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The Janus of macrophysiology： stronger effects of evolutionary history, but weaker effects of climate on upper thermal limits are reversed for lower thermal limits in ants

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Current Zoology 2018年第2期64卷 223-230页

作者： Sarah E. DIAMOND Lacy D. CHICK Department of Biology Case Western Reserve University Cleveland OH 44106 USA

Species may exhibit similar traits via different mechanisms： environmental filtering and local adaptation （geography） and shared evolutionary history （phylogeny） can each contribute to the resemblance of traits among species. Parsing trait variation into geographic and phylogenetic sources is important, as each suggests different constraints on trait evolution. Here, we explore how phylogenetic distance, geographic distance, and geographic variation in climate shape physiological tolerance of high and low temperatures using a global dataset of ant thermal tolerances. We found generally strong roles for evolutionary history and geographic variation in temperature, but essen- tially no detectable effects of spatial proximity per se on either upper or lower thermal tolerance. When we compared the relative importance of the factors shaping upper and lower tolerances, we found a much stronger role for evolutionary history in shaping upper versus lower tolerance, and a moderately weaker role for geographic variation in temperature in shaping upper tolerance when compared with lower tolerance. Our results demonstrate how geographic variation in climate and evolutionary history may have differential effects on the upper and lower endpoints of physiological tolerance. This Janus effect, where the relative contributions of geographic variation in climate and evolutionary history are reversed for lower versus upper physiological tolerances, has gained some support in the literature, and our results for ant physiological tolerances provide further evidence of this pa^ern. As the climate continues to change, the high phylogenetic conservatism of upper tolerance may suggest potential constraints on the evolution of tolerance of high temperatures.

关键词： biogeography evolutionary history latitudinal cline macrophysiology temperature thermal tolerance.

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Revisiting the evolutionary history of Pigs via De Novo Mutation Rate Estimation in A Three-generation Pedigree

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Genomics, Proteomics & Bioinformatics 2022年第6期20卷 1040-1052页

作者： Mingpeng Zhang Qiang Yang Huashui Ai Lusheng Huang State Key Laboratory of Swine Genetic Improvement and Production Technology Jiangxi Agricultural UniversityNanchang 330045China

The mutation rate used in the previous analyses of pig evolution and demographics was cursory and hence invited potential bias in inferring evolutionary ***,we estimated the de novo mutation rate of pigs as 3.6×10-9 per base per generation using high-quality whole-genome sequencing data from nine individuals in a three-generation pedigree through stringent filtering and *** this mutation rate,we re-investigated the evolutionary history of *** estimated divergence time of~10 kiloyears ago(KYA)between European wild and domesticated pigs was consistent with the domestication time of European pigs based on archaeological ***,other divergence events inferred here were not as ancient as previously *** estimates suggest that Sus speciation occurred~1.36 million years ago(MYA);European wild pigs split from Asian wild pigs only~219 KYA;and south and north Chinese wild pigs split~25 ***,our results showed that the most recent divergence event between Chinese wild and domesticated pigs occurred in the Hetao Plain,northern China,approximately 20 KYA,supporting the possibly independent domestication in northern China along the middle Yellow *** also found that the maximum effective population size of pigs was~6 times larger than estimated *** archaic migration from other Sus species originating~2 MYA to European pigs was detected during western colonization of pigs,which may affect the accuracy of previous demographic *** de novo mutation rate estimation and its consequences for demographic history inference reasonably provide a new vision regarding the evolutionary history of pigs.

