Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks
Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks
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DOI：
10.1093/molbev/msg236
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发表时间：
2004-01-01
影响因子：
10.7
通讯作者：
Kumar, S
中科院分区：
文献类型：
--
作者：
Tamura, K;Subramanian, S;Kumar, S
近一个世纪以来，黑腹果蝇一直是研究遗传学、发育、行为、生理学、进化和群体遗传学的典型模式生物。尽管强调了这一点，并且完成了其核基因组序列，但由于缺乏广泛的化石记录和生物地理数据，导致这种果蝇起源的主要物种形成事件的时间仍然难以捉摸。使用分子钟作为一种替代方法充满了核苷酸和氨基酸取代的非时钟积累。在这里，我们提出了一种新的方法，其中使用基因组突变距离来克服这些限制，并利用所有可用的基因序列数据来构建果蝇分子时间尺度。我们对来自176个核基因的2977个成对序列比较的分析显示，果蝇的长期突变时钟以每个Myr每千碱基对11.1个突变的速率运行。基于基因组突变时钟的具有里程碑意义的物种形成事件的时序表明，它与D. simulans拥有最近的共同祖先5.4 MYA，与D. erecta+D.拥有12.6 MYA。orena， 12.8 MYA与D. yakuba+D。高桥亚群为35.6 MYA， montium亚群为41.3 MYA， ananassae亚群为44.2 MYA，暗箱亚群为54.9 MYA， willistoni亚群为62.2 MYA，果蝇亚属为62.9 MYA。这些估计和其他估计与有限的生物地理和化石记录中已知的估计是一致的。果蝇进化的时间格局与古气候变化的降温格局和新生代栖息地破碎化相吻合。
Drosophila melanogaster has been a canonical model organism to study genetics, development, behavior, physiology, evolution, and population genetics for nearly a century. Despite this emphasis and the completion of its nuclear genome sequence, the timing of major speciation events leading to the origin of this fruit fly remain elusive because of the paucity of extensive fossil records and biogeographic data. Use of molecular clocks as an alternative has been fraught with non-clock-like accumulation of nucleotide and amino-acid substitutions. Here we present a novel methodology in which genomic mutation distances are used to overcome these limitations and to make use of all available gene sequence data for constructing a fruit fly molecular time scale. Our analysis of 2977 pairwise sequence comparisons from 176 nuclear genes reveals a long-term fruit fly mutation clock ticking at a rate of 11.1 mutations per kilobase pair per Myr. Genomic mutation clock-based timings of the landmark speciation events leading to the evolution of D. melanogaster show that it shared most recent common ancestry 5.4 MYA with D. simulans, 12.6 MYA with D. erecta+D. orena, 12.8 MYA with D. yakuba+D. teisseri, 35.6 MYA with the takahashii subgroup, 41.3 MYA with the montium subgroup, 44.2 MYA with the ananassae subgroup, 54.9 MYA with the obscura group, 62.2 MYA with the willistoni group, and 62.9 MYA with the subgenus Drosophila. These and other estimates are compatible with those known from limited biogeographic and fossil records. The inferred temporal pattern of fruit fly evolution shows correspondence with the cooling patterns of paleoclimate changes and habitat fragmentation in the Cenozoic.