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The concept of horizontal or lateral gene transfer (the non‐genealogical transmission of genetic material between organisms) was introduced in 1990s to explain the observed incongruence in phylogenetic reconstructions using different genes. Today, horizontal gene transfer is accepted as an important force modulating evolution of Bacteria, Archaea and unicellular eukaryotes, and evidence is rising for their role in the evolution of pluricellular eukaryotes (fungi, plants and animals). The realisation that horizontal gene transfer plays an important role in evolution of both, prokaryotes and eukaryotes, put in question the metaphor of the tree of life and the traditional view of evolution as a slow process. A more pluralistic approach to evolution is emerging that encompasses different evolutionary mechanisms operating at different levels of complexity.

This study explores the effects of microsatellite size homoplasies in the reconstruction of phylogenetic relationships and estimates of population parameters as Fixation index (FST) using as a case study a truncated microsatellite from the picote splitfin Zoogoneticus quitzeoensis. The results suggest that the use of imperfect microsatellites may have only a minor effect in phylogenetic and population studies.