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Comparative population genomics reveals glacial cycles to drive diversifications in tropical montane birds(Aves,Timaliidae)

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Avian Research 2022年第4期13卷 399-406页

作者： per g.p.ericson Martin Irestedt Department of Bioinformatics and genetics Swedish Museum of Natural HistoryP.O.Box 50007SE-10405StockholmSweden

Many bird species are specialized to live in the broadleaved,evergreen forests in the mountain regions in Southeast *** mountain habitats are not continuously distributed as the different mountain areas are separated by lowlands,which has restricted gene flow and thus contributed to the high biological diversity in this *** degree of connectivity between mountain areas has fluctuated with the pleistocene glacial cycles,being largest during the glaciations when the mountain forests spread to lower *** we study how the intermittent periods of restricted gene flow and connectivity between the populations of five montane species of babblers(Aves,Timaliidae)in Vietnam may be traced in their *** results suggest that the babbler species in the Central Highlands have been isolated from their sister-populations in northern Vietnam for between ca.585 and 380 *** two species with populations in both the Central Highlands and the Da Lat region,we found that these split at more or less the same time(440–340 kya).We also found a significant statistical correlation between the time of the splits of these populations and the lowest altitude at which they are known to occur(no similar correlation was found with the geographic distances between populations).The populations in northern Vietnam show higher genetic variation than their counterparts in South-Central Vietnam,supporting the postulate that smaller populations may have lower genetic variation than *** accordance with this,we found the lowest genetic variation in the two species with the smallest populations in the Central *** two populations also show low levels of genomic *** results show that the south-central populations of the studied babbler species are genetically distinct from their sister-populations in northern Vietnam,providing additional argument for the long-term protection of the evergreen mountain forests in Southeast Asia.

关键词： Aves Timaliidae Babblers Demographic history Fragmented distributions pleistocene glacial cycles population genomics Tropical mountain forests

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A New Enantiornithes(Aves) from the Early Cretaceous of China

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Acta geologica Sinica(English Edition) 2014年第4期88卷 1034-1040页

作者： Johan DALSTT per g.p.ericson Zhonge ZHOU Department of Vertebrate Zoology Swedish Museum of Natural History Department of geological Sciences Stockholm University Institute of Vertebrate paleontology and paleoanthropology Chinese Academy of Sciences

A new bird from the early Cretaceous Yixian Formation of Liaoning, China is described. This new species, grabauornis lingyuanensis, shares several synapomorphies with the Enantiornithes. The specimen is relatively well preserved. The skeletal morphology of grabauornis bears close resemblance to that of other Chinese members of this clade. The brachial index （the ratio between the lengths of humerus and ulna） is 0.95, which is close to the average for enantiornithine birds. It indicates that grabauornis was a rather good flyer, and the presence of an alula in the wing further testifies to this.

关键词： Enantiornithes Aves Early Cretaceous Yixian Formation Liaoning China

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Evolutionary relationships of mitogenomes in a recently radiated Old World avian family

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Avian Research 2023年第2期14卷 153-159页

作者： Wenqing Zang Zhiyong Jiang per g.p.ericson gang Song Sergei VDrovetski Takema Saitoh Fumin Lei Yanhua Qu Key Laboratory of Zoological Systematics and Evolution Institute of ZoologyChinese Academy of SciencesBeijingChina College of Life Sciences University of Chinese Academy of SciencesBeijingChina Department of Bioinformatics and genetics Swedish Museum of Natural HistoryPO Box 50007SE-10405StockholmSweden Laboratories of Analytical Biology National Museum of Natural HistorySmithsonian InstitutionWashingtonDC 20004USA U.S.geological Survey Eastern Ecological Science Center at Patuxent Research RefugeLaurelMD 20708USA Yamashina Institute for Ornithology AbikoChibaJapan Center for Excellence in Animal Evolution and genetics Chinese Academy of SciencesKunming650223China

