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Phylogeography of a dominant desert lizard reveals the synergistic effects of topography and climate dynamics on diversification in arid eastern-Central Asia
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作者 Abid Ali Da-Li Chen +5 位作者 Tatjana N.Dujsebayeva Qi Song Khayankhyarvaa Terbish Jun Li Yin Qi Xian-Guang Guo 《Zoological Research》 2025年第3期485-504,共20页
Comprehensive phylogeographic insights require the integration of evidence across diverse taxa,ecosystems,and geographical regions.However,our understanding of the arid biota of the vast Asian drylands remains limited... Comprehensive phylogeographic insights require the integration of evidence across diverse taxa,ecosystems,and geographical regions.However,our understanding of the arid biota of the vast Asian drylands remains limited.Accordingly,this study combined phylogeographic analyses with ecological niche modeling to investigate patterns of diversification and demography of the Central Asian racerunner(Eremias vermiculata),a widespread lizard inhabiting arid eastern-Central Asia(AECA).Mitochondrial DNA(mtDNA)sequences were obtained from 876 individuals across 113 localities,while three nuclear genes-CGNL1,MAP1A,andβ-fibint7-were sequenced from 204,170,and 138 individuals,respectively.Analyses identified four distinct mtDNA lineages corresponding to specific geographic subregions within the AECA,reflecting the topographic and ecological heterogeneity of the region.The detection of mito-nuclear discordance indicated the presence of complex evolutionary dynamics.Divergence dating placed the initial lineage splits at approximately 1.18 million years ago,coinciding with major tectonic activity and climatic aridification that likely promoted allopatric divergence.In particular,lineage diversification within the Tarim Basin suggests that recent environmental shifts may have contributed to genetic divergence.Demographic reconstructions revealed signatures of population expansion or range shifts across all lineages during the Last Glacial Maximum,signifying the combined influence of the unique topography and climate dynamics of the AECA on diversification and demographic change.These results highlight the need for fine-scale genomic investigations to clarify the mechanisms underlying mito-nuclear discordance and local adaptation.Such efforts are essential for advancing understanding of how genetic diversity in dryland taxa responds to environmental change,providing insights into the evolutionary adaptability of species in dynamic landscapes. 展开更多
关键词 Demographic history Ecological niche modeling Genetic structure Pleistocene climatic oscillations phylogeography
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Molecular Phylogeny and Phylogeography of Suidae 被引量:1
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作者 吴桂生 庞峻峰 张亚平 《Zoological Research》 CAS CSCD 北大核心 2006年第2期197-201,共5页
Although the Suidae animals were one of the most prosperous mammals, their taxa and phylogeny were poorly studied. To bridge this research gap, the complete mitochondrial DNA cyt b sequences (1140 bp)of one red rive... Although the Suidae animals were one of the most prosperous mammals, their taxa and phylogeny were poorly studied. To bridge this research gap, the complete mitochondrial DNA cyt b sequences (1140 bp)of one red river pig ( Potamochoerus porcus ), one bearded pig ( Sus barbatus ), and several Eurasian wild boars ( Sus scorfa ) were determined with direct PCR sequencing method. Incorporated with the sequences of other Suidae species obtained from GenBank, the phylogentic trees of Suidae species were constructed by Neighbor-Joining and Most Parsimony method. Our resuits showed that the babirousa was sister group of all other species. The African species clustered into a single clade, while the Eurasian species formed the other clade. The phylogenetic positions of the Sus species were consistent with their geographical distribution. Based on our phylogeographical results, the Sus species could be classified into three groups: (1) the relatively primitive animals from Philippine Islands (such as S. cebifrons and S. philippensis ), Sulawesi and it's adjacent islands (S. celebensis), (2) the Eurasian wild boars (S. scrofa and the mysterious S. salvanius), and (3) other pigs (such as S. barbatus and S. verrucosus), which might further diverged as the islands type (such as S. barbatus from Sumatra and Borneo) and the continental type (such as Malay Peninsula wild boar). 展开更多
关键词 SUIDAE PHYLOGENY phylogeography Mitochondrial DNA Cytochrome b PIGS
