Identifying a species tree subject to random lateral gene transfer

DOI10.1016/J.JTBI.2013.01.009MaRDI QIDQ1715215zbMATH OpenOpenAlexWikidataFDO

Authors Simone Linz, D. Huson, Michael J. Sanderson, Mike Steel

Publication date 4 February 2019

Published in Journal of Theoretical Biology (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/1211.7307

zbMATH Keywords

phylogenetic treePoisson processstatistical consistencymodeling LGT

Mathematics Subject Classification ID

Applications of graph theory (05C90) Genetics and epigenetics (92D10) Problems related to evolution (92D15)

Abstract: A major problem for inferring species trees from gene trees is that evolutionary processes can sometimes favour gene tree topologies that conflict with an underlying species tree. In the case of incomplete lineage sorting, this phenomenon has recently been well-studied, and some elegant solutions for species tree reconstruction have been proposed. One particularly simple and statistically consistent estimator of the species tree under incomplete lineage sorting is to combine three-taxon analyses, which are phylogenetically robust to incomplete lineage sorting. In this paper, we consider whether such an approach will also work under lateral gene transfer (LGT). By providing an exact analysis of some cases of this model, we show that there is a zone of inconsistency for triplet-based species tree reconstruction under LGT. However, a triplet-based approach will consistently reconstruct a species tree under models of LGT, provided that the expected number of LGT transfers is not too high. Our analysis involves a novel connection between the LGT problem and random walks on cyclic graphs. We have implemented a procedure for reconstructing trees subject to LGT or lineage sorting in settings where taxon coverage may be patchy and illustrate its use on two sample data sets.

Recommendations

• The standard lateral gene transfer model is statistically consistent for pectinate four-taxon trees
• Species trees from gene trees despite a high rate of lateral genetic transfer: a tight bound (extended abstract)
• Reconstruction of LGT networks from tri-LGT-nets
• Towards identifying lateral gene transfer events
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Cites work

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Cited in

(8)

• On partial gene transfer and its impact on gene tree reconstruction
• Detecting locus acquisition events in gene trees
• The standard lateral gene transfer model is statistically consistent for pectinate four-taxon trees
• Species trees from gene trees despite a high rate of lateral genetic transfer: a tight bound (extended abstract)
• Reconstruction of LGT networks from tri-LGT-nets
• Overlaid species forests
• Towards identifying lateral gene transfer events
• Lateral transfer in stochastic Dollo models

Describes a project that uses

Uses Software

• Dendroscope

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