Biogeography

Code:

B4007

Acronym:

B4007

Keywords
Classification	Keyword
OFICIAL	Biology

Instance: 2014/2015 - 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	10	Official Study Plan	1	-	3	21	81

Teaching language

Suitable for English-speaking students

Objectives

The module Biogeography is aimed at giving a broad perspective on spatial patterns of biodiversity. It will be given an introduction to the discipline focusing on concepts and historical research on the subject. It will be discussed the distribution of single-species and communities with emphasis on methods for representing biodiversity distribution, spatial and temporal shifts in biodiversity distribution and the distribution of terrestrial biomes. It will be reviewed major biogeographical processes that originate, shit and maintain the geographic range of biodiversity. It will be discussed major geographic trends in the distribution of biodiversity, such as gradients and hotspots, from global to local scales. It will be given an introduction to methods for analysing geographic distribution including Ecological-Niche based models and Geographical Information Systems. Finally, it will be presented the concepts, aims and work methods on Conservation Biogeography.

 

Learning outcomes and competences

The Biogeography module was developed in order to meet two main objectives. On the one hand, providing a comprehensive and integrative view of biogeography, as the area of the biological sciences that brings together knowledge from other fields, such as Ecology, Evolution, Morphology, Genetics, Systematics, or Ethology, and other sciences such as Mathematics, Physics, or Geology. On the other hand, provide students with a solid background in Biogeography in order to more easily integrate the material taught in cycles specialization degree in biology, especially in blocks of options in the areas of Statistics and Models, Geology and Geographic Information.

Working method

Presencial

Program

1. Introduction to Biogeography
1.1 The science of biogeography
1.2 The history of biogeography
 
2. Geographic distribution
2.1 Species distributions
2.1.1 Geographic distribution
2.1.2 Distribution of populations
2.2 Distribution of communities
2.2.1 Communities and ecosystems
2.2.2 Distribution of communities
2.2.3 Terrestrial biomes
 
3. Biogeographic processes
3.1 Processes that maintain distributions – ecological character / local scale
3.2 Processes that change distributions – ecological and historical character / local or global scales
3.3 Processes that originate distributions – historical character /evolutionary scale
 
4. Geographic trends in the distribution of species richness
4.1 Latitudinal gradient
4.2 Other diversity patterns
4.3 Biodiversity hotspots
4.4 Regional and local patterns
 
5. Methods for analysing geographic distributions
5.1 Indexes characterising distributions
5.2 Univariate analyses
5.3 Multivariate analyses (species distribution models and models of species richness)
5.4 Geostatistical tools
5.5 Integrative analyses
 
6. Conservation biogeography
6.1 Definitions and aims
6.2 Climate changes and reserve design
6.3 Conservation of evolutionary processes
6.4 Integrative analyses

Mandatory literature

Brown, J.H. & Lomolino, M.V. ; Biogeography, 2nd Ed. Sinauer Associates, Massachusetts, 1998

Comments from the literature

A set of scientific papers will be distributed to students.

Teaching methods and learning activities

Theoretical classes and report preparation.

Evaluation Type

Distributed evaluation without final exam

Assessment Components

designation	Weight (%)
Participação presencial	20,00
Prova oral	40,00
Trabalho escrito	40,00
Total:	100,00

Amount of time allocated to each course unit

designation	Time (hours)
Estudo autónomo	60,00
Frequência das aulas	21,00
Total:	81,00

Eligibility for exams

Attendance to a minimum of 75% of classes.

Calculation formula of final grade

The main component for the assessment is the oral presentation of a scientific paper. The students will be arranged in groups of two and each group will present a scientific paper from the present bibliographic list (except books and book chapters). It will be used the general procedures for oral presentations in congresses: 10 minutes of oral presentation (5 for each student), in English, using a PowerPoint presentation as digital support. After the presentation, it will begin a discussion period in which all students should participate. Essentially, it is aimed that the presenting-students represent the role of the authors of the paper that they are going to present, but if needed not forgetting to auto-criticize the work, and that the audience represents a group of congress-people with sharp doubts. The time of discussion will be decided case by case according to the levels of interest and participation, but it should not exceed 10 minutes. Immediately after the presentation, the students should provide a copy of the presented slides (a print of the PowerPoint file with 4 slides in each page), which will constitute the formal document for evaluation.

