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Matrilineal Genealogy of Hynobius (Caudata:Hynobiidae) and a Temporal Perspective on Varying Levels of Diversity among Lineages of Salamanders on the Japanese Islands

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Asian Herpetological Research 2012年第4期3卷 288-302页

作者： Yuchi ZHENG Rui PENG Robert W.MURPHY Masaki KURO-O Lujun HU Xiaomao ZENG Department of Herpetology Chengdu Institute of BiologyChinese Academy of Sciences Sichuan Key Laboratory of conservation biology on Endangered Wildlife College of Life SciencesSichuan University State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Centre for biodiversity and conservation biology Royal Ontario Museum Department of biology Hirosaki University

Previous work found that different Japanese lineages of salamanders had quite different levels of species and genetic diversity. Lineages vary from having one to several species and the extent of genetic variation among lineages differs substantially. Most speciose,genus Hynobius contains 18 species and several potential cryptic species. We explore genetic diversity in this genus by combining comprehensive sampling and mitochondrial DNA sequences. Based on this and previous analyses of salamanders,relative times of divergence are employed to evaluate the relationship between age and diversity among the four major lineages whose distributions broadly overlap on the islands. For Hynobius,our analyses are congruent with the previously reported high level of cryptic diversity in morphology and allozymes,particularly in species composed of non-sister matrilines. Both species and genetic diversity correlate with the relative ages of the lineages. This correlation indicates that the variation in levels of diversity can be explained,to a considerable extent,by the hypothesis that older insular lineages have accumulated greater diversity. In addition to the Korean Peninsula,H. leechii might have survived in another Pleistocene glacial refugium north of the peninsula and this refugium provided a source of colonization after the last glacial maximum.

关键词： tempo of diversification salamander Japanese Archipelago Hynobius cryptic species northern glacial refugium

Matrilineal History of the Rana longicrus Species Group(Rana,Ranidae,Anura) and the Description of a New Species from Hunan,southern China

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Asian Herpetological Research 2011年第2期2卷 61-71页

作者： Fang YAN Ke JIANG Hongman CHEN Ping FANG Jieqiong JIN Yi LI Shaoneng WANG Robert W.MURPHY Jing CHE Yaping ZHANG State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Laboratory for conservation and Utilization of Bio-resources Yunnan University Jiemuxi National Nature Reserve Maoershan National Nature Reserve Centre for biodiversity and conservation biology Royal Ontario Museum100 Queen's Park

Fieldwork in Jiemuxi National Nature Reserve, Hunan, China, discovered morphologically indis- tinguishable groups of brown frogs that bred at different, exclusive times of the year. A principal components analysis of morphometric data, molecular analyses, and the exclusive breeding season suggested the occurrence of two species. The population that breeds during the winter was found to be an undescribed species and was subsequently described as Rana jiemuxiensis sp. nov. The new cryptic species can be identified from its congeners at the same locality by having a different breeding season and a divergent DNA barcode, Six major lineages of brown frogs were resolved with high nodal support. Rana japonica, R. chaochiaoensis, R. omeimontis, and R. jiemuxiensis have independent maternal lineages. Rana hanlunica and R. maoershanensis have essentially identical maternal lineages and they appear to represent the same species. The validity of the species R. longicrus, R. zhenhaiensis, and R. culaiensis and their genealogical relationships are not resolved and deserve further study. The genealogy indicates that sympatric cryptic lineages probably widely exist in the R. longicrus group. This highlights the importance of future more fine-scaled samplings and the inclusion of nuclear genes.

