====== Material Apoio ======
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Textos, slides e material suplementar, por tema de aula.
**O material suplementar não é uma lista completa de tópicos ou literatura sobre o assunto**, mas uma coletânea parcial, pessoal e passional feita pelos professores.
À medida que a disciplina avança, incluiremos referências para artigos, livros, pessoas e //sites// que se mostrem importantes nas discussões e aulas teóricas.
Para cada tema há os seguintes textos:
* **Introdutórios**: leitura obrigatória antes da primeira aula de cada tema, seja discussão, seja exercício.
* **Para Discussão**: leitura obrigatória antes das aulas de discussão sobre cada tema.
* **Suplementares**: leitura opcional, para aprofundar-se no tema.
===== Introdução à Ecologia de comunidades =====
==== Leituras ====
===Introdutórias===
* Robert Root-Bernstein, 2008. //I don't know//. //In:// de Vitek, W., & Jackson, W. eds. The virtues of ignorance: complexity, sustainability, and the limits of knowledge.
=== Para discussão ===
* Werner, E.E. 1998. Ecological experiments and a research program in community ecology. pp 3-27 //In:// Resetarits B. & J. Bernardo. //Experimental ecology: issues and perspectives.// Oxford University Press.
* Roughgarden J. 2009. Is there a general theory of community ecology? //Biology and Philosophy// 224:521–529
==== Slides ====
* {{:aulas:aula1_introducao_2016.pdf|Palestra 1 - Introdução e histórico de Ecologia de Comunidades}}
==== Material Suplementar ====
* Levin, S. 1992. The problem of pattern and scale in ecology. Ecology 73:1943-1967.
* Scheiner, S. 2013. The ecological literature, an idea-free distribution. [[http://onlinelibrary.wiley.com/doi/10.1111/ele.12196/abstract|Ecology Letters 16: 1421–1423]]. //Belo editorial sobre a falta de teoria nos artigos de ecologia.//
* Fawcett, T.W. and Higginson, A.D., 2012. Heavy use of equations impedes communication among biologists. [[http://www.pnas.org/content/109/29/11735.full|Proceedings of the National Academy of Sciences, 109(29): 11735-11739]]. // Como a aversão à matemática impede a interação entre teoria e empiria. Veja também [[http://www.pnas.org/content/109/29/11735.full?tab=related|o debate resultante]].//
* Outros artigos sobre as diferentes vertentes na ecologia de comunidades:
* El-Hani, C.N. 2006. Generalizações Ecológicas. [[http://www.oecologiaaustralis.org/ojs/index.php/oa/article/viewArticle/249|Oecologia Australis 10 (1)]]. Uma revisão abrangente e profunda sobre o estado da teoria em ecologia, feita por um biólogo com sólida formação em filosofia da ciência.
* Austin, M.P. 1999. A silent clash of paradigms: some inconsistencies in community ecology. //Oikos 86//: 170-179.
===Modelos mecanísticos e fenomenológicos===
* [[https://dynamicecology.wordpress.com/2013/02/21/ecologists-need-to-do-a-better-job-of-prediction-part-iii-the-need-for-data|Mechanistic of phenomelogical?]] boa dicussão por Brian McGill, no blog [[https://dynamicecology.wordpress.com|Dynamic Ecology]].
* [[https://theartofmodelling.wordpress.com/2012/02/19/mechanistic-models-what-is-the-value-of-understanding|The value of mechanistic models]]: outro //post// claro e provocativo sobre modelos mecanísticos, do blog [[https://theartofmodelling.wordpress.com/|The art of modelling]].
* [[https://www.quantamagazine.org/20151216-physicists-and-philosophers-debate-the-boundaries-of-science/|A fight for the soul of science]]:de como uma teoria mecanicista na física está provocando um debate sobre a relação entre empiria e teoria.
===Criatividade e aprendizado===
* [[http://www.ted.com/talks/ken_robinson_says_schools_kill_creativity.html|How school kills creativity]], uma palestra do educador Ken Robinson no [[http://www.ted.com/|TED]].
* [[http://www.ted.com/playlists/124/ken_robinson_10_talks_on_educ.html|Top 10 talks on education at TED]], uma seleção de Ken Robinson.
* [[http://undsci.berkeley.edu/|How science really works]]: grupo da Universidade de Berkeley propõe uma concepção menos linear da criação de conhecimento.
=== Joan Roughgarden ===
* [[http://www.stanford.edu/group/roughlab/|Site do grupo de pesquisa]]
* [[http://www.nimbios.org/videos/vid_roughgarden|Vídeo de entrevista]] sobre matemática na biologia. Da ótima [[http://www.nimbios.org/videos|série de vídeos]] do [[http://www.nimbios.org|National Institute for Mathematical and Biological Syntesis]].
===== Nicho, Competição e Estutura de Comunidades =====
==== Leituras ====
=== Introdutórias ===
* Schoener, T.W. Ecological niche. Cap. I.1, The Princeton Guide to Ecology.
=== Para discussão ===
* Connell J.H. 1961. The influence of interspecific competition and other factors on the distribution of the barnacle //Chthamalus stellatus//. //Ecology// 42(4): 710-723.
* Godoy, O., Kraft, N. J., & Levine, J. M. (2014). Phylogenetic relatedness and the determinants of competitive outcomes. Ecology letters 17(7): 836-844.
==== Slides ====
* {{:aulas:competicao_nicho_estrutura_comunidades_2016.pdf|Palestra 2 - competição, nicho e estrutura de comunidades}}
==== Material Suplementar ====
* //A referência básica sobre nichos:// Jonathan M. Chase and Mathew A. Leibold, 2003. Ecological Niches: Linking Classical and Contemporary Approaches. Chicago University Press.
