Molecular Phylogenetics and Evolution
A.Y. 2023/2024
Learning objectives
The course aims to contribute to the training of master's graduates who have a full understanding of the fundamentals of evolutionary biology and of the theoretical foundation and methods used in phylogenetic reconstruction, with a special focus on molecular phylogenetics. These fundamentals will be declined both from theoretical and methodological perspectives. Objectives include clarification of how the methodological tools represent both the translation of theoretical knowledge, but also a new source of information, in turn stimulating the generation of new
theoretical formulations. The fundamental concepts of the discipline will be presented in a historical key, with particular emphasis on the main discussions, sometimes diatribes, which have accompanied the development of the different areas of experimental research and theoretical elaboration of evolutionary biology.
theoretical formulations. The fundamental concepts of the discipline will be presented in a historical key, with particular emphasis on the main discussions, sometimes diatribes, which have accompanied the development of the different areas of experimental research and theoretical elaboration of evolutionary biology.
Expected learning outcomes
At the end of the course, the student will have acquired: knowledge of the basic concepts of biological evolution (such as: fitness; natural selection; mutation; homology; analogy). Knowledge of specific issues (such as: the targets of natural selection; altruism; neutrality theory; origin of life and cells). Knowledge of evolutionary mechanisms at the molecular level. Knowledge of the principles underlying the main approaches for the reconstruction of phylogenetic trees, and their applications.
Lesson period: Second semester
Assessment methods: Esame
Assessment result: voto verbalizzato in trentesimi
Single course
This course can be attended as a single course.
Course syllabus and organization
Single session
Responsible
Lesson period
Second semester
Course syllabus
Molecular Phylogenetics:
1) The importance of molecular phylogenetics in the study of evolutionary relationships between organisms.
2) Concepts of Homology, Orthology, and Paralogy. The fate of duplicated genes. The role of gene duplication in the generation of evolutionary novelty.
3) The mode of natural selection on molecular sequences, the impact of the genetic code, the neutral theory, molecular clocks.
4) Phylogenetic trees, terminology, data formats, interpretation. Rooted and un-rooted trees, outgroups.
5) Alignment of homologous sequences: Positional homology, scoring alignments. Global vs local alignment. Pairwise and multiple alignment.
6) Database searches using sequence homology. BLAST, its strengths and weaknesses. The fasta data format.
7) Common tools for multiple sequence alignment (clustal, muscle), alignment of coding sequences/codon alignment. Masking of sequence alignment
8) Saturation of substitutions, models of substitution processes and correction of genetic distance estimates.
9) Simple distance clustering strategies (UPGMA, Neighbor Joining).
10) Maximum parsimony and its application to phylogenetics
11) Probabilistic approaches (Likelihood/Bayesian phylogenetics)
12) The bootstrap
13) Critical evaluation of phylogenetic hypotheses.
Biological Evolution:
1)Selected topics from the history of Evolutionary Biology
2) Natural Selection
3) Hierarchies and targets of natural selection
4) Altruism in biology: group selection, and kin selection, the role of sexual reproduction.
5) Phenotypic plasticity, phenotypic adaptation, genetic adaptation,
6) Epigenetic modification and epigenetic heredity
7) The Neutral Theory of molecular evolution
8) Punctuated equilibria
1) The importance of molecular phylogenetics in the study of evolutionary relationships between organisms.
2) Concepts of Homology, Orthology, and Paralogy. The fate of duplicated genes. The role of gene duplication in the generation of evolutionary novelty.
3) The mode of natural selection on molecular sequences, the impact of the genetic code, the neutral theory, molecular clocks.
4) Phylogenetic trees, terminology, data formats, interpretation. Rooted and un-rooted trees, outgroups.
5) Alignment of homologous sequences: Positional homology, scoring alignments. Global vs local alignment. Pairwise and multiple alignment.
6) Database searches using sequence homology. BLAST, its strengths and weaknesses. The fasta data format.
7) Common tools for multiple sequence alignment (clustal, muscle), alignment of coding sequences/codon alignment. Masking of sequence alignment
8) Saturation of substitutions, models of substitution processes and correction of genetic distance estimates.
9) Simple distance clustering strategies (UPGMA, Neighbor Joining).
