A likelihood framework to measure horizontal gene transfer.

@article{Linz2007ALF,
  title={A likelihood framework to measure horizontal gene transfer.},
  author={Simone Linz and Achim Radtke and Arndt von Haeseler},
  journal={Molecular biology and evolution},
  year={2007},
  volume={24 6},
  pages={
          1312-9
        }
}
We suggest a likelihood-based approach to estimate an overall rate of horizontal gene transfer (HGT) in a simplified setting. To this end, we assume that the number of occurring HGT events within a given time interval follows a Poisson process. To obtain estimates for the rate of HGT, we simulate the distribution of tree topologies for different numbers of HGT events on a clocklike species tree. Using these simulated distributions, we estimate an HGT rate for a collection of gene trees… 
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Species Trees are Recoverable from Unrooted Gene Tree Topologies Under a Constant Rate of Horizontal Gene Transfer
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It is shown that the species phylogeny can be reconstructed perfectly even when each edge of the tree has a constant probability of being the location of an LGT event, and a new reconstruction algorithm builds the tree recursively from the leaves.
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This work reformulates LCA and root inference in the framework of statistical hypothesis testing and outlines an analytical procedure to formally test competing a-priori LCA hypotheses and to infer confidence sets for the earliest speciation events in the history of a group of species.
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TLDR
The infinitely many genes model from Baumdicker, Hess and Pfaffelhuber (2010) is extended and a genealogical view is taken and a construction -- called the Ancestral Gene Transfer Graph -- of the joint genealogy of all genes in the pangenome is given.
A Bayesian Approach to Phylogenetic Networks
TLDR
A Bayesian approach to the estimation of phylogenetic network parameters is proposed which allows for different phylogenies to be inferred at different parts of the authors' DNA alignment in the presence of reticulation events, at the species level, by using the idea that a phylogenetics network can be naturally decomposed into trees.
A Bayesian method for analyzing lateral gene transfer.
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A Bayesian Markov-chain Monte Carlo-based method is presented that integrates GD, gene loss, LGT, and sequence evolution, and is applied in a genome-wide analysis of two groups of bacteria: Mollicutes and Cyanobacteria.
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