A nuclear genome assembly of an extinct flightless bird, the little bush moa.

We present a draft genome of the little bush moa (Anomalopteryx didiformis)-one of approximately nine species of extinct flightless birds from Aotearoa, New Zealand-using ancient DNA recovered from a fossil bone from the South Island. We recover a complete mitochondrial genome at 249.9× depth of coverage and almost 900 megabases of a male moa nuclear genome at ~4 to 5× coverage, with sequence contiguity sufficient to identify more than 85% of avian universal single-copy orthologs. We describe a diverse landscape of transposable elements and satellite repeats, estimate a long-term effective population size of ~240,000, identify a diverse suite of olfactory receptor genes and an opsin repertoire with sensitivity in the ultraviolet range, show that the wingless moa phenotype is likely not attributable to gene loss or pseudogenization, and identify potential function-altering coding sequence variants in moa that could be synthesized for future functional assays. This genomic resource should support further studies of avian evolution and morphological divergence.

Routes to diagnosis for hepatocellular carcinoma patients: predictors and associations with treatment and mortality.

BACKGROUND: Hepatocellular carcinoma (HCC) incidence has increased rapidly, and prognosis remains poor. We aimed to explore predictors of routes to diagnosis (RtD), and outcomes, in HCC cases. METHODS: HCC cases diagnosed 2006-2017 were identified from the National Cancer Registration Dataset and linked to Hospital Episode Statistics and the RtD metric. Multivariable logistic regression was used to explore associations between RtD, diagnosis year, 365-day mortality and receipt of potentially curative treatment. RESULTS: 23,555 HCC cases were identified; 36.1% via emergency presentation (EP), 30.2% GP referral (GP), 17.1% outpatient referral, 11.0% two-week wait and 4.6% other/unknown routes. Odds of 365-day mortality was >70% lower via GP or OP routes than EP, and odds of curative treatment 3-4 times higher. Further adjustment for cancer/cirrhosis stage attenuated the associations with curative treatment. People who were older, female, had alcohol-related liver disease, or were more deprived, were at increased risk of an EP. Over time, diagnoses via EP decreased, and via GP increased. CONCLUSIONS: HCC RtD is an important predictor of outcomes. Continuing to reduce EP and increase GP and OP presentations, for example by identifying and regularly monitoring patients at higher risk of HCC, may improve stage at diagnosis and survival.

Systems biology as a framework to understand the physiological and endocrine bases of behavior and its evolution-From concepts to a case study in birds.

Organismal behavior, with its tremendous complexity and diversity, is generated by numerous physiological systems acting in coordination. Understanding how these systems evolve to support differences in behavior within and among species is a longstanding goal in biology that has captured the imagination of researchers who work on a multitude of taxa, including humans. Of particular importance are the physiological determinants of behavioral evolution, which are sometimes overlooked because we lack a robust conceptual framework to study mechanisms underlying adaptation and diversification of behavior. Here, we discuss a framework for such an analysis that applies a "systems view" to our understanding of behavioral control. This approach involves linking separate models that consider behavior and physiology as their own networks into a singular vertically integrated behavioral control system. In doing so, hormones commonly stand out as the links, or edges, among nodes within this system. To ground our discussion, we focus on studies of manakins (Pipridae), a family of Neotropical birds. These species have numerous physiological and endocrine specializations that support their elaborate reproductive displays. As a result, manakins provide a useful example to help imagine and visualize the way systems concepts can inform our appreciation of behavioral evolution. In particular, manakins help clarify how connectedness among physiological systems-which is maintained through endocrine signaling-potentiate and/or constrain the evolution of complex behavior to yield behavioral differences across taxa. Ultimately, we hope this review will continue to stimulate thought, discussion, and the emergence of research focused on integrated phenotypes in behavioral ecology and endocrinology.

Comparative phylogeography reveals widespread cryptic diversity driven by ecology in Panamanian birds.