关键词： Pig De novo mutation rate Three-generation pedigree evolutionary history Archaic migration

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Comparative genomic analysis of Thermus provides insights into the evolutionary history of an incomplete denitrification pathway

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mLife 2022年第2期1卷 198-209页

作者： Jian-Yu Jiao Zheng-Han Lian Meng-Meng Li Nimaichand Salam En-Min Zhou Lan Liu Hong Ming Guoxing Nie Wensheng Shu Guoping Zhao Brian P.Hedlund Wen-Jun Li State Key Laboratory of Biocontrol Guangdong Provincial Key Laboratory of Plant Resources and Southern Marine Science and Engineering Guangdong Laboratory(Zhuhai)School of Life SciencesSun Yat-Sen UniversityGuangzhouChina International Joint Research Center for Karstology School of Earth SciencesYunnan UniversityKunmingChina Synthetic Biology Engineering Laboratory of Henan Province College of Life Sciences and TechnologyXinxiang Medical UniversityXinxiangChina College of Fisheries Henan Normal UniversityXinxiangChina Institute of Ecological Science School of Life ScienceSouth China Normal UniversityGuangzhouChina Institute of Synthetic Biology Shenzhen Institutes of Advanced TechnologyChinese Academy of SciencesShenzhenChina School of Life Sciences University of NevadaLas VegasNevadaUSA Nevada Institute of Personalized Medicine University of NevadaLas VegasNevadaUSA State Key Laboratory of Desert and Oasis Ecology Xinjiang Institute of Ecology and GeographyChinese Academy of SciencesUrumqiChina

Biological denitrification is a crucial process in the nitrogen biogeochemical cycle,and Thermus has been reported to be a significant heterotrophic denitrifier in terrestrial geothermal ***,neither the denitrification potential nor the evolutionary history of denitrification genes in the genus Thermus or phylum Deinococcota is well ***,we performed a comparative analysis of 23 Thermus genomes and identified denitrification genes in 15 Thermus *** confirmed that Thermus harbors an incomplete denitrification pathway as none of the strains contain the nosZ *** character state reconstructions and phylogenetic analyses showed that narG,nirS,and norB genes were acquired by the last common ancestor of Thermales and were inherited *** contrast,nirK of Thermales was acquired via two distinct horizontal gene transfers from Proteobacteria to the genus Caldithermus and from an unknown donor to the common ancestor of all known Thermus species except Thermus *** study expands our understanding of the genomic potential for incomplete denitrification in Thermus,revealing a largely vertical evolutionary history of the denitrification pathway in the Thermaceae,and supporting the important role for Thermus as an important heterotrophic denitrifier in geothermal environments.

关键词： comparative genomics denitrification evolutionary history Thermus

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Reconstructing evolutionary history of Chinese walnuts

Reconstructing evolutionary history of Chinese walnuts

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陕西省植物学会2024年学术研讨会

作者： Shaohong Zhu Rui Wang Jiayu Ma Hang Ye Ruimin Xi Meng Dang Peng Zhao Key Laboratory of Resource Biology and Biotechnology in Western China Ministry of EducationCollege of Life SciencesNorthwest University Xianyang Normal University

Members of the genus Juglans(walnuts,family Juglandaceae) are typical Tertiary relict tree *** distributed widely in China,and they are well known for their edible nuts and high-quality *** genetic structure and historical gene flow patterns of Chinese Juglans still need to resolve,and the evolutionary history of the Chinese Juglans is ***,we collected samples from total of 2,242 trees from142 populations of three walnut species(Juglans regia L.,*** Dode and *** Maxim.),and a hybrid taxon Juglans × *** samples were across all of *** analyzed population genetic structure,interspecific relationship,lineage differentiation,and the processes of speciation using 21EST-SSR genetic *** *** and *** populations clustered into one lineage,corresponding to *** of Juglans,and all *** and Juglans × hopeiensis populations(section Cardiocaryon) into a second *** ***,there was an obvious north-south genetic ***,except for seven populations of the hybrid Juglans × hopeiensis,there was almost no gene flow between the populations of section Juglans/Dioscaryon and section *** analysis showed that BIO7 [Temperature Annual Range(5-6)] was the most important predictor of allele frequency among 19 climate ***-scale phenological niche modelling further showed that the weighted average of niche occupancy of the two groups of Chinese Juglans(section Juglans/Dioscaryon and section Cardiocaryon) in the precipitation-dependent dimensions significantly overlapped,but there was a different occupation of the ecological niche under the temperature *** with the results of Ecological niche modeling(ENM) analysis,the southwest,northern and eastern regions of China are long-term stable refuges for Chinese *** results of DIYABC analysis showed that *** and *** differentiated during the Oligocene of the Tertiary period

关键词： comparative phylogeography evolutionary history gene introgression Juglans J.mandshurica J.regia

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Comparative Studies on the Genome and evolutionary history of Domestic Bactrian Camel

Comparative Studies on the Genome and Evolutionary History o...

