Genealogical trees, coalescent theory and the analysis of genetic polymorphisms

Cited by (750)

Items 201–300 of 750

1. Evaluation of haplotype callers for next-generation sequencing of viruses
   Anton Eliseev, Keylie M. Gibson, Pavel Avdeyev, D. K. Novik, Matthew L. Bendall, Marcos Pérez‐Losada, Nikita Alexeev, Keith A. Crandall · 2020 · Infection Genetics and Evolution
2. Empires and Exchanges in Eurasian Late Antiquity
   2018 · Cambridge University Press eBooks
3. Use of genomics to track bovine tuberculosis transmission
   Rowland Raymond Kao, Marian L. Price-Carter, Suelee Robbe‐Austerman · 2016 · Scientific and Technical Review (World Organisation for Animal Health)
4. Reconstructing the Evolutionary History of Powdery Mildew Lineages (Blumeria graminis) at Different Evolutionary Time Scales with NGS Data
   Fabrizio Menardo, Thomas Wicker, Beat Keller · 2017 · Genome Biology and Evolution
5. Inferring Process from Pattern in Fungal Population Genetics
   Ignazio Carbone, Linda M. Kohn · 2004 · Applied mycology and biotechnology
6. Fossorial but widespread: the phylogeography of the common spadefoot toad (Pelobates fuscus), and the role of the Po Valley as a major source of genetic variability
   A. Crottini, F. Andreone, J. Kosuch, L. Borkin, S. Litvinchuk, C. Eggert, M. Veith · 2007 · Molecular Ecology
7. Tracking the evolutionary history of Cortinarius species in section Calochroi, with transoceanic disjunct distributions
   Sigisfredo Garnica, Philipp N. Spahn, Bernhard Oertel, Joseph F. Ammirati, Franz Oberwinkler · 2011 · BMC Evolutionary Biology
8. Demographic processes shaping genetic variation
   Amy Lawton‐Rauh · 2008 · Current Opinion in Plant Biology
9. Gaussian Process‐Based Bayesian Nonparametric Inference of Population Size Trajectories from Gene Genealogies
   Julia A. Palacios, Vladimir N. Minin · 2013 · Biometrics
10. Nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae)
    Jason R. Comer, Wendy B. Zomlefer, Craig F. Barrett, Dennis Wm. Stevenson, Karolina Heyduk, Jim Leebens‐Mack · 2015 · Molecular Phylogenetics and Evolution
11. COALESCENT ANALYSES OF MULTIPLE LOCI SUPPORT A NEW ROUTE TO SPECIATION IN BIRDS
    Beatrice Kondo, Jeffrey L. Peters, Bryan B. Rosensteel, Kevin E. Omland · 2008 · Evolution
12. Mitochondrial DNA variation in the malaria vector Anopheles minimus across China, Thailand and Vietnam: evolutionary hypothesis, population structure and population history
    Bin Chen, P M Pedro, Ralph E. Harbach, Pradya Somboon, Catherine Walton, Roger Kenneth Butlin · 2010 · Heredity
13. Postglacial expansion pathways of red mangrove, Rhizophora mangle , in the Caribbean Basin and Florida
    John P. Kennedy, Maria W. Pil, C. Edward Proffitt, Walter A. Boeger, Alice M. Stanford, Donna J. Devlin · 2016 · American Journal of Botany
14. Importance of Microorganisms to Macroorganisms Invasions
    Laurent Amsellem, Carine Brouat, Olivier Duron, Stephanie S. Porter, Andreas Vilcinskas, Benoît Facon · 2016 · Advances in ecological research/Advances in Ecological Research
15. How do the type of QTL effect and the form of the residual term influence QTL detection in multi-parent populations? A case study in the maize EU-NAM population
