Ecosyste.ms: Papers

10.1038/s41437-019-0204-4

Extreme mito-nuclear discordance in a peninsular lizard: the role of drift, selection, and climate
Cited by: 24
Author(s): Pedro Henrique Bernardo, Santiago Sánchez‐Ramírez, Santiago J. Sánchez-Pacheco, Sergio Ticul Álvarez-Castañeda, Eduardo Felipe Aguilera-Miller, Fausto R. Méndez–de la Cruz, Robert W. Murphy
Software Mentions: 10
Published: almost 6 years ago

10.1002/ece3.8018

Delimitation despite discordance: Evaluating the species limits of a confounding species complex in the face of mitonuclear discordance
Cited by: 8
Author(s): Thomas J. Firneno, Justin R. O’Neill, Michael W. Itgen, Timothy A. Kihneman, Josiah H. Townsend, Matthew K. Fujita
Software Mentions: 9
Published: over 3 years ago

10.1111/eva.13120

Comparative transcriptomics of ice‐crawlers demonstrates cold specialization constrains niche evolution in a relict lineage
Cited by: 4
Author(s): Sean D. Schoville, Sabrina Simon, Ming Bai, Zachary T. Beethem, R. Yu. Dudko, Monika J. B. Eberhard, Paul B. Frandsen, Simon Küpper, Ryuichiro Machida, Max Verheij, Peter Willadsen, Xin Zhou, Benjamin Wipfler‍
Software Mentions: 8
Published: over 4 years ago

10.1111/mec.14523

Shifts in diversification rates and host jump frequencies shaped the diversity of host range among <i>Sclerotiniaceae</i> fungal plant pathogens
Cited by: 39
Author(s): Olivier Navaud, Adelin Barbacci, Andrew Taylor, John P. Clarkson, Sylvain Raffaele
Software Mentions: 8
Published: almost 7 years ago

10.1002/ece3.5597

Population structure, connectivity, and demographic history of an apex marine predator, the bull shark<i>Carcharhinus leucas</i>
Cited by: 16
Author(s): Agathe Pirog, Virginie Ravigné, Michaël C. Fontaine, Adrien Rieux, Aude Gilabert, Geremy Cliff, Éric Clua, Ryan Daly, Michael R. Heithaus, Jérémy J. Kiszka, Philip Matich, John Nevill, Amy F. Smoothey, Andrew J. Temple, Per Berggren, Sébastien Jaquemet, Hélène Magalon
Software Mentions: 8
Published: about 5 years ago

10.1038/s41598-017-02157-6

Molecular phylogenetics and biogeography of the mint tribe Elsholtzieae (Nepetoideae, Lamiaceae), with an emphasis on its diversification in East Asia
Cited by: 22
Author(s): Pan Li, Zhe-Chen Qi, Luxian Liu, Tetsuo Ohi‐Toma, Dong Kun Lee, Tsung‐Hsin Hsieh, Chengxin Fu, Kenneth M. Cameron, Ying‐Xiong Qiu
Software Mentions: 7
Published: over 7 years ago

10.1038/s41598-018-33326-w

Spotlight on islands: on the origin and diversification of an ancient lineage of the Italian wall lizard Podarcis siculus in the western Pontine Islands
Cited by: 11
Author(s): Gabriele Senczuk, Katja Havenstein, Valentina Milana, Chiara Ripa, Emanuela De Simone, Ralph Tiedemann, Riccardo Castiglia
Software Mentions: 7
Published: about 6 years ago

10.1111/mec.14932

Flower‐visitor communities of an arcto‐alpine plant—Global patterns in species richness, phylogenetic diversity and ecological functioning
Cited by: 13
Author(s): Mikko Tiusanen, Tea Huotari, Paul D. N. Hebert, Tommi Andersson, Ashley L. Asmus, Joël Bêty, Emma Davis, Jennifer Gale, Bess Hardwick, David S. Hik, Christian Körner, Richard B. Lanctot, Maarten J. J. E. Loonen, Rauni Partanen, Karissa Reischke, Sarah T. Saalfeld, Fanny Senez‐Gagnon, Paul A. Smith, Ján Šulavík, Ilkka Syvänperä, Christine Urbanowicz, Siân Williams, Paul Woodard, Yulia Zaika, Tomas Roslin
Software Mentions: 7
Published: about 6 years ago

10.1002/ece3.5111

Genetic population structure and demography of an apex predator, the tiger shark<i>Galeocerdo cuvier</i>
Cited by: 21
Author(s): Agathe Pirog, Sébastien Jaquemet, Virginie Ravigné, Geremy Cliff, Éric Clua, Bonnie J. Holmes, Nigel E. Hussey, John Nevill, Andrew J. Temple, Per Berggren, Laurent Vigliola, Hélène Magalon
Software Mentions: 7
Published: over 5 years ago

10.1111/mec.14470

Landscape attributes governing local transmission of an endemic zoonosis: Rabies virus in domestic dogs
Cited by: 50
Author(s): Kirstyn Brunker, Philippe Lemey, Denise A. Marston, Anthony R. Fooks, Ahmed Lugelo, Chanasa Ngeleja, Katie Hampson, Roman Biek
Software Mentions: 7
Published: almost 7 years ago

10.1371/journal.pone.0179557

Plio-Pleistocene phylogeography of the Southeast Asian Blue Panchax killifish, Aplocheilus panchax
Cited by: 21
Author(s): Samantha V. Beck, Gary R. Carvalho, Axel Barlow, Lukas Rüber, Heok Hui Tan, Estu Nugroho, Daisy Wowor, Siti Azizah Mohd Nor, Fabian Herder, Zainal A. Muchlisin, Mark de Bruyn
Software Mentions: 7
Published: over 7 years ago

