In this subject, the evolutionary bases of DNA and gene products are studied, and the use of genetic data in the evolutionary analyses of different species. It begins with a theoretical introduction to the essential evolutionary processes, and then the evolution of molecular sequences and genomes is analyzed. In addition, this subject has a critical practical component since essential bioinformatics is worked on and molecular phylogenetics tools are used.

This course is helpful for students interested in Molecular Evolution and those who want to work on Molecular Taxonomy or Molecular Analysis of Populations.

Skills:

1) They know and adequately use scientific terminology and the basic concepts of Molecular Evolution

2) They know the origin and distribution of genetic variability in populations or species and its evolutionary importance.

3) Interpret the processes of molecular evolution through sequence analysis, bioinformatics techniques, and construction of phylogenetic trees

4) They analyze and interpret the evolution of genomes according to the modification of their size and structure.

5) Evaluate, interpret, and synthesize data and biological information

6) They creatively integrate knowledge taught and learned independently, which allows the resolution of biological problems by applying the scientific method.

THEORY PROGRAM



BASES

Topic.- 1 Introduction. What is evolution? Evolutionary theories.



Topic.- 2 Importance of variation in evolution. Techniques for the study of variability. Variability quantification. Neutral evolution and adaptation.



Topic.- 3 Dynamics of genes in populations. Basic concepts. Hardy-Weinberg equilibrium. evolutionary mechanisms

BIOINFORMATICS

Subject.- 4 Comparison of sequences. Sequence alignments Types of alignments. Alignment methods in pairs. Multiple Alignments. Alignment assessment methods.



Topic.- 5 Bioinformatics and molecular evolution. Introduction to bioinformatics. Gene and protein databases. Comparison of sequences and genomes using bioinformatics techniques.

EVOLUTION OF MOLECULAR SEQUENCES

Topic.- 6 Evolution of protein sequences. Estimation of the number of amino acid substitutions. Substitution matrices: position-dependent and position-independent substitution methods. Genetic codes. Codon usage. Codon usage bias. The molecular clock. Variations in the rate of molecular evolution. Lineage effects. Estimation of divergence time between species.



Topic.- 7 Evolution of nucleic acid sequences. Estimation of nucleotide substitution rates. Jukes-Cantor method. Kimura's 2-parameter method. Nucleotide substitution matrices. Tamura method. Gamma distance. Synonymous and non-synonymous substitutions. Evaluation of the methods. Selection detection. Variations in substitution rates in different regions of DNA. Mitochondrial and chloroplast DNA



PHYLOGENETICS

Topic.- 8 Molecular phylogenetics. Terminology. Orthologous, paralogous, and homologous genes. Topology and types of phylogenetic trees.

Topic.- 9 Genetic distance. Metric and Euclidean distances. Distances and identities of Nei. Examples.

Topic.- 10 Reconstruction of phylogenies. Construction methods based on grouping: UPGMA and Neighbor-Joining. Construction methods based on optimization: Minimum evolution, Parsimony, and Likelihood. Assessment of the reliability of a tree. Applications of phylogenetic analysis.

EVOLUTION OF GENOMES

Topic.- 11 Evolution of the size and complexity of genes. Gene duplication. Shuffling of exons and domains.

Topic.- 12 Evolution of genomes. Structure of the composition of the genome. C-value paradox. Evolution of repeated sequences. Horizontal gene transfer. Genome evolution by duplication.



INTERNSHIP PROGRAM



1) Search for DNA and protein sequences in molecular databases.

2) Search for genetic variations in molecular databases.

3) Homology analysis of DNA and protein sequences.

4) Construction and interpretation of phylogenetic trees.

Different teaching modalities are used in this subject.

- In the master classes, the theoretical concepts and some practical examples will be explained.

- The computer practices and the seminars will be carried out in groups. The use of molecular databases, the analysis of molecular sequences, and the reconstruction of phylogenetic trees will be studied in depth.

• Continuous Assessment System
• Final Assessment System
• Tools and qualification percentages:
  • Written test to be taken (%): 60
  • Realization of Practical Work (exercises, cases or problems) (%): 10
  • Team projects (problem solving, project design)) (%): 20
  • Exhibition of works, readings ... (%): 10

(A) Continuous evaluation

The evaluation system includes written tests of different modalities (60% of the final mark), including theoretical concepts and problem-solving, and reports related to practices and in-depth work that are developed (40% of the Final note).

There will be no partial exam. It will be necessary to obtain a 4 out of 10 on the exam to compute the final grade.

