Widespread horse-based mobility arose around 2200 BCE in Eurasia.

Horses revolutionized human history with fast mobility1. However, the timeline between their domestication and their widespread integration as a means of transport remains contentious2-4. Here we assemble a collection of 475 ancient horse genomes to assess the period when these animals were first reshaped by human agency in Eurasia. We find that reproductive control of the modern domestic lineage emerged around 2200 BCE, through close-kin mating and shortened generation times. Reproductive control emerged following a severe domestication bottleneck starting no earlier than approximately 2700 BCE, and coincided with a sudden expansion across Eurasia that ultimately resulted in the replacement of nearly every local horse lineage. This expansion marked the rise of widespread horse-based mobility in human history, which refutes the commonly held narrative of large horse herds accompanying the massive migration of steppe peoples across Europe around 3000 BCE and earlier3,5. Finally, we detect significantly shortened generation times at Botai around 3500 BCE, a settlement from central Asia associated with corrals and a subsistence economy centred on horses6,7. This supports local horse husbandry before the rise of modern domestic bloodlines.

Genomic imputation of ancient Asian populations contrasts local adaptation in pre- and post-agricultural Japan.

Early modern humans lived as hunter-gatherers for millennia before agriculture, yet the genetic adaptations of these populations remain a mystery. Here, we investigate selection in the ancient hunter-gatherer-fisher Jomon and contrast pre- and post-agricultural adaptation in the Japanese archipelago. Building on the successful validation of imputation with ancient Asian genomes, we identify selection signatures in the Jomon, particularly robust signals from KITLG variants, which may have influenced dark pigmentation evolution. The Jomon lacks well-known adaptive variants (EDAR, ADH1B, and ALDH2), marking their emergence after the advent of farming in the archipelago. Notably, the EDAR and ADH1B variants were prevalent in the archipelago 1,300 years ago, whereas the ALDH2 variant could have emerged later due to its absence in other ancient genomes. Overall, our study underpins local adaptation unique to the Jomon population, which in turn sheds light on post-farming selection that continues to shape contemporary Asian populations.

Ancient mitogenomes from Pre-Pottery Neolithic Central Anatolia and the effects of a Late Neolithic bottleneck in sheep (Ovis aries).

Occupied between ~10,300 and 9300 years ago, the Pre-Pottery Neolithic site of Asikli Höyük in Central Anatolia went through early phases of sheep domestication. Analysis of 629 mitochondrial genomes from this and numerous sites in Anatolia, southwest Asia, Europe, and Africa produced a phylogenetic tree with excessive coalescences (nodes) around the Neolithic, a potential signature of a domestication bottleneck. This is consistent with archeological evidence of sheep management at Asikli Höyük which transitioned from residential stabling to open pasturing over a millennium of site occupation. However, unexpectedly, we detected high genetic diversity throughout Asikli Höyük's occupation rather than a bottleneck. Instead, we detected a tenfold demographic bottleneck later in the Neolithic, which caused the fixation of mitochondrial haplogroup B in southwestern Anatolia. The mitochondrial genetic makeup that emerged was carried from the core region of early Neolithic sheep management into Europe and dominates the matrilineal diversity of both its ancient and the billion-strong modern sheep populations.

Five-Year Outcomes from a Prospective Study on the Safety and Efficacy of Phasix-ST Mesh Use at the Hiatus During Paraesophageal Hernia Repair.

