Jose Eduardo Serrano Villavicencio

Primeiro ensaio (opcional 10/03/2017)

The importance of one simple idea

Crick's (1958) central dogma was a plausible attempt to understand how the mechanisms of transmission and expression of genetic inheritance work. This dogma was as revolutionary as problematic; the fact that this hypothesis was introduced to the scientific community under the term “dogma” caused discomfort and several critics to its postulant, mainly for the contradiction between the true meaning of this word and the scientific method. By definition, a dogma is a belief that cannot and should not be questioned, for some the use of this term was too pretentious and for others outrageous. Crick himself would recognize years later that this was an unfortunate choice of word; to him “dogma” did not mean the same that for the rest of us and decided to use this term in order to avoid the overuse of the word “hypothesis” (which had been used some years before by him when describing his Sequential hypothesis). Furthermore, he also stated that he wanted to suggest that this new conjecture was more central and more powerful but, sadly, the use of the word dogma caused perhaps more problems than it was worth. To my mind, and leaving the semantics aside, this “dogma” accomplished its mission; in 1958 we knew nothing about the processes involved in the replication of the DNA and was precisely this risk and unsupported hypothesis that encouraged several teams of scientists to try to corroborate or refute it. Although over simplistic for some, Crick´s dogma represents the cornerstone and starting point of a long process of understanding the extraordinary machinery wrapped in DNA synthesis which is still ongoing.

Correção Ana Laura (17/03/17)

Olá,
No início, apresenta bem o que será abordado ao longo do
Tem toda uma contextualização histórica a cerca do problema da palavra "dogma" usada por Crick, que está clara, mas poderia ser apenas um pouco mais objetiva, como por exemplo, estas duas partes "…the fact that this hypothesis was introduced to the scientific community under the term “dogma” caused discomfort and several critics to its postulant, mainly for the contradiction between the true meaning of this word and the scientific method." e "By definition, a dogma is a belief that cannot and should not be questioned, for some the use of this term was too pretentious and for others outrageous" poderiam ser unidas e sintetizadas por que falam basicamente a mesma coisa.
O que parece é que entre quase todo o ensaio e a última sentença há uma quebra de linearidade em relação ao assunto central do texto.

Ensaio 2 (17/03/2017)

When only good taxonomy matters

The taxonomy is suffering deep changes in different hierarchical levels, not only at genus level as species too. These changes are reflected in the disproportionate increase in both species and genera number. Most of the new genera and species (regardless the method used) have been described by researchers that cannot be called taxonomists sensu stricto. In this context, I would like to present one example of how a good taxonomist could present a robust and coherent taxonomic hypothesis. Fooden (1963) based on morphological characters and an extensive set of samples, proposed only two species of woolly monkeys (genus Lagothrix): L. lagothricha and L. flavicauda, the first with four subspecies. In a second revision and with limited sample and scarce phylogenetic evidence, these four subspecies were elevated to full species rank by Groves (2001). Nevertheless, after 50 years, new molecular evidence presented by Ruiz-García et al. (2014) and Di Fiore et al. (2015) corroborated Fooden’s (1963) original proposal. As a conclusion, regardless the methodology, the expertise and the good criteria of the taxonomist would reflect better taxonomic hypothesis.

Di Fiore A., P.B. Chaves, F.M. Cornejo, C.A. Schmitt, S. Shanee, L. Cortés-Ortiz, V. Fagundes, C. Roos and V. Pacheco. 2015. The rise and fall of a genus: Complete mtDNA genomes shed light on the phylogenetic position of yellow-tailed woolly monkeys, Lagothrix flavicauda, and on the evolutionary history of the family Atelidae (Primates: Platyrrhini). Molecular Phylogenetics and Evolution 82B: 495-510.

Fooden, J. 1963. A Revision of the Woolly Monkeys (Genus Lagothrix). Journal of Mammalogy (en inglés) 44 (2): 213-247.

Groves C. 2001. Primate taxonomy. Smithsonian Institution Scholarly Press, Washington DC.

Ruiz-García M., M. Pinedo-Castro and J. M. Shostell. 2014. How many genera and species of woolly monkeys (Atelidae, Platyrrhine, Primates) are there? The first molecular analysis of Lagothrix flavicauda, an endemic Peruvian primate species. Molecular Phylogenetics and Evolution 79: 179-198.

