Breakdown of Phylogenetic Signal: A Survey of Microsatellite Densities in 454 Shotgun Sequences from 154 Non Model Eukaryote Species
Abstract
Microsatellites are ubiquitous in Eukaryotic genomes. A more complete understanding of their origin and spread can be
gained from a comparison of their distribution within a phylogenetic context. Although information for model species is
accumulating rapidly, it is insufficient due to a lack of species depth, thus intragroup variation is necessarily ignored. As
such, apparent differences between groups may be overinflated and generalizations cannot be inferred until an analysis of
the variation that exists within groups has been conducted. In this study, we examined microsatellite coverage and motif
patterns from 454 shotgun sequences of 154 Eukaryote species from eight distantly related phyla (Cnidaria, Arthropoda,
Onychophora, Bryozoa, Mollusca, Echinodermata, Chordata and Streptophyta) to test if a consistent phylogenetic pattern
emerges from the microsatellite composition of these species. It is clear from our results that data from model species
provide incomplete information regarding the existing microsatellite variability within the Eukaryotes. A very strong
heterogeneity of microsatellite composition was found within most phyla, classes and even orders. Autocorrelation analyses
indicated that while microsatellite contents of species within clades more recent than 200 Mya tend to be similar, the
autocorrelation breaks down and becomes negative or non-significant with increasing divergence time. Therefore, the age
of the taxon seems to be a primary factor in degrading the phylogenetic pattern present among related groups. The most
recent classes or orders of Chordates still retain the pattern of their common ancestor. However, within older groups, such
as classes of Arthropods, the phylogenetic pattern has been scrambled by the long independent evolution of the lineages.
Description
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