10.1002/ece3.5406

Quaternary climate change and habitat preference shaped the genetic differentiation and phylogeography of<i>Rhodiola</i>sect.<i>Prainia</i>in the southern Qinghai–Tibetan Plateau
Cited by: 8
Author(s): Zi‐Meng Wang, Shi‐Yong Meng, Guang‐Yuan Rao
Software Mentions: 7
Published: over 5 years ago

10.1099/mgen.0.000162

Genomic survey of Clostridium difficile reservoirs in the East of England implicates environmental contamination of wastewater treatment plants by clinical lineages
Cited by: 17
Author(s): Danesh Moradigaravand, Theodore Gouliouris, Catherine Ludden, Sandra Reuter, Dorota Jamrozy, Beth Blane, Plamena Naydenova, Kim Judge, Sani H. Aliyu, Nazreen F. Hadjirin, Mark A. Holmes, Estée Török, Nicholas Brown, Julian Parkhill, Sharon J. Peacock
Software Mentions: 7
Published: almost 7 years ago

10.1099/mgen.0.000156

Assembly of highly repetitive genomes using short reads: the genome of discrete typing unit III Trypanosoma cruzi strain 231
Cited by: 23
Author(s): Rodrigo P. Baptista, João Luís Reis-Cunha, Jeremy D. DeBarry, Égler Chiari, Jessica C. Kissinger, Daniella Castanheira Bartholomeu, Andréa Mara Macedo
Software Mentions: 6
Published: over 6 years ago

10.1002/ece3.4237

Gene flow and Andean uplift shape the diversification of <i>Gasteracantha cancriformis</i> (Araneae: Araneidae) in Northern South America
Cited by: 19
Author(s): Fabian C. Salgado-Roa, Carolina Pardo‐Díaz, Eloisa Lasso, Carlos F. Arias, Vera Nisaka Solferini, Camilo Salazar
Software Mentions: 6
Published: over 6 years ago

10.1371/journal.pone.0055315

Ecological Genetics of Chinese Rhesus Macaque in Response to Mountain Building: All Things Are Not Equal
Cited by: 11
Author(s): Shan-Jin Wu, Jing Luo, Qingqing Li, Yanqin Wang, Robert W. Murphy, Christopher Blair, Shi-Fang Wu, Bisong Yue, Yaping Zhang
Software Mentions: 6
Published: almost 12 years ago

10.1111/eva.12484

Severe consequences of habitat fragmentation on genetic diversity of an endangered Australian freshwater fish: A call for assisted gene flow
Cited by: 106
Author(s): Alexandra Pavlova, Luciano B. Beheregaray, Rhys A. Coleman, Dean M. Gilligan, Katherine A. Harrisson, Brett A. Ingram, Joanne Kearns, Annika M. Lamb, Mark Lintermans, Jarod Lyon, Thuy Thi Thu Nguyen, Minami Sasaki, Zeb Tonkin, Jian D. L. Yen, Paul Sunnucks
Software Mentions: 6
Published: over 7 years ago

10.1111/mec.13914

Genome biogeography reveals the intraspecific spread of adaptive mutations for a complex trait
Cited by: 44
Author(s): Jill K. Olofsson, Matheus E Bianconi, Guillaume Besnard, Luke T. Dunning, Marjorie R. Lundgren, Hélène Holota, Maria S. Vorontsova, Oriane Hidalgo, Ilia J. Leitch, Patrik Nosil, Colin P. Osborne, Pascal‐Antoine Christin
Software Mentions: 6
Published: about 8 years ago

10.1111/j.1365-294X.2010.04961.x

Hybridization and restricted gene flow between native and introduced stocks of Alpine whitefish (Coregonus sp.) across multiple environments
Cited by: 44
Author(s): Kathrin A. Winkler, Barbara Pamminger-Lahnsteiner, Josef Wanzenböck, Steven Weiss
Software Mentions: 6
Published: almost 14 years ago

10.1111/1755-0998.12676

<scp>treespace</scp> : Statistical exploration of landscapes of phylogenetic trees
Cited by: 131
Author(s): Thibaut Jombart, Michaela Kendall, Jacob Almagro-Garcia, Caroline Colijn
Software Mentions: 6
Published: over 7 years ago

10.1099/mgen.0.000042

Introduction and establishment of fluoroquinolone-resistant Shigella sonnei into Bhutan
Cited by: 11
Author(s): Maia A. Rabaa, Duy Pham Thanh, Sirigade Ruekit, Sonam Wangchuk, Tandin Dorji, Kinzang Pem Tshering, To Nguyen Thi Nguyen, Phat Voong Vinh, Tuyen Ha Thanh, Chau Nguyen Ngoc Minh, Paul Turner, Pinaki Sar, Guy Thwaites, Kathryn E. Holt, Nicholas R. Thomson, Ladaporn Bodhidatta, Carl J. Mason, Stephen Baker
Software Mentions: 6
Published: about 9 years ago

10.1186/1471-2148-12-72

Brains, tools, innovation and biogeography in crows and ravens
Cited by: 43
Author(s): Knud A. Jønsson, Pierre‐Henri Fabre, Martin Irestedt
Software Mentions: 5
Published: almost 13 years ago

10.1371/journal.pone.0086272

Robust Regression Analysis of Copy Number Variation Data based on a Univariate Score
Cited by: 4
Author(s): Glen A. Satten, Andrew S. Allen, Morna Ikeda, Jennifer G. Mullé, Stephen T. Warren
Software Mentions: 5
Published: almost 11 years ago

10.1099/mgen.0.000199

Comparative pan-genomic analyses of Orientia tsutsugamushi reveal an exceptional model of bacterial evolution driving genomic diversity
Cited by: 10
Author(s): Amy C. Fleshman, Kristin Mullins, Jason W. Sahl, Crystal M. Hepp, Nathan C. Nieto, Kristin Wiggins, Heidie Hornstra, Daryl J. Kelly, Teik Chye Chan, Rattanaphone Phetsouvanh, Sabine Dittrich, Phonepasith Panyanivong, Daniel Paris, Paul N. Newton, Allen L. Richards, Talima Pearson
Software Mentions: 5
Published: over 6 years ago