*
* [[http://www.press.uchicago.edu/cgi-bin/hfs.cgi/00/15593.ctl|site do livro]]
* //O fantasma da competição passada:// J.H. Connell, Diversity and the coevolution of competitors, or the ghost of competition past. Oikos 35 (1980), pp. 131–138.
* Grinnell, Joseph. 1917. The niche-relationships of the California Thrasher. //The Auk 34//:427-433.
* Odling-Smee, F.J., Laland, K.N. and Feldman, M.W., 2003. Niche construction: the neglected process in evolution (No. 37). Princeton University Press. . Veja também o site dos autores da idéia ([[http://www.nicheconstruction.com/]], com vários //links// interessantes.
* Biogeography, Changing Climate and Niche Evolution Sackler Colloquium. [[http://www.pnas.org/cgi/collection/biogeography_niche|PNAS vol. 106, suplemento]]. Série de artigos sobre evolução de nichos e sua relação com distribuições geográficas.
* Wilson, W.G., Lundberg, P., Vazquez, D.P., Shurin, J.B., Smith, M.D., Langford, W., Gross, K.L. and Mittelbach, G.G., 2003. Biodiversity and species interactions: extending Lotka–Volterra community theory. Ecology Letters, 6(10): 944-952.
* Tilman, D., 1982. Resource competition and community structure. Princeton University Press. //A referência clássica para modelos mecanísticos de competição (com recurso explícito).//
== G. Evelyn Hutchinson ==
* Hutchinson, G.E. 1957. Concluding remarks. //Cold Spring Harbor Symposia on Quantitative Biology 22//: 415–427.
* Hutchinson, G.E. 1959. Homage to Santa Rosalia or Why Are There So Many Kinds of Animals? //The American Naturalist 93//:145-159.
* Uma crítica feroz e datada: Lewin, R. 1983. Santa Rosalia was a goat. //Science 221//: 636-639. {{bibliografia:lewin1983.pdf|pdf}}
* George Evelyn Hutchinson: 20 th-century ecologist. LB SLOBODKIN, NG SLACK Endeavour 23:11, 24-30, Elsevier Science, 1999. (Inclui a árvore de descendentes intelectuais de Hutchinson).
== Teoria moderna da coexistência ==
* Chesson, P., 2000. Mechanisms of maintenance of species diversity. Annual review of Ecology and Systematics, pp.343-366.
* Chesson, P., 2000. General theory of competitive coexistence in spatially-varying environments. Theoretical population biology, 58(3), pp.211-237.
* Adler P.B., Hillerislambers, J. & Levine, J.M. 2007. A niche for neutrality. Ecology Letters, 10:95-104.
* HilleRisLambers, J., Adler, P. B., Harpole, W. S., Levine, J. M., & Mayfield, M. M. (2012). Rethinking community assembly through the lens of coexistence theory. Annual Review of Ecology, Evolution, and Systematics, 43(1), 227.
* [[http://eebweb.arizona.edu/Faculty/chesson/|The Chesson Lab]]
== Estrutura filogenética de comunidades==
* Webb, C. O., Ackerly, D. D., McPeek, M. A., & Donoghue, M. J. (2002). Phylogenies and community ecology. Annual review of ecology and systematics, 475-505.
* Losos, J.B., 2008. Phylogenetic niche conservatism, phylogenetic signal and the relationship between phylogenetic relatedness and ecological similarity among species. Ecology letters, 11(10), pp.995-1003. //Esclarece a diferença entre conservação de nicho e sinal filogenético de nicho.//
== Modelagem de "nicho"==
* 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(9), 1623-1627.
===== Predação e estrutura de comunidades =====
==== Leituras ====
=== Introdutórias ===
* Holt, R.D. Predation and community organization. Cap. III.3, The Princeton Guide to Ecology.
=== Para discussão ===
* Lubchenco, J. (1978). Plant species diversity in a marine intertidal community: importance of herbivore food preference and algal competitive abilities. American Naturalist, 23-39.
* Peacor S.D., Werner E.E. 2001. The contribution of trait-mediated indirect effects to the net effects of a predator. //PNAS// 98: 3904-3908
==== Slides ====
* {{:aulas:predacao_estrutura_comunidades_2016.pdf|Palestra 3 - predação e estrutura de comunidades}}
==== Material Suplementar ====
* Schmitz O.J. Indirect Effects in Communities and Ecosystems: The Role of Trophic and Nontrophic Interactions. Cap. III.5, .
* Werner, E.E. and Peacor, S.D., 2003. A review of trait-mediated indirect interactions in ecological communities. Ecology, 84(5), pp.1083-1100.
* Estes J.A. et al. 2011. Trophic Downgrading of Planet Earth. Science 333: 301-306.
* Ohgushi, T., Schmitz, O., & Holt, R. D. (Eds.). (2012). Trait-mediated indirect interactions: ecological and evolutionary perspectives. Cambridge University Press.
* Schmitz, O.J., Krivan, V. and Ovadia, O., 2004. Trophic cascades: the primacy of trait‐mediated indirect interactions. Ecology Letters, 7(2), pp.153-163.
* Terborgh J. & Estes J.A. 2010. Trophic Cascades: Predators, Prey, and the Changing Dynamics of Nature. Island Press.
==Plasticidade==
* Relyea, R.A. and Auld, J.R., 2004. Having the guts to compete: how intestinal plasticity explains costs of inducible defences. Ecology Letters, 7(9), pp.869-875.
* Relyea, R.A., 2001. Morphological and behavioral plasticity of larval anurans in response to different predators. Ecology, 82(2), pp.523-540.
== Clássicos ==
* Huffaker, C.B. 1958. Experimental studies on predation: dispersion factors and predator-prey oscillations. [[http://www.montana.edu/screel/Webpages/Bio%20303/Huffaker1958.pdf|Hilgardia, 27, 343–383]].
