Population interconnectivity over the past 120,000 years explains distribution and diversity of Central African hunter-gatherers

The evolutionary history of African hunter-gatherers holds key insights into modern human diversity. Here, we combine ethnographic and genetic data on Central African hunter-gatherers (CAHG) to show that their current distribution and density are explained by ecology rather than by a displacement to marginal habitats due to recent farming expansions, as commonly assumed. We also estimate the range of hunter-gatherer presence across Central Africa over the past 120,000 years using paleoclimatic reconstructions, which were statistically validated by our newly compiled dataset of dated archaeological sites. Finally, we show that genomic estimates of divergence times between CAHG groups match our ecological estimates of periods favoring population splits, and that recoveries of connectivity would have facilitated subsequent gene flow. Our results reveal that CAHG stem from a deep history of partially connected populations. This form of sociality allowed the coexistence of relatively large effective population sizes and local differentiation, with important implications for the evolution of genetic and cultural diversity in Homo sapiens.

The evolutionary history of African hunter-gatherers may hold key insights into patterns and processes behind the evolution of modern human diversity. Recent genomic studies have revealed that these populations represent the oldest and most diverse human genetic lineages and have been genetically differentiated from one another since the origin of humans (1–3) (SI Appendix, Table S1). Therefore, a first question is whether their current ecological niches were also characteristic of early Homo sapiens populations. However, genetic data alone can neither determine the geographic distribution of hunter-gatherers in the past nor demonstrate a deep history of adaptation of hunter-gatherers to their current environments. In fact, various studies have proposed that farming expansions within the past 5,000 years (in particular by the ancestors of Bantu speakers) would have only recently displaced hunter-gatherers to marginalized regions less favorable to agriculture (such as rainforests and deserts) (4–7).For example, the central part of Africa, between latitudes 5°N and 5°S currently is inhabited by ∼20 scattered hunter-gatherer ethnic groups (8). These Central African hunter-gatherers (CAHG) form a genetic clade thought to have diverged from other African populations as far back as 120,000 to 200,000 years ago (2, 9). The lack of any major linguistic specificity between them is often implied to reflect extensive contacts with surrounding farmer populations (8, 10), and seen as evidence of recent displacement into marginal forest environments by expanding farming populations. However, anthropologists have remarked on the huge variability in lifestyle, habitat, techniques, and tools between CAHG (11), suggestive of long-term cultural diversification and adaptation to forest environments. Research on the drivers of demography and adaptation of CAHG populations remains extremely limited, which can be partially attributed to the lack of archaeological and osteological data resulting from a rapid disintegration of fossil remains in the rainforest’s acidic soils, in addition to social instability in the region (12). Therefore, we are still left with crucial questions regarding the time depth of occupation of Central Africa by hunter-gatherers, the breadth of the niche exploited by earlier populations in the region, and variations in levels of interconnectivity at different points in time.To address those questions, we first compiled ethnographic data on the distribution of 749 camps from 11 hunter-gatherer groups extending from West to East Central Africa. We used them as inputs for environmental niche models (ENMs) to determine the relative influence of several bioclimatic and ecological factors, as well as the presence of farming populations, on the distribution and abundance of CAHG (13, 14). Then, we used high-resolution paleoclimatic reconstructions and topographic maps to make continuous predictions about where CAHG could have lived over the past 120,000 years and the potential extension of their interaction networks. Next, we compiled all reliably dated archaeological assemblages ascribed to hunter-gatherer groups in the Congo Basin (n = 168) and confirmed the model’s ability to predict the location and date of the sites. We further contextualized genomic estimates of population divergences with changes in population densities and interpopulation connectivity predicted by our model. Last, we complemented these analyses with a detailed assessment of present and historical gene flow between nine CAHG populations (n = 265 individuals), which we used to assess recent interactions between previously diverged CAHG populations, after farming expansions. Our study therefore provides a causal link between past environmental changes and human population dynamics over evolutionary time, by predicting where and when populations across Central Africa could have exchanged genetic and/or cultural information throughout their evolutionary history.     