Widespread species often harbor unrecognized genetic diversity, and investigating the factors associated with such cryptic variation can help us better understand the forces driving diversification. Here, we identify potential cryptic species based on a comprehensive dataset of COI mitochondrial DNA barcodes from 2,333 individual Panamanian birds across 429 species, representing 391 (59%) of the 659 resident landbird species of the country, as well as opportunistically sampled waterbirds. We complement this dataset with additional publicly available mitochondrial loci, such as ND2 and cytochrome b, obtained from whole mitochondrial genomes from 20 taxa. Using barcode identification numbers (BINs), we find putative cryptic species in 19% of landbird species, highlighting hidden diversity in the relatively well-described avifauna of Panama. Whereas some of these mitochondrial divergence events corresponded with recognized geographic features that likely isolated populations, such as the Cordillera Central highlands, the majority (74%) of lowland splits were between eastern and western populations. The timing of these splits are not temporally coincident across taxa, suggesting that historical events, such as the formation of the Isthmus of Panama and Pleistocene climatic cycles, were not the primary drivers of cryptic diversification. Rather, we observed that forest species, understory species, insectivores, and strongly territorial species-all traits associated with lower dispersal ability-were all more likely to have multiple BINs in Panama, suggesting strong ecological associations with cryptic divergence. Additionally, hand-wing index, a proxy for dispersal capability, was significantly lower in species with multiple BINs, indicating that dispersal ability plays an important role in generating diversity in Neotropical birds. Together, these results underscore the need for evolutionary studies of tropical bird communities to consider ecological factors along with geographic explanations, and that even in areas with well-known avifauna, avian diversity may be substantially underestimated.

Especies extendidas frecuentemente tiene diversidad genética no reconocida, y investigando los factores asociados con esta variación críptica puede ayudarnos a entender las fuerzas que impulsan la diversificación. Aquí, identificamos especies crípticas potenciales basadas en un conjunto de datos de códigos de barras de ADN mitocondrial de 2,333 individuos de aves de Panama en 429 especies, representando 391 (59%) de las 659 especies de aves terrestres residentes del país, además de algunas aves acuáticas muestreada de manera oportunista. Adicionalmente, complementamos estos datos con secuencias mitocondriales disponibles públicamente de otros loci, tal como ND2 o citocroma b, obtenidos de los genomas mitocondriales completos de 20 taxones. Utilizando los números de identificación de código de barras (en ingles: BINs), un sistema taxonómico numérico que proporcina una estimación imparcial de la diversidad potencial a nivel de especie, encontramos especies crípticas putativas en 19% de las especies de aves terrestres, lo que destaca la diversidad oculta en la avifauna bien descrita de Panamá. Aunque algunos de estos eventos de divergencia conciden con características geográficas que probablemente aislaron las poblaciones, la mayoría (74%) de la divergencia en las tierras bajas se encuentra entre las poblaciones orientales y occidentales. El tiempo de esta divergencia no coincidió entre los taxones, sugiriendo que eventos históricos tales como la formación del Istmo de Panamá y los ciclos climáticos del pleistoceno, no fueron los principales impulsores de la especiación. En cambio, observamos asociaciones fuertes entre las características ecológicas y la divergencia mitocondriale: las especies del bosque, sotobosque, con una dieta insectívora, y con territorialidad fuerte mostraton múltiple BINs probables. Adicionalmente, el índice mano-ala, que está asociado a la capacidad de dispersión, fue significativamente menor en las especies con BINs multiples, sugiriendo que la capacidad de dispersión tiene un rol importamente en la generación de la diversidad de las aves neotropicales. Estos resultos demonstran la necesidad de que estudios evolutivos de las comunidades de aves tropicales consideren los factores ecológicos en conjunto con las explicaciones geográficos.

Spatiotemporal Variation in Hatching Success and Nestling Sex Ratios Track Rapid Movement of a Songbird Hybrid Zone.

