Steps toward accurate reconstructions of phylogenies from gene-order data

Moret, Bernard M. E.; Tang, Jijun; Wang, Li-San; Warnow, Tandy

doi:10.1016/s0022-0000(02)00007-7

Cited by 90 publications

(81 citation statements)

References 26 publications

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“…Conveniently, rearrangements (as measured by the breakpoint dissoftware has been developed to facilitate this calculation tance) that have occurred along each branch. This sug- (Moret et al 2002).…”

Section: T He Organization Of the Mitochondrial Genome Amongmentioning

confidence: 96%

“…The RGR assesses whether one genome is significantly more rearranged than anisons suggested that the relative positions of genes were similarly highly conserved, at least when comparisons other. Although developed for comparisons of the mitochondrial genome, it may also prove useful for assessing within phyla were made (Moritz et al 1987). However, more recent studies have exposed many exceptions to the statistical significance of differences in the relative rate of nuclear gene rearrangement (e.g., Coghlan and this prediction ( et al 1999) genome rearrangement, but in both cases no attempts at nomic lineages [e.g., within the Hymenoptera, Apocrita (Dowton and Austin 1999) and the nonhemipteran assessing the significance of any differences were made.…”

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confidence: 99%

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Assessing the Relative Rate of (Mitochondrial) Genomic Change

Dowton

2004

Genetics

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I report a framework for assessing whether one mitochondrial genome is significantly more rearranged than another. This relative rate of gene rearrangement test (RGR) behaves according to expectation, distinguishing between highly rearranged and mildly rearranged insect mitochondrial genomes. It may be more broadly applied to assess the relative rate of nuclear gene rearrangement. T HE organization of the mitochondrial genome amongMartin and Palumbi 1993; Rand 1994)-have been greatly facilitated by the availability of a test to compare Metazoa is remarkably uniform. Of the Ͼ300 entirely sequenced mitochondrial genomes, the vast majority statistically the relative rate of nucleotide substitution.Here, I present the framework for a relative rate of gene contain the same 37 genes, are circular, and have very little noncoding sequence (Boore 1999). Early comparrearrangement test (RGR). The RGR assesses whether one genome is significantly more rearranged than anisons suggested that the relative positions of genes were similarly highly conserved, at least when comparisons other. Although developed for comparisons of the mitochondrial genome, it may also prove useful for assessing within phyla were made (Moritz et al. 1987). However, more recent studies have exposed many exceptions to the statistical significance of differences in the relative rate of nuclear gene rearrangement (e.g., Coghlan and this prediction ( et al. 1999) genome rearrangement, but in both cases no attempts at nomic lineages [e.g., within the Hymenoptera, Apocrita (Dowton and Austin 1999) and the nonhemipteran assessing the significance of any differences were made. The framework for the RGR follows that developed hemipteroids (Shao et al. 2001b), and the Crustacea, Anomura (Morrison et al. 2002)], leading to speculaby Tajima (1993) to assess the relative rate of nucleotide substitution between two sequences. A comparison of tion that the rate of gene rearrangement is not uniform, but may sporadically increase or decrease during evolutwo sequences can reveal only the absolute number of differences between those two sequences. To determine tion.However, there is currently no means of assessing the whether one sequence is accumulating more substitusignificance of any rearrangement rate increase or detions than another, reference to a third sequence is crease-either lineages have highly rearranged genomes necessary (Figure 1). or they do not. It would be extremely useful to identify m 1 (the number of substitutions between sequence 1 the branches of the metazoan mitochondrial phylogeny and the reference sequence) and m 2 can be measured with significantly increased rates of rearrangement, as directly, and the relative rate of nucleotide divergence this would facilitate investigations of the underlying facis estimated by subtracting these two values. The signifitors associated with such rate changes. Analogously, cance of this value is assessed by performing a chi-square studies identifying factors associated with increased test, with 1 d.f.,...

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Section: T He Organization Of the Mitochondrial Genome Amongmentioning

confidence: 96%

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confidence: 99%

Assessing the Relative Rate of (Mitochondrial) Genomic Change

Dowton

2004

Genetics

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“…in GRAPPA (Moret et al, 2002) can be computed efficiently and are used as input to standard distance methods such as neighbor-joining (Saitou and Nei, 1987). A Bayesian method of this type is described by Larget and Simon (2002).…”

Section: Introductionmentioning

confidence: 99%

Alignments of mitochondrial genome arrangements: Applications to metazoan phylogeny

Fritzsch

Schlegel

Stadler

2006

Journal of Theoretical Biology

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Mitochondrial genomes provide a valuable dataset for phylogenetic studies in particular of metazoan phylogeny because of the extensive taxon sample that is available. Beyond the traditional sequence based analysis it is possible to extract phylogenetic information from the gene order. Here we present a novel approach utilizing these data based on cyclic list alignments of the gene orders. A progressive alignment approach is used to combined pairwise list alignments into a multiple alignment of gene orders. Parsimony methods are used to reconstruct phylogenetic trees, ancestral gene orders, and consensus patterns in a straightforward approach. We apply this method to study the phylogeny of protostomes based exclusively on mitochondrial genome arrangements.

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“…Many biologists have embraced this new source of data in their phylogenetic work [7,17,18], while computer scientists are slowly solving the difficult problems posed by the manipulations of these gene orders [16]. Studies conducted by our group [15,26,[29][30][31] confirm that gene-order data support very accurate reconstructions.…”

Section: Introductionmentioning

confidence: 99%

“…GRAPPA achieved a billion-fold speed-up over BPAnalysis [15]; it can analyze datasets of 13 organellar genomes in 20 minutes on a laptop. Extensive testing has shown that the trees returned by GRAPPA are better than those returned by other methods based on gene orders, such as distance-based methods and parsimony based on encodings [6,31].…”

Section: Introductionmentioning

confidence: 99%

Quartet-Based Phylogeny Reconstruction from Gene Orders

Liu

Tang

Moret

2005

Lecture Notes in Computer Science

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Abstract. Phylogenetic reconstruction based on gene rearrangements is attracting increasing attention from biologists and computer scientists. Methods used in reconstruction include distance-based methods, parsimony methods using sequence encodings, and direct optimization. The latter, pioneered by Sankoff and extended by us with the software suite GRAPPA, is the most accurate approach; however, its exhaustive nature means that it can be applied only to small datasets (of fewer than 15 taxa). While we have successfully scaled it up to 1,000 taxa by integrating it with a disk-covering method, yielding DCM-GRAPPA, the recursive decomposition in the DCM may require many levels of recursion to handle datasets with 1,000 or more taxa. In order to handle larger datasets and reduce the need for recursive decomposition, we investigate quartet-based approaches, which directly decompose the datasets into subsets of four taxa each. Such approaches have been well studied for sequence data, but not for gene-order data. We give an optimization algorithm for the NP-hard problem of computing optimal trees for each quartet, present a variation of the dyadic method (using heuristics to choose suitable short quartets), and use both in simulation studies. We find that our quartet-based method can handle more taxa than the base version of GRAPPA, thus enabling us to reduce the number of levels of recursion in DCM-GRAPPA, but is more sensitive to the rate of evolution, with error rates rapidly increasing when saturation is approached.

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Steps toward accurate reconstructions of phylogenies from gene-order data

Cited by 90 publications

References 26 publications

Assessing the Relative Rate of (Mitochondrial) Genomic Change

Assessing the Relative Rate of (Mitochondrial) Genomic Change

Alignments of mitochondrial genome arrangements: Applications to metazoan phylogeny

Quartet-Based Phylogeny Reconstruction from Gene Orders

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