In cladistic analysis, the inference of homology has been previously suggested to be at least a two-step procedure: the first step is the hypothesis of correspondence of constituent features between two or more organisms. The second step subject these character hypotheses to the test of congruence (Rieppel & Kearney, 2002). In this sense it is not just the method used for phylogenetic inference which determines the quality of relationship hypotheses. Definition and selection of characters constitute a fundamental step (in the relationship hypotheses), because with them the crucial test in phylogenetic analysis is done.
A character is a logical relation established between intrinsic attributes of two or more organisms that is rooted in observation (Rieppel, 1988). So, “a meaningful character is thus based upon a character description that can in itself be evaluated... and potentially rejected” (Riepperl & Kearney, 2002). In morphological data, there are some classical characteristics that a good character must have: topology, connectivity, and the establishment of a one-to-one relationship of the parts being compared (Rieppel & Kearney, 2002). Although, there are other attributes as function and “special similarity” that are relevant in character definition (Rieppel & Kearney, 2002; Agnarsson & Coddington, 2007). Sometimes, topology correspondence, function and special similarity could conflict and quantitative methods for choosing among different criteria are necessary (Agnarsson & Coddington, 2007).
Other problem that morphological data face is coding. When we compare features in different organisms in some way, we are assuming some correspondence (not necessary topological). So, a presence-absence coding (See Pleijel, 1999) is telling nothing about that feature correspondence, and nothing about the taxa relationship. Becasuse, what forms the evidence in a cladistic analysis is the change among the character states, not the existence of different states (Brower, 2000).
In molecular data, the problem of character definition and character coding is different. Because it is widely accepted that similarity is equivalent to homology, but as those data also have homoplasy, similarity could not be seen as homology. Therefore, a criterion for defining molecular character hypotheses is necessary (de Pinna, 1991). The characters definition with DNA (or other molecular data) could be seen as a previous step, aligning with an algorithm. Or could be seen as a direct search of the optimal trees via direct optimization of the data with which the character hypotheses change during the search (Wheeler, 1996). The second approach is preferable, while it is testing the topology directly and is exploring different possibilities of the data, not just an alignment.
Finally, congruence is the test that corroborates the character as synapomorphies. The tool that allow to asses hypotheses of relationship, and concomitantly of character evolution, is parsimony. Parsimony maximizes congruence between the characters, so it maximizes the propositions of homology (Farris, 1983; Kluge, 1997; Sober, 1998).
Agnarsson, I. & Coddington, J. A. 2007. Quantitative tests of primary homology. Cladistics.
Brower, A. 2000. Homology and the inference of systematic relationships: some historical and philosophical perspectives. In Homology and systematics, coding characters for phylogenetic analysis (eds. Scotland, R & Pennington, R. T.). Taylor & Francis.
de Pinna, M. C. C. 1991. Concepts and tests of homology in the cladistic paradigm. Cladistics.
Kluge, A. 1997. Testability and the refutation and corroboration of cladistic hypotheses. Cladistics.
Pleijel, F. 1995. On character coding for phylogenetic reconstruction. Cladistics.
Rieppel, O. & Kearney, M. 2002. Similarity. Biological Journal of the Linnean Society.
Wheeler, W. C. 1996. Optimization alignment: the end of multiple sequence alignment in phylogenetics? Cladistics.
Farris SJ. 1983. The logical basis of phylogenetic analysis. In: Platnick, NI, Funk, VA, eds. Advances in Cladistics, Vol. 2. New York: Columbia University Press.
domingo, 25 de noviembre de 2007
Homology
Homology is correspondence due to their shared ancestry. Homology assessment is a crucial step in phylogenetics analyses regardless of the type of data employed, since hypotheses of homology relate observations among taxa.
Every proposition of homology involves two stages which are associated with is generation and testing: the primary homology statement is conjectural based on similarity. The secondary level of homology is the outcome of a patter detecting analysis, the congruence test, and represents a test of the expectation that the observable match of similarities is potentially part of a retrievable regularity indicative of a general pattern (de Pinna, 1991).
When dealing with molecular data similarity guides primary homology -as in morphological characters- but there have been a tendency to believe that higher the similarity, the more likely that the sequences are homologous (Salemi and Vandamme, 2003; Patterson, 1988) where the fundamental homology statements are made at the level of the individual nucleotide bases. Conversely, the fundamental homology statement can be consider at the level of the sequence itself because the contiguous sequences are the homologous units that transform at prescribed costs among various states (Wheeler, 1999). Therefore Sequences themselves are treated as the fundamental units of homology and homology assessment is not consider a matter of aligning sequences and counting matches between them. Following “Direct Optimization’’ we can vary dynamically the primary homology hypotheses during tree search consequently the resulting hypotheses of homology are tested in conjunction with character congruence through parsimony (Wheeler, 2006). The testing of all characters against one another simultaneously constitutes the most severe test of congruence; In a phylogenetic context, the best alignment is the one that generates the most parsimonious tree when analyzed in conjunction with all relevant data (Philips, 2006).
The homology assessment have been shown to be influenced by the way we coding and the different interpretations of the criteria used to asses those statements demonstrating that the organismal variation is often conceptualized as characters and characters states in different ways (Scotland and Pennington, 2000). Even so, it is possible to have greater explicitness in the delimitation of morphological characters by detailed observation and the topologic criterion used, used in conjunction with special quality, and intermediate conditions of form (Rieppel and Kearney, 2002). In general, better guidelines concerning character conceptualization are required to help solving this.
Similarity and conjunction have proposed as tests for homology but only congruence serves to this respect. Similarity, as mentioned above, guides the assessment of the homology conjecture. Conjunction is an indicator of non-homology, but it is not specific about the pair wise comparison where non-homology is present, and depends on a specific scheme of relationship in order to refute a hypothesis of homology (de Pinna, 1991).
Every proposition of homology involves two stages which are associated with is generation and testing: the primary homology statement is conjectural based on similarity. The secondary level of homology is the outcome of a patter detecting analysis, the congruence test, and represents a test of the expectation that the observable match of similarities is potentially part of a retrievable regularity indicative of a general pattern (de Pinna, 1991).