    Vincent Garin, Valentin Wimmer, Sofiane Mezmouk, Marcos Malosetti, Fred van Eeuwijk · 2017 · Theoretical and Applied Genetics
16. Long-term population size of the North Atlantic humpback whale within the context of worldwide population structure
    Kristen Ruegg, Howard C. Rosenbaum, Eric C. Anderson, Márcia H. Engel, Anna Rothschild, C. Scott Baker, Stephen R. Palumbi · 2012 · Conservation Genetics
17. TESTING PHYLOGEOGRAPHIC HYPOTHESES IN A EURO-SIBERIAN COLD-ADAPTED LEAF BEETLE WITH COALESCENT SIMULATIONS
    Patrick Mardulyn, Yu. E. Mikhailov, Jacques M. Pasteéls · 2009 · Evolution
18. Phylogeography of surfclams, Spisula solidissima, in the western North Atlantic based on mitochondrial and nuclear DNA sequences
    Matthew P. Hare, J. R. Weinberg · 2004 · Marine Biology
19. Toward an organismal, integrative, and iterative phylogeography
    David Buckley · 2009 · BioEssays
20. Impacts of Marsh Management on Coastal-Marsh Bird Habitats
    Laura R. Mitchell, Steven W. Gabrey, Peter P. Marra, R. Michael Erwin · 2006 · Digital Commons - University of South Florida (University of South Florida)
21. Human influence on the population decline and loss of genetic diversity in a small and isolated population of Sichuan snub-nosed monkeys (Rhinopithecus roxellana)
    Zong-Fei Chang, Mao Fang Luo, Zhi Jin Liu, Jing Yang, Zuo Fu Xiang, Ming Li, Linda Vigilant · 2012 · Genetica
22. Genetic divergence and phylogeographic history of two closely related species (Leucomeris decora and Nouelia insignis) across the 'Tanaka Line' in Southwest China
    Yu-Juan Zhao, Xun Gong · 2015 · BMC Evolutionary Biology
23. Adaptive radiation in miniature: the minute salamanders of the Mexican highlands (Amphibia: Plethodontidae:Thorius)
    Sean M. Rovito, Gabriela Parra‐Olea, James Hanken, Ronald M. Bonett, David B. Wake · 2013 · Biological Journal of the Linnean Society
24. Coalescent Times and Patterns of Genetic Diversity in Species with Facultative Sex: Effects of Gene Conversion, Population Structure, and Heterogeneity
    Matthew Hartfield, Stephen Wright, Aneil F. Agrawal · 2015 · Genetics
25. Population genomic data reveal extreme geographic subdivision and novel conservation actions for the declining foothill yellow-legged frog
    Evan McCartney‐Melstad, Müge Gidiş, Howard Bradley Shaffer · 2018 · Heredity
26. PHYLOGEOGRAPHIC STRUCTURE OF THE FIRE ANT SOLENOPSIS INVICTA IN ITS NATIVE SOUTH AMERICAN RANGE: ROLES OF NATURAL BARRIERS AND HABITAT CONNECTIVITY
    Michael E. Ahrens, Kenneth G. Ross, DeWayne Shoemaker · 2005 · Evolution
27. Population genetics of tandem trypsin inhibitor genes in Arabidopsis species with contrasting ecology and life history
    Maria J. Clauss, Thomas Mitchell‐Olds · 2003 · Molecular Ecology
28. Analysis of sex‐linked sequences supports a new mammal species in Europe
    Linda Hellborg, İslam Gündüz, Maarit Jaarola · 2005 · Molecular Ecology
29. Impact of climate changes from M iddle M iocene onwards on evolutionary diversification in E urasia: Insights from the mesobuthid scorpions
    Cheng‐Min Shi, Ya-Jie Ji, Lin Liu, Lei Wang, De‐Xing Zhang · 2013 · Molecular Ecology
