Publications by authors named "Hans Ellegren"

100Publications

Recent introgression between Taiga Bean Goose and Tundra Bean Goose results in a largely homogeneous landscape of genetic differentiation.

Heredity (Edinb) 2020 Aug 26;125(1-2):73-84. Epub 2020 May 26.

Department of Evolutionary Biology, University of Uppsala, Uppsala, Sweden.

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http://dx.doi.org/10.1038/s41437-020-0322-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7413267PMC
August 2020

How Linked Selection Shapes the Diversity Landscape in Flycatchers.

Genetics 2019 05 14;212(1):277-285. Epub 2019 Mar 14.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36, Sweden.

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http://dx.doi.org/10.1534/genetics.119.301991DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6499528PMC
May 2019

The evolutionary history of grey wolf Y chromosomes.

Mol Ecol 2019 05 10;28(9):2173-2191. Epub 2019 Apr 10.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1111/mec.15054DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6850511PMC
May 2019

Footprints of adaptive evolution revealed by whole Z chromosomes haplotypes in flycatchers.

Mol Ecol 2019 05 29;28(9):2290-2304. Epub 2019 May 29.

Department of Evolutionary Biology, University of Uppsala, Uppsala, Sweden.

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http://dx.doi.org/10.1111/mec.15021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6852393PMC
May 2019

Genotype-free estimation of allele frequencies reduces bias and improves demographic inference from RADSeq data.

Mol Ecol Resour 2019 May 17;19(3):586-596. Epub 2019 Apr 17.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1111/1755-0998.12990DOI Listing
May 2019

GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes.

Genome Biol 2019 01 7;20(1). Epub 2019 Jan 7.

Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, 75236, Uppsala, Sweden.

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http://dx.doi.org/10.1186/s13059-018-1613-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6322265PMC
January 2019

A Genetic Map of Ostrich Z Chromosome and the Role of Inversions in Avian Sex Chromosome Evolution.

Genome Biol Evol 2018 08 1;10(8):2049-2060. Epub 2018 Aug 1.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala, Sweden.

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http://dx.doi.org/10.1093/gbe/evy163DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6105114PMC
August 2018

Sex-biased gene expression, sexual antagonism and levels of genetic diversity in the collared flycatcher (Ficedula albicollis) genome.

Mol Ecol 2018 09 4;27(18):3572-3581. Epub 2018 Sep 4.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1111/mec.14789DOI Listing
September 2018

Genome sequencing and conservation genomics in the Scandinavian wolverine population.

Conserv Biol 2018 12 7;32(6):1301-1312. Epub 2018 Sep 7.

Department of Ecology and Genetics, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1111/cobi.13157DOI Listing
December 2018

Natural selection beyond genes: Identification and analyses of evolutionarily conserved elements in the genome of the collared flycatcher (Ficedula albicollis).

Mol Ecol 2018 01 9;27(2):476-492. Epub 2018 Jan 9.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1111/mec.14462DOI Listing
January 2018

Abundant recent activity of retrovirus-like retrotransposons within and among flycatcher species implies a rich source of structural variation in songbird genomes.

Mol Ecol 2018 01 12;27(1):99-111. Epub 2017 Dec 12.

Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1111/mec.14439DOI Listing
January 2018

Genomic consequences of intensive inbreeding in an isolated wolf population.

Nat Ecol Evol 2018 Jan 20;2(1):124-131. Epub 2017 Nov 20.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden.

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http://dx.doi.org/10.1038/s41559-017-0375-4DOI Listing
January 2018

Whole-genome patterns of linkage disequilibrium across flycatcher populations clarify the causes and consequences of fine-scale recombination rate variation in birds.

Mol Ecol 2017 Aug 5;26(16):4158-4172. Epub 2017 Jul 5.

Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1111/mec.14197DOI Listing
August 2017

Genomewide patterns of variation in genetic diversity are shared among populations, species and higher-order taxa.

Mol Ecol 2017 Aug 27;26(16):4284-4295. Epub 2017 Jun 27.

Department of Evolutionary Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1111/mec.14195DOI Listing
August 2017

Bayesian Inference of Allele-Specific Gene Expression Indicates Abundant Cis-Regulatory Variation in Natural Flycatcher Populations.

Genome Biol Evol 2017 05;9(5):1266-1279

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Sweden.