When dealing with molecular data similarity guides primary homology -as in morphological characters- but there have been a tendency to believe that higher the similarity, the more likely that the sequences are homologous (Salemi and Vandamme, 2003; Patterson, 1988) where the fundamental homology statements are made at the level of the individual nucleotide bases. Conversely, the fundamental homology statement can be consider at the level of the sequence itself because the contiguous sequences are the homologous units that transform at prescribed costs among various states (Wheeler, 1999). Therefore Sequences themselves are treated as the fundamental units of homology and homology assessment is not consider a matter of aligning sequences and counting matches between them. Following “Direct Optimization’’ we can vary dynamically the primary homology hypotheses during tree search consequently the resulting hypotheses of homology are tested in conjunction with character congruence through parsimony (Wheeler, 2006). The testing of all characters against one another simultaneously constitutes the most severe test of congruence; In a phylogenetic context, the best alignment is the one that generates the most parsimonious tree when analyzed in conjunction with all relevant data (Philips, 2006).
The homology assessment have been shown to be influenced by the way we coding and the different interpretations of the criteria used to asses those statements demonstrating that the organismal variation is often conceptualized as characters and characters states in different ways (Scotland and Pennington, 2000). Even so, it is possible to have greater explicitness in the delimitation of morphological characters by detailed observation and the topologic criterion used, used in conjunction with special quality, and intermediate conditions of form (Rieppel and Kearney, 2002). In general, better guidelines concerning character conceptualization are required to help solving this.
Similarity and conjunction have proposed as tests for homology but only congruence serves to this respect. Similarity, as mentioned above, guides the assessment of the homology conjecture. Conjunction is an indicator of non-homology, but it is not specific about the pair wise comparison where non-homology is present, and depends on a specific scheme of relationship in order to refute a hypothesis of homology (de Pinna, 1991).
On Homology
Introduction
The importance of homology has been discused by several authors (Patterson, 1988; Wagner, 1989; de Pinna, 1991; Rieppel & Kearney, 2002; Agnarsson & Coddington, 2007). So, homology is a crucial basis in the Systematics. The most simple meaning of homology is equivalence of parts (de Pinna, 1991). In 1982, Patterson states that homology is equal to synapomorphy. So, the synapomorphic characters must be homologous. Nevertheless, the symplesiomorphic characters could be homologous (homologies at a higher level).
There are two kinds of homologies; the primary homology - conjectures or hypothesis about common origin of characters -, and the secondary homology - the tested hypothesis – (de Pinna, 1991).
The importance of homology has been discused by several authors (Patterson, 1988; Wagner, 1989; de Pinna, 1991; Rieppel & Kearney, 2002; Agnarsson & Coddington, 2007). So, homology is a crucial basis in the Systematics. The most simple meaning of homology is equivalence of parts (de Pinna, 1991). In 1982, Patterson states that homology is equal to synapomorphy. So, the synapomorphic characters must be homologous. Nevertheless, the symplesiomorphic characters could be homologous (homologies at a higher level).
There are two kinds of homologies; the primary homology - conjectures or hypothesis about common origin of characters -, and the secondary homology - the tested hypothesis – (de Pinna, 1991).
Pattern or process
A question about homology is the significance of evolutionary process in the identification of homologous characters. Implicitly, the evolutionary events are bounded to the analysis of characters (Lee, 2002). However, Brower (2000) stated that “the similarities - homologies - between taxa represent the only necessary ontological foundation for the construction of cladograms and hypotheses of taxonomic grouping”. So, the evolutionary asumptions are not necessary in the identification of homologies; but the homologous characters can be explained by evolutionary process (Rieppel & Kearney, 2002).
Equally, some authors claims that the phenomenon of circularity in homology (need of a priori topology) is undesirable because the recognition of homologous characters is conditionated to mapping of them in a initial topology. Nevertheless, the circularity is not a “big” problem, because the tested homologies (mapped hypothesis of homologies) are “tested hypothesis” attached to new set of analysis (new tests).
An inherent point in the identification of homologous characters is the character's coding. A inadequate definition of characters produces bias in the identification of homology. Some author claims that the real problem in homology is the character's coding. So, for example, there is the belief that the character's coding is linked to knowledge of researcher about taxon. So, the “eyes” of an experienced researcher would discriminate and describe “best” characters and character's states that an non-experienced researcher.
A approach used in the the character's coding was the morphometric analysis (biometry). However, the biometry is not useful in homology because the complexity of the biological estrucures and its incompatibility with the statistical multivariate analysis (Bookstein, 1994).
Tests
The three tests of homology (similarity, conjuction, and congruence) are secuencial in the identification of homology. Nevertheless, the similarity is not a test (in Popperian sense), similarity is a conjecture of homologous characters - primary homology – (de Pinna, 1991) . The conjuction and congruence (agreement in supporting the same phylogenetics relationships) are the “hard” tests of homology – the secondary homology from de Pinna - (Rieppel and Kearney, 2002). Although there is interdependece among them (tests), it not means that the three tests will be one only. So, the result is a hypothesis of homology corroborated, but they is not definitive (“true homology”).
Molecular homology
The identification of homology in molecular characters (nucleotide sequences) presents problems not found in other kinds of character data. For example, although each base position presents one of four identical states (A, C, G or T), the number of these positions is likely to vary, that is homologous nucleotide sequences may differ in length (Wheeler, 1996). Further, Patterson (1988) claims that the tests of homology in molecular characters are equal to morphological characters. However, the significance of tests (similarity, conjuction, and congruence) is different because the similarity is the most crucial test, while in morphological characters is test of congruence.
A point of discussion in the identification of homologies in molecular sequences is the need of an alignment to determine sites or homologous fragment. However, this way is considered inadequate because alignment is generated using a priori costs and asumptions. Wheeler (2003) proposes a synapomorphic-based alignment methods - Implied alignment – (IA) that identifies homologies in the topology using Direct Optimization (DO). So, Implied alignment generating all posibles alignments and all posibles homologies are analized. This method may be efficient to identify homologies. Nevertheless, the a priori asumptions are inherent to alignments.
- Agnarsson, I., & Coddington, J. A. (2007). Quantitative tests of primary homology. Cladistics, 23, 1-11.
- Brower, A. V. Z. (2000). Evolution is not an assumption of cladistics. Cladistics, 16, 143–154.