INTRODUCTION: Laparoscopic paraesophageal hernia (PEH) repair has a high hernia recurrence rate. The aim of this study was to assess the 5-year hernia recurrence rate after PEH repair using a combination of bioresorbable mesh and advanced surgical techniques to address tension as needed in a prospective group of patients. METHODS: In 2016 a prospective database was established for 50 patients undergoing primary, elective PEH repair with a new bioresorbable mesh (Phasix-ST). Intra-operatively, tension was addressed with Collis gastroplasty and / or diaphragm relaxing incisions as needed. All 50 patients from the initial study were tracked and asked to return for objective follow-up. Recurrence was considered present for any hernia > 2 cm in size. RESULTS: Objective follow-up was obtained in 27 of the original 50 patients (54%) at a median of 5.25 years after their PEH repair. Prior to the 5-year follow-up, 5 patients had a known recurrent hernia. Objective evaluation at 5 years identified an additional 3 recurrences, for a total recurrence rate of 25% (8/32 patients). The hernia recurrence rate in patients with a Collis gastroplasty was significantly lower compared to those without a Collis (7% vs 54%, p=0.008). Two patients underwent re-operation for hernia recurrence. No patient had a mesh infection or mesh erosion. CONCLUSION: The combination of Phasix-ST mesh and tension reducing techniques during PEH repair led to a 25% hernia recurrence rate at 5 years. The addition of a Collis gastroplasty led to significantly fewer hernia recurrences and is indicative of the potential for esophageal shortening in many patients with a PEH. The long-term safety and efficacy of Phasix-ST mesh in combination with surgical technique for PEH repair is confirmed.

Ancient genomes illuminate Eastern Arabian population history and adaptation against malaria.

The harsh climate of Arabia has posed challenges in generating ancient DNA from the region, hindering the direct examination of ancient genomes for understanding the demographic processes that shaped Arabian populations. In this study, we report whole-genome sequence data obtained from four Tylos-period individuals from Bahrain. Their genetic ancestry can be modeled as a mixture of sources from ancient Anatolia, Levant, and Iran/Caucasus, with variation between individuals suggesting population heterogeneity in Bahrain before the onset of Islam. We identify the G6PD Mediterranean mutation associated with malaria resistance in three out of four ancient Bahraini samples and estimate that it rose in frequency in Eastern Arabia from 5 to 6 kya onward, around the time agriculture appeared in the region. Our study characterizes the genetic composition of ancient Arabians, shedding light on the population history of Bahrain and demonstrating the feasibility of studies of ancient DNA in the region.

Sidedness in Unilateral Orofacial Clefts: A Systematic Scoping Review.

OBJECTIVE: An overview of the literature relating to the sidedness of unilateral cleft lip with or without cleft palate to map current knowledge on the cause and impact of directional asymmetry. DESIGN: Scoping review with a systematic search of Medline and Embase from inception to May 2023. PATIENTS, PARTICIPANTS: Humans born with a left or right unilateral cleft lip with or without a cleft palate. MAIN OUTCOME MEASURES: Cleft sidedness as a co-occurrence, an outcome or an exposure. RESULTS: Forty studies were eligible for inclusion and confirmed the predilection for the occurrence of left sided cleft lips; 12 studies reported cleft sidedness co-occurring with another phenotype, 11 studies report sidedness as an outcome and 17 studies as an exposure. Phenotypes which were reported to co-occur with either left or right sided clefts included congenital dental anomalies, handedness and additional congenital anomalies. Variables investigated as a potential cause of left or right sided clefts as an outcome included chromosomal anomalies, genetic variants and environmental factors. Outcomes investigated in relation to cleft sidedness as an exposure included facial anatomical features, facial growth, educational attainment, functional and psychological characteristics. More studies showed worse outcomes in right sided clefts versus left sided clefts than vice versa, although studies were inconsistent, and a quality assessment was not performed. CONCLUSIONS: The field of cleft sidedness research is expanding and there are promising early findings to differentiate cause and outcome by sidedness of the cleft.

Missed Opportunities: the Timing and Frequency of Screening Colonoscopy in Patients That Develop Esophageal Adenocarcinoma.

