Assembly of the largest squamate reference genome to date: The western fence lizard, Sceloporus occidentalis.

Spiny lizards (genus Sceloporus) have long served as important systems for studies of behavior, thermal physiology, dietary ecology, vector biology, speciation, and biogeography. The western fence lizard, Sceloporus occidentalis, is found across most of the major biogeographical regions in the western United States and northern Baja California, Mexico, inhabiting a wide range of habitats, from grassland to chaparral to open woodlands. As small ectotherms, Sceloporus lizards are particularly vulnerable to climate change, and S. occidentalis has also become an important system for studying the impacts of land use change and urbanization on small vertebrates. Here, we report a new reference genome assembly for S. occidentalis, as part of the California Conservation Genomics Project (CCGP). Consistent with the reference genomics strategy of the CCGP, we used Pacific Biosciences HiFi long reads and Hi-C chromatin-proximity sequencing technology to produce a de novo assembled genome. The assembly comprises a total of 608 scaffolds spanning 2,856 Mb, has a contig N50 of 18.9 Mb, a scaffold N50 of 98.4 Mb, and BUSCO completeness score of 98.1% based on the tetrapod gene set. This reference genome will be valuable for understanding ecological and evolutionary dynamics in S. occidentalis, the species status of the California endemic island fence lizard (S. becki), and the spectacular radiation of Sceloporus lizards.

Hybridization and Transgressive Evolution Generate Diversity in an Adaptive Radiation of Anolis Lizards.

Interspecific hybridization may act as a major force contributing to the evolution of biodiversity. Although generally thought to reduce or constrain divergence between 2 species, hybridization can, paradoxically, promote divergence by increasing genetic variation or providing novel combinations of alleles that selection can act upon to move lineages toward new adaptive peaks. Hybridization may, then, play a key role in adaptive radiation by allowing lineages to diversify into new ecological space. Here, we test for signatures of historical hybridization in the Anolis lizards of Puerto Rico and evaluate 2 hypotheses for the role of hybridization in facilitating adaptive radiation-the hybrid swarm origins hypothesis and the syngameon hypothesis. Using whole genome sequences from all 10 species of Puerto Rican anoles, we calculated D and f-statistics (from ABBA-BABA tests) to test for introgression across the radiation and employed multispecies network coalescent methods to reconstruct phylogenetic networks that allow for hybridization. We then analyzed morphological data for these species to test for patterns consistent with transgressive evolution, a phenomenon in which the trait of a hybrid lineage is found outside of the range of its 2 parents. Our analyses uncovered strong evidence for introgression at multiple stages of the radiation, including support for an ancient hybrid origin of a clade comprising half of the extant Puerto Rican anole species. Moreover, we detected significant signals of transgressive evolution for 2 ecologically important traits, head length and toepad width, the latter of which has been described as a key innovation in Anolis. [Adaptive radiation; introgression; multispecies network coalescent; phenotypic evolution; phylogenetic network; reticulation; syngameon; transgressive segregation.].

Parallel and non-parallel phenotypic responses to environmental variation across Lesser Antillean anoles.

Species whose ranges encompass substantial environmental variation should experience heterogeneous selection, potentially resulting in local adaptation. Repeated covariation between phenotype and environment across ecologically similar species inhabiting similar environments provides strong evidence for adaptation. Lesser Antillean anoles present an excellent system in which to study repeated local adaptation because most species are widespread generalists occurring throughout environmentally heterogenous island landscapes. We leveraged this natural replication to test the hypothesis that intraspecific variation in phenotype (coloration and morphology) is consistently associated with environment across 9 species of bimaculatus series anoles. We measured dorsal coloration from 173 individuals from 6 species and 16 morphological traits from 883 individuals from 9 species, spanning their island ranges. We identified striking, but incomplete, parallelism in dorsal coloration associated with annual precipitation in our study species. By contrast, we observed significant patterns of morphological isolation-by-environment in only 2 species and no signal of parallel morphological evolution. Collectively, our results reveal strong divergent natural selection by environment on dorsal coloration but not morphology.

Female dewlap ornaments are evolutionarily labile and associated with increased diversification rates in Anolis lizards.