AbstractHybridization often occurs at the parapatric range interface between closely related species, but fitness outcomes vary: hybrid offspring exhibit diverse rates of viability and reproduction compared with their parental species. The mobile hybrid zone between two chickadee congeners (Poecile atricapillus × Poecile carolinensis) has been well studied behaviorally and genetically, but the viability of hybrids and the underlying mechanisms contributing to hybrid fitness have remained unclear. To better characterize the fitness costs of hybridization in this system, we analyzed 21 years of data from four sites, including more than 1,400 breeding attempts by the two species, to show that rates of hatching success changed substantially as the zone of hybridization moved across the landscape. Admixture-associated declines in hatching success correlated with reduced proportions of heterogametic (female) offspring, as predicted by Haldane's rule. Our data support an underlying mechanism implicating genetic admixture of the homogametic (male) parent as the primary determinant of offspring sex ratio, via incompatibilities on the hemizygous Z chromosome. Our long-term study is the first to directly measure changes in fitness costs as a vertebrate hybrid zone moves, and it shows that changes in these costs are a way to track the distribution of a hybrid zone across the landscape.

Layered evolution of gene expression in "superfast" muscles for courtship.

Identifying the molecular process of complex trait evolution is a core goal of biology. However, pinpointing the specific context and timing of trait-associated changes within the molecular evolutionary history of an organism remains an elusive goal. We study this topic by exploring the molecular basis of elaborate courtship evolution, which represents an extraordinary example of trait innovation. Within the behaviorally diverse radiation of Central and South American manakin birds, species from two separate lineages beat their wings together using specialized "superfast" muscles to generate a "snap" that helps attract mates. Here, we develop an empirical approach to analyze phylogenetic lineage-specific shifts in gene expression in the key snap-performing muscle and then integrate these findings with comparative transcriptomic sequence analysis. We find that rapid wing displays are associated with changes to a wide range of molecular processes that underlie extreme muscle performance, including changes to calcium trafficking, myocyte homeostasis and metabolism, and hormone action. We furthermore show that these changes occur gradually in a layered manner across the species history, wherein which ancestral genetic changes to many of these molecular systems are built upon by later species-specific shifts that likely finalized the process of display performance adaptation. Our study demonstrates the potential for combining phylogenetic modeling of tissue-specific gene expression shifts with phylogenetic analysis of lineage-specific sequence changes to reveal holistic evolutionary histories of complex traits.

Regional variations in hepatocellular carcinoma incidence, routes to diagnosis, treatment and survival in England.

BACKGROUND: Hepatocellular carcinoma (HCC) incidence, management and survival across England were examined to determine if geographical inequalities exist. METHOD: 15,468 HCC cases diagnosed 2010-2016 were included. Age-standardised incidence rates, net survival and proportions receiving potentially curative treatment and presenting through each route to diagnosis adjusted for age at diagnosis, sex and area-based deprivation quintile, were calculated overall and by Cancer Alliance. RESULTS: HCC incidence rates increased in men from 6.2 per 100,000 in 2010 to 8.8 in 2016, and in women from 1.5 to 2.2. The highest incidence rates, found in parts of the North of England and London, were nearly double the lowest. The adjusted proportion presenting as an emergency ranged 27-41% across Cancer Alliances. Odds increased with increasing deprivation quintile and age. Only one in five patients received potentially curative treatment (range 15-28%) and odds decreased with increasing deprivation and age. One-year survival in 2013-2016 ranged 38-53%. CONCLUSION: This population-based, nationwide analysis demonstrates clear differences in HCC incidence, management and survival across England. It highlights socioeconomic-associated variation and the need for improvement in early diagnosis and curative treatment of HCC. This research should assist policymakers, service providers and clinicians to identify regions where additional training, services and resources would be best directed.

Highly Contiguous Genomes Improve the Understanding of Avian Olfactory Receptor Repertoires.

Third-generation (long-read-based) sequencing technologies are reshaping our understanding of genome structure and function. One of the most persistent challenges in genome biology has been confidently reconstructing radiations of complex gene families. Olfactory receptors (ORs) represent just such a gene family with upward of thousands of receptors in some mammalian taxa. Whereas in birds olfaction was historically an overlooked sensory modality, new studies have revealed an important role for smell. Chromosome-level assemblies for birds allow a new opportunity to characterize patterns of OR diversity among major bird lineages. Previous studies of short-read-based (second-generation) genome assemblies have associated OR gene family size with avian ecology, but such conclusions could be premature especially when new assembly methods reshape our understanding of avian OR evolution. Here we provide a fundamental characterization of OR repertoires in five recent genome assemblies, including the most recent assembly of golden-collared manakin (Manacus vitellinus). We find that short read-based assemblies systematically undercount the avian-specific gamma-c OR subfamily, a subfamily that comprises over 65% of avian OR diversity. Therefore, in contrast to previous studies, we find a high diversity of gamma-c ORs across the avian tree of life. Building on these findings, ongoing sequencing efforts and improved genome assemblies will clarify the relationship between OR diversity and avian ecology.