INTRODUCTION: Screening colonoscopy (SC) is widely accepted and has been shown to decrease the rate of colorectal cancer death. Guidelines and acceptance of screening for Barrett's esophagus (BE) are less established despite the fact that esophageal adenocarcinoma (EA) remains the fastest increasing cancer in the USA. The aim of this study was to assess the timing and frequency of SC in patients ultimately found to have EA and to evaluate the presence of symptoms and risk factors that might have prompted an esophagogastroduodenoscopy (EGD) and potentially earlier diagnosis of the EA. METHODS: A retrospective chart review was performed to identify all patients who were referred to a single center with esophageal cancer between July 2016 and November 2022. Patients with any histology other than adenocarcinoma were excluded. RESULTS: There were 221 patients referred with EA. Of these, a SC had been done prior to the diagnosis of EA in 108 patients (49%): 96 men and 12 women. A total of 203 SC had been done (range 1-7 per patient), and 47% of patients had more than 1 SC. The median interval from the last SC to the diagnosis of EA was 2.9 years. At the time of SC, gastroesophageal reflux disease (GERD) symptoms or chronic acid suppression medication use was reported by 81% of patients, and 80% had an American Society of Gastrointestinal Endoscopy (ASGE) indication for a screening EGD. Only 19 patients (18%) that had a SC had an EGD at any time prior to the diagnosis of EA, and in these patients, 74% had erosive esophagitis or BE. The EA in most patients was stage III or IV and associated with lymph node metastases. CONCLUSIONS: Nearly one-half of patients ultimately diagnosed with EA had one or more SCs, and most of these patients had GERD symptoms, were using acid suppression medications or had an ASGE indication for a screening EGD. Despite this, only 18% had an EGD prior to the EA diagnosis. The addition of an EGD at the time of SC in these patients may have allowed the detection of BE or EA at an early, endoscopically curable stage and represents a missed opportunity to intervene in the natural history of this disease.

Genomic insights into a tripartite ancestry in the Southern Ryukyu Islands.

A tripartite structure for the genetic origin of Japanese populations states that present-day populations are descended from three main ancestors: (1) the indigenous Jomon hunter-gatherers; (2) a Northeast Asian component that arrived during the agrarian Yayoi period; and (3) a major influx of East Asian ancestry in the imperial Kofun period. However, the genetic heterogeneity observed in different regions of the Japanese archipelago highlights the need to assess the applicability and suitability of this model. Here, we analyse historic genomes from the southern Ryukyu Islands, which have unique cultural and historical backgrounds compared with other parts of Japan. Our analysis supports the tripartite structure as the best fit in this region, with significantly higher estimated proportions of Jomon ancestry than mainland Japanese. Unlike the main islands, where each continental ancestor was directly brought by immigrants from the continent, those who already possessed the tripartite ancestor migrated to the southern Ryukyu Islands and admixed with the prehistoric people around the eleventh century AD, coinciding with the emergence of the Gusuku period. These results reaffirm the tripartite model in the southernmost extremes of the Japanese archipelago and show variability in how the structure emerged in diverse geographic regions.

Antiviral Evaluation of Dispirotripiperazines against Hepatitis B Virus.

Hepatitis B virus (HBV) is a hepatotropic DNA virus that replicates by reverse transcription. It chronically infects >296 million people worldwide, including ∼850,000 in the USA, and kills 820,000 annually worldwide. Current nucleos(t)ide analogue (NA) or pegylated interferon α therapies do not eradicate the virus and would benefit from a complementary antiviral drug. We performed a preliminary screen of 28 dispirotripiperazines against HBV, identifying 9 hits with EC50 of 0.7-25 µM. Compound 11826096 displays the most potent activity and represents a promising lead for future optimization. While the mechanism of action is unknown, preliminary assays limit possible targets to activities involved in RNA accumulation, translation, capsid assembly, and/or capsid stability. In addition, we built machine learning models to determine if they were able to predict the activity of this series of compounds. The novelty of these molecules indicated they were outside of the applicability domain of these models.

The Implications of Laterality in Unilateral Cleft Lip Reconstruction: A Global Survey of Cleft Surgeons.

