Lavin Matt, Herendeen Patrick S, Wojciechowski Martin F
Department of Plant Sciences, Montana State University, Bozeman, Montana 59717, USA.
Syst Biol. 2005 Aug;54(4):575-94. doi: 10.1080/10635150590947131.
Tertiary macrofossils of the flowering plant family Leguminosae (legumes) were used as time constraints to estimate ages of the earliest branching clades identified in separate plastid matK and rbcL gene phylogenies. Penalized likelihood rate smoothing was performed on sets of Bayesian likelihood trees generated with the AIC-selected GTR+ Gamma +I substitution model. Unequivocal legume fossils dating from the Recent continuously back to about 56 million years ago were used to fix the family stem clade at 60 million years (Ma), and at 1-Ma intervals back to 70 Ma. Specific fossils that showed distinctive combinations of apomorphic traits were used to constrain the minimum age of 12 specific internal nodes. These constraints were placed on stem rather than respective crown clades in order to bias for younger age estimates. Regardless, the mean age of the legume crown clade differs by only 1.0 to 2.5 Ma from the fixed age of the legume stem clade. Additionally, the oldest caesalpinioid, mimosoid, and papilionoid crown clades show approximately the same age range of 39 to 59 Ma. These findings all point to a rapid family-wide diversification, and predict few if any legume fossils prior to the Cenozoic. The range of the matK substitution rate, 2.1-24.6 x 10(-10) substitutions per site per year, is higher than that of rbcL, 1.6- 8.6 x 10(-10), and is accompanied by more uniform rate variation among codon positions. The matK and rbcL substitution rates are highly correlated across the legume family. For example, both loci have the slowest substitution rates among the mimosoids and the fastest rates among the millettioid legumes. This explains why groups such as the millettioids are amenable to species-level phylogenetic analysis with these loci, whereas other legume groups are not.
开花植物豆科(豆科植物)的第三纪宏观化石被用作时间限制,以估计在单独的质体matK和rbcL基因系统发育中确定的最早分支进化枝的年龄。对使用AIC选择的GTR + Gamma +I替代模型生成的贝叶斯似然树集进行了惩罚似然率平滑处理。从近代一直追溯到约5600万年前的明确豆科植物化石被用于将该科的茎进化枝固定在6000万年(Ma),并以100万年的间隔追溯到7000万年。显示出独特的衍征性状组合的特定化石被用于限制12个特定内部节点的最小年龄。这些限制被置于茎进化枝而非各自的冠进化枝上,以便偏向于更年轻的年龄估计。无论如何,豆科冠进化枝的平均年龄与豆科茎进化枝的固定年龄仅相差1.0至2.5百万年。此外,最古老的云实亚科、含羞草亚科和蝶形花亚科冠进化枝显示出大致相同的年龄范围,即39至59百万年。这些发现都指向了全科范围内的快速多样化,并预测在新生代之前几乎没有豆科植物化石。matK替代率的范围为每年每个位点2.1 - 24.6×10⁻¹⁰次替代,高于rbcL的范围1.6 - 8.6×10⁻¹⁰,并且密码子位置之间的速率变化更均匀。matK和rbcL替代率在豆科植物家族中高度相关。例如,在含羞草亚科中,这两个位点的替代率都是最慢的,而在崖豆族豆科植物中是最快的。这解释了为什么像崖豆族这样的类群适合用这些位点进行物种水平的系统发育分析,而其他豆科类群则不适合。