10.1002/ece3.4161

Male-biased dispersal and the potential impact of human-induced habitat modifications on the Neotropical bat<i>Trachops cirrhosus</i>
Cited by: 7
Author(s): Tanja K. Halczok, Stefan Dominik Brändel, Victoria Flores, Sébastien J. Puechmaille, Marco Tschapka, Rachel A. Page, Gerald Kerth
Software Mentions: 5
Published: over 6 years ago

10.1002/ece3.2931

Phylogeography of a widespread small carnivore, the western spotted skunk (<i>Spilogale gracilis</i>) reveals temporally variable signatures of isolation across western North America
Cited by: 11
Author(s): Adam W. Ferguson, Molly M. McDonough, Gema I. Guerra, Margaret Rheude, Jerry W. Dragoo, Loren K. Ammerman, Robert C. Dowler
Software Mentions: 5
Published: over 7 years ago

10.1002/ece3.3175

Biogeography and systematics of endemic island damselflies: The <i>Nesobasis</i> and <i>Melanesobasis</i> (Odonata: Zygoptera) of Fiji
Cited by: 10
Author(s): Christopher D. Beatty, Melissa Sánchez Herrera, Jeffrey H. Skevington, Arash Rashed, Hans Van Gossum, Scott Kelso, Thomas N. Sherratt
Software Mentions: 5
Published: over 7 years ago

10.1099/mgen.0.000539

Population structure and transmission of Mycobacterium bovis in Ethiopia
Cited by: 8
Author(s): Gizat Almaw, Getnet Abie Mekonnen, Adane Mihret, Abraham Aseffa, Hawult Taye, Andrew J. K. Conlan, Balako Gumi, Aboma Zewude, Abde Aliy, Mekdes Tamiru, Abebe Olani, Matios Lakew, Melaku Sombo, Solomon Gebre, Colette Diguimbaye, Markus Hilty, Adama Fané, Borna Müller, R. Glyn Hewinson, Richard J. Ellis, Javier Núñez-García, Eleftheria Palkopoulou, Tamrat Abebe, Gobena Ameni, Julian Parkhill, James Wood, Stefan Berg, Andries J. van Tonder
Software Mentions: 5
Published: over 3 years ago

10.1186/s12862-016-0636-x

Evolution of East Asia’s Arcto-Tertiary relict Euptelea (Eupteleaceae) shaped by Late Neogene vicariance and Quaternary climate change
Cited by: 60
Author(s): Yanan Cao, Hans Peter Comes, Shota Sakaguchi, Luyao Chen, Ying‐Xiong Qiu
Software Mentions: 5
Published: almost 9 years ago

10.1099/mgen.0.000050

Repeated local emergence of carbapenem-resistant Acinetobacter baumannii in a single hospital ward
Cited by: 44
Author(s): Mark B. Schultz, Duy Pham Thanh, Nhu Tran Do Hoan, Ryan R. Wick, Danielle J. Ingle, Jane Hawkey, D.J. Edwards, Johanna J. Kenyon, Nguyen Phu Huong Lan, James I. Campbell, Guy Thwaites, Nguyen Thi Khanh Nhu, Ruth M. Hall, Alexandre Fournier‐Level, Stephen Baker, Kathryn E. Holt
Software Mentions: 5
Published: almost 9 years ago

10.1099/jgv.0.000464

Evolution of infectious bronchitis virus in China over the past two decades
Cited by: 52
Author(s): Ye Zhao, Hui Zhang, Jing Zhao, Qi Zhong, Ji Hui Jin, Guo Zhong Zhang
Software Mentions: 5
Published: over 8 years ago

10.1111/1751-7915.12239

Detection and evolutionary analysis of picobirnaviruses in treated wastewater
Cited by: 9
Author(s): Shiwei Zhang, Ruihua Bai, Run Feng, Hongxun Zhang, Lixin Liu
Software Mentions: 5
Published: almost 10 years ago

10.1111/j.1420-9101.2010.01971.x

Habitat use affects morphological diversification in dragon lizards
Cited by: 78
Author(s): David C. Collar, James A. Schulte, Brian C. O’Meara, Jonathan B. Losos
Software Mentions: 5
Published: over 14 years ago

10.1111/jbi.12471

Speciation in the dark: diversification and biogeography of the deep‐sea gastropod genus<i>Scaphander</i>in the Atlantic Ocean
Cited by: 26
Author(s): Mari Heggernes Eilertsen, Manuel António E. Malaquias
Software Mentions: 5
Published: almost 10 years ago

10.1099/mgen.0.000271

A global to local genomics analysis of Clostridioides difficile ST1/RT027 identifies cryptic transmission events in a northern Arizona healthcare network
Cited by: 5
Author(s): Charles H. D. Williamson, Nathan E. Stone, Amalee E. Nunnally, Heidie Hornstra, David M. Wagner, Chandler C. Roe, Adam J. Vazquez, Nivedita Nandurkar, Jacob Vinocur, Joel Terriquez, John D. Gillece, Jason Travis, Darrin Lemmer, Paul Keim, Jason W. Sahl
Software Mentions: 5
Published: over 5 years ago

10.1111/jbi.12326

<i>Ficus insipida</i> subsp. <i>insipida</i> (Moraceae) reveals the role of ecology in the phylogeography of widespread Neotropical rain forest tree species
Cited by: 23
Author(s): Eurídice N. Honorio Coronado, Kyle G. Dexter, Monica F. Poelchau, Peter M. Hollingsworth, Oliver L. Phillips, R. Toby Pennington
Software Mentions: 5
Published: over 10 years ago

