Multidimensional Vector Space Representation for Convergent Evolution and Molecular Phylogeny

Kitazoe, Yasuhiro; Kishino, Hirohisa; Okabayashi, Takahisa; Watabe, Teruaki; Nakajima, Noriaki; Okuhara, Yoshiyasu; Kurihara, Yukio

doi:10.1093/molbev/msi051

Cited by 19 publications

(28 citation statements)

References 31 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…For example, armadillo has been variously placed outside the clade containing Primates, Rodents, and Laurasiatheria (Murphy et al 2001;Kitazoe et al 2004); inside Laurasiatheria (Arnason et al 2002); or inside the clade containing Primates and Rodents (Reyes et al 2004). Our results agree with Murphy et al and Kitazoe et al: we identified one repeat separating Primate/Rodent and Laurasiatheria clades from armadillo.…”

Section: Discussionsupporting

confidence: 92%

“…Recent studies (Kitazoe et al 2004;Reyes et al 2004) agree with our placement of Rodents, horse, rabbit, and hedgehog, but still leave some open questions. For example, armadillo has been variously placed outside the clade containing Primates, Rodents, and Laurasiatheria (Murphy et al 2001;Kitazoe et al 2004); inside Laurasiatheria (Arnason et al 2002); or inside the clade containing Primates and Rodents (Reyes et al 2004).…”

Section: Discussionsupporting

confidence: 68%

“…In particular, various placements of Rodents, horse, rabbit, and hedgehog have been reported, as we discuss below. More recent studies (Kitazoe et al 2004;Reyes et al 2004) have resolved many of the differences between mitochondrial and nuclear data, but leave open questions regarding the placement of armadillo and muntjak, which our results address.…”

Section: Discussionmentioning

confidence: 71%

“…We note that the phylogeny of eutherian mammals has been subject to considerable debate, as there are many instances in which previous studies reach conflicting conclusions (Amrine-Madsen et al 2003). More recent studies (Kitazoe et al 2004;Reyes et al 2004) have resolved many of the differences between mitochondrial and nuclear data. However, some open questions remain.…”

mentioning

confidence: 84%

See 3 more Smart Citations

Orthologous repeats and mammalian phylogenetic inference

Bashir

Ye²,

Price³

et al. 2005

Genome Res.

View full text Add to dashboard Cite

Determining phylogenetic relationships between species is a difficult problem, and many phylogenetic relationships remain unresolved, even among eutherian mammals. Repetitive elements provide excellent markers for phylogenetic analysis, because their mode of evolution is predominantly homoplasy-free and unidirectional. Historically, phylogenetic studies using repetitive elements have relied on biological methods such as PCR analysis, and computational inference is limited to a few isolated repeats. Here, we present a novel computational method for inferring phylogenetic relationships from partial sequence data using orthologous repeats. We apply our method to reconstructing the phylogeny of 28 mammals, using more than 1000 orthologous repeats obtained from sequence data available from the NISC Comparative Sequencing Program. The resulting phylogeny has robust bootstrap numbers, and broadly matches results from previous studies which were obtained using entirely different data and methods. In addition, we shed light on some of the debatable aspects of the phylogeny. With rapid expansion of available partial sequence data, computational analysis of repetitive elements holds great promise for the future of phylogenetic inference.[Supplemental material is available online at www.genome.org.]Repetitive elements, particularly SINEs (short interspersed elements) and LINEs (long interspersed elements), provide excellent markers for phylogenetic analysis: their mode of evolution is predominantly homoplasy-free, since they do not typically insert in the same locus of two unrelated lineages, and unidirectional, since they are not precisely excised from a locus with the flanking sequences preserved . Indeed, the use of SINEs and LINEs to elucidate phylogeny has a rich history. SINEs and LINEs have been used to show that hippopotamuses are the closest living relative of whales (Shimamura et al. 1997;Nikaido et al. 1999), to determine phylogenetic relationships among cichlid fish (Takahashi et al. 2001a,b;Terai et al. 2003), and to elucidate the phylogeny of eight Primate species, providing the strongest evidence yet that chimps are the closest living relative of humans (Salem et al. 2003). In each one of these studies, the presence or absence of a repetitive element at a specific locus in a given species was determined experimentally by PCR analysis, using flanking sequences as primers. It has been suggested that such experimental studies would not make a widespread contribution to phylogenetic inference in the short term, because the time, money, and effort needed to collect data on relatively few characters would be prohibitive (Hillis 1999). We agree that the biological methods described above are highly resource-intensive. However, the set of species with partial sequence data available is rapidly expanding. Therefore, we propose instead to determine the presence or absence of a repetitive element at specific loci in each given species, and infer the resulting phylogeny, purely by computational means. Previous work has a...