- de Pinna, M. C. C. (1991) Concepts and tests of homology in the cladistic paradigm. Cladistics, 7, 367-394.
- Lee, M. S. Y. (2002). Divergent evolution, hierarchy, and cladistics. Zoologica Scripta, 31, 217–219.
- Patterson, C. (1988). Homology in classical and molecular biology. Molecular Biology and Evolution, 5, 603-625.
- Rieppel, O., & Kearney, M. (2002) Similarity. Biological Journal of the Linnean Society, 75, 59-82.
- Wagner, G. P. (1989) The biological homology concept. Annual Reviews of Ecology and Systematics. 20, 51-69.
- Wheeler, W. C. (1996). Optimization alignment: the end of multiple sequence alignment in phylogenetics?. Cladistics, 12, 1-9.
- Wheeler, W. C. (2003) Implied alignment: a synapomorphic-based multiple alignment method and its use in cladogram search. Cladistics, 19, 261-268.
lunes, 29 de octubre de 2007
On Evidence
Evidence are a group of events that support or not a hypotesis. A pure observation not must be considered as evidence, a pure observation (observations are not bounded to theorical basis) is not evidence. The evidence's quality is related to hypotesis which it is bounded. So, all evidence is not relevant for a hypotesis. Evidence is not considered as “good” or “bad”, simply it is support a event rather other. The pure observations (without theoric basis) is considered “good” or “bad. So, in the historical sciences the observation of event is not enough, these observation must be bounded a theorical background. The “smoking gun” is a example which the evidence is obtained, but all the observations in the event ( murder) must be related to a theory. The observations that are not related to murder, it are not evidence.
domingo, 28 de octubre de 2007
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.
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.
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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domingo, 16 de septiembre de 2007
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
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.
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
- Wheeler, Q. D. and Meier, R. (Editors). 2000. Species Concepts and Phylogenetic Theory: A Debate. New York: Columbia University Press.
- de Queiroz, K. 2005. Different species problems and their resolution. Bioessays 27:1263-1269.
- 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.
- Sites J. W., Marshall. C. J. 2003 Delimiting species: a Renaissance issue in systematic biology Trends Ecol. Evol. 18: 462
- 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
- Templeton, A. R. 2001. Using phylogeographic analyses of gene trees to test species status and processes. Mol. Ecol. 10:779–791.
- 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.
- 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.
- 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
sábado, 15 de septiembre de 2007
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.
lunes, 10 de septiembre de 2007
Applying the species concepts to dengue viruses
Villabona-Arenas, C. J.
Laboratorio de Sistemática y Biogeografía, Escuela de Biología
Universidad Industrial de Santander
Figure 1
Figure 2
Figure 3
Figura 4
Tables
Laboratorio de Sistemática y Biogeografía, Escuela de Biología
Universidad Industrial de Santander
Introduction
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 constitutes a lineage of replication and occupies a particular ecological niche [1]; the virologists adopted its own species concept because they assumed that the only legitimate species concept was that of biological species [2]. The species problem has been discussed in different publications and diverse species concepts have been proposed [3, 4]. The dengue viruses are an ICTV approved species of the genus flavivirus, family flaviviridae and comprise four antigenically related but distinct serotypes (DENV-1 to DENV-4) [5, 6]. In this work I explored the change in the number of species within the dengue viruses applying different applicable concepts and I proposed one of them to be used in the virology field.
Methods
The Table 1 presents the different species concepts applied in this work. The data set included 47 published E gene sequences from worldwide isolates of each serotype deposited in Genbank (See appendix 1). The nucleotide sequences were aligned using multiple alignment with Muscle 3.6 software package (7) and optimal alignment with Poy 4.0 software package (8). The former alignment was used to reconstruct an UPGMA tree with the Muscle 3.6 software package and the latter alignment was used to reconstruct a Parsimony tree with the TNT 1.1 software package (9) using the Yellow Fever virus to root the tree. A bootstrapping with 100 replicates was used to place confidence values on groupings within the parsimony tree and a value ≥ 99% was used as the criterion by which a taxon was ranked as a species according to phylogenetic species concept (PSC) sensu Mishler and Theriot. The Parsimony tree was use also as a guide to differentiate groups within the DENV-1 and then the characters were mapped to identify species in this serotype following the PSC sensu Wheeler and Platnick
Results
The UPGMA tree is presented in Figure 1; three different cut points are shown representing different percentage of genome sequence similarity. The number of recognized species was 37, 41 and 45 for 73, 75 and 77% respectively. A parsimony tree is presented in Figure 2; the sixhighlighted groups represent the identified species using the ranking decision mentioned above. The Figure 3 shows and scheme of the diagnosed groups for the DENV-1 sequences: each line represents a position in which the respective group fixed a unique nucleotide; the diagnose groups are highlighted and a summary of the same analysis for each one serotypes is presented in Table 2.
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 constitutes a lineage of replication and occupies a particular ecological niche [1]; the virologists adopted its own species concept because they assumed that the only legitimate species concept was that of biological species [2]. The species problem has been discussed in different publications and diverse species concepts have been proposed [3, 4]. The dengue viruses are an ICTV approved species of the genus flavivirus, family flaviviridae and comprise four antigenically related but distinct serotypes (DENV-1 to DENV-4) [5, 6]. In this work I explored the change in the number of species within the dengue viruses applying different applicable concepts and I proposed one of them to be used in the virology field.
Methods
The Table 1 presents the different species concepts applied in this work. The data set included 47 published E gene sequences from worldwide isolates of each serotype deposited in Genbank (See appendix 1). The nucleotide sequences were aligned using multiple alignment with Muscle 3.6 software package (7) and optimal alignment with Poy 4.0 software package (8). The former alignment was used to reconstruct an UPGMA tree with the Muscle 3.6 software package and the latter alignment was used to reconstruct a Parsimony tree with the TNT 1.1 software package (9) using the Yellow Fever virus to root the tree. A bootstrapping with 100 replicates was used to place confidence values on groupings within the parsimony tree and a value ≥ 99% was used as the criterion by which a taxon was ranked as a species according to phylogenetic species concept (PSC) sensu Mishler and Theriot. The Parsimony tree was use also as a guide to differentiate groups within the DENV-1 and then the characters were mapped to identify species in this serotype following the PSC sensu Wheeler and Platnick
Results
The UPGMA tree is presented in Figure 1; three different cut points are shown representing different percentage of genome sequence similarity. The number of recognized species was 37, 41 and 45 for 73, 75 and 77% respectively. A parsimony tree is presented in Figure 2; the sixhighlighted groups represent the identified species using the ranking decision mentioned above. The Figure 3 shows and scheme of the diagnosed groups for the DENV-1 sequences: each line represents a position in which the respective group fixed a unique nucleotide; the diagnose groups are highlighted and a summary of the same analysis for each one serotypes is presented in Table 2.
