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
domingo, 16 de septiembre de 2007
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.
Bibliography
Amadon, D. (1949) The seventy-five per cent rule for subspecies. The Condor, 51, 250-158.
Amadon, D. (1976) Treatment of subspecies approaching species status. Systematic Zoology, 25, 161-167.
Brumfield, R.T. (2005) Mitochondrial variation in bolivian populations of the variable antshrike (Thamnophilus caerulescens). The Auk, 122, 414-432.
Cicero, C. & Johnson, N.K. (2006) Diagnosibility of subspecies: Lessons from sage sparrows (Amphispiza belli) for analysis of geographic variation in birds. The Auk, 123, 266-274.
Courtney, S.P., Blakesley, J.A., Bigley, R.E., Cody, M.L., Dumbacher, J.P., Fleischer, R.C., Franklin, A.B., Franklin, J.F., Gutiérrez, R.J., Marzluff, J.M., & Sztukowski, L. (2004) Scientific evaluation of the status of the Northern Spotted Owl. Scientific evaluation of the status of the northern spotted owl. Sustainable Ecosystems Institute, Portland, Oregon. 508 pp.
Felsenstein, J. 1989. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.
Groves, C.P., Meijaard, E. (2005) Interspecific variation in Moschiola, the Indian chevrotain. The Raffles Bulletin of Zoology, 12, 413-421.
Haig, S.M., Beever, E.A., Chambers, S.M., Draheim, H.M., Dugger, B.D., Dunham, S., Elliott-Smith, E., Fontaine, J.B., Kesler, D.C., Knaus, B.J., Lopes, L.F., Loschi, P., Mullins, T.D, & Sheffield, L.M. (2006) Taxonomic considerations in listing subspecies under the U.S. Endangered species act. Conservation Biology, 20, 1584-1594.
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
Amadon, D. (1949) The seventy-five per cent rule for subspecies. The Condor, 51, 250-158.
Amadon, D. (1976) Treatment of subspecies approaching species status. Systematic Zoology, 25, 161-167.
Brumfield, R.T. (2005) Mitochondrial variation in bolivian populations of the variable antshrike (Thamnophilus caerulescens). The Auk, 122, 414-432.
Cicero, C. & Johnson, N.K. (2006) Diagnosibility of subspecies: Lessons from sage sparrows (Amphispiza belli) for analysis of geographic variation in birds. The Auk, 123, 266-274.
Courtney, S.P., Blakesley, J.A., Bigley, R.E., Cody, M.L., Dumbacher, J.P., Fleischer, R.C., Franklin, A.B., Franklin, J.F., Gutiérrez, R.J., Marzluff, J.M., & Sztukowski, L. (2004) Scientific evaluation of the status of the Northern Spotted Owl. Scientific evaluation of the status of the northern spotted owl. Sustainable Ecosystems Institute, Portland, Oregon. 508 pp.
Felsenstein, J. 1989. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.
Groves, C.P., Meijaard, E. (2005) Interspecific variation in Moschiola, the Indian chevrotain. The Raffles Bulletin of Zoology, 12, 413-421.
Haig, S.M., Beever, E.A., Chambers, S.M., Draheim, H.M., Dugger, B.D., Dunham, S., Elliott-Smith, E., Fontaine, J.B., Kesler, D.C., Knaus, B.J., Lopes, L.F., Loschi, P., Mullins, T.D, & Sheffield, L.M. (2006) Taxonomic considerations in listing subspecies under the U.S. Endangered species act. Conservation Biology, 20, 1584-1594.
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.
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).
Evolutionary species and their delimitation.
Ana Marcela Florez Rueda
This document attempts to describe the evolutionary species concept and to provide criteria to delimit evolutionary species. The evolutionary species concept was first stated by Simpson in 1961 and restated by Wiley in 1981 as “An evolutionary species is a single lineage of ancestor-descendant populations which maintains its identity from other such lineages and which has its own evolutionary tendencies and historical fate”. Following Hening1 evolutionary species are “logical individuals bounded by speciation events with origins, existence and ends” 1 , they have an origin by cladogenesis, undergo evolution by anagenesis, and disappear by extinction. There has to be a “correlation with the species and the number of cladogenetic events that have occurred during the course of descent within a clade”1, this definition ties species to speciation and seeks for process, “divorcing species from cladogenesis destroys de distinction between tokogeny (nonhierarquical descent) and phylogeny ( hierarquical descent)”1 and this distinction is one of the premises of phylogenetic analysis.
