSCO completeness score of 97.2%. Repetitive elements span 16.6% of the genome including nearly 90% of the W chromosome. Compared with high-quality assemblies from other members of the family Corvidae, the Steller's jay genome contains a larger proportion of repetitive elements than 4 crow species (Corvus), but a lower proportion of repetitive elements than the California scrub-jay (Aphelocoma californica). This reference genome will serve as an essential resource for future studies on speciation, local adaptation, phylogeography, and conservation genetics in this species of significant biological interest.

De novo assembly of a chromosome-level reference genome for the California Scrub-Jay, Aphelocoma californica.

We announce the assembly of the first de novo reference genome for the California Scrub-Jay (Aphelocoma californica). The genus Aphelocoma comprises four currently recognized species including many locally adapted populations across Mesoamerica and North America. Intensive study of Aphelocoma has revealed novel insights into the evolutionary mechanisms driving diversification in natural systems. Additional insights into the evolutionary history of this group will require continued development of high-quality, publicly available genomic resources. We extracted high molecular weight genomic DNA from a female California Scrub-Jay from northern California and generated PacBio HiFi long-read data and Omni-C chromatin conformation capture data. We used these data to generate a de novo partially phased diploid genome assembly, consisting of two pseudo-haplotypes, and scaffolded them using inferred physical proximity information from the Omni-C data. The more complete pseudo-haplotype assembly (arbitrarily designated "Haplotype 1") is 1.35 Gb in total length, highly contiguous (contig N50 = 11.53 Mb), and highly complete (BUSCO completeness score = 97%), with comparable scaffold sizes to chromosome-level avian reference genomes (scaffold N50 = 66.14 Mb). Our California Scrub-Jay assembly is highly syntenic with the New Caledonian Crow reference genome despite ~10 million years of divergence, highlighting the temporal stability of the avian genome. This high-quality reference genome represents a leap forward in publicly available genomic resources for Aphelocoma, and the family Corvidae more broadly. Future work using Aphelocoma as a model for understanding the evolutionary forces generating and maintaining biodiversity across phylogenetic scales can now benefit from a highly contiguous, in-group reference genome.

Omicron Breakthrough Infection After Heterologous Prime-Boost Vaccination Induces a Vigorous Antibody Response.

Infection with the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron variant is usually asymptomatic or mild and appears to be poorly immunogenic at least in unvaccinated individuals. Here, we found that health care workers vaccinated with 2 doses of Sputnik V and a booster dose of ChAdOx1 mount a vigorous neutralizing-antibody response after Omicron breakthrough infection.

Neo-sex chromosome evolution and phenotypic differentiation across an elevational gradient in horned larks (Eremophila alpestris).

Genetic structure and phenotypic variation among populations are affected by both geographic distance and environmental variation across species' distributions. Understanding the relative contributions of isolation by distance (IBD) and isolation by environment (IBE) is important for elucidating population dynamics across habitats and ecological gradients. In this study, we compared phenotypic and genetic variation among Horned Lark (Eremophila alpestris) populations from 10 sites encompassing an elevational gradient from low-elevation desert scrub in Death Valley (285 a.s.l.) to high-elevation meadows in the White Mountains of the Sierra Nevada of California (greater than 3000 m a.s.l.). Using a ddRAD data set of 28,474 SNPs aligned to a high-quality reference genome, we compared genetic structure with elevational, environmental, and spatial distance to quantify how different aspects of the landscape drive genomic and phenotypic differentiation in Horned Larks. We found larger-bodied birds were associated with sites that had less seasonality and higher annual precipitation, and longer spurs occurred in soils with more clay and silt content, less sand, and finer fragments. Larks have large neo-sex chromosomes, and we found that associations with elevation and environmental variation were much stronger among neo-sex chromosomes compared to autosomes. Furthermore, we found that putative chromosomal translocations, fusions, and inversions were associated with elevation and may underlie local adaptation across an elevational gradient in Horned Larks. Our results suggest that genetic variation in Horned Larks is affected more by IBD than IBE, but specific phenotypes and genomic regions-particually on neo-sex chromosomes-bear stronger associations with the environment.

Mutualism in museums: A model for engaging undergraduates in biodiversity science.

