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Rethinking phylogeographic structure and historical refugia in the rufous-capped babbler Cyanoderma ruficeps in light of range-wide genetic sampling and paleodistributional reconstructions

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Current Zoology 2015年第5期61卷 901-909页

作者： Peter A. HOSNER Huatao LIU A. Townsend PETERSON Robert G. MOYLE Biodiversity Institute University of Kansas Lawrence Kansas 66045 USA School of Chemistry and Life Sciences Guizhou Education University Guiyang 550018 China

Combining ecological niche modeling with phylogeography has become a popular approach to understand how historical climate changes have created and maintained population structure. However, methodological choices in geographic extents and environmental layer sets employed in modeling may affect results and interpretations profoundly. Here, we infer range-wide phylogeographic structure and model ecological niches of Cyanoderrna ruficeps, and compare results to previous studies that examined this species across China's Mainland and Taiwan only. Use of dense taxon sampling of closely related species as outgroups question C. ruficeps monophyly. Furthermore, previously unsampled C. ruficeps populations from central Vietnam were closely related to disjunct western populations （Nepal, Tibet, Myanmar, Yunnan）, rather than to geographically proximate populations in northern Vietnam and eastern China. Phylogeographic structure is more complex than previously appreciated; niche model projections to Last Glacial Maximum climate scenarios identified larger areas of suitable conditions than previous studies, but potential distributional limits differed markedly between climate models employed and were dependent upon interpretation of non-analogous historical climate scenarios. Previously identified population expansion across central China may result from colonization from refugial distributions during the Last Interglacial, rather than the Last Glacial Maximum, as previously understood [Current Zoology 61 （5）： 901-909, 2015].

关键词： Biogeography Climate change Ecological niche modeling Southeast Asia Pleistocene refugia

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The Silk roads: phylogeography of Central Asian dice snakes (Serpentes: Natricidae) shaped by rivers in deserts and mountain valleys

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Current Zoology 2024年第2期70卷 150-162页

作者： Daniel Jablonski Konrad Mebert Rafaqat Masroor Evgeniy Simonov Oleg Kukushkin Timur Abduraupov Sylvia Hofmann Department of Zoology Comenius University in BratislavaBratislavaSlovakia Global Biology BirrSwitzerland Pakistan Museum of Natural History ShakarparianIslamabadPakistan Severtsov Institute of Ecology and Evolution Russian Academy of SciencesMoscowRussia T.I.Vyazemski Karadag Scientific Station-Nature Reserve—Branch of A.0.Kovalevsky Institute of Biology of the Southern Seas TheodosiaCrimea Zoological Institute of the RAS Saint PetersbourgRussia Institute of Zoology Academy of Sciences of the Republic of UzbekistanYunusabadTashkentUzbekistan Museum Koenig Bonn LIBLeibniz Institute for the Analysis of Biodiversity ChangeBonnGermany UFZ-Helmholtz Centre for Environmental Research Department of Conservation BiologyPermoserstrasse 1504318 LeipzigGermany

Influenced by rapid changes in climate and landscape features since the Miocene,widely distributed species provide suitable models to study the environmental impact on their evolution and current genetic *** dice snake Natrix tessellata,widely distributed in the Western Palearctic is one such *** aimed to resolve a detailed phylogeography of *** with a focus on the Central Asian clade with 4 and the Anatolia clade with 3 mitochondrial lineages,trace their origin,and correlate the environmental changes that affected their distribution through *** expected time of divergence of both clades began at 3.7 Mya in the Pliocene,reaching lineage differentiation approximately 1 million years *** genetic diversity in both clades is rich,suggesting different ancestral areas,glacial refugia,demographic changes,and colonization *** Caspian lineage is the most widespread lineage in Central Asia,distributed around the Caspian Sea and reaching the foothills of the Hindu Kush Mountains in Afghanistan,and Eastern European lowlands in the *** distribution is limited by deserts,moun-tains,and cold steppe ***,Kazakhstan and Uzbekistan lineages followed the Amu Darya and the Syr Darya water systems in Central Asia,with ranges delimited by the large Kyzylkum and Karakum *** the western side,there are several lineages within the Anatolia clade that converged in the central part of the peninsula with 2 being endemic to Western *** distribution of both main clades was affected by expansion from their Pleistocene glacial refugia around the Caspian Sea and in the valleys of Central Asia as well as by environmental changes,mostly through aridification.

