The use of the central dogma of molecular biology isn't so useful to understand/create historical reconstructions. The central dogma of molecular biology is an explanation of the flow of genetic information within a biological system. This dogma has also been stated as DNA, makes RNA and RNA makes protein. A historical reconstruction is a “tree” that infers evolutionary relationships between species. Historical reconstructions are built based on morphological or genetic characteristics. But we need to be careful of how we understand these genetic characteristics. When we think in a individual, the central dogma can explain the most common ways of flowing information in its life. But evolutionary events are deeper than that. For understanding the flow of genetic information in historical reconstructions we need to consider events like, for example: epigenetics, prions or lateral transference. Epigenetics can interfere in morphological characteristics of organisms and even in their fitness, all this without changing the base sequence that you use to build the trees. Lateral transferences is a kind of genetic information flow that can make the work of building trees harder if you don't identify this event. Lateral transferences can occur in different organisms that are not necessarily related, and you are seeing just an homoplastic character. For these reasons, phylogenetic studies in general are using combinations of genes and morphological characters, trying to obtain the phylogenetic signal for the groups. So, if you ignore all these different cases of flowing of genetic information, and stays with the central dogma of molecular biology you are basically staying in individual level, and not working with all the possibilities of evolutionary events that can be happening in your group.
Achei o texto claro e direto. Com parágrafos curtos e lógicos. Você falou sobre como mecanismos diferentes devem influenciar na reconstrução histórica. Faltou falar sobre as divergências do próprio código genético em si.
Ensaio 1 (17/03)
Alignment is an art. You could identify many evolutionary processes and mistakes just looking to your data. The methods that we have to build historical reconstructions are based on dichotomies that came from duplication models of DNA replication. However, this dichotomies doesn’t consider reticulation events, for example. Reticulation events, like lateral transferences, can disturb the “vertical” signal (phylogenetically related). The tip here is, look to your alignment before you use a pipeline. Pipelines will just analyze your data and give you the tree. It is interesting to understand what your pipeline gives to you before trust it.
Não tenho certeza se a sua primeira frase é um “topic sentense”, apesar de ter um único verbo na frase. Sua frase não vai direto ao ponto como sugerido pelo Daniel. Não ficou clara a relação entre “art” e os processos (mecanismos) de alinhamento.
Essa é minha única observação. Suas frases são curtas e me parecem muito boas. Elas, também, atendem as orientações do Daniel.
Ensaio 2 (24/03)
Genes used as phylogenetic markers must be neutral. Phylogenetic analysis uses substitution rate to infer relationships. We can underestimate or overestimate substitutions rates. These mistakes can occur when your site is not neutral. Sites under selective pressures are usually underestimated. That happens, because you have purifying selection acting on it. Molecular markers usually are neutral. However, in big data times it is difficult to know if everything is neutral or not. Because of that, or you understand the genes you are using or you find a way to escape from this bias. New methods can discard these “not neutral” data. Otherwise, a way to escape could be using aleatory sites to reconstructions.