Quasispecies Theory and the Behavior of RNA Viruses

A large number of medically important viruses, including HIV, hepatitis C virus, and influenza, have RNA genomes. These viruses replicate with extremely high mutation rates and exhibit significant genetic diversity. This diversity allows a viral population to rapidly adapt to dynamic environments and evolve resistance to vaccines and antiviral drugs. For the last 30 years, quasispecies theory has provided a population-based framework for understanding RNA viral evolution. A quasispecies is a cloud of diverse variants that are genetically linked through mutation, interact cooperatively on a functional level, and collectively contribute to the characteristics of the population. Many predictions of quasispecies theory run counter to traditional views of microbial behavior and evolution and have profound implications for our understanding of viral disease. Here, we discuss basic principles of quasispecies theory and describe its relevance for our understanding of viral fitness, virulence, and antiviral therapeutic strategy

The evolution and changing ecology of the African hominid oral microbiome.

The oral microbiome plays key roles in human biology, health, and disease, but little is known about the global diversity, variation, or evolution of this microbial community. To better understand the evolution and changing ecology of the human oral microbiome, we analyzed 124 dental biofilm metagenomes from humans, including Neanderthals and Late Pleistocene to present-day modern humans, chimpanzees, and gorillas, as well as New World howler monkeys for comparison. We find that a core microbiome of primarily biofilm structural taxa has been maintained throughout African hominid evolution, and these microbial groups are also shared with howler monkeys, suggesting that they have been important oral members since before the catarrhine-platyrrhine split ca. 40 Mya. However, community structure and individual microbial phylogenies do not closely reflect host relationships, and the dental biofilms of Homo and chimpanzees are distinguished by major taxonomic and functional differences. Reconstructing oral metagenomes from up to 100 thousand years ago, we show that the microbial profiles of both Neanderthals and modern humans are highly similar, sharing functional adaptations in nutrient metabolism. These include an apparent Homo-specific acquisition of salivary amylase-binding capability by oral streptococci, suggesting microbial coadaptation with host diet. We additionally find evidence of shared genetic diversity in the oral bacteria of Neanderthal and Upper Paleolithic modern humans that is not observed in later modern human populations. Differences in the oral microbiomes of African hominids provide insights into human evolution, the ancestral state of the human microbiome, and a temporal framework for understanding microbial health and disease

Temperature dependence of oxygen dynamics and community metabolism in a shallow Mediterranean macroalgal meadow (caulerpa prolifera)

Hypoxia is emerging as a major threat to marine coastal biota. Predicting its occurrence and elucidating the driving factors are essential to set successful management targets to avoid its occurrence. This study aims to elucidate the effects of warming on the likelihood of hypoxia. Highfrequency dissolved oxygen measurements have been used to estimate gross primary production (GPP), net ecosystem production (NEP) and community respiration (CR) in a shallow macroalgae (Caulerpa prolifera) ecosystem in a highly human-influenced closed Mediterranean bay. Daily averaged GPP and CR ranged from 0 to 1,240.9 and 51.4 to 1,297.3 mmol O2 m−2 day−1, respectively. The higher GPP and CRwere calculated for the same day, when daily averaged water temperature was 28.3 °C, and resulted in a negative NEP of −56.4 mmol O2 m−2 day−1. The ecosystem was net heterotrophic during the studied period, probably subsidized by allochthonous organic inputs from ground waters and from the surrounding town and boating activity. Oxygen dynamics and metabolic rates strongly depend on water temperature, with lower oxygen content at higher temperatures. The probability of hypoxic conditions increased at a rate of 0.39%°C−1 (±0.14 % °C−1). Global warming will increase the likelihood of hypoxia in the bay studied, as well as in other semienclosed bays