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Factors affecting mito-nuclear codon usage interactions in the OXPHOS system of Drosophila melanogaster

Journal of Genetics and Genomics 2008年第12期35卷 729-735页

作者： Zheng Sun Liang Ma robert w. murphy Xiansheng Zhang Daw.i Huang College of Plant Protection Shandong Agricultural University Tai＇an 271018 China Institute of Zoology Chinese Academy of Sciences Beijing 100101 China Department of Natural History Royal Ontario Museum 100 Queen＇s Park Toronto ON M5S 2C6 Canada College of Life Sciences Shandong Agricultural University Tai＇an 271018 China

Codon usage bias varies considerably among genomes and even w.thin the genes of the same genome. In eukaryotic organisms, energy production in the form of oxidative phosphorylation （OXPHOS） is the only process under control of both nuclear and mitochondrial genomes. Although factors affecting codon usage in a single genome have been studied, this has not occurred w.en both interactional genomes are involved. Consequently, w. investigated w.ether or not other factors influence codon usage of coevolved genes. w. used Drosophila melanogaster as a model organism. Our χ^2 test on the number of codons of nuclear and mitochondrial genes involved in the OXPHOS system w.s significantly different （χ^2= 7945.16, P 〈 0.01）. A plot of effective number of codons against GC3s content of nuclear genes show.d that few.genes lie on the expected curve, indicating that codon usage w.s random. Correspondence analysis indicated a significant correlation betw.en axis 1 and codon adaptation index （R = 0.947, P 〈 0.01） in every nuclear gene sequence. Thus, codon usage bias of nuclear genes appeared to be affected by translational selection. Correlation betw.en axis 1 coordinates and GC content （R = 0.814, P 〈 0.01） indicated that the codon usage of nuclear genes w.s also affected by GC composition. Analysis of mitochondrial genes did not reveal a significant correlation betw.en axis 1 and any parameter. Statistical analyses indicated that codon usages of both nDNA and mtDNA w.re subjected to context-dependent mutations.

关键词： Drosophila melanogaster oxidative phosphorylation nDNA mtDNA codon usage

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Genetic consequences of postglacial colonization by the endemic Yarkand hare (Lepus yarkandensis) of the arid Tarim Basin

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Chinese Science Bulletin 2011年第13期56卷 1370-1382页

作者： SHAN w.nJuan LIU Jiang YU Li robert w. murphy MAHMUT Halik ZHANG YaPing College of Life Sciences and Technology Xinfiang University Urumqi 830046 China Laboratory for Conservation and Utilization ofBio-resource & Key Laboratory for Microbial Resources of the Ministry of Education Yunnan University Kunming 650091 China State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Kunming 650223 China Centre for Biodiversity and Conservation Biology Royal Ontario Museum Ontario M5S 2C6 Canada

Orogenesis of the Qinghai-Tibetan Plateau,w.ich occurred in a stepw.se manner,contributed to the extreme aridity of the Tarim Basin,resulting in vulnerable and unstable *** climatic oscillations may have affected the ecosystems and,consequently,the distributions and genetic structuring of the Tarim Basin's *** used nucleotide sequence data from 2 mitochondrial (mt) DNA genes (Cyt b and the D-loop) to test hypotheses associated w.th the matrilineal and demographical histories of the Tarim Basin's endemic Yarkand hare (Lepus yarkandensis).Range-w.de sampling involving 20 populations and 224 individuals detected 126 haplotypes that clustered into 5 major lineages in both the phylogenetic tree and median-joining *** from the northern and eastern Tarim Basin shared a similar history,as did those from the w.stern and southern *** analysis and genetic diversity estimations suggested that the w.stern and southern regions might have served as glacial refugia for the Yarkand hare during Quaternary climatic *** distribution of the Yarkand hare,especially in the northern and eastern parts,probably represented 3 postglacial colonization events,dated to 0.21,0.090 and 0.054 MYA,w.ich corresponded to know. interglacial *** the relatively complete geographic isolation betw.en the eastern and southern populations,the Yarkand hare likely dispersed during postglacial periods from the southw.st to the north,and then onw.rd to the *** absence of w.ter likely forced the species into refugia,and this differed from other Pleistocene biogeographical *** demographical and historical patterns have important implications for conservation.

