BAYESIAN ANALYSIS OF BIRD OVOMUCOID: INFERRINGEVOLUTIONARY DYNAMICS AND PHYLOGENETIC RELATIONSHIPS.

Rachana Krishnamurthy

BAYESIAN ANALYSIS OF BIRD OVOMUCOID: INFERRINGEVOLUTIONARY DYNAMICS AND PHYLOGENETIC RELATIONSHIPS.

Rachana Krishnamurthy | International Journal of Animal Biotechnology and Applications | Vol 10, Issue 01 | ISSN: 2455-7315

Abstract

Objective: Ovomucoid is a serine protease inhibitor discovered in bird eggs that not only protects embryo but also has phylogenetic significance due to its potential usage as a molecular marker. They are glycoproteins that have antibacterial efficacy because they inhibit bacterial proteolytic enzymes that are essential for microbiological development. This study makes use of DNA sequence data to rebuild evolutionary connections among bird species.
Methods: Over the past decade, the incorporation of cutting-edge Bayesian analytic methods has resulted in substantial advances in the study of Phylogeny. Here, we successfully explore parameter space by integrating sophisticated Bayesian techniques, predicting divergence durations, branch lengths, and substitution rates using the software tools- BEAUti, BEAST, TreeAnnotator, Tracer, and FigTree. In general, this research demonstrates the effectiveness of Bayesian analytic methods in unraveling the rich evolutionary thread woven by bird ovomucoid. The resulting Bayesian phylogenetic tree sheds light on the evolutionary processes of bird ovomucoid over several avian families.
Results: The use of Bayesian methods along with Phylogenetic evaluation provides insights into the evolutionary connections of the seventeen bird ovomucoids. Using probabilistic statistical models could shed light on the genetic basis and hence the string that links the many avian species. The Bayesian analysis also facilitated this study by yielding information about branch lengths, and substitution rates, and hence put forth a clearer picture of evolution based on bird ovomucoid.
Conclusion: These findings help to deepen our understanding of bird ovomucoid evolution and lay the groundwork for future avian genetics and evolutionary biology study. Thus, the findings give a framework for addressing pressing questions and advancing research in the field of molecular evolution.

Keywords: Ovomucoid, Bayesian, Phylogenetic analysis, BEAUti, BEAST, FigTree, Tracer,
Molecular evolution

🔒 This is a subscription article

Full text is available to subscribers and institutional members. Please choose an option below to access it.

Subscribe Purchase this article Institutional / Login access

References

[1] Arbi, M., Souiai, O., Rego, N., Larbi, I., Naya, H., Ghram, A., & Houimel, M. (2020, April 25). Historical origins and zoonotic potential of avian influenza virus H9N2 in Tunisia revealed by Bayesian analysis and molecular characterization. Archives of Virology, 165(7), 1527–1540. https://doi.org/10.1007/s00705-020-04624-4

[2] Furlong, & Holland. (n.d.). https://bioone.org/jBayesian-Phylogenetic-Analysis-Supports Monophyly-of-Ambulacraria-and-of-Cyclostomes. BioOne Digital Library, 19(5).

[3] Fabreti, L. G., & Höhna, S. (2021, October 15). Convergence assessment for Bayesian phylogenetic analysis using MCMC simulation. Methods in Ecology and Evolution, 13(1), 77–90.

https://doi.org/10.1111/2041-210x.13727

[4] Xie, Q., Bu, W., & Zheng, L. (2005, February). The Bayesian phylogenetic analysis of the 18S rRNA sequences from the main lineages of Trichophora (Insecta: Heteroptera: Pentatomomorpha). Molecular Phylogenetics and Evolution, 34(2), 448–451. https://doi.org/10.1016/j.ympev.2004.10.015

[5] Drummond, A. J., & Rambaut, A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7(1), 214. https://doi.org/10.1186/1471-2148-7-214

[6] Winiarska-Mieczan A, Kwiecień M. Charakterystyka owomukoidu--jednego z wazniejszych alergenów pokarmowych [Avian egg's white ovomucoid as food-allergen for human]. Postepy Biochem. 2007;53(3):212-7. Polish. PMID: 18399349.

[7] De Bruyn, A., Martin, D. P., & Lefeuvre, P. (2013, December 19). Phylogenetic Reconstruction Methods: An Overview. Methods in Molecular Biology, 257–277. https://doi.org/10.1007/978-1- 62703-767-9_13

[8] Drummond, Ho, Rawlence, & Rambaut. (2007, May 17). A Rough Guide to BEAST 1.4. Retrieved August 25, 2023, from https://www.researchgate.net/profile/Nicolas- Rawlence/publication/228988177_A_Rough_Guide_to_beast_14/links/0a85e532a8d141a0e2000

000/A-Rough-Guide-to-beast-14.pdf.

