Publications by authors named "Murray P Cox"

95Publications

Dense sampling of bird diversity increases power of comparative genomics.

Authors:
Shaohong Feng Josefin Stiller Yuan Deng Joel Armstrong Qi Fang Andrew Hart Reeve Duo Xie Guangji Chen Chunxue Guo Brant C Faircloth Bent Petersen Zongji Wang Qi Zhou Mark Diekhans Wanjun Chen Sergio Andreu-Sánchez Ashot Margaryan Jason Travis Howard Carole Parent George Pacheco Mikkel-Holger S Sinding Lara Puetz Emily Cavill Ângela M Ribeiro Leopold Eckhart Jon Fjeldså Peter A Hosner Robb T Brumfield Les Christidis Mads F Bertelsen Thomas Sicheritz-Ponten Dieter Thomas Tietze Bruce C Robertson Gang Song Gerald Borgia Santiago Claramunt Irby J Lovette Saul J Cowen Peter Njoroge John Philip Dumbacher Oliver A Ryder Jérôme Fuchs Michael Bunce David W Burt Joel Cracraft Guanliang Meng Shannon J Hackett Peter G Ryan Knud Andreas Jønsson Ian G Jamieson Rute R da Fonseca Edward L Braun Peter Houde Siavash Mirarab Alexander Suh Bengt Hansson Suvi Ponnikas Hanna Sigeman Martin Stervander Paul B Frandsen Henriette van der Zwan Rencia van der Sluis Carina Visser Christopher N Balakrishnan Andrew G Clark John W Fitzpatrick Reed Bowman Nancy Chen Alison Cloutier Timothy B Sackton Scott V Edwards Dustin J Foote Subir B Shakya Frederick H Sheldon Alain Vignal André E R Soares Beth Shapiro Jacob González-Solís Joan Ferrer-Obiol Julio Rozas Marta Riutort Anna Tigano Vicki Friesen Love Dalén Araxi O Urrutia Tamás Székely Yang Liu Michael G Campana André Corvelo Robert C Fleischer Kim M Rutherford Neil J Gemmell Nicolas Dussex Henrik Mouritsen Nadine Thiele Kira Delmore Miriam Liedvogel Andre Franke Marc P Hoeppner Oliver Krone Adam M Fudickar Borja Milá Ellen D Ketterson Andrew Eric Fidler Guillermo Friis Ángela M Parody-Merino Phil F Battley Murray P Cox Nicholas Costa Barroso Lima Francisco Prosdocimi Thomas Lee Parchman Barney A Schlinger Bette A Loiselle John G Blake Haw Chuan Lim Lainy B Day Matthew J Fuxjager Maude W Baldwin Michael J Braun Morgan Wirthlin Rebecca B Dikow T Brandt Ryder Glauco Camenisch Lukas F Keller Jeffrey M DaCosta Mark E Hauber Matthew I M Louder Christopher C Witt Jimmy A McGuire Joann Mudge Libby C Megna Matthew D Carling Biao Wang Scott A Taylor Glaucia Del-Rio Alexandre Aleixo Ana Tereza Ribeiro Vasconcelos Claudio V Mello Jason T Weir David Haussler Qiye Li Huanming Yang Jian Wang Fumin Lei Carsten Rahbek M Thomas P Gilbert Gary R Graves Erich D Jarvis Benedict Paten Guojie Zhang

Nature 2020 11 11;587(7833):252-257. Epub 2020 Nov 11.

China National GeneBank, BGI-Shenzhen, Shenzhen, China.

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http://dx.doi.org/10.1038/s41586-020-2873-9DOI Listing
November 2020

Comparative genetic diversity of species causing human infections.

Parasitology 2020 11 10;147(13):1532-1537. Epub 2020 Aug 10.

Molecular Epidemiology and Public Health Laboratory, Hopkirk Research Institute, School of Veterinary Science, Massey University, Private Bag 11 222, Palmerston North, 4442, New Zealand.