关键词： biogeography colonization Eurasia genetic diversity mitochondrial DNA Paratethys refugia water snakes.

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Projected impacts of climate change and anthropogenic effects on habitat distribution of endangered Javan Hawk-Eagle in Indonesia

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Geography and Sustainability 2024年第2期5卷 241-250页

作者： Syartinilia Aryo Adhi Condro Satoshi Tsuyuki Department of Landscape Architecture Faculty of AgricultureIPB University(Bogor Agricultural University)Bogor 16680Indonesia International Research Institute for Environment and Climate Change-IPB University Collaborative Research CentreBogor 16128Indonesia Rainforest Alliance DenpasarBali 80227Indonesia Graduate School of Agricultural and Life Sciences The University of TokyoTokyo 113-8657Japan

Changing climate will jeopardize biodiversity,particularly the geographic distribution of endemic *** such species is the Javan Hawk-Eagle(JHE,Nisaetus bartelsi),a charismatic raptor found only on Java Island,***,it is crucial to develop an appropriate conservation strategy to preserve the *** niche modeling is considered a valuable tool for designing conservation plans for the *** provide an ecological niche modeling approach and transfer its model to future climate scenarios for the *** utilize various machine learning algorithms under sustainability and business-as-usual(BAU)scenarios for ***,we investigate the conservation vulnerability of the JHE,capturing multifaceted pressures on the species from climate dissimilarities and human disturbance *** study reveals that the ensemble model performs exceptionally well,with temperature emerging as the most critical factor affecting the JHE *** finding indicates that climate change will have a significant impact on the JHE *** results suggest that the JHE distribution will likely decrease by 28.41%and 40.16%from the current JHE distribution under sustainability and BAU scenarios,***,our study reveals high-potential refugia for future JHE,covering 7,596 km^(2)(61%)under the sustainability scenario and only 4,403 km^(2)(35%)under the BAU ***,effective management and planning,including habitat restoration,refugia preservation,habitat connectivity,and local community inclusivity,should be well-managed to achieve JHE conservation targets.

关键词： Climate change Ecological niche Ensemble model refugia Javan Hawk-Eagle

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Influence of slope position and aspect on the vegetation attributes and treewater relations in forests of the central Himalayas

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Journal of Mountain Science 2023年第9期20卷 2592-2602页

作者： Vidit TYAGI Surendra P.SINGH Ripu Daman SINGH Surabhi GUMBER Rajesh THADANI Rajiv PANDEY Dolphin(PG)Institute of Bio-medical and Natural Sciences Dehra Dun 248007India Central Himalayan Environment Association(CHEA) Dehradun 248007India Department of Forestry and Environmental Science DSB CampusKumaun UniversityNainital 263001India Centre for Ecology Development and Research(CEDAR) A-17 Mayfair GardensNew Delhi 110016India Indian Council of Forestry Research and Education(ICFRE) Dehra Dun 248007India