OBJECTIVE: To explore the impact of directional laterality in complete Unilateral Cleft Lip (UCL) amongst the global cleft surgeon community. DESIGN: Cross-sectional survey study. SETTING: Global distribution of online survey distributed in English and Spanish. PARTICIPANTS: Cleft surgeons from around the world. MAIN OUTCOME MEASURES: Survey participant perception of the impact of laterality on: (1) cleft presentation (2) surgical challenge and (3) surgical outcomes. RESULTS: Responses were received from 453 cleft surgeons located in 54 countries around the world. 221 (49%) had previously considered differences in patients presenting with a left- versus right-sided UCL. 95 (21%) considered right-sided clefts more difficult to reconstruct, 37 (8%) reported left-sided clefts to be more difficult and 321 (71%) reported no difference in difficulty between the cleft sides. Higher volume cleft surgeons, characterised by those reporting cleft as their principal area of practice and performing >20 cleft operations per year, were more likely to have both previously considered differences in laterality in cleft and to report right-sided unilateral cleft lip to be more difficult to primarily reconstruct. 395 (87%) did not consider surgical outcomes to be influenced by cleft laterality. CONCLUSIONS: This survey reports perceptions on cleft laterality from a large body of global surgeons and suggests a trend for increased difficulty in right-sided compared to left-sided cleft lip reconstruction, where such laterality-associated difficulty is perceived.

Diaphragmatic relaxing incisions for complex hiatal reconstruction: longer-term follow-up confirms safety, efficacy and rare complications.

BACKGROUND: Tension is an important factor in hernia repairs. Relaxing incisions to reduce tension are common with ventral hernia repairs, and techniques for relaxing incisions also exist for the hiatus. The aim of this study was to update our original experience with a diaphragm relaxing incision (DRI) in a larger group of patients with longer follow-up. METHODS: A retrospective chart review was performed to identify all patients who had a DRI between August 2016 and September 2021 during hiatal hernia repair. All DRI defects were repaired with permanent mesh remote from the esophagus. Objective follow-up was with chest x-ray, upper GI series (UGI) or both. RESULTS: Seventy-three patients had a total of 79 DRI (right in 63, left in 4, and bilateral in 6 patients), during a primary (n = 52) or redo (n = 21) hiatal hernia repair. Concomitant Collis gastroplasty was used in 38 patients (52%). A single intra-operative complication occurred where the right crus tore during a right DRI. At a median of 15 months, 78% of patients had objective follow-up. There was one hernia through a repaired right DRI (1.2%). No patient had evidence of diaphragm paralysis and there were no mesh infections. The 1-year hernia recurrence rate in these patients was 3.9%. CONCLUSIONS: A DRI can be done safely with minimal risk of intra- or post-operative complications. There was a low rate of herniation through the defect when repaired with permanent mesh. No patient developed a mesh infection despite concomitant Collis gastroplasty in 52% of patients, and there was no evidence of diaphragm paralysis on imaging studies. Further, the low rate of hiatal hernia recurrence suggests efficacy of a DRI to reduce crural closure tension. These excellent outcomes should encourage use of a DRI in patients with a difficult hiatus during hernia repair.

Lesion-level correspondence and longitudinal properties of paramagnetic rim and slowly expanding lesions in multiple sclerosis.

BACKGROUND: Paramagnetic rim lesions (PRLs) and slowly expanding lesions (SELs) have been posited as markers of chronic active lesions (CALs). OBJECTIVE: To assess the lesion-level concordance of PRLs and SELs in MS and to characterize changes in brain tissue integrity in CALs over time. METHODS: MRIs were analyzed from a substudy of AFFINITY [NCT03222973], a phase 2 trial of opicinumab in relapsing MS. Assessments included (1) identification of SELs based on longitudinal MRIs over 72 weeks, and identification of PRLs on susceptibility-weighted imaging (SWI) filtered phase images at week 72; (2) evaluation of subject-level correlation of SEL and PRL counts, volumes, and degree of lesion-level overlap between SELs and PRLs; and (3) characterization of tissue integrity over time in overlapping and non-overlapping SELs and PRLs. RESULTS: In 41 subjects, 119 chronic PRLs and 267 SELs were detected. Of 119 (39.5%) chronic PRLs, 47 co-localized with a SEL; 46/267 (17.2%) SELs co-localized with a PRL. PRLs co-localized with SELs showed expansion and worsening microstructural damage over time. SELs with and without co-localization with PRLs showed ongoing tissue damage. CONCLUSIONS: Chronic MS lesions identified as both PRL and SEL were associated with the most severe accumulation of tissue damage. TRIAL REGISTRATION: AFFINITY [NCT03222973].