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http://dx.doi.org/10.1017/S0031182020001493DOI Listing
November 2020

Papuan mitochondrial genomes and the settlement of Sahul.

J Hum Genet 2020 Oct 1;65(10):875-887. Epub 2020 Jun 1.

Laboratoire Évolution and Diversité Biologique (EDB UMR 5174), Université de Toulouse Midi-Pyrénées, CNRS, IRD, UPS, 118 route de Narbonne, Bat 4R1, 31062, Toulouse, France.

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http://dx.doi.org/10.1038/s10038-020-0781-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7449881PMC
October 2020

Plant Resistance and Susceptibility to Petal Blight Disease Are Defined by the Timing of Defense Responses.

Mol Plant Microbe Interact 2020 Jul 20;33(7):982-995. Epub 2020 May 20.

School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.

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http://dx.doi.org/10.1094/MPMI-10-19-0304-RDOI Listing
July 2020

Correction to: Archaic mitochondrial DNA inserts in modern day nuclear genomes.

BMC Genomics 2020 01 17;21(1):55. Epub 2020 Jan 17.

Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D04103, Leipzig, Germany.

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http://dx.doi.org/10.1186/s12864-020-6449-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6966873PMC
January 2020

Archaic mitochondrial DNA inserts in modern day nuclear genomes.

BMC Genomics 2019 Dec 26;20(1):1017. Epub 2019 Dec 26.

Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, D04103, Germany.

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http://dx.doi.org/10.1186/s12864-019-6392-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6933719PMC
December 2019

Chromosome-Level Reference Genome of , Causative Agent of Pecan Scab.

Mol Plant Microbe Interact 2020 Feb 2;33(2):149-152. Epub 2019 Dec 2.

Noble Research Institute, LLC, Ardmore, OK 73401, U.S.A.

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http://dx.doi.org/10.1094/MPMI-08-19-0236-ADOI Listing
February 2020

Greater genetic and regulatory plasticity of retained duplicates in Epichloë endophytic fungi.

Mol Ecol 2019 12 6;28(23):5103-5114. Epub 2019 Nov 6.

Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North, New Zealand.

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http://dx.doi.org/10.1111/mec.15275DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7004115PMC
December 2019

Sex-linked genetic diversity originates from persistent sociocultural processes at microgeographic scales.

R Soc Open Sci 2019 Aug 28;6(8):190733. Epub 2019 Aug 28.

Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand.

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http://dx.doi.org/10.1098/rsos.190733DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6731738PMC
August 2019

Reduced Virulence of an Introduced Forest Pathogen over 50 Years.

Microorganisms 2019 Oct 5;7(10). Epub 2019 Oct 5.

School of Fundamental Sciences and Bio-Protection Research Centre, Massey University, Palmerston North 4410, New Zealand.

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http://dx.doi.org/10.3390/microorganisms7100420DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6843257PMC
October 2019

Genetics, adaptation to environmental changes and archaic admixture in the pathogenesis of diabetes mellitus in Indigenous Australians.

Rev Endocr Metab Disord 2019 09;20(3):321-332

Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North, 4410, New Zealand.

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http://dx.doi.org/10.1007/s11154-019-09505-zDOI Listing
September 2019

Phylogenetic determinants of toxin gene distribution in genomes of Brevibacillus laterosporus.

Genomics 2020 01 19;112(1):1042-1053. Epub 2019 Jun 19.

Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand.

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https://linkinghub.elsevier.com/retrieve/pii/S08887543183068
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http://dx.doi.org/10.1016/j.ygeno.2019.06.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6978878PMC
January 2020

Warfare induces post-marital residence change.

J Theor Biol 2019 08 3;474:52-62. Epub 2019 May 3.

Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North, New Zealand; Te Pūnaha Matatini, New Zealand Complex Systems Research Centre, Centre of Research Excellence, New Zealand. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00225193193018
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http://dx.doi.org/10.1016/j.jtbi.2019.05.002DOI Listing
August 2019

Multiple Deeply Divergent Denisovan Ancestries in Papuans.