The species problem involves different questions one is the species concept per se (an idea of what kind of entity species are) and the other is the operational question (a methodological approach to recognizing species in a particular case)2. Several authors1,2,3 have argued for the distinction of these two questions considering it the root of the “species problem”. Operational concepts (that try to answer both questions at once) are not universal because all operational species criteria will fail in some cases3 due to missing data, or simply inapplicability, consider the biological criteria of reproductive isolation, it is not applicable to asexual species, and sometimes it is impossible to determine. But the operational question is indeed the most important and accurate operational methods are a necessity. The ESC does not provide a method for the delimitation of species, but based on it one can choose the right method to delimit evolutionary species, there is plenty of empirical data and methods that can be brought to the question of whether a group of specimens is worthy of being hypothesized as parts of an evolutionary species, and when we consider this we can see the links between this concept and other species concepts.
The operational concepts must be reinterpreted as delimitation criteria. There are more than 20 species concepts which may have a delimitation criteria, each one of them should be evaluated to see if the species that delimits are evolutionary species, here I will only evaluate four species concepts/delimitation criteria. Biological delimitation agrees with the ESC because it proves lineage independence and identity, in the few cases when this kind of data is available it should be the primary criteria, but this is as previously stated a non universal delimitation criteria, and probably the less applicable, discerning potential reproductive barriers can be difficult, time consuming, expensive, and fraught with error. Homology and genealogical concordance are delimitation criteria that agree with ESC these are embodied in the PSC (sensu Mishler and Theriot), and GSC (sensu Baum and Shaw), they take into account the process of cladogenesis, and prove lineage independence, contrary to biological delimitation this methodology is widely applicable to all the taxa and there is a lot of data available. Delimitation criteria based on PSC (sensu Wheeler and Platnick) might result in every diagnosable subpopulation be called a species ignoring its genealogy, with terminals that may have tokogenetic relationships, making the delimited species unuseful for phylogenetic analysis, this approach is at odds whit the ESC, and thus prohibited.
The ESC provides an universal idea of what The Species is, but accurate operational methods are a necessity, hopefully biologist are now in a position to shift its attention away from the endless debate about the definition of The Species and “focus instead on estimating accurately the boundaries and numbers of species and studying the diverse processes involved in their origin and maintenance”. 2
Bibliography
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., and M. R. Servedio. 2000. Species delimitation in systematics: inferring diagnostic differences between species. Proceedings of the Royal Society of London, Series B 267:631–636.
THE SPECIES CONCEPTS IN AVES
Sergio David Bolívar Leguizamón
Biology
UIS
The number of species in Aves is 9000 to 10000 approximately. Within the group, there is clinal variation and populations intergradation. The Aves were identified by ornithologists using general morphology and patterns of coloration in the feathers. This Tipological Species Concept (TSC) were used to delimit and to recognize species in many groups. However, the TSC was used to identify and delimited species in Aves indiscriminately, but the TSC is not useful to identify sibling species and groups with sympatric populations.
Since Dobzhansky (1937) and Mayr (1952), the Biological Species Concept (BSC) has been used by ornithologists, the BSC claims that a species are groups of interbreeding natural populations that are reproductively isolated from other such groups. The geographic and reproductive isolation is the criterion of delimitation in th BSC. The sympatric species are defined as subspecies by BSC. The Aves posees great quantity of subspecies, because your high polymorphism within a same species. Studies claims that the sympatric species o subspecies must be considered as “emergent species” (Mayr, 1963). Nevertheless, BSC is not applicable in the field camp, the reproductive isolation is not applicable the Aves. In laboratory conditions the breeding of much birds is not successful, and the hybrid species have the uncertainty of if they are on or two species, futhermore, the sympatric species are not easy to identify because the variation in the populations could be insignificant. In fact, the ornithologists used coloration patterns to recognize species of birds. So, genera and species are difficult to determine. However, the BSC is proclamed as the principal species concept in Ornithology.
