沉闷科学的掘墓人分享 http://blog.sciencenet.cn/u/Bearjazz

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每日翻译20190729

已有 519 次阅读 2019-7-29 16:33 |个人分类:翻译作品|系统分类:科研笔记| r8s软件, 分子钟, 昆虫, 线粒体DNA, 每百万年

#编者信息

熊荣川

明湖实验室

xiongrongchuan@126.com

http://blog.sciencenet.cn/u/Bearjazz

Relative ages of nodes were estimated   using the r8s   software (Sanderson, 2002) by fitting branch lengths of an ML tree using   penalized likelihood and a smoothing parameter of 10, chosen as optimal by   cross-validation. Absolute ages were estimated setting the split of R. aurifodina (sample 204) and R. salicursoria (sample 208) to 3.2   Mya (Pons et al., 2004). This was based on an estimate from a phylogeny of   worldwide lineages of Cicindela   sensu lato calibrated from biogegraphic evidence in North American lineages   which included only these two species to represent Rivacidela (Barraclough and Vogler, 2002). Sequence divergence   between individuals of these species was 6.0% (SD 0.14%) and hence the   estimate corresponds closely to the widely used insect mtDNA molecular clock   calibration of 2.3% per My (Brower, 1994). Lineage-through-time analyses were   obtained as a semilogarithmic plot of the number of lineages against time   since the first bifurcation (Nee et al., 1992).

使用r8s软件(Sanderson, 2002)罚分似然法的枝长拟合来估计节点的相对年龄,并通过交叉验证选择最佳平滑参数为10。估计具体年代时,将R. aurifodina(样本204)和R. salicursoria(样本208)分化时间设为3.2 个百万年(Pons et al., 2004)。这是基于一项来自全世界广义上的虎甲属(Cicindela sensu lato)系统发育研究根据生物地理学证据得到的校准时间,该系统发育中代表Rivacidela属的物种仅包括这两个(Barraclough and Vogler, 2002)。这些物种个体之间的序列差异平均为6.0%(标准差0.14%),因此,估计值与广泛使用的昆虫mtDNA分子钟校准值(每百万年变异2.3%)非常接近(Brower, 1994)。支系随时间变化的分析用一个自第一次分叉以来谱系数量相对时间的变化的半对数图来表示(Nee et al., 1992)。

Pons J, Barraclough T G, Gomez-Zurita J, et   al. Sequence-based species delimitation for the DNA taxonomy of undescribed   insects[J]. Systematic biology, 2006, 55(4): 595-609.




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