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Highly divergent sympatric lineages of Leptotila verreauxi(Aves:Columbidae)suggest a secondary contact area in the Isthmus of Tehuantepec,Mexico

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Avian Research 2024年第1期15卷 12-21页

作者： Orlando J.Espinosa-Chávez Adolfo G.Navarro-Sigüenza Hernando Rodríguez-Correa Luis A.Sánchez-González Museo de Zoología“Alfonso L.Herrera” Depto.de Biología EvolutivaFacultad de CienciasUniversidad Nacional Autonoma de MexicoApdo.Postal 70-399CP 04510Ciudad de MexicoMexico Posgrado en Ciencias Biologicas Unidad de PosgradoEdificio D1◦PisoCircuito de PosgradosCiudad UniversitariaUniversidad Nacional Autonoma de MexicoCoyoacanCP 04510CDMXMexico Escuela Nacional de Estudios Superiores Unidad Morelia Universidad Nacional Autonoma de Mexico.Antigua Carretera a Patzcuaro No.8701 Col.Ex Hacienda de San Jose de la HuertaC.P.58190MoreliaMichoacanMexico

Due to a complex geological and biotic history,the Isthmus of Tehuantepec(IT),has been long recognized as a driver for the evolutionary divergence of numerous lowland and highland taxa.Widely distributed in the lowlands of the American continent,the White-Tipped Dove(Leptotila verreauxi)is a polytypic species with 13 recognized subspecies.Four of these have been recorded in Mexico,and the distribution of three abuts at the IT,suggesting a contact zone.To estimate phylogenetic patterns,divergence times and genetic differentiation,we examined two mt DNA(ND2 and COI)and one n DNA(β-fibint 7)markers.We also used correlative ecological niche models(ENM)to assess whether ecological differences across the IT may have acted as a biogeographical boundary.We estimated paleodistributions during the Middle Holocene,Last Glacial Maximum and Last Interglacial,to evaluate the influence of climate changes on the distribution and demographic changes.Our results showed genetically distinct lineages that diverged approximately 2.5 million years ago.Climatic and ecological factors may have played a dual role in promoting differentiation,but also in the formation of a secondary contact zone in the southern IT.Our ecological niche comparisons indicated that the ecological niche of sympatric lineages at the IT are not identical,suggesting niches divergence;in addition,environmental niche models across the region indicated no abrupt biogeographic barriers,but the presence of regions with low suitability.These results suggest that genetic differentiation originated by a vicariant event probably related to environmental factors,favored the evolution of different ecological niches.Also,the absence of a biogeographic barrier but the presence of less suitable areas in the contact regions,suggest that secondary contact zones may be also maintained by climatic factors for the eastern group,but also by biotic interactions for the western group.

关键词： Biogeographical boundary Humid and dry forests Isthmus of Tehuantepec phylogeography Secondary contact

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Phylogenetic, phylogeographic and divergence time analysis of Anopheles subpictus species complex using ITS2 and COI sequences

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Asian Pacific Journal of Tropical Medicine 2024年第5期17卷 214-225,I0004-I0038页

作者： Lihini Sandaleka Muthukumarana Methsala Madurangi Wedage Samanthika Rathnayake Nissanka Kolitha De Silva Department of Zoology Faculty of Applied SciencesUniversity of Sri JayewardenepuraGangodawilaNugegodaSri Lanka Genetics and Molecular Biology Unit Faculty of Applied SciencesUniversity of Sri JayewardenepuraGangodawilaNugegodaSri Lanka Sri Lanka Institute of Biotechnology PitipanaHomagamaSri Lanka