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Chloroplast DNA-based genetic variation of Rosa roxburghii in Southwest China:Phylogeography and conservation implications 被引量:8
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作者 Min Lu Huaishan Zhang Huaming An 《Horticultural Plant Journal》 SCIE CSCD 2021年第4期286-294,共9页
Rosa roxburghii Tratt.is a well-known commercial horticultural crop in China with nutritional and medicinal value.Wild germplasms of this species are mainly distributed in Southwest China but the population is decreas... Rosa roxburghii Tratt.is a well-known commercial horticultural crop in China with nutritional and medicinal value.Wild germplasms of this species are mainly distributed in Southwest China but the population is decreasing due to continuous exploitation,habitat destruction,and fragmentation.Therefore,assessing the genetic diversity and phylogeography is essential for efficient conservation.Herein,two chloroplast intergenic spacers(trnL-trnF and accD-psaI)were investigated in 255 individuals from 29 R.roxburghii populations and 18 haplotypes(H1–H18)were identified.High levels of haplotype diversity(Hd=0.829)and nucleotide diversity(π=1.3×10^(−3))were detected in these populations.Also,the genetic variation representing 86.4%of the total variation was detected by an analysis of molecular variance.A significant correlation was established between genetic divergence and geographic distance by the Mantel test(r=0.204,P=0.04,9999 permutations),suggesting the isolation-by-distance model.A significantly higher Nst than Gst(Nst=0.257,Gst=0.136,P<0.05)indicated the phylogeographic structure of R.roxburghii.Further phylogeographic analysis revealed rapid range expansion in the population,probably between 647073 and 217848 years ago.The primary processes shaping the genetic patterns of the R.roxburghii populations included restricted gene flow with isolation distance within clades 1-8,2-3,and overall,contiguous expansion within clades 1-3 and 3-2,past fragmentation,and/or long-distance colonization within clades 1-9 and 2-2.Conservation priority should be given to the core populations GZ,FQ,DF,DS,xy,AL,LC,PB,and XY in the Yunnan-Guizhou Plateau,NZ and MX in the Qingling-Bashan mountains,and MN in the Hengduan mountains,where an in situ preservation and management strategy should be applied. 展开更多
关键词 Chloroplast DNA Genetic diversity Core population phylogeography Rosa roxburghii
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Evolutionary history and phylogeography of Scots pine (Pinus sylvestris L.) in Europe based on molecular markers 被引量:4
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作者 Endre Gy. To′th Zolta′n A. Kobolkuti +1 位作者 Andrzej Pedryc Ma′ria Hohn 《Journal of Forestry Research》 SCIE CAS CSCD 2017年第4期637-651,共15页
In this review we summarized recent historical records and molecular studies on evolutionary history and phylogeography of Scots pine with focus on the European highly fragmented distribution area of the species. Foss... In this review we summarized recent historical records and molecular studies on evolutionary history and phylogeography of Scots pine with focus on the European highly fragmented distribution area of the species. Fossilized pollen, plant micro- and macrofossil records provided evidences on the large-scale species’ range shifts and demographic changes during the Quaternary. Populations of Scots pine were documented both in the glacial (incl. full glaciation) and interglacial periods. Recolonization of Europe after the glaciation originated from the (Sub) Mediterranean areas like the Balkan Peninsula but also from around the Eastern Alps and the surroundings of the Danube plain. Fennoscandia and northern European Baltic regions were most probably colonized from two main directions, from Western Europe and from the Russian Plain. Modern history of Scots pine was hardly affected by anthropogenic activities that started to strengthen in the Bronze and Iron Age. Along with the fossil records, molecular genetic tools were used to infer the origin and putative history including migration, differentiation and demography of the species. In this paper we compiled the major publications (30) of molecular genetic studies of the past 20 years derived from distinctly inherited organelle genomes (mitochondrial, chloroplast, nuclear) revealed by different marker systems (mtDNA-cox1, -nad1, -nad3, -nad7, ISSR, cpSSR, nSSR, B-SAP, SNP). It is important to consider that different phylogeographic patterns can be drawn by the analysis of different DNA marker types. Accordingly the use of more than one marker simultaneously outlines the most sophisticated phylogeographical pattern on the genetic lineages and can reveal high differentiation of the European distribution. Combined marker systems and markers derived from coding sequences have also been used to detect species’ phylogeographic patterns, but these were rarely applied to Scots pine. Although new molecular techniques can provide higher resolution data for populations, the reviewed results can shape the direction of further studies. 展开更多
