Bayesian skyline plot inference of the Toscana virus epidemic: A decline in the effective number of infections over the last 30 years

Abstract Background Today an unprecedented amount of genetic sequence data is stored in publicly available repositories. For decades now, mitochondrial DNA (mtDNA) has been the workhorse of genetic studies, and as a result, there is a large volume of mtDNA data available in these repositories for a wide range of species. Indeed, whilst whole genome sequencing is an exciting prospect for the future, for most non-model organisms’ classical markers such as mtDNA remain widely used. By compiling existing data from multiple original studies, it is possible to build powerful new datasets capable of exploring many questions in ecology, evolution and conservation biology. One key question that these data can help inform is what happened in a species’ demographic past. However, compiling data in this manner is not trivial, there are many complexities associated with data extraction, data quality and data handling. Results Here we present the mtDNAcombine package, a collection of tools developed to manage some of the major decisions associated with handling multi-study sequence data with a particular focus on preparing sequence data for Bayesian skyline plot demographic reconstructions. Conclusions There is now more genetic information available than ever before and large meta-data sets offer great opportunities to explore new and exciting avenues of research. However, compiling multi-study datasets still remains a technically challenging prospect. The mtDNAcombine package provides a pipeline to streamline the process of downloading, curating, and analysing sequence data, guiding the process of compiling data sets from the online database GenBank.

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An Optical Analog-to-Digital Converter with Enhanced ENOB Based on MMI-Based Phase-Shift Quantization

Photonics ◽

10.3390/photonics8020052 ◽

2021 ◽

Vol 8 (2) ◽

pp. 52

Author(s):

Yue Liu ◽

Jifang Qiu ◽

Chang Liu ◽

Yan He ◽

Ran Tao ◽

...

Keyword(s):

Phase Shift ◽

Multimode Interference ◽

Analog To Digital Converter ◽

Effective Number ◽

Digital Converter ◽

Analog To Digital ◽

Mmi Coupler ◽

Simulation Results ◽

Optical Analog ◽

Optical Quantization

An optical analog-to-digital converter (OADC) scheme with enhanced bit resolution by using a multimode interference (MMI) coupler as optical quantization is proposed. The mathematical simulation model was established to verify the feasibility and to investigate the robustness of the scheme. Simulation results show that 20 quantization levels (corresponding to 4.32 of effective number of bits (ENOB)) are realized by using only 6 channels, which indicates that the scheme requires much fewer quantization channels or modulators to realize the same amount of ENOB. The scheme is robust and potential for integration.

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Sampled-based estimation of diversity sensu stricto by transforming Hurlbert diversities into effective number of species

Ecography ◽

10.1111/j.1600-0587.2011.06860.x ◽

2011 ◽

Vol 35 (7) ◽

pp. 661-672 ◽

Cited By ~ 24

Author(s):

Gilles Dauby ◽

Olivier J. Hardy

Keyword(s):

Sensu Stricto ◽

Effective Number ◽

Number Of Species

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Effect of genome composition and codon bias on infectious bronchitis virus evolution and adaptation to target tissues

BMC Genomics ◽

10.1186/s12864-021-07559-5 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Giovanni Franzo ◽

Claudia Maria Tucciarone ◽

Matteo Legnardi ◽

Mattia Cecchinato

Keyword(s):

Codon Usage ◽

Codon Bias ◽

Synonymous Codon ◽

Synonymous Codon Usage ◽

Accessory Proteins ◽

Effective Number ◽

Genome Composition ◽

Infectious Bronchitis ◽

Selective Forces ◽

Effective Number Of Codons

Abstract Background Infectious bronchitis virus (IBV) is one of the most relevant viruses affecting the poultry industry, and several studies have investigated the factors involved in its biological cycle and evolution. However, very few of those studies focused on the effect of genome composition and the codon bias of different IBV proteins, despite the remarkable increase in available complete genomes. In the present study, all IBV complete genomes were downloaded (n = 383), and several statistics representative of genome composition and codon bias were calculated for each protein-coding sequence, including but not limited to, the nucleotide odds ratio, relative synonymous codon usage and effective number of codons. Additionally, viral codon usage was compared to host codon usage based on a collection of highly expressed genes in IBV target and nontarget tissues. Results The results obtained demonstrated a significant difference among structural, non-structural and accessory proteins, especially regarding dinucleotide composition, which appears under strong selective forces. In particular, some dinucleotide pairs, such as CpG, a probable target of the host innate immune response, are underrepresented in genes coding for pp1a, pp1ab, S and N. Although genome composition and dinucleotide bias appear to affect codon usage, additional selective forces may act directly on codon bias. Variability in relative synonymous codon usage and effective number of codons was found for different proteins, with structural proteins and polyproteins being more adapted to the codon bias of host target tissues. In contrast, accessory proteins had a more biased codon usage (i.e., lower number of preferred codons), which might contribute to the regulation of their expression level and timing throughout the cell cycle. Conclusions The present study confirms the existence of selective forces acting directly on the genome and not only indirectly through phenotype selection. This evidence might help understanding IBV biology and in developing attenuated strains without affecting the protein phenotype and therefore immunogenicity.

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