The evolution of costly signalling traits has largely focused on male ornaments. However, our understanding of ornament evolution is necessarily incomplete without investigating the causes and consequences of variation in female ornamentation. Here, we study the Anolis lizard dewlap, a trait extensively studied as a male secondary sexual characteristic but present in females of several species. We characterized female dewlaps for 339 species to test hypotheses about their evolution. Our results did not support the hypothesis that female dewlaps are selected against throughout the anole phylogeny. Rather, we found that female dewlaps were evolutionary labile. We also did not find support for the adaptive hypothesis that interspecific competition drove the evolution of female dewlaps. However, we did find support for the pleiotropy hypothesis as species with larger females and reduced sexual size dimorphism were more likely to possess female dewlaps. Lastly, we found that female dewlap presence influenced diversification rates in anoles, but only secondarily to a hidden state. Our results demonstrate that female ornamentation is widespread in anoles and the traditional hypothesis of divergent selection between the sexes does not fully explain their evolution. Instead, female ornamentation is likely to be subject to complex adaptive and non-adaptive evolutionary forces.

A Pop from a Shock: A Case Report of an Unusual Cause of Achilles Tendon Rupture.

INTRODUCTION: Achilles tendon ruptures often occur during physical activity where the tendon is frequently stressed. Although rare, rupture can also result from electric shock. CASE REPORT: We present the case of a 63-year-old female who presented with pain in the lower leg after enduring an electric shock. She was diagnosed with a ruptured Achilles tendon based on physical exam and ultrasound. CONCLUSION: This case highlights an uncommon mechanism for a relatively common injury. Because Achilles tendon ruptures are frequently misdiagnosed, clinicians need to be aware of unusual causes and use tools at their disposal to ensure timely and accurate diagnosis.

A Culinary Misadventure: A Case Report of Shiitake Dermatitis.

Shiitake dermatitis is a rare cutaneous reaction that can occur after consumption of shiitake mushrooms. It is characterized by highly pruritic lesions with a distinct whip lash appearance. Management of this condition includes reassurance and providing symptomatic relief. Although most reported cases have occurred in Asia, this rash has made appearances in the Western world. Here, we report a case of a 23-year-old female in the United States who experienced this itchy ailment. A diagnosis was made based on the presence of the recognizable lesions and dietary history. She was discharged with advice to continue symptomatic care and given reassurance about her condition. Her symptoms resolved within a few weeks. As the use of shiitake mushrooms become more widespread, it is important for clinicians to be familiar with this rash and remember to take a detailed dietary history. Topics: Rash, dermatology, toxicology, shiitake mushrooms.

Varicella-Zoster as a Cause of Aseptic Meningitis in an Immunocompetent Young Patient With Skin Rash.

We present a case of aseptic meningitis due to Varicella-Zoster infection in an immunocompetent patient. Varicella-Zoster virus (VZV) causes chickenpox disease in children, teens, and young adults. Typically, it runs its course and stays dormant in nerve tissue, which can get reactivated in elderly, immunocompromised patients. Frequently, reactivation results in the painful dermatomal rash of herpes zoster, but in sporadic cases, it can cause meningitis or encephalitis in the immunocompromised population. Our case demonstrates a healthy immunocompetent adult male who presented with headache, fever, mild neck stiffness, and painless right-sided abdominal skin rash and was later diagnosed with VZV meningitis via polymerase chain reaction (PCR) of the cerebrospinal fluid (CSF). We are reporting this case due to its rarity, and the challenging nature of its diagnosis and treatment. In the hospital, he was treated with IV acyclovir for three days and discharged home on 14 days of oral valacyclovir. Our case demonstrates the importance of having a high degree of suspicion, even if the presentation is unexpected and atypical.

Genome-wide epigenetic isolation by environment in a widespread Anolis lizard.