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http://dx.doi.org/10.1093/gbe/evx080DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5434935PMC
May 2017

Covariation in levels of nucleotide diversity in homologous regions of the avian genome long after completion of lineage sorting.

Proc Biol Sci 2017 02;284(1849)

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden

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http://dx.doi.org/10.1098/rspb.2016.2756DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5326536PMC
February 2017

Inferring Individual Inbreeding and Demographic History from Segments of Identity by Descent in Flycatcher Genome Sequences.

Genetics 2017 03 18;205(3):1319-1334. Epub 2017 Jan 18.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, 75236, Sweden

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http://dx.doi.org/10.1534/genetics.116.198861DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5340341PMC
March 2017

Association mapping of morphological traits in wild and captive zebra finches: reliable within, but not between populations.

Mol Ecol 2017 Mar 6;26(5):1285-1305. Epub 2017 Feb 6.

Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, 82319, Seewiesen, Germany.

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http://dx.doi.org/10.1111/mec.14009DOI Listing
March 2017

Genomics advances the study of inbreeding depression in the wild.

Evol Appl 2016 12 23;9(10):1205-1218. Epub 2016 Oct 23.

Division of Biological Sciences University of Montana Missoula MT USA.

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http://dx.doi.org/10.1111/eva.12414DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5108213PMC
December 2016

Making sense of genomic islands of differentiation in light of speciation.

Nat Rev Genet 2017 02 14;18(2):87-100. Epub 2016 Nov 14.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.

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http://dx.doi.org/10.1038/nrg.2016.133DOI Listing
February 2017

Genomic distribution and estimation of nucleotide diversity in natural populations: perspectives from the collared flycatcher (Ficedula albicollis) genome.

Mol Ecol Resour 2017 Jul 14;17(4):586-597. Epub 2016 Nov 14.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden.

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http://doi.wiley.com/10.1111/1755-0998.12602
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http://dx.doi.org/10.1111/1755-0998.12602DOI Listing
July 2017

Increasing the power of genome wide association studies in natural populations using repeated measures - evaluation and implementation.

Methods Ecol Evol 2016 Jul 5;7(7):792-799. Epub 2016 Feb 5.

Department of Animal Ecology Evolutionary Biology Centre (EBC) Uppsala University Norbyvägen 18D SE-75236 Uppsala Sweden.

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http://dx.doi.org/10.1111/2041-210X.12535DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4950150PMC
July 2016

Direct estimate of the rate of germline mutation in a bird.

Genome Res 2016 09 13;26(9):1211-8. Epub 2016 Jul 13.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden;

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http://dx.doi.org/10.1101/gr.204669.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5052036PMC
September 2016

Determinants of genetic diversity.

Nat Rev Genet 2016 07 6;17(7):422-33. Epub 2016 Jun 6.

Institute of Evolutionary Sciences, French National Centre for Scientific Research (CNRS), University of Montpellier 2, Place E. Bataillon, Montpellier 34095, France.

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http://dx.doi.org/10.1038/nrg.2016.58DOI Listing
July 2016

High-Resolution Mapping of Crossover and Non-crossover Recombination Events by Whole-Genome Re-sequencing of an Avian Pedigree.

PLoS Genet 2016 05 24;12(5):e1006044. Epub 2016 May 24.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1371/journal.pgen.1006044DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4878770PMC
May 2016

Noninvasive genetic sampling reveals intrasex territoriality in wolverines.

Ecol Evol 2016 Mar 9;6(5):1527-36. Epub 2016 Feb 9.

Norwegian Institute for Nature Research Trondheim Norway.

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http://dx.doi.org/10.1002/ece3.1983DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4775525PMC
March 2016

Life History Traits, Protein Evolution, and the Nearly Neutral Theory in Amniotes.

Mol Biol Evol 2016 06 4;33(6):1517-27. Epub 2016 Mar 4.

UMR 5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Montpellier, France

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http://dx.doi.org/10.1093/molbev/msw033DOI Listing
June 2016

Divergence in gene expression within and between two closely related flycatcher species.

Mol Ecol 2016 05 2;25(9):2015-28. Epub 2016 Apr 2.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.

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http://dx.doi.org/10.1111/mec.13596DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4879514PMC
May 2016

PSMC analysis of effective population sizes in molecular ecology and its application to black-and-white Ficedula flycatchers.

