Deyvid Emanuel Amgarten

Hello world!
Welcome to my personal page for the course PEMARF.
Have fun :P

Optional Essay - March, 9th

Viruses and the central dogma

The flow of information from DNA molecules to RNA and thereafter to proteins is known as the Central Dogma of Molecular Biology, as first stated by Francis Crick in 1958 [1]. This dogma was the epicenter of plenty of debate in the scientific community and new directions to the flow of genetic information are now well described. Viruses are remarkable exceptions in this regard, since several studies have demonstraded RNA viruses that replicate themselves through a DNA intermediate (Retroviruses) and self-replicating RNA genomes from single and double stranded RNA viruses. Another noteworthy case refers to viruses that carry methylation proteins in the virion to target bacterial DNA and stop host transcription once and for all. This last example could be characterized as an Unknown case of transfer (Protein -> DNA), as hypothesized by Crick in 1970 [2]. As a result of the diversity of genome forms and replication mechanisms, viruses have a unique capacity of shedding light to a complete picture of the Central Dogma of Molecular Biology.

1. Crick, Francis. "On protein synthesis." Symp Soc Exp Biol. Vol. 12. No. 138-63. 1958.
2. Crick, Francis. "Central dogma of molecular biology." Nature 227.5258 (1970): 561-563.

Analisado por Livia Moura: Dado que o objetivo desse exercício é ser sucinto e direto na informação que se quer transmitir: + a primeira sentença vem com a informação principal de antemão, antes da histórica ( :D ); + creio que a segunda sentença poderia ser descartada; + na terceira sentença a frase ficou estranha, como precisando de uma finalização (n seria o "that" substituido por "can" ou similar?… posso estar enganada). + As demais ficaram boas :)

Essay 1 - March 17th

The avalanche of genomic information that scientists have been experience in the last decade is revolutionizing several areas of biology. Taxonomy and species definition are special cases in this context, since both fields are subject to classical taxonomic rules and descriptions. Techniques of environmental sequencing allow researchers to obtain entire microbial genomes without the isolation of the organism in vitro, with many completely new species been unveiled every day in all parts of the globe. Therefore, taxonomy and species definition should change to embrace genomic data and rules should be redesigned in a way that genomic/molecular data and classical descriptions could both be used in this new scenario. Biology since its very beggining is changing from exclusively descriptive approaches to include computational and quantitative methods [1], and so should do its taxonomy field.


1. Markowetz F. All biology is computational biology, 2017. PLOS Biology 15(3): e2002050. doi: 10.1371/journal.pbio.2002050

Primeira Frase, OK : Achei direta e objetiva, uma idéia clara.
Segunda frase também Ok, tem duas idéias, mas bem ralecionadas.
Terceira frase, muito longa, quebraria em duas: "Techniques of environmental sequencing (…) the organism in vitro. Therefore many new species (…)."
Frase seguinte também está longa, como já usei um "Therefore" antes começaria direto com: "Taxonomy and (…) genomic data. The rules should (…) in this nex scenario."
Ultima frase, OK.

Correção Maila

Essay 2 - March 24th

Student's understanding of the neutral theory

It is interesting to think about the bias that most scientists have regarding the importance of Darwinian selection in the evolution landscape. It is contra intuitive to think that stochastic processes (genetic drift) could be responsible by most of features we now see fixed in different populations. Darwin’s natural selection teachings permeate most undergrad courses and there is a constant repetition of its importance to evolution and biology in general. On the other hand, the neutral theory and its agent are only taught in evolution classes and/or more advanced graduation classes. This causes students to contest ideas that for them are not intuitive. The diversity arises from random mutations and the ones that are truly adaptive are thought to be very rare. Nevertheless, the majority of substitutions are thought to be neutral and they are fixed in populations through genetic drift, as many studies have shown[1,2,3]. Thus, early evolution courses in undergrad could be a way of solving this problem and make students more familiar with the neutral theory since the very beggining.


1. Kimura, Motoo (1968) Evolutionary Rate at the Molecular Level. Nature, 217:624.
2. King JL, Jukes TH. (1969). Non-Darwinian Evolution. Science 164:788-97.
3. Kimura, Motoo (1991). The neutral theory of molecular evolution: a review of recent evidence.. Jap. J. of Genetics.