Protocol and statistical analysis plan for the Antibiotic Choice On ReNal outcomes (ACORN) randomised clinical trial.

INTRODUCTION: Antibiotics are time-critical in the management of sepsis. When infectious organisms are unknown, patients are treated with empiric antibiotics to include coverage for gram-negative organisms, such as antipseudomonal cephalosporins and penicillins. However, in observational studies, some antipseudomonal cephalosporins (eg, cefepime) are associated with neurologic dysfunction while the most common antipseudomonal penicillin (piperacillin-tazobactam) is associated with acute kidney injury (AKI). No randomised control trials have compared these regimens. This manuscript describes the protocol and analysis plan for a trial designed to compare the effects of antipseudomonal cephalosporins and antipseudomonal penicillins among acutely ill patients receiving empiric antibiotics. METHODS AND ANALYSIS: The Antibiotic Choice On ReNal outcomes trial is a prospective, single-centre, non-blinded randomised trial being conducted at Vanderbilt University Medical Center. The trial will enrol 2500 acutely ill adults receiving gram-negative coverage for treatment of infection. Eligible patients are randomised 1:1 to receive cefepime or piperacillin-tazobactam on first order entry of a broad-spectrum antibiotic covering gram-negative organisms. The primary outcome is the highest stage of AKI and death occurring between enrolment and 14 days after enrolment. This will be compared between patients randomised to cefepime and randomised to piperacillin-tazobactam using an unadjusted proportional odds regression model. The secondary outcomes are major adverse kidney events through day 14 and number of days alive and free of delirium and coma in 14 days after enrolment. Enrolment began on 10 November 2021 and is expected to be completed in December 2022. ETHICS AND DISSEMINATION: The trial was approved by the Vanderbilt University Medical Center institutional review board (IRB#210591) with a waiver of informed consent. Results will be submitted to a peer-reviewed journal and presented at scientific conferences. TRIAL REGISTRATION NUMBER: NCT05094154.

DirEct versus VIdeo LaryngosCopE (DEVICE): protocol and statistical analysis plan for a randomised clinical trial in critically ill adults undergoing emergency tracheal intubation.

INTRODUCTION: Among critically ill patients undergoing orotracheal intubation in the emergency department (ED) or intensive care unit (ICU), failure to visualise the vocal cords and intubate the trachea on the first attempt is associated with an increased risk of complications. Two types of laryngoscopes are commonly available: direct laryngoscopes and video laryngoscopes. For critically ill adults undergoing emergency tracheal intubation, it remains uncertain whether the use of a video laryngoscope increases the incidence of successful intubation on the first attempt compared with the use of a direct laryngoscope. METHODS AND ANALYSIS: The DirEct versus VIdeo LaryngosCopE (DEVICE) trial is a prospective, multicentre, non-blinded, randomised trial being conducted in 7 EDs and 10 ICUs in the USA. The trial plans to enrol up to 2000 critically ill adults undergoing orotracheal intubation with a laryngoscope. Eligible patients are randomised 1:1 to the use of a video laryngoscope or a direct laryngoscope for the first intubation attempt. The primary outcome is successful intubation on the first attempt. The secondary outcome is the incidence of severe complications between induction and 2 min after intubation, defined as the occurrence of one or more of the following: severe hypoxaemia (lowest oxygen saturation <80%); severe hypotension (systolic blood pressure <65 mm Hg or new or increased vasopressor administration); cardiac arrest or death. Enrolment began on 19 March 2022 and is expected to be completed in 2023. ETHICS AND DISSEMINATION: The trial protocol was approved with waiver of informed consent by the single institutional review board at Vanderbilt University Medical Center and the Human Research Protection Office of the Department of Defense. The results will be presented at scientific conferences and submitted for publication in a peer-reviewed journal. TRIAL REGISTRATION NUMBER: ClinicalTrials.gov Registry (NCT05239195).