Objective:To address the phylogenetic and phylogeographic relationship between different lineages of Anopheles(An.)subpictus species complex in most parts of the Asian continent by maximum utilization of Internal Transcriber Spacer 2(ITS2)and cytochrome C oxidase I(COI)sequences deposited at the GenBank.Methods:Seventy-five ITS2,210 COI and 26 concatenated sequences available in the NCBI database were used.Phylogenetic analysis was performed using Bayesian likelihood trees,whereas median-joining haplotype networks and time-scale divergence trees were generated for phylogeographic analysis.Genetic diversity indices and genetic differentiation were also calculated.Results:Two genetically divergent molecular forms of An.subpictus species complex corresponding to sibling species A and B are established.Species A evolved around 37-82 million years ago in Sri Lanka,India,and the Netherlands,and species B evolved around 22-79 million years ago in Sri Lanka,India,and Myanmar.Vietnam,Thailand,and Cambodia have two molecular forms:one is phylogenetically similar to species B.Other forms differ from species A and B and evolved recently in the above mentioned countries,Indonesia and the Philippines.Genetic subdivision among Sri Lanka,India,and the Netherlands is almost absent.A substantial genetic differentiation was obtained for some populations due to isolation by large geographical distances.Genetic diversity indices reveal the presence of a long-established stable mosquito population,at mutation-drift equilibrium,regardless of population fluctuations.Conclusions:An.subpictus species complex consists of more than two genetically divergent molecular forms.Species A is highly divergent from the rest.Sri Lanka and India contain only species A and B.

关键词： Molecular systematics ITS2 COI DNA sequences Phylogeny 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

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Zoological Research 2020年第6期41卷 605-620页

作者： Alberto Gomez-Carballa Xabier Bello Jacobo Pardo-Seco Maria Luisa Perez del Molino Federico Martinon-Torres Antonio Salas Unidade de Xendtica Instituto de Ciencias Forenses(I NCI FOR)Facultade de MedicinaUniversidade de Santiago de Compostelaand GenPoB Research GroupInstituto de Investigaci6n Sanitaria(IDIS)Hospital Clinico Universitario de Santiago(SERGAS)Galicia 15706Spain Genetics Vaccines and Pediatric Infectious Diseases Research Group(GENVIP)Instituto de Investigacion Sanitaria de Santiago(IDIS)and Universidade de Santiago de Compostela(USC)Galicia 15706Spain Translational Pediatrics and Infectious Diseases Department of PediatricsHospital Clinico Universitario de Santiago de Compostela(SERGAS)Galicia 15706Spain Servicio de Microbiologia y Parasitologia Complejo Hospitalario Universitario de Santiago de CompostelaSantiago de CompostelaGalicia15706 Spain

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.

关键词： Covid-19 SARS-CoV-2 Genomics Phylogeny phylogeography

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phylogeography of Highly Pathogenic H5 Avian Influenza Viruses in China

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Virologica Sinica 2020年第5期35卷 548-555页

作者： Xiaowen Li Xueying Li Bing Xu Department of Earth System Science Tsinghua UniversityBeijing 100084China Center for Healthy Cities Institute for China Sustainable UrbanizationTsinghua UniversityBeijing 100084China

The spread of H5 highly pathogenic avian influenza viruses poses serious threats to the poultry industry,wild bird ecology and human health.Circulation of H5 viruses between poultry and wild birds is a significant public health threat in China.Thus,viral migration networks in this region need to be urgently studied.Here,we conducted molecular genetic analyses of the hemagglutinin genes of H5 highly pathogenic avian influenza viruses in multiple hosts from 2000 to 2018 in China.Our aim was to clarify the roles of different hosts in the evolution of H5 viruses.We used a flexible Bayesian statistical framework to simulate viral space diffusion and continuous-time Markov chains to infer the dynamic evolutionary process of spatiotemporal dissemination.Bayesian phylogeographic analysis of H5 viruses showed for the first time that H5 viruses in poultry and wild birds were present in Guangdong Province.Furthermore,Guangdong,Jiangsu,Shanghai and Hunan acted as the epicenters for the spread of various H5 subtypes viruses in poultry,and Henan,Shanghai,Hong Kong and Inner Mongolia acted as epicenters for the spread of various H5 subtypes viruses in wild birds.Thus,H5 viruses exhibited distinct evolutionary dynamics in poultry and wild birds.Our findings extend our understanding of the transmission and spread of highly pathogenic H5 avian influenza viruses in China.