[9] Bouckaert, Remco, et al. "Estimating Species Trees from Multilocus Data." (2012, Oct 12).Estimating Species Trees from Multilocus Data.

[10] Stein, J., Catterall, J. F., Kristo, P., Means, A. R., & O’Malley, B. W. (1980, October 1). Ovomucoid intervening sequences specify functional domains and generate protein polymorphism. Cell; Cell Press. https://doi.org/10.1016/0092-8674(80)90431-6

[11] Wei, X., Chen, M., & Cui, J. (2017, December 1). Bayesian evolutionary analysis for emerging infectious disease: an exemplified application for H7N9 avian influenza viruses. Science China-life Sciences; Springer Science+Business Media. https://doi.org/10.1007/s11427-017-

9227-6

[12] Baele, G., Lemey, P., Rambaut, A., & Suchard, M. A. (2017). Adaptive MCMC in Bayesian

phylogenetics: an application to analyzing partitioned data in BEAST. Bioinformatics, 33(12), 1798–1805. https://doi.org/10.1093/bioinformatics/btx088

[13] Osozawa, S., & Wakabayashi, J. (Year). Cicada timetree by BEAST v1.X verified the recently and exponentially increasing base substitution rates. Title of the Journal or Preprint Server, Version number. https://doi.org/10.1101/2020.12.03.409599

[14] Jose-Abrego, A., Roman, S., Laguna-Meraz, S., Rebello-Pinho, J. R., Arevalo, S. J., & Panduro, A. (2023, May 24). Tracing the evolutionary history of hepatitis B virus genotype H endemic to Mexico. Frontiers in Microbiology; Frontiers Media. https://doi.org/10.3389/fmicb.2023.1180931

[15] Hill, V., & Baele, G. (2019, July 31). Bayesian Estimation of Past Population Dynamics in BEAST 1.10 Using the Skygrid Coalescent Model. Molecular Biology and Evolution; Oxford University Press. https://doi.org/10.1093/molbev/msz172

[16] Baele, G., Ayres, D. L., Rambaut, A., Suchard, M. A., & Lemey, P. (2019, January 1). High-

Performance Computing in Bayesian Phylogenetics and Phylodynamics Using BEAGLE. Springer eBooks. https://doi.org/10.1007/978-1-4939-9074-0_23

[17] Dellicour, S., Gill, M. S., Faria, N. R., Rambaut, A., Pybus, O. G., Suchard, M. A., & Lemey, P. (2021, February 2). Relax, Keep Walking — A Practical Guide to Continuous Phylogeographic Inference with BEAST. Molecular Biology and Evolution; Oxford University Press. https://doi.org/10.1093/molbev/msab031

[18] Springer, M. S., Murphy, W. J., & Roca, A. L. (2018, April 1). Appropriate fossil calibrations and tree constraints uphold the Mesozoic divergence of solenodons from other extant mammals. Molecular Phylogenetics and Evolution; Elsevier BV. https://doi.org/10.1016/j.ympev.2018.01.007

[19] Kumar, S., Nei, M., Dudley, J. T., & Tamura, K. (2008, March 27). MEGA: A biologist- centric software for evolutionary analysis of DNA and protein sequences. Briefings in Bioinformatics; Oxford University Press. https://doi.org/10.1093/bib/bbn017

[20] Lee, J., Cho, H. Y., Lee, J. H., Ahn, D. U., Kim, K. T., & Paik, H. D. (2023, August 9). The inhibitory effect of ovomucoid from egg white on the biofilm formation by Streptococcus mutans. Journal of the Science of Food and Agriculture; Wiley. https://doi.org/10.1002/jsfa.12915

[21] Abeyrathne, E., Lee, H. Y., Jo, C., Suh, J. W., & Ahn, D. U. (2015, September 1). Enzymatic hydrolysis of ovomucoid and the functional properties of its hydrolysates. Poultry Science; Oxford University Press. https://doi.org/10.3382/ps/pev196

[22] Building phylogenetic trees from molecular data with MEGA - PubMed. (2013, May 1). PubMed. https://doi.org/10.1093/molbev/mst012

[23] OVOMUCOID | Bioseutica®. (n.d.). OVOMUCOID | Bioseutica®. https://www.bioseutica.com/products/ovomucoid#:~:text=Comprising%2011%25%20of%20the %20egg,in%20a%201%3A1%20ratio.

[24] Portugal, J. S., Allerdice, M. E. J., Moraru, G. M., King, J. W. B., Paddock, C. D., Becker, T., Smith, T. C., & Goddard, J. (2019, April 5). Molecular Phylogeny of Dermacentor parumapertus (Acari: Ixodidae) from Two Locations Within Its Geographical Range. Journal of Medical Entomology; Oxford University Press. https://doi.org/10.1093/jme/tjz042

[25] Suchard, Lemey, Baele, Ayres, Drummond, & Rambaut. (n.d.). Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evolution, 4(1).