* Huffaker, C.B., Herman, S.G. and Shea, K.P., 1963. Experimental studies on predation: complex dispersion and levels of food in an acarine predator-prey interaction. University of Calif.
* [[https://www.youtube.com/watch?v=-b_VBIhbuwM|Huffaker's balancing act]]: clip de animação do projeto [[https://www.youtube.com/channel/UC0Es673h-PyES_WAmBIA87A|Ecomotion]].
* Paine, R. T. 1966. Food web complexity and species diversity. //American Naturalist 100//: 65-75.
* Paine, R.T., 1980. Food webs: linkage, interaction strength and community infrastructure. Journal of animal ecology, 49(3), pp.667-685.
* [[https://www.youtube.com/watch?v=FsEOBZbxBr0|Life of every color and kind]], animação sobre o trabalho pioneiro de Paine. Do projeto [[https://www.youtube.com/channel/UC0Es673h-PyES_WAmBIA87A|Ecomotion]].
* Holt, R.D., 1977. Predation, apparent competition, and the structure of prey communities. Theoretical population biology, 12(2), pp.197-229.
* Hipótese do mundo verde:
* Hairston N G, Smith F E & Slobodkin L B. Community structure, population control, and competition. Amer. Naturalist 94:421-5, 1960.
* Sherrat T.M. & Wilikinson D.N. 2009. Why the world is green? Cap.7 in Big Questions in Ecology and Evolution. //Ótima revisão, com hipóteses alternativas e boa crítica à ideia original//.
* [[https://www.youtube.com/watch?v=bLs2dZvJQX4&list=PL1KbTtDlbwHC0jRQ--LsMnyAhOgVMgRB-|Cilp de animação sobre a hipótese do mundo verde]], do projeto [[https://www.youtube.com/channel/UC0Es673h-PyES_WAmBIA87A|Ecomotion]].
* J. H. Lawton and S. McNeill, “Between the devil and the deep blue sea: on the problem of being a herbivore,” in Population Dynamics, R. M. Anderson, B. D. Turner, and L. R. Taylor, Eds., Blackwell Scientific Publications, Oxford, UK, 1979.. //Clássico sobre a importância de controle //top-down// e //bottom-up// em comunidades de herbívoros.//
==Jane Lubchenco==
* [[http://en.wikipedia.org/wiki/Jane_Lubchenco|Wikipedia]]
* [[http://vimeo.com/100425703|Depoimento]] para a série //Conservation Talks//.
* [[http://mytilus.science.oregonstate.edu/|Lubchenco/Meng Lab]]
* [[http://www.compassonline.org/|Compass]]: fundação criada por Jane Lubchenco e colegas para fomentar o maior engajamento de cientistas nas políticas ambientais.
* Smith, B., Baron, N., English, C., Galindo, H., Goldman, E., McLeod, K., Miner, M. and Neeley, E., 2013. COMPASS: navigating the rules of scientific engagement. [[http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.1001552|PLoS Biol, 11(4), p.e1001552]].
* Lubchenco, J. 1998. Entering the century of the environment: a new social contract for science. Science 279: 491–497. //Sua tese sobre a responsabilidade social da ciência//.
* Lubchenco, J., & Menge, B. A. (1993). Split positions can provide a sane career track: A personal account. Bioscience, 243-248.. //Sobre o contrato pioneiro que ela e seu marido Bruce Menge propuseram à Oregon State University.//
==Conservação e comportamento==
* [[https://www.eeb.ucla.edu/Faculty/Blumstein/|Daniel Blumstein]] criou esta linha de pesquisa que, entre outras coisas, chama a atenção sobre como a evolução de respostas comportamentais de presas pode ser um problema para a sua conservação.
===== Equilíbrio em Sistemas Dinâmicos =====
==== Leituras ====
=== Introdutórias ===
* McCann, K. S. The structure and stability of food webs. Cap. III.7, Princeton Guide to Ecology.
==== Material suplementar ====
* May, R.M. 1972. Will a large complex system be stable? Nature, 238, 413-414. . O artigo clássico que estabeleceu o conceito de equilíbrio de redes tróficas como solução de um sistema de equações de Lotka-Volterra. Vale apena rastrear as citações na Web of Science.
* May, R.M. 2001. Stability and complexity in model ecosystems. Princeton Univ Press.. Nesta influente monografia Robert May desenvolve as idéias do artigo de 1972. A primeira edição é de 1973, e o livro foi re-editado na coleção [[http://press.princeton.edu/catalogs/series/plb.html|Princeton Landmarks of Biology]] em 2001.
* [[http://www.zoo.ox.ac.uk/staff/academics/may_r.htm|Biografia]] de Robert May, Barão de Oxford, no //site// da Oxford University.
* Tregonning, K. & Roberts, A.P. 1979. Complex systems which evolve towards homeostasis. Nature 281: 563-564.. Um contraponto subestimado ao artigo clássico a May (1972).
* Yodzis, P. 1980. The connectance of real ecosystems. Nature, 284, 544-545 . Um dos testes empíricos clássicos da relação negativa entre estabilidade e diversidade.
* Allesina, S. & Pascual M. 2007. Network structure, predator–prey modules, and stability in large food webs. Theoretical Ecology, 1(1), 55-64.
* Allesina, S. & Tang, S. Stability criteria for complex ecosystems.Nature 483, 205–208. Generalização das condições de equilíbrio deduzidas por May (1972).
* Allesina, S. & Tang, S. 2015. The stability–complexity relationship at age 40: a random matrix perspective. Population ecology 57: 63-75.
* McCann, K. S. 2000. The diversity-stability debate. Nature, 405(6783), 228-33.. Uma abordagem mais abrangente das relações entre complexidade e estabilidade.
