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基因组中。若能在系统发育框架下比对其分布特征，便可更全面地阐明微卫星的起源与传播规律。尽管模式物种的相关研究数据正快速积累，但受限于物种覆盖广度不足，现有数据仍存在显著局限性，进而不可避免地忽略了类群内部的遗传变异。故此，类群间的表观差异可能被过度放大，唯有先完成类群内部变异的分析，方可推导得出可靠的普遍性结论。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鸟枪测序序列，分析了其微卫星覆盖度与基序模式，旨在探究这些物种的微卫星组成是否存在一致的系统发育特征。研究结果显示，模式物种的相关数据无法完整反映真核生物界内现存的微卫星变异全貌。本研究发现，大多数门类、纲甚至目内部的微卫星组成均存在极强的异质性。自相关分析结果显示，分化时间晚于2亿年（200 Mya）的演化支内，物种的微卫星含量往往较为相似；但随着分化时间的增加，这种自相关关系会逐渐消失，甚至呈现负相关或无显著性关联。故此，分类群的演化时长似乎是消解相关类群间系统发育特征的首要驱动因素。脊索动物门中较晚分化的纲或目，仍保留着其共同祖先的微卫星组成特征。但在更为古老的类群中，例如节肢动物门的各纲，其系统发育特征已因各谱系长期独立演化而被彻底扰乱。