Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences

Ababneh, Faisal; Jermiin, Lars S.; Ma, Chunsheng; Robinson, John

doi:10.1093/bioinformatics/btl064

Cited by 122 publications

(102 citation statements)

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“…The resulting alignment contained 6913 sites from the 26 species. We then applied the matched-pairs test of symmetry [38] to the data to determine whether the sequences were consistent with evolution under globally SRH conditions. The PP -plot in Figure 7 clearly shows that the data are consistent with evolution under these conditions.…”

Section: Resultsmentioning

confidence: 99%

Statistical tests to identify appropriate types of nucleotide sequence recoding in molecular phylogenetics

et al. 2014

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BackgroundUnder a Markov model of evolution, recoding, or lumping, of the four nucleotides into fewer groups may permit analysis under simpler conditions but may unfortunately yield misleading results unless the evolutionary process of the recoded groups remains Markovian. If a Markov process is lumpable, then the evolutionary process of the recoded groups is Markovian.ResultsWe consider stationary, reversible, and homogeneous Markov processes on two taxa and compare three tests for lumpability: one using an ad hoc test statistic, which is based on an index that is evaluated using a bootstrap approximation of its distribution; one that is based on a test proposed specifically for Markov chains; and one using a likelihood-ratio test. We show that the likelihood-ratio test is more powerful than the index test, which is more powerful than that based on the Markov chain test statistic. We also show that for stationary processes on binary trees with more than two taxa, the tests can be applied to all pairs. Finally, we show that if the process is lumpable, then estimates obtained under the recoded model agree with estimates obtained under the original model, whereas, if the process is not lumpable, then these estimates can differ substantially. We apply the new likelihood-ratio test for lumpability to two primate data sets, one with a mitochondrial origin and one with a nuclear origin.ConclusionsRecoding may result in biased phylogenetic estimates because the original evolutionary process is not lumpable. Accordingly, testing for lumpability should be done prior to phylogenetic analysis of recoded data.

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Section: Resultsmentioning

confidence: 99%

Statistical tests to identify appropriate types of nucleotide sequence recoding in molecular phylogenetics

et al. 2014

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“…Following that each pair of observed and expected F matrices may be tested as in Waddell et al (2004), and the results summed. Finally, it is straightforward to extend the testing procedures of Waddell et al (2004) to include the relationship noted by Ababneh et al (2006). That is, the internal symmetry statistic of F, X 2* [F], equals X 2 [F] -GLS [F].…”

Section: Discussionmentioning

confidence: 99%

Measuring Fit of Sequence Data to Phylogenetic Model: Gain of Power Using Marginal Tests

2009

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field of phylogenetics rarely do this. Such analyses discard fundamental aspects of science as prescribed by Karl Popper. Indeed, not without cause, Popper (1978) once argued that evolutionary biology was unscientific as its hypotheses were untestable. Here we trace developments in assessing fit from Penny et al. (1982) to the present. We compare the general log-likelihood ratio (the G or G 2 statistic) statistic between the evolutionary tree model and the multinomial model with that of marginalized tests applied to an alignment (using placental mammal coding sequence data). It is seen that the most general test does not reject the fit of data to model (p~0.5), but the marginalized tests do. Tests on pair-wise frequency (F) matrices, strongly (p < 0.001) reject the most general phylogenetic (GTR) models commonly in use. It is also clear (p < 0.01) that the sequences are not stationary in their nucleotide composition.Deviations from stationarity and homogeneity seem to be unevenly distributed amongst taxa; not necessarily those expected from examining other regions of the genome. By marginalizing the 4 t patterns of the i.i.d. model to observed and expected parsimony counts, that is, from constant sites, to singletons, to parsimony informative characters of a minimum possible length, then the likelihood ratio test regains power, and it too rejects the evolutionary model with p << 0.001.Given such behavior over relatively recent evolutionary time, readers in general should maintain a healthy skepticism of results, as the scale of the systematic errors in published analyses may really be far larger than the analytical methods (e.g., bootstrap) report.Keywords: Fit of sequence data to evolutionary model, base composition stationarity, placental / eutherian mammals.Waddell, Ota and Penny

