Large-scale genomic analysis reveals the genetic cost of chicken domestication.

BACKGROUND: Species domestication is generally characterized by the exploitation of high-impact mutations through processes that involve complex shifting demographics of domesticated species. These include not only inbreeding and artificial selection that may lead to the emergence of evolutionary bottlenecks, but also post-divergence gene flow and introgression. Although domestication potentially affects the occurrence of both desired and undesired mutations, the way wild relatives of domesticated species evolve and how expensive the genetic cost underlying domestication is remain poorly understood. Here, we investigated the demographic history and genetic load of chicken domestication. RESULTS: We analyzed a dataset comprising over 800 whole genomes from both indigenous chickens and wild jungle fowls. We show that despite having a higher genetic diversity than their wild counterparts (average π, 0.00326 vs. 0.00316), the red jungle fowls, the present-day domestic chickens experienced a dramatic population size decline during their early domestication. Our analyses suggest that the concomitant bottleneck induced 2.95% more deleterious mutations across chicken genomes compared with red jungle fowls, supporting the "cost of domestication" hypothesis. Particularly, we find that 62.4% of deleterious SNPs in domestic chickens are maintained in heterozygous states and masked as recessive alleles, challenging the power of modern breeding programs to effectively eliminate these genetic loads. Finally, we suggest that positive selection decreases the incidence but increases the frequency of deleterious SNPs in domestic chicken genomes. CONCLUSION: This study reveals a new landscape of demographic history and genomic changes associated with chicken domestication and provides insight into the evolutionary genomic profiles of domesticated animals managed under modern human selection.

Controlling the Nanoscale Rotational Behaviors of Nanoparticles on the Cell Membranes: A Computational Model.

Nanoparticles prefer to bind to a membrane with a surface coated by short or rigid ligands, as shown by computer simulations. To realize such a preferred configuration, the nanoparticle can spontaneously spin itself on the membrane surface, no matter what its initial orientation is.

[Metabolism Changes of Main Active Ingredients During Liquid Fermentation of Cordyceps militaris].

Objective: To study the accumulation and changes of main active ingredients during liquid fermentation of Cordyceps militaris. Methods: The militaris varity GIM5. 270 was selected to extended fermentation time to 20 days on the basic fermentation condition. Meanwhile, the accumulation and dynamic changes of biomass, polysaccharide, cordycepic acid, adenosine and cordycepin in the fermentation system were detected by the analytical method of contents per 24 hour. Results: The foundation culture medium composed of complex nitrogen sources could reach a higher biomass level than single nitrogen sources. In addition, with the development of time, the mycelial biomass increased, the contents of polysaccharide and cordycepic acid( D-mannitol) increased firstly and then decreased, the contents of adenosine decreased gradually and cordycepin( 3-deoxy adenosine) increased gradually. Conclusion: The whole system is observed autolyzed phenomenon caused by absorbing self-generated nutrients. In this study, the dynamic changes of the main active ingredients in the fermentation system are researched and the optimum collecting time is determined, which provides evidence for reaching a better yield of the active ingredients.

Effect of safety and security equipment on patient and visitor violence towards nurses in multiple public hospitals of China during the COVID-19 pandemic: a retrospective, difference-in-difference analysis.

OBJECTIVES: This study aimed to analyse whether safety and security equipment decreased patient and visitor violence (PVV) towards nurses in the COVID-19 period and quantify to what extent safety and security equipment affects PVV. DESIGN: Controlled before and after study and difference-in-difference (DID) analysis. SETTING: A large hospital medical group, consisting of three public tertiary teaching hospitals, namely, Xinjiekou Branch, Huilongguan Branch and Xinlongze Branch of Beijing Jishuitan Hospital, located in the west and north parts of Beijing, China. PARTICIPANTS: A panel of nine departments recruited using two-step sampling method, administered online surveys in 2021 and 2022. A total of 632 eligible nurses participated in the survey in 2021 and 725 eligible nurses in 2022. MEASURES: We assessed impacts of the safety and security equipment on the PVV. The policy had been enacted in June 2020, and the corresponding measures were established after mid-December 2020, and therefore, we use a DID design to evaluate changes in nurses' PVV incidence. Departments are classified as either department installed or non installed, and nurses are classified based on their department. RESULTS: Within the treatment group, the incidence of physical PVV significantly decreased from 13.8% in 2020 to 2.0% in 2021. In the control group, the incidence of physical PVV increased from 0.6% in 2020 to 2.7% in 2021. The application of the safety and security equipment decreased the incidence of physical PVV by 13.93% (95% CI: -23.52% to -4.34%). In contrast, no difference was observed between the treatment and control groups for the incidence of psychological PVV (6.23%, 95% CI: -11.56% to 24.02%) and overall PVV (0.88, 95% CI: -20.90% to 22.66%). CONCLUSION: The safety and security equipment reduced the incidence of physical PVV towards nurses. For hospital managers in public hospitals, longer-term strategies roadmap for PVV prevention measures are needed to create a more supportive work environment in employees.

