Leibniz Institute for Natural Product Research and Infection Biology, Jena, Germany.
Mol Phylogenet Evol. 2011 Feb;58(2):404-8. doi: 10.1016/j.ympev.2010.11.028. Epub 2010 Dec 9.
The mitochondrial control region (mtCR) is a widely used genetic marker for phylogenetic, phylogeographic and population genetic inference. The analysis of mtCR in 115 Indonesian specimens of the giant tiger shrimp, Penaeus monodon, revealed 26 individuals yielding a second - apparently paralogous - sequence in addition to the putatively authentic mitochondrial haplotype. The paralogous haplotypes fell into two major haplogroups that are highly diverged with respect to the authentic mitochondrial haplotypes (average pairwise sequence divergence of 12.5% and 5.0%, respectively). A comparison with published mtCR sequences of P. monodon showed that the paralogous contaminant sequences were inadvertently included in a series of recent population genetic studies, leading to seriously compromised conclusions about genetic diversity and differentiation. The prevalence of the paralogous haplotypes throughout the sampled Indo-Pacific populations is highly skewed: From African and Indian individuals only paralogs have been sequenced, while they are completely absent from Australian individuals. This suggests that geographically unequally distributed allelic variants at binding sites of the primer pair ordinarily used to amplify mtCR in P. monodon suppressed the amplification of authentic mtCR in a wide range of samples.
线粒体控制区（mtCR）是一种广泛用于系统发育、系统地理学和种群遗传学推断的遗传标记。对 115 个印度尼西亚巨型虎虾（Penaeus monodon）标本的 mtCR 分析显示，除了假定的真实线粒体单倍型外，还有 26 个个体产生了第二个——显然是平行的——序列。平行单倍型分为两个主要单倍型组，与真实线粒体单倍型高度分化（平均成对序列差异分别为 12.5%和 5.0%）。与已发表的 P. monodon mtCR 序列的比较表明，平行污染物序列在最近的一系列种群遗传研究中被无意中包含在内，导致对遗传多样性和分化的结论严重受损。在整个取样的印度洋-太平洋种群中，平行单倍型的流行高度偏斜：从非洲和印度个体中只测序了平行序列，而澳大利亚个体中则完全没有。这表明，在通常用于扩增 P. monodon mtCR 的引物对的结合位点中，地理上分布不均的等位变异抑制了广泛样本中真实 mtCR 的扩增。
