The first heuristic for reconstructing phylogenetic trees from gene order data was introduced by ... more The first heuristic for reconstructing phylogenetic trees from gene order data was introduced by Blanchette et al.. It sought to reconstruct the breakpoint phylogeny and was applied to a variety of datasets. We present a new heuristic for estimating the breakpoint phylogeny which, although not polynomial-time, is much faster in practice than BP-Analysis. We use this heuristic to conduct a phylogenetic analysis of chloroplast genomes in the flowering plant family Campanulaceae. We also present and discuss the results of experimentation on this real dataset with three methods: our new method, BPAnalysis, and the neighbor-joining method, using breakpoint distances, inversion distances, and inversion plus transposition distances.
The breakpoint phylogeny is an optimization problem proposed by Blanchette et al. for reconstruct... more The breakpoint phylogeny is an optimization problem proposed by Blanchette et al. for reconstructing evolutionary trees from gene order data. These same authors also developed and implemented BPAnalysis (3), a heuristic method (based upon solving many instances of the travelling salesman problem) for estimating the breakpoint phylogeny. We present a new heuristic for this purpose; although not polynomial-time, our heuristic
Evolution operates on whole genomes by operations that change the order and strandedness of genes... more Evolution operates on whole genomes by operations that change the order and strandedness of genes within the genomes. This type of data presents new opportunities for discoveries about deep evolutionary rearrangement events, provided that sufficiently accurate methods can be developed to reconstruct evolutionary trees in these models [3, 6, 7, 15, 17]. A necessary component of any such method is
Journal of Computer and System Sciences - JCSS, 2003
We report on our progress in reconstructing phylogenies from gene-order data. We have developed p... more We report on our progress in reconstructing phylogenies from gene-order data. We have developed polynomial-time methods for estimating genomic distances that greatly improve the accuracy of trees obtained using the popular neighbor-joining method; we have also further improved the running time of our GRAPPA software suite through a combination of tighter bounding and better use of the bounds. We present new experimental results (that extend those we presented at ISMB'01 and WABI'01) that demonstrate the accuracy and robustness of our distance estimators under a wide range of model conditions. Moreover, using the best of our distance estimators (EDE) in our GRAPPA software suite, along with more sophisticated bounding techniques, produced spectacular improvements in the already huge speedup: whereas our earlier experiments showed a one-million-fold speedup (when run on a 512-processor cluster), our latest experiments demonstrate a speedup of one hundred million. The combination of these various advances enabled us to conduct new phylogenetic analyses of a subset of the Campanulaceae family, confirming various conjectures about the relationships among members of the subset and confirming that inversion can be viewed as the principal mechanism of evolution for their chloroplast genome. We give representative results of the extensive experimentation we conducted on both real and simulated datasets in order to validate and characterize our approaches.