10.1099/mgen.0.000201

Genomic epidemiology of the commercially important pathogen Renibacterium salmoninarum within the Chilean salmon industry
Cited by: 9
Author(s): Sion C. Bayliss, David W. Verner–Jeffreys, David Ryder, Rudy Suárez, Roxana Olvera Ramírez, Jaime Romero, Ben Pascoe, Sam Sheppard, Marcos Godoy, Edward J. Feil
Software Mentions: 5
Published: over 6 years ago

10.1111/irv.12772

Comparative epidemiology, phylogenetics, and transmission patterns of severe influenza A/H3N2 in Australia from 2003 to 2017
Cited by: 1
Author(s): Jing Xia, Dillon C. Adam, Aye Moa, Abrar Ahmad Chughtai, Ian G. Barr, Naomi Komadina, C. Raina MacIntyre
Software Mentions: 5
Published: over 4 years ago

10.1111/eva.12495

Speciation history of a species complex of<i>Primulina eburnea</i>(Gesneriaceae) from limestone karsts of southern China, a biodiversity hot spot
Cited by: 23
Author(s): Jing Wang, Bin Ai, Hanghui Kong, Ming Kang
Software Mentions: 5
Published: over 7 years ago

10.1099/mgen.0.000269

Global phylogenomics of multidrug-resistant Salmonella enterica serotype Kentucky ST198
Cited by: 57
Author(s): Jane Hawkey, Simon Le Hello, Benoît Doublet, Sophie A. Granier, René S. Hendriksen, W. Florian Fricke, Pieter‐Jan Ceyssens, Camille Gomart, Helen Billman‐Jacobe, Kathryn E. Holt, François‐Xavier Weill
Software Mentions: 5
Published: over 5 years ago

10.1186/s12862-017-0968-1

Distinct genetic differentiation and species diversification within two marine nematodes with different habitat preference in Antarctic sediments
Cited by: 21
Author(s): Freija Hauquier, Frédérik Leliaert, Annelien Rigaux, Sofie Derycke, Ann Vanreusel
Software Mentions: 5
Published: over 7 years ago

10.1111/mec.12840

Niche divergence promotes rapid diversification of East African sky island white-eyes (Aves: Zosteropidae)
Cited by: 46
Author(s): Siobhan C. Cox, Robert Prŷs-Jones, Jan Christian Habel, Bernard Amakobe, Julia J. Day
Software Mentions: 4
Published: over 10 years ago

10.1111/mec.12462

Divergent evolutionary processes associated with colonization of offshore islands
Cited by: 88
Author(s): Natália Martínková, Ross Barnett, Thomas Cucchi, Rahel Struchen, M. Pascal, Michel Pascal, Martin C. Fischer, Thomas Higham, Selina Brace, Simon Y. W. Ho, Jean‐Pierre Quéré, Paul O’Higgins, Laurent Excoffier, Gerald Heckel, A. Rus Hoelzel, Keith Dobney, Jeremy B. Searle
Software Mentions: 4
Published: over 11 years ago

10.1099/mgen.0.000263

Rapid phenotypic evolution in multidrug-resistant Klebsiella pneumoniae hospital outbreak strains
Cited by: 18
Author(s): Lucy van Dorp, Qi Wang, Liam Shaw, Mislav Acman, Ola Brønstad Brynildsrud, Vegard Eldholm, Ruobing Wang, Hua Gao, Yuyao Yin, Hongbin Chen, Chuling Ding, Rhys A. Farrer, Xavier Didelot, François Balloux, Hui Wang
Software Mentions: 4
Published: over 5 years ago

10.1186/s13742-016-0150-5

The preprocessed connectomes project repository of manually corrected skull-stripped T1-weighted anatomical MRI data
Cited by: 35
Author(s): Benjamin Puccio, James Pooley, John Pellman, Elise C. Taverna, R. Cameron Craddock
Software Mentions: 4
Published: about 8 years ago

10.1111/jbi.13525

Ancestral range reconstruction of remote oceanic island species of <i>Plantago</i> (Plantaginaceae) reveals differing scales and modes of dispersal
Cited by: 20
Author(s): Natalie Iwanycki Ahlstrand, Brecht Verstraete, Gustavo Hassemer, Stephanie Dunbar-Co, Ronald K. Hoggard, Heidi M. Meudt, Nina Rønsted
Software Mentions: 4
Published: almost 6 years ago

10.1099/mgen.0.000582

Achromobacter spp. genetic adaptation in cystic fibrosis
Cited by: 4
Author(s): Miglė Gabrielaitė, Finn C. Nielsen, Helle Krogh Johansen, Rasmus Lykke Marvig
Software Mentions: 4
Published: over 3 years ago

10.1111/jeb.12022

Loss of genetic variability in social spiders: genetic and phylogenetic consequences of population subdivision and inbreeding
Cited by: 33
Author(s): Ingi Agnarsson, Leticia Avilés, Wayne P. Maddison
Software Mentions: 4
Published: about 12 years ago

10.1002/ece3.576

Reevaluation of a classic phylogeographic barrier: new techniques reveal the influence of microgeographic climate variation on population divergence
Cited by: 15
Author(s): J. Angel Soto‐Centeno, Lisa N. Barrow, Julie M. Allen, David L. Reed
Software Mentions: 4
Published: over 11 years ago

10.1099/mgen.0.000205

Genomic surveillance of Neisseria gonorrhoeae to investigate the distribution and evolution of antimicrobial-resistance determinants and lineages
Cited by: 37
Author(s): Koji Yahara, Shuichi Nakayama, Ken Shimuta, Ken-ichi Lee, Masatomo Morita, Takuya Kawahata, Toshiro Kuroki, Yuko Watanabe, Hitomi Ohya, Mitsuru Yasuda, Takashi Deguchi, Xavier Didelot, Makoto Ohnishi
Software Mentions: 4
Published: over 6 years ago