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“…The data matrices are available from the corresponding author. Kim et al (1994) a Inferred from ITS1 sequence analysis (Yang et al 2010) b Named previously on the basis of zymodeme analysis (Xu et al 1984) c Identified as L. donovani according to the zymodeme, LON41, whereas recent analysis have shown that it is L. infantum (Ibrahim and Barker 2001) Compositional heterogeneity was evaluated using Chisquare (# 2 ) tests implemented in PAUP* 4.0b10 (Swofford 2002) and assessed using the software SeqVis v.1.5 (Ho et al 2006) to visualize and to conduct matched-pairs test of symmetry (Ababneh et al 2006). Evidence of evolution under conditions more complex than that assumed by commonly applied models (i.e., stationary, reversible, and homogeneous conditions) was inferred if the scatter of dots in the tetrahedral plots was widely dispersed and if x% of the matched-pairs test of symmetry produced p values greater than or equal to x; this procedure is consistent with that advocated by Jermiin et al (2008).…”

Section: Sequence Alignment and Analysesmentioning

confidence: 99%

Species delimitation and phylogenetic relationships of Chinese Leishmania isolates reexamined using kinetoplast cytochrome oxidase II gene sequences

et al. 2011

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Leishmaniasis is a geographically widespread disease caused by protozoan parasites belonging to the genus Leishmania and transmitted by certain species of sand fly. This disease still remains endemic in China, especially in the west and northwest frontier regions. A recent ITS1 phylogeny of Chinese Leishmania isolates has challenged some aspects for their traditional taxonomy and cladistic hypotheses of their phylogeny. However, disagreement with respect to relationships within Chinese Leishmania isolates highlights the need for additional data and analyses. Here, we test the phylogenetic relationships among Chinese isolates and their relatives by analyzing kinetoplast cytochrome oxidase II (COII) gene sequences, including 14 Chinese isolates and three isolates from other countries plus 17 sequences retrieved from GenBank. The COII gene might have experienced little substitution saturation, and its evolutionary process was likely to have been stationary, reversible, and homogeneous. Both neighbor-joining and Bayesian analyses reveal a moderately supported group comprising ten newly determined isolates, which is closely related to Leishmania tarentolae and Endotrypanum monterogeii. In combination with genetic distance analysis as well as Bayesian hypothesis testing, this further corroborates the occurrence of an undescribed species of Leishmania. Our results also suggest that (1) isolate MHOM/CN/93/GS7 and isolate IPHL/CN/77/XJ771 are Leishmania donovani; (2) isolate MHOM/CN/84/JS1 is Leishmania tropica; (3) the status referring to an isolate MRHO/CN/62/GS-GER20 from a great gerbil in Gansu, China, as Leishmania gerbilli, formerly based on multilocus enzyme electrophoresis, is recognized; and (4) E. monterogeii is nested within the genus Leishmania, resulting in a paraphyletic Leishmania. In addition, the results of this study enrich our understanding of the heterogeneity and relationships of Chinese Leishmania isolates.

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Matched-pairs tests of homogeneity with applications to homologous nucleotide sequences

Abstract: Programs written in R to do the tests on nucleotides are available from http://www.maths.usyd.edu.au/u/johnr/testsym/

Cited by 122 publications

References 20 publications

Statistical tests to identify appropriate types of nucleotide sequence recoding in molecular phylogenetics

Statistical tests to identify appropriate types of nucleotide sequence recoding in molecular phylogenetics

Measuring Fit of Sequence Data to Phylogenetic Model: Gain of Power Using Marginal Tests

Species delimitation and phylogenetic relationships of Chinese Leishmania isolates reexamined using kinetoplast cytochrome oxidase II gene sequences

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