Correção ensaio (17/03/2017)

Hola José,
Eu achei seu texto muito bom, principalmente pelo fato de desenvolver uma opinião pessoal, bem sustentada num caso concreto e focada na discussão da aula. Esse é o dever ser de um ensaio.

Segundo o exposto pelo Daniel na aula (eu não vou repetir), más se complementar:
- A voz passiva, exemplo: … were elevated…
- Poderia ter deixado mais ampla a ideia original, como proposito do seu ensaio. A ideia original eu entendo como a conclusão, mas deveria aparecer na sua frase tópico, no começo do texto. Assim seja uma tão lapidaria quanto: Most of the new genera and species (regardless the method used) have been described by researchers that cannot be called taxonomists sensu stricto. (Isso precisa ter um apoio maior que um único caso só, que é mais uma opinião sobre o caso exposto, eu acho, pelo menos.)
Obrigada pelas suas correções!

Ángela Márquez


Ensaio 3 (24/03/2017)

Darwin and his natural selection idea

Darwin´s (1856) concept of natural selection was a revolutionary idea for most of scientists at his time. Since the publication of the first edition of “On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life”, Darwin stated that he was sure that there were several factors, unknown by him, of speciation. Darwin also declared that natural selection alone would not explain by itself the vast diversity of plants and animals. Perhaps, based on misunderstandings or lack of knowledge, several scientists distorted Darwin’s idea proclaiming natural selection as the unique force of speciation. Kimura (1969) corrected and expanded the vision of the processes involved in evolution. The most important Kimura’s statement was that most of the evolutionary processes are explained by Genetic drift and not by natural selection. This idea changed profoundly our vision of evolution. Furthermore, Kimura’s (1969) agrees with Darwin’s predictive (and perhaps ignored) ideas.

Comments (Caio Gueratto):

My observations regarding the text are expressed below:

Lack of reference in the first sentence. Who says Charles Darwin`s concept was a revolutionary idea?
Lack of reference here as well: " Perhaps, based on misunderstandings or lack of knowledge, several scientists distorted Darwin’s idea proclaiming natural selection as the unique force of speciation." Which scientists?

"The most important Kimura’s statement was that most of the evolutionary processes are explained by Genetic drift and not by natural selection.". It is in passive voice and there is a grammatical issue here. Suggestion of change: kimura's most important statement was that Genetic drift explains most of the evolutionary process instead of natural selection).

Some sentences have breaks and inversions that make them more difficult to undestand than when they are not broken. An example: "…Darwin stated that he was sure that there were several factors, unknown by him, of speciation".

"This idea changed profoundly our vision of evolution." In which way? Expand a little bit more your ideas.
"Furthermore, Kimura’s (1969) agrees with Darwin’s predictive (and perhaps ignored) ideas." Which ones and how does Kimura agree? Expand a little bit more your ideas.

Ensaio 4 (31/03/2017)

Effective population size and its relation with taxonomy

The number of mammal species has rapidly increased in the last two decade. In particular, primate species are the target of a taxonomic inflation (Mace 2004). Every year new species (and genera) of primates are described. Some of these species are the result of arbitrary elevation of subspecies to the full species rank and others of molecular phylogenies that have become more common in these days. In the latter case, the main criterion for splitting species is the time of divergence between taxa. As pointed out in class, this criterion can be (and it is) used for organisms as bacteria and virus in which the Effective population size (Ne) may be calculated. I do not recall any case when the Ne had been calculated for primates. Therefore, the practice of splitting primate species (and even genera) under this criterion is harmful for taxonomy because creates a great ambiguity. For some authors 70% of divergence between two taxa should be enough for others do not. We must understand that genomics are a good complement for other methods but should not be taken as the holy grail of current taxonomy.

Ensaio 5 (05/05/2017)

The more… the better?