10.1099/mgen.0.000095

Whole genome analysis of Yersinia ruckeri isolated over 27 years in Australia and New Zealand reveals geographical endemism over multiple lineages and recent evolution under host selection
Cited by: 16
Author(s): Andrew C. Barnes, J. Delamare-Deboutteville, Nicholas Gudkovs, Cara L. Brosnahan, R. I. Guy Morrison, J Carson
Software Mentions: 4
Published: about 8 years ago

10.1002/ece3.4487

Evolutionary history of the endemic water shrew<i>Neomys anomalus</i>: Recurrent phylogeographic patterns in semi-aquatic mammals of the Iberian Peninsula
Cited by: 9
Author(s): Marina Querejeta, José Castresana
Software Mentions: 4
Published: about 6 years ago

10.1093/sysbio/syu052

Bayesian Species Delimitation Can Be Robust to Guide-Tree Inference Errors
Cited by: 52
Author(s): Chi Zhang, Bruce Rannala, Ziheng Yang
Software Mentions: 4
Published: over 10 years ago

10.1002/ece3.4861

Living on the edge: Exploring the role of coastal refugia in the Alexander Archipelago of Alaska
Cited by: 15
Author(s): Yadéeh E. Sawyer, Stephen O. MacDonald, Enrique P. Lessa, Joseph A. Cook
Software Mentions: 4
Published: almost 6 years ago

10.1099/vir.0.000035

Rapid evolution of the env gene leader sequence in cats naturally infected with feline immunodeficiency virus
Cited by: 9
Author(s): Paweł M. Bęczkowski, Joseph Hughes, Roman Biek, Annette Litster, Brian J. Willett, Margaret J. Hosie
Software Mentions: 4
Published: over 9 years ago

10.1002/ece3.3161

Cryptic lineage divergence in marine environments: genetic differentiation at multiple spatial and temporal scales in the widespread intertidal goby<i>Gobiosoma bosc</i>
Cited by: 23
Author(s): Borja Milá, James L. Van Tassell, Jatziri A. Calderón, Lukas Rüber, Rafael Zardoya
Software Mentions: 4
Published: over 7 years ago

10.1099/vir.0.000062

Genetic characterization of human coxsackievirus A6 variants associated with atypical hand, foot and mouth disease: a potential role of recombination in emergence and pathogenicity
Cited by: 51
Author(s): Eleanor Gaunt, Heli Harvala, Riikka Österback, Vattipally B. Sreenu, Emma C. Thomson, Matti Waris, Peter Simmonds
Software Mentions: 4
Published: over 9 years ago

10.1099/jgv.0.001494

Analysis of partial sequences of the RNA-dependent RNA polymerase gene as a tool for genus and subgenus classification of coronaviruses
Cited by: 9
Author(s): David A. Wilkinson, Léa Joffrin, Camille Lebarbenchon, Patrick Mavingui
Software Mentions: 3
Published: about 4 years ago

10.1099/mgen.0.000133

Phylogeographic separation and formation of sexually discrete lineages in a global population of Yersinia pseudotuberculosis
Cited by: 11
Author(s): Tristan Seecharran, Laura Kalin-Mänttäri, Katja A. Koskela, Simo Nikkari, Benjamin Dickins, Jukka Corander, Mikael Skurnik, Alan McNally
Software Mentions: 3
Published: about 7 years ago

10.1099/mgen.0.000355

Origin, genomic diversity and microevolution of the Clostridium difficile B1/NAP1/RT027/ST01 strain in Costa Rica, Chile, Honduras and Mexico
Cited by: 5
Author(s): Enzo Guerrero-Araya, Claudio Meneses, Eduardo Castro-Nallar, Ana M Guzmán D, Manuel Álvarez-Lobos, Carlos Quesada-Gómez, Daniel Paredes-Sabja, César Rodríguez
Software Mentions: 3
Published: over 4 years ago

10.1099/mgen.0.000142

Vibrio cholerae genomic diversity within and between patients
Cited by: 24
Author(s): Inès Levade, Yves Terrat, Jean-Baptiste Leducq, Ana A. Weil, Leslie M. Mayo-Smith, Fahima Chowdhury, Ashraful Islam Khan, Jacques Boncy, Josiane Buteau, Louise C. Ivers, Edward T. Ryan, Richelle C. Charles, Stephen B. Calderwood, Firdausi Qadri, Jason B. Harris, Regina C. LaRocque, B. Jesse Shapiro
Software Mentions: 3
Published: about 7 years ago

10.1099/mgen.0.000361

Bayesian reconstruction of Mycobacterium tuberculosis transmission networks in a high incidence area over two decades in Malawi reveals associated risk factors and genomic variants
Cited by: 16
Author(s): Benjamin Sobkowiak, Louis Banda, Themba Mzembe, Amelia C. Crampin, Judith R. Glynn, Taane G. Clark
Software Mentions: 3
Published: over 4 years ago

10.1099/mgen.0.000219

Genome-based transmission modelling separates imported tuberculosis from recent transmission within an immigrant population
Cited by: 10
Author(s): Diepreye Ayabina, Janne O. Rønning, Kristian Alfsnes, Nadia Debech, Ola Brønstad Brynildsrud, Trude Margrete Arnesen, Gunnstein Norheim, Anne Torunn Mengshoel, Rikard Rykkvin, Ulf R. Dahle, Caroline Colijn, Vegard Eldholm
Software Mentions: 3
Published: about 6 years ago

10.1099/mgen.0.000057

Bayesian codon substitution modelling to identify sources of pathogen evolutionary rate variation
Cited by: 4
Author(s): Guy Baele, Marc A. Suchard, Filip Bielejec, Philippe Lemey
Software Mentions: 3
Published: over 8 years ago