30. Will haplotype maps be useful for finding genes?
    Edwin J. C. G. van den Oord, Benjamin M. Neale · 2003 · Molecular Psychiatry
31. A Genomic View of the Peopling and Population Structure of India: Figure 1.
    Partha Pratim Majumder, Analabha Basu · 2014 · Cold Spring Harbor Perspectives in Biology
32. Bayesian Inference of the Evolution of a Phenotype Distribution on a Phylogenetic Tree
    M. Azim Ansari, Xavier Didelot · 2016 · Genetics
33. Monotypic status of the South American relictual marsupial Dromiciops gliroides (Microbiotheria)
    Elkin Y. Suárez-Villota, Camila A. Quercia, José J. Núñez, Milton H. Gallardo, Christopher M. T. Himes, G. J. Kenagy · 2018 · Journal of Mammalogy
34. From evidence to inference: Probing the evolution of protein interaction networks
    Oliver Ratmann, Carsten Wiuf, John W. Pinney · 2009 · HFSP journal
35. Signals of demographic expansion in Drosophila virilis
    Patricia M. Mirol, Jarkko Routtu, Anneli Hoikkala, Roger Kenneth Butlin · 2008 · BMC Evolutionary Biology
36. Reticulate Evolution
    Nathalie Gontier · 2015 · Interdisciplinary evolution research
37. Clonal Expansion and Migration of a Highly Virulent, Defoliating Lineage of Verticillium dahliae
    Michael G. Milgroom, María del Mar Jiménez-Gasco, Concepción Olivares-García, Rafael M. Jiménez-Dı́az · 2016 · Phytopathology
38. Genotyping and Coalescent Phylogenetic Analysis of Pneumocystis jiroveci from South Africa
    F. J. Lourens Robberts, Lynne D. Liebowitz, Lynda J. Chalkley · 2004 · Journal of Clinical Microbiology
39. Phylogeographic patterns of host‐race evolution in Tephritis conura (Diptera: Tephritidae)
    Thorsten Diegisser, Alfred Seitz, Jes Johannesen · 2006 · Molecular Ecology
40. The Roots of Bioinformatics
    David B. Searls · 2010 · PLoS Computational Biology
41. Patterns of mtDNA diversity in North Atlantic populations of the mussel Mytilus edulis
    Cynthia Riginos, Christine M. Henzler · 2008 · Marine Biology
42. HIV Migration Between Blood and Cerebrospinal Fluid or Semen Over Time
    Antoine Chaillon, Sara Gianella, Joel O. Wertheim, Douglas D. Richman, Sanjay R. Mehta, Davey Mitchell Smith · 2013 · The Journal of Infectious Diseases
43. Detecting glacial refugia in the Southern Ocean
    Sally C. Y. Lau, Nerida G. Wilson, Catarina N. S. Silva, Jan M. Strugnell · 2020 · Ecography
44. Phylogeny and phylogeography of the sword-tailed newt, Cynops ensicauda (Amphibia: Caudata), as revealed by nucleotide sequences of mitochondrial DNA
    A Tominaga, Hidetoshi Ota, Masafumi Matsui · 2009 · Molecular Phylogenetics and Evolution
45. Sorting through the chaff, nDNA gene trees for phylogenetic inference and hybrid identification of annual sunflowers (Helianthus sect. Helianthus)
    Michael L. Moody, Loren H. Rieseberg · 2012 · Molecular Phylogenetics and Evolution
46. Archaic inheritance: supporting high-altitude life in Tibet
    Emilia Huerta‐Sánchez, Fergal Casey · 2015 · Journal of Applied Physiology
47. A climate change context for the decline of a foundation tree species in south-western Australia: insights from phylogeography and species distribution modelling
    Eleftheria Dalmaris, Cristina E. Ramalho, Pieter Poot, Erik J. Veneklaas, Margaret Mary Byrne · 2015 · Annals of Botany
48. Genetic continuity of brood‐parasitic indigobird species
    Kristina M. Sefc, Robert B. Payne, Michael D. Sorenson · 2005 · Molecular Ecology
49. Genetic divergence does not predict change in ornament expression among populations of stalk‐eyed flies
    John G. Swallow, Lisa E. Wallace, Sarah J. Christianson, Philip Johns, Gerald S. Wilkinson · 2005 · Molecular Ecology
50. Robust and Accurate Bayesian Inference of Genome-Wide Genealogies for Large Samples