Figure 1
Figure 2
Figure 3
Figura 4
Tables
Discussion
It has been shown in Figure 1 that minor differences in the percentages used to discriminate species lead to changes in the number of encountered species. The determination of such percentages is subjective and there is indeed no simple relationship between the extent of genome sequence similarity and the affiliation of a single virus to a particular species: the imaginary data matrix presented in Figure 4 shows a problematic case in which the sequence number 4 has the same similarity value with both of the other two set of sequences which are clearly different between them, therefore a level of genome similarity fails to identify the members of species. Mishler and Theriot (3) have proposed that organisms are grouped into taxa using as grouping criterion the evidence for monophyly and at the same time they have suggested to use as criterion by which a taxon is ranked as a species the amount of character support for putative groups or involve biological criteria in better known organisms. The application of ranking decisions, as in the percentage rules, is arbitrary to some extent and suggests that species are artificial constructs in the minds of researchers. On the other hand the PSC sensu Mishler and Theriot raise the idea that species are the result of phylogenetic analyses of the organisms. Hennig (10) described phylogenetic analysis as a means of reconstructing hierarchic descent relationships among species; the phylogenetic history is retrievable above the level of species, in part because of the emergence of hierarchical relations marked by character transformations; and consequently using a phylogenetic analysis to determine species is rather circular. The PSC sensu Wheeler and Platnick (3) shows that it is possible to have a species concept that avoids rampant subjectivity and furthermore applicable to viruses. The identified species in the Figure 4 are just based on characters and such species can be diagnosed by a unique combination of character states. While is some cases The PSC sensu Mishler and Theriot sometimes present a putative group as one species (the case of Dengue Virus type 1 in Figure 2) in which according to the PSC sensu Wheeler and Platnick is possible to identify multiple species, diagnosed even by a unique fixed mutation. This point highlights a particular aspect of the PSC sensu Wheeler and Platnick: it may result in an enormous number of species. In the other hand it looks that the recognizable groups that have been called genotypes (6) inside each one of the dengue virus serotypes somehow could be equated with the diagnosable species reported here using PSC sense Wheeler and Platnick. In this respect is possible that the dengue virologists misinterpret their study units because they often use as classification guides epidemiology and/or disease clinical presentations. As thousands of sequences of viral genomes are continuously added to databases, there is an increasing tendency to rely almost exclusively on molecular data for virus classification (11). Here I introduced PSC that represents a unit species concept that also can be applied to the virology field using molecular data: a concept that aims to recognize the lineages that perpetuate more in the nature avoiding the arbitrary in the decisions for their identification and recognizing species like real entities, as diagnosable lineages by their characters.
It has been shown in Figure 1 that minor differences in the percentages used to discriminate species lead to changes in the number of encountered species. The determination of such percentages is subjective and there is indeed no simple relationship between the extent of genome sequence similarity and the affiliation of a single virus to a particular species: the imaginary data matrix presented in Figure 4 shows a problematic case in which the sequence number 4 has the same similarity value with both of the other two set of sequences which are clearly different between them, therefore a level of genome similarity fails to identify the members of species. Mishler and Theriot (3) have proposed that organisms are grouped into taxa using as grouping criterion the evidence for monophyly and at the same time they have suggested to use as criterion by which a taxon is ranked as a species the amount of character support for putative groups or involve biological criteria in better known organisms. The application of ranking decisions, as in the percentage rules, is arbitrary to some extent and suggests that species are artificial constructs in the minds of researchers. On the other hand the PSC sensu Mishler and Theriot raise the idea that species are the result of phylogenetic analyses of the organisms. Hennig (10) described phylogenetic analysis as a means of reconstructing hierarchic descent relationships among species; the phylogenetic history is retrievable above the level of species, in part because of the emergence of hierarchical relations marked by character transformations; and consequently using a phylogenetic analysis to determine species is rather circular. The PSC sensu Wheeler and Platnick (3) shows that it is possible to have a species concept that avoids rampant subjectivity and furthermore applicable to viruses. The identified species in the Figure 4 are just based on characters and such species can be diagnosed by a unique combination of character states. While is some cases The PSC sensu Mishler and Theriot sometimes present a putative group as one species (the case of Dengue Virus type 1 in Figure 2) in which according to the PSC sensu Wheeler and Platnick is possible to identify multiple species, diagnosed even by a unique fixed mutation. This point highlights a particular aspect of the PSC sensu Wheeler and Platnick: it may result in an enormous number of species. In the other hand it looks that the recognizable groups that have been called genotypes (6) inside each one of the dengue virus serotypes somehow could be equated with the diagnosable species reported here using PSC sense Wheeler and Platnick. In this respect is possible that the dengue virologists misinterpret their study units because they often use as classification guides epidemiology and/or disease clinical presentations. As thousands of sequences of viral genomes are continuously added to databases, there is an increasing tendency to rely almost exclusively on molecular data for virus classification (11). Here I introduced PSC that represents a unit species concept that also can be applied to the virology field using molecular data: a concept that aims to recognize the lineages that perpetuate more in the nature avoiding the arbitrary in the decisions for their identification and recognizing species like real entities, as diagnosable lineages by their characters.
References
1. Van Regenmortel, M.H.V. and Mahy, B.W.J., 2004. Emerging issues in virus taxonomy. Emerg. Infect. Dis. 10, 8–13.Van Regenmortel, M.H.V., 2006. Virologists, taxonomy and the demands of logic. Arch. Virol. 151, in press.