The quantitative assessment will be based in six criteria:

1) Participation in classes: it will be evaluated the levels of interest and participation along classes

2) Duration of oral presentation: the presentation should not exceed 10 minutes

3) Slide contents: it will be evaluated the contents of slides to detect if these are appropriate for the oral presentation and if the information is correctly presented

4) Slide clarity: it will be evaluated the form how the information is presented in the slides

5) Oral presentation: it will be evaluated the capacity for oral presentation of the scientific paper

6) General discussion: it will be evaluated the level of participation in the discussion of the paper

 

Each one of these criteria is applied individually, which means that two students from the same group might have distinct evaluations.

Classification improvement

Improving the marking may be achieved through the oral presentation of a scientific paper to be decided. The presentation will be individual.

Observations

BIBLIOGRAPHY

Anderson, R.P., Gómez-Laverde, M., & Peterson, T. (2002) Geographical distributions of spiny pocket mice in South America: insights from predictive models. Global Ecology & Biogeography 11, 131-141.

Araújo, M.B., Nogués-Bravo, D., Diniz-Filho, J.A.F., Haywood, A.M., Valdes, P.J., & Rahbek, C. (2007) Quaternary climate changes explain diversity among reptiles and amphibians. Ecography 38, 8-15.

Arif, S., Adams, D.C., & Wicknick, J.A. (2007) Bioclimatic modelling, morphology, and behaviour reveal alternative mechanisms regulating the distributions of two parapatric salamander species. Evolutionary Ecology Research 9, 843-854.

Bauer, J.T. & Peterson, A.T. (2005) Visualizing environmental correlates of species geographical range limits. Diversity and Distributions 11, 275-278.

Brito, J.C., Acosta, A.L., Álvares, F., & Cuzin, F. (2009) Biogeography and conservation of taxa from remote regions: An application of ecological-niche based models and GIS to North-African Canids. Biological Conservation 142, 3020-3029.

Brown, J.H. & Lomolino, M.V. (1998) Biogeography, 2^nd Ed. Sinauer Associates, Massachusetts.

Carstens, B.C. & Richards, C.L. (2007) Integrating coalescent and ecological niche modeling in comparative phylogeography. Evolution 61, 1439-1454.

Casazza, G., Zappa, E., Mariotti, M.G., Médail, F., & Minuto, L. (2008) Ecological and historical factors affecting distribution pattern and richness of endemic plant species: the case of the Maritime and Ligurian Alps hotspot. Diversity and Distributions 14, 47-58.

Cordellier, M. & Pfenninger, M. (2009) Inferring the past to predict the future: climate modelling predictions and phylogeography for the freshwater gastropod Radix balthica (Pulmonata, Basommatophora). Molecular Ecology 18, 534-544.

de Jong, H. (1998) In search of historical biogeographic patterns in the western Mediterranean terrestrial fauna. Biological Journal of the Linnean Society 65, 99-164.

Filipe, A.F., Araújo, M.B., Doadrio, I., Angermeier, P.L., & Collares-Pereira, M.J. (2009) Biogeography of Iberian freshwater fishes revisited: the roles of historical versus contemporary constraints. Journal of Biogeography doi:10.1111/j.1365-2699.2009.02154.x.

Gómez, A. & Luntz, D.H. (2006) Refugia within refugia: patterns of phylogeographic concordance in the Iberian Peninsula. Phylogeography of Southern European Refugia (ed. by S. Weiss and N. Ferrand), pp. 155-188. Springer.

Graham, C.H., Smith, T.B., & Languy, M. (2005) Current and historical factors influencing patterns of species richness and turnover of birds in the Gulf of Guinea highlands. Journal of Biogeography 32, 1371-1384.

