Molecular Methods in Biological Diversity Analysis

Code:

B4038

Acronym:

B4038

Keywords
Classification	Keyword
OFICIAL	Biology

Instance: 2014/2015 - 1S

Active?	Yes
Responsible unit:	Department of Biology
Course/CS Responsible:	Master in Biodiversity, Genetics and Evolution

Cycles of Study/Courses

Acronym	No. of Students	Study Plan	Curricular Years	Credits UCN	Credits ECTS	Contact hours	Total Time
M:BGE	20	Official Study Plan	1	-	6	42	162

Teaching language

English

Objectives

The main objective of the course is to provide students a deep understanding of the use of molecular tools in the study and comprehension of biological diversity. Complementing the different theoretical aspects related with the development, measurement and analysis of molecular markers a special effort will be dedicated to the contact with diverse laboratory techniques and analytical tools related with molecular data, with special emphasis on the DNA and RNA level.

Learning outcomes and competences

Aquisition and strengthening of the theoretical knowledge and concepts on the analysis of molecular genetic variation. Aquisition of basic laboratory skills on the use of different techniques of molecular genetic analysis.

Working method

Presencial

Program

Part 1 - Covers the evolutionary principles to introduce the natural mechanisms how genetic structure and diversity originates. The content provides the necessary background for interpretation and analysis of genotypic data developed by molecular methods. 

Part 2 – Demonstration of the principles of molecular genetics necessary to understand its implications for molecular measurement of genetic diversity. It covers molecular genetics DNA structure and organization, nuclear and cytoplasmic DNA, transcription and translation, protein structure to, gene organization and its implication for sequence divergence. Mutational mechanisms and mutation rate variation in different organisms and molecular markers. It’s Implications in population genetic diversity. Genetic diversiy analyses of diploid and haploid genomes.

Part 3 - Laboratory methods for DNA analyses. Samples conservation; methods applied to different types of samples and objectives. Theoretical background for DNA isolation, detection methods, Enzymatic reaction, restriction, ligation and DNA amplification: conditions, parameters and polymerase systems. Different PCR strategies. Variations to conventional PCR: qPCR. Polymerase errors and consequences. Primers design. Primer labelling. Southern and Northern blots. DNA Sequencing methods.

Part 4 - Laboratory methods to detect genetic variation. Historical perspective from electrophoretic analysis of proteins to genomic analysis. The use of different markersystems using restriction enzymes: AFLPs and RFLps. Construction of microssatelites libraries. Mutation rates and evolutionary models of microssatelites. Genotyping and applications. Development and genotyping of SNps. The use of SNPs arrays. Data analysis. Distinction between dominant and codominant markers.

Part 5 - New developments in next generation sequencing and its potential use for evolutionary biology research are introduced. The lecture covers the conceptual background of whole genome sequencing, laboratory workflow, Analysis principle, detection principle for different platforms, and potential applications for molecular evolutionary biology related studies using different genome downsizing strategies.

Part 6 - it will be given a broad overview on what RNA molecules are and on the methods currently used based on RNA molecules, with a few examples of how these methods are applied to address common questions in evolutionary biology, conservation, and other biological fields. Specific topics will focus on: Introduction to what is the RNA. RNA extraction: methods and problems related to it. Uses of RNA: gene characterization; gene expression analyses (microarray, qRT-PCR) RNA-seq (transcriptomics); fields of application of the above-mentioned techniques.

Mandatory literature

Avise John C.; Molecular markers, natural history, and evolution. ISBN: 978-0-87893-041-8 0-87893-041-8
Singer Maxine; Genes & genomes. ISBN: 978-0-935702-17-0
Hillis D, Moritz C, Mable B; Molecular systematics, Sinauer , 1996

Complementary Bibliography

Fred W Allendorf, Paul Hohenlohe, Gordon Luikart; Genomics and the future of conservation genetics, Nature Reviews Genetics, 11 , 697-709, 2010
I. Keller, O. Seehausen; Thermal adaptation and ecological speciation, Molecular Ecology, 21, 782-799
Christopher Bird, Iria Fernandez-Silva, Derek Skillings, Robert Toonen; Sympatric speciation in the post 'Modern Systhesis' Era of evolutionary biology, Evol Biol, 39: 158-180
J Huggett, K Dheda, S Bustin, A Zumla; Real-time RT-PCR normalization; strategies and considerations, Genes and Immunity, 1-6, 2005
Pal Olsvik, Kai Lie, Ann-Elise Jordal, Tom Nielsen, Ivar Hordvik; Evaluation of potential reference genes in real-time RT-PCR studies of Atlantic salmon, BMC Molecular Biology, 6:21, 2005
P Gayral, L Weinert, Y Chiari, ; Next-generation sequencing of transcriptomes: a guide to RNA isolation in nonmodel animals, Molecular Ecology Resources, 11, 650-661, 2011
V Cahais, P Gayral, G Tsagkogeorga, J Melo-Ferreira, M Ballenghien, L Weinert, Y Chiari, K Belkhir, V Ranwez, N Galtier; Reference-free transcriptome assembly in non-model animals from next-generation sequencing data, Molecular Ecology Resources
Y C Li, AB Korol, T Fahima, E Nevo; Microsatellites within genes: structure, function, and evolution, Molecular Biology and Evolution, 21, 991, 2004
G Luikart, PR England, D Tallmon, S Jordan, P Taberlet; The power and promise of population genomics: from genotyping to genome typing., Nature Reviews Genetics, 4, 981-994 , 2003
C Schlotterer; The evolution of molecular markers – just a matter of fashion? , Nature Reviews Genetics, 5, 63-68, 2004
D Zhang, GM Hewitt; Nuclear DNA analyses in genetic studies of populations: practice, problems and prospects., Molecular Ecology, 12, 563-584, 2003

Comments from the literature

Scientific papers distributed to students.

Teaching methods and learning activities

Theoretical classes, discussion of scientific papers, laboratory work with analysis of results and elaboration of a report with tutorial supervision

Evaluation Type

Distributed evaluation without final exam

Assessment Components

designation	Weight (%)
Participação presencial	20,00
Teste	50,00
Trabalho laboratorial	30,00
Total:	100,00

Amount of time allocated to each course unit

designation	Time (hours)
Frequência das aulas	25,00
Trabalho laboratorial	10,00
Total:	35,00

Eligibility for exams

Conclusion of the laboratory work and respective report.

Attendance of a minimum of 50% of the theoretical course.

 

 

Calculation formula of final grade

The students will be requested to: 1) write a report covering the procedures in the laboratory (30/100) and 2) written test on key concepts discussed in the theoretical components of the course (50/100); 3)presence and participation in classes (20/100). 

Classification improvement

Improvement of the theoretical and practical classification could be obtained through a final written examination (80/100)