===== Resiliência e Estados Múltiplos =====
==== Leituras ====
=== Introdutórias ===
* Scheffer, M. 2009. Alternative Stable States. In: Critical Transitions in Nature and Society, Chapter II, pp. 11-36, Princenton University Press.
=== Para discussão ===
* Blindow I. et al. 1993. Long-term pattern of alternative stable states in two shallow eutrophic lakes. Freshwater Biology 30: 159-167.
* Persson et al. 2007. Culling prey promotes predator recovery — alternative states in a whole-lake experiment. Science 316: 1743-1746., [[http://www.sciencemag.org/content/316/5832/1743/suppl/DC1|Supporting online material]].
==== Slides ====
* {{:aulas:aula4_resil_estados_multilp_2016.pdf|Palestra 4 - Resiliência e estados múltiplos}}
==== Material suplementar====
===Básico===
* Lewontin, RC. 1969. The meaning of stability. Brookhaven Symp Biol 22:13–23.
* Holling C.S. 1973. Resilience and stability of ecological systems. Annu. Rev. Ecol. Syst. 4: 1-23.
* May, R.M. 1977. Thresholds and breakpoints in ecosystems with a multiplicity of stable states. //Nature// 269: 471-477.
* Scheffer, M. 2009. Critical Transitions in Nature and Society. Princeton Univ. Press.
===Revisões e estudos de caso===
* Scheffer, M. et al. 2001. Catastrophic shifts in ecosystems. //Nature// 413: 591-596.
* Beisner, B.E. et al. 2003. Alternative stable states in ecology. //Front. Ecol. Environ.// 1: 376–382.
* Elmqvist et al. 2003. Response diversity, ecosystem change, and resilience. //Frontiers in Ecology and Environment//1: 488–494.
* Folke, C. et al. 2004. Regime shifts, resilience, and biodiversity in ecosystem management. //Annu. Rev. Ecol. Evol. Syst.// 35: 557–81.
* Grimm, V. & Wissel, C. 1997. Babel, or the ecological stability discussions: an inventory and analysis of terminology and a guide for avoiding confusion. //Oecologia// 109: 323–334.
* Staver et al. 2011. The Global Extent and Determinants of Savanna and Forest as Alternative Biome States.
* Peterson, G. et al. 1998. Ecological Resilience,Biodiversity, and Scale. //Ecosystems// 1: 6–18.
* Scheffer, M. et al. 2009. Early-warning signals for critical transitions. //Nature// 461: 53-59.
* Scheffer, M., Carpenter, S.R., Lenton, T.M., Bascompte, J., Brock, W., Dakos, V., et al. (2012). Anticipating Critical Transitions. Science, 338, 344–348.
* Schröder, A. et al. 2005. Direct experimental evidence for alternative stable states: a review. //Oikos// 110: 3-19.
* van Nes, E.H. & Scheffer, M. 2004. Large species shifts triggered by small forces. //Am. Nat. //164: 255-266.
* Walker, B. et al. 2004. Resilience, Adaptability and Transformability in Social–ecological Systems. //Ecology and Society// 9:5.
* Pardini et al. 2010. Beyond the fragmentation threshold hypothesis: regime shifts in biodiversity across fragmented landscapes.[[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0013666|PLoS ONE 5 e13666]]
* Hirota et al. 2011. Global resilience of tropical forest and savanna to critical transitions. Science 334: 232-235.
* E.C. Zeeman, Catastrophe Theory, Scientific American, April 1976; pp. 65–70, 75–83.
* Lansing, J.S., 2003. Complex adaptive systems. Annual review of anthropology, pp.183-204.
* Dakos, V., Carpenter, S. R., Brock, W. A., Ellison, A. M., Guttal, V., Ives, A. R., ... & Scheffer, M. (2012). Methods for detecting early warnings of critical transitions in time series illustrated using simulated ecological data. [[http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0041010#s5|PloS one, 7(7), e41010]].
==André de Roos==
* [[https://staff.fnwi.uva.nl/a.m.deroos/|Site]]
* de Roos, A.M. and Persson, L., 2013. Population and community ecology of ontogenetic development. Princeton University Press.
=== Sites ===
* [[http://www.resalliance.org/|Resilience Alliance]]
* [[http://www.early-warning-signals.org/|Early warnings toolbox]]
===== Biogeografia de ilhas =====
==== Leituras ====
=== Introdutórias ===
* Gotelli, N.J. 2007 Ecologia. Cap. 7 - Biogeografia de ilhas. Pp. 159-181. Ed. Planta. .
=== Para discussão ===
* Simberloff, D. & Wilson, E. 1969. Experimental zoogeography of islands: the colonization of empty islands Ecology, //Ecology 50//: 278-296
* Alonso, D., Pinyol‐Gallemí, A., Alcoverro, T., & Arthur, R. 2015. Fish community reassembly after a coral mass mortality: higher trophic groups are subject to increased rates of extinction. Ecology letters, 18(5), 451-461.
==== Material suplementar====
Wilson, E. O., & Simberloff, D. S. (1969). Experimental zoogeography of islands: defaunation and monitoring techniques. Ecology, 267-278.. Descrição detalhada do experimento de defaunação. Mesmo uma leitura rápida ajudará muito a discussão.
* MacArthur, R.M. & Wilson, E.O. 1967. The theory of island biogeography. Princeton Univ. Press.
* Revisão recente sobre a história e estado da arte da teoria. Essencial para quem quiser se aprofundar:
* Losos, J. & Ricklefs, R. (Eds.) The Theory of Island Biogeography Revisited. Princenton University Press.
* [[http://onlinelibrary.wiley.com/subject/code/000046/homepage/new_island_biology_virtual_issue.htm?campaign=wlytk-41856.2182523148|Island Biogeography Special Issue]] do Journal of Biogeography. "//The papers featured in this virtual issue illustrate the breadth and vitality of recent advances in island biogeography.// "
* Wilson, Edward O. Naturalist. Island Press, 2006.