关键词：塔里木盆地北部叶尔羌野兔遗传后果干旱殖民化冰后期生态系统

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Conserved sequences identify the closest living relatives of primates

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Zoological Research 2019年第6期40卷 532-540页

作者： Mei-Ling Zhang Ming-Li Li Adeola Oluw.kemi Ayoola robert w. murphy Dong-Dong w. Yong Shao Department of Acute Infectious Diseases Control and Prevention Yunnan Provincial Centre for Disease Control and PreventionKunming Yunnan 650022China State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of SciencesKunming Yunnan 650223China Centre for Biodiversity and Conservation Biology Royal Ontario MuseumToronto M5S 2C6Canada Kunming College of Life Science University of the Chinese Academy of SciencesKunming Yunnan 650223China

Elucidating the closest living relatives of extant primates is essential for fully understanding important biological processes related to the genomic and phenotypic evolution of primates, especially of humans. How.ver, the phylogenetic placement of these primate relatives remains controversial, w.th three primary hypotheses currently espoused based on morphological and molecular evidence. In the present study, w. used tw. algorithms to analyze differently partitioned genomic datasets consisting of 45.4 Mb of conserved non-coding elements and 393 kb of concatenated coding sequences to test these hypotheses. w. assessed different genomic histories and compared w.th other molecular studies found solid support for colugos being the closest living relatives of primates. Our phylogeny show.d Cercopithecinae to have low.levels of nucleotide divergence, especially for Papionini, and gibbons to have a high rate of divergence. The MCMCtree comprehensively updated divergence dates of early evolution of Primatomorpha and Primates.

关键词： Phylogeny Colugos Primates Conserved non-coding elements Divergence time

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A new.species of the genus Raorchestes(Anura:Rhacophoridae) from Yunnan Province, China

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Zoological Research 2019年第6期40卷 558-563页

作者： Yun-He w. Chatmongkon Suw.nnapoom Kai Xu Jin-Min Chen Jie-Qiong Jin Hong-Man Chen robert w. murphy Jing Che State Key Laboratory of Genetic Resources and Evolution State Kunming Institute of ZoologyChinese Academy of SciencesKunming Yunnan 650223China Kunming College of Life Science University of the Chinese Academy of SciencesKunming Yunnan 650204China School of Agriculture and Natural Resources University of PhayaoPhayao 56000Thailand Centre for Biodiversity and Conservation Biology Royal Ontario MuseumToronto Ontario M5S 2C6Canada

DEAR EDITOR,A new.bush frog species, Raorchestes cangyuanensis sp. nov., from Cangyuan, Yunnan Province, China, is described based on morphological and molecular analyses. It differs from all know. congeners by a combination of the follow.ng characters: body size small, adult snout-vent length (SVL) 16.1–20.0 mm in males (n=3);tympanum indistinct;tips of all fingers and toes expanded into discs w.th circummarginal grooves;rudimentary w.bbing betw.en toes;fingers and toes w.th lateral dermal fringes;inner and outer metacarpal tubercles present;heels meeting w.en limbs held at right angles to body;crotch w.th a distinct black patch;discs of fingers and toes orange;male w.th external single subgular vocal sac and reddish nuptial pad at the base of first finger.

关键词： Raorchestes Yunnan

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A new.species of the genus Xenophrys(Anura:Megophryidae) from northern Thailand

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Zoological Research 2019年第6期40卷 564-574页

作者： Yun-He w. Chatmongkon Suw.nnapoom Nikolay A. Poyarkov,Jr. Parinya Paaw.ngkhanant Kai Xu Jie-Qiong Jin robert w. murphy Jing Che State Key Laboratory of Genetic Resources and Evolution State Kunming Institute of ZoologyChinese Academy of SciencesKunming Yunnan 650223China Kunming College of Life Science University of the Chinese Academy of SciencesKunming Yunnan 650204China Southeast Asia Biodiversity Research Institute Chinese Academy of SciencesYezin Nay Pyi Taw 05282Myanmar School of Agriculture and Natural Resources University of PhayaoPhayao 56000Thailand Department of Vertebrate Zoology Biological FacultyLomonosov Moscow State UniversityMoscow 119991Russia Joint Russian-Vietnamese Tropical Research and Technological Center 63 Nguyen Van Huyen RoadNghia DoCau GiayHanoiVietnam Centre for Biodiversity and Conservation Biology Royal Ontario MuseumToronto M5S 2C6Canada

DEAR EDITOR,Species of Xenophrys are conserved morphologically and live primarily in forests. In Thailand, the genus harbors many cryptic species. Herein w. report the collection of specimens from Doi Inthanon, Chiang Mai Province, northern Thailand, w.ich w.re identified previously as X. minor. Molecular and morphological analyses find that these specimens differ significantly from other know. congeners, and therefore w. describe a new.species. Further, our phylogenetic analyses indicate that X. latidactyla is a junior synonym of X. palpebralespinosa.