Epigenetic changes can provide a pathway for organisms to respond to local environmental conditions by influencing gene expression. However, we still know little about the spatial distribution of epigenetic variation in natural systems, how it relates to the distribution of genetic variation and the environmental structure of the landscape, and the processes that generate and maintain it. Studies examining spatial patterns of genetic and epigenetic variation can provide valuable insights into how ecological and population processes contribute to epigenetic divergence across heterogeneous landscapes. Here, we perform a comparative analysis of spatial genetic and epigenetic variation based on 8,459 single nucleotide polymorphisms (SNPs) and 8,580 single methylation variants (SMVs) from eight populations of the Puerto Rican crested anole, Anolis cristatellus, an abundant lizard in the adaptive radiations of anoles on the Greater Antilles that occupies a diverse range of habitats. Using generalized dissimilarity modelling and multiple matrix regression, we found that genome-wide epigenetic differentiation is strongly correlated with environmental divergence, even after controlling for the underlying genetic structure. We also detected significant associations between key environmental variables and 96 SMVs, including 42 located in promoter regions or gene bodies. Our results suggest an environmental basis for population-level epigenetic differentiation in this system and contribute to better understanding how environmental gradients structure epigenetic variation in nature.

Close-kin mating, but not inbred parents, reduces hatching rates and offspring quality in a threatened tortoise.

Inbreeding depression, the reduction in fitness due to mating of related individuals, is of particular conservation concern in species with small, isolated populations. Although inbreeding depression is widespread in natural populations, long-lived species may be buffered from its effects during population declines due to long generation times and thus are less likely to have evolved mechanisms of inbreeding avoidance than species with shorter generation times. However, empirical evidence of the consequences of inbreeding in threatened, long-lived species is limited. In this study, we leverage a well-studied population of gopher tortoises, Gopherus polyphemus, to examine the role of inbreeding depression and the potential for behavioural inbreeding avoidance in a natural population of a long-lived species. We tested the hypothesis that increased parental inbreeding leads to reduced hatching rates and offspring quality. Additionally, we tested for evidence of inbreeding avoidance. We found that high parental relatedness results in offspring with lower quality and that high parental relatedness is correlated with reduced hatching success. However, we found that hatching success and offspring quality increase with maternal inbreeding, likely due to highly inbred females mating with more distantly related males. We did not find evidence for inbreeding avoidance in males and outbred females, suggesting sex-specific evolutionary trade-offs may have driven the evolution of mating behaviour. Our results demonstrate inbreeding depression in a long-lived species and that the evolution of inbreeding avoidance is shaped by multiple selective forces.

Phenotypic integration between claw and toepad traits promotes microhabitat specialization in the Anolis adaptive radiation.

The performance of an organism in its environment frequently depends more on its composite phenotype than on individual phenotypic traits. Thus, understanding environmental adaptation requires investigating patterns of covariation across functionally related traits. The replicated adaptive radiations of Greater Antillean Anolis lizards are characterized by ecological and morphological convergence, thus, providing an opportunity to examine the role of multiple phenotypes in microhabitat adaptation. Here, we examine integrated claw and toepad morphological evolution in relation to habitat partitioning across the adaptive radiations of Greater Antillean anoles. Based on analysis of 428 specimens from 57 species, we found that different aspects of claw morphology were associated with different perch dimensions, with claw height positively associated with perch diameter and claw curvature positively associated with perch height. Patterns of integration also varied across claw and toepad traits, likely driven by correlative selection for performance on smoother and rougher substrates. Finally, rates of evolution differed between claw and toepad traits, with claw length evolving faster than all other traits despite having no predicted functional importance. Our results highlight the multivariate nature of phenotypic adaptation and suggest that phenotypic integration across Greater Antillean anoles is driven by fine-scale correlative selection based on structural habitat specialization.

Sodium ion channel alkaloid resistance does not vary with toxicity in aposematic Dendrobates poison frogs: An examination of correlated trait evolution.