Subjectivity is a big handicap in systematics. This subjectivity is reflected in the different interpretations that scientists from the same result. At the end, how many differences separate the genus A from the genus B? This is a complicated issue because here with deal with a very complex philosophical debate. In order to illustrate this problem, I would like to present the case of the New World Monkeys (hereafter NWM) genera. The number of NWM genera has increased in the last two decades. If we push a little bit our memories and remember the classics Napier (1976) or Hershkovitz (1977), both proposed 16 genera of NWM. Groves (2001) proposed 17 genera of NWM. After a phylogenetic analysis based on 20 cranial characters and an unknown number of specimens, Groves (2001) concluded that Lagothrix flavicauda was more closely related to the spider monkeys (genus Ateles) and did not to the wooly monkeys (genus Lagothrix). Using his phylogenetic result Groves decided to revive the monotypic genus Oreonax proposed by Thomas (1927) for L. flavicauda. Rosenberger and Matthews (2008) replicated and extended Groves’ study and showed that his results were probably a sampling artifact. These results undermined the logic of reviving Oreonax as a formal genus for flavicauda. More recently, several splits of NWM genera have been proposed. The capuchins monkeys (genus Cebus) are now divided into Sapajus (tufted capuchins) and Cebus (untufted capuchins). Tamarins (genus Saguinus) into Leontocebus and Saguinus. Titi monkeys (genus Callicebus) into Cheracebus, Plectorocebus, and Callicebus. As you can notice, we have now approximately 22 genera of NWM. This is an unusual and very particular phenomenon among medium and large mammals. The majority of these taxonomic changes are based on phylogenetic analysis, which found that different clades of the same monophyletic group had distinct divergence times. Thus, any single clade should deserve a new generic name. This tendency of splitting well-known monophyletic clades into smaller groups is affecting the current primate taxonomy. However, what do we win with all these new genera? To me, only taxonomic noise. The main question is: are not these animals the same thing more or less? Continuing to recognize the long-established and monophyletic genera Cebus, Callicebus, and Saguinus, and as subgenus, these “new genera”, will allow a more efficient communication among scientists. Facilitating this communication is the task of taxonomists.

References

Groves C. 2001. Primate taxonomy. Smithsonian Institution Scholarly Press, Washington DC.

Hershkovitz P. 1977. Living New World monkeys, volume 1: (Platyrrhini) with an introduction to primates. University of Chicago Press, Chicago.

Napier P.H. 1976. Catalogue of Primates in the British Museum (Natural History). Part I: Families Callitrichidae and Cebidae. British Museum, London.

Rosenberger A.L. & L. Matthews. 2008. Oreonax-not a genus. Neotropical Primates 15(1):8-12.

Thomas O. 1927. A remarkable new monkey from Peru. Annals and magazine of natural history 9(19):156–157.

Comments (by Caio Gueratto):

This is a good text. The point you want to make is clear for me. There are some things to say, though.

- There are words missing/ without a clear sense. I could see this in two sentences:
"This subjectivity is reflected in the different interpretations that scientists from the same result." (Maybe "scientists have"?)
"This is a complicated issue because here with deal with a very complex philosophical debate" (Maybe "we" instead of "with"?)

-Passive voice. I could count many of them in this paragraph. Some examples are below:
"More recently, several splits of NWM genera have been proposed."
"The capuchins monkeys (genus Cebus) are now divided into.."
"The majority of these taxonomic changes are based on phylogenetic analysis…"
Besides these examples, I think there are two or three more.

If these you correct these two points, the text will be very good.

Ensaio 6 (12/05/2017)

Phenetics vs Cladistics

Cladistics can be defined as the study of the pathways of evolution. In this context, cladists are more interested in classifying organisms based on their evolutionary lineage. As a result of their studies (regardless the method) cladists obtain a tree-like network that expresses such ancestor-descendant relationships, called cladogram. On the other hand, Phenetics is the study of relationships among a group of organisms based on the degree of similarity between them. In other words, it is an attempt to classify organisms based on overal similarity, typically in morphology, without regard for their evolutionary relationships. In this case, the result is a tree-like network expressing phenetic relationships called phenogram.
After several (and not very friendly) debates between the developers of each method phenetics was almost forgotten. In this century, phenetics’ resurgence has brought a large list of “new users” which are using this method. Some of these new users are not worried about to study organisms as a whole, but as a number. The idea of quantifying everything (even some biological elements or concepts) is conquering the biological thought in these days.

Comentário por Lyslaine Sato:
O texto está bem escrito. A topic sentence introduzindo o assunto discorrido na sequência. A construção do texto abordando fenética e cladística ficou bem interessante.

Ensaio 7 (19/05/2017)

Weak topology and weak bootstrap are a good argument?