Cell 2019 05 11;177(4):1010-1021.e32. Epub 2019 Apr 11.

Statistics and Bioinformatics Group, School of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.02.035DOI Listing
May 2019

Global population genomics of the forest pathogen Dothistroma septosporum reveal chromosome duplications in high dothistromin-producing strains.

Mol Plant Pathol 2019 06 1;20(6):784-799. Epub 2019 Apr 1.

Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa.

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http://dx.doi.org/10.1111/mpp.12791DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6637865PMC
June 2019

Complex epigenetic regulation of alkaloid biosynthesis and host interaction by heterochromatin protein I in a fungal endophyte-plant symbiosis.

Fungal Genet Biol 2019 04 4;125:71-83. Epub 2019 Feb 4.

School of Fundamental Sciences and the BioProtection Research Centre, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand. Electronic address:

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http://dx.doi.org/10.1016/j.fgb.2019.02.001DOI Listing
April 2019

Human Perceptions of Megafaunal Extinction Events Revealed by Linguistic Analysis of Indigenous Oral Traditions.

Hum Ecol Interdiscip J 2018 4;46(4):461-470. Epub 2018 Jun 4.

4Faculty of Māori and Indigenous Studies, University of Waikato, Private Bag 3105, Hamilton, 3240 New Zealand.

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http://dx.doi.org/10.1007/s10745-018-0004-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6133014PMC
June 2018

Epichloë hybrida, sp. nov., an emerging model system for investigating fungal allopolyploidy.

Mycologia 2017 25;109(5):715-729. Epub 2018 Jan 25.

a Institute of Fundamental Sciences, Massey University , Private Bag 11 222, Palmerston North 4410 , New Zealand.

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http://dx.doi.org/10.1080/00275514.2017.1406174DOI Listing
November 2018

Kinship structures create persistent channels for language transmission.

Proc Natl Acad Sci U S A 2017 12 20;114(49):12910-12915. Epub 2017 Nov 20.

Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North 4410, New Zealand.

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http://dx.doi.org/10.1073/pnas.1706416114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5724253PMC
December 2017

Complex Patterns of Admixture across the Indonesian Archipelago.

Mol Biol Evol 2017 10;34(10):2439-2452

Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.

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http://dx.doi.org/10.1093/molbev/msx196DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5850824PMC
October 2017

Genomic admixture tracks pulses of economic activity over 2,000 years in the Indian Ocean trading network.

Sci Rep 2017 06 7;7(1):2919. Epub 2017 Jun 7.

Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse UMR 5288 CNRS, Université Toulouse III, Université de Toulouse, Toulouse, France.

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http://dx.doi.org/10.1038/s41598-017-03204-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5462752PMC
June 2017

The last sea nomads of the Indonesian archipelago: genomic origins and dispersal.

Eur J Hum Genet 2017 08 17;25(8):1004-1010. Epub 2017 May 17.

Equipe de Médecine Evolutive, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse UMR-5288, Université de Toulouse, Toulouse, France.

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http://dx.doi.org/10.1038/ejhg.2017.88DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5567155PMC
August 2017

Genomic Data Quality Impacts Automated Detection of Lateral Gene Transfer in Fungi.

G3 (Bethesda) 2017 04 3;7(4):1301-1314. Epub 2017 Apr 3.

Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand

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http://dx.doi.org/10.1534/g3.116.038448DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5386878PMC
April 2017

The Case of the Missing Ancient Fungal Polyploids.

Am Nat 2016 Dec 26;188(6):602-614. Epub 2016 Sep 26.

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http://dx.doi.org/10.1086/688763DOI Listing
December 2016

Reconstructing Demography and Social Behavior During the Neolithic Expansion from Genomic Diversity Across Island Southeast Asia.

Genetics 2016 Dec 28;204(4):1495-1506. Epub 2016 Sep 28.

Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand

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http://dx.doi.org/10.1534/genetics.116.191379DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5161281PMC
December 2016

Genomic analyses inform on migration events during the peopling of Eurasia.

Authors:
Luca Pagani Daniel John Lawson Evelyn Jagoda Alexander Mörseburg Anders Eriksson Mario Mitt Florian Clemente Georgi Hudjashov Michael DeGiorgio Lauri Saag Jeffrey D Wall Alexia Cardona Reedik Mägi Melissa A Wilson Sayres Sarah Kaewert Charlotte Inchley Christiana L Scheib Mari Järve Monika Karmin Guy S Jacobs Tiago Antao Florin Mircea Iliescu Alena Kushniarevich Qasim Ayub Chris Tyler-Smith Yali Xue Bayazit Yunusbayev Kristiina Tambets Chandana Basu Mallick Lehti Saag Elvira Pocheshkhova George Andriadze Craig Muller Michael C Westaway David M Lambert Grigor Zoraqi Shahlo Turdikulova Dilbar Dalimova Zhaxylyk Sabitov Gazi Nurun Nahar Sultana Joseph Lachance Sarah Tishkoff Kuvat Momynaliev Jainagul Isakova Larisa D Damba Marina Gubina Pagbajabyn Nymadawa Irina Evseeva Lubov Atramentova Olga Utevska François-Xavier Ricaut Nicolas Brucato Herawati Sudoyo Thierry Letellier Murray P Cox Nikolay A Barashkov Vedrana Skaro Lejla Mulahasanovic Dragan Primorac Hovhannes Sahakyan Maru Mormina Christina A Eichstaedt Daria V Lichman Syafiq Abdullah Gyaneshwer Chaubey Joseph T S Wee Evelin Mihailov Alexandra Karunas Sergei Litvinov Rita Khusainova Natalya Ekomasova Vita Akhmetova Irina Khidiyatova Damir Marjanović Levon Yepiskoposyan Doron M Behar Elena Balanovska Andres Metspalu Miroslava Derenko Boris Malyarchuk Mikhail Voevoda Sardana A Fedorova Ludmila P Osipova Marta Mirazón Lahr Pascale Gerbault Matthew Leavesley Andrea Bamberg Migliano Michael Petraglia Oleg Balanovsky Elza K Khusnutdinova Ene Metspalu Mark G Thomas Andrea Manica Rasmus Nielsen Richard Villems Eske Willerslev Toomas Kivisild Mait Metspalu

Nature 2016 Oct 21;538(7624):238-242. Epub 2016 Sep 21.

Estonian Biocentre, Tartu, Estonia.

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http://dx.doi.org/10.1038/nature19792DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5164938PMC
October 2016

Malagasy Genetic Ancestry Comes from an Historical Malay Trading Post in Southeast Borneo.

Mol Biol Evol 2016 09 5;33(9):2396-400. Epub 2016 Jul 5.

Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse UMR 5288 CNRS, Université Toulouse III, Université de Toulouse, Toulouse, France

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http://dx.doi.org/10.1093/molbev/msw117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4989113PMC
September 2016

Contrasting Linguistic and Genetic Origins of the Asian Source Populations of Malagasy.

Sci Rep 2016 05 18;6:26066. Epub 2016 May 18.

Evolutionary Medicine Group, Laboratoire d'Anthropologie Moléculaire et Imagerie de Synthèse UMR-5288, Université de Toulouse, Toulouse, France.

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http://dx.doi.org/10.1038/srep26066DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4870696PMC
May 2016

High Frequency Haplotypes are Expected Events, not Historical Figures.

F1000Res 2015 4;4:666. Epub 2015 Sep 4.

Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4722684PMC
http://dx.doi.org/10.12688/f1000research.7023.2DOI Listing
February 2016

Draft Genome Sequences of Three Strains of Geobacillus stearothermophilus Isolated from a Milk Powder Manufacturing Plant.

Genome Announc 2015 Oct 15;3(5). Epub 2015 Oct 15.