Mol Ecol 2016 Mar 15;25(5):1058-72. Epub 2016 Feb 15.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden.

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http://dx.doi.org/10.1111/mec.13540DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4793928PMC
March 2016

Whole-genome resequencing of extreme phenotypes in collared flycatchers highlights the difficulty of detecting quantitative trait loci in natural populations.

Mol Ecol Resour 2016 May 24;16(3):727-41. Epub 2015 Dec 24.

Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala, 75236, Sweden.

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http://dx.doi.org/10.1111/1755-0998.12498DOI Listing
May 2016

GC-biased gene conversion links the recombination landscape and demography to genomic base composition: GC-biased gene conversion drives genomic base composition across a wide range of species.

Bioessays 2015 Dec 7;37(12):1317-26. Epub 2015 Oct 7.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1002/bies.201500058DOI Listing
December 2015

The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds.

PLoS Biol 2015 Aug 18;13(8):e1002224. Epub 2015 Aug 18.

Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1371/journal.pbio.1002224DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4540587PMC
August 2015

Third Report on Chicken Genes and Chromosomes 2015.

Authors:
Michael Schmid Jacqueline Smith David W Burt Bronwen L Aken Parker B Antin Alan L Archibald Chris Ashwell Perry J Blackshear Clarissa Boschiero C Titus Brown Shane C Burgess Hans H Cheng William Chow Derrick J Coble Amanda Cooksey Richard P M A Crooijmans Joana Damas Richard V N Davis Dirk-Jan de Koning Mary E Delany Thomas Derrien Takele T Desta Ian C Dunn Matthew Dunn Hans Ellegren Lél Eöry Ionas Erb Marta Farré Mario Fasold Damarius Fleming Paul Flicek Katie E Fowler Laure Frésard David P Froman Valerie Garceau Paul P Gardner Almas A Gheyas Darren K Griffin Martien A M Groenen Thomas Haaf Olivier Hanotte Alan Hart Julien Häsler S Blair Hedges Jana Hertel Kerstin Howe Allen Hubbard David A Hume Pete Kaiser Darek Kedra Stephen J Kemp Christophe Klopp Kalmia E Kniel Richard Kuo Sandrine Lagarrigue Susan J Lamont Denis M Larkin Raman A Lawal Sarah M Markland Fiona McCarthy Heather A McCormack Marla C McPherson Akira Motegi Stefan A Muljo Andrea Münsterberg Rishi Nag Indrajit Nanda Michael Neuberger Anne Nitsche Cedric Notredame Harry Noyes Rebecca O'Connor Elizabeth A O'Hare Andrew J Oler Sheila C Ommeh Helio Pais Michael Persia Frédérique Pitel Likit Preeyanon Pablo Prieto Barja Elizabeth M Pritchett Douglas D Rhoads Charmaine M Robinson Michael N Romanov Max Rothschild Pierre-François Roux Carl J Schmidt Alisa-Sophia Schneider Matthew G Schwartz Steve M Searle Michael A Skinner Craig A Smith Peter F Stadler Tammy E Steeves Claus Steinlein Liang Sun Minoru Takata Igor Ulitsky Qing Wang Ying Wang Wesley C Warren Jonathan M D Wood David Wragg Huaijun Zhou

Cytogenet Genome Res 2015 14;145(2):78-179. Epub 2015 Jul 14.

Department of Human Genetics, University of Würzburg, Würzburg, Germany.

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http://dx.doi.org/10.1159/000430927DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5120589PMC
October 2015

Resolving Evolutionary Relationships in Closely Related Species with Whole-Genome Sequencing Data.

Syst Biol 2015 Nov 17;64(6):1000-17. Epub 2015 Jul 17.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1093/sysbio/syv045DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4604831PMC
November 2015

Quantitative Mass Spectrometry Reveals Partial Translational Regulation for Dosage Compensation in Chicken.

Mol Biol Evol 2015 Oct 24;32(10):2716-25. Epub 2015 Jun 24.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden

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http://dx.doi.org/10.1093/molbev/msv147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4576709PMC
October 2015

A prezygotic transmission distorter acting equally in female and male zebra finches Taeniopygia guttata.

Mol Ecol 2015 Aug 17;24(15):3846-59. Epub 2015 Jul 17.

Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Eberhard-Gwinner-Str., 82319, Seewiesen, Germany.