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. Wheeler, Q. D. and Meier, R. (Editors). 2000. Species Concepts and Phylogenetic Theory: A Debate. New York: Columbia University Press
4. Goldstein, P.Z. and DeSalle, R. 2000. Phylogenetic species, nested hierarchies, and character fixation. Cladistics 16: 364-384.
5. Henchal, E. and Putnak, R. 1990. The Dengue Viruses. Clinical Microbiology Reviews, 3 (4), 376-396
6. Rico-Hesse, R. 2003. Microevolution and virulence of dengue viruses. Adv Virus Res 59: 315-341.
7. Edgar, Robert C., 2004, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.
8. Varón A., Vinh L.S., Bomash I., Wheeler W.C., 2007. POY 4.0 Beta 1665. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php
9. Goloboff, P., Farris J. S., and Nixon K. T.N.T.: Tree Analysis Using New Technology. Program and Documentation, available from the authors, and at www.zmuc.dk/public/phylogeny
10. Hennig, W. 1966. Phylogenetic systematics. University of Illinois, Urbana, Illinois. 263 p.
Calisher, C.H., Horzinek, M.C., Mayo, M.A., Ackermann, H.W., Maniloff, J., 1995. Sequence analyses and a unifying system of virus taxonomy: consensus via consent. Arch. Virol. 140, 2093–2099
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. Wheeler, Q. D. and Meier, R. (Editors). 2000. Species Concepts and Phylogenetic Theory: A Debate. New York: Columbia University Press
4. Goldstein, P.Z. and DeSalle, R. 2000. Phylogenetic species, nested hierarchies, and character fixation. Cladistics 16: 364-384.
5. Henchal, E. and Putnak, R. 1990. The Dengue Viruses. Clinical Microbiology Reviews, 3 (4), 376-396
6. Rico-Hesse, R. 2003. Microevolution and virulence of dengue viruses. Adv Virus Res 59: 315-341.
7. Edgar, Robert C., 2004, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.
8. Varón A., Vinh L.S., Bomash I., Wheeler W.C., 2007. POY 4.0 Beta 1665. American Museum of Natural History. http://research.amnh.org/scicomp/projects/poy.php
9. Goloboff, P., Farris J. S., and Nixon K. T.N.T.: Tree Analysis Using New Technology. Program and Documentation, available from the authors, and at www.zmuc.dk/public/phylogeny
10. Hennig, W. 1966. Phylogenetic systematics. University of Illinois, Urbana, Illinois. 263 p.
Calisher, C.H., Horzinek, M.C., Mayo, M.A., Ackermann, H.W., Maniloff, J., 1995. Sequence analyses and a unifying system of virus taxonomy: consensus via consent. Arch. Virol. 140, 2093–2099
Delimiting species by GCPSR
Ana Marcela Florez Rueda
The most important question regarding the species problem is species delimitation, species are fundamental units of systematic, ecological and evolutionary studies and the accurate documentation and delimitation of species is increasingly important as the species diversity of the world's biota is increasingly reduced and threatened. (1)
Using ESC, one can reinterpret other species concepts as operational criteria useful for delimitation of independent lineages ie. species. This work focuses on Phylogenetic Species Recognition, having as a criterion monophyly as in the PSC (sensu Mishler and Theriot)(2), the drawback of this type of PSR is that individuals are grouped very well, but the decision about where to place the limit of the species is subjective. PSR can avoid the subjectivity of determining the limits of a species by relying on the concordance of more than one gene genealogy (3,4). Genealogical Concordance Phylogenetic Species Recognition (GCPSR) has become feasible for most groups of organisms due to the increased ease of obtaining large amounts of nucleic acid sequence data. The strength GCPSR lies in its comparison of more than one gene genealogy, where the different gene trees are concordant they have the same tree topology due to fixation of formerly polymorphic loci following genetic isolation; these concordant branches connect species. Fig. 1 Conflict among gene trees is likely to be due to recombination among individuals within a species, and the transition from concordance to conflict determines the limits of species (5)
Fig. 1. Simultaneous analysis of three gene genealogies shows how the transition from concordance among branches to incongruity among branches can be used to diagnose species.(5)A prevailing theme that emerges from studies that use concordance of multiple gene genealogies to recognize species boundaries is that recognizes additional genetically isolated species that had not been recognized previously, due to the lack of taxonomically informative morphological characters (phenotypic simplicity or plasticity) or incomplete reproductive isolation among species (5). This is the case of some Neurospora species, in which the reproductive success of crosses with species-specific tester strains has been used to assign most Neurospora individuals to one of five outbreeding biological species: N. crassa, N. intermedia, N. sitophila, N. tetrasperma, and N. discreta but N. crassa and N.intermedia are assumed to be closely related sibling species between which reproductive isolation may not be complete(6), the purpose of this analyses is to test if these are independent lineages through GCPSR, the same aproach is going to be used to delimite species of the mygalomorph spider Antrodiaetus riversi(7). It is expected that the combined data set due to presence of all the evidence of the loci shows a better resolution in the species delimitation.
Methods
Data sets
Neurospora data set : four microsatellite loci were analysed (DMG, TMI, TML, QMA) with 15 sequences per loci representing the five outbreeding biological species: N. crassa, N. intermedia, N. sitophila, N. tetrasperma, and outgroup Neurospora species (N. dodgei, N. galapagosensis, N. africana, and N. lineolata), these sequences were retrieved from the GenBank website under accessions AY225899– AY225949, from Dettman 2003 work(6).
Antrodiaetus riversi data set: two mitocondrial and one nuclear loci were retrieved from the genebank website, number of accesions, gene specification and accesions numbers respectively for each locus follows: 37 accesions for 28S ribosomal RNA gene (DQ898772 - DQ898808), 36 accesions for 12S ribosomal RNA gene (DQ898809 - DQ898844) and 36 accesions for cytochrome oxidase subunit I (COI) gene (DQ898845- DQ898880). In the combined data set a total of 10 terminals were used as outgroup including species from genus Aliatypus, Atypoides and
Antrodiaetus.
Tree searches
The reconstruction of the genealogy between terminals was assesed using direct optimization method as implemented in POY 4.0 (8), for each single locus data set as well as for the combined data set, two different matrix cost were used one of equal costs 111 and one that favours transitions and penalizes transversions and gaps 421. The search strategy was a initial build of 100 Wagner trees posterior selection of the unique trees with minimal cost that then were summited to branch permutation with SPR followed by TBR, 50 bootstraps replicates were run to determine support values on each of the single locus data sets and in combined analyses of all the loci for each case.