Deletion or replacement of the second EGF-like domain of protein S results in loss of APC cofactor activity

Human protein S (PS), a cofactor of anticoagulant-activated protein C (APC), is a modular protein containing 4 epidermal growth factor (EGF)-like domains. EGF1 appears to mediate PS interaction with APC, but the roles of EGFs 2, 3, and 4 are less clear. We synthesized PS variants lacking single EGF domains (EGF2, 3, or 4) and assessed their APC cofactor activity in a factor Va inactivation assay. The variant lacking EGF2 (variant 134) showed the most dramatic loss of activity (approximately 10% of recombinant wild-type PS activity). Replacement of EGF2 by an additional EGF3 (variant 1334) resulted in a comparable loss of activity, suggesting that the loss of a specific rather than "spacer" function of EGF2 was responsible. We confirmed that the variant 134 had a functional gamma-carboxyglutamic acid (Gla) domain and that EGF1 was correctly folded. This is the first clear evidence that EGF2 is required for the expression of PS activity.     

Development of a synthetic peptide-based tartrate-resistant acid phosphatase radioimmunoassay for the measurement of bone resorption in rat serum

Selective markers of bone turnover provide a convenient and reproducible alternative to the complex and expensive histochemical techniques used commonly to study the effect of pharmacological agents and the pathogenesis of bone disease in the ovariectomized (OVX) rat model. One marker, which has been specifically linked to terminally differentiated osteoclasts and, thus, provides useful insight at cellular levels, is type-5 tartrate-resistant acid phosphatase (TRACP). We describe the development of a TRACP radioimmunoassay (RIA), which requires synthetic peptide for antibody development. To develop the RIA, polyclonal antibodies were generated in goats against a synthetic peptide, DPSVRHQRKCY, corresponding to amino acid residues 267–275 of the rat type-5 TRACP sequence. In the RIA, 50 μl of rat serum, 100 μl of goat anti-TRACP antibodies, and 100 μl of tracer were incubated overnight. The antibody-bound fraction was separated, counted, and unknown values were calculated by comparison with the peptide calibrator. Rat serum shows parallelism with the synthetic peptide calibrator used in the RIA. The sensitivity of the RIA was 24.7 μg/l, and the measuring range was 19–2476 μg/l. The average intra-assay coefficients of variation for (CV) two controls were less than 7%. The average dilution and spike recoveries were 107% and 87%, respectively. We applied our peptide-based RIA to study bone resorption in an OVX rat model. TRACP concentrations in serum in 12-week-old OVX Sprague Dawley rats were 14%–22% (P < 0.05) higher than those in the sham-operated rats, and TRACP concentrations in OVX rats treated with estradiol were 24%–32% lower (P < 0.01) than those in the vehicle-treated OVX group. Similarly, as compared with those in OVX rats, TRACP concentrations decreased to those of sham levels in OVX rats receiving 10 μg/kg per day of alendronate for 10 days. In addition, the TRACP levels determined by RIA showed a significant correlation with serum C-telopeptide (type-I collagen) concentrations (r = 0.56; P < 0.001) measured by an enzyme-linked immunosorbent assay (ELISA) developed earlier for the rat model. In conclusion, we have developed a TRACP RIA that could be used to monitor the rate of bone resorption in the rat model. Received: June 18, 2001 / Accepted: October 26, 2001     

Ileocecectomy is definitive treatment for advanced appendicitis.