While the need for understanding the effects of topographical factors on forest structure and function is well recognized,comprehensive studies are *** study evaluates the effect of slope aspect and slope position on water relations and forest attributes across six forest types occurring between 400 m and 2600 m altitude in the Central Himalaya(27°-38°N).We found that predawn tree water potential and soil water potential were generally higher on moist north slope aspect(-0.78±0.05 MPa and-3.34±0.18 MPa,respectively)than dry south slope aspect(-0.82±0.18 MPa and-3.77±0.18 MPa,respectively).Across six different forests,these values were higher at hill base(-0.71±0.06 MPa and-2.77±0.19 MPa,tree predawn water potential and soil water potential,respectively)than other topographical *** favorable effect of north aspect and hill base was also observed in maintaining soil water and tree water potential during the dry *** attributes,such as species richness,unique species and plant density were also generally higher on north slope and hill base than southern aspect and lowest at hill *** forest types,the hill base provided shelter to 46 unique species,compared to 16-18 at the other positions,thus emphasizing its importance as refugia for species to survive climate change induced *** favorable conditions of hill base position not only contribute to increase in alpha diversity,but also to extended species distributional range.

关键词： Hill base Himalaya refugia Unique species Water relation

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Evolutionary history and phylogeography of Scots pine (Pinus sylvestris L.) in Europe based on molecular markers

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Journal of Forestry Research 2017年第4期28卷 637-651页

作者： Endre Gy. To′th Zolta′n A. Kobolkuti Andrzej Pedryc Ma′ria Hohn Department of Botany Szent Istva′n University Me′nesi u′t 44Budapest 1118 Hungary Department of Genetics and Plant Breeding Szent Istva′n UniversityMe′nesi u′t 44Budapest 1118Hungary

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 h

关键词： Molecular genetic markers Phylogeography Pinus sylvestris Quaternary history refugia

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Origin area and migration route: Chloroplast DNA diversity in the arctic-alpine plant Koenigia islandica

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Science China Earth Sciences 2014年第8期57卷 1760-1770页

作者： LONG Cong MIN YunJiang ZHAO XiuXia YANY ChunLei SUN Hang Lü HouYuan TANG LingYu ZHOU ZhongZe School of Resources and Environmental Engineering Anhui University Anhui Biodiversity Information Center Department of Biological and Pharmaceutical Engineering West Anhui University Key Laboratory for Plant Diversity and Biogeography of East Asia Kunming Institute of Botany Chinese Academy of Sciences Institute of Geology and Geophysics. Chinese Academy of Sciences Nanjing Institute of Geology and Palaeontology Chinese Academy of Sciences

The Hengduan Mountains(henceforth H-D Mountains) on the Tibet Plateau are a distribution and diversity center for many alpine genera. We examine patterns of genetic variation in an arctic-alpine plant to evaluate the possibility that the H-D Mountains constitute the area of origin of the species as well as to uncover postglacial migration routes. 220 individuals of the arctic-alpine plant Koenigia islandica were sampled from 26 populations distributed in western China and northern Finland. DNA haplotypes were identified using restriction site analysis of two chloroplast DNA intergene spacer regions, atpB-rbcL and trnL-trnF. We examined the geographical distribution of haplotype diversity in relation to latitude, and also compared various indices of diversity in putatively glaciated and unglaciated regions. Patterns of migration were inferred using nested clade analysis. A total of 25 haplotypes were detected. High haplotype diversity was found in the H-D Mountains. H3 and its radiated haplotypes were distributed in the Himalayas. Two haplotypes were fixed concurrently in the H-D Mountains and northern Finland. High genetic diversity of K. islandica and high species diversity of K. islandica are expected in the origin area. Our observations suggest that the H-D Mountains are not only the place of origin of K. islandica, but also the refugia for K. islandica on the Tibet Plateau. What is more, the migration route for the arctic-alpine plant K. islandica must have originated in the region defined by the H-D Mountains in western China extending northward to the Arctic circumpolar, and moved westward along the Himalayas, then northward across the Altay Mountains and the Central Siberian Plateau at different time periods.