    Yun Kai Deng, Rasmus Nielsen, Yun S. Song · 2024 · bioRxiv (Cold Spring Harbor Laboratory)
51. Healthcare-associated outbreak of meticillin-resistant Staphylococcus aureus bacteraemia: role of a cryptic variant of an epidemic clone
    Ruth R. Miller, James Richard Price, Elizabeth M. Batty, Xavier Didelot, D H Wyllie, Tanya Golubchik, Derrick W. Crook, J. Paul, Tim Peto, Daniel J. Wilson et al. · 2013 · Journal of Hospital Infection
52. Phylogenetic analysis of the genusRasbora(Teleostei: Cyprinidae)
    Te Yu Liao, S. Kullander, Fang Fang · 2009 · Zoologica Scripta
53. Bayesian hypothesis testing supports long-distance Pleistocene migrations in a European high mountain plant (Androsace vitaliana, Primulaceae)
    Christopher J. Dixon, Peter Schönswetter, Pablo Vargas, Siegrun Ertl, Gerald M. Schneeweiss · 2009 · Molecular Phylogenetics and Evolution
54. Molecular Epidemiology and Genetic History of Hepatitis C Virus Subtype 3a Infection in Thailand
    Srunthron Akkarathamrongsin, Pitchaya Hacharoen, Pisit Tangkijvanich, Apiradee Theamboonlers, Yasuhito Tanaka, Masashi Mizokami, Yong Poovorawan · 2013 · Intervirology
55. Implications of mitochondrial DNA polyphyly in two ecologically undifferentiated but morphologically distinct migratory birds, the masked and white‐browed woodswallows Artamus spp. of inland Australia
    Leo Joseph, Thomas Wilke, José ten Have, R. Terry Chesser · 2006 · Journal of Avian Biology
56. Allele phasing is critical to revealing a shared allopolyploid origin of Medicago arborea and M. strasseri (Fabaceae)
    Jonna Sofia Eriksson, Filipe Sousa, Yann Bertrand, Alexandre Antonelli, Bengt Oxelman, Bernard E. Pfeil · 2018 · BMC Evolutionary Biology
57. Molecular techniques in phytoplankton research: from allozyme electrophoresis to genomics
    Arnout de Bruin, Bastiaan Willem Ibelings, Ellen van Donk · 2003 · Hydrobiologia
58. On the need for integrative phylogenomics, and some steps toward its creation
    Eric P Bapteste, Richard M. Burian · 2010 · Biology & Philosophy
59. Population Genetic Analysis of Tomato spotted wilt virus on Peanut in North Carolina and Virginia
    A. C. Kaye, James W. Moyer, E. J. Parks, Ignazio Carbone, Marc A. Cubeta · 2010 · Phytopathology
60. Models of RNA virus evolution and their roles in vaccine design
    Samuel Ojosnegros, Niko Beerenwinkel · 2010 · Immunome Research
61. The diversity, evolution and epidemiology of plant viruses: A phylogenetic view
    Israel Pagán · 2018 · Infection Genetics and Evolution
62. Exploring the potential of nuclear and mitochondrial sequencing data generated through genome‐skimming for plant phylogenetics: A case study from a clade of neotropical lianas
    Luiz Henrique M. Fonseca, Lúcia G. Lohmann · 2019 · Journal of Systematics and Evolution
63. Implications of barrier ephemerality in geogenomic research
    Raúl Araya‐Donoso, Sarah M Baty, Pedro Alonso‐Alonso, María José Sanín, Benjamin T. Wilder, Adrián Munguía‐Vega, Greer Dolby · 2022 · Journal of Biogeography
64. Inference Under a Wright-Fisher Model Using an Accurate Beta Approximation
    Paula Tataru, Thomas M Bataillon, Asger Hobolth · 2015 · Genetics
65. Estimating change rates of genetic markers using serial samples: applications to the transposon IS6110 in Mycobacterium tuberculosis
    Noah A. Rosenberg, Anthony George Tsolaki, Mark M. Tanaka · 2003 · Theoretical Population Biology
66. Integrating patterns across multiple genetic markers to infer spatial processes
    Robert G. Latta · 2006 · Landscape Ecology
67. Great cities look small
    Aaron Sim, Sophia N. Yaliraki, Mauricio Barahona, Michael P. H. Stumpf · 2015 · Journal of The Royal Society Interface