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http://dx.doi.org/10.1111/mec.13281DOI Listing
August 2015

Temporal Dynamics of Avian Populations during Pleistocene Revealed by Whole-Genome Sequences.

Curr Biol 2015 May 16;25(10):1375-80. Epub 2015 Apr 16.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden.

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http://dx.doi.org/10.1016/j.cub.2015.03.047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4446789PMC
May 2015

Genome-wide association mapping in a wild avian population identifies a link between genetic and phenotypic variation in a life-history trait.

Proc Biol Sci 2015 05;282(1806):20150156

Department of Animal Ecology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala 75236, Sweden.

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http://dx.doi.org/10.1098/rspb.2015.0156DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4426624PMC
May 2015

Evolutionary consequences of DNA methylation on the GC content in vertebrate genomes.

G3 (Bethesda) 2015 Jan 15;5(3):441-7. Epub 2015 Jan 15.

Department of Ecology and Genetics, Uppsala University, SE-752 36 Uppsala, Sweden.

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http://g3journal.org/lookup/doi/10.1534/g3.114.015545
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http://dx.doi.org/10.1534/g3.114.015545DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4349097PMC
January 2015

Whole-genome analyses resolve early branches in the tree of life of modern birds.

Authors:
Erich D Jarvis Siavash Mirarab Andre J Aberer Bo Li Peter Houde Cai Li Simon Y W Ho Brant C Faircloth Benoit Nabholz Jason T Howard Alexander Suh Claudia C Weber Rute R da Fonseca Jianwen Li Fang Zhang Hui Li Long Zhou Nitish Narula Liang Liu Ganesh Ganapathy Bastien Boussau Md Shamsuzzoha Bayzid Volodymyr Zavidovych Sankar Subramanian Toni Gabaldón Salvador Capella-Gutiérrez Jaime Huerta-Cepas Bhanu Rekepalli Kasper Munch Mikkel Schierup Bent Lindow Wesley C Warren David Ray Richard E Green Michael W Bruford Xiangjiang Zhan Andrew Dixon Shengbin Li Ning Li Yinhua Huang Elizabeth P Derryberry Mads Frost Bertelsen Frederick H Sheldon Robb T Brumfield Claudio V Mello Peter V Lovell Morgan Wirthlin Maria Paula Cruz Schneider Francisco Prosdocimi José Alfredo Samaniego Amhed Missael Vargas Velazquez Alonzo Alfaro-Núñez Paula F Campos Bent Petersen Thomas Sicheritz-Ponten An Pas Tom Bailey Paul Scofield Michael Bunce David M Lambert Qi Zhou Polina Perelman Amy C Driskell Beth Shapiro Zijun Xiong Yongli Zeng Shiping Liu Zhenyu Li Binghang Liu Kui Wu Jin Xiao Xiong Yinqi Qiuemei Zheng Yong Zhang Huanming Yang Jian Wang Linnea Smeds Frank E Rheindt Michael Braun Jon Fjeldsa Ludovic Orlando F Keith Barker Knud Andreas Jønsson Warren Johnson Klaus-Peter Koepfli Stephen O'Brien David Haussler Oliver A Ryder Carsten Rahbek Eske Willerslev Gary R Graves Travis C Glenn John McCormack Dave Burt Hans Ellegren Per Alström Scott V Edwards Alexandros Stamatakis David P Mindell Joel Cracraft Edward L Braun Tandy Warnow Wang Jun M Thomas P Gilbert Guojie Zhang

Science 2014 Dec;346(6215):1320-31

China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China. Centre for Social Evolution, Department of Biology, Universitetsparken 15, University of Copenhagen, DK-2100 Copenhagen, Denmark.

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http://dx.doi.org/10.1126/science.1253451DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4405904PMC
December 2014

Early mesozoic coexistence of amniotes and hepadnaviridae.

PLoS Genet 2014 Dec 11;10(12):e1004559. Epub 2014 Dec 11.

Department of Evolutionary Biology (EBC), Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1371/journal.pgen.1004559DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4263362PMC
December 2014

Genomic identification and characterization of the pseudoautosomal region in highly differentiated avian sex chromosomes.

Nat Commun 2014 Nov 7;5:5448. Epub 2014 Nov 7.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.

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http://dx.doi.org/10.1038/ncomms6448DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4272252PMC
November 2014

Patterns of sequencing coverage bias revealed by ultra-deep sequencing of vertebrate mitochondria.