Spatial heterogeneity in the strength or agents of selection can lead to geographic variation in ecologically important phenotypes. Many dendrobatid frogs sequester alkaloid toxins from their diets and often exhibit fixed mutations at NaV1.4, a voltage-gated sodium ion channel associated with alkaloid toxin resistance. Yet previous studies have noted an absence of resistance mutations in individuals from several species known to sequester alkaloid toxins, suggesting possible intraspecific variation for alkaloid resistance in these species. Toxicity and alkaloid profiles vary substantially between populations in several poison frog species (genus Dendrobates) and are correlated with variation in a suite of related traits such as aposematic coloration. If resistance mutations are costly, due to alterations of channel gating properties, we expect that low toxicity populations will have reduced frequencies and potentially even the loss of resistance alleles. Here, we examine whether intraspecific variation in toxicity in three dendrobatid frogs is associated with intraspecific variation in alleles conferring toxin resistance. Specifically, we examine two species that display marked variation in toxicity throughout their native ranges (Dendrobates pumilio and D. granuliferus) and one species with reduced toxicity in its introduced range (D. auratus). However, we find no evidence for population-level variation in alkaloid resistance at NaV1.4. In fact, contrary to previous studies, we found that alkaloid resistance alleles were not absent in any populations of these species. All three species exhibit fixed alkaloid resistance mutations throughout their ranges, suggesting that these mutations are maintained even when alkaloid sequestration is substantially reduced.

Marital Status and Outcomes in Patients With Cardiovascular Disease.

BACKGROUND: Being unmarried is associated with decreased survival in the general population. Whether married, divorced, separated, widowed, or never-married status affects outcomes in patients with cardiovascular disease has not been well characterized. METHODS AND RESULTS: A prospective cohort (inception period 2003-2015) of 6051 patients (mean age 63 years, 64% male, 23% black) undergoing cardiac catheterization for suspected or confirmed coronary artery disease was followed for a median of 3.7 years (interquartile range: 1.7-6.7 years). Marital status was stratified as married (n=4088) versus unmarried (n=1963), which included those who were never married (n=451), divorced or separated (n=842), or widowed (n=670). The relationship between marital status and primary outcome of cardiovascular death and myocardial infarction was examined using Cox regression models adjusted for clinical characteristics. There were 1085 (18%) deaths from all causes, 688 (11%) cardiovascular-related deaths, and 272 (4.5%) incident myocardial infarction events. Compared with married participants, being unmarried was associated with higher risk of all-cause mortality (hazard ratio [HR]: 1.24; 95% confidence interval [CI], 1.06-1.47), cardiovascular death (HR: 1.45; 95% CI, 1.18-1.78), and cardiovascular death or myocardial infarction (HR: 1.52; 95% CI, 1.27-1.83). Compared with married participants, the increase in cardiovascular death or myocardial infarction was similar for the participants who were divorced or separated (HR: 1.41; 95% CI, 1.10-1.81), widowed (HR: 1.71; 95% CI, 1.32-2.20), or never married (HR: 1.40; 95% CI, 0.97-2.03). The findings persisted after adjustment for medications and other socioeconomic factors. CONCLUSIONS: Marital status is independently associated with cardiovascular outcomes in patients with or at high risk of cardiovascular disease, with higher mortality in the unmarried population. The mechanisms responsible for this increased risk require further study.

Assessment of Commonly Used Frailty Markers for High- and Extreme-Risk Patients Undergoing Transcatheter Aortic Valve Replacement.

BACKGROUND: The effect of frailty on outcomes after transcatheter aortic valve replacement (TAVR) remains incompletely understood. The objective of this study was to evaluate the performance of four commonly used frailty markers as predictors of early and late outcomes among patients undergoing TAVR. METHODS: A review was performed of 361 high- and extreme-risk patients undergoing TAVR from 2011 to 2015. Four frailty variables were assessed: serum albumin (g/dL), 5-m walk (seconds), grip strength (kg), and Katz index of independence in activities of daily living. Logistic regression was used to examine the association between the frailty indicators and 30-day composite of mortality, stroke, new heart block requiring permanent pacemaker, major or life-threatening bleeding, acute renal failure, major vascular complication, and 30-day readmission rate. Minimum distance to the perfect point (0, 1) was performed to delineate a cutoff point for each frailty indicator, and risk models were compared using receiver-operating characteristics curves. RESULTS: The composite of outcomes occurred in 28% of patients. Serum albumin, activities of daily living, and 5-m walk were independent predictors for 30-day composite outcomes, but only albumin was predictive of 30-day mortality. A new frailty model (four frailty indicators, age, and sex) to predict 30-day mortality was created and compared with The Society of Thoracic Surgeons predicted risk of mortality. Better discrimination was found with the new frailty model (area under the curve 0.74 versus 0.58). New individual frailty variable cutoff values were found to predict our composite of events. CONCLUSIONS: Among high- and extreme-risk patients undergoing TAVR, our new frailty model was more discriminative of 30-day mortality than The Society of Thoracic Surgeons predicted risk of mortality. New cutoff values for frailty indicators were identified and will require further validation.

