A genetic method for dating ancient genomes provides a direct estimate of human generation interval in the last 45,000 years

The study of human evolution has been revolutionized by inferences from ancient DNA analyses. Key to these studies is the reliable estimation of the age of ancient specimens. High-resolution age estimates can often be obtained using radiocarbon dating, and, while precise and powerful, this method has some biases, making it of interest to directly use genetic data to infer a date for samples that have been sequenced. Here, we report a genetic method that uses the recombination clock. The idea is that an ancient genome has evolved less than the genomes of present-day individuals and thus has experienced fewer recombination events since the common ancestor. To implement this idea, we take advantage of the insight that all non-Africans have a common heritage of Neanderthal gene flow into their ancestors. Thus, we can estimate the date since Neanderthal admixture for present-day and ancient samples simultaneously and use the difference as a direct estimate of the ancient specimen’s age. We apply our method to date five Upper Paleolithic Eurasian genomes with radiocarbon dates between 12,000 and 45,000 y ago and show an excellent correlation of the genetic and ¹⁴C dates. By considering the slope of the correlation between the genetic dates, which are in units of generations, and the ¹⁴C dates, which are in units of years, we infer that the mean generation interval in humans over this period has been 26–30 y. Extensions of this methodology that use older shared events may be applicable for dating beyond the radiocarbon frontier.Ancient DNA analyses have transformed research into human evolutionary history, making it possible to directly observe genetic variation patterns that existed in the past, instead of having to infer them retrospectively (1). To interpret findings from an ancient specimen, it is important to have an accurate estimate of its age. The current gold standard is radiocarbon dating, which is applicable for estimating dates for samples up to 50,000 y old (2). This method is based on the principle that, when a living organism dies, the existing ¹⁴C starts decaying to ¹⁴N with a half-life of ∼5,730 y (3). By measuring the ratio of ¹⁴C to ¹²C in the sample and assuming that the starting ratio of carbon isotopes is the same everywhere in the biosphere, the age of the sample is inferred. A complication is that carbon isotope ratios vary among carbon reservoirs (e.g., marine, freshwater, atmosphere) and over time. Thus, ¹⁴C dates must be converted to calendar years using calibration curves based on other sources, including annual tree rings (dendrochronology) or uranium-series dating of coral (2). Such calibrations, however, may not fully capture the variation in atmospheric carbon. In addition, contamination of a sample by modern carbon, introduced during burial or by handling afterwards, can make a sample seem younger than it actually is (2). The problem is particularly acute for samples that antedate 30,000 y ago because they retain very little original ¹⁴C.Here, we describe a genetic approach for dating ancient samples, applicable in cases where DNA sequence data are available, as is becoming increasingly common (1). This method relies on the insight that an ancient genome has experienced fewer generations of evolution compared with the genomes of its living (i.e., extant) relatives. Because recombination occurs at an approximately constant rate per generation, the accumulated number of recombination events provides a molecular clock for the time elapsed or, in the case of an ancient sample, the number of missing generations since it ceased to evolve. This idea is referred to as “branch shortening” and estimates of missing evolution can be translated into absolute time in years by using an estimate of the mean age of reproduction (generation interval) or an independent calibration point such as human–ape divergence time.Branch shortening has been used in studies of population history, for inferring mutation rates, and for establishing time scales for phylogenic trees in humans and other species (4, 5). It was first applied for dating ancient samples on a genome-wide scale by Meyer et al. (6), who used the mutation clock (instead of the recombination clock as proposed here) to estimate the age of the Denisova finger bone, which is probably older than 50,000 y, and has not been successfully radiocarbon dated (6). Specifically, the authors compared the divergence between the Denisova and extant humans and calibrated the branch shortening relative to human–chimpanzee (HC) divergence time. The use of ape divergence time for calibration, however, relies on estimates of mutation rate that are uncertain (7). In particular, recent pedigree studies have yielded a yearly mutation rate that is approximately twofold lower than the one obtained from phylogenetic methods (7). In addition, comparison with HC divergence relies on branch-shortening estimates that are small relative to the total divergence of millions of years, so that even very low error rates in allele detection can bias estimates. These issues lead to substantial uncertainty in estimated age of the ancient samples, making this approach impractical for dating specimens that are tens of thousands of years old, a time period that encompasses the vast majority of ancient human samples sequenced to date.Given the challenges associated with the use of the mutation clock, here we explore the possibility of using a molecular clock based on the accumulation of crossover events (the recombination clock), which is measured with high precision in humans (8). In addition, instead of using a distant outgroup, such as chimpanzees, we rely on a more recent shared event that has affected both extant and ancient modern humans and is therefore a more reliable fixed point on which to base the dating. Previous studies have documented that most non-Africans derive 1–4% ancestry from Neanderthals from an admixture event that occurred ∼37,000–86,000 y before present (yBP) (9, 10), with some analyses proposing a second event (around the same time) into the ancestors of East Asians (11, 12). Because the vast majority of ancient samples sequenced to date were discovered in Eurasia (with estimated ages of ∼2,000–45,000 yBP), postdate the Neanderthal admixture, and show evidence of Neanderthal ancestry, we used the Neanderthal gene flow as the shared event.The idea of our method is to estimate the date of Neanderthal gene flow separately for the extant and ancient genomes. Because the ancient sample is closer in time to the shared Neanderthal admixture event, we expect that the inferred dates of Neanderthal admixture will be more recent in ancient genomes (by an amount that is directly determined by the sample’s age) compared with the dates in the extant genomes. The difference in the dates thus provides an estimate of the amount of missing evolution: that is, the age of the ancient sample. An illustration of the idea is shown in SI Appendix, Fig. S1. An assumption in our approach is that the Neanderthal admixture into the ancestors of modern humans occurred approximately at the same time and that the same interbreeding events contributed to the ancestry of all of the non-African samples being compared. Deviations from this model could lead to incorrect age estimates. Our method is not applicable for dating genomes that do not have substantial Neanderthal ancestry, such as sub-Saharan African genomes.To date the Neanderthal admixture event, we used the insight that gene flow between genetically distinct populations, such as Neanderthals and modern humans, introduces blocks of archaic ancestry into the modern human background that break down at an approximately constant rate per generation as crossovers occur (13–15). Thus, by jointly modeling the decay of Neanderthal ancestry and recombination rates across the genome, we can estimate the date of Neanderthal gene flow, measured in units of generations. Similar ideas have been used to estimate the time of admixture events between contemporary human populations (14–16), as well as between Eurasians and Neanderthals (9, 17). An important feature of our method is that it is expected to give more precise results for samples that are older because these samples are closer in time to the Neanderthal introgression event, thus it is easier to accurately estimate the time of the admixture event for them. Thus, unlike ¹⁴C dating, the genetic approach becomes more reliable with age and, in that regard, complements ¹⁴C dating.     