== Relação espécie-área ==
* Tjørve, E. (2009). Shapes and functions of species–area curves (II): a review of new models and parameterizations. Journal of Biogeography 36: 1435-1445..
* Dengler, J. (2009). Which function describes the species–area relationship best? A review and empirical evaluation. Journal of Biogeography 36, 728–744.
===== Teorias Neutras da biodiversidade =====
==== Leituras ====
=== Introdutórias ===
* Alonso, D., R. S. Etienne, and A. J. Mckane 2006. The merits of neutral theory. Trends in Ecology & Evolution 21: 451-457.
* Harpole, W. (2010) Neutral Theory of Species Diversity. [[https://www.nature.com/scitable/knowledge/library/neutral-theory-of-species-diversity-13259703|Nature Education Knowledge 3(10):60]]
=== Para discussão ===
* Hubbell, S.P. 1979. Tree dispersion, abundance, and diversity in a tropical dry forest. Science 203: 1299-1309.
* Levine, J. M., & HilleRisLambers, J. (2009). The importance of niches for the maintenance of species diversity. Nature, 461(7261), 254-257.
==== Material suplementar====
== Teorias que Hubbel Usou ==
* Kendall, D.G. 1948. On the Generalized "Birth-and-Death" Process. //Ann. Math. Statist. 19:// 1-15. [[http://projecteuclid.org/DPubS?service=UI&version=1.0&verb=Display&handle=euclid.aoms/1177730285|artigo completo]] na página do [[http://projecteuclid.org/DPubS?Service=UI&version=1.0&verb=Display&handle=euclid|Projeto Euclides]].
* Ewens, W. J. (1972). The sampling theory of selectively neutral alleles. Theoretical Population Biology 3 (1), 87-112.
* Caswell, H. 1976. Community structure: a neutral model analysis. //Ecological Monographs 46//: 327-354.
* Excelente livro básico sobre modelos estocásticos. Há [[http://dedalus.usp.br/F/F8NPQ6CNFN5DT8VIR1BLRIN9B7CJHLA725QQ4TDFHGMYVKFF7X-08453?func=item-global&doc_library=USP01&doc_number=000933996&year=&volume=&sub_library=IB|um exemplar]] na biblioteca do IB. O capítulo 2 cobre os modelos básicos de deriva em populações:
* Renshaw, E. 1991. Modelling biological populations in space and time Cambridge University Press.
== A proposta por Stephen Hubbell ==
* O livro (referência básica, mas nem sempre didática quanto ao modelo):
* Hubbell, S.P. (2001). The Unified Neutral Theory of Biodiversity and Biogeography. Princeton University Press.
* Hubbell, S. P. (2005). Neutral theory in community ecology and the hypothesis of functional equivalence. Functional ecology, 19(1), 166-172. //Artigo em que Hubbel rebate críticas sobre a premissa de equivalência ecológicas.//
* Harpole, W. (2010) Neutral Theory of Species Diversity. [[http://www.nature.com/scitable/knowledge/library/neutral-theory-of-species-diversity-13259703|Nature Education Knowledge 3(10):60]], apresentação básica para graduandos, do projeto [[http://www.nature.com/scitable|Scitable]].
* Um pacote em R para simulação e ajuste dos modelos de distribuição de espécies previstos pela teoria. **A introdução é uma excelente explicação da teoria**:
* Hankin, R. 2007. Introducing untb, an R Package For Simulating Ecological Drift Under the Unified Neutral Theory of Biodiversity. Journal of Statistical Software 22: 12 [[http://www.jstatsoft.org/v22/i12/]].
* Rosindell, J., Hubbell, S. P. & Etienne, R. S. 2011. The Unified Neutral Theory of Biodiversity and Biogeography at Age Ten. Trends in Ecology & Evolution 26:340-348. . Ótima revisão sobre o tema e seu impacto.
* Chave, J. Competition, Neutrality, and Community Organization. Cap. III.2, The Princeton Guide to Ecology.
==Alternativas e desenvolvimentos==
* Tilman, D., 2004. Niche tradeoffs, neutrality, and community structure: a stochastic theory of resource competition, invasion, and community assembly. Proceedings of the National Academy of Sciences of the United States of America, 101(30), pp.10854-10861.
* Gravel, D., Canham, C.D., Beaudet, M. and Messier, C., 2006. Reconciling niche and neutrality: the continuum hypothesis. Ecology letters, 9(4), pp.399-409.
* Scheffer, M. and van Nes, E.H., 2006. Self-organized similarity, the evolutionary emergence of groups of similar species. Proceedings of the National Academy of Sciences, 103(16), pp.6230-6235.
* Rosindell, J., Cornell, S.J., Hubbell, S.P. and Etienne, R.S., 2010. Protracted speciation revitalizes the neutral theory of biodiversity. Ecology Letters, 13(6), pp.716-727.
== Brian McGill ==
* [[http://www.brianmcgill.org/|Página na internet]]
* [[http://dynamicecology.wordpress.com/|Blog]] de Jeremy Fox, para o qual colabora.
* Uma boa revisão da evidência empírica até a época, com comparações com outros modelos neutros: Brian J. McGill, Brian A. Maurer, Michael D. Weiser (2006) EMPIRICAL EVALUATION OF NEUTRAL THEORY. Ecology: Vol. 87, No. 6, pp. 1411-1423.
== Estabilização x Diversificação ==
* Connell, J. H., 1978. Diversity in tropical rain forests and coral reefs. //Science 199//: 1302-1310.
* Comentário de Connell sobre o impacto deste artigo, em seu [[http://garfield.library.upenn.edu/classics1987/A1987K668500001.pdf|ensaio]] para a [[http://garfield.library.upenn.edu/classics.html|Citation Classics Library]] da ISI.
