Publications by authors named "Hendrik-Jan Megens"

82Publications

Prioritizing sequence variants in conserved non-coding elements in the chicken genome using chCADD.

PLoS Genet 2020 09 23;16(9):e1009027. Epub 2020 Sep 23.

Animal Breeding and Genomics Group, Wageningen University & Research, 6708 PB, Wageningen, The Netherlands.

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http://dx.doi.org/10.1371/journal.pgen.1009027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7535126PMC
September 2020

Parallel Genetic Origin of Foot Feathering in Birds.

Mol Biol Evol 2020 09;37(9):2465-2476

Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands.

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http://dx.doi.org/10.1093/molbev/msaa092DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7475038PMC
September 2020

pCADD: SNV prioritisation in Sus scrofa.

Genet Sel Evol 2020 Feb 7;52(1). Epub 2020 Feb 7.

Bioinformatics Group, Wageningen University & Research, 6708 PB, Wageningen, The Netherlands.

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http://dx.doi.org/10.1186/s12711-020-0528-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7006094PMC
February 2020

The type of bottleneck matters: Insights into the deleterious variation landscape of small managed populations.

Evol Appl 2020 Feb 30;13(2):330-341. Epub 2019 Sep 30.

Department of Animal Sciences, Animal Breeding and Genomics Wageningen University & Research Gelderland The Netherlands.

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http://dx.doi.org/10.1111/eva.12872DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6976952PMC
February 2020

Impact of merging commercial breeding lines on the genetic diversity of Landrace pigs.

Genet Sel Evol 2019 Oct 29;51(1):60. Epub 2019 Oct 29.

Centre for Genetic Resources, the Netherlands, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, The Netherlands.

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http://dx.doi.org/10.1186/s12711-019-0502-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6819590PMC
October 2019

Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe.

Authors:
Laurent A F Frantz James Haile Audrey T Lin Amelie Scheu Christina Geörg Norbert Benecke Michelle Alexander Anna Linderholm Victoria E Mullin Kevin G Daly Vincent M Battista Max Price Kurt J Gron Panoraia Alexandri Rose-Marie Arbogast Benjamin Arbuckle Adrian Bӑlӑşescu Ross Barnett László Bartosiewicz Gennady Baryshnikov Clive Bonsall Dušan Borić Adina Boroneanţ Jelena Bulatović Canan Çakirlar José-Miguel Carretero John Chapman Mike Church Richard Crooijmans Bea De Cupere Cleia Detry Vesna Dimitrijevic Valentin Dumitraşcu Louis du Plessis Ceiridwen J Edwards Cevdet Merih Erek Aslı Erim-Özdoğan Anton Ervynck Domenico Fulgione Mihai Gligor Anders Götherström Lionel Gourichon Martien A M Groenen Daniel Helmer Hitomi Hongo Liora K Horwitz Evan K Irving-Pease Ophélie Lebrasseur Joséphine Lesur Caroline Malone Ninna Manaseryan Arkadiusz Marciniak Holley Martlew Marjan Mashkour Roger Matthews Giedre Motuzaite Matuzeviciute Sepideh Maziar Erik Meijaard Tom McGovern Hendrik-Jan Megens Rebecca Miller Azadeh Fatemeh Mohaseb Jörg Orschiedt David Orton Anastasia Papathanasiou Mike Parker Pearson Ron Pinhasi Darko Radmanović François-Xavier Ricaut Mike Richards Richard Sabin Lucia Sarti Wolfram Schier Shiva Sheikhi Elisabeth Stephan John R Stewart Simon Stoddart Antonio Tagliacozzo Nenad Tasić Katerina Trantalidou Anne Tresset Cristina Valdiosera Youri van den Hurk Sophie Van Poucke Jean-Denis Vigne Alexander Yanevich Andrea Zeeb-Lanz Alexandros Triantafyllidis M Thomas P Gilbert Jörg Schibler Peter Rowley-Conwy Melinda Zeder Joris Peters Thomas Cucchi Daniel G Bradley Keith Dobney Joachim Burger Allowen Evin Linus Girdland-Flink Greger Larson

Proc Natl Acad Sci U S A 2019 08 12;116(35):17231-17238. Epub 2019 Aug 12.

The Palaeogenomics & Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford OX1 3TG, United Kingdom;

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http://dx.doi.org/10.1073/pnas.1901169116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6717267PMC
August 2019

Deleterious alleles in the context of domestication, inbreeding, and selection.

Evol Appl 2019 Jan 8;12(1):6-17. Epub 2018 Sep 8.

Animal Breeding and Genomics Wageningen University & Research Wageningen The Netherlands.

