LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites

Area of Science:

• Evolutionary biology
• Computational phylogenetics

Background:

• Phylogenetic models often assume a uniform evolutionary process, which can be an oversimplification.
• Changes in selection or drift can alter evolutionary processes over time, affecting sequence evolution.
• Varying proportions of variable sites across lineages can impact phylogenetic tree reconstruction accuracy, especially over long evolutionary distances.

Purpose of the Study:

• To introduce a novel phylogenetic model that accounts for lineage-specific changes in the proportion of variable sites.
• To assess the impact of lineage-specific evolutionary processes on phylogenetic reconstruction.

Main Methods:

• Development of LineageSpecificSeqgen, an extension of the seq-gen program.
• Implementation of simulations allowing changes in the proportion of variable sites and their switching rates.
• Branch lengths are interpreted as substitutions per variable site, not per site, enabling independent rate specification.

Main Results:

• LineageSpecificSeqgen can generate DNA and amino acid sequence alignments reflecting lineage-specific evolutionary dynamics.
• The model allows for independent control over substitution rates of variable sites and the proportion of invariable sites.
• This provides a means to simulate sequences under more realistic, non-homogeneous evolutionary scenarios.

Conclusions:

• LineageSpecificSeqgen facilitates the testing of existing phylogenetic models against sequences with lineage-specific evolution.
• The program aids in developing new methods for detecting lineage-specific evolutionary processes in empirical data.
• It supports the creation of improved phylogenetic methods that can accommodate such evolutionary complexities.