关键词： Ranajiemuxiensis Ranajaponica group phylogeny genealogy DNA barcode cryptic species

The gap in research on polyploidization between plants and vertebrates:model systems and strategic challenges

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Science Bulletin 2015年第17期60卷 1471-1478页

作者： Jing Chai Yuebo Su Feng Huang Shaojun Liu Min Tao Robert W.Murphy Jing Luo Laboratory of conservation and Utilization of Bio-resources and Key Laboratory for Animal Genetic Diversity and Evolution of High Education in Yunnan Province School of Life SciencesYunnan University State Key Laboratory of Genetic Resources and Evolution and Yunnan Laboratory of Molecular biology of Domestic Animals Kunming Institute of Zoology Chinese Academy of Sciences Kunming College of Life Science University of Chinese Academy of Sciences College of Life Sciences Hunan Normal University Centre for biodiversity and conservation biology Royal Ontario Museum

Polyploidization via whole-genome duplications （WGD） is a common phenomenon in organisms. However, investigations into this phenomenon differ greatly between plants and animals. Recent research on polyploid plants illustrates the immediate changes that follow WGDs and the mechanisms behind in both genetic and epigenetic consequences. Unfortunately, equivalent questions remain to be explored in animals. Enlightened by botanical research, the study of polyploidization in vertebrates involves the identification of model animals and the establishment of strategies. Here we review and compare the research on plants and vertebrates while considering intrageneric or intraspecific variation in genome size. Suitable research methods on recently established poly- ploidy systems could provide important clues for under- standing what happens after WGDs in vertebrates. The approach yields insights into survival and the rarity of polyploidization in vertebrates. The species of Carassius and the allopolyploid system of goldfish × common carp hybridization appear to be suitable models for unraveling the evolution and adaptation of polyploid vertebrates.

关键词： Polyploidization Recurrent WGD events Genome size variation Next-generation sequencing

How many species of Apodemus and Rattus occur in China？ A survey based on mitochondrial cyt b and morphological analyses

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Zoological Research 2018年第5期39卷 309-320页

作者： Shao-Ying Liu Kai He Shun-De Chen Wei Jin Robert W.Murphy Ming-Kun Tang Rui Liao Feng-Jun Li Sichuan Academy of Forestry Chengdu Sichuan 610081 China Kunming Institute of Zoology Chinese Academy of Sciences Kunming Yunnan 650223 China College of Life Sciences Sichuan Normal University Chengdu Sichuan 610066 China Centre for biodiversity and conservation biology Royal Ontario Museum Toronto M5S 2C6 Canada

Apodemus （mice） and Rattus （rats） are the top rodent reservoirs for zoonoses in China,yet little is known about their *** reexamined the alpha diversity of these two genera based on a new collection of specimens from China and their cyt b sequences in *** also tested whether species could be identified using external and craniodental measurements *** from 147 specimens of Apodemus and 233 specimens of Rattus were used for morphological *** analysed 74 cyt b sequences of Apodemus and 100 cyt b sequences of Rattus to facilitate phylogenetic *** demonstrated that nine species of Apodemus and seven species of Rattus,plus a new subspecies of Rattus nitidus,are distributed in *** component analysis using external and craniodental measurements revealed that measurements alone could not separate the recognized *** occurrence of Rattus pyctoris in China remains uncertain.

关键词： Alpha diversity Apodemus DNA-barcoding Rattus Taxonomy Phylogenies New subspecies

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 WenJuan 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,which occurred in a stepwise 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 with the matrilineal and demographical histories of the Tarim Basin's endemic Yarkand hare (Lepus yarkandensis).Range-wide 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 western and southern *** analysis and genetic diversity estimations suggested that the western 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,which corresponded to known interglacial *** the relatively complete geographic isolation between the eastern and southern populations,the Yarkand hare likely dispersed during postglacial periods from the southwest to the north,and then onward to the *** absence of water 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

Reproductive Behavior and Underwater Calls in the Emei Mustache Toad,Leptobrachium boringii

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Asian Herpetological Research 2011年第4期2卷 199-215页