Primary liver cancer in the UK: Incidence, incidence-based mortality, and survival by subtype, sex, and nation.

BACKGROUND & AIMS: The incidence of primary liver cancer (PLC) is increasing in Western Europe. To understand trends over time and the current burden in the UK, a detailed analysis of the epidemiology of PLC and its subtypes was conducted. METHODS: Data on PLCs diagnosed during 1997-2017 were obtained from population-based, nationwide registries in the UK. European age-standardised incidence (ASR) and incidence-based mortality rates (ASMR) per 100,000 person-years were calculated overall and by sex and UK-nation. Annual percentage change in rates was estimated using Joinpoint regression. One-, 2-, and 5-year age-standardised net survival was estimated. RESULTS: A total of 82,024 PLCs were diagnosed. Both hepatocellular carcinoma (HCC) incidence and mortality rates trebled (ASR 1.8-5.5 per 100,000, ASMR 1.3-4.0). The rate of increase appeared to plateau around 2014/2015. Scottish men consistently had the highest HCC incidence rates. PLC survival increased, driven by a substantial increase in the proportion that are HCC (as prognosis is better than other PLCs) and in HCC survival (change in 1-year survival 24-47%). Intrahepatic cholangiocarcinoma was the most common PLC in women and 1-year survival improved from 22.6% to 30.5%. CONCLUSIONS: PLC incidence has been increasing rapidly but, as most risk factors are modifiable, it is largely a preventable cancer. This rate of increase has slowed in recent years, possibly attributable to effective treatment for hepatitis C. As other risk factors such as obesity and diabetes remain prevalent in the UK, it is unlikely the considerable burden of this disease will abate. While improvements in survival have been made, over half of patients are not alive after 1 year, therefore further progress in prevention, early detection, and treatment innovation are needed. LAY SUMMARY: Many more people are getting liver cancer, particularly the subtype hepatocellular carcinoma, than 20 years ago. Men in Scotland are most likely to get liver cancer and to die from it. Survival after liver cancer diagnosis is getting longer but still less than half are alive after 1 year.

An Acoustic Password Enhances Auditory Learning in Juvenile Brood Parasitic Cowbirds.

How does a naive, young animal decide from which adults to learn behavior? Obligate brood parasitic birds, including brown-headed cowbirds (Molothrus ater), face a particular challenge in learning species-specific behaviors; they lay their eggs in the nest of another species, and juveniles are raised without exposure to adult conspecifics. Nevertheless, male cowbirds need to learn a conspecific song to attract appropriate mates, and female cowbirds need to learn to identify conspecific males for mating. Traditionally, it was thought that parasitic bird species rely purely on instinctual species recognition [1-4], but an alternative is that a species-specific trait serves as a "password" [5], a non-learned cue for naive animals that guides decisions regarding from whom to learn. Here, we tested the hypothesis that the adult "chatter call" enhances the learning of specific songs in juvenile cowbirds. We exposed acoustically naive juvenile male and female cowbirds to songs paired with chatter calls and found that the chatter call enhanced song production learning in males and induced a neurogenomic profile of song familiarity in females, even for heterospecific songs. Thus, a combination of experience-independent and -dependent mechanisms converges to explain how young cowbirds emerge from another species' nest yet learn behaviors from conspecifics. Identifying whether such password-based mechanisms relate to perceptual and behavioral learning in non-parasitic taxa will contribute to our general understanding of the development of social recognition systems.

Validation of an algorithm using inpatient electronic health records to determine the presence and severity of cirrhosis in patients with hepatocellular carcinoma in England: an observational study.