68. Heterogeneity in Genetic Diversity among Non-Coding Loci Fails to Fit Neutral Coalescent Models of Population History
    Jeffrey L. Peters, Trina E. Roberts, Kevin S. Winker, Kevin G. McCracken · 2012 · PLoS ONE
69. Salinity tolerance explains the contrasting phylogeographic patterns of two swimming crabs species along the tropical western Atlantic
    Pedro Augusto Peres, Fernando Luís Medina Mantelatto · 2020 · Evolutionary Ecology
70. Colonization history of the high‐arctic pink‐footed gooseAnser brachyrhynchus
    Minna Ruokonen, Tomas Aarvak, Jesper Johannes Madsen · 2004 · Molecular Ecology
71. Functional primate genomics—leveraging the medical potential
    Wolfgang Enard · 2012 · Journal of Molecular Medicine
72. Plant adaptation and speciation studied by population genomic approaches
    Masaru Bamba, Yawako W. Kawaguchi, Takashi Tsuchimatsu · 2018 · Development Growth & Differentiation
73. PHYLOGEOGRAPHIC STRUCTURE OF THE FIRE ANTSOLENOPSIS INVICTAIN ITS NATIVE SOUTH AMERICAN RANGE: ROLES OF NATURAL BARRIERS AND HABITAT CONNECTIVITY
    Michael E. Ahrens, Kenneth G. Ross, DeWayne Shoemaker · 2005 · Evolution
74. Gene tree discordance and coalescent methods support ancient intergeneric hybridisation between Dasymaschalon and Friesodielsia (Annonaceae)
    Xing Guo, Daniel C. Thomas, RICHARD M. K. SAUNDERS · 2018 · Molecular Phylogenetics and Evolution
75. Multiple Merger Genealogies in Outbreaks of Mycobacterium tuberculosis
    Fabrizio Menardo, Sébastien Gagneux, Fabian Freund · 2020 · Molecular Biology and Evolution
76. Cytochrome b polymorphisms and population structure of two species of Alouatta (Primates)
    Fabrícia Ferreira do Nascimento, Cibele Rodrigues Bonvicino, F.C.D. da Silva, Maria Paula Cruz Schneider, Hector Nicolas Seuánez · 2004 · Cytogenetic and Genome Research
77. Molecular evidence supports the distinction between Xanthoria parietina and X. aureola (Teloschistaceae, lichenized Ascomycota)
    Louise Lindblom, Stefan Ekman · 2005 · Mycological Research
78. Phylodynamic analysis to inform prevention efforts in mixed HIV epidemics
    Erik Volz, Nicaise Ndembi, Rebecca G. Nowak, Gustavo H. Kijak, John Alechenu Idoko, Patrick Dakum, Walter Royal, Stefan Baral, Mark R Dybul, William A. Blattner et al. · 2017 · Virus Evolution
79. Population Genetic Analysis of an Eastern U.S. Wheat Powdery Mildew Population Reveals Geographic Subdivision and Recent Common Ancestry with U.K. and Israeli Populations
    Ryan Parks, Ignazio Carbone, Joseph Paul Murphy, Christina Cowger · 2009 · Phytopathology
80. Genealogies in simple models of evolution
    Éric Brunet, Bernard Derrida · 2016
81. Contrasting phylogeographic patterns and demographic history in closely related species of Daphnia longispina group (Crustacea: Cladocera) with focus on North-Eastern Eurasia
    E. I. Zuykova, Evgeniy Simonov, Nickolai A. Bochkarev, Sergey A. Abramov, Natalia G. Sheveleva, Alexey A. Kotov · 2018 · PLoS ONE
82. Species formation and geographical range evolution in a genus of Central American cloud forest salamanders (Dendrotriton)
    Sean M. Rovito, David B. Wake, Theodore J. Papenfuss, Gabriela Parra‐Olea, Luis Antonio Muñoz Alonso, Carlos Roberto Vásquez-Almazán · 2012 · Journal of Biogeography
83. Phylogeography of Pinus subsection Australes in the Caribbean Basin
    Lev Jardón‐Barbolla, Patrícia Valério, Gretel Geada López, Alejandra Vázquez‐Lobo, Daniel Piñero · 2010 · Annals of Botany
84. Phylogeny and biogeography of the Anderson’s crocodile newt, Echinotriton andersoni (Amphibia: Caudata), as revealed by mitochondrial DNA sequences
    Masanao Honda, Masafumi Matsui, A Tominaga, Hidetoshi Ota, Satoshi Tanaka · 2012 · Molecular Phylogenetics and Evolution