10.1099/mgen.0.000180

Bordetella pertussis population dynamics and phylogeny in Japan after adoption of acellular pertussis vaccines
Cited by: 18
Author(s): Aldert Zomer, Nao Otsuka, Yukihiro Hiramatsu, Kazunari Kamachi, Naoko Nishimura, Takao Ozaki, Jan Poolman, Jeroen Geurtsen
Software Mentions: 3
Published: over 6 years ago

10.1099/mgen.0.000094

Genome-scale rates of evolutionary change in bacteria
Cited by: 165
Author(s): Sebastián Duchêne, Kathryn E. Holt, François‐Xavier Weill, Simon Le Hello, Jane Hawkey, D.J. Edwards, Mathieu Fourment, Edward C. Holmes
Software Mentions: 3
Published: about 8 years ago

10.1099/mgen.0.000052

Five decades of genome evolution in the globally distributed, extensively antibiotic-resistant Acinetobacter baumannii global clone 1
Cited by: 91
Author(s): Kathryn E. Holt, Johanna J. Kenyon, Mohammad Hamidian, Mark B. Schultz, Derek Pickard, Gordon Dougan, Ruth M. Hall
Software Mentions: 3
Published: almost 9 years ago

10.1371/journal.pcbi.1008380

On the inference of complex phylogenetic networks by Markov Chain Monte-Carlo
Cited by: 10
Author(s): Charles-Elie Rabier, Vincent Berry, Marnus Stoltz, João dos Santos, Wensheng Wang, Jean-Christophe Glaszmann, Fabio Pardi, Céline Scornavacca
Software Mentions: 3
Published: over 3 years ago

10.1371/journal.pone.0161713

Multilocus Analyses Reveal Postglacial Demographic Shrinkage of Juniperus morrisonicola (Cupressaceae), a Dominant Alpine Species in Taiwan
Cited by: 7
Author(s): Chi‐Cheng Huang, Tsai Wen Hsu, Hao Ven Wang, Zin Huang Liu, Yi-Yen Chen, Chi Te Chiu, Chao Huang, Kuo Hsiang Hung, Tzen‐Yuh Chiang
Software Mentions: 3
Published: over 8 years ago

10.1371/journal.pone.0186690

Phylogeography of the termite Macrotermes gilvus and insight into ancient dispersal corridors in Pleistocene Southeast Asia
Cited by: 7
Author(s): G Veera Singham, Ahmad Sofiman Othman, Chow‐Yang Lee
Software Mentions: 3
Published: about 7 years ago

10.1371/journal.pone.0037068

The Impact of Human Conflict on the Genetics of Mastomys natalensis and Lassa Virus in West Africa
Cited by: 37
Author(s): Aude Lalis, Raphaël Leblois, Émilie Lecompte, Christiane Denys, Jan ter Meulen, Thierry Wirth
Software Mentions: 3
Published: over 12 years ago

10.1002/ece3.7358

Genetic divergence between isolated populations of the North Island New Zealand Rifleman (<i>Acanthisitta chloris granti</i>) implicates ancient biogeographic impacts rather than recent habitat fragmentation
Cited by: 1
Author(s): Sarah J. Withers, Stuart Parsons, Márk E. Hauber, Alistair Kendrick, Shane Lavery
Software Mentions: 3
Published: over 3 years ago

10.1002/ece3.2393

Phylogeographic structure in long‐tailed voles (Rodentia: Arvicolinae) belies the complex Pleistocene history of isolation, divergence, and recolonization of Northwest North America's fauna
Cited by: 10
Author(s): Yadéeh E. Sawyer, Joseph A. Cook
Software Mentions: 3
Published: over 8 years ago

10.1111/eva.12151

Evidence that hepatitis C virus genome partly controls infection outcome
Cited by: 4
Author(s): Matthew Hartfield, Rowena A. Bull, Peter A. White, Andrew R. Lloyd, Fabio Luciani, Samuel Alizon
Software Mentions: 3
Published: over 10 years ago

10.3390/genes12060862

Improved Models of Coalescence Ages of Y-DNA Haplogroups
Cited by: 2
Author(s): Iain McDonald
Software Mentions: 3
Published: over 3 years ago

10.1111/irv.12131

Identification of group <scp>B</scp> respiratory syncytial viruses that lack the 60‐nucleotide duplication after six consecutive epidemics of total <scp>BA</scp> dominance at coastal <scp>K</scp> enya
Cited by: 18
Author(s): Charles N. Agoti, Caroline W. Gitahi, Graham F. Medley, Patricia A. Cane, D. James Nokes
Software Mentions: 3
Published: over 11 years ago

10.1111/irv.12715

Toward unified molecular surveillance of RSV: A proposal for genotype definition
Cited by: 39
Author(s): Stephanie Goya, Mónica Galiano, Inne Nauwelaers, Alfonsina Trento, Peter Openshaw, Alicia Mistchenko, Maria Zambon, Mariana Viegas
Software Mentions: 3
Published: almost 5 years ago

10.1111/jzs.12110

Gene flow, population growth and a novel substitution rate estimate in a subtidal rock specialist, the black‐faced blenny<i><scp>T</scp>ripterygion delaisi</i>(<scp>P</scp>erciformes,<scp>B</scp>lennioidei,<scp>T</scp>ripterygiidae) from the<scp>A</scp>driatic<scp>S</scp>ea
Cited by: 15
Author(s): Stephan Koblmüller, Bernd Steinwender, Sara Weiß, Kristina M. Sefc
Software Mentions: 3
Published: about 9 years ago

10.1111/j.1365-2699.2010.02472.x

Phylogeography of the dark kangaroo mouse, Microdipodops megacephalus: cryptic lineages and dispersal routes in North America’s Great Basin
Cited by: 16
Author(s): John C. Hafner, Nathan S. Upham
Software Mentions: 3
Published: almost 14 years ago