* Scheffer, M., van Nes, E. H., April 2006. Self-organized similarity, the evolutionary emergence of groups of similar species. Proceedings of the National Academy of Sciences of the United States of America 103 (16), 6230-6235. [[http://www.pnas.org/content/103/16/6230.long]]
* Adler P.B., Hillerislambers, J. & Levine, J.M. 2007. A niche for neutrality. //Ecology Letters, 10//:95-104.
* Vaja também material sobre a teoria moderna da coexistência, na seção sobre [[#material_suplementar1|nicho e competição]].
===== Metacomunidades =====
==== Leituras ====
=== Introdutórias ===
* Leibold. M.A. Spatial and Metacommunity Dynamics in Biodiversity. Cap. III.8, The Princeton Guide to Ecology.
=== Para discussão ===
* Warren, P.H. 1996. The effects of between-habitat dispersal rate on protist communities and metacommunities in microcosms at two spatial scales. Oecologia 105: 132–140.
* Venail, P.A. et al. 2008. Diversity and productivity peak at intermediate dispersal rate in evolving metacommunities. Nature 452: 210–215.
==== Slides ====
* {{:aulas:deriva_e_dispersao_2016.pdf|Palestra 5 - Deriva e dispersão}}
==== Material suplementar====
* Leibold, M.A. et al. 2004. The metacommunity concept: a framework for multi-scale community ecology. Ecology Letters 7: 601–613.
* Leibold, M.A. 2011. The metacommunity concept and its theoretical underpinnings. **In:** Scheiner & Willig (Eds) Theory in Ecology.
* Holyoak, M., Leibold, M. A. & Holt, R. D. 2005. Metacommunities: spatial dynamics and ecological communities. University of Chicago Press. [[http://books.google.com/books?hl=en&lr=&id=J4iy6Jl0a0MC&oi=fnd&pg=PR1&dq=Metacommunities:+Spatial+Dynamics+and+Ecological+Communities&ots=zb5rDmZu5f&sig=YJY2tDMdOF5YBf1Q1D7kdOvUWl4|Google books]]. Disponível na [[http://dedalus.usp.br/F/NVU11DNHEDBLGY7J5SKDBKNEK3DICC8C2KHL8M4XM2MSS32PGJ-61368?func=item-global&doc_library=USP01&doc_number=001835584&year=&volume=&sub_library=IB|biblioteca do IB-USP]]
* Logue, J. B., Mouquet, N., Peter, H. & Hillebrand, H. 2011. Empirical approaches to metacommunities: a review and comparison with theory. Trends in Ecology & Evolution, 26(9). . Boa revisão dos principais conceitos e estudos empíricos.
* Hubert, N., Calcagno, V., Etienne, R.S. and Mouquet, N., 2015. Metacommunity speciation models and their implications for diversification theory. Ecology letters, 18(8), pp.864-881.
* Mouquet N. and Loreau, M. (2003). Community patterns in source-sink metacommunities. American Naturalist, 162: 544-557.
* Winegardner, A.K., Jones, B.K., Ng, I.S., Siqueira, T. and Cottenie, K., 2012. The terminology of metacommunity ecology. Trends Ecol Evol, 27: 253-254.
* Heino, J., Melo, A.S., Siqueira, T., Soininen, J., Valanko, S. and Bini, L.M., 2015. Metacommunity organisation, spatial extent and dispersal in aquatic systems: patterns, processes and prospects. Freshwater Biology, 60(5): 845-869.
* Amarasekare, P. 2000. The geometry of coexistence. Biol J Linnean Soc 71: 1-31.
* Chesson, P., 1998. Recruitment limitation: a theoretical perspective. Australian Journal of Ecology, 23(3): 234-240.
* Hanski, I. and Gilpin, M.E., 1997. Metapopulation biology. Academic Press.
* Hanski, I. and Gaggiotti, O.E., 2004. Ecology, genetics, and evolution of metapopulations. Academic Press.
==Reação-difusão e espaço explícito==
* Skellam, J.G., 1951. Random dispersal in theoretical populations. Biometrika, 38(1/2), pp.196-218.
* Law, R., Murrell, D.J. and Dieckmann, U., 2003. Population growth in space and time: spatial logistic equations. Ecology, 84(1), pp.252-262.
* Maciel, G.A. and Lutscher, F., 2013. How individual movement response to habitat edges affects population persistence and spatial spread. The American Naturalist, 182(1), pp.42-52. //Do físico brasileiro [[https://scholar.google.com.br/citations?user=qwSSGIQAAAAJ|Gabriel Maciel]], prêmio [[http://esa.org/theory/awards|"Outstanding Ecological Theory Paper"]]// da Ecological Society of America em seu centenário.
==Richard Levins==
* Levins, R. 1969. Some demographic and genetic consequences of environmental heterogeneity for biological control. Bulletin of the Entomological Society of America 15: 237–240. //Artigo em que propôs o seu modelo de dinâmica de metapopulações//.
* [[http://www.hsph.harvard.edu/levins85/fond-reminiscences-by-colleagues-and-students-of-richard-levins-phd/|Fond reminiscence of Richard Levins]]: testemunhos de cientistas influenciadas por Richard Levins, na comemoração de seus 85 anos.
* [[http://www.hsph.harvard.edu/news/features/in-memoriam-richard-levins-ecologist-biomathematician-and-philosopher-of-science/|Obituário]] da Harvard School of Public Health
* [[https://www.jacobinmag.com/2016/01/richard-levins-obituary-biological-determinism-dialectics|The people's scientist]], belo obituário que destaca o compromisso social de Richard Levins.
===== Processos históricos e biogeográficos =====
==== Leituras ====
=== Introdutórias ===
* Ricklefs, R. E. 1987. Community diversity: relative roles of local and regional processes. //Science 235//: 167-171.