关键词： Influenza H5 viruses phylogeography Spatial dispersion Population dynamics China

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phylogeography and morphometric variation in the Cinnamon Hummingbird complex:Amazilia rutila(Aves:Trochilidae)

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Avian Research 2021年第4期12卷 509-525页

作者： Melisa Vázquez-López Nandadevi Córtes-Rodríguez Sahid M.Robles-Bello Alfredo Bueno-Hernández Luz E.Zamudio-Beltrán Kristen Ruegg Blanca E.Hernández-Baños Museo de Zoología Facultad de CienciasUniversidad Nacional Autónoma de MéxicoApartado Postal04510 Mexico CityMexico Department of Biology Ithaca CollegeIthacaNY 14850USA Museo de Zoología Facultad de Estudios Superiores ZaragozaUniversidad Nacional Autónoma de MéxicoMexico CityMexico Department of Biology Colorado State UniversityFort CollinsCO 80523USA

Background:The Mesoamerican dominion is a biogeographic area of great interest due to its complex topography and distinctive climatic history.This area has a large diversity of habitats,including tropical deciduous forests,which house a large number of endemic species.Here,we assess phylogeographic pattern,genetic and morphometric variation in the Cinnamon Hummingbird complex Amazilia rutila,which prefers habitats in this region.This resident species is distributed along the Pacific coast from Sinaloa—including the Tres Marías Islands in Mexico to Costa Rica,and from the coastal plain of the Yucatán Peninsula of Mexico south to Belize.Methods:We obtained genetic data from 85 samples of A.rutila,using 4 different molecular markers(mtDNA:ND2,COI;nDNA:ODC,MUSK)on which we performed analyses of population structure(median-joining network,STRU CTU RE,FST,AMOVA),Bayesian and Maximum Likelihood phylogenetic analyses,and divergence time estimates.In order to evaluate the historic suitability of environmental conditions,we constructed projection models using past scenarios(Pleistocene periods),and conducted Bayesian Skyline Plots(BSP)to visualize changes in population sizes over time.To analyze morphometric variation,we took measurements of 5 morphological traits from 210 study skins.We tested for differences between sexes,differences among geographic groups(defined based on genetic results),and used PCA to examine the variation in multivariate space.Results:Using mtDNA,we recovered four main geographic groups:the Pacific coast,the Tres Marías Islands,the Chiapas region,and the Yucatán Peninsula together with Central America.These same groups were recovered by the phylogenetic results based on the multilocus dataset.Demography based on BSP results showed constant population size over time throughout the A.rutila complex and within each geographic group.Ecological niche model projec-tions onto past scenarios revealed no drastic changes in suitable conditions,but revealed some possible refuges.Mor-phometric results showed m

关键词： Amazilia rutila Genetic structure Genetic variation phylogeography Tres Marías Islands Trochilidae Tropical deciduous forest

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phylogeography and Cryptic Species Diversity of Paramesotriton caudopunctatus Species Group(Salamandridae: Paramesotriton) in Guizhou, China

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Asian Herpetological Research 2021年第2期12卷 188-200页

作者： Tao LUO Huamei WEN Kai GAO Jun ZHOU Jiang ZHOU School of Karst Science Guizhou Normal UniversityGuiyang 550001GuizhouChina School of Life Sciences Central China Normal UniversityWuhan 430000HubeiChina Key Laboratory for Biodiversity ami Ecological Engineering of Ministry of Education College of Life SciencesBeijing Normal UniversityBeijing 100875China