Graham, C.H. & Hijmans, R.J. (2006) A comparison of methods for mapping species ranges and species richness. Global Ecology & Biogeography 15, 578-587.

Lozier, J.D., Aniello, P., & Hickerson, M.J. (2009) Predicting the distribution of Sasquatch in western North America: anything goes with ecological niche modelling. Journal of Biogeography 36, 1623-1627.

Marmion, M., Parviainen, M., Luoto, M., Heikkinen, R.K.. & Thuiller, W. (2009) Evaluation of consensus methods in predictive species distribution modelling. Diversity and Distributions, 15, 59-69.

Martínez-Freiría, F., Sillero, N., Lizana, M., & Brito, J.C. (2008) GIS-based niche models identify environmental correlates sustaining a contact zone between three species of European vipers. Diversity and Distributions 14, 452-461.

Patten, M.A. & Smith-Patten, B.D. (2008) Biogeographical boundaries and Monmonier's algorithm: a case study in the northern Neotropics. Journal of Biogeography 35, 407-416.

Peterson, A.T. & Nyári, Á.S. (2007) Ecological niche conservatism and Pleistocene refugia in the thrush-like mourner,  Schiffornis sp., in the Neotropics. Evolution 62, 173-183.

Raxwhorty, C.J., Ingram, C.M., Rabibisoa, N., & Pearson, R.G. (2007) Applications of ecological niche modeling for species delimitation: a review and empirical evaluation using day geckos (Phelsuma) from Madagascar. Systematic Biology 56, 907-923.

Richards, C.L., Carstens, B.C., & Knowles, L.L. (2007) Distribution modelling and statistical phylogeography: an integrative framework for generating and testing alternative biogeographical hypotheses. Journal of Biogeography 34, 1833-1845.

Shepard, D.B. & Burbrink, F.T. (2009) Phylogeographic and demographic effects of Pleistocene climatic fluctuations in a montane salamander, Plethodon fourchensis. Molecular Ecology 18, 2243-2262.

Sillero, N., Brito, J.C., Skidmore, A.K., & Toxopeus, A.G. (2009) Biogeographical patterns derived from remote sensing variables: the amphibians and reptiles of the Iberian Peninsula. Amphibia-Reptilia 30, 185-206.

Smith, S.A., Stephens, P.R., & Wiens, J.J. (2005) Replicate patterns of species richness, historical biogeography, and phylogeny in Holarctic treefrogs. Evolution 59, 2433-2450.

Strasburg, J.L., Kearney, M., Moritz, C., & Templeton, A.R. (2007) Combining phylogeography with distribution modeling: multiple Pleistocene range expansions in a parthenogenetic gecko from the Australian arid zone. PLoS ONE 2, e760.

Swenson, N.G. & Howard, D.J. (2005) Clustering of contact zones, hybrid zones, and phylogeographic breaks in North America. The American Naturalist 166, 581-591.

Swenson, N.G. (2008) The past and future influence of geographic information systems on hybrid zone, phylogeographic and speciation research. Journal of Evolutionary Biology 21, 421-434.

Thuiller, W., Lavorel, S., Araújo, M.B., Sykes, M.T., & Prentice, I.C. (2005) Climate change threats to plant diversity in Europe. Proceedings National Acad.Science USA 102, 8245-8250.

Thuiller, W., Broennimann, O., Hughes, G., Alkemade, J.R.M., Midgley, G.F., & Corsi, F. (2006) Vulnerability of African mammals to anthropogenic climate change under conservative land transformation assumptions. Global Change Biology 12, 424-440.

Waltari, E., Hijmans, R.J., Peterson, A.T., Nyári, Á.S., Perkins, S.L., & Guralnick, R.P. (2007) Locating Pleistocene refugia: comparing phylogeographic and ecological niche model predictions. PLoS ONE 2, e563.

Waltari, E. & Guralnick, R.P. (2009) Ecological niche modelling of montane mammals in the Great Basin, North America: examining past and present connectivity of species across basins and ranges. Journal of Biogeography 36, 148-161.