=== Para discussão ===
* Tilman, D., 1997. Community invasibility, recruitment limitation, and grassland biodiversity. Ecology, 78: 81-92.
* Lessard, J. P., Borregaard, M. K., Fordyce, J. A., Rahbek, C., Weiser, M. D., Dunn, R. R., & Sanders, N. J. (2012). Strong influence of regional species pools on continent-wide structuring of local communities. Proceedings of the Royal Society B: Biological Sciences, 279(1727), 266-274.
==== Slides ====
{{:aulas:processos_historicos_e_biogeograficos_2016.pdf|}}
==== Material suplementar====
==Fundadores==
* Cornell H.V. 1985. Local and regional richness of Cynipine gall wasps on California oaks. Ecology 66: 1247-1260.
* Lawton, J.H., 1982. Vacant niches and unsaturated communities: a comparison of bracken herbivores at sites on two continents. The Journal of Animal Ecology, pp.573-595.
* Jenkins D.G. & Ricklefs, R.E. 2011. Biogeography and ecology: two views of one world. [[http://rstb.royalsocietypublishing.org/content/366/1576.toc|Special Issue do Phil Trans Royal Soc]].
* Kingsland, S. 1995. Modeling nature-Episodes in the history of population ecology. The Chicago University Press, Chicago. Excelente história da teoria ecológica. Há [[http://dedalus.usp.br/F/F8NPQ6CNFN5DT8VIR1BLRIN9B7CJHLA725QQ4TDFHGMYVKFF7X-17652?func=item-global&doc_library=USP01&doc_number=000519541&year=&volume=&sub_library=IB|um exemplar na biblioteca do IB]]. O último capítulo e posfácio abordam a retomada da história em uma ecologia dominada pelos modelos de dinâmica local.
* Ricklefs, R.E. & Schluter, D. 1993. Species diversity in ecological communities: historical and geographical perspectives. University of Chicago Press, Chicago.
* Wiens, J.J. & Donoghue, M.J. 2004. Historical biogeography, ecology and species richness. TREE 19: 639-644.
* Wiens J.J. 2011. The niche, biogeography and species interactions. Phil. Trans. R. Soc. B 366: 2336-2350.
* Whittaker, R. H. (1972). Evolution and measurement of species diversity. Taxon, 213-251.
==Desenvolvimentos==
* Loreau M. 2000. Are communities saturated? On the relationships between alpha, beta and gamma diversity. Ecology Letters 3: 73-76.
* Shurin, J.B. 2000. Dispersal limitation, invasion resistance, and the structure of pond zooplankton communities. Ecology 81: 3074–3086.
* Mittelbach G.G. et al. 2007. Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography. Ecology Letters 10: 315–331.
* Harrison S. & Cornell H. 2008. Toward a better understanding of the regional causes of local community richness. Ecology Letters 11: 969–979.
* Ricklefs, R.E. 2008. Disintegration of the ecological community. The American Naturalist 172:741-750.
* Brooker, R.W., Callaway, R.M., Cavieres, L., Kikvidze, Z., Lortie, C.J., Michalet, R., Pugnaire, F.I., et al. 2009. Don’t diss integration: a comment on Ricklefs's disintegrating communities. The American naturalist, 174(6), 919-27
* Ricklefs, R.E. 2009. A Brief Response to Brooker et al.’s Comment. The American Naturalist, 174(6), 928-931.
* Wiens, J.J., Ackerly, D.D., Allen, A.P., Anacker, B.L., Buckley, L.B., Cornell, H.V., Damschen, E.I., Jonathan Davies, T., Grytnes, J.A., Harrison, S.P. and Hawkins, B.A., 2010. Niche conservatism as an emerging principle in ecology and conservation biology. Ecology letters, 13(10), pp.1310-1324. //Do special issue://
* [[http://rstb.royalsocietypublishing.org/content/366/1576|Biogeography and ecology: two views of one world]], Special issue, Phil. Trans. Royal Soc, 2011.
* Lessard, J.-P., Belmaker, J., Myers, J. a, Chase, J. M., & Rahbek, C. (2012). Inferring local ecological processes amid species pool influences. Trends in ecology & evolution, 27(11), 600–7.
* Gonçalves-Souza, T. et al. 2013. A critical analysis of the ubiquity of linear local–regional richness relationships. Oikos 122: 961–966.
* Mittelbach, G. G., & Schemske, D. W. 2015.Ecological and evolutionary perspectives on community assembly. Trends in ecology & evolution, 30(5), 241-247.
* Hubert, N., Calcagno, V., Etienne, R.S. and Mouquet, N., 2015. Metacommunity speciation models and their implications for diversification theory. Ecology letters, 18(8), pp.864-881. //Revisão de como evolução, dispersão e processos locais têm sido abordados pela vertente de metacomunidades.//
==Estudos de caso==
* Wiens, J. J., Graham, C. H., Moen, D. S., Smith, S. A. & Reeder, T.W. 2006 Evolutionary and ecological causes of the latitudinal diversity gradient in hylid frogs: treefrog trees unearth the roots of high tropical diversity. Am. Nat. 168, 579–596.
* Wiens, J.J., Parra-Olea, G., García-París, M. and Wake, D.B., 2007. Phylogenetic history underlies elevational biodiversity patterns in tropical salamanders. Proceedings of the Royal Society of London B: Biological Sciences, 274(1612), pp.919-928.
* Pärtel, M., 2002. Local plant diversity patterns and evolutionary history at the regional scale. Ecology, 83(9), pp.2361-2366.
===== Integrando abordagens ======
==== Leitura para discussão ====
* Vellend, M. 2010. Conceptual synthesis in community ecology. //The Quaterly Review of Biology// 85: 183-206.
