lunes, 6 de septiembre de 2010

Does the phylogenetic Species Category exist in virus?

Jiménez- Silva C. L.
Universidad Industrial de Santander.
Laboratorio de Sistematica y Biogeografia

Phylogenetic specie is the smallest diagnosable group identified as an ancestor-descendant populations evolving separately from others (Cacraft, 1983). The species can be considered a species level, among all those available in the hierarhy Phylogenetic. Only monophyletic groups can be recognized and formally named taxa. This principle is based on the groups which include all the descendants of a single common ancestor are the only groups with real and natural existence in relation to the evolutionary process (De Luna and Mishler, 1996). The real existence of the species gives genealogical relationships with other group of organisms, their historical behavior, so it is considered that the species are different because they have diverged evolutionarily. Wiley (1978) supports this assertion by suggesting that the species is a single lineage of ancestral-descendant populations, they retain their identity from other lineages and have their own evolutionary tendencies and historical fate.

According to the above and the ontological status of phylogenetic species suggests that instead of viewing species as natural kinds we should think of them as individuals (Ghiselin, 1974 and Hull, 1978). Given the class/individual distinction, Ghiselin and Hull argue that species are individuals, not classes. Their argument assumes that the term ‘species’ is a theoretical term in evolutionary theory, so their argument focuses on the role of ‘species’ in that theory. Here is Hull's version of the argument, which can be dubbed the ‘evolutionary unit argument.’ Since Darwin, species have been considered units of evolution. The "individuals" can you discover connectors or space - time, ie, the status of "individual" at a time and place particle is linked to another state at another time and space site for historical connections (Dupré 2001, Reydon de 2003, y Crane 2004). From this concept and its ontological status is to intend whether the phylogenetic Species exist in virus Category.

The idea that species are individuals has a number of implications. For one, the relationship between an organism and its species is not a member/class relation but a part/whole relation. An organism belongs to a particular species only if it is appropriately causally connected to the other organisms in that species. The organisms of a species must be parts of a single evolving lineage (Hull, 1978). If belonging to a species turns on an organism's insertion in a lineage, then qualitative similarity can be misleading. Two organisms may be very similar morphologically, genetically, and behaviorally, but unless they belong to the same spatiotemporally continuous lineage they cannot belong to the same species.

Virus Species

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 (Van Regenmortel & Mahy, 2004). This definition applies for viruses like units called "classes", in a biological classification scheme, an individual organism or a virus can be a member of several abstract classes like a species or a genus. Class membership must be distinguished from the so-called ‘‘part-whole’’ relationship which exists only between two concrete objects, one being a part of the other in the way, for instance, that cells and organs are parts of an organism. It is not possible for a concrete object like a virus to be ‘‘part’’ of an abstract entity like a species (similarly a thought cannot be part of an object). The mixing of logical categories has led to much debate in viral taxonomy (Bos, 2003; Van Regenmortel, 2003).

A class is defined by properties that are constant and immutable. This allows members of such a class to be recognized with absolute certainty since one or more property is necessarily present in every member of the class. Virus families, for instance, are universal classes because they consist of members, all of which share a number of defining properties that are both necessary and sufficient for class membership. Allocating a virus to a family is thus an easy task since a few structural or chemical attributes will suffice to allocate the virus to a particular family. (Van Regenmortel, 2006).

Classifying viruses consists in inventing taxonomic classes like particular families or species and allocating individual viruses to these classes in order to achieve some order whereby similar viral agents are grouped together. The failure to distinguish between real objects such as organisms and viruses and the mental constructions and abstractions needed to build up any classification system has been a fertile source of confusion in taxonomy (Van Regenmortel, 2003) Distinguishing between real, tangible objects like viruses (i.e. concrete individuals) and mental constructs like virus species and genera (i.e. classes) that exist only in the mind is a basic requirement for clear thinking. Although a taxonomic class is defined by properties possessed by concrete objects, it is an abstract, conceptualized collection, i.e. a mental construct.

Returning to the phylogenetic species concept, this raises the real Existence of the species Conceived as discrete units, ie, restricted in space and time. Inconsistent with the vision Referred to by (ICTV), Which Takes the virus species as a class being these, units exist independent and unrestricted that teporales or spatial boundaries. If we encuena that "classes" are abstractions, ie, a mental construct, missing reality. The concept proposed by De Luna and Mishler (1996), on the phylogenetic concept where raise the species as a group with real existence in relation to the natural evolutionary process. The virus species is not wonderful to hang phylogenetic species category and be closer to a nominalist concept (real missing) or phenetic.

