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This Week in PNAS: Feb 23, 2016

In the early, online edition of the Proceedings of the National Academy of Sciences, Los Alamos National Lab researchers explore phylogenetic patterns that may appear when trying to untangle disease transmission dynamics in an epidemiological investigation. The team used a mathematical framework called coalescent theory to come up with half a dozen phylogenetic tree topologies using HIV-1 sequences from two individuals suspected of being epidemiologically linked. Results from the analyses indicate that phylogenetic relationships are influenced not only by transmission direction, but also by the presence or absence of still-to-be-sampled individuals who are epidemiological intermediates in the transmission chain. "Our systematic classification and evaluation of expected topologies should make future interpretation of phylogenetic results in epidemiological investigations more objective and informative," study authors write.

A team from the US, UK, and Spain searches for sponge sequences that could serve as molecular markers of early animal life. The researchers focused on sterol-coding sequences in four sponge outgroup animals — the choanoflagellate Salpingoeca rosetta, the filasterean Capsaspora owczarzaki, and the Sphaeroforma arctica and Creolimax fragrantissima ichthypsporeans — to retrace their ability to make the precursor of a sterane compound that's been detected in rocks dated at between 540 million and 650 million years old. From phylogenetic trees produced for enzymes involved in this process, they argue that algae and sponges likely evolved the ability to produce sterane precursors independently, though this appears to have occurred earlier on in the sponge lineage.

In an effort to understand bats' ability to carry so many potentially dangerous viruses without themselves becoming sick, researchers from Australia and Singapore sequenced and mapped genes at the type I interferon locus in the Australian black flying fox bat, Pteropus alecto. The team detected fewer interferon genes than anticipated based on prior studies of other mammals. Nevertheless, three interferon alpha genes seemed to be continuously turned on and expressed in bat tissues, even in the absence of immune system stimulation. "This unusual pattern of [interferon-alpha] expression has not been described in any other species to our knowledge," the authors write, "and has important implications for the role of innate immunity in the ability of bats to coexist with viruses in the absence of disease."