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http://doi.wiley.com/10.1111/eva.12691
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http://dx.doi.org/10.1111/eva.12691DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6304688PMC
January 2019

The impact of genome editing on the introduction of monogenic traits in livestock.

Genet Sel Evol 2018 04 16;50(1):18. Epub 2018 Apr 16.

Wageningen University & Research Animal Breeding and Genomics, PO Box 338, 6700 AH, Wageningen, The Netherlands.

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http://dx.doi.org/10.1186/s12711-018-0389-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5902981PMC
April 2018

A survey of functional genomic variation in domesticated chickens.

Genet Sel Evol 2018 04 16;50(1):17. Epub 2018 Apr 16.

Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, 6700 AH, Wageningen, The Netherlands.

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http://dx.doi.org/10.1186/s12711-018-0390-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5902831PMC
April 2018

The effects of recent changes in breeding preferences on maintaining traditional Dutch chicken genomic diversity.

Heredity (Edinb) 2018 12 28;121(6):564-578. Epub 2018 Mar 28.

Animal Breeding and Genetics Group, Wageningen University & Research, Wageningen, The Netherlands.

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http://dx.doi.org/10.1038/s41437-018-0072-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6221889PMC
December 2018

Early and late feathering in turkey and chicken: same gene but different mutations.

Genet Sel Evol 2018 03 22;50(1). Epub 2018 Mar 22.

Wageningen University and Research Animal Breeding and Genomics, P.O. Box 338, 6700 AH, Wageningen, The Netherlands.

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http://dx.doi.org/10.1186/s12711-018-0380-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5863816PMC
March 2018

A systematic survey to identify lethal recessive variation in highly managed pig populations.

BMC Genomics 2017 Nov 9;18(1):858. Epub 2017 Nov 9.

Wageningen University & Research, Animal Breeding and Genomics, Wageningen, The Netherlands.

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http://dx.doi.org/10.1186/s12864-017-4278-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5680825PMC
November 2017

A history of hybrids? Genomic patterns of introgression in the True Geese.

BMC Evol Biol 2017 08 22;17(1):201. Epub 2017 Aug 22.

Resource Ecology Group, Wageningen University & Research, Droevendaalsesteeg 3a, 6708 PB, Wageningen, the Netherlands.

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http://dx.doi.org/10.1186/s12862-017-1048-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5568201PMC
August 2017

A tree of geese: A phylogenomic perspective on the evolutionary history of True Geese.

Mol Phylogenet Evol 2016 08 24;101:303-313. Epub 2016 May 24.

Resource Ecology Group, Wageningen University, Droevendaalsesteeg 3a, 6708 PB Wageningen, The Netherlands.

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http://dx.doi.org/10.1016/j.ympev.2016.05.021DOI Listing
August 2016

The Use of Genomics in Conservation Management of the Endangered Visayan Warty Pig (Sus cebifrons).

Int J Genomics 2016 16;2016:5613862. Epub 2016 Mar 16.

Animal Breeding and Genomics Centre (ABGC), Wageningen University, 6708 PB Wageningen, Netherlands.

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http://dx.doi.org/10.1155/2016/5613862DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4812450PMC
April 2016

Evolutionary patterns of Toll-like receptor signaling pathway genes in the Suidae.

BMC Evol Biol 2016 Feb 9;16:33. Epub 2016 Feb 9.

Department of Animal Sciences, University of Illinois, at Urbana-Champaign, Urbana, Illinois, 61801, USA.

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http://dx.doi.org/10.1186/s12862-016-0602-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4748524PMC
February 2016

Evidence for adaptation of porcine Toll-like receptors.

Immunogenetics 2016 Mar 23;68(3):179-89. Epub 2015 Dec 23.

Department of Animal Sciences, University of Illinois, Urbana-Champaign, IL, 61801, USA.

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http://dx.doi.org/10.1007/s00251-015-0892-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4759233PMC
March 2016

Increased Mycoplasma hyopneumoniae Disease Prevalence in Domestic Hybrids Among Free-Living Wild Boar.

Ecohealth 2015 Dec 21;12(4):571-9. Epub 2015 Sep 21.

Resource Ecology Group, Wageningen UR, Droevendaalsesteeg 3a, 6708PB, Wageningen, The Netherlands.

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http://dx.doi.org/10.1007/s10393-015-1062-zDOI Listing
December 2015

TRES: Identification of Discriminatory and Informative SNPs from Population Genomic Data.

J Hered 2015 Sep-Oct;106(5):672-6. Epub 2015 Jul 2.

