The primary objective of this course is to provide doctoral students with an advanced understanding of the theoretical foundations, computational methodologies, and research applications of molecular phylogenetics in animal science. The course covers the principles of phylogenetic inference based on DNA sequence data, molecular evolution models, phylogenetic tree reconstruction methods, molecular clock approaches, the assessment of genetic relationships among populations, and the application of bioinformatics tools for evolutionary analyses. Particular emphasis is placed on the use of molecular phylogenetic approaches for the characterization and conservation of animal genetic resources, the assessment of biodiversity, the investigation of domestication processes, the elucidation of genetic relationships among breeds and populations, the evolutionary interpretation of genomic data, and the development of sustainable animal breeding strategies. Upon successful completion of the course, students will be able to critically evaluate phylogenetic analyses, develop appropriate analytical frameworks for evolutionary studies, and integrate contemporary molecular phylogenetic methodologies into original research in animal genetics, genomics, and breeding.

1- Fundamental concepts of molecular phylogenetics, its role in evolutionary biology, and applications in animal science. 2- Molecular markers and DNA sequence data: mitochondrial DNA, nuclear DNA, and genomic markers. 3- Sequence alignment, data quality assessment, and preparation of datasets for phylogenetic analyses. 4- Models of molecular evolution, nucleotide substitution models, and model selection approaches. 5- Phylogenetic tree reconstruction methods: UPGMA, Neighbor-Joining, Maximum Parsimony, Maximum Likelihood, and Bayesian inference. 6- Evaluation of phylogenetic tree reliability: bootstrap analysis, posterior probabilities, and comparison of tree topologies. 7- Molecular clock approaches, evolutionary time estimation, and demographic history of populations. 8- Applications of molecular phylogenetics in the characterization of animal genetic resources, biodiversity assessment, and domestication studies. 9- Phylogenomics, genome-wide phylogenetic analyses, and the use of bioinformatics software (e.g., MEGA, BEAST, MrBayes, IQ-TREE, and RAxML). 10- Current advances in molecular phylogenetics, critical evaluation of scientific literature, and advanced research applications.