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General functions to transform associate data to host data, and their use in phylogenetic inference from sequences with intra-individual variability.

Göker M, Grimm GW - BMC Evol. Biol. (2008)

Bottom Line: The results agree well with these three measures and the datasets examined as well as with the theoretical predictions and previous results in the literature.Regarding cloned sequences, the formulae have a high potential to accurately reflect evolutionary relationships within angiosperm genera, and to identify hybrids and ancestral taxa.These results corroborate earlier ones which showed that treelikeness measures are a valuable tool in comparative studies of biological distance functions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Organismic Botany, Eberhard-Karls-University, Auf der Morgenstelle 1, Tübingen, Germany. markus.goeker@uni-tuebingen.de

ABSTRACT

Background: Amongst the most commonly used molecular markers for plant phylogenetic studies are the nuclear ribosomal internal transcribed spacers (ITS). Intra-individual variability of these multicopy regions is a very common phenomenon in plants, the causes of which are debated in literature. Phylogenetic reconstruction under these conditions is inherently difficult. Our approach is to consider this problem as a special case of the general biological question of how to infer the characteristics of hosts (represented here by plant individuals) from features of their associates (represented by cloned sequences here).

Results: Six general transformation functions are introduced, covering the transformation of associate characters to discrete and continuous host characters, and the transformation of associate distances to host distances. A pure distance-based framework is established in which these transformation functions are applied to ITS sequences collected from the angiosperm genera Acer, Fagus and Zelkova. The formulae are also applied to allelic data of three different loci obtained from Rosa spp. The functions are validated by (1) phylogeny-independent measures of treelikeness; (2) correlation with independent host characters; (3) visualization using splits graphs and comparison with published data on the test organisms. The results agree well with these three measures and the datasets examined as well as with the theoretical predictions and previous results in the literature. High-quality distance matrices are obtained with four of the six transformation formulae. We demonstrate that one of them represents a generalization of the Sørensen coefficient, which is widely applied in ecology.

Conclusion: Because of their generality, the transformation functions may be applied to a wide range of biological problems that are interpretable in terms of hosts and associates. Regarding cloned sequences, the formulae have a high potential to accurately reflect evolutionary relationships within angiosperm genera, and to identify hybrids and ancestral taxa. These results corroborate earlier ones which showed that treelikeness measures are a valuable tool in comparative studies of biological distance functions.

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Gap treatment vs. Delta values. Delta values plotted against the gap treatment applied in CON or MOD character-character transformations and in computation of p distances. For further explanations, see legend to Fig. 2.
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Figure 4: Gap treatment vs. Delta values. Delta values plotted against the gap treatment applied in CON or MOD character-character transformations and in computation of p distances. For further explanations, see legend to Fig. 2.

Mentions: The different character and distance transformation functions resulted in even more pronounced differences regarding the treelikeness of the matrices (Fig. 3). ENT distances rather uniformly produced high DV (0.293–0.329). Treelikeness of CON matrices was even lower in some cases, whereas variability was much higher (0.216 – 0.346). MIN and PBC DV were generally much lower and similar in size to each other, but variability was more pronounced in the latter. MOD and FRQ achieved the lowest DV and were also similar in the variance of their treelikeness. In general, DV were lower if distance matrices were inferred and gaps were treated as a 5thcharacter state (Fig. 4).


General functions to transform associate data to host data, and their use in phylogenetic inference from sequences with intra-individual variability.

Göker M, Grimm GW - BMC Evol. Biol. (2008)

Gap treatment vs. Delta values. Delta values plotted against the gap treatment applied in CON or MOD character-character transformations and in computation of p distances. For further explanations, see legend to Fig. 2.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2291458&req=5

Figure 4: Gap treatment vs. Delta values. Delta values plotted against the gap treatment applied in CON or MOD character-character transformations and in computation of p distances. For further explanations, see legend to Fig. 2.
Mentions: The different character and distance transformation functions resulted in even more pronounced differences regarding the treelikeness of the matrices (Fig. 3). ENT distances rather uniformly produced high DV (0.293–0.329). Treelikeness of CON matrices was even lower in some cases, whereas variability was much higher (0.216 – 0.346). MIN and PBC DV were generally much lower and similar in size to each other, but variability was more pronounced in the latter. MOD and FRQ achieved the lowest DV and were also similar in the variance of their treelikeness. In general, DV were lower if distance matrices were inferred and gaps were treated as a 5thcharacter state (Fig. 4).

Bottom Line: The results agree well with these three measures and the datasets examined as well as with the theoretical predictions and previous results in the literature.Regarding cloned sequences, the formulae have a high potential to accurately reflect evolutionary relationships within angiosperm genera, and to identify hybrids and ancestral taxa.These results corroborate earlier ones which showed that treelikeness measures are a valuable tool in comparative studies of biological distance functions.

View Article: PubMed Central - HTML - PubMed

Affiliation: Organismic Botany, Eberhard-Karls-University, Auf der Morgenstelle 1, Tübingen, Germany. markus.goeker@uni-tuebingen.de

ABSTRACT

Background: Amongst the most commonly used molecular markers for plant phylogenetic studies are the nuclear ribosomal internal transcribed spacers (ITS). Intra-individual variability of these multicopy regions is a very common phenomenon in plants, the causes of which are debated in literature. Phylogenetic reconstruction under these conditions is inherently difficult. Our approach is to consider this problem as a special case of the general biological question of how to infer the characteristics of hosts (represented here by plant individuals) from features of their associates (represented by cloned sequences here).

Results: Six general transformation functions are introduced, covering the transformation of associate characters to discrete and continuous host characters, and the transformation of associate distances to host distances. A pure distance-based framework is established in which these transformation functions are applied to ITS sequences collected from the angiosperm genera Acer, Fagus and Zelkova. The formulae are also applied to allelic data of three different loci obtained from Rosa spp. The functions are validated by (1) phylogeny-independent measures of treelikeness; (2) correlation with independent host characters; (3) visualization using splits graphs and comparison with published data on the test organisms. The results agree well with these three measures and the datasets examined as well as with the theoretical predictions and previous results in the literature. High-quality distance matrices are obtained with four of the six transformation formulae. We demonstrate that one of them represents a generalization of the Sørensen coefficient, which is widely applied in ecology.

Conclusion: Because of their generality, the transformation functions may be applied to a wide range of biological problems that are interpretable in terms of hosts and associates. Regarding cloned sequences, the formulae have a high potential to accurately reflect evolutionary relationships within angiosperm genera, and to identify hybrids and ancestral taxa. These results corroborate earlier ones which showed that treelikeness measures are a valuable tool in comparative studies of biological distance functions.

Show MeSH
Related in: MedlinePlus