[26] Suchard, M. A., Christina M. R. Kitchen, Sinsheimer, J. S., & Weiss, R. E. (2003). Hierarchical Phylogenetic Models for Analyzing Multipartite Sequence Data. Systematic Biology, 52(5), 649–664. http://www.jstor.org/stable/3651067

How to cite this article

APA

Krishnamurthy, R. (2024). BAYESIAN ANALYSIS OF BIRD OVOMUCOID: INFERRINGEVOLUTIONARY DYNAMICS AND PHYLOGENETIC RELATIONSHIPS.. International Journal of Animal Biotechnology and Applications, 10(01).

MLA

Krishnamurthy, Rachana. “BAYESIAN ANALYSIS OF BIRD OVOMUCOID: INFERRINGEVOLUTIONARY DYNAMICS AND PHYLOGENETIC RELATIONSHIPS..” International Journal of Animal Biotechnology and Applications, vol. 10, no. 01, 2024.

Chicago

Rachana Krishnamurthy. “BAYESIAN ANALYSIS OF BIRD OVOMUCOID: INFERRINGEVOLUTIONARY DYNAMICS AND PHYLOGENETIC RELATIONSHIPS..” International Journal of Animal Biotechnology and Applications 10, no. 01 (2024).

Vancouver

Krishnamurthy R. BAYESIAN ANALYSIS OF BIRD OVOMUCOID: INFERRINGEVOLUTIONARY DYNAMICS AND PHYLOGENETIC RELATIONSHIPS.. International Journal of Animal Biotechnology and Applications. 2024;10(01).

BibTeX

@article{KrishnamurthyR2024,
author = {Rachana Krishnamurthy},
title = {BAYESIAN ANALYSIS OF BIRD OVOMUCOID: INFERRINGEVOLUTIONARY DYNAMICS AND PHYLOGENETIC RELATIONSHIPS.},
journal = {International Journal of Animal Biotechnology and Applications},
year = {2024},
volume = {10},
number = {01},
issn = {2455-7315},
url = {https://journalspub.com/publication/uncategorized/article=11145}
}

► Necessary Cookies Always Active

Necessary cookies enable essential site features like secure log-ins and consent preference adjustments. They do not store personal data.

► Functional Cookies Remark

Functional cookies support features like content sharing on social media, collecting feedback, and enabling third-party tools.

► Analytical Cookies Remark

Analytical cookies track visitor interactions, providing insights on metrics like visitor count, bounce rate, and traffic sources.

► Advertisement Cookies Remark

Advertisement cookies deliver personalized ads based on your previous visits and analyze the effectiveness of ad campaigns.

Rachana Krishnamurthy | International Journal of Animal Biotechnology and Applications | Vol 10, Issue 01 | ISSN: 2455-7315

Abstract

Keywords: Ovomucoid, Bayesian, Phylogenetic analysis, BEAUti, BEAST, FigTree, Tracer,
Molecular evolution

🔒 This is a subscription article

Full text is available to subscribers and institutional members. Please choose an option below to access it.

Subscribe Purchase this article Institutional / Login access

References

[2] Furlong, & Holland. (n.d.). https://bioone.org/jBayesian-Phylogenetic-Analysis-Supports Monophyly-of-Ambulacraria-and-of-Cyclostomes. BioOne Digital Library, 19(5).

[3] Fabreti, L. G., & Höhna, S. (2021, October 15). Convergence assessment for Bayesian phylogenetic analysis using MCMC simulation. Methods in Ecology and Evolution, 13(1), 77–90.

https://doi.org/10.1111/2041-210x.13727

[5] Drummond, A. J., & Rambaut, A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7(1), 214. https://doi.org/10.1186/1471-2148-7-214

000/A-Rough-Guide-to-beast-14.pdf.

[9] Bouckaert, Remco, et al. "Estimating Species Trees from Multilocus Data." (2012, Oct 12).Estimating Species Trees from Multilocus Data.

9227-6

[12] Baele, G., Lemey, P., Rambaut, A., & Suchard, M. A. (2017). Adaptive MCMC in Bayesian

phylogenetics: an application to analyzing partitioned data in BEAST. Bioinformatics, 33(12), 1798–1805. https://doi.org/10.1093/bioinformatics/btx088

[16] Baele, G., Ayres, D. L., Rambaut, A., Suchard, M. A., & Lemey, P. (2019, January 1). High-

Performance Computing in Bayesian Phylogenetics and Phylodynamics Using BEAGLE. Springer eBooks. https://doi.org/10.1007/978-1-4939-9074-0_23

[22] Building phylogenetic trees from molecular data with MEGA - PubMed. (2013, May 1). PubMed. https://doi.org/10.1093/molbev/mst012

[23] OVOMUCOID | Bioseutica®. (n.d.). OVOMUCOID | Bioseutica®. https://www.bioseutica.com/products/ovomucoid#:~:text=Comprising%2011%25%20of%20the %20egg,in%20a%201%3A1%20ratio.