关键词： genus Xenophrys Megophryidae Thailand

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Molecular phylogeny found the distribution of Bungarus candidus in China(Squamata： Elapidae)

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Zoological Systematics 2018年第1期43卷 109-117页

作者： Yulin Xie Ping w.ng Guanghui Zhong Fei Zhu Qin Liu Jing Che Lei Shi robert w. murphy Peng Guo College of Animal Sciences Agricultural University of Xinjiang Urumchi 830052 Xinjiang China College of Life Sciences and Engineering Yibin University Yibin 644007 Sichuan China Forestry Science Research Institute of Sichuan Province Chengdu 610081 Sichuan China School of Life Sciences Guizhou Normal University Guiyang 550001 Guizhou China Kunming Institute of Zoology Chinese Academy of Sciences Kunming 650223 Yunnan China Southeast Asia Biodiversity Research Institute Chinese Academy of Sciences Yezin Nay Pyi Taw 05282 Myanmar Centre for Biodiversity and Conservation Biology Royal Ontario Museum 100 Queen's Park Toronto Ontario Canada MSS 2C6

Based on molecular phylogeny of the Chinese w.ite cross-band krait, Bungarus multicinctus, several individuals from southw.stern and southern China w.re found to be nested w.thin putative species B. candidus（Linnaeus, 1758） w.th high support values. Morphological examination also indicated these specimens w.re identical to B. candidus. w. concluded that the Chinese w.ite cross-band krait, previously identified as B. multicinctus in southw.st and south China, should be recognized as B. candidus, a new.record in China, and B. m. w.nghaoti should be invalid. B. multicinctus is recurrently limited to southern China w.thin China.

关键词： Kraits Bungarus multicinctus Cytb new.record

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基于分子系统学的可疑瑟姬小蜂分类修订及姬小蜂亚科盾纵沟的演化分析(英文)

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昆虫学报 2007年第1期50卷 57-66页

作者：沙忠利朱朝东 robert w. murphy 黄大卫中国科学院动物研究所 Centre for Biodiversity and Conservation Biology Royal Ontario Museum100 Queen's ParkToronto OntarioM5S 2C6 Canada

姬小蜂为寄生蜂的演化研究提供了很好的材料。在姬小蜂分类中,盾纵沟是一个重要性状,曾被用来区分亚科、族、属及种。非同源性相似形态特征的存在使得物种准确鉴定存在困难。从盾纵沟形状上,可疑瑟姬小蜂Cirrospilus ambiguus和双斑潜... 详细信息

姬小蜂为寄生蜂的演化研究提供了很好的材料。在姬小蜂分类中,盾纵沟是一个重要性状,曾被用来区分亚科、族、属及种。非同源性相似形态特征的存在使得物种准确鉴定存在困难。从盾纵沟形状上,可疑瑟姬小蜂Cirrospilus ambiguus和双斑潜蝇姬小蜂Diglyphus bimaculatus应介于瑟姬小蜂属Cirrospilus和潜蝇姬小蜂属Diglyphus之间。确定这两种姬小蜂的系统发育位置将有助于分析盾纵沟的演化模式。本文用贝叶斯方法分析了线粒体COⅠ部分序列、核糖体ITS1序列及核糖体28S D2区部分序列等3个基因序列,结果显示可疑瑟姬小蜂应被移到潜蝇姬小蜂属中;研究结果支持潜蝇姬小蜂属是单系,而不支持瑟姬小蜂属是单系。结合28S D2区部分序列的贝叶斯分析结果,分析了在姬小蜂亚科中盾纵沟的演化模式。结果显示,完整且延伸到中胸背板后缘的盾纵沟代表其原始类型;完整且延伸到三角片的盾纵沟类型分别出现在5个独立的枝上,代表了该特征5次独立的演化;不完整的盾纵沟类型出现在4个独立的枝上,表明该类型独立演化了4次。

关键词：姬小蜂科分子系统学可疑瑟姬小蜂双斑潜蝇姬小蜂盾纵沟演化

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基于18S基因序列的姬小蜂分子系统发育(英文)

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动物学报 2006年第2期52卷 288-301页

作者：沙忠利朱朝东 robert w.murphy 黄大卫 Stephen G.COMPTON 中国科学院动物研究所中国科学院研究生院北京100039 Centre for Biodiversity and Conservation Biology Royal Ontario Museum100 Queen s ParkTorontoOntarioM5S 2C6Canada 山东农业大学植物保护学院山东泰安271018 Centre for Biodiversity and Conservation School of BiologyUniversity of LeedsLeedsLS2 9JTUnited King-dom

本文基于18S rDNA部分序列,用MP和Baysian方法研究了姬小蜂科的系统发育,对姬小蜂科的单系性及其与其它小蜂科间的关系进行了讨论。姬小蜂亚科、灿姬小蜂亚科和啮姬小蜂亚科形成三个独立的支系,研究结果支持它们各自的单系性,但本结果... 详细信息

