Fossil calibration of molecular divergence infers a moderate mutation rate and recent radiations for Pinus
Fossil calibration of molecular divergence infers a moderate mutation rate and recent radiations for Pinus
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DOI：
10.1093/molbev/msl131
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发表时间：
2007-01-01
影响因子：
10.7
通讯作者：
Cronn, Richard
中科院分区：
文献类型：
--
作者：
Ann, Willyard;Syring, John;Cronn, Richard
松树的沉默突变率估计值相差50倍，从被子植物到植物中报道的最慢的。这些差异要么反映了非凡的基因组过程，要么反映了不一致的化石校准，它们对种群和生物地理推断产生了重要影响。在这里，我们估计突变率从4松属物种，代表主要谱系使用11个核和4个叶绿体位点。在松属亚属的分歧与最古老的叶化石subg。Strobus（始新世; 45 MYA）或最近发表的subg。Strobus木化石（白垩纪; 8500万年）。这些校准确定了松属190-102 MYA的起源，并给出了核和叶绿体基因组的绝对沉默率估计值分别为0.70-1.31 × 10（-9）和0.22-0.42 × 10（-9）·位点（-1）·年（-1）。这些速率比被子植物慢约4至20倍，但与许多以前的估计不同，它们与松树中观察到的每代高有害突变率更一致。从细胞核和叶绿体基因组的年表显示，亚属的分歧约占一半的时间，因为松从云杉分歧，随后的辐射发生最近。通过扩大采样，包括松的系统发育多样性，我们预测，最现存的子部分分歧在中新世。此外，subsect. Australales，Ponderosae和Contortae，包含50多个现存物种，在5百万年的时间跨度内辐射，最近开始于18百万年。一个始新世的松树亚属分歧（使用叶化石）并不冲突与化石为基础的估计松云杉分裂，但白垩纪的分歧使用木材化石容纳渐新世化石，可能代表现代的亚类。由于同质性和极性的字符状态尚未测试的化石松分配，化石和校准节点的选择代表了一个重要的不确定性来源。基于几条证据线（包括协议与年龄推断使用校准以外的松），我们的结论是，85 MYA校准在分歧的松树亚属提供了一个合理的下限，年龄和突变率估计的进一步完善将需要综合检查松树化石的历史。
Silent mutation rate estimates for Pinus vary 50-fold, ranging from angiosperm-like to among the slowest reported for plants. These differences either reflect extraordinary genomic processes or inconsistent fossil calibration, and they have important consequences for population and biogeographical inferences. Here we estimate mutation rates from 4 Pinus species that represent the major lineages using 11 nuclear and 4 chloroplast loci. Calibration was tested at the divergence of Pinus subgenera with the oldest leaf fossil from subg. Strobus (Eocene; 45 MYA) or a recently published subg. Strobus wood fossil (Cretaceous; 85 MYA). These calibrations place the origin of Pinus 190-102 MYA and give absolute silent rate estimates of 0.70-1.31 x 10(-9) and 0.22-0.42 x 10(-9).site(-1).year(-1) for the nuclear and chloroplast genomes, respectively. These rates are approximately 4- to 20-fold slower than angiosperms, but unlike many previous estimates, they are more consistent with the high per-generation deleterious mutation rates observed in pines. Chronograms from nuclear and chloroplast genomes show that the divergence of subgenera accounts for about half of the time since Pinus diverged from Picea, with subsequent radiations occurring more recently. By extending the sampling to encompass the phylogenetic diversity of Pinus, we predict that most extant subsections diverged during the Miocene. Moreover, subsect. Australes, Ponderosae, and Contortae, containing over 50 extant species, radiated within a 5 Myr time span starting as recently as 18 MYA. An Eocene divergence of pine subgenera (using leaf fossils) does not conflict with fossil-based estimates of the Pinus-Picea split, but a Cretaceous divergence using wood fossils accommodates Oligocene fossils that may represent modern subsections. Because homoplasy and polarity of character states have not been tested for fossil pine assignments, the choice of fossil and calibration node represents a significant source of uncertainty. Based on several lines of evidence (including agreement with ages inferred using calibrations outside of Pinus), we conclude that the 85 MYA calibration at the divergence of pine subgenera provides a reasonable lower bound and that further refinements in age and mutation rate estimates will require a synthetic examination of pine fossil history.