From the Department of Informatics, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece (Kavakiotis, Ntelidou, Tsoumakas, and Vlahavas); Department of Genetics, Development & Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece (Triantafyllidis and Alexandri); and Wageningen University, Animal Breeding and Genomics Centre, Wageningen, The Netherlands (Megens, Crooijmans, and Groenen).

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http://dx.doi.org/10.1093/jhered/esv044DOI Listing
January 2016

Copy number variation in the speciation of pigs: a possible prominent role for olfactory receptors.

BMC Genomics 2015 Apr 22;16:330. Epub 2015 Apr 22.

Animal Breeding and Genomics Centre, Wageningen University, 6700 AH, Wageningen, The Netherlands.

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http://dx.doi.org/10.1186/s12864-015-1449-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4413995PMC
April 2015

Adaptive Evolution of Toll-Like Receptors (TLRs) in the Family Suidae.

PLoS One 2015 20;10(4):e0124069. Epub 2015 Apr 20.

Department of Animal Sciences, University of Illinois, Urbana-Champaign, Illinois, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0124069PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4404360PMC
February 2016

Evolution of Tibetan wild boars.

Nat Genet 2015 Mar;47(3):188-9

Animal Breeding and Genomics Group, Wageningen University, Wageningen, the Netherlands.

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http://dx.doi.org/10.1038/ng.3197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4455000PMC
March 2015

Testing models of speciation from genome sequences: divergence and asymmetric admixture in Island South-East Asian Sus species during the Plio-Pleistocene climatic fluctuations.

Mol Ecol 2014 11 5;23(22):5566-74. Epub 2014 Nov 5.

Animal Breeding and Genomics Group, Wageningen University, De Elst 1, Wageningen, WD, 6708, The Netherlands.

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http://dx.doi.org/10.1111/mec.12958DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4245187PMC
November 2014

Untangling the hybrid nature of modern pig genomes: a mosaic derived from biogeographically distinct and highly divergent Sus scrofa populations.

Mol Ecol 2014 Aug 16;23(16):4089-102. Epub 2014 Jun 16.

Animal Breeding and Genomics Centre, Wageningen University, De Elst 1 Zodiac, P.O. Box 338, Wageningen, 6708WD, the Netherlands.

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http://dx.doi.org/10.1111/mec.12807DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4225523PMC
August 2014

Conservation genomic analysis of domestic and wild pig populations from the Iberian Peninsula.

BMC Genet 2013 Oct 30;14:106. Epub 2013 Oct 30.

Departamento de Producción Animal, Fac, de Veterinaria, Área de Genética, C,P,30100 Murcia, Spain.

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http://dx.doi.org/10.1186/1471-2156-14-106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3840735PMC
October 2013

Signatures of diversifying selection in European pig breeds.

PLoS Genet 2013 Apr 25;9(4):e1003453. Epub 2013 Apr 25.

The Roslin Institute and Royal Dick School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1003453DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3636142PMC
April 2013

Analyses of pig genomes provide insight into porcine demography and evolution.

Authors:
Martien A M Groenen Alan L Archibald Hirohide Uenishi Christopher K Tuggle Yasuhiro Takeuchi Max F Rothschild Claire Rogel-Gaillard Chankyu Park Denis Milan Hendrik-Jan Megens Shengting Li Denis M Larkin Heebal Kim Laurent A F Frantz Mario Caccamo Hyeonju Ahn Bronwen L Aken Anna Anselmo Christian Anthon Loretta Auvil Bouabid Badaoui Craig W Beattie Christian Bendixen Daniel Berman Frank Blecha Jonas Blomberg Lars Bolund Mirte Bosse Sara Botti Zhan Bujie Megan Bystrom Boris Capitanu Denise Carvalho-Silva Patrick Chardon Celine Chen Ryan Cheng Sang-Haeng Choi William Chow Richard C Clark Christopher Clee Richard P M A Crooijmans Harry D Dawson Patrice Dehais Fioravante De Sapio Bert Dibbits Nizar Drou Zhi-Qiang Du Kellye Eversole João Fadista Susan Fairley Thomas Faraut Geoffrey J Faulkner Katie E Fowler Merete Fredholm Eric Fritz James G R Gilbert Elisabetta Giuffra Jan Gorodkin Darren K Griffin Jennifer L Harrow Alexander Hayward Kerstin Howe Zhi-Liang Hu Sean J Humphray Toby Hunt Henrik Hornshøj Jin-Tae Jeon Patric Jern Matthew Jones Jerzy Jurka Hiroyuki Kanamori Ronan Kapetanovic Jaebum Kim Jae-Hwan Kim Kyu-Won Kim Tae-Hun Kim Greger Larson Kyooyeol Lee Kyung-Tai Lee Richard Leggett Harris A Lewin Yingrui Li Wansheng Liu Jane E Loveland Yao Lu Joan K Lunney Jian Ma Ole Madsen Katherine Mann Lucy Matthews Stuart McLaren Takeya Morozumi Michael P Murtaugh Jitendra Narayan Dinh Truong Nguyen Peixiang Ni Song-Jung Oh Suneel Onteru Frank Panitz Eung-Woo Park Hong-Seog Park Geraldine Pascal Yogesh Paudel Miguel Perez-Enciso Ricardo Ramirez-Gonzalez James M Reecy Sandra Rodriguez-Zas Gary A Rohrer Lauretta Rund Yongming Sang Kyle Schachtschneider Joshua G Schraiber John Schwartz Linda Scobie Carol Scott Stephen Searle Bertrand Servin Bruce R Southey Goran Sperber Peter Stadler Jonathan V Sweedler Hakim Tafer Bo Thomsen Rashmi Wali Jian Wang Jun Wang Simon White Xun Xu Martine Yerle Guojie Zhang Jianguo Zhang Jie Zhang Shuhong Zhao Jane Rogers Carol Churcher Lawrence B Schook