Environmentally heterogeneous mountains provide opportunities for rapid diversification and *** family prunellidae(accentors)is a group of birds comprising primarily mountain specialists that have recently radiated across the palearctic *** rapid diversification poses challenges to resolving their *** we sequenced the complete mitogenomes and estimated the phylogeny using all 12(including 28 individuals)currently recognized species of *** reconstructed the mitochondrial genome phylogeny using 13 protein-coding genes of 12 species and 2 Eurasian Tree Sparrows(passer montanus).phylogenetic relationships were estimated using a suite of analyses:maximum likelihood,maximum parsimony and the coalescent-based *** times were estimated by implementing a Bayesian relaxed clock model in *** on the BEAST time-calibrated tree,we implemented an ancestral area reconstruction using RASp *** phylogenies based on the maximum likelihood,maximum parsimony and SVDquartets approaches support a clade of large-sized accentors(subgenus Laiscopus)to be sister to all other accentors with small size(subgenus prunella).In addition,the trees also support the sister relationship of *** and ***+*** with 100%bootstrap support,but the relationships among the remaining eight species in the prunella clade are poorly *** species cluster in different positions in the three phylogenetic trees and the nodes are often poorly *** five nodes separating the seven species diverged simultaneously within less than half million years(i.e.,between 2.71 and 3.15 million years ago),suggesting that the recent radiation is likely responsible for rampant incomplete lineage sorting and gene tree *** area reconstruction indicates a central palearctic region origin for *** study highlights that whole mitochondrial genome phylogeny can resolve major lineages within prun

关键词： Incomplete lineage sorting Mitochondrial genome Mountain specialists Radiation

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A crowd-sourced genomic project to assess hybrid content in a rare avian vagrant(Azure Tit Cyanistes cyanus(pallas,1770))

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Avian Research 2023年第4期14卷 545-552页

作者： Martin Irestedt Filip Thorn per g.p.ericson Hein van grouw Yaroslav A.Red'kin Alexander Hellquist Frank Johansson Johan A.A.Nylander Department of Bioinformatics and genetics Swedish Museum of Natural HistoryStockholmSweden Department of Zoology Stockholm University Sweden Bird group Department of Life SciencesNatural History MuseumTringUnited Kingdom Zoological Museum Lomonosov Moscow State UniversityMoscowRussia Institute of Biological problems of Cryolithozone SB RAS YakutskRussia Department of Women's and Children's Health Uppsala UniversitySweden Department of Ecology and genetics Uppsala UniversityUppsalaSweden

The aim of this study was to correlate plumage variation with the amount of genomic hybrid content in hybrids between Azure Tits Cyanistes cyanus(pallas,1770)and European Blue Tit Cyanistes caeruleus(Linnaeus,1758),by re-sequencing the genomes of museum specimens of non-hybrids and presumed hybrids with varying *** project was funded by crowdsourcing and initiated when two presumed Azure Tits,observed by hundreds of Swedish birdwatchers,were rejected as hybrids based on minor plumage deviations assumed to indicate hybrid contents from the European Blue *** results confirm that hybrids with intermediate plumages,so called pleske’s Tits,are first generation hybrids(F1 hybrids).Individuals,whose plumages are similar to Azure Tits,but assessed as hybrids based on minor plumage deviations,are all backcrosses but vary in their degree of hybrid ***,some individuals morphologically recognized as pure Azure Tits expressed similar degrees of hybrid *** results indicate that:(1)hybrid content may be widespread in Azure Tits in the western part of its habitat distribution;(2)plumage deviation in backcrosses is not linearly correlated with the genetic degree of hybrid origin;and(3)all Azure Tits observed in Europe outside its natural distribution may have some degree of hybrid *** therefore suggest that it is very difficult to phenotypically single out hybrids beyond first generation *** argue that decreased sequencing costs and improved analytical tools open the doors for museomic crowd-sourced projects that may not address outstanding biological questions but have a major interest for lay citizens such as birdwatchers.