GCPSR
A clade was recognized as an independent evolutionary lineage if it satisfied either of two criteria: 1. Genealogical concordance: the clade was present in the majority (3/4) of the single-locus genealogies. This criterion revealed the genealogical patterns shared among loci, regardless of levels of support.(3,4,5,6) 2. Genealogical nondiscordance: the clade appeared with bootstrap support values SV(1.0) in at least one single-locus genealogy, and was not contradicted in any other single-locus genealogy at the same level of support. This criterion prohibited poorly supported nonmonophyly at one locus from undermining well-supported monophyly at another locus.(6)
Results and discusion
Table 1. Sumarized results for all the searches under the two set cost used 111 and 421.
Based on the genealogical concordance criterion 4 species were recognized in the Antrodiaetus riversi complex. figs 2-5.
- Sp1(purple) appears with 1.00 support value (SV) in the 28S ribosomal RNA gene, and in the 12S ribosomal RNA gene SV(1.0) , and was not contradicted in any other single-locus genealogy.
- Sp2 (orange/red) appears in the in the 28S ribosomal RNA gene, and in the 12S ribosomal RNA gene and combined data set with SV(1.0) The orange clade is also present in the cytochrome oxidase subunit I gene tree found using equal cost SV(1.0).
- Sp3(green): is consistently present in all the topologies found.
- Sp4(blue): was found in in the 28S ribosomal RNA gene, and in the 12S ribosomal RNA gene with SV(0.8) .
The results of the combined data set did not behave as expected, none of the species delimited based on the single locus gene trees, was supported in the combined data set.
Fig2. Results of single gene 12S ribosomal RNA, four species identified, identical results for both matrix cost used.
Fig3. Results of single gene cytochrome oxidase subunit I gene tree found with equal cost. No species delimited by SV(1.0)The topology found with the differential matrix cost is different but also no species were found delimited by SV(1.0)
Fig4. Results of single 28S ribosomal RNA gene, four species identified, identical results for both matrix cost used.
Fig5. Results combined data set with differential matrix costs, pecies 2 and 3 delimited with no support. Results with equal cost yield different topology with less resolution ie. no species delimited.
Neurospora species
The results obtained from the analyses supports the independence of the lineages and thus the species status of Neurospora crassa, Neurospora intermedia and Neurospora tetrasperma. figs 6-10
- The two Neurospora intermedia accesions (in blue) were present as an independent lineage in the DGM and in the TML topologies as well as in the combined analysis with SV(1.0)
- Neurospora tetrasperma and accesion FGSC8815 (in green) clustered together as a species in the TMI, TML and combined analysis with SV(1.0).
- The three accesions of N. crassa plus accesion FGSC8834 (in red) , were found to be a species with SV(1.0) in the TML and combined analysis. Also in the QMA topology the highest SV(0.9) was for two different clades belonging to this species.
- Although the TMI and DGM topologies show clades containing N. crassa and N. intermedia SV(1.0, 0.80) respectively, the well supported clades SV(1.0) present in the TML topology for each species were not contradicted at the same level of support.
fig 6. Results for TML microsatellite sequence data set with equal cost matrix. Identical results were obtained with differential matrix cost.
fig 7. Results for DGM microsatellite sequence data set with equal cost matrix. Identical results were obtained with differential matrix cost.
fig8. Results for QMA microsatellite sequence data set with equal cost matrix. 
fig 9. Results for TMI microsatellite sequence data set with equal cost matrix. Identical results were obtained with differential matrix cost.
Fig10. Results combined data set with equal costs species delimited with no support except N. intermedia, results with equal cost yield different topology with less resolution ie. no species delimited.
Bibliography
- Wiens, J. J., and M. R. Servedio. 2000. Species delimitation in systematics: Inferring diagnostic differences between species. Proc. R. Soc. London Ser. B. 267:631–636.
- Wheeler, Q. D. and Meier, R. (Editors). 2000. Species Concepts and Phylogenetic Theory: A Debate. New York: Columbia University Press.
- Avise, J. C., and R. M. Ball. 1990. Principles of genealogical concordance in species conceptsa and biological taxonomy. Pp. 45– 67 in D. Futuyma and J. Antonovics, eds. Oxford surveys in evolutionary biology. Oxford Univ. Press, Oxford, U.K
- Baum, D. A., and K. L. Shaw. 1995. Genealogical perspectives on the species problem. Pp. 289–303 in P. C. Hoch and A. G. Stephenson, eds. Experimental and molecular approaches to plant biosystematics. Missouri Botanical Garden, St. Louis, MO.
- Taylor, J. W., D. J. Jacobson, S. Kroken, T. Kasuga, D. M. Geiser,D. S. Hibbett, and M. C. Fisher. 2000. Phylogenetic speciesrecognition and species concepts in fungi. Fungal Genet. Biol. 31:21–32.
- 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.
- 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.
- Varón, A., Vinh, L. S., Bomash, I. & Wheeler, W. C. 2007. POY 4.0 Beta 1983. American Museum of Natural History. ttp://research.amnh.org/scicomp/projects/poy/php
The Amadon's rule: is applicable really?
Sergio David Bolívar Leguizamón
Escuela Biología
UIS
Introduction
Infraspecific taxa are important in discussions of biodiversity because they represent evolutionary potential within a species (Haig et al, 2006). So, the Linnaean rank of subspecies became prevalent during the mid-twentieth century with the emergence of the biological species concept (Zink, 2004). Subspecies have functioned as units in at least three roles, namely in classifications, evolutionary theories and, more recently, conservation plans, without strong tests of how well they function in these roles (Zink, 2004). There are several statistical methods to delimit subspecies. Among them, the Amadon's rule or 75% rule claims that two populations belong to the different subspecies if the 75% of individuals in a population A is separable by same character from all members (+99%) of a overlapping population B (Amadon, 1949). For characters that occur as separate states, such as presence or absence of a plumage pattern or mtDNA haplotype or clade, the test involves a simple contingency table analysis. For continuously varying, normally distributed traits, such as measurements of body size, the rule involves comparison of the two distributions via their means, standard deviations and the expectation of 75% non-overlap from a t-distribution (Courtney et al, 2004). Several studies has used the Amadon's rule, but they is based in morphological characters (Patton & Unitt, 2002). A study on the feasibility of Amadon's rule in molecular sequences from three species of Pyrrhura (Psittacidae: Aves) will be made. A analysis of genetic distances and grouping will be used to deduce if the Amadon's rule is applicable to molecular characteres.