Evolution operates on whole genomes through direct rearrangements of genes, such as inversions, t... more Evolution operates on whole genomes through direct rearrangements of genes, such as inversions, transpositions, and inverted transposi- tions, as well as through operations, such as dupli- cations, losses, and transfers, that also affect the gene content of the genomes. Because these events are rare relative to nucleotide substitutions, gene order data offer the possibility of resolving ancient branches in the
We report on our progress in reconstructing phylogenies from gene-order data. We have developed p... more We report on our progress in reconstructing phylogenies from gene-order data. We have developed polynomial-time methods for estimating genomic distances that greatly improve the accuracy of trees obtained using the popular neighbor-joining method; we have also further improved the running time of our GRAPPA software suite through a combination of tighter bounding and better use of the bounds. We present new experimental results (that extend those we presented at ISMB'01 and WABI'01) that demonstrate the accuracy and robustness of our distance estimators under a wide range of model conditions. Moreover, using the best of our distance estimators (EDE) in our GRAPPA software suite, along with more sophisticated bounding techniques, produced spectacular improvements in the already huge speedup: whereas our earlier experiments showed a one-million-fold speedup (when run on a 512-processor cluster), our latest experiments demonstrate a speedup of one hundred million. The combination of these various advances enabled us to conduct new phylogenetic analyses of a subset of the Campanulaceae family, confirming various conjectures about the relationships among members of the subset and confirming that inversion can be viewed as the principal mechanism of evolution for their chloroplast genome. We give representative results of the extensive experimentation we conducted on both real and simulated datasets in order to validate and characterize our approaches.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2000
Multiple sequence alignment is typically the first step in estimating phylogenetic trees, with th... more Multiple sequence alignment is typically the first step in estimating phylogenetic trees, with the assumption being that as alignments improve, so will phylogenetic reconstructions. Over the last decade or so, new multiple sequence alignment methods have been developed to improve comparative analyses of protein structure, but these new methods have not been typically used in phylogenetic analyses. In this paper, we report on a simulation study that we performed to evaluate the consequences of using these new multiple sequence alignment methods in terms of the resultant phylogenetic reconstruction. We find that while alignment accuracy is positively correlated with phylogenetic accuracy, the amount of improvement in phylogenetic estimation that results from an improved alignment can range from quite small to substantial. We observe that phylogenetic accuracy is most highly correlated with alignment accuracy when sequences are most difficult to align, and that variation in alignment accuracy can have little impact on phylogenetic accuracy when alignment error rates are generally low. We discuss these observations and implications for future work.
Motivation: Phylogenetic analyses often produce thou- sands of candidate trees. Biologists resolv... more Motivation: Phylogenetic analyses often produce thou- sands of candidate trees. Biologists resolve the conflict by computing the consensus of these trees. Single-tree con- sensus as postprocessing methods can be unsatisfactory due to their inherent limitations. Results: In this paper we present an alternative approach by using clustering algorithms on the set of candidate trees. We propose bicriterion problems, in particular
We report on new techniques we have developed for reconstructing phylogenies on whole genomes. Ou... more We report on new techniques we have developed for reconstructing phylogenies on whole genomes. Our mathematical techniques include new polynomialtime methods for bounding the inversion length of a candidate tree and new polynomial-time methods for estimating genomic distances which greatly improve the accuracy of neighbor-joining analyses. We demonstrate the power of these techniques through an extensive performance study based upon simulating genome evolution under a wide range of model conditions. Combining these new tools with standard approaches (fast reconstruction with neighborjoining, exploration of all possible refinements of strict consensus trees, etc.) has allowed us to analyze datasets that were previously considered computationally impractical. In particular, we have conducted a complete phylogenetic analysis of a subset of the Campanulaceae family, confirming various conjectures about the relationships among members of the subset and about the principal mechanism of evolution for their chloroplast genome. We give representative results of the extensive experimentation we conducted on both real and simulated datasets in order to validate and characterize our approaches. We find that our techniques provide very accurate reconstructions of the true tree topology even when the data are generated by processes that include a sig-¡
Chaucer's Canterbury Tales consists of loosely-connected stories, appearing in many different ord... more Chaucer's Canterbury Tales consists of loosely-connected stories, appearing in many different orders in extant manuscripts. Differences in order result from rearrangements by scribes during copying, and may reveal relationships among manuscripts. Identifying these relationships is analogous to determining evolutionary relationships among organisms from the order of genes on a genome. We use gene order analysis to construct a stemma for the Canterbury Tales. This stemma shows relationships predicted by earlier scholars, reveals new relationships, and shares features with a word variation stemma. Our results support the idea that there was no established order when the first manuscripts were written.