Genome assembly of autotetraploid Actinidia arguta highlights adaptive evolution and enables dissection of important economic traits.

Actinidia arguta, the most widely distributed Actinidia species and the second cultivated species in the genus, can be distinguished from the currently cultivated Actinidia chinensis on the basis of its small and smooth fruit, rapid softening, and excellent cold tolerance. Adaptive evolution of tetraploid Actinidia species and the genetic basis of their important agronomic traits are still unclear. Here, we generated a chromosome-scale genome assembly of an autotetraploid male A. arguta accession. The genome assembly was 2.77 Gb in length with a contig N50 of 9.97 Mb and was anchored onto 116 pseudo-chromosomes. Resequencing and clustering of 101 geographically representative accessions showed that they could be divided into two geographic groups, Southern and Northern, which first diverged 12.9 million years ago. A. arguta underwent two prominent expansions and one demographic bottleneck from the mid-Pleistocene climate transition to the late Pleistocene. Population genomics studies using paleoclimate data enabled us to discern the evolution of the species' adaptation to different historical environments. Three genes (AaCEL1, AaPME1, and AaDOF1) related to flesh softening were identified by multi-omics analysis, and their ability to accelerate flesh softening was verified through transient expression assays. A set of genes that characteristically regulate sexual dimorphism located on the sex chromosome (Chr3) or autosomal chromosomes showed biased expression during stamen or carpel development. This chromosome-level assembly of the autotetraploid A. arguta genome and the genes related to important agronomic traits will facilitate future functional genomics research and improvement of A. arguta.

Effect of lipopolysaccharide mediating early- and late- activated THP-1 macrophages on ECV304 endothelial cell dysfunction: dysregulation of secretion of VEGF and proliferation and migration of ECV304.

OBJECTIVE: To investigate the different effects of lipopolysaccharide (LPS) mediating early and late activated THP-1 macrophages (Mφ) on ECV304 endothelial cell dysfunction: dysregulation of secretion of VEGF and proliferation, and migration of ECV304. METHODS: The inflammatory Mφ was divided into early phase (2 h) group and late phase (24 h) group according the different exposure time to LPS. Then the inflammatory Mφ and ECV304 were co-cultured via transwell chambers in both non-contacting and contacting systems. The levels of VEGF were determined by ELISA, and the proliferation index and apoptosis of ECV304 were analyzed by FACSCalibur. The migration of ECV304 was tested by modified Boyden chamber assay. RESULTS: The level of VEGF and the proliferation of ECV304 cell were increased more apparently in early-phase Mφ-treated group. But the proportion of early apoptotic and late apoptotic/necrotic cells in late-phase Mφ-treated group were higher than that of the former. Migration rate of ECV304 was enhanced in early-phase Mφ-treated group. All those effects were more significant in contacting system comparing with no-contacting system. CONCLUSION: Early-activated macrophages (mediated by LPS) could increase the secretion of VEGF and promote the proliferation and migration of ECV304; while the late-activated macrophages could promote/enhance the apoptosis of ECV304 more significant in contacting system when (it was) compared with no-contacting system.

Effects of Musca domestica cecropin on the adhesion and migration of human hepatocellular carcinoma BEL-7402 cells.

