Evidence

A hypothesis is a conjecture, a speculation, a hunch, framed in such a way that it can be tested. The result from this test is accepted, until new evidence is available and regarded (Gee, 1999). But, testing a hypothesis requires that it makes a prediction that can be checked by observation, and we make observations in order to learn about things that we do not observe (Sober, 1999). Our observations, then goes far from the mere action of sensing an object, and that's why our observations are always full of theory. Although, when we test competing hypotheses we use the same tools for doing observations, and the theoretical machinery could be regarded as auxiliary hypotheses that do not alter the test result.

Cladistics, is a historical science, then it emphasis in analyzing and shapering traces at the light of a hypothesis (Cleland, 2002). In cladistic analysis a hypotheses is a presume relationship between taxa (a monophyletic group), and the evidence that 'corroborates' a group, are the synapomorphies (Patterson, 1988). But, at the beginning of the analysis there are not synapomorphies, just characters, observations that need a theoretical context. However, that a theoretical construct is necessary for evidence interpretation that is not an excuse for not seeing it with out bias about what it tells (i.e., adaptation, change sequence).

Because our hypotheses and methods always could be refined, and we would never have all the information any presumption is susceptible of being accepted or refuted in the light of new evidence.

On Evidence sensu CJ

The evidence consists of observations that are compatible with a hypothesis. These observations must be collected systematically in an attempt to avoid the bias inherent to observations that has been used as evidence in the past. In this sense what we call evidence depends on its informativeness regarding the hypothesis and is presumed to be true used in support of the hypotheses that are presumed to be falsifiable. Therefore the evidence goes toward supporting a hypothesis.

Cladistics or phylogenetic systematics groups organisms by their share derived characters. Taxa that share many derived characters are grouped more closely together than those that do not. Tree-like relationship diagrams called "cladograms" results showing hypothesized relationships. The evidence that organisms are related comes from homologies between them. The observable parts, or attributes, of organisms which can be examined for homology are characters. Therefore In these hypothesized relationships, the characters are considered the evidence.

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Rebuttal from PSC

Erika Jazmín Parada Vargas

The transference of the knowledge is part of any activity, and the basic research in biology is not the exception. As the species are the basic units which different biological programs work with, (and not all the researchers are experts in the groups) a feasible way to communicate its necessary. That system or classification needs to reflect the history of the group, in which the species are contained.

Although the delimitation of the species is related to the classification, they are not the same. The inference about the history of the groups is an after activity to its delimitation (Davis & Nixon, 1992). The PSC (sensu Wheeler & Platnick, 2000), has the advantage that is not worried about the evolutionary mechanisms that have caused the species, but the way how could we distinguish them. The way we could distinguish among species is the unique combination of character states.

As the species are not external, and our knowledge about the organisms is not immaculate, we need a concept not based on abstract or unpractical characteristics (i.e., niche, reproductive isolation, percentage rules). But on observational features, the unique combination of character states of the PSC gives us a testable hypothesis. (Wheeler & Platnick, 2000).

Davis, J. I. & Nixon, K. C. Populations, Genetic Variation, and the Delimitation of Phylogenetic Species Systematic Biology, 1992, 41, 421-435

Wheeler, Q. D. and Meier, R. (Editors). 2000. Species Concepts and Phylogenetic Theory: A Debate. New York: Columbia University Press

Rebuttal from the ESC

The species concepts should answer the question of what is a species? rather than, How can we delimite species?. Several authors have argued for the distinction of these two questions considering it the root of the “species problem”1, 2,3. The ESC is not relaxed in the true nature of species, and is only answering the first question. The SC that are operational are thus not species concepts, should be reinterpreted as delimitation methods of ES 2. The fact that ESC does not provide a clear delimitation criteria is not a weakness, it is indeed one of the advantages of this SC that permits to use not only one delimitation method but almost all methods are suitable for this purpose 4.

Evolutionary species can be delimited by a number of methods, I will present some works in which ESC is used and ES are delimited. Wiens and Penkrot5 review three approaches for species delimitation (tree-based with DNA data and tree-based and character-based with morphological data) in Sceloporus lizards, Also as in my previous empirical post and other works 6,7,8,9 genealogical concordance of multiple gene trees is a criteria to delimit ES, the results of this analysis are independent lineages regardless of whether in the analyses one looks for pattern or for process. Sites and Marshall4 present a review with nine methods with empirical examples to delimite ES. Disagreement between species boundaries inferred from different data types raises several important questions 5, each particular case has its own way to approach delimitation, and the decision of assigning species boundaries and hierarchy implicit in it should be based on the previous knowledge of the study group and its variability, as well as availability of the data.