Systematists study how a group of genes or organisms evolved. These biologists now have set their... more Systematists study how a group of genes or organisms evolved. These biologists now have set their sights on the Tree of Life challenge: to reconstruct the evolutionary history of all known living organisms. A typical phylogenetic reconstruction starts with biomolecular data, such as DNA sequences for modern organisms, and builds a tree, or phylogeny, for these sequences that represents a
The first heuristic for reconstructing phylogenetic trees from gene order data was introduced by ... more The first heuristic for reconstructing phylogenetic trees from gene order data was introduced by Blanchette et al.. It sought to reconstruct the breakpoint phylogeny and was applied to a variety of datasets. We present a new heuristic for estimating the breakpoint phylogeny which, although not polynomial-time, is much faster in practice than BP-Analysis. We use this heuristic to conduct a phylogenetic analysis of chloroplast genomes in the flowering plant family Campanulaceae. We also present and discuss the results of experimentation on this real dataset with three methods: our new method, BPAnalysis, and the neighbor-joining method, using breakpoint distances, inversion distances, and inversion plus transposition distances.
The breakpoint phylogeny is an optimization problem proposed by Blanchette et al. for reconstruct... more The breakpoint phylogeny is an optimization problem proposed by Blanchette et al. for reconstructing evolutionary trees from gene order data. These same authors also developed and implemented BPAnalysis (3), a heuristic method (based upon solving many instances of the travelling salesman problem) for estimating the breakpoint phylogeny. We present a new heuristic for this purpose; although not polynomial-time, our heuristic
Evolution operates on whole genomes by operations that change the order and strandedness of genes... more Evolution operates on whole genomes by operations that change the order and strandedness of genes within the genomes. This type of data presents new opportunities for discoveries about deep evolutionary rearrangement events, provided that sufficiently accurate methods can be developed to reconstruct evolutionary trees in these models [3, 6, 7, 15, 17]. A necessary component of any such method is
Journal of Computer and System Sciences - JCSS, 2003
We report on our progress in reconstructing phylogenies from gene-order data. We have developed p... more We report on our progress in reconstructing phylogenies from gene-order data. We have developed polynomial-time methods for estimating genomic distances that greatly improve the accuracy of trees obtained using the popular neighbor-joining method; we have also further improved the running time of our GRAPPA software suite through a combination of tighter bounding and better use of the bounds. We present new experimental results (that extend those we presented at ISMB'01 and WABI'01) that demonstrate the accuracy and robustness of our distance estimators under a wide range of model conditions. Moreover, using the best of our distance estimators (EDE) in our GRAPPA software suite, along with more sophisticated bounding techniques, produced spectacular improvements in the already huge speedup: whereas our earlier experiments showed a one-million-fold speedup (when run on a 512-processor cluster), our latest experiments demonstrate a speedup of one hundred million. The combination of these various advances enabled us to conduct new phylogenetic analyses of a subset of the Campanulaceae family, confirming various conjectures about the relationships among members of the subset and confirming that inversion can be viewed as the principal mechanism of evolution for their chloroplast genome. We give representative results of the extensive experimentation we conducted on both real and simulated datasets in order to validate and characterize our approaches.