Millennium-old pathogenic Mendelian mutation discovery for multiple osteochondromas from a Gaelic Medieval graveyard.

Only a limited number of genetic diseases are diagnosable in archaeological individuals and none have had causal mutations identified in genome-wide screens. Two individuals from the Gaelic Irish Medieval burial ground of Ballyhanna, Co. Donegal, showed evidence of bone tumours consistent with the autosomal dominant condition multiple osteochondromas. Genome sequencing of the earlier individual uncovered a missense mutation in the second exon of EXT1, a specific lesion that has been identified in several modern patients. The later individual lacked this but displayed a novel frameshift mutation leading to a premature stop codon and loss of function in the same gene. These molecular confirmations of a paleopathological diagnosis within a single rural ancient context are surprisingly disjunct, given the observation of clusters of this disease in modern isolated populations and a de novo mutation rate of only 10%.

Abnormal response after multiple rapid swallow provocation is not predictive of post-operative dysphagia following a tailored fundoplication approach.

INTRODUCTION: The aim was to evaluate the clinical significance of multiple rapid swallows (MRS) during high-resolution manometry (HRM) prior to fundoplication. Despite pre-operative HRM, up to 38% of patients report post-fundoplication dysphagia. Suggestion that MRS improves prediction of dysphagia after fundoplication has not been investigated when using a tailored approach. We hypothesize response to MRS is predictive of dysphagia after tailored fundoplication. METHODS: A retrospective cohort study was performed on patients undergoing HRM with MRS provocation 5/2019-7/2021 at a single institution. Patients who underwent subsequent index laparoscopic fundoplication, without peptic stricture or achalasia, were included. After performing standard 10-swallow HRM, MRS provocation was performed. Patient-reported dysphagia frequency scores were collected at initial consultation and post-operative follow-up. At least weekly symptoms were considered clinically significant. Normal MRS response was defined as adequate deglutitive inhibition and MRS contractile response. Fundoplications were tailored based on standard HRM values. RESULTS: HRM was performed in 1201 patients, 220 met inclusion criteria. Clinically significant pre-operative dysphagia was reported by 85 (38.6%). Patients undergoing partial fundoplication (n = 123, 55.9%) had lower mean distal contractile integer, distal esophageal contraction amplitude, and percent peristalsis (p < 0.005). Post-operatively, 120 (54.5%) were without dysphagia, 59 (26.8%) had improved dysphagia, 26 (11.8%) had unchanged dysphagia, and 15 (6.8%) reported new dysphagia. There was no statistical difference in early or late dysphagia outcome between tailored fundoplication groups (p = 0.69). On univariate and multivariate analysis, neither MRS response, nor standard HRM metrics were significantly associated with post-operative dysphagia. Younger age (OR 0.96, 95% CI 0.94-0.986, p = 0.042) and the presence of pre-operative dysphagia (OR 2.54, 95% CI 1.17-5.65, p = 0.015) were significant predictors of post-operative dysphagia. CONCLUSION: The risk of clinically significant dysphagia post-fundoplication is low when using a tailored approach based on standard HRM metrics. Additional data provided by MRS does not add to surgical decision-making using the investigated approach.

Design, synthesis, and biological evaluation of novel sulfamoylbenzamide derivatives as HBV capsid assembly modulators.