Bos, L., 2003. Virus nomenclature; continuing topicality. Arch. Virol. 148, 1235–1246.

Crane, J. 2004, “On the Metaphysics of Species”, Philosophy of Science, 71: 156–173

Cracraft, J. 1983. Species concepts and speciation analysis. Current Ornithology, 1, 159–187.

Dupré, J., 2001, “In Defense of Classification”, Studies in the History and Philosophy of Biology and the Biomedical Sciences, 32: 203–219.

Ghiselin, M., 1974, “A Radical Solution to the Species Problem”, Systematic Zoology, 23: 536–544

Hull, D., 1978, “A Matter of Individuality”, Philosophy of Science, 45: 335–360
Reydon, T., 2003, “Species Are Individuals Or Are They?” Philosophy of Science, 70: 49–56.

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., 2003. Viruses are real, virus species are man-made taxonomic constructions. Arch. Virol. 148, 2481–2488.

Van Regenmortel, M.H.V., 2006. Virologists, taxonomy and the demands of logic. Arch. Virol. 151, in press.

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Evaluation of genetic recombination on phylogenetics relationships in Dengue virus

A. Susana Ortiz Bae
Laboratorio de Sistematica y Biogeografia


Genetic recombination in RNA viruses is an evolutionary process defined as the exchange of genetic information from two or more nucleotide sequences into recombinant progeny virus (Mahy, 2009). This mechanism apparently plays a significant role in the generation of genetic diversity especially important under adverse conditions (Worobey et al. 1999). Despite above, the process is a rare event in natural populations of Dengue virus in which through a copy-choice mechanism, the polymerase switches between parental viral molecules during replication (Lai, 1992). However, the approximate inference of recombination can be based regarding their effect on genealogy as events that can change or not the final topology or branch lengths and therefore can disrupt the pattern of phylogenetic relationships between viral sequences (Wiuf et al. 2000). Given that many recombinant sequences are mosaics comprising regions with quite different phylogenetic histories, this study evaluated the effect of genetic recombination on phylogenetics relationships in Dengue virus type 1 sequence, based on the detection of conflicting phylogenic signals under parsimony criterion.


Viral recombinants , parental and no recombinants sequences from dengue strains used in this study were provide from the analysis reported by Chen et al. (2008) and Worobey et al. (1999). Prior to the analysis of these sequences was constructed a data set and recombination events were simulated between regions of the serotypes with the aim to detect sensitivity to genetic recombination in the inter-serotype level. The sequences from literature, was partitioned in specific coding regions corresponding to recombination breakpoints and were aligned, then the the phylogenetic relationships were reconstructed under phylogenetic inference criteria such as parsimony implementing heuristic method and finally the pattern of relationships were summarized on a strict consensus. Representative sequences from Denv-2, Denv-3 and Denv4 were used as outgroups to root the tree.

Results and Discussion

Based on phylogenies inferred from the structural and non-structural regions, the results pointed differential levels of resolution and rearrangement of the parental sequences as recombinant sequences were eliminated depending on the analyzed partition. This was clearly seen given the pattern of phylogenetic relationships between Philippines84 with Nauru74 and ARG992 strains which are closely related in the region encoding the capside. On the other hand, from the region encoding the membrane (prM/M) protein the Philippines84 strain diverges to associate with Thailand80 strain while the region coding for envelope (E) protein and at the junction with the membrane protein (preM/E), Phylippines84 is reassociated with both viral sequences Nauru74 and Thailand80 which indicates these sequences as parental of Philippines84 in a higher or lower component depending on the partition analyzed and corroborates Philippines84 as descendant of one ancestor that derived independently.
Moreover, despite the reassociations between Thailand80 strains with Philippines84, this was never dissociated from its parental sequence Jamaica77 which indicates an important contribution of this sequence to the genetic diversity of Thailand80. Concerning the strain BR 90, although suggested by Woorobey et al. (1999) no clearly evidenced the pattern of relationships with its parental sequences Jamaica77 and Singapore90 when new sequences are incorporated into the analysis, however seems that Jamaica77 classified as genotype VI represent a significant component in the C and preM regions while Singapore90 classified as genotype I, contributes most notably to E and junction preM/E regions. Such discordant relationships and different topologies between regions within the same sequence may suggest the existence of intra-serotype mosaic genomes produced by recombination between divergent parent lineages (Worebey and Holmes, 1999).

