Data from: Breakdown of phylogenetic signal: a survey of microsatellite densities in 454 shotgun sequences from 154 non model eukaryote species

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.

微卫星（microsatellite）广泛存在于真核生物（Eukaryote）基因组中。要全面理解其起源与传播规律，可通过在系统发育（phylogenetic）框架下比较其分布特征实现。尽管模式物种的相关研究数据正快速积累，但因物种覆盖深度不足，类群内的变异往往被忽略。因此，类群间的表观差异可能被夸大，唯有开展类群内变异分析，方能得出可靠的一般性结论。

本研究针对来自8个远缘门类（刺胞动物门Cnidaria、节肢动物门Arthropoda、有爪动物门Onychophora、苔藓动物门Bryozoa、软体动物门Mollusca、棘皮动物门Echinodermata、脊索动物门Chordata以及链形植物门Streptophyta）的154个真核生物物种的454鸟枪测序（shotgun sequencing）序列，分析其微卫星覆盖度与基序模式，以检验这些物种的微卫星组成是否存在一致的系统发育模式。

研究结果表明，模式物种的数据无法完整反映真核生物中现存的微卫星变异情况。绝大多数门类、纲乃至目级类群内部，微卫星组成均存在极强的异质性。自相关分析显示，尽管分化时间晚于200 Mya（百万年前）的演化支（clade）内的物种，其微卫星含量往往较为相似，但随着分化时间增加，自相关关系会逐渐瓦解，甚至呈现负相关或无显著性。因此，类群（taxon）的演化时长似乎是削弱相关类群间系统发育模式的核心因素。最晚分化的脊索动物纲或目类群，仍保留其共同祖先的系统发育模式。但在更为古老的类群中，比如节肢动物的各纲，其系统发育模式已因各支系长期独立演化而被打乱。