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A continental-wide perspective: the genepool of nuclear encoded ribosomal DNA and single-copy gene sequences in North American Boechera (Brassicaceae).

Kiefer C, Koch MA - PLoS ONE (2012)

Bottom Line: Together with the network analysis confirming this result this can be interpreted as an indication for multiple, independent, and rapid diversification events.Our results provide first direct evidence for enormous reticulate evolution in the entire genus and give further insights into the evolutionary history of this complex genus on a continental scale.In addition two novel single-copy gene markers, orthologues of the Arabidopsis thaliana genes At2g25920 and At3g18900, were analyzed for subsets of taxa and confirmed the findings obtained through the ITS data.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.

ABSTRACT
74 of the currently accepted 111 taxa of the North American genus Boechera (Brassicaceae) were subject to pyhlogenetic reconstruction and network analysis. The dataset comprised 911 accessions for which ITS sequences were analyzed. Phylogenetic analyses yielded largely unresolved trees. Together with the network analysis confirming this result this can be interpreted as an indication for multiple, independent, and rapid diversification events. Network analyses were superimposed with datasets describing i) geographical distribution, ii) taxonomy, iii) reproductive mode, and iv) distribution history based on phylogeographic evidence. Our results provide first direct evidence for enormous reticulate evolution in the entire genus and give further insights into the evolutionary history of this complex genus on a continental scale. In addition two novel single-copy gene markers, orthologues of the Arabidopsis thaliana genes At2g25920 and At3g18900, were analyzed for subsets of taxa and confirmed the findings obtained through the ITS data.

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Statistical Parsimony network based on the 24 most frequent ITS types.The nodes of the network have been replaced by pie diagrams depicting ITS type sharing by different taxa; taxa which occurred only once or twice all over the network are coloured in grey (light gray 1, dark grey 2); the overall frequency of the ITS types is given within the pie charts.
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pone-0036491-g001: Statistical Parsimony network based on the 24 most frequent ITS types.The nodes of the network have been replaced by pie diagrams depicting ITS type sharing by different taxa; taxa which occurred only once or twice all over the network are coloured in grey (light gray 1, dark grey 2); the overall frequency of the ITS types is given within the pie charts.

Mentions: The 24 ITS types, on which the most simplified network was based, were selected according to their frequency (>5), their position in the Bayesian analysis (on the large polytomy or basal in a lineage containing several ITS types) and their central position in the network based on 149 ITS types. Those selection criteria were applied in order to get an easier insight into the relationship only of ancestral ITS types in a form which also allowed the presentation of ITS type sharing among taxa. The network based on those 24 ITS types contained resolved as well as reticulate connections (Figure 1). ITS type H (most frequent and most shared in the dataset) was found to be central to the network. Clockwise the following lineages (in the sense of connections) directly derived from ITS type H could be identified: a lineage comprising the ITS types AD (n = 34), ER (n = 16) and AB (n = 7); a lineage represented by ITS type I only (n = 13); a lineage comprising ITS types GX (n = 15) and AR (n = 6); a lineage comprising ITS types AC (n = 14), AU (n = 13) and EU (n = 9). The relationships between the other lineages were more complex. ITS types F (n = 21), G (n = 16), BT (n = 19) and Z (n = 9) were derived from H but had also reticulate connections among each other. ITS type F was connected to H by one missing ITS type and to G (n = 16). G was also connected to BT (n = 19) and BT to Z (n = 9) by three missing ITS types. Z in turn was connected to H and the lineage of ITS type OG by four mutational steps which closed the circle connection of these ITS types. From the missing ITS type connecting H and F, a lineage comprising ITS types V (n = 11), T (n = 16), AZ (n = 20), E (n = 36), L (n = 34), C (n = 16) and R (n = 7) was derived. This lineage was unique because it was almost specific to Boechera stricta, a well defined sexual species, and its putative hybrid Boechera “divaricarpa”. The aforementioned ITS type F (n = 21) was ancestor to ITS type EV (n = 26). ITS type BX (n = 6) was derived from ITS type BT.