Transjugular intrahepatic portosystemic shunt in cirrhosis: An exhaustive critical update

More than five decades after it was originally conceptualized as rescue therapy for patients with intractable variceal bleeding, the transjugular intrahepatic portosystemic shunt(TIPS) procedure continues to remain a focus of intense clinical and biomedical research. By the impressive reduction in portal pressure achieved by this intervention, coupled with its minimally invasive nature, TIPS has gained increasing acceptance in the treatment of complications of portal hypertension. The early years of TIPS were plagued by poor long-term patency of the stents and increased incidence of hepatic encephalopathy. Moreover, the diversion of portal flow after placement of TIPS often resulted in derangement of hepatic functions, which was occasionally severe. While the incidence of shunt dysfunction has markedly reduced with the advent of covered stents, hepatic encephalopathy and instances of early liver failure continue to remain a significant issue after TIPS. It has emerged over the years that careful selection of patients and diligent post-procedural care is of paramount importance to optimize the outcome after TIPS. The past twenty years have seen multiple studies redefining the role of TIPS in the management of variceal bleeding and refractory ascites while exploring its application in other complications of cirrhosis like hepatic hydrothorax, portal hypertensive gastropathy, ectopic varices, hepatorenal and hepatopulmonary syndromes, non-tumoral portal vein thrombosis and chylous ascites. It has also been utilized to good effect before extrahepatic abdominal surgery to reduce perioperative morbidity and mortality. The current article aims to review the updated literature on the status of TIPS in the management of patients with liver cirrhosis.     

