title: Impact of deep coalescence and recombination on the estimation of phylogenetic relationships among species using AFLP markers.
abstract: Deep coalescence and the nongenealogical pattern of descent caused by recombination have emerged as a common problem for phylogenetic inference at the species level. Here we use computer simulations to assess whether AFLP-based phylogenies are robust to the uncertainties introduced by these factors. Our results indicate that phylogenetic signal can prevail even in the face of extensive deep coalescence allowing recovering the correct species tree topology. The impact of recombination on tree accuracy was related to total tree depth and species effective population size. The correct tree topology could be recovered upon many simulation settings due to a trade-off between the conflicting signals resulting from intra-locus recombination and the benefits of the joint consideration of unlinked loci that better matched overall the true species tree. Errors in tree topology were not only determined by deep coalescence, but also by the timing of divergence and the tree-building errors arising from an insufficient number of characters. DNA sequences generally outperformed AFLPs upon any simulated scenario, but this difference in performance was nearly negligible when a sufficient number of AFLP characters were sampled. Our simulations suggest that the impact of deep coalescence and intra-locus recombination on the reliability of AFLP trees could be minimal for effective population sizes equal to or lower than 10,000 (typical of many vertebrates and tree plants) given tree depths above 0.02 substitutions per site.
authors.affiliation: Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, 36310 Vigo, Spain. Electronic address: mariajesus@uvigo.es.
authors.forename: María Jesús
authors.initials: MJ
authors.lastname: García-Pereira
authors.affiliation: Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, 36310 Vigo, Spain. Electronic address: acraaj@uvigo.es.
authors.forename: Antonio
authors.initials: A
authors.lastname: Carvajal-Rodríguez
authors.affiliation: Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala 75236-SE, Sweden. Electronic address: simon.whelan@ebc.uu.se.
authors.forename: Simon
authors.initials: S
authors.lastname: Whelan
authors.affiliation: Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, 36310 Vigo, Spain. Electronic address: armando@uvigo.es.
authors.forename: Armando
authors.initials: A
authors.lastname: Caballero
authors.affiliation: Departamento de Bioquímica, Genética e Inmunología, Facultad de Biología, Universidad de Vigo, 36310 Vigo, Spain. Electronic address: hquesada@uvigo.es.
authors.forename: Humberto
authors.initials: H
authors.lastname: Quesada
mesh_terms: D054458:Amplified Fragment Length Polymorphism Analysis / Q000379:methods*; D000818:Animals; D001483:Base Sequence; D003198:Computer Simulation; D008957:Models, Genetic; D010802:Phylogeny; D011995:Recombination, Genetic; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA
keywords: AFLP; Computer simulation; Deep coalescence; Phylogenetic inference; Recombination