Recursos

Sequências para atividade de Filogenômica

Os transcriptomas dos quatro taxons terminais podem ser baixados no link a seguir:

https://drive.google.com/drive/folders/1CXJ4lhS-WqV-wJZOcYkew20Yqf6b6D2T?usp=drive_link

Aulas Online

Aula 2

https://youtu.be/CzWJvAUHwAI

Aula 3

https://youtu.be/gD14Hrqkzz8

Aula 4

https://youtu.be/ibVo1R34LCU

Aula 5

https://youtu.be/2ltx-0aRnz4

Aula 6

https://youtu.be/KWWGVVsji24

Aula 8

https://youtu.be/jKj22Zbc5ow

Aula 9

https://youtu.be/LhCMp6pKOG0

aula 10

https://youtu.be/u2VW6_lpSQg

Literatura para Aulas

Aula 1

• Crick, F (August 1970). Central dogma of molecular biology. Nature. 227 (5258): 561–3.
• Koonin, E.V., Novozhilov, A.S., 2009. Origin and evolution of the genetic code: The universal enigma. IUBMB Life 61, 99–111. doi:10.1002/iub.146
• Pray, L. (2008) What is a gene? Colinearity and transcription units. Nature Education 1(1):97

Aula 2

Para ter uma noção geral, vejam o vídeo e os dois artigos Khan Academy abaixo.

• Replicação
• Reparo

Para aprofundar, o melhor é livros-texto

• Alberts et al. (2002) Molecular Biology of the Cell, 4th edition - Capítulo 5: DNA Replication, Repair, and Recombination. Qualquer outra edição serve!

Aula 3

Observações: Os artigos de 68 e 69 são os que originaram toda a teoria e debate. O de 1991 apresenta uma excelente explicação, porém é bem mais longo. Para os mais inclinados morfologicamente, o artigo de Gould e Lewontin demonstra que o mesmo tipo de raciocínio também surgiu nas discussões morfológicas na década de 70, porém é uma leitura bem mais complicada e que envolve diversos outros conceitos, e certamente merece uma sessão de discussão própria.

• Kimura, Motoo (1968) Evolutionary Rate at the Molecular Level. Nature, 217:624.
• King JL, Jukes TH. (1969). Non-Darwinian Evolution. Science 164:788-97.
• Kimura, Motoo (1991). The neutral theory of molecular evolution: a review of recent evidence.. Jap. J. of Genetics.
• Gould SJ, Lewontin RC (1979). The Spandrels of San Marco. Proc. Royal Soc. B, 205:581.

Aula 4

• Charlesworth, Brian. "Effective population size and patterns of molecular evolution and variation." Nature Reviews Genetics 10.3 (2009): 195-205.

• Simulador PopGen Simulador

• Hartl, Daniel L., and Andrew G. Clark. "Principles of population genetics." (1998). Livro texto, qualquer edição serve.

Aula 5

• O'hara R. J. 1993. Systematic generalization, historical fate and the species problem. Systematic Biology, 42:231-246.

• Baum D. A. & Offner S. 2008. Phylogenics & tree-thinking. The American Biology Teacher, 70:222–229.

• Baum D. A., Smith S. D. & Donovan S. S. 2005. The tree-thinking challenge. Science, 310:979–980.

• Sandvik H. 2008. Tree thinking cannot taken for granted: challenges for teaching phylogenetics. Theory in Biosciences, 127:45–51.

• O’hara R. J. 1997. Population thinking and tree thinking in systematics. Zoologica Scripta, 26:323–329.

Aula 6

• Tutorial UPGMA Prof. Fernando Portella

• Capítulo de semelhança em qualquer livro de filogenética.

Aula 8

• Felsenstein, J. 1988. “Phylogenies from Molecular Sequences: Inference and Reliability.” Annual Review of Genetics 22 (1): 521–565. doi:10.1146/annurev.ge.22.120188.002513.

• Holder, Mark, and Paul O. Lewis. 2003. “Phylogeny Estimation: Traditional and Bayesian Approaches.” Nature Reviews Genetics 4 (4) (April): 275–284. doi:10.1038/nrg1044.

• Tem muitos no Youtube, eu gostei deste

Aula 9

• David Posada - Selecting models of evolution.

• Sullivan J. & Joyce P. 2005. Model Selection in Phylogenetics. Annual Review of Ecology, Evolution, and Systematics, 36:445–466.

• Le, S.Q., Gascuel, O., 2008. An Improved General Amino Acid Replacement Matrix. Mol Biol Evol 25, 1307–1320. doi:10.1093/molbev/msn067

Aula 10

• Giribet G., 2007. Efficient tree searches with available algorithms. Evol Bioinform Online 3: 341–356.

Aula 11

• Graur, Dan, and William Martin. "Reading the entrails of chickens: molecular timescales of evolution and the illusion of precision." TRENDS in Genetics 20.2 (2004): 80-86.]

• Donoghue, Philip CJ, and Ziheng Yang. "The evolution of methods for establishing evolutionary timescales." Phil. Trans. R. Soc. B 371.1699 (2016): 20160020.

• Kumar, Sudhir. "Molecular clocks: four decades of evolution." Nature Reviews Genetics 6.8 (2005): 654-662.

Aula 12

• Pagel, Mark, Andrew Meade, and Daniel Barker. "Bayesian estimation of ancestral character states on phylogenies." Systematic biology 53.5 (2004): 673-684.

• Swofford, David L., and Wayne P. Maddison. "Reconstructing ancestral character states under Wagner parsimony." Mathematical Biosciences 87.2 (1987): 199-229.

Literatura Sobre Escrita Científica

Elements of Style

Strunk & White Elements of Style Website do "livrinho"

Strunk & White Elements of Style "livrinho"

Strunk & White Elements of Style livro

Strunk & White simplificado

Outros recursos

Livros Gilson Volpato
Artigos Gilson Volpato

Moore A. 2013. On the state of scientific English and how to improve it – Part 1. Bioessays 35: 409–409.
Moore A. 2013. On the state of scientific English and how to improve it – Part 2. BioEssays 35: 497–497.
Moore A. 2013. On the state of Scientific English and how to improve it – Part 3. BioEssays 35: 667–667.
Moore A. 2013. On the state of scientific English and how to improve it – Part 4. BioEssays 35: 925–925.
Moore A. 2014. On the state of scientific English and how to improve it – Part 5. BioEssays 36: 331–331.
Moore A. 2014. On the State of Scientific English and How to Improve It – Part 6. BioEssays 36: 541–541.