85. A Coalescent Model of Recombination Hotspots
    Carsten Wiuf, David Posada · 2003 · Genetics
86. Are solitary and gregarious Mormon crickets (Anabrus simplex, Orthoptera, Tettigoniidae) genetically distinct?
    Nathan W. Bailey, Darryl T. Gwynne, Michael Gordon Ritchie · 2005 · Heredity
87. The evolutionary history of the common chloroplast genome ofArabidopsis thalianaandA. suecica
    Mattias Jakobsson, Torbjörn Säll, Christina Lind‐Halldén, Christer Halldén · 2006 · Journal of Evolutionary Biology
88. On the Use of Star-Shaped Genealogies in Inference of Coalescence Times
    Noah A. Rosenberg, Aaron E. Hirsh · 2003 · Genetics
89. Robust and accurate Bayesian inference of genome-wide genealogies for hundreds of genomes
    Yun Kai Deng, Rasmus Nielsen, Yun S. Song · 2025 · Nature Genetics
90. Assessment of the historical population size of an endangered bird, the black‐faced spoonbill (Platalea minor) by analysis of mitochondrial DNA diversity
    Carol K. L. Yeung, C.‐T. Yao, Y.‐C. Hsu, J.‐P. Wang, Shou‐Hsien Li · 2005 · Animal Conservation
91. The genetic structure of adders (Vipera berus) in Fennoscandia: congruence between different kinds of genetic markers
    M. CARLSSON, Linda Söderberg, Håkan Tegelström · 2004 · Molecular Ecology
92. The landscape of nucleotide diversity in Drosophila melanogaster is shaped by mutation rate variation
    Gustavo Valadares Barroso, Julien Yann Dutheil · 2023 · Peer Community Journal
93. POPULATION STRUCTURE AND MITOCHONDRIAL POLYPHYLY IN NORTH AMERICAN GADWALLS (ANAS STREPERA)
    Jeffrey L. Peters, Kevin E. Omland · 2007 · The Auk
94. Integrating Sequence Capture and Restriction Site-Associated DNA Sequencing to Resolve Recent Radiations of Pelagic Seabirds
    Joan Ferrer, Helen F. James, R. Terry Chesser, Vincent Bretagnolle, Jacob González‐Solís, Julio Rozas, Marta Riutort, Andreanna J. Welch · 2021 · Systematic Biology
95. Population genetic analyses of plant pathogens: new challenges and opportunities
    Celeste C. Linde · 2009 · Australasian Plant Pathology
96. Genes and Languages
    Robert McMahon · 2004 · Public Health Genomics
97. The interplay between habitat availability and population differentiation: a case study on genetic and morphological structure in an inland wader (Charadriiformes)
    Yvonne I. Verkuil, Theunis Piersma, Joop Jukema, Jos C. E. W. Hooijmeijer, Leo Zwarts, Allan J. Baker · 2012 · Biological Journal of the Linnean Society
98. Bayesian logistic regression using a perfect phylogeny
    Taane Gregory Clark, Maria De Iorio, Robert Griffiths · 2006 · Biostatistics
99. Correction: Genetic Patterns in European Geometrid Moths Revealed by the Barcode Index Number (BIN) System
    Axel Hausmann, H. Charles J. Godfray, Peter Huemer, Marko Mutanen, Rodolphe Rougerie, Erik J. van NIEUKERKEN, Sujeevan Ratnasingham, Paul D. N. Hebert · 2013 · PLoS ONE
100. A Genomic View of the Pleistocene Population History of Asia
     Martin Sikora · 2017 · Current Anthropology