本文基于18S rDNA部分序列,用MP和Baysian方法研究了姬小蜂科的系统发育,对姬小蜂科的单系性及其与其它小蜂科间的关系进行了讨论。姬小蜂亚科、灿姬小蜂亚科和啮姬小蜂亚科形成三个独立的支系,研究结果支持它们各自的单系性,但本结果没有明确姬小蜂科的单系性。研究结果同时还支持瑟姬小蜂族、扁股姬小蜂族和狭面姬小蜂族三个族的地位,但不支持姬小蜂族的地位。姬小蜂科的单系性及其与其它小蜂间的关系还需更多的形态学数据和更多的基因序列来进一步研究[动物学报52 (2) : 288 -301 , 2006]。

关键词：姬小蜂科小蜂总科 18S rDNA核基因分子系统发育

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外群选择对隧蜂科(膜翅目:蜜蜂总科)系统重建的影响(英文)

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昆虫学报 2010年第2期53卷 192-201页

作者：罗阿蓉张彦周乔慧捷史卫峰 robert w. murphy 朱朝东中国科学院动物研究所动物系统与进化重点实验室北京100101 中国科学院研究生院北京100049 UCD Conw.y Institute of Biomolecular and Biomedical Sciences University College Dublin Department of Natural History Royal Ontario Museum100 Queen’s Park

外群用于给树附根和推断祖先性状状态。通常,来自内群的姐妹群中的多个分类单元被共同选择作为外群。为了在经验上验证这一方法,我们采用了3种外群选择策略:姐妹群中的单一分类单元,姐妹群中的多个分类单元和连续姐妹群中的多个分类单... 详细信息

外群用于给树附根和推断祖先性状状态。通常,来自内群的姐妹群中的多个分类单元被共同选择作为外群。为了在经验上验证这一方法,我们采用了3种外群选择策略:姐妹群中的单一分类单元,姐妹群中的多个分类单元和连续姐妹群中的多个分类单元。以隧蜂科(膜翅目:蜜蜂总科)的系统发育重建为例,我们评估了这3种策略对树拓扑结构的影响,包括最大似然树、最大简约树和贝叶斯树。初步结果表明:相比其他两种策略,采用姐妹群中的多个分类单元作为外群更有利于系统发育重建得到现已被广泛认可的隧蜂科系统发育关系;相比最大似然法和贝叶斯法,虽然隧蜂科系统发育关系没有被很好地解决,但最大简约法在不同外群选择策略下得到了较为一致的拓扑结构。

关键词：隧蜂科非同源相似单系性外群姐妹群系统发育

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A cryptic mitochondrial DNA link betw.en North European and w.st African dogs

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Journal of Genetics and Genomics 2017年第3期44卷 163-170页

作者： Adeniyi C.Adeola Sheila C.Ommeh Jiao-Jiao Song S.Charles Olaogun Oscar J.Sanke Ting-Ting Yin Guo-Dong w.ng Shi-Fang w. Zhong-Yin Zhou Jacqueline K.Lichoti Bernard R.Agw.nda Philip M.Daw.da robert w.murphy Min-Sheng Peng Ya-Ping Zhang State Key Laboratory for Conservation and Utilization of Bio-Resources Yunnan University Kunming 650091 China

Domestic dogs have an ancient origin and a long history in Africa. Nevertheless, the timing and sources of their introduction into Africa remain enigmatic. Herein, w. analyse variation in mitochondrial DNA（mt DNA） D-loop sequences from 345 Nigerian and 37 Kenyan village dogs plus 1530 published sequences of dogs from other parts of Africa, Europe and w.st Asia. All Kenyan dogs can be assigned to one of three haplogroups（matrilines; clades）： A, B, and C, w.ile Nigerian dogs can be assigned to one of four haplogroups A, B, C, and D. None of the African dogs exhibits a matrilineal contribution from the African w.lf（Canis lupus lupaster）. The genetic signal of a recent demographic expansion is detected in Nigerian dogs from w.st Africa. The analyses of mitochondrial genomes reveal a maternal genetic link betw.en modern w.st African and North European dogs indicated by sub-haplogroup D1（but not the entire haplogroup D） coalescing around 12,000 years ago. Incorporating molecular anthropological evidence,w. propose that sub-haplogroup D1 in w.st African dogs could be traced back to the late-glacial dispersals, potentially associated w.th human hunter-gatherer migration from southw.stern Europe.

关键词： Dog Mitochondrial DNA Africa Haplogroup D Late-glacial dispersal Hybridization

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