Museums have an untapped potential to engage students in hands-on learning. Here, we describe the development of a tiered museum-based program at the University of California, Berkeley as a model for engaging undergraduates in biodiversity science. This decade-long effort to increase student participation in collections demonstrates the mutual benefits of undergraduate involvement. Museums benefit from critical help in collections care and an increased intellectual vitality, while students simultaneously gain essential research skills and an unparalleled exposure to biodiversity. Five first steps to creating a program are: dedicate a coordinator, offer credit, diversify participation, create a tiered structure, and build community.

Phenotypic and genetic introgression across a moving woodpecker hybrid zone.

In hybrid zones in which two divergent taxa come into secondary contact and interbreed, selection can maintain phenotypic diversity despite widespread genetic introgression. Red-breasted (Sphyrapicus ruber) and red-naped (S. nuchalis) sapsuckers meet and hybridize along a narrow contact zone that stretches from northern California to southern British Columbia. We found strong evidence for changes in the structure of this hybrid zone across time, with significant temporal shifts in allele frequencies and in the proportions of parental phenotypes across the landscape. In addition to these shifts, we found that differences in plumage predict genetic differences (R2  = 0.80), suggesting that plumage is a useful proxy for assessing ancestry. We also found a significant bimodal distribution of hybrids across the contact zone, suggesting that premating barriers may be driving reproductive isolation, perhaps as a result of assortative mating based on plumage differences. However, despite evidence of selection and strong patterns of population structure between parental samples, we found only weak patterns of genetic divergence. Using museum specimens and genomic data, this study of sapsuckers provides insight into the ways in which phenotypic and genetic structure have changed over a 40-year period, as well as insight into the mechanisms that may contribute to the maintenance of the hybrid zone over time.

Robotic Radical Hysterectomy After Concomitant Chemoradiation in Locally Advanced Cervical Cancer: A Prospective Phase II Study.

STUDY OBJECTIVE: To assess the feasibility of total robotic radical surgery (TRRS) in patients with locally advanced cervical cancer (LACC) who receive chemoradiation therapy (CT/RT). DESIGN: A prospective (preplanned) study of a nonrandomized controlled trial (Canadian Task Force classification level 2). SETTING: Catholic University of the Sacred Hearth, Rome, Italy. PATIENTS: Between September 2013 and January 2016, a total of 40 patients with LACC (Fédération Internationale de Gynécologie et d'Obstétrique stage IB2-III) were enrolled in the study. INTERVENTIONS: Robotic radical hysterectomy (RRH) plus pelvic and/or aortic lymphadenectomy was attempted within 6 weeks after CT/RT. The feasibility of TRRS as well as the rate, pattern, and severity of early and late postoperative complications were analyzed. MEASUREMENTS AND MAIN RESULTS: After CT/RT, 29 patients (72.5%) underwent type B2 RRH, and 11 (27.5%) underwent type C1 RRH. Pelvic lymphadenectomy was performed in all cases. TRRS was successful in 39 of 40 cases (feasibility rate = 97.5%). In patients successfully completing TRRS, the median operating time was 185 minutes (range, 100-330 minutes), and the median blood loss was 100 mL (range, 50-300 mL). The median time of hospitalization counted from the first postoperative day was 2 days (range, 1-4 days). No intraoperative complications were recorded. During the observation period (median = 18 months; range, 4-28 months), 9 of 40 (22.5%) experienced postoperative complications, for a total number of 12 complications. As of April 2016, recurrence of disease was documented in 5 cases (12.5%). CONCLUSION: TRRS is feasible in LACC patients administered preoperative CT/RT, providing perioperative outcomes comparable with those registered in early-stage disease, and LACC patients receiving neoadjuvant chemotherapy.

Robotic Versus Laparoscopic Staging for Early Ovarian Cancer: A Case-Matched Control Study.