作者： Yuchi ZHENG Dingqi RAO Robert W.MURPHY Xiaomao ZENG Department of Herpetology Chengdu Institute of BiologyChinese Academy of Sciences Key Laboratory of Zoological Systematics and Evolution Institute of ZoologyChinese Academy of Sciences State Key Laboratory of Genetic Resources and Evolution Kunming Institute of ZoologyChinese Academy of Sciences Centre for biodiversity and conservation biology Royal Ontario Museum100 Queen’s ParkToronto M5S 2C6OntarioCanada

The Emei mustache toad, Leptobrachium boringii （Megophryidae）, is terrestrial but breeds in permanent streams. Primarily, it has a polygynous mating system and polyandry also occurs. The species vigorously defends submerged nest sites. We report on a reproductive study at Mt. Emei, western China conducted in 2004, 2006, 2007, 2009, and 2011 during the breeding season. Males produce both advertisement and courtship calls underwater, and the latter differs from the former in having an additional trill-like last note of low intensity. Females might determine the oviposition location and hence the egg mass location. A low, submissive posture can be adopted by the male to avoid being attacked by other males. When fighting, the maxillary nuptial spines are employed as weapons, and males hold their opponents on their spines with the forelimbs that enlarge during the breeding season. Male body size and the quantity of fight wounds on its ventral side are positively correlated. Satellite male mating might exist in L. boringii. Additionally, underwater calls from another population of this species and a population of L. leishanense generally are similar to those of the population from Mt. Emei.

关键词： advertisement call courtship call underwater call male combat male weaponry nest inspection satellite male reproductive tactic

Comparative multi-locus assessment of modern Asian newts(Cynops, Paramesotriton, and Pachytriton:Salamandridae) in southern China suggests a shared biogeographic history

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Zoological Research 2022年第5期43卷 706-718页

作者： Zhi-Yong Yuan Yun-Ke Wu Fang Yan Robert W.Murphy Theodore J.Papenfuss David B.Wake Ya-Ping Zhang Jing Che State Key Laboratory of Genetic Resources and Evolution&Yunnan Key Laboratory of biodiversity and Ecological Security of Gaoligong Mountain Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China Key Laboratory of Freshwater Fish Reproduction and Development(Ministry of Education) School of Life SciencesSouthwest UniversityChongqing 400715China Department of Ecology and Evolutionary biology Cornell UniversityIthaca 14850USA College of Life Science Yunnan UniversityKunmingYunnan 650091China Centre for biodiversity and conservation biology Royal Ontario MuseumTorontoOntario M5S 2C6Canada museum of Vertebrate Zoology University of CaliforniaBerkeleyCA 94720USA

Evolutionary biologists are always interested in deciphering the geographic context of diversification,therefore they introduced the concept of comparative phylogeography, which helps to identify common mechanisms that contribute to shared genetic structures among organisms from the same ***, we used multi-locus genetic data along with environmental data to investigate shared phylogeographic patterns among three Asianendemic newt genera, Cynops, Paramesotriton and Pachytriton, which occurred in montane/submontane streams or ponds in southern China. Our 222samples from 78 localities covered the entire range of the three genera and represented the largest dataset of this group to date. We reconstructed matrilineal genealogies from two protein-coding,mitochondrial genes, and gene network from two nuclear genes. We also estimated divergence times of major cladogenetic events and used occurrence data to evaluate niche difference and similarity between lineages. Our results revealed a common basal split in all three genera that corresponds to the separation of two geographic terrains of southern *** ancient divergence occurred during middle to late Miocene and likely correlate with paleoclimatic fluctuations caused by the uplift of the Qinghai-Xizang (Tibet) Plateau (QTP).Particularly,the strengthening and weakening of Asian summer monsoons during the Miocene may have profoundly impacted southern China and led to repeatedly vicariance in those ***,despite differences in realized niches between lineages,there is no evidence for divergence of fundamental *** of old newt matriline lineages in mountains of southern China suggests that the region acts as both museums and cradles of *** on those results,we advocate a multi-pronged protection strategy for newts in the three genera.