This study was designed to explore the effects of Musca domestica antimicrobial peptides cecropin on the adhesion and migration of human hepatocellular carcinoma BEL-7402 cells. The adhesive and migratory capacities were determined by adhesion assay and transwell assay, respectively. The changes in microvilli of tumor cells were determined by scanning electron microscopy (SEM). Western blotting and quantitative polymerase chain reaction (qPCR) were carried out to determine the expression levels of proteins related to adhesion and migration, such as matrix metalloproteinase-2 (MMP2), tissue inhibitors of metalloproteinase-2 (TIMP2), and epithelial cadherin (E-cadherin). We found that Musca domestica cecropin inhibited the adhesion and migration of BEL-7402 cells, which also displayed curling microvilli, increased ball structures on cell surface, gradually broken connections between tumor cells, and even disappeared microvilli on some cells. The expression of MMP2 was significantly reduced after cecropin treatment, while the levels of TIMP2 and E-cadherin were significantly increased. These results suggest that Musca domestica cecropin inhibits the adhesion and migration of human hepatocellular carcinoma BEL-7402 cells by destroying the microvilli of tumor cells and changing the expression of MMP2, TIMP2 and E-cadherin.

Expression of a novel dual-functional protein--the antimicrobial peptide LL-37 fused with human acidic fibroblast growth factor in Escherichia coli.

Human acidic fibroblast growth factor (haFGF) stimulates repair of delayed healing which still remains a tremendously world-wide issue. However, most of the patients with delayed healings have to face another creeping problem - microbial infection, which is one of the most frequent complications that still lead to wound healing failure. LL-37/hCAP-18 is the only cathelicidin-derived antimicrobial peptide found in human with a wide range of antimicrobial activities. In the present study, a novel hybrid protein combining LL-37 with haFGF was designed. The DNA sequence encoding recombination fusion protein LL-37-haFGF was subcloned into the pET-21b vector for protein expression in Escherichia coli strain BL21 (DE3). The recombinant protein was expressed as a His-tagged protein and purified using a combination of Ni affinity and CM-Sepharose chromatography at a purity of 95.43% as detected by RP-HPLC and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE). Antimicrobial activity assays showed that the purified LL-37-haFGF had improved antimicrobial activities in vitro compared with LL-37. Methylthiazoletetrazolium (MTT) assay showed that the purified LL-37-haFGF also had a distinct mitogenic activity in NIH 3T3 cells. These data suggests the recombinant protein LL-37-haFGF has pharmaceutical potential for applications in wound healing.

[Research advances on circumsporozoite protein of Plasmodium].

Circumsporozoite protein (CSP) is found in all the mature malaria parasites, which forms a dense coat on the sporozoite's surface. CSPs contain approximately 400 amino acids and are organized into three domains: an N-terminal domain containing a conserved pentapeptide called region I, a highly repetitive species-specific central domain, and a C-terminal domain containing another conserved sequence called region II. It has been reported that the CSP fulfills vital roles in invading to the mosquito's salivary glands, binding sporozoite to liver cells, and inactivating host cell protein synthesis machinery. Recently, researches pointed out that both of the vaccine and the targeted-drug-delivery-system based on CSP antigen reveal an immense prospect. This review presents a compilation of the protein at the molecular characterization, function and application level that have been described to date.

Development of a prediction model for enteral feeding intolerance in intensive care unit patients: A prospective cohort study.

BACKGROUND: Enteral nutrition (EN) is essential for critically ill patients. However, some patients will have enteral feeding intolerance (EFI) in the process of EN. AIM: To develop a clinical prediction model to predict the risk of EFI in patients receiving EN in the intensive care unit. METHODS: A prospective cohort study was performed. The enrolled patients' basic information, medical status, nutritional support, and gastrointestinal (GI) symptoms were recorded. The baseline data and influencing factors were compared. Logistic regression analysis was used to establish the model, and the bootstrap resampling method was used to conduct internal validation. RESULTS: The sample cohort included 203 patients, and 37.93% of the patients were diagnosed with EFI. After the final regression analysis, age, GI disease, early feeding, mechanical ventilation before EN started, and abnormal serum sodium were identified. In the internal validation, 500 bootstrap resample samples were performed, and the area under the curve was 0.70 (95%CI: 0.63-0.77). CONCLUSION: This clinical prediction model can be applied to predict the risk of EFI.

The Exploration of the Antibacterial Mechanism of FE(3+) against Bacteria.

This study demonstrated that the bacteria could adsorb Fe(3+) and reduce Fe(3+) to Fe(2+). Iron had significant bacteriostatic effects, which were directly proportional to the iron concentration and under the influence of pH and chelator. It presumed that the inhibition of Fe(3+) acts through the formation of hydroxyl free radicals.

[The target of Musca domestica cecropin on human hepatocellular carcinoma BEL-7402 cells].