The Paramesotriton caudopunctatus species group is mainly distributed in the karst mountain ecosystems of Guizhou, China. Although some species have been included in previous phylogenetic studies, the evolutionary relationships and divergence-time of members of this species group as a whole remain unexplored. In this study, we report the sequencing of one protein coding mitochondrial gene fragment(ND2) and one nuclear gene(POMC), and use a combination of phylogenetic analyses and coalescent simulations to explore the cryptic diversity and evolutionary history of the P. caudopunctatus species group. Phylogenetic relationships revealed that the P. caudopunctatus species group is composed of two major groups, i. e., East Clade and Western-South Clade. The divergence-time and ancestral area estimation suggested that the P. caudopunctatus species group likely originated in the Doupeng Mountains in Guizhou, China at 12.34 Ma(95% HPD: 8.30–14.73), and intraspecific divergence began at about 2.17 Ma(95% HPD: 1.39–2.97). This timing coincides with the orogenesis of the Miaoling Mountains during the Late Miocene to early Pleistocene. The delimitation of species in the P. caudopunctatus species group supports the existence of the currently identified species, and consensus was confirmed across methods for the existence of least to two cryptic species within what has been traditionally considered to be P. caudopunctatus species group. This study is of significance for understanding the species formation, dispersal, and diversity of the tailed amphibians in the karst mountains ecosystem of Guizhou and the role of the Miaoling Mountains as a geographical barrier to species dispersal.

关键词： P.caudopunctatus species group phylogeography cryptic diversity biogeography species delimitation Guizhou

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Comparative mitogenome phylogeography of two anteater genera (Tamandua and Myrmecophaga;Myrmecophagidae, Xenarthra): Evidence of discrepant evolutionary traits

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Zoological Research 2021年第5期42卷 525-547页

作者： Manuel Ruiz-García Daniel Pinilla-Beltrán Oscar E.Murillo-García Christian Miguel Pinto Jorge Brito Joseph Mark Shostell Laboratorio de Genética de Poblaciones Molecular-Biología Evolutiva Departamento de BiologíaFacultad de CienciasPontificia Universidad JaverianaBogotáDC 110231Colombia Grupo de Investigación en Ecología Animal Departamento de BiologíaFacultad de Ciencias Naturales y ExactasUniversidad del ValleApartado AéreoCali 25360Colombia Instituto de Ciencias Biológicas Escuela Politécnica NacionalQuito 17012759Ecuador Instituto Nacional de Biodiversidad(INABIO) Quito 170135Ecuador Math Science and Technology DepartmentUniversity of Minnesota CrookstonCrookstonMN 56716USA

The species within Xenarthra(sloths,anteaters,and armadillos)are quintessential South American mammals.Of the three groups,Vermilingua(anteaters)contains the fewest extant and paleontological species.Here,we sampled and sequenced the entire mitochondrial genomes(mitogenomes)of two Tamandua species(Tamandua tetradactyla and T.mexicana)(n=74)from Central and South America,as well as Myrmecophaga tridactyla(n=41)from South America.Within Tamandua,we detected three different haplogroups.The oldest(THI)contained many specimens with the T.tetradactyla morphotype(but also several with the T.mexicana morphotype)and originated in southeastern South America(currently Uruguay)before moving towards northern South America,where the THII haplogroup originated.THII primarily contained specimens with the T.mexicana morphotype(but also several with the T.tetradactyla morphotype)and was distributed in Central America,Colombia,and Ecuador.THI and THII yielded a genetic distance of 4%.THII originated in either northern South America or“in situ”in Central America with haplogroup THIII,which consisted of~50%T.mexicana and 50%T.tetradactyla phenotypes.THIII was mostly located in the same areas as THII,i.e.,Central America,Ecuador,and Colombia,though mainly in the latter.The three haplogroups overlapped in Colombia and Ecuador.Thus,T.tetradactyla and T.mexicana were not reciprocally monophyletic.For this reason,we considered that a unique species of Tamandua likely exists,i.e.,T.tetradactyla.In contrast to Tamandua,M.tridactyla did not show different morphotypes throughout its geographical range in the Neotropics.However,two very divergent genetic haplogroups(MHI and MHII),with a genetic distance of~10%,were detected.The basal haplogroup,MHI,originated in northwestern South America,whereas the more geographically derived haplogroup,MHII,overlapped with MHI,but also expanded into central and southern South America.Thus,Tamandua migrated from south to north whereas Myrmecophaga migrated from north to south.Our results also showed that tem

