PLOS Papers Look at Reference Bias Effects in Ancient Genomics, More

In PLOS Genetics, a duo from Uppsala University searches for reference bias and its potential consequences for population genomics studies on ancient human populations. The team reasoned that ancient DNA analyses based on low-coverage or fragmented sequence data are apt to produce sequences that map to multiple sites in reference genomes, while making heterozygous sites seem homozygous. Based on their analyses of reference bias, mapping quality, and related SNP patterns in dozens of published ancient human, Neanderthal, or Denisovan sequences, the authors found that "reference bias has the potential to cause minor but significant differences in the results of downstream analyses such as population allele sharing, heterozygosity estimates, and estimates of archaic ancestry."

A team from Japan, Malawi, and Zambia considers genetic diversity in tsetse fly (Glossina morsitans morsitans) representatives from sites in where the fly serves as a vector for the human African trypanosomiasis-causing parasite Trypanosoma brucei rhodesiense. As they report in PLOS Neglected Tropical Diseases, the researchers profiled partial mitochondrial cytochrome oxidase gene 1 sequences in 108 tsetse flies from five parts of Zambia or Malawi that are prone to human African trypanosomiasis, looking at 10 microsatellite markers in 99 of the flies. The genetic features found in the tsetse flies pointed distinct clusters in eastern and western parts of the Great Rift Valley, for example, while highlighting a tsetse fly population in Malawi's Kasungu National Park that resembled flies in the Luangwa river basin in Zambia.

For a paper in PLOS One, researchers from Brazil retrace hepatitis B virus dynamics in 11 countries in the Americas, focusing on Brazilian isolates from the widespread "D" genotype and their relationship to HBV isolates found in other parts of the Americas. The team sequenced 39 HBV isolates from patients in Brazil, comparing them with more than 1,100 complete or partial HBV genome sequences from the Americas available in the GenBank database to reconstruct historical HBV migrations. "Spatiotemporal reconstruction analyses using short-term substitution rates suggested times of the most recent common ancestor for the American HBV/D sub-genotypes [coincide] with mass migratory movements to the Americas during the 19^th and 20^th centuries," the authors report.