Evolution operates on whole genomes through direct rearrangements of genes, such as inversions, t... more Evolution operates on whole genomes through direct rearrangements of genes, such as inversions, transpositions, and inverted transposi- tions, as well as through operations, such as dupli- cations, losses, and transfers, that also affect the gene content of the genomes. Because these events are rare relative to nucleotide substitutions, gene order data offer the possibility of resolving ancient branches in the
We report on our progress in reconstructing phylogenies from gene-order data. We have developed p... more We report on our progress in reconstructing phylogenies from gene-order data. We have developed polynomial-time methods for estimating genomic distances that greatly improve the accuracy of trees obtained using the popular neighbor-joining method; we have also further improved the running time of our GRAPPA software suite through a combination of tighter bounding and better use of the bounds. We present new experimental results (that extend those we presented at ISMB'01 and WABI'01) that demonstrate the accuracy and robustness of our distance estimators under a wide range of model conditions. Moreover, using the best of our distance estimators (EDE) in our GRAPPA software suite, along with more sophisticated bounding techniques, produced spectacular improvements in the already huge speedup: whereas our earlier experiments showed a one-million-fold speedup (when run on a 512-processor cluster), our latest experiments demonstrate a speedup of one hundred million. The combination of these various advances enabled us to conduct new phylogenetic analyses of a subset of the Campanulaceae family, confirming various conjectures about the relationships among members of the subset and confirming that inversion can be viewed as the principal mechanism of evolution for their chloroplast genome. We give representative results of the extensive experimentation we conducted on both real and simulated datasets in order to validate and characterize our approaches.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2000
Multiple sequence alignment is typically the first step in estimating phylogenetic trees, with th... more Multiple sequence alignment is typically the first step in estimating phylogenetic trees, with the assumption being that as alignments improve, so will phylogenetic reconstructions. Over the last decade or so, new multiple sequence alignment methods have been developed to improve comparative analyses of protein structure, but these new methods have not been typically used in phylogenetic analyses. In this paper, we report on a simulation study that we performed to evaluate the consequences of using these new multiple sequence alignment methods in terms of the resultant phylogenetic reconstruction. We find that while alignment accuracy is positively correlated with phylogenetic accuracy, the amount of improvement in phylogenetic estimation that results from an improved alignment can range from quite small to substantial. We observe that phylogenetic accuracy is most highly correlated with alignment accuracy when sequences are most difficult to align, and that variation in alignment accuracy can have little impact on phylogenetic accuracy when alignment error rates are generally low. We discuss these observations and implications for future work.
Motivation: Phylogenetic analyses often produce thou- sands of candidate trees. Biologists resolv... more Motivation: Phylogenetic analyses often produce thou- sands of candidate trees. Biologists resolve the conflict by computing the consensus of these trees. Single-tree con- sensus as postprocessing methods can be unsatisfactory due to their inherent limitations. Results: In this paper we present an alternative approach by using clustering algorithms on the set of candidate trees. We propose bicriterion problems, in particular
We report on new techniques we have developed for reconstructing phylogenies on whole genomes. Ou... more We report on new techniques we have developed for reconstructing phylogenies on whole genomes. Our mathematical techniques include new polynomialtime methods for bounding the inversion length of a candidate tree and new polynomial-time methods for estimating genomic distances which greatly improve the accuracy of neighbor-joining analyses. We demonstrate the power of these techniques through an extensive performance study based upon simulating genome evolution under a wide range of model conditions. Combining these new tools with standard approaches (fast reconstruction with neighborjoining, exploration of all possible refinements of strict consensus trees, etc.) has allowed us to analyze datasets that were previously considered computationally impractical. In particular, we have conducted a complete phylogenetic analysis of a subset of the Campanulaceae family, confirming various conjectures about the relationships among members of the subset and about the principal mechanism of evolution for their chloroplast genome. We give representative results of the extensive experimentation we conducted on both real and simulated datasets in order to validate and characterize our approaches. We find that our techniques provide very accurate reconstructions of the true tree topology even when the data are generated by processes that include a sig-¡
Chaucer's Canterbury Tales consists of loosely-connected stories, appearing in many different ord... more Chaucer's Canterbury Tales consists of loosely-connected stories, appearing in many different orders in extant manuscripts. Differences in order result from rearrangements by scribes during copying, and may reveal relationships among manuscripts. Identifying these relationships is analogous to determining evolutionary relationships among organisms from the order of genes on a genome. We use gene order analysis to construct a stemma for the Canterbury Tales. This stemma shows relationships predicted by earlier scholars, reveals new relationships, and shares features with a word variation stemma. Our results support the idea that there was no established order when the first manuscripts were written.
Systematists study how a group of genes or organisms evolved. These biologists now have set their... more Systematists study how a group of genes or organisms evolved. These biologists now have set their sights on the Tree of Life challenge: to reconstruct the evolutionary history of all known living organisms. A typical phylogenetic reconstruction starts with biomolecular data, such as DNA sequences for modern organisms, and builds a tree, or phylogeny, for these sequences that represents a
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