TrExML: a maximum-likelihood approach for extensive tree-space
  exploration

Wolf, Marty J.; Easteal, Simon; Kahn, Margaret; McKay, Brendan D.; Jermiin, Lars S.

doi:10.1093/bioinformatics/16.4.383

Cited by 35 publications

(22 citation statements)

References 10 publications

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“…The asterisk shows the proposed point of genome duplication. The same topology was obtained for a tree that omitted the bottom five species, and by TREXML (18). A. gossypii data are from ref.…”

Section: Resultsmentioning

confidence: 97%

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Gene order evolution and paleopolyploidy in hemiascomycete yeasts

Wong

Butler

Wolfe

2002

Proc. Natl. Acad. Sci. U.S.A.

133

100

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The wealth of comparative genomics data from yeast species allows the molecular evolution of these eukaryotes to be studied in great detail. We used ''proximity plots'' to visually compare chromosomal gene order information from 14 hemiascomycetes, including the recent Gé nolevures survey, to Saccharomyces cerevisiae. Contrary to the original reports, we find that the Gé nolevures data strongly support the hypothesis that S. cerevisiae is a degenerate polyploid. Using gene order information alone, 70% of the S. cerevisiae genome can be mapped into ''sister'' regions that tile together with almost no overlap. This map confirms and extends the map of sister regions that we constructed previously by using duplicated genes, an independent source of information. Combining gene order and gene duplication data assigns essentially the whole genome into sister regions, the largest gap being only 36 genes long. The 16 centromere regions of S. cerevisiae form eight pairs, indicating that an ancestor with eight chromosomes underwent complete doubling; alternatives such as segmental duplications can be ruled out. Gene arrangements in Kluyveromyces lactis and four other species agree quantitatively with what would be expected if they diverged from S. cerevisiae before its polyploidization. In contrast, Saccharomyces exiguus, Saccharomyces servazzii, and Candida glabrata show higher levels of gene adjacency conservation, and more cases of imperfect conservation, suggesting that they split from the S. cerevisiae lineage after polyploidization. This finding is confirmed by sequences around the C. glabrata TRP1 and IPP1 loci, which show that it contains sister regions derived from the same duplication event as that of S. cerevisiae.

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Section: Resultsmentioning

confidence: 97%

“…The contiguous sequence between the 5Ј end of the SSU gene and the 3Ј end of the LSU gene (5,873 aligned sites) was aligned by using T COFFEE (16) and analyzed by the NJ method as implemented in CLUSTALW (17), and by TREXML (18).…”

Section: Methodsmentioning

confidence: 99%

Gene order evolution and paleopolyploidy in hemiascomycete yeasts

Wong

Butler

Wolfe

2002

Proc. Natl. Acad. Sci. U.S.A.

133

100

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“…There was substantial base composition heterogeneity at codon position 3, so nucleotides at these sites were recoded as purine/pyrimidine. The alignments were analyzed using the maximum likelihood program TrExML (Wolf et al, 2000), which implements the F84 model of nucleotide substitutions. Using an iterative approach, we estimated a transition/transversion ratio of 1.86 and relative rates of change of 2.26, 1.00, and 7.32 at codon positions 1, 2, and 3, respectively, for the species tree.…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Many Parallel Losses of infA from Chloroplast DNA during Angiosperm Evolution with Multiple Independent Transfers to the Nucleus