10.1111/jeb.12211

Reproductive isolation and patterns of genetic differentiation in a cryptic butterfly species complex
Cited by: 56
Author(s): Vlad Dincă, Christer Wiklund, Vladimir A. Lukhtanov, Ullasa Kodandaramaiah, Karin Norén, Leonardo Dapporto, Niklas Wahlberg, Roger Vila, Magne Friberg
Software Mentions: 3
Published: over 11 years ago

10.1038/srep24041

Contributions of historical and contemporary geographic and environmental factors to phylogeographic structure in a Tertiary relict species, Emmenopterys henryi (Rubiaceae)
Cited by: 39
Author(s): Yonghua Zhang, Ian Wang, Hans Peter Comes, Hua Peng, Ying‐Xiong Qiu
Software Mentions: 3
Published: over 8 years ago

10.1099/vir.0.026666-0

A complex hepatitis B virus (X/C) recombinant is common in Long An county, Guangxi and may have originated in southern China
Cited by: 27
Author(s): Zhong-Liao Fang, Stephane Hué, Caroline Sabin, Guojian Li, Jin-Ye Yang, Qin-Yan Chen, Kong-Xiong Fang, Huang Ji, Xueyan Wang, Tim J. Harrison
Software Mentions: 3
Published: about 14 years ago

10.7717/peerj.11338

Comparative phylogeography uncovers evolutionary past of Holarctic dragonflies
Cited by: 4
Author(s): Manpreet Kohli, Marie Djernæs, Melissa Sánchez Herrera, Göran Sahlén, Erik M. Pilgrim, Thomas J. Simonsen, Kent Olsen, Jessica L. Ware
Software Mentions: 2
Published: over 3 years ago

10.1111/j.1365-294X.2012.05456.x

Extensive range persistence in peripheral and interior refugia characterizes Pleistocene range dynamics in a widespread Alpine plant species (<i>Senecio carniolicus</i>, Asteraceae)
Cited by: 41
Author(s): Pedro Escobar García, Manuela Winkler, Ruth Flatscher, Michaela Sonnleitner, Jana Krejčíková, Jan Suda, Karl Hülber, Gerald M. Schneeweiss, Peter Schönswetter
Software Mentions: 2
Published: almost 13 years ago

10.1099/vir.0.039370-0

Origin and fate of A/H1N1 influenza in Scotland during 2009
Cited by: 14
Author(s): Samantha Lycett, Nigel J. McLeish, Christopher Robertson, William F. Carman, Gregory J. Baillie, James McMenamin, Andrew Rambaut, Peter Simmonds, Mark Woolhouse, Andrew J. Leigh Brown
Software Mentions: 2
Published: over 12 years ago

10.1111/mec.13586

Inferences from tip‐calibrated phylogenies: a review and a practical guide
Cited by: 112
Author(s): Adrien Rieux, François Balloux
Software Mentions: 2
Published: over 8 years ago

10.1111/mec.12374

Water‐level fluctuations and metapopulation dynamics as drivers of genetic diversity in populations of three Tanganyikan cichlid fish species
Cited by: 30
Author(s): Bruno Nevado, Selma Mautner, Christian Sturmbauer, Erik Verheyen
Software Mentions: 2
Published: over 11 years ago

10.1099/mgen.0.000357

Visualizing variation within Global Pneumococcal Sequence Clusters (GPSCs) and country population snapshots to contextualize pneumococcal isolates
Cited by: 22
Author(s): Rebecca A. Gladstone, Stephanie Lo, Richard Goater, Corin Yeats, Benjamin A. Taylor, James Hadfield, John A. Lees, Nicholas J. Croucher, Andries J. van Tonder, Leon J. Bentley, F X Quah, Anne J. Blaschke, Nicole L Pershing, Carrie L. Byington, Balaji Veeraraghavan, Waleria Hryniewicz, Betuel Sigaúque, K L Ravikumar, Samanta Cristine Grassi Almeida, Theresa J. Ochoa, Pak‐Leung Ho, Mignon du Plessis, Kedibone Ndlangisa, Jennifer Cornick, Brenda Kwambana-Adams, Rachel Benisty, Susan Nzenze, Shabir A. Madhi, Paulina A. Hawkins, Andrew J. Pollard, Dean Everett, Martín Antonio, Ron Dagan, Keith P. Klugman, Anne von Gottberg, Ben J. Metcalf, Y Li, Bernard Beall, Lesley McGee, Robert F. Breiman, David M. Aanensen, Stephen D. Bentley
Software Mentions: 2
Published: over 4 years ago

10.1099/mgen.0.000111

Genomic epidemiology of a national outbreak of post-surgical Mycobacterium abscessus wound infections in Brazil
Cited by: 20
Author(s): Izzy Everall, Christiane Lourenço Nogueira, Josephine M. Bryant, Leonor Sánchez-Busó, Érica Chimara, Rafael da Silva Duarte, Jesus Pais Ramos, Karla Valéria Batista Lima, Maria Luíza Lopes, Moisés Palaci, André Kipnis, Fernanda Monego, R. Andres Floto, Julian Parkhill, Sylvia Cardoso Leão, Simon R. Harris
Software Mentions: 2
Published: over 7 years ago

10.1111/mec.15329

Ancient DNA suggests modern wolves trace their origin to a Late Pleistocene expansion from Beringia
Cited by: 63
Author(s): Liisa Loog, Olaf Thalmann, Mikkel Holger S. Sinding, Verena J. Schuenemann, Angela R. Perri, Mietje Germonpré, Hervé Bocherens, Kelsey E. Witt, José Alfredo Samaniego Castruita, Marcela Sandoval Velasco, Inge Lundstrøm, Nathan Wales, Gontran Sonet, Laurent Frantz, Hannes Schroeder, Jane Budd, Elodie‐Laure Jimenez, Sergey Fedorov, Boris Gasparyan, Andrew W. Kandel, Martina Lázničková‐Galetová, Hannes Napierala, Hans Peter Uerpmann, Pavel A. Nikolskiy, Elena Y. Pavlova, Vladimir V. Pitulko, Karl Heinz Herzig, Ripan S. Malhi, Eske Willerslev, Anders J. Hansen, Keith Dobney, M. Thomas P. Gilbert, Johannes Krause, Greger Larson, Anders Eriksson, Andrea Manica
Software Mentions: 2
Published: almost 5 years ago

