Palumbi S R, Cipriano F
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
J Hered. 1998 Sep-Oct;89(5):459-64. doi: 10.1093/jhered/89.5.459.
DNA sequence analysis is a powerful tool for identifying the source of samples thought to be derived from threatened or endangered species. Analysis of mitochondrial DNA (mtDNA) from retail whale meat markets has shown consistently that the expected baleen whale in these markets, the minke whale, makes up only about half the products analyzed. The other products are either unregulated small toothed whales like dolphins or are protected baleen whales such as humpback, Bryde's, fin, or blue whales. Independent verification of such mtDNA identifications requires analysis of nuclear genetic loci, but this is technically more difficult than standard mtDNA sequencing. In addition, evolution of species-specific sequences (i.e., fixation of sequence differences to produce reciprocally monophyletic gene trees) is slower in nuclear than in mitochondrial genes primarily because genetic drift is slower at nuclear loci. When will use of nuclear sequences allow forensic DNA identification? Comparison of neutral theories of coalescence of mitochondrial and nuclear loci suggests a simple rule of thumb. The "three-times rule" suggests that phylogenetic sorting at nuclear loci is likely to produce species-specific sequences when mitochondrial alleles are reciprocally monophyletic and the branches leading to the mtDNA sequences of a species are three times longer than the average difference observed within species. A preliminary test of the three-times rule, which depends on many assumptions about the species and genes involved, suggests that blue and fin whales should have species-specific sequences at most neutral nuclear loci, whereas humpback and fin whales should show species-specific sequences at fewer nuclear loci. Partial sequences of actin introns from these species confirm the predictions of the three-times rule and show that blue and fin whales are reciprocally monophyletic at this locus. These intron sequences are thus good tools for the identification of these species and will afford a chance to identify putative hybrid blue/fin whales thought to have entered the retail market after 1989.
DNA序列分析是一种强大的工具，可用于识别被认为源自受威胁或濒危物种的样本来源。对零售鲸鱼肉市场的线粒体DNA（mtDNA）分析一直表明，这些市场中预期的须鲸——小须鲸，仅占所分析产品的约一半。其他产品要么是未受监管的小型齿鲸，如海豚，要么是受保护的须鲸，如座头鲸、布氏鲸、长须鲸或蓝鲸。对此类mtDNA鉴定进行独立验证需要分析核基因座，但这在技术上比标准的mtDNA测序更困难。此外，物种特异性序列的进化（即序列差异的固定以产生相互单系的基因树）在核基因中比在线粒体基因中更慢，主要是因为遗传漂变在核基因座处更慢。何时使用核序列进行法医DNA鉴定？线粒体和核基因座合并的中性理论比较提出了一个简单的经验法则。“三倍法则”表明，当线粒体等位基因相互单系且导致一个物种的mtDNA序列的分支比物种内观察到的平均差异长三倍时，核基因座处的系统发育分类可能会产生物种特异性序列。对三倍法则的初步测试依赖于许多关于所涉及物种和基因的假设，结果表明，蓝鲸和长须鲸在大多数中性核基因座上应该有物种特异性序列，而座头鲸和长须鲸在较少的核基因座上应该显示物种特异性序列。来自这些物种的肌动蛋白内含子的部分序列证实了三倍法则的预测，并表明蓝鲸和长须鲸在该基因座上是相互单系的。因此，这些内含子序列是鉴定这些物种的良好工具，并且将提供机会识别被认为在1989年后进入零售市场的推定杂交蓝鲸/长须鲸。