关键词： Amphibian Comparative phylogeography Qinghai-Xizang(Tibet)Plateau East Asian monsoons Ecological niche modeling Species museums and cradles

Testing Hypotheses of Pleistocene Population History Using Coalescent Simulations: Refugial Isolation and Secondary Contact in Pseudepidalea raddei (Amphibia: Bufonidae)

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Asian Herpetological Research 2012年第2期3卷 103-113页

作者： Bingjun DONG Jing CHE Li DING Song HUANG Robert W.MURPHY Ermi ZHAO Yaping ZHANG Key Laboratory for Bio-resources and Eco-environment (Ministry of Education) College of Life Sciences Sichuan University College of Chemistry and Life Sciences Shenyang Normal University State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences Chengdu Institute of biology Chinese Academy of Sciences Department of biology Huangshan University Centre for biodiversity and conservation biology Department of Natural History Royal Ontario Museum 100 Queen's Park

The impact of the Quaternary glaciation on eastern China’s local fauna and flora is a topic of considerable interest. We use mitochondrial DNA(mtDNA) sequences and coalescent simulations to test two general biogeographic hypotheses related to the effect of the Pleistocene climatic fluctuations on a widespread, eastern Chinese amphibian, Pseudepidalea raddei. Genealogical reconstructions are made and they detect major western and eastern lineages, which overlap in northwestern China, and possibly indicate the secondary contact of the populations that had entered the region from separate glacial refugia. Coalescent tests rejected alternative hypotheses of fragmentation of either a widespread ancestor or panmixia. The tests instead supported the hypothesis of geographic isolation and a remarkable dispersal pattern in one of the lineages. Though the Pleistocene climatic events are known to have affected the historical distributions and intra-specific divergence of Chinese squamates, coalescent and non-coalescent demographic analyses indicated that the toad P. raddei was not adversely affected by glacial cycling. Presumably, an increase in the amount of climatically mild habitats in East Asia is due to the development of monsoons since the Mid-late Pleistocene is responsible for the relatively mild effects.

关键词： Mongolian toad Pleistocene refugia phylogeography biogeography

Comparative sensitivity to environmental variation and human disturbance of Asian tapirs (Tapirus indicus) and other wild ungulates in Thailand

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Integrative Zoology 2012年第4期7卷 389-399页

作者： Antony J.LYNAM Naruemon TANTIPISANUH Wanlop CHUTIPONG Dusit NGOPRASERT Megan C.BAKER Passanan CUTTER George GALE Shumpei KITAMURA Robert STEINMETZ Ronglarp SUKMASUANG Somying THUNHIKORN Global conservation Program Wildlife Conservation Society(WCS)BronxNYUSA IUCN/SSC Tapir Specialist Group BangkokThailand conservation Ecology Program King Mongkut’s University of Technology ThonburiBangkokThailand center for Species Survival Smithsonian Conservation Biology InstituteFront RoyalVirginiaUSA conservation biology Program University of MinnesotaSt.PaulMinnesotaUSA museum of Nature and Human Activities SandaJapan WWF Thailand BangkokThailand Department of Forest biology Kasetsart UniversityBangkokThailand Wildlife Research Division Department of National ParksWildlife and Plants ConservationBangkokThailand

Southeast Asia’s tropical forests suffer the highest rates of deforestation and disturbance of any on Earth,with poorly understood impacts on native *** tapirs(Tapirus indicus)are among the least studied of the large mammals in these *** records from 9 camera trap surveys in 7 of the largest(>1000 km2)pro-tected area complexes,we assessed the influence of environmental variation and human-induced disturbance on tapir *** were detected at 13%of locations sampled,significantly associated with evergreen for-est(P40%over the past 20 *** recommend surveys to fill gaps in the understanding of the status in lesser-known protected areas,research to better understand the fine-scale environmental influences on behavior and habitats of tapirs,and other forest un-gulates,and continued legal status for tapirs in the highest category of protection.

关键词： Asian tapir camera traps conservation logistic regression ungulates