Nevertheless, other alternatives were emerged, as The Phylogenetics Species Concept (Cracraft, 1983; Nixon & Wheeler, 1990), offers a new vision about species and the asumptions about them. PSC (sensu Cracraft, 1983) is based in recognition of characters and monophyly (ancestry-descent), the PSC (sensu Cracraft,1983) claims that the species must be reproductively cohesive and diagnosable. For Cracraft, the species concept has three key elements: Reproductive cohesion, diagnosability, and a criterion for ranking populations at the species-level. The PSC (sensu Cracraft, 1983) offers greater theorical ans empirical support that BSC.
In the Ornithology, the delimitation of subspecies is bounded to great debate and discusion, some researchs claims that the populational variation must be treated as polimorphisms within of a species, on the other hand, researchs states that the “subspecies” hierarchy is very important in the classification and use of taxa.
In field camp, there are several statistical methods to delimit species, the Amadon's rule or 75% rule claims that two populations belong to the same species if the 75% of individuals in a population A posses the same character (or character state) that the 99% of a population B (Amadon, 1949). This statistical method was used by Patton & Unitt (2002), Meijaard & Groves (2004), and Cicero & Johnson (2006). The 75% rule is defined to mean that before a population is given subspecific status at least 75% of the individuals comprising it must be separable from +99% of the individuals of all other populations of the same species which may overlap with it as regards the geographically variable characters (Amadon, 1949).
The Methodology is based in statistical analysis, where the presence of trait of interest is plotted in the population and this is calculated for the others populations, and the comparisons are made. The standard deviation and media are calculated for the traits or characters of the population, if the standard deviation is not enough among the characters of populations (75%), then the population are the same species. But if the differentiation among the two populations in a character is > that 75%, the character separates the two populations in two subspecies.
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.
It rule provides a quantitative method to evaluate distinctiveness and in which to make subspecies designations (Patten and Unitt 2002). Nevertheless, the 75% rule is not strict, because sample effects or data's nature. Other approach similar to Amadon's rule are the 99% rule that is based on the same argument.
At least in Aves and for morphological data (Patton & Unitt, 2002; Meijaard & Groves, 2004; Cicero & johnson, 2006), the Amadon's rule is a way to delimit species and subspecies in sympatric populations. However, molecular analysis apply this method are non-existence, or they are few.
The PSC (sensu Cracraft, 1983) is more applicable and useful that the BSC (Mayr, 1952). The subspecies must be vievew as polimorphic populations, where the populational variation must be significative to postule new subspecies. The Amadon's rule (75%) is ambiguous because is usseful with morpholgical traits, but it is not quite applicable in molecular caracteres.
Bibliography
Sergio David Bolívar Leguizamón
Biology
UIS
The number of species in Aves is 9000 to 10000 approximately. Within the group, there is clinal variation and populations intergradation. The Aves were identified by ornithologists using general morphology and patterns of coloration in the feathers. This Tipological Species Concept (TSC) were used to delimit and to recognize species in many groups. However, the TSC was used to identify and delimited species in Aves indiscriminately, but the TSC is not useful to identify sibling species and groups with sympatric populations.
Since Dobzhansky (1937) and Mayr (1952), the Biological Species Concept (BSC) has been used by ornithologists, the BSC claims that a species are groups of interbreeding natural populations that are reproductively isolated from other such groups. The geographic and reproductive isolation is the criterion of delimitation in th BSC. The sympatric species are defined as subspecies by BSC. The Aves posees great quantity of subspecies, because your high polymorphism within a same species. Studies claims that the sympatric species o subspecies must be considered as “emergent species” (Mayr, 1963). Nevertheless, BSC is not applicable in the field camp, the reproductive isolation is not applicable the Aves. In laboratory conditions the breeding of much birds is not successful, and the hybrid species have the uncertainty of if they are on or two species, futhermore, the sympatric species are not easy to identify because the variation in the populations could be insignificant. In fact, the ornithologists used coloration patterns to recognize species of birds. So, genera and species are difficult to determine. However, the BSC is proclamed as the principal species concept in Ornithology.