关键词： Crowdsourcing Cyanistes cyanus Hybridization Museomics

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鸟类形态特征的同质性比较

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动物学杂志 2024年第3期59卷 321-336页

作者：郑雪星 per g.p.ericson 屈延华中国科学技术大学生命科学与医学部合肥230026 中国科学院动物研究所动物进化与系统学院重点实验室北京100010 瑞典自然历史博物馆瑞典斯德哥尔摩50007

鸟类作为脊椎动物中的主要类群之一,其内部演化关系一直是动物学研究的重点。形态特征及分子特征在推断鸟类内部类群间的系统发育关系时被广泛应用,但长久以来受制于同质性的影响,不同形态特征难以得到一致的系统发育关系。随着基因组... 详细信息

鸟类作为脊椎动物中的主要类群之一,其内部演化关系一直是动物学研究的重点。形态特征及分子特征在推断鸟类内部类群间的系统发育关系时被广泛应用,但长久以来受制于同质性的影响,不同形态特征难以得到一致的系统发育关系。随着基因组测序技术及分析方法的快速发展,基于大量DNA序列数据所建的物种树成为领域内普遍认可的鸟类系统发育关系。在此基础之上,重新挖掘形态特征的研究价值成为可能。本研究基于prum发表于2015年的鸟类科级水平系统发育树,比较了不同形态特征同质性水平的差异,讨论了形态特征对于提高分子特征系统发育信号及分子树支持率的作用。研究发现,不同种类形态特征的同质性水平存在显著的差异,以一致性指数为标准,杂项特征(包括神经、肌腱及肠道的特征)的得分显著高于骨学特征和肌学特征(ppp<0.05),也提高了分子树的支持率。综上所述,不同的形态特征在同质性水平的得分上具有显著差异,在分子特征上加入形态特征既能够提高分子特征的系统发育信号,也能够提高分子树的支持率。

关键词：形态特征同质性水平一致性指数系统发育信号支持率

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Rapid phenotypic evolution with shallow genomic differentiation during early stages of high elevation adaptation in Eurasian Tree Sparrows

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National Science Review 2020年第1期7卷 113-127页

作者： Yanhua Qu Chunhai Chen Ying Xiong Huishang She Yong E Zhang Yalin Cheng Shane Du Bay Dongming Li per g p ericson Yan Hao Hongyuan Wang Hongfeng Zhao gang Song Hailin Zhang Ting Yang Chi Zhang Liping Liang Tianyu Wu Jinyang Zhao Qiang gao Weiwei Zhai Fumin Lei Key Laboratory of Zoological Systematics and Evolution Institute of Zoology Chinese Academy of Sciences BgI genomics BGI-Shenzhen University of Chinese Academy of Sciences Center for Excellence in Animal Evolution and genetics Chinese Academy of Sciences Committee on Evolutionary Biology University of Chicago Life Sciences Section Integrative Research Center Field Museum of Natural History Key Laboratory of Animal physiology Biochemistry and Molecular Biology of Hebei Province College of Life Sciences Hebei Normal University Department of Bioinformatics and genetics Swedish Museum of Natural History College of Life Sciences Shaanxi Normal University China National gene Bank BGI-Shenzhen Human genetics Genome Institute of Singapore Agency for Science Technology and Research

Known as the ‘third polar region’, the Qinghai-Tibet plateau represents one of the harshest highland environments in the world and yet a number of organisms thrive there. previous studies of birds, animals and humans have focused on well-differentiated populations in later stages of phenotypic divergence. The adaptive processes during the initial phase of highland adaptation remain poorly understood. We studied a human commensal, the Eurasian Tree Sparrow, which has followed human agriculture to the Qinghai-Tibet plateau. Despite strong phenotypic differentiation at multiple levels, in particular in muscle-related phenotypes, highland and lowland populations show shallow genomic divergence and the colonization event occurred within the past few thousand years. In a one-month acclimation experiment investigating phenotypic plasticity, we exposed adult lowland tree sparrows to a hypoxic environment and did not observe muscle changes. Through population genetic analyses, we identified a signature of polygenic adaptation, whereby shifts in allele frequencies are spread across multiple loci, many of which are associated with muscle-related processes. Our results reveal a case of positive selection in which polygenic adaptation appears to drive rapid phenotypic evolution, shedding light on early stages of adaptive evolution to a novel environment.