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提升骆驼产业科技含量，打造骆驼行业知名品牌——第二届（2013）中国骆驼大会

作者： Siriguleng Yu Jirimutu Temuulen Ming Linag Yi Li Sirendalai Sanchir Sarentuya Key Laboratory of Dairy Biotechnology and Engineering Ministry of Education College of Food Science and EngineeringInner Mongolia Agricultural University Inner Mongolia Camel Protection Association College of Veterinary Science Inner Mongolia Agricultural University

INTRODUCTION The factual origin of the domestic bactrian camel remain *** the archaeozoological record shows that fully domesticated bactrian camels were present in the third millennium BC and subsequently spread into much of Central ***,our knowledge about the origins and migration history of domestic bactrian camels remains ***,camels have acquired many special

关键词： Domestic bactrian camel Genome evolutionary history

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Conservation priority of global Galliformes species based on phylogenetic diversity

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Integrative Zoology 2014年第3期9卷 340-348页

作者： Youhua CHEN Department of Zoology University of British ColumbiaVancouverBCCanada Department of Renewable Resources University of AlbertaEdmontonAB T6G 2H1Canada

In this study,based on phylogenetic diversity(PD),I develop a conservation strategy for Galliformes species around the world.A cladogram of 197 Galliformes species derived from a previous study was used for calculating PD *** length is an important aspect of the phylogenetic information a tree can convey,but 2 traditionally-used metrics,the number of phylogenetic groups to which a taxon belongs(I)and the proportion that each taxon contributes to the total diversity of the group(W),are fully node-based and do not take branch length into ***,to measure PD more appropriately,I combined a branch-related metric,pendant edge(P),in addition to I and W.A final combined rank for Galliformes species was obtained by summing the ranks of the 3 *** results showed that the 5%top priority species for conserving evolutionary potential were Galloperdix lunulata,Haematortyx sanguiniceps,Margaroperdix madagarensis,Syrmaticus soemmerringii,Coturnix pectoralis,Polyplectron napoleonis,Alectoris melanocephala,Xenoperdix udzungwensis,Afropavo congensis and Syrmaticus *** current species priority ranking based on pylogenetic diversity and the official International Union for Conservation of Nature(IUCN)ranking of Galliformes species was significantly correlated when considering the 5 categories of IUCN(critical endangered,endangered,vulnerable,near threatened and least concern).This indicated the feasibility of introducing the PD index into the network of IUCN regional Red List *** 5%top priority countries selected using the complementarity principle possessing diversified Galliformes genetic resources were China,Indonesia,Mexico,India,Colombia,Australia,Brazil,Angola,Congo and Japan(in descending order).China,Indonesia,Mexico,Brazil,India and Colombia are consistently selected among the 4 top priority sets of richness,rarity,endemicity and *** result indicated that the priority result from PD is highly congruent with conventio

关键词： complementarity conservation priority evolutionary history IUCN Red List

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Scan of the endogenous retrovirus sequences across the swine genome and survey of their copy number variation and sequence diversity among various Chinese and Western pig breeds

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Zoological Research 2022年第3期43卷 423-441页

作者： Jia-Qi Chen Ming-Peng Zhang Xin-Kai Tong Jing-Quan Li Zhou Zhang Fei Huang Hui-Peng Du Meng Zhou Hua-Shui Ai Lu-Sheng Huang State Key Laboratory for Swine Genetic Improvement and Production Technology Jiangxi Agricultural UniversityNanchangJiangxi 330045China

