Genome-Wide EST Data Mining Approaches to Resolving Incongruence of Molecular Phylogenies

Shan, Yunfeng; Gras, Régis

doi:10.1007/978-1-4419-5913-3_27

Cited by 5 publications

(4 citation statements)

References 33 publications

(70 reference statements)

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“…The sequences of 43 nuclear protein-encoding genes were downloaded from GenBank through the National Center for Biotechnology Information http://www.ncbi.nlm.nih.gov/ using the program SeqMiner.pl [ 28 ]. These 43 genes were previously analyzed using the genome-scale approach of concatenated genes; however, the sequence length of some genes was different [Additional file 1 : Supplemental Table S1].…”

Section: Methodsmentioning

confidence: 99%

43 genes support the lungfish-coelacanth grouping related to the closest living relative of tetrapods with the Bayesian method under the coalescence model

Shan

Gras

2011

BMC Res Notes

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BackgroundSince the discovery of the "living fossil" in 1938, the coelacanth (Latimeria chalumnae) has generally been considered to be the closest living relative of the land vertebrates, and this is still the prevailing opinion in most general biology textbooks. However, the origin of tetrapods has not been resolved for decades. Three principal hypotheses (lungfish-tetrapod, coelacanth-tetrapod, or lungfish-coelacanth sister group) have been proposed.FindingsWe used the Bayesian method under the coalescence model with the latest published program (Bayesian Estimation of Species Trees, or BEST) to perform a phylogenetic analysis for seven relevant taxa and 43 nuclear protein-coding genes with the jackknife method for taxon sub-sampling. The lungfish-coelacanth sister group was consistently reconstructed with the Bayesian method under the coalescence model in 17 out of 21 taxon sets with a Bayesian posterior probability as high as 99%. Lungfish-tetrapod was only inferred from BCLS and BACLS. Neither coelacanth-tetrapod nor lungfish-coelacanth-tetrapod was recovered out of all 21 taxon sets.ConclusionsOur results provide strong evidence in favor of accepting the hypothesis that lungfishes and coelacanths form a monophyletic sister-group that is the closest living relative of tetrapods. This clade was supported by high Bayesian posterior probabilities of the branch (a lungfish-coelacanth clade) and high taxon jackknife supports.

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Section: Methodsmentioning

confidence: 99%

43 genes support the lungfish-coelacanth grouping related to the closest living relative of tetrapods with the Bayesian method under the coalescence model

Shan

Gras

2011

BMC Res Notes

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“…Data mining has been applied with success in many areas of science such as Biology [5]- [8], Astronomy [9]- [13] and Medicine [14] [15] just to mention some. In particular, due to the multisystem nature of Earth sciences, we consider that the incorporation of data mining to this discipline would provide a new perspective to analyze old problems and would likely suggest new ones [16]- [21].…”

Section: Introductionmentioning

confidence: 99%

Data Mining of Historic Hydrogeological and Socioeconomic Data Bases of the Toluca Valley, Mexico

López-Corona¹,

Fuentes²,

Morales-Casique³

et al. 2016

JWARP

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In this paper we used several data mining techniques to analyze the coevolution of hydrogeological and socioeconomical data for the Toluca Valley in Mexico. We found non trivial relations between two historic data bases that make clear that groundwater and economy may be much more linked than it was thought before. In particular, we found that hydrogeological data trends change during economical crisis and election years in Mexico. This shows that different macroeconomical policies implemented by several administrations have a direct impact in the way groundwater is used. We also found that hydrogoelogical data evolve in the direction of population transformation from rural to urban, which could represent a whole paradigm shift in groundwater management with profound repercussions in policy making.

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“…In spite of the positive aspects, however, multiple markers inconsistency does represent a problem with actual data 5–8. The overwhelming and rapidly accumulating amounts of molecular data have just scratched the surface of the problem 9.…”

Section: Introductionmentioning

confidence: 99%

“…In spite of the positive aspects, however, multiple markers inconsistency does represent a problem with actual data. 5–8 The overwhelming and rapidly accumulating amounts of molecular data have just scratched the surface of the problem. 9 It is clear that different genes present distinct probabilities of efficiently recovering the correct tree and that a careful marker selection has been shown to be more important than the choice of a tree-building method.…”

Section: Introductionmentioning

confidence: 99%

Efficiency of Nuclear and Mitochondrial Markers Recovering and Supporting Known Amniote Groups

Lambret-Frotté

Perini

Russo

2012

Evol Bioinform Online

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We have analysed the efficiency of all mitochondrial protein coding genes and six nuclear markers (Adora3, Adrb2, Bdnf, Irbp, Rag2 and Vwf) in reconstructing and statistically supporting known amniote groups (murines, rodents, primates, eutherians, metatherians, therians). The efficiencies of maximum likelihood, Bayesian inference, maximum parsimony, neighbor-joining and UPGMA were also evaluated, by assessing the number of correct and incorrect recovered groupings. In addition, we have compared support values using the conservative bootstrap test and the Bayesian posterior probabilities. First, no correlation was observed between gene size and marker efficiency in recovering or supporting correct nodes. As expected, tree-building methods performed similarly, even UPGMA that, in some cases, outperformed other most extensively used methods. Bayesian posterior probabilities tend to show much higher support values than the conservative bootstrap test, for correct and incorrect nodes. Our results also suggest that nuclear markers do not necessarily show a better performance than mitochondrial genes. The so-called dependency among mitochondrial markers was not observed comparing genome performances. Finally, the amniote groups with lowest recovery rates were therians and rodents, despite the morphological support for their monophyletic status. We suggest that, regardless of the tree-building method, a few carefully selected genes are able to unfold a detailed and robust scenario of phylogenetic hypotheses, particularly if taxon sampling is increased.

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Genome-Wide EST Data Mining Approaches to Resolving Incongruence of Molecular Phylogenies

Cited by 5 publications

References 33 publications

43 genes support the lungfish-coelacanth grouping related to the closest living relative of tetrapods with the Bayesian method under the coalescence model

43 genes support the lungfish-coelacanth grouping related to the closest living relative of tetrapods with the Bayesian method under the coalescence model

Data Mining of Historic Hydrogeological and Socioeconomic Data Bases of the Toluca Valley, Mexico

Efficiency of Nuclear and Mitochondrial Markers Recovering and Supporting Known Amniote Groups

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