Nevertheless, other alternatives were emerged, as The Phylogenetics Species Concept (Cracraft, 1983; Nixon & Wheeler, 1990), offers a new vision about species and the asumptions about them. PSC (sensu Cracraft, 1983) is based in recognition of characters and monophyly (ancestry-descent), the PSC (sensu Cracraft,1983) claims that the species must be reproductively cohesive and diagnosable. For Cracraft, the species concept has three key elements: Reproductive cohesion, diagnosability, and a criterion for ranking populations at the species-level. The PSC (sensu Cracraft, 1983) offers greater theorical ans empirical support that BSC.
In the Ornithology, the delimitation of subspecies is bounded to great debate and discusion, some researchs claims that the populational variation must be treated as polimorphisms within of a species, on the other hand, researchs states that the “subspecies” hierarchy is very important in the classification and use of taxa.
In field camp, there are several statistical methods to delimit species, the Amadon's rule or 75% rule claims that two populations belong to the same species if the 75% of individuals in a population A posses the same character (or character state) that the 99% of a population B (Amadon, 1949). This statistical method was used by Patton & Unitt (2002), Meijaard & Groves (2004), and Cicero & Johnson (2006). The 75% rule is defined to mean that before a population is given subspecific status at least 75% of the individuals comprising it must be separable from +99% of the individuals of all other populations of the same species which may overlap with it as regards the geographically variable characters (Amadon, 1949).
The Methodology is based in statistical analysis, where the presence of trait of interest is plotted in the population and this is calculated for the others populations, and the comparisons are made. The standard deviation and media are calculated for the traits or characters of the population, if the standard deviation is not enough among the characters of populations (75%), then the population are the same species. But if the differentiation among the two populations in a character is > that 75%, the character separates the two populations in two subspecies.
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.
It rule provides a quantitative method to evaluate distinctiveness and in which to make subspecies designations (Patten and Unitt 2002). Nevertheless, the 75% rule is not strict, because sample effects or data's nature. Other approach similar to Amadon's rule are the 99% rule that is based on the same argument.
At least in Aves and for morphological data (Patton & Unitt, 2002; Meijaard & Groves, 2004; Cicero & johnson, 2006), the Amadon's rule is a way to delimit species and subspecies in sympatric populations. However, molecular analysis apply this method are non-existence, or they are few.
The PSC (sensu Cracraft, 1983) is more applicable and useful that the BSC (Mayr, 1952). The subspecies must be vievew as polimorphic populations, where the populational variation must be significative to postule new subspecies. The Amadon's rule (75%) is ambiguous because is usseful with morpholgical traits, but it is not quite applicable in molecular caracteres.
Bibliography
- Amadon, D. (1949) The seventy-five per cent rule for subspecies. The Condor, 51, 250-158.
- Cicero, C. & Johnson, N.K. (2006) Diagnosibility of subspecies: Lessons from sage sparrows (Amphispiza belli) for analysis of geographic variation in birds. The Auk, 123, 266-274.
- Courtney, S.P., Blakesley, J.A., Bigley, R.E., Cody, M.L., Dumbacher, J.P., Fleischer, R.C., Franklin, A.B., Franklin, J.F., Gutiérrez, R.J., Marzluff, J.M., & Sztukowski, L. (2004) Scientific evaluation of the status of the Northern Spotted Owl. Scientific evaluation of the status of the northern spotted owl. Sustainable Ecosystems Institute, Portland, Oregon. 508 pp.
- Cracraft, J. (1997) Species concepts in systematics and conservation biology – an ornithological viewpoint. Species The units of biodiversity. Ed. Chapman & Hall, 325-339.
- Groves, C.P., Meijaard, E. (2005) Interspecific variation in Moschiola, the Indian chevrotain. The Raffles Bulletin of Zoology, 12, 413-421.
- Mayr, E. (2000) The biological species concept. Species concepts and phylogenetics theory, Ed. Columbia University Press, pp 17-29.
- Patten, M.A., & Unitt, P. (2002) Diagnosibility versus mean differences of sage sparrow subspecies. The Auk, 119, 26-35.
Virus Species: A Controversy
A virus is an infectious agent composed by a genomic nucleic acid covered by several protective layers. In 1991, the International Committee on Taxonomy of Viruses (ICTV) endorsed the following definition of virus species: a virus species is a polythetic class of viruses that constitute a replicating lineage and occupy a particular ecological niche(1). The rationale for applying the species concept in virology is that viruses are biological entities and not chemicals: they possess genes, replicate, specialize, evolve and occupy specific ecological niches. The virologists adopted its own concept because they assumed that the only legitimate species concept was that of biological species defined by sexual reproduction, gene pools and reproductive isolation(2). However, within the multiplicity of species definitions just a reduced number of virologists, if any, have kept in mind the application of the phylogenetic species concept (PSC) into the virology field. The goal of this document is to present some fails of the virological concept of species and to introduce the PSC as an alternative in this field.