Nature 2012 Nov;491(7424):393-8

Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708 WD, Wageningen, The Netherlands.

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http://www.umass.edu/vetimm/docs/Groenen_etal_2012.pdf
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http://www.nature.com/doifinder/10.1038/nature11622
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http://dx.doi.org/10.1038/nature11622DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3566564PMC
November 2012

Strong signatures of selection in the domestic pig genome.

Proc Natl Acad Sci U S A 2012 Nov 14;109(48):19529-36. Epub 2012 Nov 14.

Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden.

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http://dx.doi.org/10.1073/pnas.1217149109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3511700PMC
November 2012

Development of a genetic tool for product regulation in the diverse British pig breed market.

BMC Genomics 2012 Nov 15;13:580. Epub 2012 Nov 15.

The Roslin Institute and (Royal) Dick School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.

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http://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2
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http://dx.doi.org/10.1186/1471-2164-13-580DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3499217PMC
November 2012

Global lack of flyway structure in a cosmopolitan bird revealed by a genome wide survey of single nucleotide polymorphisms.

Mol Ecol 2013 Jan 30;22(1):41-55. Epub 2012 Oct 30.

Resource Ecology Group, Wageningen University, PO Box 47, 6700 AA, Wageningen, The Netherlands.

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http://dx.doi.org/10.1111/mec.12098DOI Listing
January 2013

Signatures of selection in the genomes of commercial and non-commercial chicken breeds.

PLoS One 2012 27;7(2):e32720. Epub 2012 Feb 27.

Animal Breeding and Genomics Centre, Wageningen University and Research Centre, Wageningen, The Netherlands.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0032720PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3287981PMC
August 2012

Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis.

PLoS Biol 2010 Sep 7;8(9). Epub 2010 Sep 7.

Avian Immunobiology Laboratory, Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, Virginia, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1000475DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2935454PMC
September 2010

Regional regulation of transcription in the chicken genome.

BMC Genomics 2010 Jan 14;11:28. Epub 2010 Jan 14.

Animal Breeding and Genomics Centre, Wageningen University, Marijkeweg 40, 6709 PG, Wageningen, the Netherlands.

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http://dx.doi.org/10.1186/1471-2164-11-28DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2817690PMC
January 2010

Preliminary insight into the age and origin of the Labeobarbus fish species flock from Lake Tana (Ethiopia) using the mtDNA cytochrome b gene.

Mol Phylogenet Evol 2010 Feb 28;54(2):336-43. Epub 2009 Oct 28.

Experimental Zoology Group, Wageningen Institute of Animal Sciences (WIAS), Wageningen University, Marijkeweg 40, 6700 AH Wageningen, The Netherlands.

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http://dx.doi.org/10.1016/j.ympev.2009.10.029DOI Listing
February 2010

Linkage disequilibrium decay and haplotype block structure in the pig.

Genetics 2008 May;179(1):569-79

Animal Breeding and Genomics Centre, Wageningen UR, 6700AH, Wageningen, The Netherlands.

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http://dx.doi.org/10.1534/genetics.107.084277DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2390633PMC
May 2008

Tempo of speciation in a butterfly genus from the Southeast Asian tropics, inferred from mitochondrial and nuclear DNA sequence data.

Mol Phylogenet Evol 2004 Jun;31(3):1181-96

Institute of Evolutionary and Ecological Sciences, Leiden University, Leiden, The Netherlands.

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http://dx.doi.org/10.1016/j.ympev.2003.10.002DOI Listing
June 2004