The tree alignment problem

Abstract

BackgroundThe inference of homologies among DNA sequences, that is, positions in multiple genomes that share a common evolutionary origin, is a crucial, yet difficult task facing biologists. Its computational counterpart is known as the multiple sequence alignment problem. There are various criteria and methods available to perform multiple sequence alignments, and among these, the minimization of the overall cost of the alignment on a phylogenetic tree is known in combinatorial optimization as the Tree Alignment Problem. This problem typically occurs as a subproblem of the Generalized Tree Alignment Problem, which looks for the tree with the lowest alignment cost among all possible trees. This is equivalent to the Maximum Parsimony problem when the input sequences are not aligned, that is, when phylogeny and alignments are simultaneously inferred.ResultsFor large data sets, a popular heuristic is Direct Optimization (DO). DO provides a good tradeoff between speed, scalability, and competitive scores, and is implemented in the computer program POY. All other (competitive) algorithms have greater time complexities compared to DO. Here, we introduce and present experiments a new algorithm Affine-DO to accommodate the indel (alignment gap) models commonly used in phylogenetic analysis of molecular sequence data. Affine-DO has the same time complexity as DO, but is correctly suited for the affine gap edit distance. We demonstrate its performance with more than 330,000 experimental tests. These experiments show that the solutions of Affine-DO are close to the lower bound inferred from a linear programming solution. Moreover, iterating over a solution produced using Affine-DO shows little improvement.ConclusionsOur results show that Affine-DO is likely producing near-optimal solutions, with approximations within 10% for sequences with small divergence, and within 30% for random sequences, for which Affine-DO produced the worst solutions. The Affine-DO algorithm has the necessary scalability and optimality to be a significant improvement in the real-world phylogenetic analysis of sequence data.

Systematics of the Neotropical GenusLeptodactylusFitzinger, 1826 (Anura: Leptodactylidae): Phylogeny, the Relevance of Non-molecular Evidence, and Species Accounts

“…The most complex parental care reported includes attendance and active defense of eggs and larvae in Leptodactylus latrans (Fernández and Fernández, 1921;Gallardo, 1964b;Vaz-Ferreira and Gehrau, 1974, 1986 and L. insularum (Wells and Bard, 1988;Vaira, 1997;Ponssa, 2001). Furthermore, several studies have reported the female communicating with the larval school.…”

“…Behavioral characters were scored based on data from many studies, including Cei (1949aCei ( , b, 1980, Gallardo (1958Gallardo ( , 1964a, Sexton (1962), Heatwole et al (1965), Pisanó and Barbieri (1965), Heyer and Silverstone (1969), Lescure (1972Lescure ( , 1979, Barrio (1973), Heyer and Bellin (1973), Heyer (1974a, b;, Philibosian et al (1974), Muedeking and Heyer (1976), Heyer and Rand (1977), Toft and Duellman (1979), Downie (1984Downie ( , 1989Downie ( , 1990Downie ( , 1994Downie ( , 1996, Lescure and Letellier (1983), Aichinger (1985), Solano (1987), Martins (1988), Wells and Bard (1988), Caldwell and Lopez (1989), Gascon (1991), Rodriguez (1992), Pisanó et al (1993), Rodrí-guez and Duellman (1994), Cardoso and Heyer (1995), De la Riva (1995, Lamar and Wild (1995), Vaira (1997), Prado et al (2000), Freitas et al (2001), Lewis et al (2001), Ponssa (2001), Almeida and Angulo (2002), Prado et al (2002), Prado and Haddad (2003), Readin and Jofré (2003), França et al (2004), Giaretta and Kokubum (2004), Gibson and Buley (2004), …”

High resolution images for Phylogeny, taxonomic revision, and character evolution of the genera Chiasmocleis and Syncope (Anura, Microhylidae) in Amazonia, with descriptions of three new species.

“…Phylogenetic analyses were performed under direct optimization (Wheeler, 1996;Varó n and Wheeler, 2012) in POY 5.0 (Varó n et al, 2013) using equal weights for all transformations (substitutions and insertion/deletion events) and the parsimony optimality criterion. Justifications for 6 Two terminals from the de Sá et al (2012) dataset, Chiasmocleis bassleri (voucher number NMPGV 71148) and Syncope antenori (QCAZ 23824) do not have Genbank numbers for the 16S fragment given in the manuscript.…”

A simple method to test the reproducibility of the phylogenetic reconstructions: the molecular systematics of cyanobacteria as a case study

“…Earlier reports (oGden & rosenBerG 2007;Liu et al 2009;sedaGhatinia et al 2009;Löytynoja et al 2012;Varon & WheeLer 2012), employed either simulated data or simulated differences from a known data set, such that a "true-alignment" and a "true-tree" were known. These provided benchmark tools to score any experimenatlly-obtained output against.…”