A novel clinical decision support algorithm for constructing complete medication histories.

A patient's complete medication history is a crucial element for physicians to develop a full understanding of the patient's medical conditions and treatment options. However, due to the fragmented nature of medical data, this process can be very time-consuming and often impossible for physicians to construct a complete medication history for complex patients. In this paper, we describe an accurate, computationally efficient and scalable algorithm to construct a medication history timeline. The algorithm is developed and validated based on 1 million random prescription records from a large national prescription data aggregator. Our evaluation shows that the algorithm can be scaled horizontally on-demand, making it suitable for future delivery in a cloud-computing environment. We also propose that this cloud-based medication history computation algorithm could be integrated into Electronic Medical Records, enabling informed clinical decision-making at the point of care.

Depression and chest pain in patients with coronary artery disease.

BACKGROUND: Depression is common in patients with coronary artery disease (CAD) and is associated with more frequent chest pain. It is however unclear whether this is due to differences in underlying CAD severity. We sought to determine [1] whether depressive symptoms are associated with chest pain independently of CAD severity, [2] whether improvement in depressive symptoms over time is associated with improvement in chest pain and [3] whether the impact of revascularization on chest pain differs between patients with and without depression. METHODS AND RESULTS: 5158 patients (mean age 63±12years, 65% male, 20% African American) undergoing cardiac catheterization completed the Seattle Angina Questionnaire (SAQ) and Patient Health Questionnaire-8 (PHQ-8) to assess angina severity and screen for depression, respectively, both at baseline and between 6 and 24months of follow-up. We found significant correlations between PHQ-8 scores and angina frequency (SAQ-AF, r=-0.28), physical limitation (SAQ-PL, r=-0.32) and disease perception (SAQ-DS r=-0.37, all P<0.001), which remained significant after adjustment for clinical characteristics, CAD severity, and anti-depressant use. Improvement in depressive symptoms at follow-up was associated with improvement in angina subscales (SAQ-AF ß 1.34, P<0.001), SAQ-PL ß 1.85, P<0.001), and SAQ-DS (ß 2.12, P<0.001), independently of CAD severity or revascularization. Patients with depression who underwent revascularization had less improvement in chest pain frequency than those without depressive symptoms. CONCLUSIONS: Depression is associated with angina, independently of CAD severity. Patients with depression may not derive as adequate symptomatic benefit from revascularization as those without. Whether treatment of underlying depression improves chest pain needs to be further studied.

Common methods for fecal sample storage in field studies yield consistent signatures of individual identity in microbiome sequencing data.

Field studies of wild vertebrates are frequently associated with extensive collections of banked fecal samples-unique resources for understanding ecological, behavioral, and phylogenetic effects on the gut microbiome. However, we do not understand whether sample storage methods confound the ability to investigate interindividual variation in gut microbiome profiles. Here, we extend previous work on storage methods for gut microbiome samples by comparing immediate freezing, the gold standard of preservation, to three methods commonly used in vertebrate field studies: lyophilization, storage in ethanol, and storage in RNAlater. We found that the signature of individual identity consistently outweighed storage effects: alpha diversity and beta diversity measures were significantly correlated across methods, and while samples often clustered by donor, they never clustered by storage method. Provided that all analyzed samples are stored the same way, banked fecal samples therefore appear highly suitable for investigating variation in gut microbiota. Our results open the door to a much-expanded perspective on variation in the gut microbiome across species and ecological contexts.

An Observational Study to Evaluate the Usability and Intent to Adopt an Artificial Intelligence-Powered Medication Reconciliation Tool.