Methods
The mitochondrial sequences (mtDNA) of three species (24 populations) within of genera Pyrrhura were collected from GenBank (accessions number see Table 1), the populations are found in Peru, Brazil, and Bolivia. Populations from Pyrrhura picta (7), Pyrrhura roseifrons (7), and Pyrrhura snethlageae (10) were sampled (Table 1). The sequences were aligned in Bioedit (multiple alignment in ClustalW) version 7.0.4.1 (2005). The genetic analiysis were made in Phylip version 3.67 (Felsenstein, 2007). The software dnadist and Neighbor (Phylip v. 3.67) were used to calculate genetic distances between sequences and grouping of populations, respectively. The Neighbor-Joinning and UPGMA methods were used to grouping the distance's matrix generated by dnadist.
Table 1.
Results
Within of Pyrrhura picta are main two groups: the "Baramita + Iwokrama Reserve" group (Guyana) and the Guyanan "Acari + Baramita" group. The Brazilian population of Vila Sumuru forms a outgroup within of the P. Picta. However, the genetic variation in not significant among the two groups and the Brazilian population (0.004795 with population Baramita) see Table 2 and Fig. 1.
Pyrrhura roseifrons forms three groups. First, the Madre de Dios group with a variation of 0.017780 and 0.017381 with two populations from Contamana, respectively. Nevertheless, one sample fron Contamana posses a little divergence with population from Madre de Dios (0.008630). the Pucallpa's populations forms a defined group without variation between the samples (see Table 3).
The Pyrrhura snethlageae species is not forms sepatated groups, two groups divides the species: the "Alta Floresta + Nazaré" group (Brazil) and the "Santa Cruz + Porto Velho + Jacarecanga" group. The genetic distances between the populations from Alta Floresta and the populations from Santa Cruz is high - 0.011401 - (see Table 4).
Generally, the variation between populations from the three species (P. picta, P. roseifrons, and P. snethlageae) in not significant, and they are lower that 75%. So, the Amadon rule is not applicable to separated population (allopatric). In sympatric populations (samples from Alta Floresta) there is not variation.
Discussion
When a species becomes divided into more or less isolated subpopulations, the latter initially vary genetically because of differences in the original founding individuals
(founder principle, Mayr, 1954). Subsequently, differentiation will continue at varying rates so long as these populations remain more or less isolated geographicaIIy (Amadon, 1976).
The clinal variation and the polimorphism are consequences of this differentiation. In Aves, the morphological variation is complex because the confused coloration patterns (Ribas et al, 2006; Burmfield, 2005). Statistical approaches as the Amadon's rule (Amadon, 1949) were stablished to delimit subspecies. However, the genetic diversification within populations of Pyrrhura is not significant, and the differentiation is very lower that 75%. The geographic distances between the populations may be the main causes, so, the relation among the variation and the geographic distances is showed in the genetic distances among the populations of P. roseifrons (Madre de Dios, Peru) and the others populations of P. roseifrons. The population from Madre de Dios (Peru) is more distant and its differentiation is major.
The 75% rule (Amadon, 1949) was used in morphological studies (Patton & Unitt, 2002; Cicero & Johnson, 2006; Groves & Meijaard, 2005). The Amadon's rule is useful in morphological data because the characteristics of these data. In morphological data, the given values are not attached to the variations ocurred in molecular sequences (there are not transversions for example). So, the Amadon's rule is not feasible to apply it to molecular characters. Other reason to reject the application of the Amadon's rule is that the sympatric populations within a species are not posses significant molecular variation, because events of interbreeding or short genetic distances. The complex patterns of plumaje and the morphological characters could be the results of a little variation in the genome of individuals, so, the variation among populations is not greater that 75%.
The limits of the sympatric subspecies (mainly endemics) must be analyzed carefully, the study of the morphological and genetic variation within them is the first step to delimit it. The most appropriate approach is the recognition of yours characters. The statistical methods similar to the Amadon's rule are good as a primary approach, but the phylogenetic analysis of characters is essential. The conservation of subspecies must be based in a efficient delimitation of the populations based in the recognition of yours characters.
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Hall, T.A. 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl. Acids. Symp. Ser. 41:95-98.
Patten, M.A., & Unitt, P. (2002) Diagnosibility versus mean differences of sage sparrow subspecies. The Auk, 119, 26-35.
Ribas, C., Joseph, L., & Miyaki, C.Y. (2006) Molecular systematics and the patterns of diversification in Pyrrhura (Psittacidae), with special reference to the Picta-Leucotis complex. The Auk, 123, 660-680.
Zink, R.M. (2004) The role of subspecies in obscuring avian biological diversity and misleading conservation policy. Proceedings The Royal Society Biological Sciences, 271, 561-564.
Sergio David Bolívar Leguizamón
Escuela Biología
UIS
Introduction
Infraspecific taxa are important in discussions of biodiversity because they represent evolutionary potential within a species (Haig et al, 2006). So, the Linnaean rank of subspecies became prevalent during the mid-twentieth century with the emergence of the biological species concept (Zink, 2004). Subspecies have functioned as units in at least three roles, namely in classifications, evolutionary theories and, more recently, conservation plans, without strong tests of how well they function in these roles (Zink, 2004). There are several statistical methods to delimit subspecies. Among them, the Amadon's rule or 75% rule claims that two populations belong to the different subspecies if the 75% of individuals in a population A is separable by same character from all members (+99%) of a overlapping population B (Amadon, 1949). For characters that occur as separate states, such as presence or absence of a plumage pattern or mtDNA haplotype or clade, the test involves a simple contingency table analysis. For continuously varying, normally distributed traits, such as measurements of body size, the rule involves comparison of the two distributions via their means, standard deviations and the expectation of 75% non-overlap from a t-distribution (Courtney et al, 2004). Several studies has used the Amadon's rule, but they is based in morphological characters (Patton & Unitt, 2002). A study on the feasibility of Amadon's rule in molecular sequences from three species of Pyrrhura (Psittacidae: Aves) will be made. A analysis of genetic distances and grouping will be used to deduce if the Amadon's rule is applicable to molecular characteres.
