Trails: Tree reconstruction of ancestry using incomplete lineage sorting

TY - JOUR

T1 - Trails

T2 - Tree reconstruction of ancestry using incomplete lineage sorting

AU - Rivas-González, Iker

AU - Schierup, Mikkel H

AU - Wakeley, John

AU - Hobolth, Asger

N1 - Copyright: © 2024 Rivas-González et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

PY - 2024/2

Y1 - 2024/2

N2 - Genome-wide genealogies of multiple species carry detailed information about demographic and selection processes on individual branches of the phylogeny. Here, we introduce TRAILS, a hidden Markov model that accurately infers time-resolved population genetics parameters, such as ancestral effective population sizes and speciation times, for ancestral branches using a multi-species alignment of three species and an outgroup. TRAILS leverages the information contained in incomplete lineage sorting fragments by modelling genealogies along the genome as rooted three-leaved trees, each with a topology and two coalescent events happening in discretized time intervals within the phylogeny. Posterior decoding of the hidden Markov model can be used to infer the ancestral recombination graph for the alignment and details on demographic changes within a branch. Since TRAILS performs posterior decoding at the base-pair level, genome-wide scans based on the posterior probabilities can be devised to detect deviations from neutrality. Using TRAILS on a human-chimp-gorilla-orangutan alignment, we recover speciation parameters and extract information about the topology and coalescent times at high resolution.

AB - Genome-wide genealogies of multiple species carry detailed information about demographic and selection processes on individual branches of the phylogeny. Here, we introduce TRAILS, a hidden Markov model that accurately infers time-resolved population genetics parameters, such as ancestral effective population sizes and speciation times, for ancestral branches using a multi-species alignment of three species and an outgroup. TRAILS leverages the information contained in incomplete lineage sorting fragments by modelling genealogies along the genome as rooted three-leaved trees, each with a topology and two coalescent events happening in discretized time intervals within the phylogeny. Posterior decoding of the hidden Markov model can be used to infer the ancestral recombination graph for the alignment and details on demographic changes within a branch. Since TRAILS performs posterior decoding at the base-pair level, genome-wide scans based on the posterior probabilities can be devised to detect deviations from neutrality. Using TRAILS on a human-chimp-gorilla-orangutan alignment, we recover speciation parameters and extract information about the topology and coalescent times at high resolution.

KW - Animals

KW - Humans

KW - Genetic Speciation

KW - Hominidae/genetics

KW - Pan troglodytes/genetics

KW - Phylogeny

KW - Genetics, Population

KW - Models, Genetic

U2 - 10.1371/journal.pgen.1010836

DO - 10.1371/journal.pgen.1010836

M3 - Journal article

C2 - 38330138

SN - 1553-7390

VL - 20

JO - PLOS Genetics

JF - PLOS Genetics

IS - 2

M1 - e1010836

ER -