STUDY OBJECTIVE: To evaluate the feasibility, surgical outcome, and oncologic results observed after robotic staging compared with conventional laparoscopic staging for patients with early-stage ovarian cancer patients. DESIGN: A retrospective cohort study (Canadian Task Force classification II-2). SETTING: Catholic University of the Sacred Heart, Rome, Italy. PATIENTS: Ninety-six patients underwent minimally invasive staging for presumed stage I ovarian cancer; 32 underwent the robotic approach (cases), and 64 underwent the laparoscopic approach (controls). MEASUREMENTS AND MAIN RESULTS: There was no statistically significant difference between the 2 approaches with regard to final Fédération Internationale de Gynécologie et d'Obstétrique stage, histology, and grade of tumors. In the whole series, 15 patients (15.6%) were upstaged, with no statistically significant difference between the 2 groups. The median number of pelvic lymph nodes removed was 14 (range, 3-42) and 11 (range, 2-29) in the robotic and laparoscopic groups (p = .235), respectively. The median number of aortic lymph nodes removed was 11 (range, 3-26) and 12 (range, 1-39) in the robotic and laparoscopic groups (p = .263), respectively. The operative time was significantly shorter in the robotic group compared with the laparoscopic group (p = .043), whereas the amount of estimated blood loss was similar (p = .691). No difference was found in terms of early and postoperative complications. Overall, 72 patients were considered as requiring adjuvant treatment. Two patients experienced peritoneal recurrence. CONCLUSION: The present study suggests that there is no relevant difference between the robotic and laparoscopic approaches in staging early-stage ovarian cancer. Further prospective trials are needed to confirm our results.

[Health literacy and diabetes control in patients attending a university outpatient clinic in Argentina]. / Alfabetización en salud y control de la diabetes en pacientes de un hospital universitario de Argentina.

Health literacy (HL) is a measure of a patient ability to read, understand and to take decisions on medical instructions. Patients with inadequate HL have poorer health outcomes than those with adequate HL. There is little information on HL levels in diabetic patients in Argentina. The aim of this study was to explore the association between HL and glycemic control in diabetic patients from a university hospital in Argentina. HL was assessed with the Short Assessment of Health Literacy for Spanish-speaking Adults (SAHLSA), glycemic control through glycosylated hemoglobin A1c (HbA1c); 156 patients (58% women) took part in the study. Average SAHLSA score was 35 (range: 11-50). Patients with inadequate values of HL had HbA1c of 8.15% vs. 7.15% among those with adequate HL (p = 0.0001). The multiple linear regression shows that inadequate HL was significantly associated with poorer glycemic control (ß = -0.05 IC 95% -0.07; -0.02, p < 0.001). Efforts should focus on developing interventions to improve glycemic control among patients with inadequate HL.

Genetic sequence data reveals widespread sharing of Leucocytozoon lineages in corvids.

Leucocytozoon, a widespread hemosporidian blood parasite that infects a broad group of avian families, has been studied in corvids (family: Corvidae) for over a century. Current taxonomic classification indicates that Leucocytozoon sakharoffi infects crows and related Corvus spp., while Leucocytozoon berestneffi infects magpies (Pica spp.) and blue jays (Cyanocitta sp.). This intrafamily host specificity was based on the experimental transmissibility of the parasites, as well as slight differences in their morphology and life cycle development. Genetic sequence data from Leucocytozoon spp. infecting corvids is scarce, and until the present study, sequence data has not been analyzed to confirm the current taxonomic distinctions. Here, we predict the phylogenetic relationships of Leucocytozoon cytochrome b lineages recovered from infected American Crows (Corvus brachyrhynchos), yellow-billed magpies (Pica nuttalli), and Steller's jays (Cyanocitta stelleri) to explore the host specificity pattern of L. sakharoffi and L. berestneffi. Phylogenetic reconstruction revealed a single large clade containing nearly every lineage recovered from the three host species, while showing no evidence of the expected distinction between L. sakharoffi and L. berestneffi. In addition, five of the detected lineages were recovered from both crows and magpies. This absence of the previously described host specificity in corvid Leucocytozoon spp. suggests that L. sakharoffi and L. berestneffi be reexamined from a taxonomic perspective.

Speciation in Western Scrub-Jays, Haldane's rule, and genetic clines in secondary contact.

