Apodemus （mice） and Rattus （rats） are the top rodent reservoirs for zoonoses in China,yet little is known about their diversity.We reexamined the alpha diversity of these two genera based on a new collection of sp...Apodemus （mice） and Rattus （rats） are the top rodent reservoirs for zoonoses in China,yet little is known about their diversity.We reexamined the alpha diversity of these two genera based on a new collection of specimens from China and their cyt b sequences in GenBank.We also tested whether species could be identified using external and craniodental measurements exclusively.Measurements from 147 specimens of Apodemus and 233 specimens of Rattus were used for morphological comparisons.We analysed 74 cyt b sequences of Apodemus and 100 cyt b sequences of Rattus to facilitate phylogenetic estimations.Results demonstrated that nine species of Apodemus and seven species of Rattus,plus a new subspecies of Rattus nitidus,are distributed in China.Principal component analysis using external and craniodental measurements revealed that measurements alone could not separate the recognized species.The occurrence of Rattus pyctoris in China remains uncertain.展开更多
One of the many problems that are considered to be NP-Hard is the Multiple Sequence Alignment one that initially requires, as for any other of its siblings, a specific encoding schema and design of the main functional...One of the many problems that are considered to be NP-Hard is the Multiple Sequence Alignment one that initially requires, as for any other of its siblings, a specific encoding schema and design of the main functionalities of the heuristics algorithm being implemented and executed. This paper intends to discuss our proposed generic implementation of the Simulated Annealing, inspired for the procedure of cooling and shaping methods of metals. In our algorithm, we attempted to add some executions tracing functionalities in order to help later analysis for initial parameters tuning. On another hand, we also tried to get closer in our attempt to mimic the cooling of metals, but giving it an option to run under different cooling schedules. We proposed a few schedules that seemed to be studied and/or used in many algorithm implementations.展开更多
This document elaborates on the generic implementation one of the main heuristics algorithms verified through its quick application to a biology problem requiring to find out an optimal sequences tree topology. In ord...This document elaborates on the generic implementation one of the main heuristics algorithms verified through its quick application to a biology problem requiring to find out an optimal sequences tree topology. In order to solve this problem, categorized as Non-Polynomial Hard (NP-Hard), “to minimize differences between given (leaf) and/or derived (parent) sequences”, many popular methods are used. “The higher the number of given sequences is, the more advisable and efficient it would be to go towards heuristics as they would provide a close-enough solution faster, as for instance genetic algorithms amongst others do. Thus, as part of a larger research in Heuristics and phylogenies, this paper aims to suggest a generic advanced flexible implementation of the Genetic Algorithm verified by a “general way to encode the problem into instances of different heuristic algorithms” as mentioned in our first reference below. The proposed algorithm will also present a chronology traceability feature for further analysis and potential improvements.展开更多
基金funded by the National Natural Science Foundation of China(3147011031301869+3 种基金31670388)Key Research Program of the Chinese Academy of Sciences(KJZD-EW-L07)Yunnan Applied Basic Research Projects(2014FB176)China Postdoctoral Science Foundation(2015M570801)
文摘Apodemus （mice） and Rattus （rats） are the top rodent reservoirs for zoonoses in China,yet little is known about their diversity.We reexamined the alpha diversity of these two genera based on a new collection of specimens from China and their cyt b sequences in GenBank.We also tested whether species could be identified using external and craniodental measurements exclusively.Measurements from 147 specimens of Apodemus and 233 specimens of Rattus were used for morphological comparisons.We analysed 74 cyt b sequences of Apodemus and 100 cyt b sequences of Rattus to facilitate phylogenetic estimations.Results demonstrated that nine species of Apodemus and seven species of Rattus,plus a new subspecies of Rattus nitidus,are distributed in China.Principal component analysis using external and craniodental measurements revealed that measurements alone could not separate the recognized species.The occurrence of Rattus pyctoris in China remains uncertain.
文摘One of the many problems that are considered to be NP-Hard is the Multiple Sequence Alignment one that initially requires, as for any other of its siblings, a specific encoding schema and design of the main functionalities of the heuristics algorithm being implemented and executed. This paper intends to discuss our proposed generic implementation of the Simulated Annealing, inspired for the procedure of cooling and shaping methods of metals. In our algorithm, we attempted to add some executions tracing functionalities in order to help later analysis for initial parameters tuning. On another hand, we also tried to get closer in our attempt to mimic the cooling of metals, but giving it an option to run under different cooling schedules. We proposed a few schedules that seemed to be studied and/or used in many algorithm implementations.
文摘This document elaborates on the generic implementation one of the main heuristics algorithms verified through its quick application to a biology problem requiring to find out an optimal sequences tree topology. In order to solve this problem, categorized as Non-Polynomial Hard (NP-Hard), “to minimize differences between given (leaf) and/or derived (parent) sequences”, many popular methods are used. “The higher the number of given sequences is, the more advisable and efficient it would be to go towards heuristics as they would provide a close-enough solution faster, as for instance genetic algorithms amongst others do. Thus, as part of a larger research in Heuristics and phylogenies, this paper aims to suggest a generic advanced flexible implementation of the Genetic Algorithm verified by a “general way to encode the problem into instances of different heuristic algorithms” as mentioned in our first reference below. The proposed algorithm will also present a chronology traceability feature for further analysis and potential improvements.
基金the Chinese Academy of Sciences Visiting Professorship Scheme(2011T1S20)the National Natural Science Foundation of China(31000258,31470306,31260038,31460159)+3 种基金the Key Laboratory of Plant Diversity and Biogeography of East AsiaKunming Institute of Botany(KIB)&the Chinese Academy of Sciences(2014CB954100)Guangxi Natural Science Foundation(2015GXNSFBB139004&2015GXNSFBA139105)Guangxi Forest Science&Technology Foundation(Gui Lin Ke Zi〔2014〕No.27)
基金The Natural Science Foundation of Yunnan Province (2007C099M)the National Natural Science Foundation of China(30970332, 30730017)the National Basic Research Program of China 973 Program (2007CB411600)
