Phylogenetic signal in AFLP data sets

Area of Science:

• Molecular Systematics
• Phylogenetics
• Population Genetics

Background:

• Amplified fragment length polymorphism (AFLP) markers are valuable for molecular systematics.
• AFLP data presents challenges for phylogenetic interpretation, including fragment non-independence, homology, and heterozygote identification.

Purpose of the Study:

• To examine AFLP data sets of Lactuca s.l. for the presence of phylogenetic signal.
• To assess the phylogenetic utility of AFLP markers and compare them with internal transcribed spacer (ITS) data.

Main Methods:

• Phylogenetic signal detection using tree length distribution skewness (g1) tests, permutation tail probability (PTP) tests, and relative apparent synapomorphy analysis (RASA).
• Branch support assessment via bootstrap, jackknife, and decay analysis.
• Congruence testing between AFLP and ITS datasets using partition homogeneity test (PHT) and Templeton test.

Main Results:

• Analytical studies indicated the presence of phylogenetic signal within the AFLP data sets.
• Some incongruence was observed between AFLP and ITS optimal parsimony trees (MPTs).
• AFLPs were found to be informative at lower taxonomic levels than ITS sequences in Lactuca s.l. and other groups.

Conclusions:

• AFLP markers possess significant phylogenetic signal, supporting their use in molecular systematic studies.
• While generally congruent with ITS data, AFLP and ITS markers provide information at different taxonomic resolutions.
• Tentative estimates for AFLP phylogenetic informativeness relative to ITS sequence divergence are suggested.