关键词 Molecular genetic markers phylogeography Pinus sylvestris Quaternary history REFUGIA
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Limited gene flow and partial isolation phylogeography of Himalayan snowcock Tetraogallus himalayensis based on part mitochondrial D-loop sequences 被引量:5
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作者 Xiaoli WANG Jiangyong QU +2 位作者 Naifa LIU Xinkang BAO Sen SONG 《Current Zoology》 SCIE CAS CSCD 北大核心 2011年第6期758-767,共10页
Himalayan snowcock Tetraogallus himalayensis are distributed in alpine and subalpine areas in China. We used mi- tochondrial DNA control-region data to investigate the origin and past demographic change in sixty-seven... Himalayan snowcock Tetraogallus himalayensis are distributed in alpine and subalpine areas in China. We used mi- tochondrial DNA control-region data to investigate the origin and past demographic change in sixty-seven Himalayan snowcock T. himalayensis. The fragments of 1155 nucleotides from the control region of mitochondrial DNA were sequenced, and 57 poly- morphic positions defined 37 haplotypes. A high level of genetic diversity was detected in all populations sampled and may be associated isolation of the mountains and habitat fragmentation and deterioration from Quaternary glaciations. In the phylogenetic tree, all haplotypes grouped into four groups: clade A (Kunlun Mountains clade), clade B (Northern Qinghai-Tibetan Plateau clade), clade C (Tianshan Mountains clade) and clade D (Kalakunlun Mountains clade). We found a low level of gene flow and significant genetic differentiation among all populations. Based on divergence time we suggest that the divergence of Himalayan snowcock occurred in the middle Pleistocene inter-glaciation, and expansion occurred in the glaciation. Analysis of mtDNA D-loop sequences confirmed demographic population expansion, as did our non-significant mismatch distribution analysis. In conclusion, limited gene flow and a pattern of partial isolation phylogeographic was found in geographic populations of T. hima- layansis based on the analysis on mtDNA D-loop sequences [Current Zoology 57 (6): 758-767, 2011]. 展开更多
关键词 Tetraogallus himalayensis Mitochondrial DNA control-region phylogeography
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Phylogeography of SARS-CoV-2 pandemic in Spain:a story of multiple introductions,micro-geographic stratification,founder effects,and super-spreaders 被引量:3
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作者 Alberto Gomez-Carballa Xabier Bello +3 位作者 Jacobo Pardo-Seco Maria Luisa Perez del Molino Federico Martinon-Torres Antonio Salas 《Zoological Research》 SCIE CAS CSCD 2020年第6期605-620,共16页
Spain has been one of the main global pandemic epicenters for coronavirus disease 2019(COVID-19).Here,we analyzed>41000 genomes(including>26000 high-quality(HQ)genomes)downloaded from the GISAID repository,inclu... Spain has been one of the main global pandemic epicenters for coronavirus disease 2019(COVID-19).Here,we analyzed>41000 genomes(including>26000 high-quality(HQ)genomes)downloaded from the GISAID repository,including 1245(922 HQ)sampled in Spain.The aim of this study was to investigate genome variation of novel severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)and reconstruct phylogeographic and transmission patterns in Spain.Phylogeographic analysis suggested at least 34 independent introductions of SARS-CoV-2 to Spain at the beginning of the outbreak.Six lineages spread very successfully in the country,probably favored by super-spreaders,namely,A2 a4(7.8%),A2 a5(38.4%),A2 a10(2.8%),B3 a(30.1%),and B9(8.7%),which accounted for 87.9% of all genomes in the Spanish database.One distinct feature of the Spanish SARS-Cov-2 genomes was the higher frequency of B lineages(39.3%,mainly B3 a+B9)than found in any other European country.While B3 a,B9,(and an important sub-lineage of A2 a5,namely,A2 a5 c)most likely originated in Spain,the other three haplogroups were imported from other European locations.The B3 a strain may have originated in the Basque Country from a B3 ancestor of uncertain