show abstract

Section: Discussionsupporting

confidence: 92%

Section: Discussionsupporting

confidence: 68%

Section: Discussionmentioning

confidence: 71%

mentioning

confidence: 84%

See 2 more Smart Citations

Orthologous repeats and mammalian phylogenetic inference

Bashir

Ye²,

Price³

et al. 2005

Genome Res.

View full text Add to dashboard Cite

show abstract

“…It may be more common than widely believed but difficult to detect, or it may simply have been overlooked (11)(12)(13)(14).…”

mentioning

confidence: 99%

Evidence for an ancient adaptive episode of convergent molecular evolution

Castoe

Koning

Kim

et al. 2009

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

301

272

View full text Add to dashboard Cite

Documented cases of convergent molecular evolution due to selection are fairly unusual, and examples to date have involved only a few amino acid positions. However, because convergence mimics shared ancestry and is not accommodated by current phylogenetic methods, it can strongly mislead phylogenetic inference when it does occur. Here, we present a case of extensive convergent molecular evolution between snake and agamid lizard mitochondrial genomes that overcomes an otherwise strong phylogenetic signal. Evidence from morphology, nuclear genes, and most sites in the mitochondrial genome support one phylogenetic tree, but a subset of mostly amino acid-altering substitutions (primarily at the first and second codon positions) across multiple mitochondrial genes strongly supports a radically different phylogeny. The relevant sites generally evolved slowly but converged between ancient lineages of snakes and agamids. We estimate that Ϸ44 of 113 predicted convergent changes distributed across all 13 mitochondrial protein-coding genes are expected to have arisen from nonneutral causes-a remarkably large number. Combined with strong previous evidence for adaptive evolution in snake mitochondrial proteins, it is likely that much of this convergent evolution was driven by adaptation. These results indicate that nonneutral convergent molecular evolution in mitochondria can occur at a scale and intensity far beyond what has been documented previously, and they highlight the vulnerability of standard phylogenetic methods to the presence of nonneutral convergent sequence evolution.adaptation ͉ convergence ͉ phylogenetics ͉ reptile

show abstract

A novel approach to phylogenetic trees:d‐Dimensional geometric Steiner trees

et al. 2008

View full text Add to dashboard Cite

We suggest a novel distance-based method for the determination of phylogenetic trees. It is based on multidimensional scaling and Euclidean Steiner trees in highdimensional spaces. Preliminary computational experience shows that the use of Euclidean Steiner trees for finding phylogenetic trees is a viable approach. Experiments also indicate that the new method is comparable with results produced by neighbor joining (Saitou and Nei, Mol Biol Evol 4 (1987), 406-425).

show abstract

Multidimensional Vector Space Representation for Convergent Evolution and Molecular Phylogeny

Cited by 19 publications

References 31 publications

Orthologous repeats and mammalian phylogenetic inference

Orthologous repeats and mammalian phylogenetic inference

Evidence for an ancient adaptive episode of convergent molecular evolution

A novel approach to phylogenetic trees:d‐Dimensional geometric Steiner trees

Contact Info

Product

Resources

About