Essay 3 - March 31st

Infinite size populations

Species with assumed infinite population sizes may pose as exceptions to the neutral theory of evolution. Most of substitutions observed in different populations are thought to be fixed by random drift of the allele’s frequency, as first stated in [1]. However, the effective population size modulates how genetic drift and natural select act upon the frequency of alleles [2]. Species with enormous population sizes (e.g. bacteria and viruses) may amplify the effects of selection upon alleles that confers differential fitness to the organism. Thus, different from small size population, most of diversity observed in bacterial and viral populations would be a result of natural selection action. Nevertheless, what seems to actually occur is that most of modifications slightly decreases or increases the fitness of its carrier [3]. In this context, selection is more pronounced in infinite size populations when compared with small size populations. In other words, we are more likely to see nearly neutral (increasing or decreasing the fitness) modifications in small size populations than we are of seeing slightly deleterious modifications in infinite size populations.

Avaliação Livia: Achei muito bom. Pode-se ver a aplicação das técnicas aprendidas em aula durante a leitura do texto. :)


1. Kimura, Motoo (1968) Evolutionary Rate at the Molecular Level. Nature, 217:624.
2. Charlesworth, Brian. "Effective population size and patterns of molecular evolution and variation." Nature Reviews Genetics 10.3 (2009): 195-205.
3. Ohta, Tomoko (1973-11-09). "Slightly Deleterious Mutant Substitutions in Evolution". Nature. 246 (5428): 96–98

Essay 4: May 5th

Phylogenetic trees are the core display of evolutionary biology and frequently subjective to misunderstandings caused by tips or topologies not carefully thought [1]. The act of thinking the display of a tree can make an important difference in the understanding of the concepts transmitted by it. Even more if we consider that tree diagrams have been used for different purposes, as for clustering or demonstrating similarity for example. This use may give the specific idea of similarity among the clades when the tree is actually showing a historic relationship. Therefore, tree thinking should be a fundamental part of evolution training for biology students, as reading and understanding maps is for beginning geography students [2].


[1] Baum D. A., Smith S. D. & Donovan S. S. 2005. The tree-thinking challenge. Science, 310:979–980.
[2] O'hara R. J. 1993. Systematic generalization, historical fate and the species problem. Systematic Biology, 42:231-246.

Correção por Jorge

Parágrafo bacana. O primeira sentença poderia ser dividida em duas, dando as mais força a cada uma. Eu seria uma pouco mais direto em alguns casos como "The act of thinking the display of a tree can make…" para "Thinking about tree display makes…". Eu também incluiria um "such as" no lugar de "as" na terceira linha. Acho que é isso, parabéns. Espero ter ajudado.

Essay 5: May 12th

Brief discussion of methods to phylogenetic reconstruction

There are different methods for phylogenetic reconstruction that may be more suitable depending on the researcher’s purpose. Methods based on distance-matrices are usually fast and computationally efficient, but lack the statistical robustness of other methods and present limitations regarding the modeling of modifications in a sequence. UPGMA is a clustering algorithm that sequentially link least different pair of sequences (analyses with molecular data). The neighbor joining (NJ) [1] method tries to correct several assumptions of the UPGMA method and is very used to assess preliminary relationship among sequences. On the other hand, the maximum likelihood (ML) [2] method is based on standard techniques to infer probability distributions and, therefore, assign probabilities to a particular possible tree. This method is very robust and thought to be suitable to analyses of distant related sequences. However, it requires a great deal of computation, which is sometimes intractable. Thus, it seems that NJ trees are useful for “first glances” at sequence alignment data, while ML would be indicated to produce a robust phylogenetic tree with small sets of OTUs and molecular characters.


[1] Saitou, Naruya, and Masatoshi Nei. "The neighbor-joining method: a new method for reconstructing phylogenetic trees." Molecular biology and evolution 4.4 (1987): 406-425.
[2] Yang, Ziheng. "PAML: a program package for phylogenetic analysis by maximum likelihood." Computer applications in the biosciences: CABIOS 13.5 (1997): 555-556.

Correção por Rosana Cunha

Texto muito bom Deyvid. Sua "topic sentence" está objetiva e resumindo bem a temática que será abordada ao longo parágrafo. Linguagem telegráfica e com sentido completo das ideias. Breve conclusão do raciocínio ao terminar o texto, ótima construção! Vou fazer apenas umas pequenas correções no inglês, só questão de gramática mesmo. Parabéns, gostei muito de como você desenvolveu o assunto.
- "but they lack the statistical"
- "to analyses of distant related sequences" - essa frase está estranha, depois você dá uma olhada pra ver se minha crítica é válida.