10.1099/vir.0.000155

Influenza A virus evolution and spatio-temporal dynamics in Eurasian wild birds: a phylogenetic and phylogeographical study of whole-genome sequence data
Cited by: 23
Author(s): Nicola S. Lewis, Josanne H. Verhagen, Z. Javakhishvili, Colin A. Russell, Pascal Lexmond, Kim B. Westgeest, Theo M. Bestebroer, Rebecca Halpin, Xudong Lin, Amy Ransier, Nadia Fedorova, Timothy B. Stockwell, Neus Latorre‐Margalef, Björn Olsén, Gavin J. D. Smith, Justin Bahl, David E. Wentworth, Jonas Waldenström, Ron A. M. Fouchier, Miranda de Graaf
Software Mentions: 2
Published: over 9 years ago

10.1099/jgv.0.001198

Increased predominance of HIV-1 CRF01_AE and its recombinants in the Philippines
Cited by: 12
Author(s): Yue Chen, Bhavna Hora, Todd DeMarco, Regina Berba, Heidi Register, Sylvia Faye Hood, Meredith Carter, Mars Stone, Andrea L. Pappas, Ana M. Sánchez, Michael P. Busch, Thomas N. Denny, Feng Gao
Software Mentions: 2
Published: almost 6 years ago

10.1099/mgen.0.000141

Population structure of Escherichia coli O26 : H11 with recent and repeated stx2 acquisition in multiple lineages
Cited by: 26
Author(s): Yoshitoshi Ogura, Yasuhiro Gotoh, Takehiko Itoh, Mitsuhiko Sato, Kazuko Seto, Shyuji Yoshino, Junko Isobe, Yoshiki Etoh, Mariko Kurogi, Keiko Kimata, Eriko Maeda, Denis Piérard, Masahiro Kusumoto, Masato Akiba, Kiyoshi Tominaga, Yumi Kirino, Yuki Kato, Katsuhiko Shirahige, Tadasuke Ooka, Nozomi Ishijima, Ken-ichi Lee, Sunao Iyoda, Jacques Mainil, Tetsuya Hayashi
Software Mentions: 2
Published: about 7 years ago

10.1099/mgen.0.000242

Evolution of a clade of Acinetobacter baumannii global clone 1, lineage 1 via acquisition of carbapenem- and aminoglycoside-resistance genes and dispersion of ISAba1
Cited by: 28
Author(s): Mohammad Hamidian, Jane Hawkey, Ryan R. Wick, Kathryn E. Holt, Ruth M. Hall
Software Mentions: 2
Published: almost 6 years ago

10.1111/jbi.12611

Diversification of clearwing butterflies with the rise of the Andes
Cited by: 49
Author(s): Dunnya De‐Silva, Marianne Élias, Keith R. Willmott, James Mallet, Julia J. Day
Software Mentions: 2
Published: about 9 years ago

10.1099/mgen.0.000147

Multi-clonal evolution of multi-drug-resistant/extensively drug-resistant Mycobacterium tuberculosis in a high-prevalence setting of Papua New Guinea for over three decades
Cited by: 30
Author(s): Arnold Bainomugisa, Evelyn Lavu, Stenard Hiashiri, S. S. Majumdar, A. Honjepari, Rendi Moke, Paison Dakulala, Grant A. Hill-Cawthorne, Sushil Pandey, Ben J. Marais, Chris Coulter, Lachlan Coin
Software Mentions: 2
Published: almost 7 years ago

10.1099/mgen.0.000323

Differential dynamics and impacts of prophages and plasmids on the pangenome and virulence factor repertoires of Shiga toxin-producing Escherichia coli O145:H28
Cited by: 27
Author(s): Keiji Nakamura, Kazunori Murase, Mitsuhiko Sato, Atsushi Toyoda, Takehiko Itoh, Jacques Mainil, Denis Piérard, Shuji Yoshino, Keiko Kimata, Junko Isobe, Kazuko Seto, Yoshiki Etoh, Hiroshi Narimatsu, Shioko Saito, Jun Yatsuyanagi, Ken-ichi Lee, Sunao Iyoda, Makoto Ohnishi, Tadasuke Ooka, Yasuhiro Gotoh, Tetsuya Hayashi
Software Mentions: 2
Published: almost 5 years ago

10.1099/mgen.0.000161

A novel prophage identified in strains from Salmonella enterica serovar Enteritidis is a phylogenetic signature of the lineage ST-1974
Cited by: 6
Author(s): Bruno D’Alessandro, Victoria Pérez Escanda, Lucía Balestrazzi, Andrés Iriarte, Derek Pickard, Lucía Yim, José A. Chabalgoity, Laura Betancor
Software Mentions: 2
Published: almost 7 years ago

10.1111/2041-210X.12466

The effect of genetic structure on molecular dating and tests for temporal signal
Cited by: 109
Author(s): Gemma G. R. Murray, Fang Wang, Ewan M. Harrison, Gavin K. Paterson, Alison E. Mather, Simon R. Harris, Mark A. Holmes, Andrew Rambaut, John J. Welch
Software Mentions: 2
Published: over 9 years ago

10.1099/vir.0.000077

Phylodynamic analysis of avian infectious bronchitis virus in South America
Cited by: 38
Author(s): Ana Marandino, Ariel Pereda, Gonzalo Tomás, Martı́n Hernández, Gregorio Iraola, María Isabel Craig, Diego Hernández, Alejandro Banda, Pedro Villegas, Yanina Panzera, Rubén Pérez
Software Mentions: 2
Published: over 9 years ago