sábado, 1 de septiembre de 2007

Virus Species: A Controversy

A virus is an infectious agent composed by a genomic nucleic acid covered by several protective layers. In 1991, the International Committee on Taxonomy of Viruses (ICTV) endorsed the following definition of virus species: a virus species is a polythetic class of viruses that constitute a replicating lineage and occupy a particular ecological niche(1). The rationale for applying the species concept in virology is that viruses are biological entities and not chemicals: they possess genes, replicate, specialize, evolve and occupy specific ecological niches. The virologists adopted its own concept because they assumed that the only legitimate species concept was that of biological species defined by sexual reproduction, gene pools and reproductive isolation(2). However, within the multiplicity of species definitions just a reduced number of virologists, if any, have kept in mind the application of the phylogenetic species concept (PSC) into the virology field. The goal of this document is to present some fails of the virological concept of species and to introduce the PSC as an alternative in this field.

Viruses are intracellular parasites and are tangible, concrete entities, located in space and time that can be handled experimentally. Some authors(1, 2, 3) have proposed that the virus species, on the other hand, are abstractions that exist only in the mind. They realize that all biological classifications are conceptual constructions created by researchers for the purpose of introducing order in the bewildering variety of biological objects. In the same way, they emphasize that the categories used for building a classification such as families, genera and even species are not found in nature but are abstractions invented by human minds and concludes that species are thus not objects that will ever be encountered by researchers in their handling of viruses. It looks that those authors don't distinct between the species category within the Linnaean hierarchy of taxonomic categories and the taxon (group), that is ranked at the species level within that hierarchy. My interpretation aims to the view that species are concrete entities with a definite position in space and time rather than abstract classes with an indefinite origin in time; if we see species just as classes lead us to quite arbitrary decisions for their diagnose.

The virological definition of species means that no single property can be used as a defining property of a virus species and highlights that the major advantage of defining species as polythetic classes is that it makes it possible to accommodate, within a species, individual viruses that lack one or other characteristic that would normally be considered typical of the species(1, 2). It seems that for the virologists is problematic to have an enormous number of species because they group as a species clearly differentiated viruses. As has been(4) stressed: if it is advisable to recognize every lineage characterized even by just a fixed mutation and the goal of distinguishing species is to thereby recognize the end-products of evolution, should we seek to suppress naming large numbers of species where large numbers of differentiated end-products exist?. It have been have mentioned
(1, 2) that it is the inherent variability of the members of a virus species that prevents a single discriminating character such a certain percentage of genome sequence dissimilarity to be used as a valid criterion for defining a species; instead of that percentage the virological concept of species proposes to use certain degree of properties similarity as is contemplate of what a polythetic class is (Each member possesses several of the diagnostic properties but no single defining property is present in all the members of the class). The PSC sensu Wheeler and Platnick define species as the smallest aggregation of (sexual) populations or (asexual) lineages diagnosable by a unique combination of character states(4); I deem that the use of percentages of similarity/dissimilarity will be rather arbitrary and irrational and that the PSC mentioned represents a unit species concept for all biological fields because is based on observable characters and avoids rampant subjectivity. Moreover, I consider that we do not create species as have been accentuated(2, 3); instead of it we identify and diagnose them by its character states.

On the other hand pair-wise sequence comparisons (PASC) have been used to produce multimodal distributions where the peaks are usually equated with clusters of sequences corresponding to groups of viral strains, species and genera(3). I consider that such PASC are just useful for delineating clusters of viruses but not to delineate species. The nucleotide sequences similarity percentages shows that, similarity, but we cannot expect to diagnose that two viruses belong to the same specie because of theirs nucleotide/amino-acid sequence identity degree. Furthermore, PASC on their own cannot provide clear cut quantitative criteria for distinguishing between different clusters and the clusters value percentage changes in different families. Consequently a level of genome homology fails to establish membership in a species.