关键词： denovo genome early stage adaptation high elevation muscle phenotypes polygenic adaptation regulatory evolution

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欧亚大陆三种广布鸟类比较谱系生物地理学

欧亚大陆三种广布鸟类比较谱系生物地理学

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第十二届全国鸟类学术研讨会暨第十届海峡两岸鸟类学术研讨会

作者：张瑞莹宋刚屈延华 per Alstrm per g.p.ericson Jon Fjelds 杨晓君 Anton Kristin Alexander M.Shestopalov Jae Chun Choe 雷富民中国科学院动物研究所中国科学院遗传与发育生物学研究所 Swedish Species Information Centre Swedish University of Agricultural SciencesSE-75007 Uppsala Sweden Swedish Museum of Natural History SE-10405 StockholmSweden Centre of Macroecology Evolution and ClimateZoological MuseumUniversity of CopenhagenUniversitetsparken 152100 Copenhagen Denmark 中国科学院昆明动物研究所 Institute of Forest Ecology Slovak Academy of SciencesSK-96053 ZvolenSlovakia Novosibirsk State University and State Research Center of Virology and Biotechnology "Vector" NovosibirskRussia Division of EcoScience Ewha Womans University Seodaemun-gu Daehyun-dong 11-1SeoulKorea

现有的鸟类谱系生物地理学研究多偏重于欧洲地区,对欧亚大陆广布种类的遗传格局比较及形成机制研究涉及较少。本论文对喜鹊(pica pica)、大山雀(parus major)及沼泽山雀(poecilepalustris)的欧亚大陆整体格局进行比较并基于线粒体及核... 详细信息

现有的鸟类谱系生物地理学研究多偏重于欧洲地区,对欧亚大陆广布种类的遗传格局比较及形成机制研究涉及较少。本论文对喜鹊(pica pica)、大山雀(parus major)及沼泽山雀(poecilepalustris)的欧亚大陆整体格局进行比较并基于线粒体及核基因分析,结果显示,三种鸟类均呈现出欧亚大陆北部种群与亚洲东部种群间的深度谱系分歧,分化时间在第三纪晚期/第四纪早期。种群动态重建结果显示,三个物种各支系内种群扩张时间在0.03-0.13MYA,与欧亚大陆北部分支相比,亚洲东部、南部的分支经历了更长的种群历史或更早的种群扩张。

关键词：比较谱系生物地理学欧亚大陆中亚-蒙新干旱区种群动态

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A revised generic classification of the jelly lichens, Collemataceae

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Fungal Diversity 2014年第1期64卷 275-293页

作者： Mónica A.g.Otálora per M.Jørgensen Mats Wedin Department of Botany Swedish Museum of Natural HistoryP.O.Box 50007SE-10405 StockholmSweden Department of Natural History Bergen University MuseumAllégt.41Box 78005020 BergenNorway

phylogenetic studies have shown the need for a revised circumscription of generic boundaries in the jelly lichens(Collemataceae).Using a four-marker dataset from a recently published phylogeny of Collemataceae,we tested the monophyly of ten morphologically well-characterized *** achieve this,we performed Bayesian and maximum likelihood *** monophyly of the ten morphological groups was *** order to reconcile molecular and morphological data into a formal classification,we here propose new generic delimitations in *** and Leptogium are re-circumscribed and six old generic names are resurrected to accommodate the Collema Crispum-group(Blennothallia),the Collema Tenax-group(Enchylium),the Collema Cristatum-group(Lathagrium),the Collema Occultatum-group(Rostania),the former small Leptogium species(Scytinium),and Leptogium diffractum(pseudoleptogium).In addition,two new genera are described to accommodate Collema multipartitum(Callome)and the Collema Italicum-group(paracollema).The presence/absence of a eucortex,which was earlier used as the cardinal character to define genera in the family,is still useful,but only in combination with other traits such as thallus habit(size),lobe size,ascospore characteristics,thallus anatomical structure,and habitat preference.A key to the genera is *** are designated for Collema marginale Hoffm.,Synechoblastus nigrescens(Huds.)Trevis.,Eucollema(Cromb.)Horw.,Collema section Enchylium Ach.,Collema section Lathagrium Ach.,Collema *** Ach.,Collema section Scytinium Ach.,Collemodium *** Lamy,and Homodium *** Olivier.

