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PLoS One
2012 Jan 01;77:e40861. doi: 10.1371/journal.pone.0040861.
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Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 non model eukaryote species.
Meglécz E
,
Nève G
,
Biffin E
,
Gardner MG
.
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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.
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22815847
???displayArticle.pmcLink???PMC3397955 ???displayArticle.link???PLoS One
Figure 1. Phylogenetic tree of the animal species studied.The cutoff limits used for autocorrelation analyses of microsatellite coverage are indicated in red.
Figure 2. Phylogenetic tree of the plant species studied.The cutoff limits used for autocorrelation analyses of microsatellite coverage are indicated in red.
Figure 3. Autocorrelation analyses of total microsatellite coverage.(A) Plants, (B) Animals, (C) Chordates, (D) Arthropods. Red symbols: P<0.05, grey symbols: P≥0.05.
Figure 4. Microsatellite coverage by phyla.Microsatellite coverage is the number of bases of microsatellites (di-hexanucleotide motifs) per Mb of DNA.
Figure 5. Microsatellite and homopolymer coverage by repeat unit length for plants and Metazoa without Chordata.Microsatellite coverage is the number of bases of microsatellites per Mb of DNA. Coverages of different motifs of the same repeat unit length (mono-hexa) are pooled. Note that the scales of the horizontal axes are different. Species follow the same order as in Dataset S1 and in Figures 1 and 2.
Figure 6. Microsatellite and homopolymer coverage by repeat unit length for Chordata.Microsatellite coverage is the number of bases of microsatellites per Mb of DNA. Coverages of different motifs of the same repeat unit length (mono-hexa) are pooled. Species follow the same order as in Dataset S1 and in Figure 1.
Figure 7. Proportion of A/T and C/G homopolymers for each species.(A) Chordates, (B) Animals without Chordata (C) Plants; species follow the same order as in Dataset S1 and in Figures 1 and 2.
Figure 8. Proportion of all four dinucleotide motifs within the total dinucleotide microsatellite coverage for each species.(A) Chordates, (B) Animals without Chordata (C) Plants; species follow the same order as in Dataset S1 and in Figures 1 and 2.
Figure 9. Proportion of all ten trinucleotide motifs within the total trinucleotide microsatellite coverage for each species.(A) Chordates, (B) Animals without Chordata (C) Plants; species follow the same order as in Dataset S1 and in Figures 1 and 2.
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