OBJECTIVES: Outcomes in hepatocellular carcinoma (HCC) are determined by both cancer characteristics and liver disease severity. This study aims to validate the use of inpatient electronic health records to determine liver disease severity from treatment and procedure codes. DESIGN: Retrospective observational study. SETTING: Two National Health Service (NHS) cancer centres in England. PARTICIPANTS: 339 patients with a new diagnosis of HCC between 2007 and 2016. MAIN OUTCOME: Using inpatient electronic health records, we have developed an optimised algorithm to identify cirrhosis and determine liver disease severity in a population with HCC. The diagnostic accuracy of the algorithm was optimised using clinical records from one NHS Trust and it was externally validated using anonymised data from another centre. RESULTS: The optimised algorithm has a positive predictive value (PPV) of 99% for identifying cirrhosis in the derivation cohort, with a sensitivity of 86% (95% CI 82% to 90%) and a specificity of 98% (95% CI 96% to 100%). The sensitivity for detecting advanced stage cirrhosis is 80% (95% CI 75% to 87%) and specificity is 98% (95% CI 96% to 100%), with a PPV of 89%. CONCLUSIONS: Our optimised algorithm, based on inpatient electronic health records, reliably identifies and stages cirrhosis in patients with HCC. This highlights the potential of routine health data in population studies to stratify patients with HCC according to liver disease severity.

The Glasgow Prognostic Score at the Time of Palliative Esophageal Stent Insertion is a Predictive Factor of 30-Day Mortality and Overall Survival.

BACKGROUND: Optimizing the timing of esophageal stent insertion is a challenge, partly due to difficulty predicting survival in advanced malignancy. The Glasgow prognostic score (GPS) is a validated tool for predicting survival in a number of cancers. GOALS: To assess the utility of the GPS in predicting 30-day mortality and overall survival postesophageal stent insertion. STUDY: Patients at a tertiary referral center who had received an esophageal stent for palliation of dysphagia were included if they had a measurement of albumin and C-reactive protein (CRP) in the week preceding the procedure (n=209). Patients with both an elevated CRP (>10 mg/L) and hypoalbuminemia (<35 g/L) were given a GPS score of 2 (GPS2). Patients with only one of these abnormalities were assigned as GPS1 and those with normal CRP and albumin were assigned as GPS0. Clinical and pathologic parameters were also collected to assess for potential confounding factors in the survival analysis. RESULTS: Increasing GPS was associated with 30-day mortality; for patients with GPS0, 30-day mortality was 5% (2/43), for GPS1 it was 23% (26/114), and for GPS2 it was 33% (17/52). The adjusted hazard ratio for overall poststent mortality was 1.6 (95% confidence interval, 1.1-2.4; P=0.02) for GPS1 and 2.4 (95% confidence interval, 1.5-3.8; P<0.001) for GPS2 patients compared with GPS0. CONCLUSIONS: GPS is an independent prognostic factor of 30-day mortality and overall survival after esophageal stent insertion. It is a potential adjunct to clinical assessment in identifying those patients at high-risk of short-term mortality poststent.

DAF-16/FOXO regulates homeostasis of essential sleep-like behavior during larval transitions in C. elegans.

Sleep homeostasis, which refers to the maintenance of sleep amount or depth following sleep deprivation, indicates that sleep and sleep-like states serve fundamental functions that cannot be bypassed [1]. Homeostasis of sleep-like behavior is observed during C. elegans lethargus, a 2-3 hr behavioral quiescent period that occurs during larval state transitions [2]. Here, we report a role for DAF-16/FOXO, a transcription factor that is active under conditions of stress [3], in the response to deprivation of lethargus quiescence. Forced locomotion during lethargus results in nuclear translocation of DAF-16. The formation of dauer larvae, a developmental state promoted by daf-16, is increased in response to quiescence deprivation. daf-16 mutants show an impaired homeostatic response to deprivation of lethargus quiescence and are hypersensitive to the lethal effects of forced locomotion during lethargus. DAF-16 expression in muscle cells, but not in neurons, is sufficient to restore a homeostatic response to deprivation of quiescence, pointing to a role for muscle in sleep homeostasis. These findings are relevant to clinical observations of altered metabolic signaling in response to sleep deprivation and suggest that these signaling pathways may act in nonneuronal tissue to regulate sleep behaviors.