Essay 6: May 19th

Selfish genetic elements

Selfish genetic elements are self-replicating DNA sequences that are spread through organisms from the three domains of life, and viruses [1-4]. Dawkins in 1976 proposed that human being and other animals are nothing more than carrier machines for these selfish elements [5]. Despite of the discussions about the unit of selection, these mobile elements are present in all sort of genomes and may have implications to the fitness of an organism [6]. For instance, a VDE homing endonuclease element may affect growth and sporulation behavior in Sacharomyces cerevisae [7]. Moreover, homing endonucleases are present in several copies in phage genomes such as the Phage T4, and they may have implication in the mosaicism of phage genomes [4]. Thus, selfish genetic elements are important components in our understanding of the genetic relationship stablished in a genome and its implication to the fitness of the organism.

[1] Peterson, Peter A., and John R. Laughnan. "Mobile elements in plants." Critical reviews in plant sciences 6.2 (1987): 105-208.
[2] Berg, Douglas E., and Claire M. Berg. "The prokaryotic transposable element Tn5." Nature Biotechnology 1.5 (1983): 417-435.
[3] Brügger, Kim, et al. "Mobile elements in archaeal genomes." FEMS microbiology letters 206.2 (2002): 131-141.
[4] Amgarten, Deyvid, et al. "Three novel Pseudomonas phages isolated from composting provide insights into the evolution and diversity of tailed phages." BMC genomics 18.1 (2017): 346.
[5] Dawkins, Richard. "Th e Selfish Gene." NewYorkCity: OxfordUniversityPress (1976).
[6] Kazazian, Haig H. "Mobile elements: drivers of genome evolution." science 303.5664 (2004): 1626-1632.
[7] Giraldo-Perez, Paulina, and Matthew R. Goddard. "A parasitic selfish gene that affects host promiscuity." Proceedings of the Royal Society of London B: Biological Sciences 280.1770 (2013): 20131875.

Correção Maila:
1. Começou com uma frase inicial clara e direta trazendo a idéia principal.
2. na segunda frase eu deixaria apenas "human" e não "human being" - tive que reler mais de uma vez para fazer sentido.
3. Já que você citou a a homing endonuclease em Sacharomyces cerevisae, acho que você poderia, dizer a implicação dessa alteração em crescimento e esporulação, só citar, acho que deixaria mais completo.
4. finalizou bem o parágrafo.
Muito bom

Essay 7: May 26th

Model selection in phylogenetic analysis

The selection of an appropriate substitution model is a fundamental step in phylogenetic analyses. It is responsible for estimating the substitution parameters and thereby, for determining the tree topology and historic inferences. Software such as RaxML [1] and ProtTest [2] are able to test several available models and provide information in order the user can choose the most appropriate one. The tests are based in the reconstruction of distance preliminary trees and they are assessed using likelihood ration test [3] or information criteria [4]. Therefore, using the best fitting model to one’s data can produce a more robust and coherent phylogeny.

[1] Stamatakis, Alexandros. "RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies." Bioinformatics 30.9 (2014): 1312-1313.
[2] Abascal, Federico, Rafael Zardoya, and David Posada. "ProtTest: selection of best-fit models of protein evolution." Bioinformatics 21.9 (2005): 2104-2105.
[3] Lewis, Fraser, Adam Butler, and Lucy Gilbert. "A unified approach to model selection using the likelihood ratio test." Methods in Ecology and Evolution 2.2 (2011): 155-162.
[4] Bozdogan, Hamparsum. "Model selection and Akaike's information criterion (AIC): The general theory and its analytical extensions." Psychometrika 52.3 (1987): 345-370.

Comentário: Lyslaine Sato
A frase inicial apresenta o assunto abordado no texto. Escrita clara, objetiva e com referências. O seu parágrafo foi bem construído, contém a introdução, o desenvolvimento/argumentação e a última frase concluindo a sua ideia.