Infectious Disease Research Centre, Institute of Veterinary, Animal and Biomedical Sciences, Massey University, Palmerston North, New Zealand

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http://dx.doi.org/10.1128/genomeA.00939-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4611674PMC
October 2015

Fungal endophyte infection of ryegrass reprograms host metabolism and alters development.

New Phytol 2015 Dec 25;208(4):1227-40. Epub 2015 Aug 25.

Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5049663PMC
http://dx.doi.org/10.1111/nph.13614DOI Listing
December 2015

Molecular Cloning and Functional Analysis of Gene Clusters for the Biosynthesis of Indole-Diterpenes in Penicillium crustosum and P. janthinellum.

Toxins (Basel) 2015 Jul 23;7(8):2701-22. Epub 2015 Jul 23.

Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.

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http://dx.doi.org/10.3390/toxins7082701DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4549719PMC
July 2015

Relaxed Observance of Traditional Marriage Rules Allows Social Connectivity without Loss of Genetic Diversity.

Mol Biol Evol 2015 Sep 12;32(9):2254-62. Epub 2015 May 12.

Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand

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http://dx.doi.org/10.1093/molbev/msv102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4540962PMC
September 2015

Genome-wide gene expression dynamics of the fungal pathogen Dothistroma septosporum throughout its infection cycle of the gymnosperm host Pinus radiata.

Mol Plant Pathol 2016 Feb 2;17(2):210-24. Epub 2015 Jun 2.

Bio-Protection Research Centre, Institute of Fundamental Sciences, Massey University, Palmerston North, 4474, New Zealand.

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http://dx.doi.org/10.1111/mpp.12273DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4746707PMC
February 2016

Reconstructing Past Admixture Processes from Local Genomic Ancestry Using Wavelet Transformation.

Genetics 2015 Jun 7;200(2):469-81. Epub 2015 Apr 7.

Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North 4442, New Zealand

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http://dx.doi.org/10.1534/genetics.115.176842DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4492373PMC
June 2015

A recent bottleneck of Y chromosome diversity coincides with a global change in culture.

Authors:
Monika Karmin Lauri Saag Mário Vicente Melissa A Wilson Sayres Mari Järve Ulvi Gerst Talas Siiri Rootsi Anne-Mai Ilumäe Reedik Mägi Mario Mitt Luca Pagani Tarmo Puurand Zuzana Faltyskova Florian Clemente Alexia Cardona Ene Metspalu Hovhannes Sahakyan Bayazit Yunusbayev Georgi Hudjashov Michael DeGiorgio Eva-Liis Loogväli Christina Eichstaedt Mikk Eelmets Gyaneshwer Chaubey Kristiina Tambets Sergei Litvinov Maru Mormina Yali Xue Qasim Ayub Grigor Zoraqi Thorfinn Sand Korneliussen Farida Akhatova Joseph Lachance Sarah Tishkoff Kuvat Momynaliev François-Xavier Ricaut Pradiptajati Kusuma Harilanto Razafindrazaka Denis Pierron Murray P Cox Gazi Nurun Nahar Sultana Rane Willerslev Craig Muller Michael Westaway David Lambert Vedrana Skaro Lejla Kovačevic Shahlo Turdikulova Dilbar Dalimova Rita Khusainova Natalya Trofimova Vita Akhmetova Irina Khidiyatova Daria V Lichman Jainagul Isakova Elvira Pocheshkhova Zhaxylyk Sabitov Nikolay A Barashkov Pagbajabyn Nymadawa Evelin Mihailov Joseph Wee Tien Seng Irina Evseeva Andrea Bamberg Migliano Syafiq Abdullah George Andriadze Dragan Primorac Lubov Atramentova Olga Utevska Levon Yepiskoposyan Damir Marjanovic Alena Kushniarevich Doron M Behar Christian Gilissen Lisenka Vissers Joris A Veltman Elena Balanovska Miroslava Derenko Boris Malyarchuk Andres Metspalu Sardana Fedorova Anders Eriksson Andrea Manica Fernando L Mendez Tatiana M Karafet Krishna R Veeramah Neil Bradman Michael F Hammer Ludmila P Osipova Oleg Balanovsky Elza K Khusnutdinova Knut Johnsen Maido Remm Mark G Thomas Chris Tyler-Smith Peter A Underhill Eske Willerslev Rasmus Nielsen Mait Metspalu Richard Villems Toomas Kivisild

Genome Res 2015 Apr 13;25(4):459-66. Epub 2015 Mar 13.

