Limits...
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.

Show MeSH

Related in: MedlinePlus

Neighbor-Net splits graph based on PBC-inferred distances: Acer section Acer. This graph largely agrees with the results of [9]: Individuals (bold labels) of the same taxon ('species') and intrasectional group (A0 to B4) cluster together. The position of potentially hybrid individuals (hd 1, of 2, sv4b) is pronounced and is directly visible from the graph because of the large proximal box-like portions. These hybrid individuals exhibit ITS clones of different evolutionary origin (ITS homoeologues), highlighted for the example of individual sv4b. Clones of this individual either represented A. ibericum-type or group B1-type homoeologues. Related edge bundles (reddish, bluish) can be addressed in the graph. Green squares correspond to individuals that exhibited recombinant (chimeric) clones (see text).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2291458&req=5

Figure 9: Neighbor-Net splits graph based on PBC-inferred distances: Acer section Acer. This graph largely agrees with the results of [9]: Individuals (bold labels) of the same taxon ('species') and intrasectional group (A0 to B4) cluster together. The position of potentially hybrid individuals (hd 1, of 2, sv4b) is pronounced and is directly visible from the graph because of the large proximal box-like portions. These hybrid individuals exhibit ITS clones of different evolutionary origin (ITS homoeologues), highlighted for the example of individual sv4b. Clones of this individual either represented A. ibericum-type or group B1-type homoeologues. Related edge bundles (reddish, bluish) can be addressed in the graph. Green squares correspond to individuals that exhibited recombinant (chimeric) clones (see text).

Mentions: Naturally, the similarity between the reconstructed networks correlates with the congruence between the underlying distance matrices. The four transformation methods (FRQ, MIN, MOD and PBC) that resulted in high correlations with morphology and in low DV produced very similar Neighbor-Net splits graphs (details not shown, but Additional file 1 contains all distance matrices calculated for import in SplitsTree, as well as the pair-wise correlations between all distance matrices). In the following, we thus focus on the description of the networks based on PBC distances. The PBC-inferred network of Acer section Acer (Fig. 9) exhibited two general elements. First, genetically unambiguous individuals (or local groups of co-occurring, taxonomically identical individuals) clustered according to their taxonomic affiliations ("species" and "subspecies") and the intra-sectional groups A0 to B4 (Fig. 9). Each group, except for group B2, was characterized by prominent parallel edges and a rather treelike appearance in the corresponding portions of the graph. Second, three individuals were placed as terminals of large box-like structures: (1) hd 1, representing a putative hybrid of A. heldreichii and A. pseudoplatanus (A. × pseudo-heldreichii), (2) of 2, material from a historical herbarium sheet of A. obtusifolium from Syria, and (3) sv4b, a morphologically unequivocal A. sempervirens individual from Crete. All three individuals were characterized by potential ITS homoeologues [9]. Aside these two major features, the following could be observed: The individual us 11, taxonomically treated as A. cf. monspessulanum, was placed near the center of the graph; the most prominent edge bundles related it to group B1 or A2. The center of the graph was dominated by relatively short edges; however, the two most prominent central edges related group B1 to group B2, and group A1 to the (potential) outgroup A0.


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)

Neighbor-Net splits graph based on PBC-inferred distances: Acer section Acer. This graph largely agrees with the results of [9]: Individuals (bold labels) of the same taxon ('species') and intrasectional group (A0 to B4) cluster together. The position of potentially hybrid individuals (hd 1, of 2, sv4b) is pronounced and is directly visible from the graph because of the large proximal box-like portions. These hybrid individuals exhibit ITS clones of different evolutionary origin (ITS homoeologues), highlighted for the example of individual sv4b. Clones of this individual either represented A. ibericum-type or group B1-type homoeologues. Related edge bundles (reddish, bluish) can be addressed in the graph. Green squares correspond to individuals that exhibited recombinant (chimeric) clones (see text).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 9: Neighbor-Net splits graph based on PBC-inferred distances: Acer section Acer. This graph largely agrees with the results of [9]: Individuals (bold labels) of the same taxon ('species') and intrasectional group (A0 to B4) cluster together. The position of potentially hybrid individuals (hd 1, of 2, sv4b) is pronounced and is directly visible from the graph because of the large proximal box-like portions. These hybrid individuals exhibit ITS clones of different evolutionary origin (ITS homoeologues), highlighted for the example of individual sv4b. Clones of this individual either represented A. ibericum-type or group B1-type homoeologues. Related edge bundles (reddish, bluish) can be addressed in the graph. Green squares correspond to individuals that exhibited recombinant (chimeric) clones (see text).
Mentions: Naturally, the similarity between the reconstructed networks correlates with the congruence between the underlying distance matrices. The four transformation methods (FRQ, MIN, MOD and PBC) that resulted in high correlations with morphology and in low DV produced very similar Neighbor-Net splits graphs (details not shown, but Additional file 1 contains all distance matrices calculated for import in SplitsTree, as well as the pair-wise correlations between all distance matrices). In the following, we thus focus on the description of the networks based on PBC distances. The PBC-inferred network of Acer section Acer (Fig. 9) exhibited two general elements. First, genetically unambiguous individuals (or local groups of co-occurring, taxonomically identical individuals) clustered according to their taxonomic affiliations ("species" and "subspecies") and the intra-sectional groups A0 to B4 (Fig. 9). Each group, except for group B2, was characterized by prominent parallel edges and a rather treelike appearance in the corresponding portions of the graph. Second, three individuals were placed as terminals of large box-like structures: (1) hd 1, representing a putative hybrid of A. heldreichii and A. pseudoplatanus (A. × pseudo-heldreichii), (2) of 2, material from a historical herbarium sheet of A. obtusifolium from Syria, and (3) sv4b, a morphologically unequivocal A. sempervirens individual from Crete. All three individuals were characterized by potential ITS homoeologues [9]. Aside these two major features, the following could be observed: The individual us 11, taxonomically treated as A. cf. monspessulanum, was placed near the center of the graph; the most prominent edge bundles related it to group B1 or A2. The center of the graph was dominated by relatively short edges; however, the two most prominent central edges related group B1 to group B2, and group A1 to the (potential) outgroup A0.

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