Similarly for GD23_95 strain, phylogenetic trees based on recombinants and non-recombinants regions showed that the variation in the sequence on the topology generated under Parsimony criterion is nor a strong indication of its recombinant condition, opposite to that found by Chen et al. (2008) by the neighbor-joining method, then such a definition could be an artifact. Additionally, given the elimination of the putative recombinant sequences on the topology, we often observe an improvement in the resolution of phylogenetic relationships, except in the preM region where three sequences were localizated in the same clade. Nonetheless this response was nor evident on topologies where the GD23_95 strain was eliminated, which could promote a false positive. Finally, it is important to note that although not recover a general pattern of phylogenetic relationships, each partition reflects a hypothesis that despite being different between these may be clouded by the presence of recombinant sequences which may contain regions with very different evolutionary histories within individual strains present.


Phylogenetic approaches can provide a method for detecting and characterizing recombination events among conflicting phylogenetic signals in gene sequence data with different patterns of relationship for different sequence regions in Dengue viruses, however, is necessary be careful in the some affirmations about recombinant events given that different regions pointed different patterns of phylogenetic relationships and regions non-recombinants don’t imply resolution on this relationships.

Lai, M.M.C., 1992. RNA recombination in animal and plant viruses. Microbiol. Rev. 56, 61–79.
Mahy, B., 2009. The Dictionary of virology. Elsevier, 4ed. 518p.
Wiuf, C. & Hein, J., 2000. Genetics 155, 451–462.
Worobey, M., Rambaut, A., Holmes, E.C., 1999. Widespread intraserotype recombination in natural populations of dengue virus. Proc. Natl. Acad. Sci. U.S.A. 96, 7352–7357.
Worobey, M., Holmes, E.C., 1999. Evolutionary aspects of recombination in RNA viruses. Mol. Journal of General Virology , 80, 2535±2543
Delimitation biological species in genus
Acanthoxyla (Phasmidae) using
mitochondrial and nuclear DNA
Gualdrón-Diaz J. C.

1. Introduction

From the broader perspective of evolutionary theory, delimiting species is im-
portant in the context of understanding many evolutionary mechanism and pro-
cesses(Sites & Marshall, 2003). The species boundary will define the limist
within or across which evolutionary processes operate (Barton & Gale , 1993).
Species are also routinely used as fundamental units of analysis in biogeogra-
phy, ecology, macroevolution and conservation biology (Brown et al., 1996) and
a better understanding of these larger scale processes requires that systema-
tists employ methods to delimit objectively and rigorously what species are in
There have been many proposals for the conceptual and practical handling of
species and among these, the biological species concept (Mayr, 1942) has been
the most thoroughly promoted and most widely accepted. One of the more
frequently stated deficiencies of the BSC is its inapplicability to uniparental
organisms (Foottit, 1997). The parthenogenesis is a common phenomenon in
the Animal Kingdom. It has been estimated that there are over 1000 obligately
parthenogenetic species situated over a broad range of taxa and over 15000
species which reproduce by cyclic parthenogenesis (White, 1978; Bell, 1982).
In stick insects(phasmids) the hybrid speciation and parthenogenesis both
appear to be unusually common phenomena (Bullini, 1994). In New Zealand
thera are parthenogenetic populations of otherwise sexual species of Clitarchus
and Argosarchus (Salmon, 1991). However, genus Acanthoxyla is entirely parthenogenetic. It comprises eight species without males and no closely related bisexual species (Jewell & Brock, 2002). This eight Acanthoxyla species exhibit a degree of morphological diversity not evident in any other New Zealand stick insects genus (Morgan & Trewick, 2005). The aim of this work is to make a nested clade analysis and phylogeography of haplotypes using nuclear and mitochondrial DNA to delineate species Acanthoxyla (Phasmatidae).

2. Materials and Methods

Five different genes of the genera Acanthoxyla and Clitarchus were used. 21
localities of New Zealand and 171 sequences in total of both genera were ana-
lyzed (fig. 1). Three were sequences nuclear genes, elongation factor 1x (EF1x),
phosphoglucose isomerase(PGI) and the large ribosomal subunit (28S) and two
were mitochondrial, cytochrome oxidase subunits I and II (COI-II) listed in
Buckley et al. (2008). The sequences have been deposited in GenBank under
accession EU492930-EU493090; Two operational criteria to delimit specie were
used, nested clade analysis (NCA)and phylogeographic analysis sensu Avise.
The nucleotide sequences were aligned using multiple alignment with Mus-
cle 3.6 software package. The nested clade analysis conducted using the ANECA software, which implements programs TCSv2.1 and GEODIS for analysis(Panchal, 2007). Haplotype networks were reconstructed in TCS v2.1. Then examined the relationship between haplotype/clades and geography through a statistical analysis of permutations, using the program GEODIS. For the phylogeographic analysis sensu Avise (Avise et al, 1987): ML bootstrap analysis (1000 permutations) were realized using the softwate Phyml 3.0 (Guindon & Gascuel, 2003).