Estonian Biocentre, Tartu, 51010, Estonia; Division of Biological Anthropology, University of Cambridge, Cambridge, CB2 1QH, United Kingdom;

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https://bib.irb.hr/datoteka/715300.2015_Genome_Res._Karmin-A
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http://genome.cshlp.org/lookup/doi/10.1101/gr.186684.114
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http://dx.doi.org/10.1101/gr.186684.114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4381518PMC
April 2015

Draft Genome Sequence of the Filamentous Fungus Penicillium paxilli (ATCC 26601).

Genome Announc 2015 Mar 12;3(2). Epub 2015 Mar 12.

Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand

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http://dx.doi.org/10.1128/genomeA.00071-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4357747PMC
March 2015

HyLiTE: accurate and flexible analysis of gene expression in hybrid and allopolyploid species.

BMC Bioinformatics 2015 Jan 16;16. Epub 2015 Jan 16.

Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.

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http://dx.doi.org/10.1186/s12859-014-0433-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4300824PMC
January 2015

A flexible theoretical representation for the temporal dynamics of structured populations as paths on polytope complexes.

J Math Biol 2015 Sep 12;71(3):735-66. Epub 2014 Oct 12.

Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand,

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http://dx.doi.org/10.1007/s00285-014-0841-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4532729PMC
September 2015

Isolation, contact and social behavior shaped genetic diversity in West Timor.

J Hum Genet 2014 Sep 31;59(9):494-503. Epub 2014 Jul 31.

Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.

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http://dx.doi.org/10.1038/jhg.2014.62DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4521296PMC
September 2014

SMARTPOP: inferring the impact of social dynamics on genetic diversity through high speed simulations.

BMC Bioinformatics 2014 Jun 9;15:175. Epub 2014 Jun 9.

Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University Palmerston North, New Zealand.

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http://dx.doi.org/10.1186/1471-2105-15-175DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4064502PMC
June 2014

An interspecific fungal hybrid reveals cross-kingdom rules for allopolyploid gene expression patterns.

PLoS Genet 2014 Mar 6;10(3):e1004180. Epub 2014 Mar 6.

Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand.

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http://dx.doi.org/10.1371/journal.pgen.1004180DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3945203PMC
March 2014

Climate change influenced female population sizes through time across the Indonesian archipelago.

Hum Biol 2013 Feb-Jun;85(1-3):135-52

Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.

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http://dx.doi.org/10.3378/027.085.0306DOI Listing
April 2015

Fragmentation of an aflatoxin-like gene cluster in a forest pathogen.

New Phytol 2013 Apr 1;198(2):525-35. Epub 2013 Mar 1.

Bio-Protection Research Centre, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.

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http://dx.doi.org/10.1111/nph.12161DOI Listing
April 2013

Reconstructing past changes in locus-specific recombination rates.

BMC Genet 2013 Feb 25;14:11. Epub 2013 Feb 25.

Institute of Fundamental Sciences, Massey University, Private Bag 11 222, Palmerston North 4442, New Zealand.

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http://dx.doi.org/10.1186/1471-2156-14-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3605148PMC
February 2013

The Indonesian archipelago: an ancient genetic highway linking Asia and the Pacific.

J Hum Genet 2013 Mar 24;58(3):165-73. Epub 2013 Jan 24.

Department of Anthropology, University of Arizona, Tucson, AZ, USA.