A continental-wide perspective: the genepool of nuclear encoded ribosomal DNA and single-copy gene sequences in North American Boechera (Brassicaceae).

Kiefer C, Koch MA - PLoS ONE (2012)

Statistical Parsimony network based on the 24 most frequent ITS types.The nodes of the network have been replaced by pie diagrams depicting ITS type sharing by different taxa; taxa which occurred only once or twice all over the network are coloured in grey (light gray 1, dark grey 2); the overall frequency of the ITS types is given within the pie charts.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3351400&req=5

pone-0036491-g001: Statistical Parsimony network based on the 24 most frequent ITS types.The nodes of the network have been replaced by pie diagrams depicting ITS type sharing by different taxa; taxa which occurred only once or twice all over the network are coloured in grey (light gray 1, dark grey 2); the overall frequency of the ITS types is given within the pie charts.
Mentions: The 24 ITS types, on which the most simplified network was based, were selected according to their frequency (>5), their position in the Bayesian analysis (on the large polytomy or basal in a lineage containing several ITS types) and their central position in the network based on 149 ITS types. Those selection criteria were applied in order to get an easier insight into the relationship only of ancestral ITS types in a form which also allowed the presentation of ITS type sharing among taxa. The network based on those 24 ITS types contained resolved as well as reticulate connections (Figure 1). ITS type H (most frequent and most shared in the dataset) was found to be central to the network. Clockwise the following lineages (in the sense of connections) directly derived from ITS type H could be identified: a lineage comprising the ITS types AD (n = 34), ER (n = 16) and AB (n = 7); a lineage represented by ITS type I only (n = 13); a lineage comprising ITS types GX (n = 15) and AR (n = 6); a lineage comprising ITS types AC (n = 14), AU (n = 13) and EU (n = 9). The relationships between the other lineages were more complex. ITS types F (n = 21), G (n = 16), BT (n = 19) and Z (n = 9) were derived from H but had also reticulate connections among each other. ITS type F was connected to H by one missing ITS type and to G (n = 16). G was also connected to BT (n = 19) and BT to Z (n = 9) by three missing ITS types. Z in turn was connected to H and the lineage of ITS type OG by four mutational steps which closed the circle connection of these ITS types. From the missing ITS type connecting H and F, a lineage comprising ITS types V (n = 11), T (n = 16), AZ (n = 20), E (n = 36), L (n = 34), C (n = 16) and R (n = 7) was derived. This lineage was unique because it was almost specific to Boechera stricta, a well defined sexual species, and its putative hybrid Boechera “divaricarpa”. The aforementioned ITS type F (n = 21) was ancestor to ITS type EV (n = 26). ITS type BX (n = 6) was derived from ITS type BT.

Bottom Line: Together with the network analysis confirming this result this can be interpreted as an indication for multiple, independent, and rapid diversification events.Our results provide first direct evidence for enormous reticulate evolution in the entire genus and give further insights into the evolutionary history of this complex genus on a continental scale.In addition two novel single-copy gene markers, orthologues of the Arabidopsis thaliana genes At2g25920 and At3g18900, were analyzed for subsets of taxa and confirmed the findings obtained through the ITS data.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Developmental Biology, Max Planck Institute for Plant Breeding Research, Cologne, Germany.

ABSTRACT
74 of the currently accepted 111 taxa of the North American genus Boechera (Brassicaceae) were subject to pyhlogenetic reconstruction and network analysis. The dataset comprised 911 accessions for which ITS sequences were analyzed. Phylogenetic analyses yielded largely unresolved trees. Together with the network analysis confirming this result this can be interpreted as an indication for multiple, independent, and rapid diversification events. Network analyses were superimposed with datasets describing i) geographical distribution, ii) taxonomy, iii) reproductive mode, and iv) distribution history based on phylogeographic evidence. Our results provide first direct evidence for enormous reticulate evolution in the entire genus and give further insights into the evolutionary history of this complex genus on a continental scale. In addition two novel single-copy gene markers, orthologues of the Arabidopsis thaliana genes At2g25920 and At3g18900, were analyzed for subsets of taxa and confirmed the findings obtained through the ITS data.

Show MeSH