Human hepatocellular carcinoma BEL-7402 cells were treated with 50 micromol/L Musca domestica cecropin for 12 h, and observed under scanning electron microscope. The effect of Musca domestica cecropin labeled with FITC (FITC-cecropin) on BEL-7402 cells was detected by laser scanning confocal microscopy. The scanning electron microscopy showed that most microvilli on the surface of BEL-7402 cells disappeared at 12 h after cecropin treatment. The laser scanning confocal microscopy revealed that most FITC-cecropin combined with BEL-7402 cell membrane, and partly in the cytoplasm.

Benefits of Early Ambulation in Elderly Patients Undergoing Lumbar Decompression and Fusion Surgery: A Prospective Cohort Study.

OBJECTIVE: To evaluate the effects of early ambulation on elderly patients' postoperative physical functional outcomes, complications, 90-day readmission rate, and the length of postoperative hospital stay. METHODS: This is a prospective cohort study conducted between June 2019 and December 2019. The study enrolled 86 elderly patients (39 males) with newly diagnosed lumbar degenerative disease undergoing single-segment decompression and fusion surgerywere enrolled. Of all 86 patients, 39 voluntarily joined the early ambulation group, and 47 joined the regular ambulation group. The early ambulation group included patients ambulated within 4 h postoperatively, whereas the regular ambulation group included patients who were ambulatory at a minimum of 24 h after surgery. Participants' baseline characteristics, surgical information, ambulation ability, degree of pain, functional scores, postoperative complications, 90-day readmission rate, and length of postoperative hospital stay were recorded. RESULTS: Participants' baseline demographic characteristics were balanced between the early ambulation group and the regular ambulation group. The operative time and blood loss were similar between groups. The time before the first-time ambulation was 4 ± 0.5 h in the early ambulation group and 28 ± 4.5 h in the regular ambulation group. Ambulating distance was significantly longer in the early ambulation group compared with the regular ambulation group on the 1st (63 ± 45 vs 23 ± 60 m), the 2nd (224 ± 100 vs 101 ± 130 m), and the 3rd (280 ± 102.5 vs 190 ± 170 m) ambulation days based on generalized estimating equation analyses. Generalized estimating equation analyses also demonstrated that the ambulating time was longer in the early ambulation group compared with the regular ambulation group on the 1st (10 ± 5 vs 10 ± 5 min), the 2nd (19 ± 7 vs 15 ± 5 min), and the 3rd (22 ± 16.5 vs 27 ± 12 min) ambulation days. Patients in the regular ambulation group experienced a higher degree of pain than the early ambulation group patients, with an odds ratio of 1.627 (P = 0.002). Short-term functional independence was superior in the early ambulation group, with a lower Roland-Morris disability questionnaire score (P = 0.008) and Oswestry disability index (P < 0.001). The incidences of postoperative urinary retention (early ambulation group: 7.7%, regular ambulation group: 25.5%, P = 0.030) and ileus (early ambulation group: 0%, regular ambulation group: 12.8%, P = 0.030) were significantly higher in the regular ambulation group. The prevalence of at least one complication rate was significantly lower in the early ambulation group than in the regular ambulation group (early ambulation group, 23.1%; regular ambulation group, 46.8%, P = 0.022). The duration of indwelling of the drainage catheter was shorter in the early ambulation group (early ambulation group, 68 ± 24 h; regular ambulation group, 78 ± 20 h, P = 0.001), and the length of the postoperative hospital stay was also shorter in the early ambulation group (early ambulation group, 4 ± 0 days; regular ambulation group: 5 ± 2 days, P < 0.001). However, there was no statistical difference in the 90-day readmission rate between groups. CONCLUSION: Early ambulation improved patients' postoperative functional status, decreased the incidence of complications, and shortened postoperative hospital stay in elderly patients undergoing lumbar decompression and fusion surgery.

[Concurrent Collection of Ammonia Gas and Aerosol Ammonium in Urban Beijing During National Celebration Days Utilizing an Acid-Coated Honeycomb Denuder in Combination with a Filter System].