BMC Genomics 2014 Jun 12;15:467. Epub 2014 Jun 12.

Department of Ecology and Genetics, Uppsala University, Uppsala SE-75236, Sweden.

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http://dx.doi.org/10.1186/1471-2164-15-467DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4070552PMC
June 2014

A high-density linkage map enables a second-generation collared flycatcher genome assembly and reveals the patterns of avian recombination rate variation and chromosomal evolution.

Mol Ecol 2014 Aug 17;23(16):4035-58. Epub 2014 Jun 17.

Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden.

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http://dx.doi.org/10.1111/mec.12810DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4149781PMC
August 2014

Estimation of linkage disequilibrium and interspecific gene flow in Ficedula flycatchers by a newly developed 50k single-nucleotide polymorphism array.

Mol Ecol Resour 2014 Nov 26;14(6):1248-60. Epub 2014 May 26.

Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, SE-752 36, Uppsala, Sweden.

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http://dx.doi.org/10.1111/1755-0998.12270DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4368375PMC
November 2014

Old but not (so) degenerated--slow evolution of largely homomorphic sex chromosomes in ratites.

Mol Biol Evol 2014 Jun 10;31(6):1444-53. Epub 2014 Mar 10.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden

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http://dx.doi.org/10.1093/molbev/msu101DOI Listing
June 2014

Demographic divergence history of pied flycatcher and collared flycatcher inferred from whole-genome re-sequencing data.

PLoS Genet 2013 Nov 7;9(11):e1003942. Epub 2013 Nov 7.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1371/journal.pgen.1003942DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820794PMC
November 2013

Genome sequencing and population genomics in non-model organisms.

Authors:
Hans Ellegren

Trends Ecol Evol 2014 Jan 17;29(1):51-63. Epub 2013 Oct 17.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden. Electronic address:

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http://dx.doi.org/10.1016/j.tree.2013.09.008DOI Listing
January 2014

Transcriptome sequencing reveals the character of incomplete dosage compensation across multiple tissues in flycatchers.

Genome Biol Evol 2013 ;5(8):1555-66

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

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https://academic.oup.com/gbe/article-lookup/doi/10.1093/gbe/
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http://dx.doi.org/10.1093/gbe/evt114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3762201PMC
December 2013

Twisted signatures of GC-biased gene conversion embedded in an evolutionary stable karyotype.

Mol Biol Evol 2013 Jul 5;30(7):1700-12. Epub 2013 Apr 5.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1093/molbev/mst067DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3684855PMC
July 2013

Sampling strategies for species trees: the effects on phylogenetic inference of the number of genes, number of individuals, and whether loci are mitochondrial, sex-linked, or autosomal.

Mol Phylogenet Evol 2013 May 11;67(2):358-66. Epub 2013 Feb 11.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.

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http://linkinghub.elsevier.com/retrieve/pii/S105579031300059
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http://dx.doi.org/10.1016/j.ympev.2013.02.002DOI Listing
May 2013

Genome-wide analysis in chicken reveals that local levels of genetic diversity are mainly governed by the rate of recombination.

BMC Genomics 2013 Feb 8;14:86. Epub 2013 Feb 8.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvagen 18D, SE-752 36, Uppsala, Sweden.

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http://dx.doi.org/10.1186/1471-2164-14-86DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3600008PMC
February 2013

Lack of dosage compensation accompanies the arrested stage of sex chromosome evolution in ostriches.

Mol Biol Evol 2013 Apr 16;30(4):806-10. Epub 2013 Jan 16.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1093/molbev/mst009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3603317PMC
April 2013

The evolutionary causes and consequences of sex-biased gene expression.

Nat Rev Genet 2013 Feb;14(2):83-7

Department of Biology II, University of Munich (LMU), Grosshaderner Strasse 2, 82152 Planegg-Martinsried, Germany.

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http://dx.doi.org/10.1038/nrg3376DOI Listing
February 2013

Inferring the demographic history of European Ficedula flycatcher populations.

BMC Evol Biol 2013 Jan 2;13. Epub 2013 Jan 2.

Department of Evolutionary Biology, Evolutionary Biology Centre (EBC), Uppsala University, Norbyvägen 18D, Uppsala, SE-752 36, Sweden.

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http://dx.doi.org/10.1186/1471-2148-13-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3556140PMC
January 2013

The genomic landscape of species divergence in Ficedula flycatchers.

