Won Hyosig, Renner Susanne S
Department of Biology, University of Missouri-St. Louis, 8001 Natural Bridge Road, St. Louis, Missouri 63121, USA.
Syst Biol. 2006 Aug;55(4):610-22. doi: 10.1080/10635150600812619.
Most implementations of molecular clocks require resolved topologies. However, one of the Bayesian relaxed clock approaches accepts input topologies that include polytomies. We explored the effects of resolved and polytomous input topologies in a rate-heterogeneous sequence data set for Gnetum, a member of the seed plant lineage Gnetales. Gnetum has 10 species in South America, 1 in tropical West Africa, and 20 to 25 in tropical Asia, and explanations for the ages of these disjunctions involve long-distance dispersal and/or the breakup of Gondwana. To resolve relationships within Gnetum, we sequenced most of its species for six loci from the chloroplast (rbcL, matK, and the trnT-trnF region), the nucleus (rITS/5.8S and the LEAFY gene second intron), and the mitochondrion (nad1 gene second intron). Because Gnetum has no fossil record, we relied on fossils from other Gnetales and from the seed plant lineages conifers, Ginkgo, cycads, and angiosperms to constrain a molecular clock and obtain absolute times for within-Gnetum divergence events. Relationships among Gnetales and the other seed plant lineages are still unresolved, and we therefore used differently resolved topologies, including one that contained a basal polytomy among gymnosperms. For a small set of Gnetales exemplars (n = 13) in which rbcL and matK satisfied the clock assumption, we also obtained time estimates from a strict clock, calibrated with one outgroup fossil. The changing hierarchical relationships among seed plants (and accordingly changing placements of distant fossils) resulted in small changes of within-Gnetum estimates because topologically closest constraints overrode more distant constraints. Regardless of the seed plant topology assumed, relaxed clock estimates suggest that the extant clades of Gnetum began diverging from each other during the Upper Oligocene. Strict clock estimates imply a mid-Miocene divergence. These estimates, together with the phylogeny for Gnetum from the six combined data sets, imply that the single African species of Gnetum is not a remnant of a once Gondwanan distribution. Miocene and Pliocene range expansions are inferred for the Asian subclades of Gnetum, which stem from an ancestor that arrived from Africa. These findings fit with seed dispersal by water in several species of Gnetum, morphological similarities among apparently young species, and incomplete concerted evolution in the nuclear ITS region.
分子钟的大多数实现方式都需要确定的拓扑结构。然而，贝叶斯宽松时钟方法之一接受包含多歧分支的输入拓扑结构。我们在种子植物谱系买麻藤目中的一个成员——买麻藤属的速率异质序列数据集中，探究了确定的和多歧的输入拓扑结构的影响。买麻藤属在南美洲有10个物种，在热带西非有1个物种，在热带亚洲有20到25个物种，对这些间断分布的年代解释涉及长距离扩散和/或冈瓦纳大陆的解体。为了解决买麻藤属内部的亲缘关系，我们对其大部分物种的六个基因座进行了测序，这些基因座分别来自叶绿体（rbcL、matK和trnT - trnF区域）、细胞核（rITS/5.8S和LEAFY基因的第二个内含子）以及线粒体（nad1基因的第二个内含子）。由于买麻藤属没有化石记录，我们依靠其他买麻藤目以及种子植物谱系松柏类、银杏、苏铁和被子植物的化石来约束分子钟，并获得买麻藤属内部分歧事件的绝对时间。买麻藤目与其他种子植物谱系之间的亲缘关系仍未解决，因此我们使用了不同分辨率的拓扑结构，包括一个在裸子植物中包含基部多歧分支的拓扑结构。对于一小部分买麻藤目样本（n = 13），其中rbcL和matK满足时钟假设，我们还从一个严格时钟获得了时间估计，该时钟用一个外类群化石进行校准。种子植物之间不断变化的层次关系（以及相应地遥远化石的位置变化）导致买麻藤属内估计值的微小变化，因为拓扑上最接近的约束优先于更遥远的约束。无论假设的种子植物拓扑结构如何，宽松时钟估计表明，现存的买麻藤属分支在上新世晚期开始彼此分化。严格时钟估计意味着中新世中期分化。这些估计值，连同来自六个组合数据集的买麻藤属系统发育，意味着买麻藤属的单一非洲物种不是曾经冈瓦纳分布的残余。推断买麻藤属亚洲亚分支在中新世和上新世有范围扩张，其起源于一个从非洲到达的祖先。这些发现与几种买麻藤属物种通过水进行种子传播、明显年轻物种之间的形态相似性以及细胞核ITS区域不完全的协同进化相吻合。