关键词： Classification Collemataceae Cyanolichens Jelly lichens Test of monophyly

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Advances in Microgeophysics for Engineering and Cultural Heritage

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Journal of China University of geosciences 2009年第3期20卷 626-639页

作者： p L Cosentino p Capizzi g Fiandaca R Martorana p Messina Department of Chemistry and physics of the Earth and Applications to geo-Resources and Natural Risks Geophysical Section University of PalermoPalermo Italy

A large number of unconventional investigations have been implemented, tested, and validated in the field of microgeophysics, with the aim being to solve specific diagnostic and/or monitoring problems regarding civil engineering and cultural heritage studies. The investigations were carried out using different tomographic 2D and 3D approaches as well as different energy sources, namely sonic, ultrasonic and electromagnetic （radar） waves, electric potential fields, and infrared thermography. Many efforts have been made to modify instruments and procedures in order to improve the resolution of the surveys as well as to greatly reduce the time of the measurements without any loss of information. The main new methodologies here discussed are the sonic imprint, the global tomographic traveltime, the electrical resistivity tomography, and the control of external films （patinas） grown on stone monuments. The results seem to be very promising and suggest that it is the moment to dedicate time and effort to this new branch of geophysics, so that these methodologies can be used even more to diagnose, monitor, and safeguard not only engineering buildings and large structures but also ancient monuments and cultural artifacts, like pottery, statues, etc..

关键词： microgeophysics engineering cultural heritage tomography electrical sonic ultrasonic ground penetrating radar (gpR).

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Flotation techniques to improve viability of Juniperus polycarpos seed lots

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Journal of Forestry Research 2017年第2期28卷 231-239页

作者： Abolfazl Daneshvar Mulualem Tigabu Asaddollah Karimidoost per Christer Odén Southern Swedish Forest Research Centre Swedish University of Agricultural SciencesP.O.Box 49SE-230 53 AlnarpSweden Department of Natural Resources Gonbad Kavoos UniversityShahid Fallahi StreetP.O.Box 163GonbadIran Agriculture and Natural Resources Research Center of golestan province Beheshti Ave.P.O.Box ***GorganIran

The germination of freshly collected Juniperus polycarpos（K. Koch） seeds is very low and attributed to the large proportion of nonviable seeds in the seed ***, the aim of this study was to improve seed lot quality by removing nonviable seeds using two flotation techniques： incubation-drying-separation（IDS） and modified specific gravity（MSg） separation. We examined different IDS conditions（the specific incubation time, subsequent drying time and sorting media） for effectively sorting out nonviable seeds; and tested the feasibility of modified Sg separation, which involved soaking seeds in water for a certain period before sorting in different concentrations of sucrose solution. Viable seeds were expected to absorb and metabolically bind more water during soaking than dead seeds could, and hence be sorted effectively depending on the viscosity of the sucrose solution. The viability of the seeds that floated or sank was determined in a topographical tetrazolium chloride（TTC） test. For the IDS trial,7 days incubation followed by 9 h of drying and sedimentation in pure water or 200 g L-1sucrose solution identified, respectively, 75 and 82 % of the seeds as viable（sunken） seeds. For the MSg trail, 77 % viable seeds were recovered in the sunken fraction when seeds were soaked for 48 h then immediately sorted in 600 g L-1sucrose solution. In both cases, the loss of viable seeds in the discarded floating fraction was only 4 %. The results demonstrate that both IDS and MSg separation techniques substantially improved seed lot viability, but MSg separation is simple and needs no modern seed handling facility, and its efficacy relies on seed mass（due to the initial soaking） and the specific density and viscosity of the flotation medium.

关键词： viable viability sorting sucrose tetrazolium incubation subsequent viscosity proportion immediately

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