It is a misunderstanding when ESC is equated to BSC, they are enormously different SC, first, the universality of the concept, ESC is applicable to all the forms of life, and BSC only to sexual forms. Second, ESC does not have as the only and predominant method for species delimitation the biological criteria, it is not the goal to find reproductive isolation or genetic distances, the goal is to identify independent lineages, with all the evidence available. Reproductive isolation, even thought it is strong evidence of lineage independence it is the hardest to obtain, almost never available. The strength of this concept is precisely to be open about evidence and methods, and surely we can not restrict ourselves to reproductive isolation as the only evidence.

When I stated that under the PSC ( sensu Wheeler and Plantnik ) every subpopulation will be named a species, I was not worried about number of resulting species, but the relationships among them, i.e. tokogenetic relationships within a species, following Hennig’s emphasis in differentiating tokogeny (parent-offspring relationships) from phylogeny, descent relationships among certain groups of organisms (i.e., species). In a ES there shouldn’t be tokogenetic relationships, is in this way (allowing species within there is tokogenetics relationships), that there is a genealogy denial in the PSC, no matter if in the posterior phylogenetic analyses this presents a problem or not.

References

1. Wheeler, Q. D. and Meier, R. (Editors). 2000. Species Concepts and Phylogenetic Theory: A Debate. New York: Columbia University Press.
2. de Queiroz, K. 2005. Different species problems and their resolution. Bioessays 27:1263-1269.
3. Wiens, J. J., M. R. Servedio. 2000. Species delimitation in systematics: Inferring diagnostic differences between species. Proc. R. Soc. London Ser. B. 267:631–636.
4. Sites J. W., Marshall. C. J. 2003 Delimiting species: a Renaissance issue in systematic biology Trends Ecol. Evol. 18: 462
5. Wiens, J.J. and Penkrot, T.A. 2002.Delimiting species using DNA and morphological variation and discordant species limits in spiny lizards (Sceloporus). Syst. Biol. 51, 69–91
6. Templeton, A. R. 2001. Using phylogeographic analyses of gene trees to test species status and processes. Mol. Ecol. 10:779–791.
7. Dettman, J. R., D. J. Jacobson, and J. W. Taylor. 2003. A multilocus genealogical approach to phylogenetic species recognition in the model eukaryote Neurospora. Evolution 57:2703-2720.
8. Starrett J. and Marshal H. (2007) Multilocus genealogies reveal multiple cryptic species and biogeographical complexity in the California turret spider Antrodiaetus riversi (Mygalomorphae, Antrodiaetidae). Molecular Ecology 16:3, 583–604.
9. Taylor, J. W., D. J. Jacobson, S. Kroken, T. Kasuga, D. M. Geiser,D. S. Hibbett, and M. C. Fisher. 2000. Phylogenetic species recognition and species concepts in fungi. Fungal Genet. Biol. 31:21–32.
   
   
   

"Virus Species: A Controversy" (Rebuttal)

When you name and classify, that’s taxonomy in practice. The goal for taxonomy is to name things in order to place them in an intuitive invented classification that can suggest relationships and meaningful associations. In The Linnaenan hierarchy of taxonomic the organism are classified in a ranked hierarchy, starting with domains and then turned (in a simplified way) into phyla, orders, families, genera and species. Groups of organisms at any of these ranks are called taxa. Species taxa are the individual lineages we call ‘species’ (thus Homo sapiens is a species taxa). The species category is a more inclusive entity. The species category is the class of all species taxa. In that way all taxonomic classes are abstract concepts, constructions fabricated by the mind and not real entities as species taxa (as diagnosable lineages) which are located in space and time and that we encounter in our handling of viruses. I empathized this distinction because the virologist see the species mainly as classes [1] and then ascribe some properties to that class as disease clinical presentations [2]. Ascribing properties to species (a polythetic class in the virology field!) and allocating individuals in those not only means to consider species as abstracts classes, in fact it might no reflect natural relationships (like to use the utility or threaten that vertebrates represents to humans to allocate vertebrates in particular species). As virus diseases became recognized, the causative viruses were given names in different languages that often reflected the symptoms of the corresponding diseases as well as the hosts or organs that become infected [1]. The international Committee on Taxonomy of Viruses (ICTV) decided in 1998, to confer the status of official species names to the English common names of viruses and introduced a typography using italics and a capital initial to indicate that these names correspond to species. Names are simply signs or labels that refer to specific species, therefore I do not see a problem in naming species until all available combination of letters and numbers in our vocabulary are exhausted.

