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（Microsatellites）广泛存在于真核生物基因组中。若能在系统发育框架下比较其分布特征，可更全面地理解微卫星的起源与扩散机制。尽管模式物种的相关研究数据正快速积累，但受限于物种覆盖深度不足，现有数据必然会忽略类群内的变异情况。如此一来，类群间的表观差异可能被夸大，唯有开展类群内变异分析后，才能得出可靠的普适性结论。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鸟枪法测序数据，分析其微卫星覆盖度与基序模式，旨在检验这些物种的微卫星组成是否存在一致的系统发育特征。研究结果清晰表明，基于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。本研究发现，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。自相关分析结果显示，分化时间晚于2亿年前（200 Mya）的演化支内，物种的微卫星含量往往较为相似；但随着分化时间增加，自相关模式会被打破，相关系数变为负值或不再具有统计学显著性。因此，类群的演化时长似乎是削弱相关类群间系统发育特征的核心因素。脊索动物门中分化最晚的纲或目类群，仍保留其共同祖先的系统发育特征模式。但对于演化时长更久的类群，如节肢动物门的各纲，其系统发育特征已因各支系长期独立演化而被打乱。