关键词： origin area refugia migration route phylogeography biogeology Koenigia islandica

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Mitochondrial phylogeography of the Iberian endemic frog Rana iberica,with implications for its conservation

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Current Zoology 2018年第6期64卷 755-764页

作者： Jose TEIXEIRA Helena GONCALVES Nuno FERRAND Mario GARCIA-PARiS Ernesto RECUERO Centro Interdisciplinar de Investigacao Marinha e Ambiental (CIIMAR) Terminal de Cruzeiros do Porto de LeixoesMatosinhos 4450-208Portugal Centro de Investigacao em Biodiversidade e Recursos Geneticos (CIBIO-InBIO) Universidade do PortoRua Padre Armando QuintasVairao 4485-661Portugal Museu de Historia Natural e da Cieneia da Universidade do Porto (MHNC-UP) Praca Gomes TeixeiraPorto 4099-002Portugal Departamento de Biologia Faculdade de Ciencias da Universidade do PortoPorto 4099-002Portugal Museo Nacional de Ciencias Naturales (MNCN-CSIC) Calle de Jose Gutierrez Abascal2Madrid 28006Spain

Genetic characterization of species using phylogeographic approaches represents a basic reference to understand their evolutionary history as well as to identify conservation priorities to protect areas of particular interest regarding evolutionary *** in well-studied regions such information is lacking for the majority of species,including many endemic species with reduced distribution *** investigate the phylogeographic pattern of the Iberian frog Rana iberica,an endemic amphibian restricted to Central and North-Western Iberian *** mitochondrial sequences,we reconstruct the phylogeographic history of the species to test the effect of Quaternary climate changes on the evolutionary diversification of lineages,that is,the differentiation of mitochondrial lineages and the formation of genetic diversity melting pots,and integrate phylogeographic evidence for future conservation *** results indicate the existence of 3 main mitochondrial lineages differentiated during the Upper *** historical demographic analyses and climatic niche modeling show a strong effect of glacial climate changes,suggesting recurrent range contractions and *** such circumstances,differentiation took place most likely by isolation in allopatric interglacial *** lineage admixture in northern Portugal generated a broad mixed zone with highest nucleotide *** its particular evolutionary potential,its reduced distribution and eventual threats under current climate change scenario,conservation priorities should focus on the isolated lineage from Sierra de Guadalupe.

关键词： climate niche modeling conservation demography glacial refugia phylogeegraphy Amphibia

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Genomic and mitochondrial evidence of ancient isolations and extreme introgression in the four-lined snake

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Current Zoology 2020年第1期66卷 99-111页

作者： Evanthia THANOU Panagiotis KORNILIOS Petros LYMBERAKIS Adam D.LEACHE Department of Biology University of WashingtonSeattleWAUSA The Molecular Ecology Backshop LoutrakiGreece Institute of Evolutionary Biology(CSIC-Universitat Pompeu Fabra) BarcelonaSpain Natural History Museum of Crete University of CreteIrakleioGreece

Comparing mitochondrial and genomic phylogenies is an essential tool for investigating speciation processes,because each genome carries different inheritance properties and evolutionary ***,mitonuclear discordance may arise from ecological adaptation,historic isolation,population size changes,and sex-biased *** related taxa are expected to experience gene flow;however,this may not be true for insular populations or populations isolated in *** four-lined snake Elaphe quatuorlineata has a fragmented distribution,separating populations of the Italian and Balkan Peninsulas,whereas several insular Aegean populations of significantly smaller body size(Cyclades island group and Skyros Island,Greece)are currently considered distinct *** constructed the species-tree phylogeny of this species utilizing genome-wide single nucleotide polymorphisms and a gene-tree based on complete cytochrome b sequences,aiming to detect convergence and discrepancies between biparentally and maternally inherited *** structuring,phylogenetic patterns and migration events among geographically defined lineages supported our hypothesis of isolation in multiple *** biogeographical barriers did not restrict subsequent dispersal,extensive genetic exchange occurred between mainland Balkan *** process has led to the mitochondrial sweep of an ancestral mitolineage that survived only in peripheral(East Greece)and insular populations(North Cyclades and Skyros).The Central Cyclades represent an ancient lineage for both molecular markers that emerged almost 3.3 *** their distinct morphology,insular *** populations should be the future focus of an extensive sampling,especially since the mitonuclear discordance observed in this species could be related to ecological adaptations,such as the island-dwarfism phenomenon.