Capsid assembly modulators (CAMs) represent a novel class of antiviral agents targeting hepatitis B virus (HBV) capsid to disrupt the assembly process. NVR 3-778 is the first CAM to demonstrate antiviral activity in patients infected with HBV. However, the relatively low aqueous solubility and moderate activity in the human body halted further development of NVR 3-778. To improve the anti-HBV activity and the drug-like properties of NVR 3-778, we designed and synthesized a series of NVR 3-778 derivatives. Notably, phenylboronic acid-bearing compound 7b (EC50 = 0.83 ± 0.33 µM, CC50 = 19.4 ± 5.0 µM) displayed comparable anti-HBV activity to NVR 3-778 (EC50 = 0.73 ± 0.20 µM, CC50 = 23.4 ± 7.0 µM). Besides, 7b showed improved water solubility (328.8 µg/mL, pH 7) compared to NVR 3-778 (35.8 µg/mL, pH 7). Size exclusion chromatography (SEC) and quantification of encapsidated viral RNA were used to demonstrate that 7b behaves as a class II CAM similar to NVR 3-778. Moreover, molecular dynamics (MD) simulations were conducted to rationalize the structure-activity relationships (SARs) of these novel derivatives and to understand their key interactions with the binding pocket, which provide useful indications for guiding the further rational design of more effective anti-HBV drugs.

A novel lineage of the Capra genus discovered in the Taurus Mountains of Turkey using ancient genomics.

Direkli Cave, located in the Taurus Mountains of southern Turkey, was occupied by Late Epipaleolithic hunters-gatherers for the seasonal hunting and processing of game including large numbers of wild goats. We report genomic data from new and published Capra specimens from Direkli Cave and, supplemented with historic genomes from multiple Capra species, find a novel lineage best represented by a ~14,000 year old 2.59 X genome sequenced from specimen Direkli4. This newly discovered Capra lineage is a sister clade to the Caucasian tur species (Capra cylindricornis and Capra caucasica), both now limited to the Caucasus region. We identify genomic regions introgressed in domestic goats with high affinity to Direkli4, and find that West Eurasian domestic goats in the past, but not those today, appear enriched for Direkli4-specific alleles at a genome-wide level. This forgotten 'Taurasian tur' likely survived Late Pleistocene climatic change in a Taurus Mountain refuge and its genomic fate is unknown.

The genomic history and global expansion of domestic donkeys.

Donkeys transformed human history as essential beasts of burden for long-distance movement, especially across semi-arid and upland environments. They remain insufficiently studied despite globally expanding and providing key support to low- to middle-income communities. To elucidate their domestication history, we constructed a comprehensive genome panel of 207 modern and 31 ancient donkeys, as well as 15 wild equids. We found a strong phylogeographic structure in modern donkeys that supports a single domestication in Africa ~5000 BCE, followed by further expansions in this continent and Eurasia and ultimately returning to Africa. We uncover a previously unknown genetic lineage in the Levant ~200 BCE, which contributed increasing ancestry toward Asia. Donkey management involved inbreeding and the production of giant bloodlines at a time when mules were essential to the Roman economy and military.

Predicted structure of the hepatitis B virus polymerase reveals an ancient conserved protein fold.

Hepatitis B virus (HBV) chronically infects >250 million people. It replicates by a unique protein-primed reverse transcription mechanism, and the primary anti-HBV drugs are nucleos(t)ide analogs targeting the viral polymerase (P). P has four domains compared to only two in most reverse transcriptases: the terminal protein (TP) that primes DNA synthesis, a spacer, the reverse transcriptase (RT), and the ribonuclease H (RNase H). Despite being a major drug target and catalyzing a reverse transcription pathway very different from the retroviruses, HBV P has resisted structural analysis for decades. Here, we exploited computational advances to model P. The TP wrapped around the RT domain rather than forming the anticipated globular domain, with the priming tyrosine poised over the RT active site. The orientation of the RT and RNase H domains resembled that of the retroviral enzymes despite the lack of sequences analogous to the retroviral linker region. The model was validated by mapping residues with known surface exposures, docking nucleic acids, mechanistically interpreting mutations with strong phenotypes, and docking inhibitors into the RT and RNase H active sites. The HBV P fold, including the orientation of the TP domain, was conserved among hepadnaviruses infecting rodent to fish hosts and a nackednavirus, but not in other non-retroviral RTs. Therefore, this protein fold has persisted since the hepadnaviruses diverged from nackednaviruses >400 million years ago. This model will advance mechanistic analyses into the poorly understood enzymology of HBV reverse transcription and will enable drug development against non-active site targets for the first time.