Since 2013, the Chinese government implemented the Air Pollution Prevention and Control Action Plan. As a result, the atmospheric concentrations of sulfate reduced significantly, whereas the nitrate concentrations remain relatively high due to the excess of ammonia (NH3). To date, there is no official observation network monitoring NH3 concentrations in China. Previous studies have focused on NH3 or ammonium (NH4+) separately. These limitations hinder a complete understanding of their dynamic changes due to the rapid gas-to-particle conversion. In this study, the concentrations of NH3 and NH4+ were measured concurrently in urban Beijing during autumn 2019 utilizing an acid-coated denuder-filter combination with a time resolution from 2 h (PM2.5>35 µg·m-3) to 5 h (PM2.5<35 µg·m-3). The mean concentrations of NH3 and NH4+ during the study were (4.1±2.9)µg·m-3 and (1.7±1.4) µg·m-3, respectively. The temporal patterns of NH3 or NH4+ coincided with that of PM2.5, CO, and NO2 throughout the sampling period. The diurnal distributions of NH3 were bimodal, both on polluted (PM2.5>75 µg·m-3) and non-polluted (PM2.5<75 µg·m-3) days, peaking at 21:30-05:30 and 05:30-08:30, respectively. The NH3 concentrations on polluted days were relatively lower during 17:30-21:30, which may be related to higher wind speeds. In contrast to NH3, NH4+ had an obvious peak during 17:30-21:30 due to the formation of ammonium nitrate. The meteorological conditions favor the gas-to-particle conversion on polluted days, resulting in a lower NH3/NH4+ ratio of 0.8. However, this value may reach 2.8 on non-polluted days. The concentrations of NH3, CO, NO2, SO2, and PM2.5 in the emission control period showed a significant increase greater than or comparable to those in the non-control period by 54.2%, 40.4%, 33.3%, 0%, and 49.4%, respectively. This result shows that the stagnant conditions offset the benefit of emission control actions implemented during and before the National Celebration Day.

The high diversity of SARS-CoV-2-related coronaviruses in pangolins alerts potential ecological risks.

Understanding the zoonotic origin and evolution history of SARS-CoV-2 will provide critical insights for alerting and preventing future outbreaks. A significant gap remains for the possible role of pangolins as a reservoir of SARS-CoV-2 related coronaviruses (SC2r-CoVs). Here, we screened SC2r-CoVs in 172 samples from 163 pangolin individuals of four species, and detected positive signals in muscles of four Manis javanica and, for the first time, one M. pentadactyla. Phylogeographic analysis of pangolin mitochondrial DNA traced their origins from Southeast Asia. Using in-solution hybridization capture sequencing, we assembled a partial pangolin SC2r-CoV (pangolin-CoV) genome sequence of 22 895 bp (MP20) from the M. pentadactyla sample. Phylogenetic analyses revealed MP20 was very closely related to pangolin-CoVs that were identified in M. javanica seized by Guangxi Customs. A genetic contribution of bat coronavirus to pangolin-CoVs via recombination was indicated. Our analysis revealed that the genetic diversity of pangolin-CoVs is substantially higher than previously anticipated. Given the potential infectivity of pangolin-CoVs, the high genetic diversity of pangolin-CoVs alerts the ecological risk of zoonotic evolution and transmission of pathogenic SC2r-CoVs.

Expression of the antimicrobial peptide cecropin fused with human lysozyme in Escherichia coli.

Lysozyme is an abundant, cationic antimicrobial protein that plays an important role in host defense. It targets the beta (1-4) glycosidic bond between N-acetylglucosamine and N-acetylmuramic residues that make up peptidoglycan, making lysozyme highly active against Gram-positive bacteria. However, lysozyme alone is inactive against Gram-negative bacteria because it cannot reach the peptidoglycan layer. Cecropins are cationic molecules with a wide range of antimicrobial activities. The main target for these peptides is the cytoplasmic membrane. We resume that cecopin may disrupt the outer membrane, giving the enzyme access to the peptidoglycan in cell wall. So in the present study, novel hybrid protein combining Musca domestica cecropin (Mdc) with human lysozyme (Hly) was designed. The DNA sequence encoding recombination fusion protein Mdc-hly was cloned into the pET-32a vector for protein expression in Escherichia coli strain BL21 (DE3). The protein was expressed as a His-tagged fusion protein, and the Mdc-hly was released from the fusion by enterokinase cleavage and separated from the carrier thioredoxin. Antimicrobial activity assays showed that the recombinant fusion protein Mdc-hly has improved in vitro antimicrobial activity and action spectrum compared to Mdc and hly. Mdc-hly may have important potential application as a future safely administered human drug and food additive.

[Effect of er'zhi tiangui granule on metabonomics and level of Ca2+ in follicle fluid in patients after in vitro fertilization and embryo transfer].