The qualifications obtained in memories and works will be saved for the extraordinary call if the student so wishes.

* In the case of continuous assessment, students may waive the call within a period that, at least, will be up to one month before the end date of the teaching period for the subject. This resignation must be submitted in writing to the teaching staff responsible for the subject.

(B) In the case of the final evaluation, students must submit in writing to the teaching staff responsible for the subject the waiver of continuous evaluation within a maximum period of 9 weeks from the beginning of the subject.



For students subject to continuous and final evaluation, it will be enough not to take the final test for the final grade for the subject to be "not submitted" or "not submitted."

academic ethics

During the development of the evaluation tests, the use of books, notes, or notes, as well as telephone, electronic, computer, or other devices or devices, by the students will be prohibited. Only a calculator is allowed. In any case of dishonest or fraudulent practice, the provisions of the protocol on academic ethics and prevention of dishonest or fraudulent practices in assessment tests and academic work at the UPV/EHU will be applied.

Ebaluazio-sistema ohiko deialdiaren berdina izango da.

The evaluation system will be the same as in the ordinary call. Failure to submit to the final test will mean renouncing the evaluation call and will be recorded as a Not Presented.

academic ethics
During the development of the evaluation tests, the use of books, notes, or notes, as well as telephone, electronic, computer, or other devices or devices, by the students will be prohibited. Only a calculator is allowed. In any case of dishonest or fraudulent practice, the provisions of the protocol on academic ethics and prevention of dishonest or fraudulent practices in assessment tests and academic work at the UPV/EHU will be applied.

Basic bibliography

Fontdevila, A., Moya, A. 2003. Evolución. Origen, adaptación y divergencia de las especies.

Ed. Síntesis. Madrid.

Freeman, S., Herron, J.C. 2002. Análisis evolutivo. Pearson Educación S.A. Madrid

Graur, D., Li, W.-H. 2000. Fundamentals of Molecular Evolution. Sinauer Associates.

Hedrick, P. W. 2005. Genetics of Populations. 3rd ed. Jones and Bartlett Pub. Boston.

Higss, P.G., Attwood, T.K. 2005. Bioinformatics and Molecular Evolution. Blackwell Publishing.

Li, W.-H. 1997. Molecular Evolution. Sinauer. MS.

Nei, M., Kumar, S. 2000. Molecular Evolution and Phylogenetics. Oxford University Press.

In-depth bibliography

Attwood, T.K. & D.J. Parry-Smith. 1999. Introduction to Bioinformatics.
Addison Wesley Longman Limited, Edimburgo.
Baxevanis, A.D., Ouellette, B.F.F. 2001. Bioinformatics. A practical guide
to the analysis of genes and proteins. 2nd ed. Wiley-InterScience
Brown, T.A. 2007. Genomes 3rd ed. Garland Science
Gibson, G., Muse, S.V. 2004. A primer of genome science. 2nd ed. Sinauer
Harvey, P.H., Leigh Browin, A.J., Maynard Smith J, Nee, S. 1996.
New uses for new phylogenies. Oxford
Higgins, D., Taylor, W. 2000. Bioinformatics. Sequence, structure and databanks.
Oxford University
Mount, D.W. 2001. Bioinformatics. Sequence and Genome analysis. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York
Salemi, M., Vandamme, A.-M. 2005 The Phylogenetic Handbook. A practical
approach to DNA and Protein phylogeny. Cambridge University Press. Cambridge.

Journals

Nature, Science, Proceedings of the National Academy of Science
Trends in Ecology and Evolution, Trends in Genetics, Ann. Rev. Ecol. Evol.
Biology and Molecular Evolution, Evolution, Journal of Molecular Evolution, Molecular Phylogenetics and Evolution
BMC Evolutionary Biology, BMC Genomics, Genome Biology

Web addresses

Historia de la evolución: http://www.ucmp.berkeley.edu/history/evolution.html
Darwin en la red: http://pages.britishlibrary.net/charles.darwin
Darwin y Wallace: http://www.inform.umd.edu/PBIO/darwin/darwindex.html
Mendel: http://www.mendelweb.org/
Historia de la Genética: http://www.es.embnet.org/~lmc/Genética3.html
http://evolution.berkeley.edu
http://www.eseb.org
http://www.nature.com/scitable/topic/Evolutionary-Genetics-13
http://wps.prenhall.com/esm_freeman_evol_3/12/3315/848837.cw/index.html
http://www.ncbi.nlm.nih.gov/Entrez