Estimating genome-wide phylogenies using probabilistic topic modeling

Inferring the evolutionary history of species or populations with genome-wide data is gaining ground, but computational constraints still limit our abilities in this area. We developed an alignment-free method to infer the genome-wide species tree and implemented it in the Python package TopicContml. The method uses probabilistic topic modeling (specifically, Latent Dirichlet Allocation or LDA) to extract ‘topic’ frequencies from k-mers, which are derived from multilocus DNA sequences. These extracted frequencies then serve as an input for the program Contml in the PHYLIP package, which is used to generate a species tree. We evaluated the performance of our method with biological and simulated data sets: a data set with 14 DNA sequence loci from 78-92 haplotypes from two Australian bird species distributed in 9 populations; a second data set of 5162 loci from 80 mammal species; and a third data set of 67317 autosomal loci and 4157 X-chromosome loci of 6 species in the Anopheles gambiae complex, and several simulated data sets. Our empirical results and simulated data suggest that our method is efficient and statistically accurate. We also assessed the uncertainty of the estimated relationships among clades using a bootstrap procedure for aligned sequence data and for k-mer data.

Methods
PacBio HiFi reads were generated from DNA isolated from four birds: a Woodhouse's Scrub-Jay (Aphelocoma woodhouseii, specimen MCZ:Orn:365326); a Yucatan Jay (Cyanocorax yucatanicus, specimen MCZ:Orn:365269); Tataupa Tinamou (Crypturellus tataupa); and White-throated Tinamou (Tinamus guttatus). DNA was isolated using Qiagen Magattract, and the concentration was estimated using a TapeStation. The DNA of the two tinamous was sequenced on a PacBio HiFi Revio DNA sequencer at the Faculty of Arts & Sciences Bauer Core, Harvard University, and the DNA from the two jays was sequenced on a PacBio HiFi machine at the DNA Sequencing & Genotyping Center at the University of Delaware.