BACKGROUND: Haldane's Rule, the tendency for the heterogametic sex to show reduced fertility in hybrid crosses, can obscure the signal of gene flow in mtDNA between species where females are heterogametic. Therefore, it is important when studying speciation and species limits in female-heterogametic species like birds to assess the signature of gene flow in the nuclear genome as well. We studied introgression of microsatellites and mtDNA across a secondary contact zone between coastal and interior lineages of Western Scrub-Jays (Aphelocoma californica) to test for a signature of Haldane's Rule: a narrower cline of introgression in mtDNA compared to nuclear markers. RESULTS: Our initial phylogeographic analysis revealed that there is only one major area of contact between coastal and interior lineages and identified five genetic clusters with strong spatial structuring: Pacific Slope, Interior US, Edwards Plateau (Texas), Northern Mexico, and Southern Mexico. Consistent with predictions from Haldane's Rule, mtDNA showed a narrower cline than nuclear markers across a transect through the hybrid zone. This result is not being driven by female-biased dispersal because neutral diffusion analysis, which included estimates of sex-specific dispersal rates, also showed less diffusion of mtDNA. Lineage-specific plumage traits were associated with nuclear genetic profiles for individuals in the hybrid zone, indicating that these differences are under genetic control. CONCLUSIONS: This study adds to a growing list of studies that support predictions of Haldane's Rule using cline analysis of multiple loci of differing inheritance modes, although alternate hypotheses like selection on different mtDNA types cannot be ruled out. That Haldane's Rule appears to be operating in this system suggests a measure of reproductive isolation between the Pacific Slope and interior lineages. Based on a variety of evidence from the phenotype, ecology, and genetics, we recommend elevating three lineages to species level: A. californica (Pacific Slope); A. woodhouseii (Interior US plus Edwards Plateau plus Northern Mexico); A. sumichrasti (Southern Mexico). The distinctive Edwards Plateau population in Texas, which was monophyletic in mtDNA except for one individual, should be studied in greater detail given habitat threat.

Do hormones influence women's sex? Sexual activity over the menstrual cycle.

INTRODUCTION: In mammals, the effects of ovarian steroids influence sexual behavior. In humans, there are a few studies that take into account if ovulation occurs. AIM: The study aims to investigate if a woman's sexuality changes during the week and over the menstrual cycle, and if so, in what way. METHODS: This is a prospective cohort study; 1,957 heterosexual women were involved over the period January 2004-December 2011. Two subgroups were taken into consideration, women having a partner and singles. MAIN OUTCOME MEASURE: Sexual interview and the Female Sexual Function Index and Female Sexual Distress Scale questionnaires were used to exclude women with sexual dysfunction. Women with ovulation confirmed by sonography were enrolled. Women were given diary cards on which to report their daily sexual activity. Serum concentrations of estradiol, progesterone, total testosterone, sex hormone binding globulin, and free androgen index were measured during the follicular, periovular, and luteal phase of the menstrual cycle. RESULTS: One thousand one hundred eighty women (age range 18-40 years) were included in the analyses. Of them, 925 had a heterosexual relationship and 255 were single. Women with a partner had more sexual activity during the weekend, while the singles had a constant sexual activity over the week. The sexual activity of singles was higher during the ovulatory phase and lower during menses than that of the women with a partner. A linear correlation between sexual activity and androgenic hormonal profile during the menstrual cycle in women with and without a partner was observed. CONCLUSIONS: Ovarian steroids modulate a woman's sexual activity. This aspect was more evident in singles than in women having a partner, in which a variety of nonhormonal factors can have a role.

Quality of sexual life of women using the contraceptive vaginal ring in extended cycles: preliminary report.

OBJECTIVE: To evaluate the quality of the sexual life of healthy women who are using a contraceptive vaginal ring (CVR) in extended cycles. METHODS: Fifty-two women (18 to 32 years old) seeking hormonal contraception were enrolled in this prospective study. Women were to use a CVR releasing daily 15 µg of ethinylestradiol (EE) and 120 µg of etonogestrel (ENG) for 63 days, followed by a four-day hormone-free interval, for two such extended cycles. At baseline and at the first (day 63-73) and second (day 126-134) follow-ups the Female Sexual Function Index (FSFI) and the Short Form-36 (SF-36) questionnaires were administered to investigate, respectively, sexual behaviour and the quality of life (QoL). The Female Sexual Distress Scale (FSDS) was used to verify whether sexual dysfunction caused significant personal distress to the woman. RESULTS: The FSFI and FSDS scores obtained at the first and second follow-up appointments detected an improvement with respect to the baseline score (p < 0.05). QoL measures of body pain, general health and emotional role improved at the first follow-up visit (p < 0.05); at the second one, all variables showed improvement (p < 0.05). CONCLUSION: According to these preliminary data the CVR in extended cycles could improve the sexual function and the QoL of women.