[Objective]The aim was to prove that the mitochondrial genes of Cyt b and 12S rRNA with different evolutional rates have effects on the topological structures of phylogenetic trees.[Method]The complete sequences of Cy...[Objective]The aim was to prove that the mitochondrial genes of Cyt b and 12S rRNA with different evolutional rates have effects on the topological structures of phylogenetic trees.[Method]The complete sequences of Cyt b and 12S rRNA from 15 species in 12 families of snakes were downloaded and extracted from GenBank,while their molecular phylogenetic trees were constructed by Maximum Likelihood（ML） method with GTR ＋I ＋G substitute model based on PAUP4.0 software.[Result]With the same software,methods and species,the difference in topological structures of phylogenetic trees was mainly due to different evolutional rates of Cyt b and 12S rRNA genes.[Conclusion]In studies on phylogenetic trees,aimed to different research species and purposes,phylogenetic trees should be constructed by choosing the correct and appropriate genes.展开更多
In the paper, related research and progress of molecular clock hypothesis were summarized, including definition of molecular clock, supporting proofs, contro- versy, significance and perfection, application and accomp...In the paper, related research and progress of molecular clock hypothesis were summarized, including definition of molecular clock, supporting proofs, contro- versy, significance and perfection, application and accompanying challenges.展开更多
To improve the performance of Saitou and Nei＇s algorithm （SN） and Studier and Keppler＇s improved algorithm （SK） for constructing neighbor-joining phylogenetic trees and reduce the time complexity of the computat...To improve the performance of Saitou and Nei＇s algorithm （SN） and Studier and Keppler＇s improved algorithm （SK） for constructing neighbor-joining phylogenetic trees and reduce the time complexity of the computation, a fast algorithm is proposed. The proposed algorithm includes three techniques. First, a linear array A[N] is introduced to store the sum of every row of the distance matrix （the same as SK）, which can eliminate many repeated computations. Secondly, the value of A [i] is computed only once at the beginning of the algorithm, and is updated by three elements in the iteration. Thirdly, a very compact formula for the sum of all the branch lengths of operational taxonomic units （OTUs） i and j is designed, and the correctness of the formula is proved. The experimental results show that the proposed algorithm is from tens to hundreds times faster than SN and roughly two times faster than SK when N increases, constructing a tree with 2 000 OTUs in 3 min on a current desktop computer. To earn the time with the cost of the space and reduce the computations in the innermost loop are the basic solutions for algorithms with many loops.展开更多
3D traveltime calculation is widely used in seismic exploration technologies such as seismic migration and tomography. The fast marching method （FMM） is useful for calculating 3D traveltime and has proven to be effi...3D traveltime calculation is widely used in seismic exploration technologies such as seismic migration and tomography. The fast marching method （FMM） is useful for calculating 3D traveltime and has proven to be efficient and stable. However, it has low calculation accuracy near the source, which thus gives it low overall accuracy. This paper proposes a joint traveltime calculation method to solve this problem. The method firstly employs the wavefront construction method （WFC）, which has a higher calculation accuracy than FMM in calculating traveltime in the small area near the source, and secondly adopts FMM to calculate traveltime for the remaining grid nodes. Due to the increase in calculation precision of grid nodes near the source, this new algorithm is shown to have good calculation precision while maintaining the high calculation efficiency of FMM, which is employed in most of the computational area. Results are verified using various numerical models.展开更多
基金Supported by Natural Science Fund in Guangdong(915102600100-0003)Project for Excellent Young Scientists and Engineers in Guangdong Academy of Sciences(200804)Fund of Open Laboratory for Protection and Utilization of Wildlife in Guangdong(200901)~~
文摘[Objective]The aim was to prove that the mitochondrial genes of Cyt b and 12S rRNA with different evolutional rates have effects on the topological structures of phylogenetic trees.[Method]The complete sequences of Cyt b and 12S rRNA from 15 species in 12 families of snakes were downloaded and extracted from GenBank,while their molecular phylogenetic trees were constructed by Maximum Likelihood（ML） method with GTR ＋I ＋G substitute model based on PAUP4.0 software.[Result]With the same software,methods and species,the difference in topological structures of phylogenetic trees was mainly due to different evolutional rates of Cyt b and 12S rRNA genes.[Conclusion]In studies on phylogenetic trees,aimed to different research species and purposes,phylogenetic trees should be constructed by choosing the correct and appropriate genes.
基金Supported by Hunan Education Reform ProjectEducation Reform Project of Hunan University of Humanities,Science and Technology(RKJGY1101)~~
文摘In the paper, related research and progress of molecular clock hypothesis were summarized, including definition of molecular clock, supporting proofs, contro- versy, significance and perfection, application and accompanying challenges.
文摘To improve the performance of Saitou and Nei＇s algorithm （SN） and Studier and Keppler＇s improved algorithm （SK） for constructing neighbor-joining phylogenetic trees and reduce the time complexity of the computation, a fast algorithm is proposed. The proposed algorithm includes three techniques. First, a linear array A[N] is introduced to store the sum of every row of the distance matrix （the same as SK）, which can eliminate many repeated computations. Secondly, the value of A [i] is computed only once at the beginning of the algorithm, and is updated by three elements in the iteration. Thirdly, a very compact formula for the sum of all the branch lengths of operational taxonomic units （OTUs） i and j is designed, and the correctness of the formula is proved. The experimental results show that the proposed algorithm is from tens to hundreds times faster than SN and roughly two times faster than SK when N increases, constructing a tree with 2 000 OTUs in 3 min on a current desktop computer. To earn the time with the cost of the space and reduce the computations in the innermost loop are the basic solutions for algorithms with many loops.
基金supported by NSFC(Nos.41274120,41404085,and 41504084)
文摘3D traveltime calculation is widely used in seismic exploration technologies such as seismic migration and tomography. The fast marching method （FMM） is useful for calculating 3D traveltime and has proven to be efficient and stable. However, it has low calculation accuracy near the source, which thus gives it low overall accuracy. This paper proposes a joint traveltime calculation method to solve this problem. The method firstly employs the wavefront construction method （WFC）, which has a higher calculation accuracy than FMM in calculating traveltime in the small area near the source, and secondly adopts FMM to calculate traveltime for the remaining grid nodes. Due to the increase in calculation precision of grid nodes near the source, this new algorithm is shown to have good calculation precision while maintaining the high calculation efficiency of FMM, which is employed in most of the computational area. Results are verified using various numerical models.
