Conservation Genetics

Code:

B4027

Acronym:

B4027

Keywords
Classification	Keyword
OFICIAL	Biology

Instance: 2021/2022 - 2S

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	14	Official Study Plan	1	-	6	42	162

Teaching language

English

Objectives

The main goal of this course is to apply the basis of theoretical and practical of evolutionary biology and population genetics on the conservation of biological diversity. In particular, aims to explain and demonstrate how the recent advances in Evolutionray biology and molecular genetics can help in maintaining the species and/or populations as dynamic entities, capable to survive to environmental changes, and thus minimizing their extinction risk.

Learning outcomes and competences

It is expected that students acquire theoretical and practical knowledge in conservation genetiics in order to develop skills that allow proper identification and evaluation of endangered species or populations and to prepare conservation plans, particularly for rare and illusive species. Additionally, it is intended that students solidify skills in oral and written presentation, analysis, interpretation and application of scientific results.

Working method

Presencial

Pre-requirements (prior knowledge) and co-requirements (common knowledge)

na

Program

1. Why we need to preserve biodiversity. The value of biodiversity. Brief review of the causes of biodiversity loss. Extinction vortex. Main international conventions for preserving biodiversity. UICN criteria. Threatened species in Europe, Spain and Portugal
2. Introduction to conservation genetics. From the conservation biology to the conservation genetics. The aims of conservation genetics. Steps to follow in conservation genetics. The problem of small populations.
3. Sampling techniques and samples preservation. How to preserve biological samples for DNA analysis. Methods for extracting difficult DNA (in feces, feathers, etc). Brief summary of molecular markers characteristics. How to select the best molecular markers for conservation genetics purposes.
4. Estimating genetic diversity through DNA markers: Microsatellites, DNA sequences, SNPs. Detecting population structure, fragmentation, isolation and migration. The problems of small populations. Real and effective population’s sizes. Evolutionary significant units (ESU) and Management Units (MU). Genetics monitoring and Landscape genetics
5. Hybrisation vs Conservation. Consequences of population fragmentation and hybridization. Natural and anthropogenic hybridization. Consequences of hybridization. Methods for detecting hybridization.
6. gNIS - genetic Non-Invasive Sampling. Advantages and disadvantages. Specificities in collecting non-invasive samples. Selection of molecular markers for non-invasive genetics. DNA extraction of non-invasive samples. PCR adjustments and pos-PCR procedures. Problems: allele dropout; false alleles and contaminations.
7. Application of gNIS in conservation and wildlife management. Species and sex identification. Pedigrees and individuals assignments to species and populations. Applications in controlling illegal hunting and trade of threatened species. Animal forensics.
8. From conservation genetics to conservation genomics. The advantages of genomic information on conservation. Understanding the local adaptation. Detection of selection.
9. Case studies in Conservation genetics.
10. Field work. Visit and pratical classes in a natural area. Collecting biological samples in terrestrial vertebrates, meeting with researches, scientific discussions based on pratical conservation exmples. 
11. Seminar “Conservation genetics: presentation of case studies”, by students. Open to other students and researchers..

Mandatory literature

Mills L. Scott; Conservation of wildlife populations. ISBN: 9780470671498
Allendorf Frederick William; Conservation and the genetics of population. ISBN: 978-1-4051-2145-3
Frankham Richard 1942-; Introduction to conservation genetics. ISBN: 978-0-521-70271-3
Avise John C.; Molecular markers, natural history, and evolution. ISBN: 978-0-87893-041-8 0-87893-041-8

Teaching methods and learning activities

Theoretical classes using multimedia. Discussion of concepts.
Discussion of scientific papers in topics related to the program.
Practical classes using different software for data analysis in conservation genetics (Structure, GenAlex, Cervus, etc).

This course includes pratical classes in  a biological field station (3 days), laboratory work and computacional analysis.