Etiology of acute, non-malaria, febrile illnesses in Jayapura, northeastern Papua, Indonesia

We conducted a prospective, inpatient fever study in malaria-endemic Papua, Indonesia to determine non-malaria fever etiologies. Investigations included malaria blood films, blood culture, paired serologic samples analysis for dengue, Japanese encephalitis, leptospirosis, scrub typhus, murine typhus, and spotted fever group rickettsia. During 1997-2000, 226 patients (127 males and 99 females) 1-80 years of age (median age = 25 years) were enrolled. Positive blood cultures (n = 34, 15%) were obtained for Salmonella Typhi (n = 13), Escherichia coli (n = 8), Streptococcus pneumoniae (n = 6), Staphylococcus aureus (n = 5), Streptococcus pyogenes (n = 1), and Klebsiella pneumoniae (n = 1). Twenty (8.8%) patients were positive for leptospirosis by polymerase chain reaction. Eighty (35.4%) of 226 patients had ≥ 1 positive serology, diagnostic for 15 rickettsial and 9 dengue cases. Acid-fast bacilli-positive sputum was obtained from three patients. Most common confirmed (81 of 226, 35.8%)/suspected diagnoses were typhoid fever (n = 41), pneumonia (n = 29), leptospirosis (n = 28), urinary tract infections (n = 20), rickettsioses (n = 19), dengue (n = 17), and meningitis/encephalitis (n = 15). There were 17 deaths, 7 (46.7%) were caused by meningitis/encephalitis. Multiple positive serologic results and few confirmed diagnoses indicate the need for improved diagnostics.     

Standard curves for mid arm circumference and mid-arm/head circumference ratio in newborns

One Thousand singleton neonates, between 28 and 44 weeks of estimated gestational age (EGA) were measured within 48 hours of their birth for upper mid-arm circumference (MAC), head circumference (HC) and birth weight (BW). Regression analysis was used to draw standard curves for MAC versus EGA and mid-arm circumference/head circumference ratio (MAC/HC) versus EGA. Correlation coefficients were 0.961 for MAC versus EGA and 0.889 for MAC/HC versus EGA (p < 0.001). MAC, MAC/HC and HC were also highly correlated with birth weight (p < 0.001). These standard curves make available a discriminating method for evaluation of intra-uterine growth and a noninvasive technique for following somatic protein status in growing preterm infants.     

Prostate cancer diagnosis,staging and survival

Prostate cancer is the most common malignancy in men and the second most common cancer related death. Through research, we have found that African–American men and men with a family history of prostate cancer have a significantly higher risk of prostate cancer. In the 90's the mortality rate from prostate cancer decreased, presumably due to PSA testing. Patients with organ-confined tumors, particularly if they have a moderate Gleason score have an excellent chance of long-term survival with radical prostatectomy or external beam radiation therapy. Advances in detecting micrometastatic disease are needed to further impact on this disease.     

The effect of a supplementary protein food containing fish flour,groundnut flour and bengal gram flour and fortified with vitamins on the growth and nutritional status of children

Summary A feeding experiment extending over a period of six months was carried out on 58 boys, aged 6 to 12 years, in a local boarding home in Mysore, to assess the effects of supplementing their diet daily, with 40 gm. of a protein food based on 2∶1∶1 blend of groundnut flour, Bengal gram flour and fish flour (from oil sardine) fortified with vitamins A and D, thiamine and riboflavin. The children were paired according to initial height and weight and the members of each pair allotted at random to the control and experimental groups. Values for weight, height, nutritional status, haemoglobin level and red blood cell count were recorded at the beginning and end of the experiment, for subjects in the control and experimental groups. All the children in the experimental group relished the protein supplement and none complained of digestive trouble. A highly significant increase in height, weight, red blood cell count and haemoglobin level of the subjects receiving the protein food supplement was observed as compared with the control group. Eighty per cent. of the subjects in the experimental group improved in their nutritional status as compared with only seventeen per cent. in the control group. None in the experimental group showed deterioration whereas seventeen per cent. of the subjects in the control group showed deterioration in their nutritional status. From the Central Food Technological Research Institute, Mysore. An erratum to this article is available at .     

Cholecysto-hydatid cyst fistula.

A 27-year-old woman developed recurrent hydatid of liver. CT scan showed unilocular cysts in segments IV and VII. Intraoperatively, there was a fistulous communication between the gall bladder and the cyst in segment IV. Partial pericystectomy along with cholecystectomy was done for the segment IV cyst; percutaneous aspiration, instillation and re-aspiration using hypertonic saline was done for the cyst in segment VII. This was followed by albendazole treatment.