Neanderthal and modern human noses
3D reconstruction of Neanderthal skulls based on CT scans. Image courtesy of A. Balzeau (Musée de l’Homme, Paris, France).
Both Neanderthals and modern humans settled in cold, dry Eurasian environments. This development may have required adaptations in internal nasal anatomy that facilitated warming and humidification of air before it reached the lungs, but a lack of soft-tissue evidence in the Neanderthal fossil record has made confirming this hypothesis difficult. S. de Azevedo et al. (pp. 12442–12447) analyzed nasal morphologies of 38 Argentineans—26 of southwestern European (SWE) ancestry and 12 recent northeastern Asian (NEA) migrants—and two fossil Neanderthals. The authors determined the main differences in nasal bone morphology between Neanderthals and modern humans, enabling inference and digital reconstruction of the Neanderthal nasal soft tissue. The authors used computational fluid dynamics to simulate breathing in Neanderthals, SWE modern humans, and NEA modern humans. Air warming and humidifying was most rapid in the NEA model, due to significantly longer fluid residence times compared with the other models. Air warming and humidifying was also more rapid in the Neanderthal model than in the SWE model. Analysis of nasal configurations within and between populations indicated selection for a particular configuration in modern human populations living in cold environments. According to the authors, the results suggest that cold-adapted nasal morphology may have evolved independently in Neanderthals and modern humans. — B.D.
Detecting short-term historical population trends
Geographical density of radiocarbon dates in the second case study. Basemap created using ESRI ArcGIS software.
Researchers rely on historical documents and oral accounts to form hypotheses about past demographic events. Simulation methods based on archeological radiocarbon data are proving increasingly useful for independently assessing historical demographic changes while avoiding bias, which can result from overreliance on hypothesis-confirming data and models. Kevan Edinborough et al. (pp. 12436–12441) refined an established radiocarbon-based simulation method to enable rigorous tests of short-duration population trends that last between 100 and 200 years. In the first case study, the authors tested the approach using simulated radiocarbon data for the European Black Death/bubonic plague. Simulation of a random sample of 1,000 radiocarbon dates between AD 1000 and 1700 accurately reflected the population crash that occurred between AD 1300 and 1400. In the second case study, the authors applied the simulation method to test the accuracy of oral records of descendant Tsimshian First Nation communities from the Prince Rupert Harbor region of British Columbia, Canada. Using a regional database of 523 radiocarbon dates derived from archaeological sites, the authors identified a population decline between 1,200 and 1,000 years ago, consistent with oral accounts describing the short-term abandonment of territories along the northern coast of British Columbia around that time. According to the authors, the refined simulation method allows rigorous testing of demographic predictions derived from a range of historical sources. — J.W.
Effectiveness and production of influenza vaccines
Eggs for growing influenza virus. Image courtesy of the CDC/Emily Cramer.
Influenza viruses, such as H3N2, continuously acquire hemagglutinin (HA) glycoprotein mutations that prevent the binding of human antibodies, posing a challenge to vaccine development. The 2016–2017 influenza season in the Northern Hemisphere was dominated by 3C.2a H3N2 viruses, which emerged during the 2014–2015 influenza season and were predicted to possess a new HA glycosylation site. Although the 2016–2017 influenza seasonal vaccine includes the 3C.2a H3N2 strain, the egg-adapted vaccine version lacks the putative glycosylation site, and the vaccine appears to exhibit only moderate effectiveness against H3N2 infections. Seth Zost et al. (pp. 12578–12583) report that glycosylation differences between the H3N2 circulating strains and egg-adapted vaccine versions likely contributed to the reduced effectiveness of the vaccine during the 2016–2017 influenza season. The authors analyzed serum from ferrets and humans exposed to the egg-adapted H3N2 vaccine strain, and found that the antibodies that were elicited poorly neutralized the 3C.2a H3N2 virus. Additionally, ferrets infected with the current circulating H3N2 strain, which possesses the glycosylation site, and humans vaccinated with a baculovirus-derived vaccine, which possesses the glycosylation site motif, mounted antibody responses that efficiently recognized the glycosylated 3C.2a H3N2 virus. According to the authors, the findings highlight challenges facing the production of influenza vaccines in eggs, and offer insight into the limited effectiveness of the 2016–2017 influenza vaccine. — C.S.
Single-cell genome sequencing and haplotyping
Computer-aided design depicting a technology for improving genome sequencing.
The accurate identification of genetic variants in single-cell genomes could enable a variety of clinical applications. Currently, accurately detecting such variants remains challenging due to the limitations of DNA sequencing methods. Wai Keung Chu et al. (pp. 12512–12517) report a method for improving the accuracy of single-cell genome sequencing and haplotyping called single-stranded sequencing using microfluidic reactors (SISSOR). The method uses a microfluidic processor that consists of modules for single-cell capture, cell lysis and strand separation, partitioning, and amplification. Once single-cell double-stranded chromosomal DNA molecules are separated, the DNA fragments are randomly distributed and partitioned into 24 identical nanoliter compartments for amplification using multiple displacement amplification techniques. The amplified products are then retrieved from each compartment, converted to barcoded sequencing libraries, and sequenced with Illumina short-read sequencing-by-synthesis methods. The authors demonstrated SISSOR using three single cells from the human PGP1 fibroblast cell line. Overall, the error rate of SISSOR sequencing was below 10-8, yielding 4 possible errors in 351 Mb. Prior to haplotype assembly, the average DNA fragment length was approximately 500 kb, 5- to 10-fold longer than lengths achieved using dilution methods. According to the authors, the method might improve the accuracy of single-cell genome sequencing and provide longer haplotype lengths than current approaches. — C.S.