关键词： Anteaters Genetic diversity Mitogenomes Myrmecophaga Neotropics phylogeography Spatial structure Tamandua

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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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phylogeography of Gyrodactylus konovalovi(Monogenoidea:Gyrodactylidae) in the Qinling Mountains in Central China

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Zoological Systematics 2020年第4期45卷 243-258页

作者： Tao Chen Xiaoning Chen Biao Wang Jianzhen Nie Ping You College of Life Sciences Shaanxi Normal UniversityXi’an 710062P.R.China Faculty of Basic Medical Sciences and Guangxi Key Laboratory of Diabetic Systems Medicine Guilin Medical UniversityGuilin 541199P.R.China

Gyrodactylus konovalovi is an ectoparasite on the Amur minnow(Rhynchocypris lagowskii)that is widely distributed in the cold fresh waters of East Asia.In the present study,the phylogeography of G.konovalovi and the distribution of its host in the Qinling Mountains are examined.A total of 102 parasite specimens was sequenced for the mitochondrial cytochrome oxidase subunit 1(cox1)gene,and 43 haplotypes were obtained.The ratio of substitution sites(dN/dS)was 0.016 and indicated strongly purifying selection.Haplotype diversity(h)and nucleotide diversity(π)of suprapopulations of G.konovalovi varied widely between distinct localities from the Qinling Mountains.Phylogenetic trees based on Bayesian inference(BI),maximum likelihood(ML)and maximum parsimony(MP)methods and network analysis revealed that all haplotypes were consistently well-supported in three different lineages A,B,and C,indicating a significant geographic distribution pattern.There was a significant positive correlation between genetic differentiation(Fst)and geographic distance(Pphylogeography of G.konovalovi was shaped by climatic oscillation and geological events,such as orogenesis,drainage capture changes and vicariance,during the Pleistocene in the Qinling Mountains in central China.

关键词： Gyrodactylus konovalovi Qinling Mountains phylogeography cox1 population expansion

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Genetic structure and phylogeography of a relict tree fern,Sphaeropteris brunoniana (Cyatheaceae) from China and Laos inferred from cpDNA sequence variations:Implications for conservation

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Journal of Systematics and Evolution 2011年第1期49卷 72-79页

作者： 1,2 Zi-Juan WANG 1 Kai-Yun GUAN 1 (Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650204, China) 2 (Graduate University of Chinese Academy of Sciences, Beijing 100049, China) (Kunming Institute of Botany Chinese Academy of Sciences Kunming 650204 China) (Graduate University of Chinese Academy of Sciences Beijing 100049 China)

In this study, we analyzed the genetic structure and phylogeography of Sphaeropteris brunoniana from China and Laos. Combining cpDNA trnL-trnF and atpB-rbcL sequence variations, five haplotypes were identi- fied from the 10 investigated populations. Moderate haplotype diversity (h = 0.66580) and low nucleotide diver- sity (π = 0.23 × 10 ?3 ) were detected. The S. brunoniana in Yunnan region had much higher genetic diversity (h = 0.60195, π = 0.35 × 10 ?3 ) than that of Hainan–Laos (h = 0.00000, π = 0.00). A high level of genetic differentiation (94.74%) between the two regions was revealed by AMOVA. Nested clade analysis identified two major clusters of the five haplotypes, one clade in the Yunnan region and the other in Hainan–Laos. The analysis indicated that restricted gene flow with isolation by distance and allopatric fragmentation were likely the major processes that shaped the spatial distribution of the haplotypes. The isolated distribution of clades implied the emergence of independent refugia of this species in each region during Quaternary glaciations. The Yunnan populations frequently contained an ancestral haplotype, and most of them harbored other descendent haplotypes. Based on the distribution pattern of haplotypes and the nested clade analysis results, the Yunnan region potentially had several refugia of this species during glacial periods, whereas the Hainan populations were probable new colonizations.

关键词： atpB-rbcL Hainan–Laos phylogeography Sphaeropteris brunoniana trnL-trnF Yunnan.

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