Methods
The mitochondrial sequences (mtDNA) of three species (24 populations) within of genera Pyrrhura were collected from GenBank (accessions number see Table 1), the populations are found in Peru, Brazil, and Bolivia. Populations from Pyrrhura picta (7), Pyrrhura roseifrons (7), and Pyrrhura snethlageae (10) were sampled (Table 1). The sequences were aligned in Bioedit (multiple alignment in ClustalW) version 7.0.4.1 (2005). The genetic analiysis were made in Phylip version 3.67 (Felsenstein, 2007). The software dnadist and Neighbor (Phylip v. 3.67) were used to calculate genetic distances between sequences and grouping of populations, respectively. The Neighbor-Joinning and UPGMA methods were used to grouping the distance's matrix generated by dnadist.
Table 1.
Results
Within of Pyrrhura picta are main two groups: the "Baramita + Iwokrama Reserve" group (Guyana) and the Guyanan "Acari + Baramita" group. The Brazilian population of Vila Sumuru forms a outgroup within of the P. Picta. However, the genetic variation in not significant among the two groups and the Brazilian population (0.004795 with population Baramita) see Table 2 and Fig. 1.
Pyrrhura roseifrons forms three groups. First, the Madre de Dios group with a variation of 0.017780 and 0.017381 with two populations from Contamana, respectively. Nevertheless, one sample fron Contamana posses a little divergence with population from Madre de Dios (0.008630). the Pucallpa's populations forms a defined group without variation between the samples (see Table 3).
The Pyrrhura snethlageae species is not forms sepatated groups, two groups divides the species: the "Alta Floresta + Nazaré" group (Brazil) and the "Santa Cruz + Porto Velho + Jacarecanga" group. The genetic distances between the populations from Alta Floresta and the populations from Santa Cruz is high - 0.011401 - (see Table 4).
Generally, the variation between populations from the three species (P. picta, P. roseifrons, and P. snethlageae) in not significant, and they are lower that 75%. So, the Amadon rule is not applicable to separated population (allopatric). In sympatric populations (samples from Alta Floresta) there is not variation.
Discussion
When a species becomes divided into more or less isolated subpopulations, the latter initially vary genetically because of differences in the original founding individuals
(founder principle, Mayr, 1954). Subsequently, differentiation will continue at varying rates so long as these populations remain more or less isolated geographicaIIy (Amadon, 1976).
The clinal variation and the polimorphism are consequences of this differentiation. In Aves, the morphological variation is complex because the confused coloration patterns (Ribas et al, 2006; Burmfield, 2005). Statistical approaches as the Amadon's rule (Amadon, 1949) were stablished to delimit subspecies. However, the genetic diversification within populations of Pyrrhura is not significant, and the differentiation is very lower that 75%. The geographic distances between the populations may be the main causes, so, the relation among the variation and the geographic distances is showed in the genetic distances among the populations of P. roseifrons (Madre de Dios, Peru) and the others populations of P. roseifrons. The population from Madre de Dios (Peru) is more distant and its differentiation is major.
The 75% rule (Amadon, 1949) was used in morphological studies (Patton & Unitt, 2002; Cicero & Johnson, 2006; Groves & Meijaard, 2005). The Amadon's rule is useful in morphological data because the characteristics of these data. In morphological data, the given values are not attached to the variations ocurred in molecular sequences (there are not transversions for example). So, the Amadon's rule is not feasible to apply it to molecular characters. Other reason to reject the application of the Amadon's rule is that the sympatric populations within a species are not posses significant molecular variation, because events of interbreeding or short genetic distances. The complex patterns of plumaje and the morphological characters could be the results of a little variation in the genome of individuals, so, the variation among populations is not greater that 75%.
The limits of the sympatric subspecies (mainly endemics) must be analyzed carefully, the study of the morphological and genetic variation within them is the first step to delimit it. The most appropriate approach is the recognition of yours characters. The statistical methods similar to the Amadon's rule are good as a primary approach, but the phylogenetic analysis of characters is essential. The conservation of subspecies must be based in a efficient delimitation of the populations based in the recognition of yours characters.
Bibliography
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Patten, M.A., & Unitt, P. (2002) Diagnosibility versus mean differences of sage sparrow subspecies. The Auk, 119, 26-35.
Ribas, C., Joseph, L., & Miyaki, C.Y. (2006) Molecular systematics and the patterns of diversification in Pyrrhura (Psittacidae), with special reference to the Picta-Leucotis complex. The Auk, 123, 660-680.
Zink, R.M. (2004) The role of subspecies in obscuring avian biological diversity and misleading conservation policy. Proceedings The Royal Society Biological Sciences, 271, 561-564.
sábado, 1 de septiembre de 2007
Species with-out evolutionary assumptions
Erika Jazmín parada Vargas.
The Species concept and its delimitation are old problems in biology and multiple debates have been done since multiple disciplines (Cracraft, 2000). Here is presented The Phylogenetic Species Concept (PSC) (sensu Wheeler and Platnick), and are showed some of its advantages.
By definition (for PSC) a species is “the smallest aggregation of populations or lineages diagnosable by a unique combination of character states in comparable individuals (Semaphoronts) (Wheeler & Platnick, 2000). It is important to make the distinction between the PSC and the monophyletic species concept (sensu Mishler and Theriot), because the second one is based on the concept of shared derived characters, called synapomorphies (in this case autapomorphies, because they belongs to a single group, and the monophyletic groups are defined by the autapomorphies (Pleijel, 1999)). “If two or more individuals or populations share a derived character then they are assumed to be more closely related than individuals or populations lacking that character” (Goldstein & DeSallle, 2001). But whether or not some individuals within a particular species are more or less closely related to one another than to members of another phylogenetic species is irrelevant to the reconstruction of relationships among species (Goldstein & DeSallle, 2001).
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