In pig-to-human xenotransplantation,the transmission risk of porcine endogenous retroviruses(PERVs)is of great ***,the distribution of PERVs in pig genomes,their genetic variation among Eurasian pigs,and their evolutionary history remain *** scanned PERVs in the current pig reference genome(assembly Build 11.1),and identified 36 long complete or near-complete PERVs(lc PERVs)and 23 short incomplete PERVs(si PERVs).Besides three known PERVs(PERV-A,-B,and-C),four novel types(PERV-JX1,-JX2,-JX3,and-JX4)were detected in this *** to evolutionary analyses,the newly discovered PERVs were more ancient,and PERV-Bs probably experienced a bottleneck~0.5 million years ago(Ma).By analyzing63 high-quality porcine whole-genome resequencing data,we found that the PERV copy numbers in Chinese pigs were lower(32.0±4.0)than in Western pigs(49.1±6.5).Additionally,the PERV sequence diversity was lower in Chinese pigs than in Western *** the lc PERV copy numbers,PERV-A and-JX2 in Western pigs were higher than in Chinese ***,Bama Xiang(BMX)pigs had the lowest PERV copy number(27.8±5.1),and a BMX individual had no PERV-C and the lowest PERV copy number(23),suggesting that BMX pigs were more suitable for screening and/or modification as xenograft ***,we identified 451 PERV transposon insertion polymorphisms(TIPs),of which 86 were shared by all 10 Chinese and Western pig *** findings provide systematic insights into the genomic distribution,variation,evolution,and possible biological function of PERVs.

关键词： PERVs Chinese and Western pigs Copy number variation evolutionary history Biological function prediction

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Three-dimensional reconstruction of Late Miocene Trapa from eastern Zhejiang Province,China:Insights into its phytogeography and evolution

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Journal of Palaeogeography 2024年第4期13卷 954-970页

作者： Liang Xiao Man Yuan De-Shuang Ji Li-Yan Guo Xiang-Chuan Li Xing Wang Jia-Nan Wang Jia-Qi Liang Mei-Ting Wang School of Earth Science and Resources and Key Laboratory of Western Mineral Resources and Geological Engineering of the Ministry of EducationChang'an UniversityXi'an 710054Shaanxi ProvinceChina State Key Laboratory of Palaeobiology and Stratigraphy Nanjing Institute of Geology and PalaeontologyChinese Academy of SciencesNanjing 210008Jiangsu ProvinceChina Shaanxi Key Laboratory of Early Life and Environments Northwest UniversityXi'an 710069Shaanxi ProvinceChina State Key Laboratory of Continental Dynamics Northwest UniversityXi'an 710069Shaanxi ProvinceChina

Abundant plant fossils were found in the Upper Miocene Shengxian Formation,eastern Zhejiang Province,China,among which Trapa belongs to a dominant *** fossil fruits of Trapa were well preserved with abundant ***,due to compaction during fossilization,Trapa fruits were often flattened,leading to the loss of some characteristic ***,a bias in taxonomic and phylogenetic studies would occur when such studies were based on these fruit *** this study,we present the first quantitative three-dimensional reconstruction of compressed Trapa fruit fossils to restore their original morphology prior to *** approach provides a novel perspective for the identification and classification of compressed fruit *** three-dimensional reconstruction of Trapa fruit fossils enabled accurate comparisons with extant *** subsequently identified it as a new species,named Trapa radiatiformis *** ***.,revealing differences from previously known taxa of ***,our comparison suggests that the long lower horns and residual stalk may represent inherent characteristics of early Trapa ***,these traits gradually degenerated during fruit evolution,resulting in morphological simplification during geological *** with primitive features exhibits good resemblance to Trapa natans fruit characteristics,which means it may be an ancestor of *** summarize the palaeogeographic distribution of fossil Trapa using previously published literature and demonstrate that the genus was mostprosperous in the Miocene and exhibited the same distribution as that at ***,through detailed morphological comparisons between Trapa and Hemitrapa fruits,along with phylogenetic analysis within the Primotrapa genus itself,we propose a homology between Trapa and Hemitrapa,suggesting that they could have a common ancestor.