关键词： Aegean Islands Elaphe quatuorlineata species-tree genome-wide SNPs mitochondrial introgression phylogeography refugia within refugia

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Phylogeography of regional fauna on the Tibetan Plateau: A review

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Progress in Natural Science:Materials International 2009年第7期19卷 789-799页

作者： Shujuan Yanga, Hailiang Dongb,c, Fumin Lei d a State Key Laboratory of Geological Processes and Mineral Resources, China University of Geosciences, Beijing 100083, China b Geomicrobiology Laboratory, China University of Geosciences, Beijing 100083, China c Department of Geology, Miami University, Oxford, OH 45056, USA d Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China State Key Laboratory of Geological Processes and Mineral Resources China University of Geosciences Beijing 100083 China Geomicrobiology Laboratory China University of Geosciences Beijing 100083 China Department of Geology Miami University Oxford OH 45056 USA Institute of Zoology Chinese Academy of Sciences Beijing 100101 China

The studies of uplift and glaciations of the Tibetan Plateau are summarized, and a series of recent case studies of the endemic species based on DNA sequences are detailed. In general, these molecular data show that all the organisms originated from Early Pliocene to Late Miocene, and then multi-stages of divergence/speciation occurred within each taxa following their original occupation on the plateau, mainly as a result of periodic glacial cycles and geographic isolation. The regional fauna may have undergone several range contractions and expansions during the Pleistocene glaciations. However, the population expansion and refugia may vary in space, time, and extent. The regional fauna of the Tibetan Plateau may be combinations of ancient movement from adjacent zoogeographical regions, speciation in situ, and postglacial colonization from adjacent areas. Geomorphic and climatic changes on the plateau definitely have a remarkable influence on the regional and adjacent biogeographic patterns, and the mechanism is very complex.

关键词： Divergence refugia Postglacial colonization Phylogeography Regional fauna Tibetan Plateau

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Molecular Phylogeny and Evolution of Two Rhacophorus Species Endemic to Mainland Japan

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Asian Herpetological Research 2019年第2期10卷 86-104页

作者： Masafumi MATSUI Yasuhiro KAWAHARA Kanto NISHIKAWA Seiji IKEDA Koshiro ETO Yusuke MIZUNO Graduate School of Human and Environmental Studies Kyoto UniversityYoshida Nihonmatsu-choSakyo-kuKyoto 606-8501Japan Hagi City Museum Horiuchi 355HagiYamaguchi 758-0057Japan Hiroshima University Museum Kagamiyama 1-1-1Higashi Hiroshima CityHiroshima 739-8524Japan Kitakyushu Museum of Natural History and Human History Higashida 2-4-1Yahatahigashi-kuKitakyushuFukuoka 805-0071Japan Takahari 4-1002 Meito-kuNagoya 465-0061Japan

We conducted molecular phylogenetic analyses of Japanese Rhacophorus species, especially of R. schlegelii and R. arboreus from the mainland, based on samples encompassing their known distribution ranges, and discussed about evolutionary history of Rhacophorus species within Japan. The common ancestor of Japanese Rhacophorus, except for R. owstoni from southern Ryukyus, was estimated to have diverged from a lineage occurring mainly in China about 7 MYBP. Both R. schlegelii and R. arboreus are genetically largely divergent between regions of eastern and western Japan, and this seems to have been promoted mainly by retreat to refugia. Retreats of the two species to different refugia sometimes in the past seem to have led restricted distribution of R. schlegelii in eastern and R. arboreus in western Japan, and brought their intraspecific variation patterns in morphology and breeding habit.

关键词： glacial period mitochondrial DNA differentiation refugia Rhacophorus arboreus Rhacophorus schlegelii

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