[25] Suchard, Lemey, Baele, Ayres, Drummond, & Rambaut. (n.d.). Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evolution, 4(1).

How to cite this article

APA

MLA

Chicago

Vancouver

Krishnamurthy R. BAYESIAN ANALYSIS OF BIRD OVOMUCOID: INFERRINGEVOLUTIONARY DYNAMICS AND PHYLOGENETIC RELATIONSHIPS.. International Journal of Animal Biotechnology and Applications. 2024;10(01).

BibTeX

@article{KrishnamurthyR2024,
author = {Rachana Krishnamurthy},
title = {BAYESIAN ANALYSIS OF BIRD OVOMUCOID: INFERRINGEVOLUTIONARY DYNAMICS AND PHYLOGENETIC RELATIONSHIPS.},
journal = {International Journal of Animal Biotechnology and Applications},
year = {2024},
volume = {10},
number = {01},
issn = {2455-7315},
url = {https://journalspub.com/publication/uncategorized/article=11145}
}

Rachana Krishnamurthy | International Journal of Animal Biotechnology and Applications | Vol 10, Issue 01 | ISSN: 2455-7315

Abstract

Keywords: Ovomucoid, Bayesian, Phylogenetic analysis, BEAUti, BEAST, FigTree, Tracer,
Molecular evolution

🔒 This is a subscription article

Full text is available to subscribers and institutional members. Please choose an option below to access it.

Subscribe Purchase this article Institutional / Login access

References

[2] Furlong, & Holland. (n.d.). https://bioone.org/jBayesian-Phylogenetic-Analysis-Supports Monophyly-of-Ambulacraria-and-of-Cyclostomes. BioOne Digital Library, 19(5).

[3] Fabreti, L. G., & Höhna, S. (2021, October 15). Convergence assessment for Bayesian phylogenetic analysis using MCMC simulation. Methods in Ecology and Evolution, 13(1), 77–90.

https://doi.org/10.1111/2041-210x.13727

[5] Drummond, A. J., & Rambaut, A. (2007). BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evolutionary Biology, 7(1), 214. https://doi.org/10.1186/1471-2148-7-214

000/A-Rough-Guide-to-beast-14.pdf.

[9] Bouckaert, Remco, et al. "Estimating Species Trees from Multilocus Data." (2012, Oct 12).Estimating Species Trees from Multilocus Data.

9227-6

[12] Baele, G., Lemey, P., Rambaut, A., & Suchard, M. A. (2017). Adaptive MCMC in Bayesian

phylogenetics: an application to analyzing partitioned data in BEAST. Bioinformatics, 33(12), 1798–1805. https://doi.org/10.1093/bioinformatics/btx088

[16] Baele, G., Ayres, D. L., Rambaut, A., Suchard, M. A., & Lemey, P. (2019, January 1). High-

Performance Computing in Bayesian Phylogenetics and Phylodynamics Using BEAGLE. Springer eBooks. https://doi.org/10.1007/978-1-4939-9074-0_23

[22] Building phylogenetic trees from molecular data with MEGA - PubMed. (2013, May 1). PubMed. https://doi.org/10.1093/molbev/mst012

[23] OVOMUCOID | Bioseutica®. (n.d.). OVOMUCOID | Bioseutica®. https://www.bioseutica.com/products/ovomucoid#:~:text=Comprising%2011%25%20of%20the %20egg,in%20a%201%3A1%20ratio.

[25] Suchard, Lemey, Baele, Ayres, Drummond, & Rambaut. (n.d.). Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evolution, 4(1).

How to cite this article

APA

MLA

Chicago

Vancouver

Krishnamurthy R. BAYESIAN ANALYSIS OF BIRD OVOMUCOID: INFERRINGEVOLUTIONARY DYNAMICS AND PHYLOGENETIC RELATIONSHIPS.. International Journal of Animal Biotechnology and Applications. 2024;10(01).

BibTeX

@article{KrishnamurthyR2024,
author = {Rachana Krishnamurthy},
title = {BAYESIAN ANALYSIS OF BIRD OVOMUCOID: INFERRINGEVOLUTIONARY DYNAMICS AND PHYLOGENETIC RELATIONSHIPS.},
journal = {International Journal of Animal Biotechnology and Applications},
year = {2024},
volume = {10},
number = {01},
issn = {2455-7315},
url = {https://journalspub.com/publication/uncategorized/article=11145}
}