OBJECTIVE: To explore the mechanism of action of Er'zhi Tiangui Granule (ETG) in improving quality of oocytes by observing metabonomics and level of calcium ion in follicle fluid, and to investigate the impacts of calcium ion, cholinesterase (ChE) and creatinine (CCr) levels in human follicle fluid on the quality of oocytes and outcome of pregnancy in patients after in vitro fertilization and embryo transfer (IVF-ET). METHODS: Fifty-seven patients after IVF-ET were randomly assigned to two groups: the trial group (27 patients) and the control group (30 patients), both were treated with conventional Western medical treatment, but ETG and Liuwei Dihuang Granule (LDG) was given respectively to the two groups additionally. Changes of Shen-asthenia syndrome, amount of oocyte obtained, fertilization rate, cleavage rate, high-quality embryo rate and pregnancy rate, levels of calcium ion, ChE and Cr in follicle fluid, and metabonomics in the two groups were observed and compared. RESULTS: After treatment, scores of Shen-asthenia syndrome 8.30 +/- 1.46, fertilization rate 0.82 +/- 0.09, cleavage rate 0.97 +/- 0.07 and high-quality embryos rate 0.51 +/- 0.18 in the trial group were all better than those in the control group (9.16 +/- 1.15, 0.74 +/- 0.18, 0.91 +/- 0.10, 0.41 +/- 0.09, respectively, P<0.05); metabonomics principal component analysis showed that in the trial group, the principal component in follicle fluid distributed mainly in the section I, and that in the control group distributed mainly in the section II, showing significant difference between the two groups; while in most pregnant patients, it distributed in the section I. The Ca2+ concentration in the trial group was significantly higher than that in the control group (P<0.05). Levels of ChE and Cr in the trial group were higher than those in the control group, but the difference between them was insignificant. CONCLUSION: ETG is better than LDG in regulating metabonomics, Ca2+ concentration, improving the quality of oocyte and embryo, and increasing pregnant rate in patients after IVF-ET.

[Source Apportionment of Atmospheric Ammonia: Sensitivity Test Based on Stable Isotope Analysis in R Language].

Ammonia (NH3) is an important precursor of fine particles and nitrogen deposition. It is critical to identify and quantify the sources of NH3 before the implementation of a mitigation strategy. Stable isotope analysis in R (SIAR) has potential with regard to the source apportionment of NH3, but its reliability is closely related to the signatures (δ15N-NH3) of emission sources. Based on SIAR, we found that the agricultural contribution varied significantly with mean δ15N-NH3 values of endmember input. In contrast, both the contributions of fossil fuel and NH3 slip showed low sensitivity against the change of endmember input. Moreover, the agricultural contribution changed by about 20% due to the variations in agricultural endmember mean values. Such a change is five times that due to the variations in endmember standard deviation values. Notably, regardless of the number of input sources tested, "non-agricultural source" was the dominant source of NH3 during hazy days in January 2013 in Beijing. Since various agricultural sources showed large variations in δ15N-NH3, future studies should focus on the endmember signatures of agricultural sources to further reduce the uncertainty in SIAR-based NH3 source apportionment.

863 genomes reveal the origin and domestication of chicken.

Despite the substantial role that chickens have played in human societies across the world, both the geographic and temporal origins of their domestication remain controversial. To address this issue, we analyzed 863 genomes from a worldwide sampling of chickens and representatives of all four species of wild jungle fowl and each of the five subspecies of red jungle fowl (RJF). Our study suggests that domestic chickens were initially derived from the RJF subspecies Gallus gallus spadiceus whose present-day distribution is predominantly in southwestern China, northern Thailand and Myanmar. Following their domestication, chickens were translocated across Southeast and South Asia where they interbred locally with both RJF subspecies and other jungle fowl species. In addition, our results show that the White Leghorn chicken breed possesses a mosaic of divergent ancestries inherited from other subspecies of RJF. Despite the strong episodic gene flow from geographically divergent lineages of jungle fowls, our analyses show that domestic chickens undergo genetic adaptations that underlie their unique behavioral, morphological and reproductive traits. Our study provides novel insights into the evolutionary history of domestic chickens and a valuable resource to facilitate ongoing genetic and functional investigations of the world's most numerous domestic animal.

Author Correction: 863 genomes reveal the origin and domestication of chicken.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.