用形态分类和ITS序列分析法对湖南桂东黄菌进行了鉴定,用基于Bayians理论和Markov chain Monte Carl(MCMC)算法的MrBayes3.1.2软件,将桂东黄菌与Genbank中牛肝菌科40个物种85个ITS序列进行系统发育树分析。结果表明,以欧洲缘盖牛肝菌(Bo...用形态分类和ITS序列分析法对湖南桂东黄菌进行了鉴定,用基于Bayians理论和Markov chain Monte Carl(MCMC)算法的MrBayes3.1.2软件,将桂东黄菌与Genbank中牛肝菌科40个物种85个ITS序列进行系统发育树分析。结果表明,以欧洲缘盖牛肝菌(Boletus appendiculatus)ITS序列为外群,湖南桂东黄菌与来自浙江庆元的所谓"缘盖牛肝菌"的两个序列以97%的后概率聚为一支,并与云南小美牛肝菌(Boletus speciosus)之ITS序列以79%的后概率聚为一支,而与欧洲缘盖牛肝菌ITS序列相比,谱系关系相距较远。认为,桂东黄菌的科学名称应为小美牛肝菌,庆元所产原名为缘盖牛肝菌的种类也应更正为小美牛肝菌。用MrBayes软件进行ITS序列分析的方法,对于在缺乏模式标本的情况下,难以准确识别的大型菌物种类的鉴定不失为一种可资借鉴的有效方法。鉴于小美牛肝菌较高的食用价值和强劲的市场需求,有必要加强栽培、促产等方面的研究。展开更多
We propose a simple statistical approach for using Dispersal-Vicariance Analysis （DIVA） software to infer biogeographic histories without fully bifurcating trees. In this approach, ancestral ranges are first optimiz...We propose a simple statistical approach for using Dispersal-Vicariance Analysis （DIVA） software to infer biogeographic histories without fully bifurcating trees. In this approach, ancestral ranges are first optimized for a sample of Bayesian trees. The probability P of an ancestral range r at a node is then calculated as P（rY） = ∑t^n=1 F（rY）t Pt where Y is a node, and F（rY） is the frequency of range r among all the optimal solutions resulting from DIVA optimization at node Y, t is one of n topologies optimized, and Pt is the probability of topology t. Node Y is a hypothesized ancestor shared by a specific crown lineage and the sister of that lineage ＂x＂, where x may vary due to phylogenetic uncertainty （polytomies and nodes with posterior probability 〈 100%）. Using this method, the ancestral distribution at Y can be estimated to provide inference of the geographic origins of the specific crown group of interest. This approach takes into account phylogenetic uncertainty as well as uncertainty from DIVA optimization. It is an extension of the previously described method called Bayes-DIVA, which pairs Bayesian phylogenetic analysis with biogeographic analysis using DIVA. Further, we show that the probability P of an ancestral range at Y calculated using this method does not equate to pp＊F（rY） on the Bayesian consensus tree when both variables are 〈 100%, where pp is the posterior probability and F（rY） is the frequency of range r for the node containing the specific crown group. We tested our DIVA-Bayes approach using Aesculus L., which has major lineages unresolved as a polytomy. We inferred the most probable geographic origins of the five traditional sections of Aesculus and ofAesculus californica Nutt. and examined range subdivisions at parental nodes of these lineages. Additionally, we used the DIVA-Bayes data from Aesculus to quantify the effects on biogeographic inference of including two wildcard fossil taxa in phylogenetic analysis. Our analysis resolved the geographic ranges of the parental nodes of the lineages of Aesculus with moderate to high probabilities. The probabilities were greater than those estimated using the simple calculation ofpp＊F（rY） at a statistically significant level for two of the six lineages. We also found that adding fossil wildcard taxa in phylogenetic analysis generally increased P for ancestral ranges including the fossil＇s distribution area. The AP was more dramatic for ranges that include the area of a wildcard fossil with a distribution area underrepresented among extant taxa. This indicates the importance of including fossils in biogeographic analysis. Exmination of range subdivision at the parental nodes revealed potential range evolution （extinction and dispersal events） along the stems ofA. californica and sect. Parryana.展开更多
基金supported by the 100 Young Talents Program of Chinese Academy of Sciences and partly supported by the Strategic Priority Research Program of Chinese Academy of Sciences (XDB26000000)~~
基金Supported by the Priority Programs in Science and Technology,Fujian Province(No.2010Y0010)the Priority Programin 863Project in China(No.2011AA02A114)~~
基金a National Science Foundation (USA) grant made to Xiang(DEB-0444125)supported by a NSF grant funded to D.E.Soltis (DEB-0090283)
文摘We propose a simple statistical approach for using Dispersal-Vicariance Analysis （DIVA） software to infer biogeographic histories without fully bifurcating trees. In this approach, ancestral ranges are first optimized for a sample of Bayesian trees. The probability P of an ancestral range r at a node is then calculated as P（rY） = ∑t^n=1 F（rY）t Pt where Y is a node, and F（rY） is the frequency of range r among all the optimal solutions resulting from DIVA optimization at node Y, t is one of n topologies optimized, and Pt is the probability of topology t. Node Y is a hypothesized ancestor shared by a specific crown lineage and the sister of that lineage ＂x＂, where x may vary due to phylogenetic uncertainty （polytomies and nodes with posterior probability 〈 100%）. Using this method, the ancestral distribution at Y can be estimated to provide inference of the geographic origins of the specific crown group of interest. This approach takes into account phylogenetic uncertainty as well as uncertainty from DIVA optimization. It is an extension of the previously described method called Bayes-DIVA, which pairs Bayesian phylogenetic analysis with biogeographic analysis using DIVA. Further, we show that the probability P of an ancestral range at Y calculated using this method does not equate to pp＊F（rY） on the Bayesian consensus tree when both variables are 〈 100%, where pp is the posterior probability and F（rY） is the frequency of range r for the node containing the specific crown group. We tested our DIVA-Bayes approach using Aesculus L., which has major lineages unresolved as a polytomy. We inferred the most probable geographic origins of the five traditional sections of Aesculus and ofAesculus californica Nutt. and examined range subdivisions at parental nodes of these lineages. Additionally, we used the DIVA-Bayes data from Aesculus to quantify the effects on biogeographic inference of including two wildcard fossil taxa in phylogenetic analysis. Our analysis resolved the geographic ranges of the parental nodes of the lineages of Aesculus with moderate to high probabilities. The probabilities were greater than those estimated using the simple calculation ofpp＊F（rY） at a statistically significant level for two of the six lineages. We also found that adding fossil wildcard taxa in phylogenetic analysis generally increased P for ancestral ranges including the fossil＇s distribution area. The AP was more dramatic for ranges that include the area of a wildcard fossil with a distribution area underrepresented among extant taxa. This indicates the importance of including fossils in biogeographic analysis. Exmination of range subdivision at the parental nodes revealed potential range evolution （extinction and dispersal events） along the stems ofA. californica and sect. Parryana.