10) Maximum parsimony and its application to phylogenetics
11) Probabilistic approaches (Likelihood/Bayesian phylogenetics)
12) The bootstrap
13) Critical evaluation of phylogenetic hypotheses.
Biological Evolution:
1)Selected topics from the history of Evolutionary Biology
2) Natural Selection
3) Hierarchies and targets of natural selection
4) Altruism in biology: group selection, and kin selection, the role of sexual reproduction.
5) Phenotypic plasticity, phenotypic adaptation, genetic adaptation,
6) Epigenetic modification and epigenetic heredity
7) The Neutral Theory of molecular evolution
8) Punctuated equilibria
Prerequisites for admission
A solid basic understanding of the fundamental concepts of molecular biology: Genome replication, Transcription, Translation, the nature of the genetic code, the polymerase chain reaction.
Teaching methods
The course presented as 2 teaching units (Molecular Phylogenetics [4cfu] and Biological Evolution [2cfu])
The Molecular Phylogenetics teaching unit consists of 3cfu (24hours) of frontal teaching and one cfu (16 hours) of computer-based practical sessions in an informatics lecture theatre. Activities, closely supervised by teachers, will include use of public databases to retrieve sequences for phylogenetic analyses, alignment of molecular sequences, evaluation of alignments, implementation of phylogenetic approaches that are presented in the lecture course. All practical approaches will use open databases and free software tools which may be used on any standard operating system (Windows/MacOS/Linux).
The Biological Evolution teaching unit consists of 2 cfu (16 hours) of frontal teaching, where specific subjects pertinent to evolutionary biology will be considered in seminar-style lectures
The Molecular Phylogenetics teaching unit consists of 3cfu (24hours) of frontal teaching and one cfu (16 hours) of computer-based practical sessions in an informatics lecture theatre. Activities, closely supervised by teachers, will include use of public databases to retrieve sequences for phylogenetic analyses, alignment of molecular sequences, evaluation of alignments, implementation of phylogenetic approaches that are presented in the lecture course. All practical approaches will use open databases and free software tools which may be used on any standard operating system (Windows/MacOS/Linux).
The Biological Evolution teaching unit consists of 2 cfu (16 hours) of frontal teaching, where specific subjects pertinent to evolutionary biology will be considered in seminar-style lectures
Teaching Resources
Materials (book chapters (pdf), relevant articles (pdf), links to resources and software) will be provided by the teacher through the Ariel website and through a dedicates Microsoft Teams group. Students are strongly recommended to inscribe to the teams group as it provides an invaluable platform for interaction between students and with the teacher outside of the classroom and facilitates the teacher providing assistance with the
Assessment methods and Criteria
The final vote for the course will consist of a weighted (4:2) mean of the votes obtained for separate evaluation of the two teaching units.
For the Molecular Phylogenetics teaching unit the evaluation will be based on a short report prepared by students. Students will choose a gene to study from a list curated by the teacher and will be expected to prepare a dataset to examine phylogenetic relationships between vertebrate groups, to execute a series of phylogenetic analyses strategies, and to interpret and discuss their results within a clearly defined framework to be explained and clarified by the teacher. Final reports and intermediate datasets will be submitted electronically.
This work may be performed individually or in groups of 2 students (who will be awarded identical votes for their contribution)
For the Biological Evolution teaching unit, the vote will be based on an oral exam. Students can prepare a topic of their choice, but the questions can also relate to other parts of the program.
For the Molecular Phylogenetics teaching unit the evaluation will be based on a short report prepared by students. Students will choose a gene to study from a list curated by the teacher and will be expected to prepare a dataset to examine phylogenetic relationships between vertebrate groups, to execute a series of phylogenetic analyses strategies, and to interpret and discuss their results within a clearly defined framework to be explained and clarified by the teacher. Final reports and intermediate datasets will be submitted electronically.
This work may be performed individually or in groups of 2 students (who will be awarded identical votes for their contribution)
For the Biological Evolution teaching unit, the vote will be based on an oral exam. Students can prepare a topic of their choice, but the questions can also relate to other parts of the program.
BIO/11 - MOLECULAR BIOLOGY - University credits: 6
Lessons: 48 hours
Educational website(s)
Professor(s)
Reception:
Thursday 14.00 - 17.00
Via Celoria 26, Tower B, 2nd floor