et al. 2001

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We used DNA sequencing and gel blot surveys to assess the integrity of the chloroplast gene infA , which codes for translation initiation factor 1, in Ͼ 300 diverse angiosperms. Whereas most angiosperms appear to contain an intact chloroplast infA gene, the gene has repeatedly become defunct in ‫ف‬ 24 separate lineages of angiosperms, including almost all rosid species. In four species in which chloroplast infA is defunct, transferred and expressed copies of the gene were found in the nucleus, complete with putative chloroplast transit peptide sequences. The transit peptide sequences of the nuclear infA genes from soybean and Arabidopsis were shown to be functional by their ability to target green fluorescent protein to chloroplasts in vivo. Phylogenetic analysis of infA sequences and assessment of transit peptide homology indicate that the four nuclear infA genes are probably derived from four independent gene transfers from chloroplast to nuclear DNA during angiosperm evolution. Considering this and the many separate losses of infA from chloroplast DNA, the gene has probably been transferred many more times, making infA by far the most mobile chloroplast gene known in plants. INTRODUCTIONMany genes have been lost from the chloroplast genome during plant and algal evolution. Most of these losses occurred in the murky interval between the original endosymbiosis of a cyanobacterium (with perhaps 2000 proteincoding genes) and the last common ancestor of all existing chloroplast genomes (with ‫ف‬ 210 protein-coding genes; . Many other genes were lost during the early evolution of photosynthetic eukaryotes, often in parallel in different algal lineages, and some of these losses were the result of gene transfers to the nuclear genome . During the evolution of land plants, relatively few changes occurred to the set of genes found in chloroplast DNA (cpDNA) Palmer and Delwiche, 1998). Nonetheless, the most recent changes are likely to provide the most information about the evolutionary mechanisms involved.Among the six completely sequenced chloroplast genomes from angiosperms (excluding the nonphotosynthetic plant Epifagus virginiana ; Wolfe et al., 1992a), 74 proteincoding genes are held in common and an additional five are present in only some species. These five genes are accD , ycf1 , and ycf2 (pseudogenes in rice and maize; Hiratsuka et al., 1989;Maier et al., 1995), rpl23 (pseudogene in spinach; Thomas et al., 1988), and infA (pseudogene in tobacco, Arabidopsis, and Oenothera elata ; Shinozaki et al., 1986;Wolfe et al., 1992b;Sato et al., 1999; Hupfer et al., 2000). Other chloroplast gene losses in angiosperms that have been confirmed by sequencing include rpl22 , rps16 , and ycf4 (open reading frame 184), all of which have been lost in 1 To whom correspondence should be addressed. E-mail (in Dublin) khwolfe@tcd.ie; fax 353-1-6798558. 646The Plant Cell some or all legumes (Gantt et al., 1991;Nagano et al., 1991; Doyle et al., 1995; K.H. Wolfe, unpublished data), and ycf2 and ndhF , both of which have been lost ...

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“…Provably correct solutions to ML are currently limited to some special cases of four-leaf model trees, exhaustive searches through tree space that use heuristics for scoring trees are limited to about ten taxa, and heuristic searches through tree space using similar heuristics for scoring trees are typically limited to fewer than 100 taxa. Various software packages provide heuristics for ML, including PAUP* (Swofford, 2001), Phylip (Felsenstein, 1993), FastDNAml (Olsen et al, 1994), PhyML (Guindon and Gascuel, 2003), and TrExML (Wolf et al, 2000).…”

Section: Maximum Likelihoodmentioning

confidence: 99%

Advances in Phylogeny Reconstruction from Gene Order and Content Data

Moret¹,

Warnow²

2005

Methods in Enzymology

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Genomes can be viewed in terms of their gene content and the order in which the genes appear along each chromosome. Evolutionary events that affect the gene order or content are "rare genomic events" (rarer than events that affect the composition of the nucleotide sequences) and have been advocated by systematists for inferring deep evolutionary histories. This chapter surveys recent developments in the reconstruction of phylogenies from gene order and content, focusing on their performance under various stochastic models of evolution. Because such methods are currently quite restricted in the type of data they can analyze, we also present current research aimed at handling the full range of whole-genome data.

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TrExML: a maximum-likelihood approach for extensive tree-space exploration

Abstract: TreeGen, TrExML, and the sequence data used to test the programs are available from the following two WWW sites: http://whitetail.bemidji.msus. edu/trexml/and http://jcsmr.anu.edu.au/dmm/humgen.+ ++html.

Cited by 35 publications

References 10 publications

Gene order evolution and paleopolyploidy in hemiascomycete yeasts

Gene order evolution and paleopolyploidy in hemiascomycete yeasts

Many Parallel Losses of infA from Chloroplast DNA during Angiosperm Evolution with Multiple Independent Transfers to the Nucleus

Advances in Phylogeny Reconstruction from Gene Order and Content Data

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