Viruses are intracellular parasites and are tangible, concrete entities, located in space and time that can be handled experimentally. Some authors(1, 2, 3) have proposed that the virus species, on the other hand, are abstractions that exist only in the mind. They realize that all biological classifications are conceptual constructions created by researchers for the purpose of introducing order in the bewildering variety of biological objects. In the same way, they emphasize that the categories used for building a classification such as families, genera and even species are not found in nature but are abstractions invented by human minds and concludes that species are thus not objects that will ever be encountered by researchers in their handling of viruses. It looks that those authors don't distinct between the species category within the Linnaean hierarchy of taxonomic categories and the taxon (group), that is ranked at the species level within that hierarchy. My interpretation aims to the view that species are concrete entities with a definite position in space and time rather than abstract classes with an indefinite origin in time; if we see species just as classes lead us to quite arbitrary decisions for their diagnose.
The virological definition of species means that no single property can be used as a defining property of a virus species and highlights that the major advantage of defining species as polythetic classes is that it makes it possible to accommodate, within a species, individual viruses that lack one or other characteristic that would normally be considered typical of the species(1, 2). It seems that for the virologists is problematic to have an enormous number of species because they group as a species clearly differentiated viruses. As has been(4) stressed: if it is advisable to recognize every lineage characterized even by just a fixed mutation and the goal of distinguishing species is to thereby recognize the end-products of evolution, should we seek to suppress naming large numbers of species where large numbers of differentiated end-products exist?. It have been have mentioned(1, 2) that it is the inherent variability of the members of a virus species that prevents a single discriminating character such a certain percentage of genome sequence dissimilarity to be used as a valid criterion for defining a species; instead of that percentage the virological concept of species proposes to use certain degree of properties similarity as is contemplate of what a polythetic class is (Each member possesses several of the diagnostic properties but no single defining property is present in all the members of the class). The PSC sensu Wheeler and Platnick define species as the smallest aggregation of (sexual) populations or (asexual) lineages diagnosable by a unique combination of character states(4); I deem that the use of percentages of similarity/dissimilarity will be rather arbitrary and irrational and that the PSC mentioned represents a unit species concept for all biological fields because is based on observable characters and avoids rampant subjectivity. Moreover, I consider that we do not create species as have been accentuated(2, 3); instead of it we identify and diagnose them by its character states.
On the other hand pair-wise sequence comparisons (PASC) have been used to produce multimodal distributions where the peaks are usually equated with clusters of sequences corresponding to groups of viral strains, species and genera(3). I consider that such PASC are just useful for delineating clusters of viruses but not to delineate species. The nucleotide sequences similarity percentages shows that, similarity, but we cannot expect to diagnose that two viruses belong to the same specie because of theirs nucleotide/amino-acid sequence identity degree. Furthermore, PASC on their own cannot provide clear cut quantitative criteria for distinguishing between different clusters and the clusters value percentage changes in different families. Consequently a level of genome homology fails to establish membership in a species.
PSC are recognized by unique combinations of constantly distributed characters and it’s compatible with phylogenetic theory because speciation events are marked by character transformations. It is a concept that applies equally to all conceivable speciation processes and biological entities (including viruses), representing a unit species concept. It aims to recognize the end-products of evolutionary processes and units of formal scientific nomenclature and as a final point the PSC concept meets the main requirement placed upon the species in virology: to achieve some rational order whereby some viral agents are grouped together.
References
1. Van Regenmortel, M.H.V. and Mahy, B.W.J., 2004. Emerging issues in virus taxonomy. Emerg. Infect. Dis. 10, 8–13.
2. Van-Regenmortel, M.H.V., 2007. Virus species and virus identification: Past and current controversies. Infection Genetics and Evolution 7(1): 133-144
3. Van Regenmortel, M.H.V., 2003. Viruses are real, virus species are man-made taxonomic constructions. Arch. Virol. 148, 2481–2488.