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http://dx.doi.org/10.1038/jhg.2012.154DOI Listing
March 2013

Dothistromin genes at multiple separate loci are regulated by AflR.

Fungal Genet Biol 2013 Feb 1;51:12-20. Epub 2012 Dec 1.

Bio-Protection Research Centre, Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand.

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http://dx.doi.org/10.1016/j.fgb.2012.11.006DOI Listing
February 2013

The guanine nucleotide exchange factor RIC8 regulates conidial germination through Gα proteins in Neurospora crassa.

PLoS One 2012 31;7(10):e48026. Epub 2012 Oct 31.

Department of Plant Pathology and Microbiology and Institute for Integrative Genome Biology, University of California Riverside, Riverside, California, USA.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0048026PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3485287PMC
April 2013

A small cohort of Island Southeast Asian women founded Madagascar.

Proc Biol Sci 2012 Jul 21;279(1739):2761-8. Epub 2012 Mar 21.

Institute of Molecular BioSciences, Massey University, Private Bag 11 222, Palmerston North, New Zealand.

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http://dx.doi.org/10.1098/rspb.2012.0012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3367776PMC
July 2012

Genetic continuity across a deeply divergent linguistic contact zone in North Maluku, Indonesia.

BMC Genet 2011 Nov 18;12:100. Epub 2011 Nov 18.

Department of Biological Sciences, Northern Arizona University, Flagstaff, Arizona, USA.

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http://dx.doi.org/10.1186/1471-2156-12-100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3252253PMC
November 2011

Population growth of Mexican free-tailed bats (Tadarida brasiliensis mexicana) predates human agricultural activity.

BMC Evol Biol 2011 Apr 1;11:88. Epub 2011 Apr 1.

Department of Biology, Grand Valley State University, Allendale, MI 49401, USA.

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http://dx.doi.org/10.1186/1471-2148-11-88DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3080819PMC
April 2011

What triggers grass endophytes to switch from mutualism to pathogenism?

Plant Sci 2011 Feb 16;180(2):190-5. Epub 2010 Oct 16.

Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand.

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http://dx.doi.org/10.1016/j.plantsci.2010.10.002DOI Listing
February 2011

Exploring molecular signaling in plant-fungal symbioses using high throughput RNA sequencing.

Plant Signal Behav 2010 Nov 1;5(11):1353-8. Epub 2010 Nov 1.

Institute of Molecular BioSciences, Massey University, Palmerston North, New Zealand.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3115233PMC
http://dx.doi.org/10.4161/psb.5.11.12950DOI Listing
November 2010

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data.

BMC Bioinformatics 2010 Sep 27;11:485. Epub 2010 Sep 27.

Institute of Molecular BioSciences, Massey University, Palmerston North 4442, New Zealand.

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http://dx.doi.org/10.1186/1471-2105-11-485DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2956736PMC
September 2010

The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genes.

Nat Genet 2010 Oct 29;42(10):830-1. Epub 2010 Aug 29.

Arizona Research Laboratories, Division of Biotechnology, University of Arizona, Tucson, Arizona, USA.

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http://dx.doi.org/10.1038/ng.651DOI Listing
October 2010

A question of scale: Human migrations writ large and small.

BMC Biol 2010 Jul 21;8:98. Epub 2010 Jul 21.

Institute of Molecular BioSciences, Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand.

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http://dx.doi.org/10.1186/1741-7007-8-98DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2908064PMC
July 2010

Disruption of signaling in a fungal-grass symbiosis leads to pathogenesis.

Plant Physiol 2010 Aug 2;153(4):1780-94. Epub 2010 Jun 2.

Institute of Molecular BioSciences, Massey University, Palmerston North, 4442, New Zealand.

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http://dx.doi.org/10.1104/pp.110.158451DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2923905PMC
August 2010

Major east-west division underlies Y chromosome stratification across Indonesia.

Mol Biol Evol 2010 Aug 5;27(8):1833-44. Epub 2010 Mar 5.