Although appendectomy is the most commonly performed emergency operation septic complications of appendectomy remain a major source of morbidity. Historically, advanced appendicitis has been treated by appendectomy with cecostomy and/or drainage tubes. Our objective was to evaluate the use of ileocecal resection for the immediate treatment of advanced appendicitis. We examined the cases of all patients undergoing ileocecal resection for appendicitis from August 1989 through April 2000. There were 92 patients (60 male and 32 female) with a median age of 34 (range 6-71). Abdominal pain was present in 98 per cent of patients with duration of 5.1+/-0.6 days. Right lower quadrant tenderness was present in 91 per cent with accompanying right lower quadrant mass in 30 per cent. Temperature on admission was 38.0+/-0.1 degrees C with a white blood cell count of 15,300+/-500. Preoperative radiological studies included abdominal X-rays (33), contrast enemas (two), CT scans (41), and abdominal ultrasound (17); these studies yielded a correct preoperative diagnosis in 89 per cent. Previous appendectomy had been performed in six patients with failed percutaneous drainage of intra-abdominal abscesses in five. There were 94 cecal resections performed in 92 patients. The extent of surgical resection varied between patients and ranged from partial cecectomy (34) to ileocecectomy (55) to ileocecectomy with diverting ileostomy (five). Intra-abdominal abscesses were present at operation in 46 cases (50%), and drains were placed in 38 (41%). Skin incisions were packed open in most cases (65); there was skin closure in 27. There was no mortality encountered in this period. There were 25 complications in 23 patients (25%). Complications included postoperative abscess (10; 11%), wound infection (10; 11%), partial small bowel obstruction (two) and pulmonary embolus (one). Reoperation was required in seven patients and CT-guided percutaneous drainage in five patients. Anastomic leaks occurred in two cases of partial cecectomy and required conversion to ileocecectomy. Mean hospital stay was 10.5+/-1.0 days with adjusted hospital costs of $31,689+/-3018. We conclude that definitive treatment of advanced appendicitis can be performed by resection of the involved areas of the ileocecum. This can be accomplished with a primary anastomosis obviating the need for ileostomy and secondary operation. This aggressive surgical approach may reduce infectious complications and reduce hospital costs.     

A preoperative prognostic nomogram for solid enhancing renal tumors 7 cm or less amenable to partial nephrectomy

PURPOSE: Small renal masses are increasing in incidence. Most tumors 7 cm or less are treated with radical or partial nephrectomy but clinicians are increasingly relying on ablative therapies and observation for some small renal masses. We present novel nomograms that predict the likelihood of benign, likely indolent or potentially aggressive pathological findings based only on readily identifiable preoperative factors. MATERIALS AND METHODS: Information on all partial nephrectomies performed at a single institution was collected in an institutional review board approved registry. Using retrospectively collected data on all 862 patients who underwent partial nephrectomy for a single, solid, enhancing, clinical T1 (7 cm or less) tumor between 1999 and 2005 tumors were classified as benign or malignant. Grade 3 clear cell renal cell carcinoma, grade 4 renal cell carcinoma of any type and any renal cell carcinoma with vascular, fat or collecting system invasion were considered potentially aggressive. The likelihood of benign, likely indolent or potentially aggressive pathological findings was modeled using multivariable logistic regression models based on age, gender, radiographic tumor size, symptoms at presentation and smoking history. RESULTS: Of 862 small renal masses 20% were benign and 80% were malignant but only 30% of cancers (24% of small renal masses) were potentially aggressive. All 11 patients with systemic symptoms had cancer. The remaining 851 patients underwent further analysis. Factors that were most strongly associated with the likelihood of benign pathology were age, gender, tumor size and smoking history. A nomogram constructed to predict benign histology proved to be relatively accurate and discriminating (bootstrap corrected concordance index 0.644) and calibrated. Small renal masses in older men and younger women were more likely to be benign. With regard to differentiating indolent from potentially aggressive cancers, only advanced age was independently significant on multivariate analysis (p <0.005). The nomogram for this outcome performed with limited ability (concordance index 0.557). CONCLUSIONS: Clinical factors provide substantial predictive ability to predict benign vs malignant pathology for small renal masses amenable to partial nephrectomy. Although most of these small renal masses are benign or indolent, our ability to predict potentially aggressive cancer in this population remains limited.