geographic origin,whereas B9 likely emerged in Madrid.The time of the most recent common ancestor(TMRCA)of SARS-CoV-2 suggested that the first coronavirus entered the country around 11 February 2020,as estimated from the TMRCA of B3 a,the first lineage detected in the country.Moreover,earlier claims that the D614 G mutation is associated to higher transmissibility is not consistent with the very high prevalence of COVID-19 in Spain when compared to other countries with lower disease incidence but much higher frequency of this mutation(56.4% in Spain vs.82.4% in rest of Europe).Instead,the data support a major role of genetic drift in modeling the micro-geographic stratification of virus strains across the country as well as the role of SARS-CoV-2 super-spreaders. 展开更多
关键词 Covid-19 SARS-CoV-2 GENOMICS PHYLOGENY phylogeography
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Phylogeography and Characteristics of Phosphorus Efficiency of Secondary Core Collection for Rice Landraces in Yunnan Province 被引量:3
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作者 ZENG Ya-wen DU Juan +5 位作者 PU Xiao-ying YANG Shu-ming YANG Tao WEI Ming-liang ZHANG Hao ZHOU Guo-hua 《Agricultural Science & Technology》 CAS 2011年第4期592-596,共5页
[Objective] The paper was to explore the causes of phosphorus(P)efficiency of rice in Yunnan Province,and to provide strategy for ecological and environmental protection.[Method]Using 703 accessions of secondary core ... [Objective] The paper was to explore the causes of phosphorus(P)efficiency of rice in Yunnan Province,and to provide strategy for ecological and environmental protection.[Method]Using 703 accessions of secondary core collections from 16 prefectures of five regions in Yunnan Province,two treatments of low available P(6.26mg/kg)versus normal P(available P 40mg/kg),and invalid P(available P 0.02 mg/kg)versus normal P(available P 70 mg/kg)were set,and zonal characteristics of phosphorus efficiency and the activation characteristics of invalid P of rice landraces were investigated.[Result] Phosphorus efficiency and the activation characteristics of invalid P in soils from rice landraces of Yunnan Province had the similar identification indexes,viz.the relative indexes of four traits(tillering ability or effective panicle,root weight,biomass,and straw weight)could be the screening indexes of gene type of secondary core collection with phosphorus efficiency,which also reflected the zonal characteristics of phosphorus efficiency and the activation characteristics of invalid P in soils of 16 prefectures among five regions.On the contrary,the relative panicle length,node length under panicle,leaf length,leaf width and plant height could only be the assistant indexes of identification for phosphorus efficiency.There were similar zonal characteristics between phosphorus efficiency and the activation characteristics of invalid P in soils of rice landraces in Yunnan Province.[Conclusion] The study had great importance to the conservation and utilization of biological diversity,which would make contribution to second green revolution of "less input,multiple output,promote health,and protect the environment". 展开更多
关键词 Phosphorus efficiency phylogeography CHARACTERISTICS Secondary core collection Rice landraces
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Molecular systematics, population genetics and phylogeography on planarians(Platyhelminths: Turbellaria): A brief review of molecular markers 被引量:2
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作者 Hecai Zhang Tiange Hu +1 位作者 Changying Shi Guangwen Chen 《Zoological Systematics》 CSCD 2019年第3期177-184,共8页
Due to their characteristics, such as powerful regeneration capability, high susceptibility to xenobiotics, wide distribution and weak dispersion ability, planarians are used as ideal test animals in several research ... Due to their characteristics, such as powerful regeneration capability, high susceptibility to xenobiotics, wide distribution and weak dispersion ability, planarians are used as ideal test animals in several research fields, and planarianology has become a more and more active subject. This paper reviews the research progress of planarians from the aspects of molecular phylogeny, molecular taxonomy, population genetics and phylogeography, and also summarizes the corresponding molecular markers applied. Moreover, the future direction and tendency in this field is briefly analyzed and prospected. 展开更多
关键词 PLANARIAN MOLECULAR marker MOLECULAR phylogeny MOLECULAR taxonomy population genetics phylogeography
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