ARL Division of Biotechnology, University of Arizona, AZ, USA.

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http://dx.doi.org/10.1093/molbev/msq063DOI Listing
August 2010

A new deep branch of eurasian mtDNA macrohaplogroup M reveals additional complexity regarding the settlement of Madagascar.

BMC Genomics 2009 Dec 14;10:605. Epub 2009 Dec 14.

CNRS FRE 2960, Laboratoire d'Anthropobiologie, Université de Toulouse, Toulouse III Paul sabatier, 31073 Toulouse cedex 3, France.

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http://dx.doi.org/10.1186/1471-2164-10-605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808327PMC
December 2009

Accuracy of molecular dating with the rho statistic: deviations from coalescent expectations under a range of demographic models.

Authors:
Murray P Cox

Hum Biol 2008 Aug;80(4):335-57

Arizona Research Laboratories, University of Arizona, AZ 85721, USA.

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http://dx.doi.org/10.3378/1534-6617-80.4.335DOI Listing
August 2008

Sex-biased evolutionary forces shape genomic patterns of human diversity.

PLoS Genet 2008 Sep 26;4(9):e1000202. Epub 2008 Sep 26.

ARL Division of Biotechnology, University of Arizona, Tucson, Arizona, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2538571PMC
September 2008

Male dominance rarely skews the frequency distribution of Y chromosome haplotypes in human populations.

Proc Natl Acad Sci U S A 2008 Aug 14;105(33):11645-50. Epub 2008 Aug 14.

Department of Anthropology, University of Arizona, Tucson, AZ 85721, USA.

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http://dx.doi.org/10.1073/pnas.0710158105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2575272PMC
August 2008

A novel DNA sequence database for analyzing human demographic history.

Genome Res 2008 Aug 20;18(8):1354-61. Epub 2008 May 20.

Institute for Human Genetics and Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA 94143, USA.

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http://dx.doi.org/10.1101/gr.075630.107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2493425PMC
August 2008

A Polynesian motif on the Y chromosome: population structure in remote Oceania.

Hum Biol 2007 Oct;79(5):525-35

Arizona Research Laboratories, University of Arizona, Tucson, AZ 85721, USA.

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http://dx.doi.org/10.1353/hub.2008.0004DOI Listing
October 2007

Coevolution of languages and genes on the island of Sumba, eastern Indonesia.

Proc Natl Acad Sci U S A 2007 Oct 3;104(41):16022-6. Epub 2007 Oct 3.

Department of Anthropology, University of Arizona, 1009 East South Campus Drive, Tucson, AZ 85721, USA.

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http://dx.doi.org/10.1073/pnas.0704451104DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2042155PMC
October 2007

Recombination-filtered genomic datasets by information maximization.

Bioinformatics 2007 Jul 22;23(14):1851-3. Epub 2007 May 22.

Arizona Research Laboratories-Biotechnology, University of Arizona, Tucson, AZ 85721, USA.

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http://dx.doi.org/10.1093/bioinformatics/btm253DOI Listing
July 2007

Y-chromosome diversity is inversely associated with language affiliation in paired Austronesian- and Papuan-speaking communities from Solomon Islands.

Am J Hum Biol 2006 Jan;18(1):35-50

Leverhulme Centre for Human Evolutionary Studies, Department of Biological Anthropology, University of Cambridge, Downing Street, Cambridge, United Kingdom.

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http://doi.wiley.com/10.1002/ajhb.20459
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January 2006

Indonesian mitochondrial DNA and its opposition to a Pleistocene era origin of proto-Polynesians in island southeast Asia.

Authors:
Murray P Cox

Hum Biol 2005 Apr;77(2):179-88

Leverhulme Centre for Human Evolutionary Studies, Department of Biological Anthropology, University of Cambridge, Downing Street, Cambridge CB2 3DZ, United Kingdom.

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http://dx.doi.org/10.1353/hub.2005.0037DOI Listing
April 2005