BACKGROUND: Medication reconciliation (the process of creating an accurate list of all medications a patient is taking) is a widely practiced procedure to reduce medication errors. It is mandated by the Joint Commission and reimbursed by Medicare. Yet, in practice, medication reconciliation is often not effective owing to knowledge gaps in the team. A promising approach to improve medication reconciliation is to incorporate artificial intelligence (AI) decision support tools into the process to engage patients and bridge the knowledge gap. OBJECTIVE: The aim of this study was to improve the accuracy and efficiency of medication reconciliation by engaging the patient, the nurse, and the physician as a team via an iPad tool. With assistance from the AI agent, the patient will review his or her own medication list from the electronic medical record (EMR) and annotate changes, before reviewing together with the physician and making decisions on the shared iPad screen. METHODS: In this study, we developed iPad-based software tools, with AI decision support, to engage patients to "self-service" medication reconciliation and then share the annotated reconciled list with the physician. To evaluate the software tool's user interface and workflow, a small number of patients (10) in a primary care clinic were recruited, and they were observed through the whole process during a pilot study. The patients are surveyed for the tool's usability afterward. RESULTS: All patients were able to complete the medication reconciliation process correctly. Every patient found at least one error or other issues with their EMR medication lists. All of them reported that the tool was easy to use, and 8 of 10 patients reported that they will use the tool in the future. However, few patients interacted with the learning modules in the tool. The physician and nurses reported the tool to be easy-to-use, easy to integrate into existing workflow, and potentially time-saving. CONCLUSIONS: We have developed a promising tool for a new approach to medication reconciliation. It has the potential to create more accurate medication lists faster, while better informing the patients about their medications and reducing burden on clinicians.

Efficient Genome-Wide Sequencing and Low-Coverage Pedigree Analysis from Noninvasively Collected Samples.

Research on the genetics of natural populations was revolutionized in the 1990s by methods for genotyping noninvasively collected samples. However, these methods have remained largely unchanged for the past 20 years and lag far behind the genomics era. To close this gap, here we report an optimized laboratory protocol for genome-wide capture of endogenous DNA from noninvasively collected samples, coupled with a novel computational approach to reconstruct pedigree links from the resulting low-coverage data. We validated both methods using fecal samples from 62 wild baboons, including 48 from an independently constructed extended pedigree. We enriched fecal-derived DNA samples up to 40-fold for endogenous baboon DNA and reconstructed near-perfect pedigree relationships even with extremely low-coverage sequencing. We anticipate that these methods will be broadly applicable to the many research systems for which only noninvasive samples are available. The lab protocol and software ("WHODAD") are freely available at www.tung-lab.org/protocols-and-software.html and www.xzlab.org/software.html, respectively.

Influence of Ambient Illumination on the Use of Olfactory and Visual Signals by a Nocturnal Hawkmoth During Close-Range Foraging.

As a goal-directed behavior, foraging for nectar functions on the basis of a sequence of innate stereotyped movements mainly regulated by sensory input. The operation of this inherited program is shaped by selective pressures acting on its efficiency, which is largely dependent upon the way the system handles sensory information. Flowers offer a wealth of signals, from odors acting as distant attractants, to colors eliciting approximation and feeding responses, to textures guiding feeding responses toward a reservoir of nectar. Thus, animals use different signals in the regulation of particular motor outputs. Nevertheless, the use of these sensory signals can be user-specific (e.g. species, motivation, experience, learning) as well as context-dependent (e.g. spatiotemporal patterns of stimulation, availability of signals, multimodal integration). The crepuscular/nocturnal hawkmoths Manduca sexta experience a wide range of illuminations during their foraging activity, which raises the question of how these environmental changes might affect the use of two important floral signals, odor and visual display. In a flight cage, we explored the use of these signals under different illuminances. Under conditions of starlight and crescent moonlight, moths showed very low levels of responsiveness to unscented feeders (artificial flowers). However, responsiveness was recovered either by increasing illumination, or by offering olfactory signals. Additionally, we recorded a bias toward white over blue feeders under dim conditions, which disappeared with increasing illumination. We discuss how this kind of experimental manipulation may provide insights to the study of how innate behavioral programs, and their underlying neural substrates, overcome selective forces imposed by the uncertainty of natural, ever-changing environments.