Influence of substitution model selection on protein phylogenetic tree reconstruction

Probabilistic phylogenetic tree reconstruction is traditionally performed under a best-fitting substitution model of molecular evolution previously selected according to diverse statistical criteria. Interestingly, some recent studies proposed that this procedure is unnecessary for phylogenetic tree reconstruction leading to a debate in the field. In contrast to DNA sequences, phylogenetic tree reconstruction from protein sequences is traditionally based on empirical exchangeability matrices that can differ among taxonomic groups and protein families. Considering this aspect, here we investigated the influence of selecting a substitution model of protein evolution on phylogenetic tree reconstruction by the analyses of real and simulated data. We found that phylogenetic tree reconstructions based on a selected best-fitting substitution model of protein evolution are the most accurate, in terms of topology and branch lengths, compared with those derived from substitution models with amino acid replacement matrices far from the selected best-fitting model, especially when the data has large genetic diversity. Indeed, we found that substitution models with similar amino acid replacement matrices produce similar reconstructed phylogenetic trees, suggesting the use of substitution models as similar as possible to a selected best-fitting model when the latter cannot be used. Therefore, we recommend the use of the traditional protocol of selection among substitution models of evolution for protein phylogenetic tree reconstruction.Universidade de Vigo/CISUGAgencia Estatal de Investigación | Ref. PID2019-107931GA-I0

Consequences of genetic recombination on protein folding stability

Genetic recombination is a common evolutionary mechanism that produces molecular diversity. However, its consequences on protein folding stability have not attracted the same attention as in the case of point mutations. Here, we studied the effects of homologous recombination on the computationally predicted protein folding stability for several protein families, finding less detrimental effects than we previously expected. Although recombination can affect multiple protein sites, we found that the fraction of recombined proteins that are eliminated by negative selection because of insufficient stability is not significantly larger than the corresponding fraction of proteins produced by mutation events. Indeed, although recombination disrupts epistatic interactions, the mean stability of recombinant proteins is not lower than that of their parents. On the other hand, the difference of stability between recombined proteins is amplified with respect to the parents, promoting phenotypic diversity. As a result, at least one third of recombined proteins present stability between those of their parents, and a substantial fraction have higher or lower stability than those of both parents. As expected, we found that parents with similar sequences tend to produce recombined proteins with stability close to that of the parents. Finally, the simulation of protein evolution along the ancestral recombination graph with empirical substitution models commonly used in phylogenetics, which ignore constraints on protein folding stability, showed that recombination favors the decrease of folding stability, supporting the convenience of adopting structurally constrained models when possible for inferences of protein evolutionary histories with recombination.Agencia Estatal de Investigación | Ref. PID2019-107931GA-I00/AEI/10.13039/501100011033Agencia Estatal de Investigación | Ref. PID2019-109041GBC22/10.13039/501100011033Ministerio de Economía y Competitividad | Ref. RYC-2015-18241Financiado para publicación en acceso aberto: Universidade de Vigo/CISU

Full polarization control for fiber optical quantum communication systems using polarization encoding

A real-time polarization control system employing two nonorthogonal reference signals multiplexed in either time or wavelength with the data signal is presented. It is shown, theoretically and experimentally, that complete control of multiple polarization states can be attained employing polarization controllers in closed-loop configuration. Experimental results show that negligible added penalties, corresponding to an average added optical Quantum Bit Error Rate of 0.044%, can be achieved with response times smaller than 10 ms, without significant introduction of noise counts in the quantum channel.Comment: 6 pages, 5 figures. Submitted to Optics Expres

Efficient upconversion of sub-THz radiation in a high-Q whispering gallery resonator

We demonstrate efficient upconversion of sub-THz radiation into the optical domain in a high-Q whispering gallery mode resonator with quadratic optical nonlinearity. The 5x10^{-3} power conversion efficiency of continuous wave 100GHz signal is achieved with only 16 mW of optical pump.Comment: This revision is limited to discussion of only optical WGMs coupled with the external Rf field. Discussion of RF WGMs is now posted separatel

Feasibility of quantum key distribution through dense wavelength division multiplexing network

In this paper, we study the feasibility of conducting quantum key distribution (QKD) together with classical communication through the same optical fiber by employing dense-wavelength-division-multiplexing (DWDM) technology at telecom wavelength. The impact of the classical channels to the quantum channel has been investigated for both QKD based on single photon detection and QKD based on homodyne detection. Our studies show that the latter can tolerate a much higher level of contamination from the classical channels than the former. This is because the local oscillator used in the homodyne detector acts as a "mode selector" which can suppress noise photons effectively. We have performed simulations based on both the decoy BB84 QKD protocol and the Gaussian modulated coherent state (GMCS) QKD protocol. While the former cannot tolerate even one classical channel (with a power of 0dBm), the latter can be multiplexed with 38 classical channels (0dBm power each channel) and still has a secure distance around 10km. Preliminary experiment has been conducted based on a 100MHz bandwidth homodyne detector.Comment: 18 pages, 5 figure