The task of defining species is commonly confounded with the task of identifying the member of species. The PSC sensu Wheeler and Platnick define species as the smallest aggregation of lineages diagnosable by a unique combination of character states [3]. The definition says nothing about how to identify particular species. For each one species there is a unique combination of character states (morphological, molecular, etc) that allows us to identify them. The only objective of the PSC is to recognize the lineages that perpetuate more in the nature avoiding the arbitrary in the decisions for their identification because it is based mainly on characters.

References

1.Van Regenmortel, M.H.V., 2003. Viruses are real, virus species are man-made taxonomic constructions. Arch. Virol. 148, 2481–2488.

2. ICTVdB - The Universal Virus Database, version 4.http//www.ncbi.nlm.nih.gov/ICTVdb/ICTVdB/

3. Wheeler, Q. D. and Meier, R. (Editors). 2000. Species Concepts and Phylogenetic Theory: A Debate. New York: Columbia University Press

The Species Concepts in Aves: Rebuttal

The Cracraft's concept states that a "desirable" Phylogenetic Species Concept must have a "parental pattern of ancestry and descent" component. However, this component is not a rule in other views on the Phylogenetic Species Concept (Wheeler & Platnick, 2000). Because its theorical and practical content, the Phylogenetic Species Concept (Wheeler & Platnick, 2000) is more adequate approach in the debate of species, the diagnosibility by unique combinations of characters-states is a good method in the recognition and delimitation of species. The combination of characters shown the homologies between the groups and it is a good estimate of your relationships. Other Cracraft's requeriment (a criterion for ranking populations at the species-level) is not important in the definition of species, it is a way to organize the names and groups within the Linnaean rank.

The Amadon's rule is a statistical approach to delimit subspecies (Amadon, 1949), the logic of the 75% rule is that the differences among two populations can be statistically measured using the quantity of variation in the populations (Patten & Unitt, 2002). However, the rule is not applicable in many issues because its instability when it is applied to molecular data. Therefore, the 75% rule is "wrong" to delimit subspecies. Wilson and Brown (1953), and Mallet (2001) have been criticized the qualitative definitions as arbitrary because some groups classified qualitatively as subspecies are not differentiated based on multiple characters.

In many studies, the subspecies have functioned as units in at least three roles, namely in classifications, evolutionary theories and, more recently, conservation plans. So, the Linnaean rank of subspecies became prevalent with the emergence of the Biological Species Concept “BSC” (Zink, 2004). In Aves, the ornithologists have spent considerable effort refining and debating subspecies concepts (Wiens 1982). Traditionally, subspecies have been defined by morphological traits or color variations, but recent critics are concerned that these traits may not reflect underlying genetic structure and phylogenies (Haig et al, 2006). Despite the criticisms ( the incongruence among dataset or between molecular and morphological characters), recent studies in which researchers used multiple criteria (e.g., morphological, behavioral, and genetic characters) have confirmed that many subspecies are evolutionarily definable entities. Thus, although subspecies definitions may have been too liberally applied by some early taxonomists, this does not invalidate the concept of subspecies as meaningful biological entities. The subspecies are a useful hierarchy to identify and fit the variable populations within a species.

In the real life, the ornithologists used the coloration pattern to identify different groups. Some strategies are not easy applicable, or they are inconsistent. For example, within the BSC might lead one to assume that partial reproductive isolation would be an appropriate criterion for subspecies recognition. Nevertheless, there is little evidence outside of Drosophila that this criterion has been routinely employed (Haig et al, 2006), Others strategies are difficult because your methodological requirement. Generally, the TSC is "useful" to identify taxa in early approaches, but the character's recognition is essential to delimit and analyze species.

Populations versus species in historical reconstructions.