Groves (2001), in a forced attempt to apply the Phylogenetic Species Concept to the entire order Primates, proposed one more genus of New World Monkey. Although I already spoke about the resurrection of Oreonax in the “ensaio 5”, I would like to expose a different approach of Groves’ work, the topology of its topology. Groves’ Atelidae phylogeny was largely criticized. One of the first critics was the unknown taxa used in his analysis, some species were explicitly informed and some remain as sp. (as in the case of Ateles). Another critic was the number of characters used in the analysis, 20 morphological characters. Finally, Groves presented a tree obtained with a Parsimony analysis in which two bootstrap indexes were shown (67 in both cases), and consistency and retention index of 0.667 and 0.538, respectively. All the evidence pointed out that the topology of that tree was unsupported and contradictory to the evolutionary history already known for several years. Matthews and Rosenberger (2008) replicated and extended Groves’ study. These authors corroborated that Groves’ tree topology that supported his decision of maintaining Oreonax as valid genus only when using Alouatta as outgroup. They finally argued that Groves’ phylogeny has a biasing effect in parsimony analysis and that the cladistic rationale for resurrecting the Oreonax generic distinction for Lagothrix flavicauda was based on an artifact of idiosyncratic sampling within the study group below the genus level. This case shows us that, regardless any logic, some researchers take advantage of their reputation in order to publish some controversial works.

Correção Ana Laura

O seu texto é muito claro e muito bom.
A única crítica que faço é ao fato de haver muitas frases longas.

Ensaio 8 (26/05/2017)

If it is popular, should I use it?

Talking in class about models that we may (or should) use in our studies, I realize something interesting. The lack of criterion of some colleagues when choosing the most appropriate model for their phylogenies is quite striking. When performing my masters’ dissertation, I decided to use parsimony for my data. Some colleagues asked me why I was using that. They argued that Bayesian analyses are now more popular. They clearly ignored the basis of each model, when and how should you use different models according your data. For my purposes and the nature of my data, morphological characters, a Bayesian analysis is not applicable. This is not uncommon in recent studies. We, as users, should know (at least) when a model will fit for our analyses. Probably some researchers we will understand the algorithms and the complex processes involved in the development of each model, perhaps I will never do that. Nevertheless, for the rest of us, a basic background that support our decision of which model will be more suitable for our analyses is needed.

Correção por Camila Chabi (02/05/17)
Seu ensaio esta muito bem escrito, didático e direto. Parabéns! Mas seguem poucas sugestões para melhora-lo:
1-Siguindo as dicas do prof, direcione seu texto à um público alvo;
2- Tente sempre utilizar alguma referência bibliográfica;
3- Entendi o contexto que vc utilizou, mas talvez seria melhor construir as frases como outra colocação,impessoal ou na terceira pessoa (é apenas uma sugestão, talvez posso estar equivocada!) por exemplo: "should I use it" por "should we use it".

Ensaio 9 (02/06/2017)

Once again…The more… the better?

There is a new tendency on recent molecular-based phylogenetic studies that I would like to present. I certainly ignored the mathematics behind the different models and optimization criteria that we saw in class (I am not that pretentious). However, I have learned that in this case, you may be able of using all the available methods in phylogenetics but that does not guarantee that you are reaching the absolute truth. It seems highly probable that if you present your work in which you applied several methods in order to obtain the same result, your work will look “stronger”. You can even decorate it with fancy words (loved by revisers and editors) like “my result is highly significant” from something that you applied 0 statistics.

Ensaio 10 (09/06/2017)