==== Material suplementar ====
* Lawton, J.H. 1999. Are there general laws in ecology? Oikos 84: 177-192
* Lawton, J.H., 1992. (Modest) advice for graduate students. Oikos, 65: 361-362.
* Simberloff, D. 2004. Community ecology: is it time to move on? The American Naturalist, 163: 787–799.
* El-Hani, C.N. 2006. Generalizações Ecológicas. [[http://www.oecologiaaustralis.org/ojs/index.php/oa/article/viewArticle/249|Oecologia Australis 10 (1)]]. Uma revisão abrangente e profunda sobre o estado da teoria em ecologia, feita por um biólogo com sólida formação em filosofia da ciência.
* Population dynamics from first principles. Capítulo 2 do livro Complex Population Dynamics, de Peter Turchin, Princeton Univ Press, 2003. //Uma excelente síntese da lógica de construção de teoria a partir de primeiros pricípios, mais bem sucedida na Ecologia de Populações do que na Ecologia de Comunidades.//
* [[https://dynamicecology.wordpress.com/2016/01/13/why-do-some-ecologists-have-evolution-envy/comment-page-1/|Why do (some) ecologists have evolution envy?]], post de Vellend sobre as consequências da sua proposta.
* [[http://www.theguardian.com/commentisfree/2013/dec/09/how-journals-nature-science-cell-damage-science|How journals like Nature and Science are damaging science]]: uma crítica de Randy Schekman, pêmio Nobel de medicina.
=== Escala e importância de cada processo===
* Hoekstra, T. W., Allen, T. F., & Flather, C. H. (1991). Implicit scaling in ecological research. Bioscience, 148-154.
* Vellend, M., Srivastava, D. S., Anderson, K. M., Brown, C. D., Jankowski, J. E., Kleynhans, E. J., ... & Xue, X. (2014). Assessing the relative importance of neutral stochasticity in ecological communities. Oikos, 123(12), 1420-1430.
=== Lacuna ciência-prática ===
* Pardini, R., Rocha, P. L. B., El-Hani, C., Pardini, F. Challenges and opportunities for bridging the research-implementation gap in ecological science and management in Brazil. In: Conservation Biology: Voices from the Tropics (N.S. Sodhi, L. Gibson & P.H. Raven). Wiley-Blackwell, pp. 77-85. {{:aulas:10_pardini_etal_voices_from_the_tropics_2013.pdf|pdf}}
* Rigueira , D. M. G , Coutinho , S. L. , Pinto-Leite , C. M. , Sarno , V. L. C. , Estavillo , C. , Campos , S. , Dias , V. S. , de Barros , C. and Chastinet , A. ( 2013 ) Perda de hábitat, leis ambientais e conhecimento científico: proposta de critérios para a avaliação dos pedidos de supressão de vegetação . Revista Caititu , 1 , 21–42. doi: 10.7724/caititu.2013.v1.n1.d03
===== Outros Tópicos =====
==== Estatística e análise de padrões ====
* Crítica de Richard Lewontin à ANOVA:
* O Artigo original: Lewontin, R.C. 1974. The analysis of variance and the analysis of causes. Am. J. Hum. Genet. 26: 400-411 (reprinted in Int J Epidemiol 35:520-525) .
* Comentários do autor, 32 anos depois:
* Comentários de outros autores, em seção especial sobre o artigo, no [[http://ije.oxfordjournals.org/content/vol35/issue3/index.dtl#REPRINTS_AND_REFLECTIONS|International Journal of Epidemiology]].
* Veja também o livro: Levins, R. & Lewontin, R.C. 1985. //The Dialectical Biologist//. Cambridge, Harvard University Press.
==== Food webs ====
== Gary Polis ==
* Polis, G.A. 1991. Complex trophic interactions in deserts: an empirical critique of food web theory. Am. Nat. 138, 123–155.
* Polis, G.A. 1996. Food Web Complexity and Community Dynamics. The American Nuturalist: 147 :813-846.
* Obituários no [[http://www.nytimes.com/2000/04/01/us/gary-allan-polis-53-an-expert-on-scorpions-and-desert-ecology.html|NY Times]] e da {{:bibliografia:polis_obituary_bas.pdf|Marshall University}}.
==== Modelos Nulos ====
* Manly, B.F.J. 2007. Randomization, bootstrap and Monte Carlo methods in biology, third edition. Chapman & Hall/CRC.
* Cody,M.L. & Diamond, J.M. 1975 (Eds). Ecology and evolution of communities. Massachusetts, Belknap Press.
* Strong, D.R., Simberloff, D., Abele, L.G., Thistle, A.B. 1984 (Eds). Ecological communities: conceptual issues and the evidence. Princeton Univ. Press.
== Nicholas Gotelli: ==
* [[http://www.uvm.edu/~ngotelli/homepage.html|Página]] na internet, com //links// para o pacote Ecosim, publicações, incluindo referência básica sobre modelos nulos (de onde veio a figura deste wiki):
* Gotelli, N.J., and G.R. Graves. 1996. Null Models in Ecology. Smithsonian Institution Press, Washington, DC. [[http://www.uvm.edu/~ngotelli/nullmodelspage.html|pdf]].
== Robert Colwell: ==
* [[http://viceroy.eeb.uconn.edu/|Página]] na internet, com muitos //links// para artigos, programas, e muito mais, incluindo:
* [[http://viceroy.eeb.uconn.edu/RangeModel|RangeModel]], programa para testar modelos nulos de distribuição geográfica de espécies.
* [[http://viceroy.eeb.uconn.edu/RangeModelPages/MDEReferences.htm|Lista extensiva de publicações]] sobre a hipótese do //Mid-Domain Effect//.
===== Em resumo =====
{{ :woordle2016.png}}
Nuvem de palavras dos títulos das leituras obrigatórias, feita com [[http://www.wordle.net]].