关键词： Trapa Late miocene Shengxian formation Three-dimensional reconstruction Phytogeographic history evolutionary history

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Genomic Variations in the Tea Leafhopper Reveal the Basis of Its Adaptive Evolution

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Genomics, Proteomics & Bioinformatics 2022年第6期20卷 1092-1105页

作者： Qian Zhao Longqing Shi Weiyi He Jinyu Li Shijun You Shuai Chen Jing Lin Yibin Wang Liwen Zhang Guang Yang Liette Vasseur Minsheng You State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops Institute of Applied EcologyFujian Agriculture and Forestry UniversityFuzhou 350002China Institute of Rice Fujian Academy of Agricultural SciencesFuzhou 350018China Tea Research Institute Fujian Academy of Agricultural SciencesFuzhou 350001China Center for Genomics and Biotechnology Fujian Agriculture and Forestry UniversityFuzhou 350002China Department of Biological Sciences Brock UniversitySt.CatharinesON L2S 3A1Canada

Tea green leafhopper(TGL),Empoasca onukii,is of biological and economic *** numerous studies,the mechanisms underlying its adaptation and evolution remain ***,we use previously untapped genome and population genetics approaches to examine how the pest adapted to different environmental variables and thus has expanded *** complete a chromosome-level assembly and annotation of the *** genome,showing notable expansions of gene families associated with adaptation to chemoreception and *** signals indicating balancing selection highlight metabolic pathways involved in adaptation to a wide range of tea varieties grown across ecologically diverse *** of genetic variations among 54 *** samples unveil the population structure and evolutionary history across different tea-growing regions in *** results demonstrate that the genomic changes in key pathways,including those linked to metabolism,circadian rhythms,and immune system functions,may underlie the successful spread and adaptation of *** work highlights the genetic and molecular basis underlying the evolutionary success of a species with broad economic impacts,and provides insights into insect adaptation to host plants,which will ultimately facilitate more sustainable pest management.

关键词： Tea green leafhopper Genomic variation Population genetics Local adaptation evolutionary history

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Assessing genome-wide adaptations associated with range expansion in the pink rice borer, Sesamia inferens

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Insect Science 2024年第5期31卷 1617-1630页

作者： Hongran Li Yan Peng Chao Wu Zhimin Li Luming Zou Kaikai Mao Junfen Ping Ryan Buck Scott Monahan Arun Sethuraman Yutao Xiao Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Gene Editing Technologies(Hainan)Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong ProvinceChina Department of Biology San Diego State UniversityCAUSA Department of Ecology&evolutionary Biology University of CaliforniaLos AngelesCAUSA

Understanding the genetic basis of adaptive evolution following habitat expan-sion can have important implications for pest *** pink rice borer(PRB),Sesamia inferens(Walker),is a destructive pest of rice that was historically restricted to regions south of 34o N latitude in ***,with changes in global climate and farming practices,the distribution of this moth has progressively expanded,en-compassing most regions in North ***,3 highly differentiated subpopulations were discovered using high-quality single-nucleotide polymorphism and structural vari-ant datasets across China,corresponding to northern,southern China regions,and the Yunnan-Guizhou Plateau,with significant patterns of isolation by geographic and envi-ronmental *** estimates of evolutionary history indicate asymmetric migration with varying population sizes across the 3 *** sweep analyses esti-mated strong selection at insect cuticle glycine-rich cuticular protein genes which are as-sociated with enhanced desiccation adaptability in the northern group,and at the histone-lysine-N-methyltransferase gene associated with range expansion and local adaptation in the Shandong *** findings have significant implications for the development of effective strategies to control this pest.

关键词： desiccation adaptability evolutionary history genetic adaptation phylo-geography Sesamia inferens

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