Essay 8: June 2nd

Viral diversity on the biosphere

Viruses are the most abundant biological entities on earth, with the estimated number of 1031 particle in total [1]. Despite of their huge abundance in particles, a little more than 3200 different genomes of double-stranded DNA and retro RNA viruses are deposited in the NCBI database [2]. This diversity is thought to be much greater, since next generation sequence techniques and metagenomics have shown that known species are extremely biased to our methods of cultivation [3]. An example of this bias was demonstrated by a recent work published in Nature, where the authors managed to discovery 125,000 new partial viral genomes obtained from metagenomic samples of different environments on the biosphere [4]. In the same line, another article reported the discovery of 15,222 epipelagic and mesopelagic viral populations obtained by sampling oceans of the globe [5]. As the authors discuss in both articles, these are astonished evidence for the great diversity on earth’s virome.

[1] Bergh, Øivind, et al. "High abundance of viruses found in aquatic environments." Nature 340.6233 (1989): 467-468.
[2] Reddy, T. B. K., et al. "The Genomes OnLine Database (GOLD) v. 5: a metadata management system based on a four level (meta) genome project classification." Nucleic acids research 43.D1 (2015): D1099-D1106.
[3] Rappé, Michael S., and Stephen J. Giovannoni. "The uncultured microbial majority." Annual Reviews in Microbiology 57.1 (2003): 369-394.
[4] Paez-Espino, David, et al. "Uncovering Earth’s virome." Nature 536.7617 (2016): 425-430.
[5] Roux, Simon, et al. "Ecogenomics and potential biogeochemical impacts of globally abundant ocean viruses." Nature (2016).

Comentário por Lyslaine Sato:
O parágrafo foi bem escrito. Utilizou linguagem clara e objetiva para transmitir a mensagem. Contém a introdução, o desenvolvimento/argumentação e a última frase concluindo a sua ideia.

Essay 9: June 9th

Biotic factors driving evolution

Interactions among organisms constitute an important factor driving evolution and speciation. The Red Queen hypothesis proposes that organisms must constantly adapt and evolve simply to survive while pitted against ever-evolving opposing organisms [1]. In other words, they must keep running (evolving), to keep at the same place (same fitness). In this line, parasite-host species perform an arms race to keep up the pace of resistance by the host and new mechanisms of infection by the parasite. For instance, bacteriophages and the bacteria they infect are in a constant arms race, as discussed in [2]. Besides parasitism, mutualism, predation and competition also have the potential to drive adaptation and evolution of an organism. It is worth noting, however, that abiotic factors may also play a role in adaptation, as well as stochastic processes [3].

[1] Van Valen L. (1973): "A New Evolutionary Law", Evolutionary Theory 1, p. 1-30.
[2] Vasu, Kommireddy, Easa Nagamalleswari, and Valakunja Nagaraja. "Promiscuous restriction is a cellular defense strategy that confers fitness advantage to bacteria." Proceedings of the National Academy of Sciences 109.20 (2012): E1287-E1293.
[3] Venditti, C., Meade, A., & Pagel, M. (2010). Phylogenies reveal new interpretation of speciation and the Red Queen. Nature, 463 (7279), 349–352.

Essay 10: June 20th

Comentários sobre a disciplina e auto-avaliação

Como reflexão geral sobre a disciplina, acredito que foi muito útil para a minha formação acadêmica e coerente com sua proposta inicial. O foco na escrita acadêmica com os ensaios semanais e feedback dos alunos sobre o texto foi um dos pontos fortes da disciplina. Abordagem muito interessante permitir que os alunos exercitem a escrita e revisão de textos acadêmicos. Além disso, os seminários abordaram temas que complementaram assuntos importantes de evolução molecular que não foram expostos diretamente em aula. A abordagem utilizada na prova também foi interessante, simulando prova de concursos. E o conteúdo das aulas foi coerente com o cronograma e contribuiu com um arcabouço teórico importante para o trabalho que venho desenvolvendo.

Eu talvez esperasse um pouco mais de profundidade nos assuntos abordados nas aulas expositivas. Porém entendo as limitações de tempo e a escolha do professor por este recorte. Em mais de uma ocasião ficou claro a opção por proporcionar o básico aos alunos de forma que eles possam correr atrás dos assuntos mais aprofundados.

De maneira geral, avalio o meu desempenho na disciplina como satisfatório. Fiz todas as atividades propostas e participei das discussões em sala de aula. A disciplina contribuiu sem dúvida nenhuma para o meu repertório de conhecimentos relacionados a evolução. Destaco pontos sobre o tamanho efetivo das populações e sua influência nos processos evolutivos e pontos sobre os métodos de ML e busca em árvores.

Minha nota: 1.0

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