3 Results and Discussion

3.1 Nested clade analysis

The cladistic analysis of haplotypes for mitochondrial genes shows 10 clades for
both COI and COII, in terms of nuclear genes, 28S, PGI and EF1x, there are
9, 11 and 7 respectively clades, but none of them considers the fragmentation
allopatric pattern as inferred from the clades formed. Therefore can not assign
the species status of these genera using this method since only fragmentation
allopatric is the important biological implication of the NCA to infer species
status (Templeton 2001).
Patterns inferred from the clades formed were restricted gene flow with iso-
lation by distance, contiguous range expansion and restricted gene flow with
isolation by distance (restricted dispersal by distance in non-sexual species) for
COII genes, EF1x and PGI, respectively. The 28S and COI gene showed Incon-
clusive outcome.

3.2 Phylogeographic analysis sensu Avise

The phylogeographic analysis, with mitochondrial genes (COI-COII) reveals the
presence of two different groups, which have a high value of confidence limits
(fig. 2-3), according to Avise (1995) assert that to infer species status requires a
confidence limit ( 95%) therefore they deserve the status of species. By contrast
with the results obtained using nuclear DNA cladograms show low resolution
and with diverging results obtained with mitochondrial DNA, in the analysis
with the 28S gene, showed levels very low limits of confidence, the evidence
suggests an clagograma unresolved with this type of gene. Similar results were
obtained through EF1x and PGI genes, however these if you showed higher
values of confidence limit (fig. 4-6).

Given the resutlados obtained, it appears that for the nested clade analsis
neither nuclear nor mitochondrial DNA showed species status. As for the re-
sults obtained with the phylogeographic analysis, differences in the phylogenetic relationships of the genus Acanthoxyla haplotypes generated with mitochondrial DNA with respect to nuclear. The mitochondrial DNA results show that only A. inermis and A. geisovii deserve species status.

4. References

Avise, J. C., Arnold, J., Ball, R. M., Bermingham, E., Lamb, T., Neigel, L. E., Reeb, C. A. & Saunders, N. C., 1987. Intraspecific phylogeography: The mitocondrial DNA bridge between population ge­netics and systematics. Annual Review in Ecology and Systematics, 18: 489–522.

Bell, G. 1982. The Masterpiece of Nature. The Evolution and Genetics of Sexuality, University of California Press, Berkeley and Los Angeles

Buckley T.R., Attanayake D., Park D., Ravidran S., Jewell T.R., Normark B.B. 2008. Investigating hybridization in the parthenogenetic New Zealand stick insects Acanthoxyla (Phasmatodea) using single-copy nuclear loci. Molecular Phylogenetics and Evolution 48: 335-349.

Bullini L. 1994. Origin and evolution of animal hybrid species. Trends Ecol. Evol. 9:422-426.

Guindon S. & Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Systematic Biology, 52(5):696-704, 2003.

Jewell T., Brock, P.D. 2002. A review of the New Zealand stick insects: new genera synonymy, keys and a catalogue. J. Orthopteran Res. 11, 189-197.

Mayr, E. 1942. Systematics and the Origin of Species from the Viewpoint of a Zoologist. Columbia University Press: New York.

Panchal, M. (2007), 'The automation of Nested Clade Phylogeographic Analysis', bioinformatics 23, 509-510.

Salmon, J.T., 1991. The Stick Insects of New Zealand. Redd, Auckland, New Zealand.

Sites J. W. Jr., Marshall J. C. 2003. Delimiting species: A Renaissance issue in systematic biology. Trends Ecol. Evol. ;18:462-470.

Templeton AR (2001) Using phylogeographic analyses of gene trees to test species status and processes. Molecular Ecology, 10, 779–791.

White, M.J.D. 1978. Modes of Speciation, W.H, Freeman and Company, San Francisco.

5. Figures

Figure 1. Map of New Zealand showing sampling localities

Figura 2. Maximun likelihood gene trees for the mtDNA data (COII). Numbers above branches are bootstrap value.

Figura 3. Maximun likelihood gene trees for the mtDNA data (COI). Numbers above branches are bootstrap value.

Figura 4. Maximun likelihood gene trees for the 28S data. Numbers above branches are bootstrap value

Figura 5. Maximun likelihood gene trees for the PGI data. Numbers above branches are bootstrap value.

Figura 6. Maximun likelihood gene trees for the EF1 data. Numbers above branches are bootstrap value.