4. Wheeler, Q. D. and Meier, R. (Editors). 2000. Species Concepts and Phylogenetic Theory: A Debate. New York: Columbia University Press
Viruses are intracellular parasites and are tangible, concrete entities, located in space and time that can be handled experimentally. Some authors(1, 2, 3) have proposed that the virus species, on the other hand, are abstractions that exist only in the mind. They realize that all biological classifications are conceptual constructions created by researchers for the purpose of introducing order in the bewildering variety of biological objects. In the same way, they emphasize that the categories used for building a classification such as families, genera and even species are not found in nature but are abstractions invented by human minds and concludes that species are thus not objects that will ever be encountered by researchers in their handling of viruses. It looks that those authors don't distinct between the species category within the Linnaean hierarchy of taxonomic categories and the taxon (group), that is ranked at the species level within that hierarchy. My interpretation aims to the view that species are concrete entities with a definite position in space and time rather than abstract classes with an indefinite origin in time; if we see species just as classes lead us to quite arbitrary decisions for their diagnose.
The virological definition of species means that no single property can be used as a defining property of a virus species and highlights that the major advantage of defining species as polythetic classes is that it makes it possible to accommodate, within a species, individual viruses that lack one or other characteristic that would normally be considered typical of the species(1, 2). It seems that for the virologists is problematic to have an enormous number of species because they group as a species clearly differentiated viruses. As has been(4) stressed: if it is advisable to recognize every lineage characterized even by just a fixed mutation and the goal of distinguishing species is to thereby recognize the end-products of evolution, should we seek to suppress naming large numbers of species where large numbers of differentiated end-products exist?. It have been have mentioned(1, 2) that it is the inherent variability of the members of a virus species that prevents a single discriminating character such a certain percentage of genome sequence dissimilarity to be used as a valid criterion for defining a species; instead of that percentage the virological concept of species proposes to use certain degree of properties similarity as is contemplate of what a polythetic class is (Each member possesses several of the diagnostic properties but no single defining property is present in all the members of the class). The PSC sensu Wheeler and Platnick define species as the smallest aggregation of (sexual) populations or (asexual) lineages diagnosable by a unique combination of character states(4); I deem that the use of percentages of similarity/dissimilarity will be rather arbitrary and irrational and that the PSC mentioned represents a unit species concept for all biological fields because is based on observable characters and avoids rampant subjectivity. Moreover, I consider that we do not create species as have been accentuated(2, 3); instead of it we identify and diagnose them by its character states.
On the other hand pair-wise sequence comparisons (PASC) have been used to produce multimodal distributions where the peaks are usually equated with clusters of sequences corresponding to groups of viral strains, species and genera(3). I consider that such PASC are just useful for delineating clusters of viruses but not to delineate species. The nucleotide sequences similarity percentages shows that, similarity, but we cannot expect to diagnose that two viruses belong to the same specie because of theirs nucleotide/amino-acid sequence identity degree. Furthermore, PASC on their own cannot provide clear cut quantitative criteria for distinguishing between different clusters and the clusters value percentage changes in different families. Consequently a level of genome homology fails to establish membership in a species.
PSC are recognized by unique combinations of constantly distributed characters and it’s compatible with phylogenetic theory because speciation events are marked by character transformations. It is a concept that applies equally to all conceivable speciation processes and biological entities (including viruses), representing a unit species concept. It aims to recognize the end-products of evolutionary processes and units of formal scientific nomenclature and as a final point the PSC concept meets the main requirement placed upon the species in virology: to achieve some rational order whereby some viral agents are grouped together.
References
1. Van Regenmortel, M.H.V. and Mahy, B.W.J., 2004. Emerging issues in virus taxonomy. Emerg. Infect. Dis. 10, 8–13.
2. Van-Regenmortel, M.H.V., 2007. Virus species and virus identification: Past and current controversies. Infection Genetics and Evolution 7(1): 133-144
3. Van Regenmortel, M.H.V., 2003. Viruses are real, virus species are man-made taxonomic constructions. Arch. Virol. 148, 2481–2488.
4. Wheeler, Q. D. and Meier, R. (Editors). 2000. Species Concepts and Phylogenetic Theory: A Debate. New York: Columbia University Press
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