Software

Cervus
GenAlex
Structure

keywords

Natural sciences
Natural sciences > Biological sciences > Biodiversity > Biodiversity characterisation
Natural sciences > Biological sciences > Biodiversity > Sustainable exploitation

Evaluation Type

Distributed evaluation with final exam

Assessment Components

designation	Weight (%)
Participação presencial	10,00
Prova oral	30,00
Trabalho escrito	60,00
Total:	100,00

Amount of time allocated to each course unit

designation	Time (hours)
Apresentação/discussão de um trabalho científico	2,00
Estudo autónomo	50,00
Frequência das aulas	20,00
Trabalho de campo	12,00
Trabalho de investigação	40,00
Trabalho escrito	30,00
Trabalho laboratorial	8,00
Total:	162,00

Eligibility for exams

Participation in classes, report and presentation on a critical analysis of a scientific paper.

Calculation formula of final grade

Participation and performance during classes (2), report on critical analysis of scientific paper (12) and oral presentation (6).

Examinations or Special Assignments

Written Rreport and oral presentation

Special assessment (TE, DA, ...)

na

Classification improvement

Report on a critical analysis of  a scientific paper, with an oral exam, is  necessary. Participation in classes is maintained.

Observations

Books:
Allendorf, F. & Luikart, G. (2013). Conservation and the Genetics of Populations. Wiley-Blackwell, 2st edition.
Avise, J. (2004). Molecular Markers, Natural History, and Evolution. Sinauer Associates, 2nd edition.
Carrol, S. P. & Fox, C. W. (2008). Conservation Biology. Evolution in action. Oxford, 1st Edition.
Frankham, R., Ballou, J.D. & Briscoe, D.A. (2010). Introduction to Conservation Genetics. Cambridge University Press, 2nd edition.
Mills, S. (2013). Conservation of Wildlife Populations: Demography, Genetics and Management. Wiley-Blackwell, 2st edition.

Papers:
Barbosa S, Mestre F, White TA, Paupério J, Alves PC, Searle JB (2018). Integrative approaches to guide conservation decisions: Using genomics to define conservation units and functional corridors. Molecular Ecololy. 27:3452-3465. doi: 10.1111/mec.14806. Epub 2018 Aug 13.
Beja-Pereira, A., Oliveira, R., Alves, P.C., Schwartz, M.K. & Luikart., G. (2009). Advancing ecological understandings through technological transformations in non-invasive genetics. Molecular Ecology Resources 9, 1279–1301.
Ferreira CM, Sabino-Marques H, Paupério J, Barbosa S, Costa P, Encarnação C, Pita R, Beja P, Mira A, Searle JB and Alves PC* (2018). The applicability of non-invasive genetic sampling for monitoring small mammal metapopulations. European Journal of Wildlife Research, 64: 46.
Oliveira, R., Castro, D., Godinho, R., Luikart, G. & Alves, P.C. (2010). Species identification using a small nuclear gene fragment: application to sympatric wild carnivores from South-western Europe. Conservation Genetics 11.
Oliveira, R., Godinho, R., Randi, E. & Alves, P.C. (2008). Hybridization vs conservation: are domestic cats threatening the genetic integrity of European wildcat (Felis silvestris silvestris) populations in Iberian Peninsula? Philosophical Transactions of the Royal Society, Biological Sciences, 363: 2953-2961. 
Shafer AB, Wolf J,Alves PC,Bergström L,Colling G, Dalén L,De Meester L,Ekblom, R,Fior S,Hajibabaei M,Hoezel AR,Hoglund J,Jensen E,Krützen M,Norman A,Österling E M,Ouborg J,Piccolo J,Primmer C, Reed F,Roumet M,Salmona J,Schwartz M, Segelbacher G,Thaulow J, Valtonen M,Vergeer P,Weissensteiner M.Wheat C, Vilà C,Zieliński P. (2016). Reply to Gardner et al. Trends in Ecology & Evolution, 31: 83 – 84.