New software to detect horizontal gene transfer in microbiomes: from forage to the rumen

HypothesisHorizontal gene transfer (HGT) is the sharing of genetic material between organisms that are not in a vertical relationship of inheritance i.e. between parents and offspring. HGT is widely recognized as a mechanism for evolutionary adaptation. While it is has been studied in bacteria and archaea for some time, it is also being seen of increasing importance for understanding eukaryotic evolution. Recent reviews of HGT emphasise the need to develop better computational methods to detect HGT, especially in eukaryotes. Approaches to detecting HGT events can be divided into two. The first involves the construction of phylogenetic trees using sequence alignment, to detect differences between the evolutionary history of a species and the evolutionary history of individual gene sequences. The second approach involves the analysis of properties intrinsic to genome sequences i.e. the patterns of order and disorder, repeats, codon usage biases, and k-mer content (k-mers are small oligonucleotides). These approaches are collectively known as alignment-free sequence analysis: Dr Swain has recently published a novel machine learning methodology that demonstrates how alignment-free methods can be improved through calibration using training data sets. We hypothesise that our novel process of calibrating alignment-free methods will give significant performance gains over existing approaches. The process of calibration indicates the optimal parameter set to use, and provides a probability score for the likelihood of detecting a true positive. Calibration can be performed in different ways, according to the sequence feature to be detected. These probabilities can then be amalgamated e.g. using Bayesian statistics, and combined with phylogeny analysis. This approach is superior to existing approaches because they estimate appropriate parameters, and cannot allocate probability scores. Our improved approach to HGT detection will generate novel insights into systems where HGT...