A new trend: splitting genera

There is a new trend in recent Primatology, splitting genera based on their divergence time. This tendency is mainly being imposed by molecular biologists, which (in some cases) do not have a familiarity with the group their studies are focused on. The logic is simple: Goodman et al. (1998) produced time-based taxonomic classification criterion and proposed that primate species that diverged from 11 to 7 Ma (million years ago) should be recognized as separate genera. This criterion has been recently applied in genera as Cebus (Lynch-Alfaro et al., 2012), Saguinus (Buckner et al., 2015), and Callicebus (Byrne et al., 2016). These splits have been accepted by some primatologist (mainly in ecological and conservation studies), and have been criticized by others (Rosenberger, 2012; Gutiérrez and Marinho-Filho, 2017). The critics are focused in the meaningless splits of well-known monophyletic groups which do not accomplish anything than using the name at the subgenus level could not. In my opinion, one of the most worrying problems whit these new taxonomic arrangements is the difficulty in communication among scientists. Take as an example the genus Callicebus. Hershkovitz (1990) recognized 13 species and 17 subspecies of this genus. Some years later, van Roosmalen (2002) decided (without any argument) to elevated to the full species rank all the Hershkovitz’s subspecies and, describing two more species, the number of species raised to 32. At least four more Callicebus species were described in recent years, so far 36 species of this genus (a difficult number of species to handle with). Byrne et al. (2016) proposed to split the genus Callicebus into three different genera (Plectorocebus, Cheracebus and Callicebus). Now imagine this scenario, in which genus should be placed the specific name moloch? Callicebus, Plectorocebus, or Cheracebus? Imagine asking yourself that question 36 times. The question here is: aren’t these animals the same thing, more or less? We should refuse these poor arguments to create new genera as the divergence time perhaps until we have a better understanding of how genes work and how we should interpret new molecular evidence.

References

Buckner JC, Lynch Alfaro JW, Rylands AB, Alfaro ME. 2015. Biogeography of the marmosets and tamarins (Callitrichidae). Molecular Phylogenetics and Evolution 82: 413-425.

Byrne H, Rylands AB, Carneiro JC, Lynch-Alfaro JW, Bertuol F, da Silva MNF, Messias M, Groves CP, Mittermeier RA, Farias I, Hrbek T, Schneider H, Sampaio I, Boubli JP. 2016. Phylogenetic relationships of the New World titi monkeys (Callicebus): first appraisal of taxonomy based on molecular evidence. Frontiers in Zoology 13:10.

Gutiérrez EE & Marinho-Filnho J. 2017. The Mammalian Faunas Endemic to the Cerrado and the Caatinga. ZooKeys 644: 105–57.

Hershkovitz P. 1990. Titis, new world monkeys of the genus Callicebus (Cebidae, Platyrrhini): A preliminary taxonomic review. Fieldiana Zoology 55: 1–109.

Lynch Alfaro JW, Boubli JP, Olson LE, Di Fiore A, Wilson B, Gutiérrez-Espeleta GA, Schulte M, Neitze S, Ross V, Schwocho D, Farias I, Janson C, Alfaro ME. 2012. Explosive pleistocene range expansion leads to widespread Amazonian sympatry between robust and gracile capuchin monkeys. J Biogeogr 39:272–288.

Rosenberger AL. 2012. New World monkey nightmares: science, art, use, and abuse (?) in platyrrhine taxonomic nomenclature. American Journal of Primatology 74: 692–695.

van Roosmalen MGM, van Roosmalen T, and Mittermeier RA. 2002. A taxonomic review of the titi monkeys, genus Callicebus Thomas, 1903, with the description of two new species, Callicebus bernhardi and Callicebus stephennashi, from Brazilian Amazonia. Neotropic Primates 10:1-52.

Ensaio final (23/06/2017)

In these days the majority of works in my field (mammals’ systematics and taxonomy) are based on molecular data. Before starting this course, I was almost forced to pull the part of methods of each paper I had in my hands. I felt really doubtful because I heard from colleagues questions like: have you seen that new species of primate? It has a molecular phylogeny and everything… it must be a valid species! After reading these cutting edge articles, I knew that something was wrong in some of them but I could not say what. I decided to improve my knowledge about genetics and the molecular approach used in these days. The PEMARF course offered me a great opportunity to enter the molecular world from zero. Due to this course, I had to start from the basics, reading classics of molecular literature. In my opinion, one of the strongest points of this course was exactly that, to focus on the basics. I think that one of my biggest mistakes, in the past, was trying to understand complex and fancy molecular methods disregarding the core concepts in which these methods are based on. At the end of this course, my vision is completely different from that from some months ago. I learned how to interpret results that I was unable to understand at the beginning of the year. Furthermore, now I feel confident to opine if the method used in these works is the most appropriate in each case. I think that the balance of the course is broadly more positive than negative. Although I do not know how to perform that kind of analyses (and it was not the course’s goal), I feel prepared to take more advanced courses in this matter. In my opinion, one point that could be enhanced is the part of models (Maximum likelihood, etc.). Perhaps elaborate a little more about each model, talking about the application and criticism of these models.
My self-evaluation is 1.

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