PSC are recognized by unique combinations of constantly distributed characters and it’s compatible with phylogenetic theory because speciation events are marked by character transformations. It is a concept that applies equally to all conceivable speciation processes and biological entities (including viruses), representing a unit species concept. It aims to recognize the end-products of evolutionary processes and units of formal scientific nomenclature and as a final point the PSC concept meets the main requirement placed upon the species in virology: to achieve some rational order whereby some viral agents are grouped together.



References

1. Van Regenmortel, M.H.V. and Mahy, B.W.J., 2004. Emerging issues in virus taxonomy. Emerg. Infect. Dis. 10, 8–13.
2. Van-Regenmortel, M.H.V., 2007. Virus species and virus identification: Past and current controversies. Infection Genetics and Evolution 7(1): 133-144
3. Van Regenmortel, M.H.V., 2003. Viruses are real, virus species are man-made taxonomic constructions. Arch. Virol. 148, 2481–2488.
4. Wheeler, Q. D. and Meier, R. (Editors). 2000. Species Concepts and Phylogenetic Theory: A Debate. New York: Columbia University Press

3 comentarios:

Salva dijo...

Bueno, a mi siempre me molesta un poko las notas/papers donde se enfatiza mucho en la 'racionalidad' del metodo defendido y la 'irracionalidad'/ 'arbitrariedad'/ 'subjetidad' de sus rivales! Si algo se ataco como arbitrio o cualkier otro adjetivo peyorativo, debe mostrarse en donde y porke se comete la arbitrariedad!

En general, yo soy un defensor del PSC, pero hay unas cosas ke me dejaron dudas ;)

En primer lugar, cual es la verdadera diferencia entre la especie como 'grupo' y como categoria? y en la misma vena, cual es la diferencia entre el 'la entidad concreta' y la 'clase abstracta'? Como cosa curiosa eas 'diferencias' son marcadas mas por los defensores del concepto biologico y el evolutivo, donde depronto (ni idea como!) esas diferencais parecen claras, bajo la PSC poko (nada en realidad!)importa si la especie es o no solo un rango, o si es una clase, entidad o individuo!

Un punto interesante que deberia ser explorado, es la consecuencia de tener muchos nombres... la respuesta de wheeler y platnick es mas una pregunta retorica y creo ke todo defensor de el PSC debe proporcionar una respuesta clara a ella! Cosa ke en esta nota desafortunademente no esta :S

Por cierto, el PSC es explicitamente nominalista, y por ello pareceria valido achacarle el 'problema' ke en realidad crea las especies (las define con un objetivo especifico conveniente) mas ke las identifica!

Saludos pues y ojala la critica sirva ;)!
Salva

Pd. Por cierto... hay algun carcacter que sea no observable?

Pd2. Se ve ke los virologos no saben nada de sistematica, no? xD

iGoR dijo...

Buenas..Cristian tiene razon en decir que usar "grados o niveles" de similaridad es arbitrario, pues en general no hay forma de hacer un cut-off cuantitativo con algun sentido biologico..si es o no irracional hacerlo es lo que sobraria...

El problema de la definicion vs. la identificacion requiere que uno este preocupado por si estamos usando las herramientas "reales" (cualquier cosa que eso sea) en Biologia. La operacion que ofrece el PSC tiene sentido biologico por que como bien San Hennig bendito nos dice: la especiacion esta acompaniada por transformacion de uno o varios caracteres. Asi que yo no me preocuparia por la distincion ;)

Salva tiene razon en que nosotros los defensores del PSC sieempreee seremos atacados con el mismo argumento de que vamos a incrementar las paginas de los checklist jeje!..Segun un articulo publicado en 2004 el PSC es responsable de haber incrementado en 48% el numero de especies reconocidas por el (guacala!) BSC .

shaylito dijo...

Si se usa un criterio como PSC es obvio que van a cambiar los limites, los virólogos usan afirmaciones clínicas para hacer inteligibles sus unidades, no seria mas bien como difícil generar una especie que puede o no tener los mismos síntomas que otra? o usamos como criterio adicional la sintomatología? y como manejar tal posible "desborde" nomenclatural!