耐药细菌的适应性代价及补偿性进化

细菌在获得抗生素耐药性后易于产生适应性代价(fitness cost)，表现为在没有抗生素存在时，与野生型菌株相比，耐药性突变株的生存能力、转移速率和毒力的降低。然而，耐药菌可通过进化恢复其适应性，这种能使适应性上升的过程称为“补偿性进化(compensatory evolution)”。本文综述了耐药菌的适应性代价产生的原因、研究方法、研究进展及补偿性进化的机制，并讨论了适应性代价研究过程中存在的问题及展望。     

Insights into the epidemic characteristics and evolutionary history of the novel porcine circovirus type 3 in southern China

Porcine circovirus type 3 (PCV 3) is a newly identified circovirus from swine in the USA , China and Poland. This novel circovirus has been associated with porcine dermatitis and nephropathy syndrome (PDNS ), reproductive failure and multisystemic inflammation; moreover, PCV 3 poses a potential threat to the swine industry. In this retrospective study, a phylogenetic analysis was conducted to address the epidemiology and evolutionary dynamics of this novel circovirus. The total positive sample rate of PCV 3 was 26.7% (76/285) and has increased gradually over the past 3 years. Of these PCV 3‐positive samples, 22.3% (17/76) were coinfected with PCV 2. PCV 3 can be detected in multiple sample types with different positive rates, and the positive rate is highest among stillborn. We also divide PCV 3 into three clades (PCV 3a, PCV 3b and PCV 3c) based on two amino acid mutations (A24V and R27K) on the cap protein in this study. In addition, the origin of PCV 3 was approximately 1966 and may have originated from a bat‐associated circovirus. Our results suggested that PCV 3 is widely distributed in southern China and has been circulating in swine herds for nearly half a century. PCV 3 has evolved into different clades caused by mutations in cap proteins; thus, further research on PCV 3 epidemiology should be conducted.     

Recombination and Positive Selection Differentially Shaped the Diversity of Betacoronavirus Subgenera

The Betacoronavirus genus of mammal-infecting viruses includes three subgenera (Sarbecovirus, Embecovirus, and Merbecovirus), in which most known human coronaviruses, including SARS-CoV-2, cluster. Coronaviruses are prone to host shifts, with recombination and positive selection possibly contributing to their high zoonotic potential. We analyzed the role of these two forces in the evolution of viruses belonging to the Betacoronavirus genus. The results showed that recombination has been pervasive during sarbecovirus evolution, and it is more widespread in this subgenus compared to the other two. In both sarbecoviruses and merbecoviruses, recombination hotspots are clearly observed. Conversely, positive selection was a less prominent force in sarbecoviruses compared to embecoviruses and merbecoviruses and targeted distinct genomic regions in the three subgenera, with S being the major target in sarbecoviruses alone. Overall, the results herein indicate that Betacoronavirus subgenera evolved along different trajectories, which might recapitulate their host preferences or reflect the origins of the presently available coronavirus sequences.     

On the origins of hierarchy in complex networks

Hierarchy seems to pervade complexity in both living and artificial systems. Despite its relevance, no general theory that captures all features of hierarchy and its origins has been proposed yet. Here we present a formal approach resulting from the convergence of theoretical morphology and network theory that allows constructing a 3D morphospace of hierarchies and hence comparing the hierarchical organization of ecological, cellular, technological, and social networks. Embedded within large voids in the morphospace of all possible hierarchies, four major groups are identified. Two of them match the expected from random networks with similar connectivity, thus suggesting that nonadaptive factors are at work. Ecological and gene networks define the other two, indicating that their topological order is the result of functional constraints. These results are consistent with an exploration of the morphospace, using in silico evolved networks.     

Structure of the archaeal head-tailed virus HSTV-1 completes the HK97 fold story

It has been proposed that viruses can be divided into a small number of structure-based viral lineages. One of these lineages is exemplified by bacterial virus Hong Kong 97 (HK97), which represents the head-tailed dsDNA bacteriophages. Seemingly similar viruses also infect archaea. Here we demonstrate using genomic analysis, electron cryomicroscopy, and image reconstruction that the major coat protein fold of newly isolated archaeal Haloarcula sinaiiensis tailed virus 1 has the canonical coat protein fold of HK97. Although it has been anticipated previously, this is physical evidence that bacterial and archaeal head-tailed viruses share a common architectural principle. The HK97-like fold has previously been recognized also in herpesviruses, and this study expands the HK97-like lineage to viruses from all three domains of life. This is only the second established lineage to include archaeal, bacterial, and eukaryotic viruses. Thus, our findings support the hypothesis that the last common universal ancestor of cellular organisms was infected by a number of different viruses.     

Radiolarians decreased silicification as an evolutionary response to reduced Cenozoic ocean silica availability

It has been hypothesized that increased water column stratification has been an abiotic “universal driver” affecting average cell size in Cenozoic marine plankton. Gradually decreasing Cenozoic radiolarian shell weight, by contrast, suggests that competition for dissolved silica, a shared nutrient, resulted in biologic coevolution between radiolaria and marine diatoms, which expanded dramatically in the Cenozoic. We present data on the 2 components of shell weight change—size and silicification—of Cenozoic radiolarians. In low latitudes, increasing Cenozoic export of silica to deep waters by diatoms and decreasing nutrient upwelling from increased water column stratification have created modern silica-poor surface waters. Here, radiolarian silicification decreases significantly (r = 0.91, P < 0.001), from ≈0.18 (shell volume fraction) in the basal Cenozoic to modern values of ≈0.06. A third of the total change occurred rapidly at 35 Ma, in correlation to major increases in water column stratification and abundance of diatoms. In high southern latitudes, Southern Ocean circulation, present since the late Eocene, maintains significant surface water silica availability. Here, radiolarian silicification decreased insignificantly (r = 0.58, P = 0.1), from ≈0.13 at 35 Ma to 0.11 today. Trends in shell size in both time series are statistically insignificant and are not correlated with each other. We conclude that there is no universal driver changing cell size in Cenozoic marine plankton. Furthermore, biologic and physical factors have, in concert, by reducing silica availability in surface waters, forced macroevolutionary changes in Cenozoic low-latitude radiolarians.