%0 Report %1 minh2007b %A Minh, Bui Quang %A Klaere, Steffen %A von Haeseler, Arndt %C Cambridge %D 2007 %K biodiversity_conservation dynamic_programming phylogenetic_diversity phylogenetic_network split_system %N NI07090 %T Phylogenetic Diversity on Split Networks %X In biodiversity conservation, one is interested in selecting a subset of taxa for preservation priority. Phylogenetic diversity (PD) provides a quantitative measure for taxon selection on phylogenetic trees. In particular, PD is the total length of the minimal subtree induced by the selected taxa. Recently, it has been shown that on trees the maximal PD score and the corresponding subset of taxa can be computed by a greedy algorithm. However, if evolution is not treelike and networks are a more appropriate illustration of phylogenetic relationships, then the greedy strategy no longer works. Here, we will extend the notion of PD to phylogenetic networks. To this end, we suggest a dynamic programming algorithm (PD-NET) which guarantees the computation of optimal PD scores and PD sets for circular networks, a commonly encountered category of networks. PD-NET has polynomial time complexity. Finally we apply PD-NET to biological data and compare the resulting PD sets to the selection of taxa derived from a tree. The outcome indicates that it is advisable to include also non-treelike effects when dealing with conservation questions.

@techreport{minh2007b, abstract = {In biodiversity conservation, one is interested in selecting a subset of taxa for preservation priority. Phylogenetic diversity (PD) provides a quantitative measure for taxon selection on phylogenetic trees. In particular, PD is the total length of the minimal subtree induced by the selected taxa. Recently, it has been shown that on trees the maximal PD score and the corresponding subset of taxa can be computed by a greedy algorithm. However, if evolution is not treelike and networks are a more appropriate illustration of phylogenetic relationships, then the greedy strategy no longer works. Here, we will extend the notion of PD to phylogenetic networks. To this end, we suggest a dynamic programming algorithm (PD-NET) which guarantees the computation of optimal PD scores and PD sets for circular networks, a commonly encountered category of networks. PD-NET has polynomial time complexity. Finally we apply PD-NET to biological data and compare the resulting PD sets to the selection of taxa derived from a tree. The outcome indicates that it is advisable to include also non-treelike effects when dealing with conservation questions.}, added-at = {2009-05-14T15:10:44.000+0200}, address = {Cambridge}, author = {Minh, Bui Quang and Klaere, Steffen and von Haeseler, Arndt}, biburl = {https://www.bibsonomy.org/bibtex/2b519a4702b80c8adc33ed1ab62f06f88/compevol}, institution = {Isaac Newton Institute}, interhash = {63abe9eb61a95438800663bfde2d7522}, intrahash = {b519a4702b80c8adc33ed1ab62f06f88}, key = {PLG}, keywords = {biodiversity_conservation dynamic_programming phylogenetic_diversity phylogenetic_network split_system}, number = {NI07090}, timestamp = {2009-05-14T15:10:44.000+0200}, title = {Phylogenetic Diversity on Split Networks}, year = 2007 }