Nature 2012 Nov 24;491(7426):756-60. Epub 2012 Oct 24.

Dept of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.

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http://dx.doi.org/10.1038/nature11584DOI Listing
November 2012

High levels of gene expression explain the strong evolutionary constraint of mitochondrial protein-coding genes.

Mol Biol Evol 2013 Feb 15;30(2):272-84. Epub 2012 Oct 15.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1093/molbev/mss238DOI Listing
February 2013

The genomic signature of sexual selection in the genetic diversity of the sex chromosomes and autosomes.

Evolution 2012 Jul 23;66(7):2138-49. Epub 2012 Feb 23.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden.

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http://dx.doi.org/10.1111/j.1558-5646.2012.01586.xDOI Listing
July 2012

QTL and quantitative genetic analysis of beak morphology reveals patterns of standing genetic variation in an Estrildid finch.

Mol Ecol 2012 Aug 13;21(15):3704-17. Epub 2012 Jun 13.

Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Seewiesen, Germany.

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http://dx.doi.org/10.1111/j.1365-294X.2012.05661.xDOI Listing
August 2012

Recombination drives vertebrate genome contraction.

PLoS Genet 2012 3;8(5):e1002680. Epub 2012 May 3.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

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https://dx.plos.org/10.1371/journal.pgen.1002680
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3342960PMC
September 2012

Heterozygosity-fitness correlations in zebra finches: microsatellite markers can be better than their reputation.

Mol Ecol 2012 Jul 3;21(13):3237-49. Epub 2012 May 3.

Max Planck Institute for Ornithology, Eberhard-Gwinner-Str. 8, 82319 Seewiesen, Germany.

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July 2012

QTL linkage mapping of zebra finch beak color shows an oligogenic control of a sexually selected trait.

Evolution 2012 Jan 20;66(1):18-30. Epub 2011 Sep 20.

Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden.

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http://doi.wiley.com/10.1111/j.1558-5646.2011.01431.x
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January 2012

QTL linkage mapping of wing length in zebra finch using genome-wide single nucleotide polymorphisms markers.

Mol Ecol 2012 Jan 24;21(2):329-39. Epub 2011 Nov 24.

Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden.

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January 2012

Significant selective constraint at 4-fold degenerate sites in the avian genome and its consequence for detection of positive selection.

Genome Biol Evol 2011 31;3:1381-9. Epub 2011 Oct 31.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1093/gbe/evr112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3242499PMC
April 2012

Emergence of male-biased genes on the chicken Z-chromosome: sex-chromosome contrasts between male and female heterogametic systems.

Authors:
Hans Ellegren

Genome Res 2011 Dec 25;21(12):2082-6. Epub 2011 Aug 25.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.

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http://dx.doi.org/10.1101/gr.119065.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3227098PMC
December 2011

Substitution rate variation at human CpG sites correlates with non-CpG divergence, methylation level and GC content.

Genome Biol 2011 Jun 22;12(6):R58. Epub 2011 Jun 22.

Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, Uppsala, Sweden.

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http://dx.doi.org/10.1186/gb-2011-12-6-r58DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218846PMC
June 2011

Dynamic evolution of base composition: causes and consequences in avian phylogenomics.

Mol Biol Evol 2011 Aug 4;28(8):2197-210. Epub 2011 Apr 4.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1093/molbev/msr047DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3144382PMC
August 2011

Evolutionary constraint in flanking regions of avian genes.

Mol Biol Evol 2011 Sep 4;28(9):2481-9. Epub 2011 Apr 4.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1093/molbev/msr066DOI Listing
September 2011

Sex-chromosome evolution: recent progress and the influence of male and female heterogamety.

Authors:
Hans Ellegren

Nat Rev Genet 2011 Mar 8;12(3):157-66. Epub 2011 Feb 8.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvgen 18D, SE752 36 Uppsala, Sweden.

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http://dx.doi.org/10.1038/nrg2948DOI Listing
March 2011

A guide to the genomics of ecological speciation in natural animal populations.

Ecol Lett 2011 Jan 12;14(1):9-18. Epub 2010 Nov 12.

Department of Ecology and Genetics, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.

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http://dx.doi.org/10.1111/j.1461-0248.2010.01546.xDOI Listing
January 2011

No evidence for Z-chromosome rearrangements between the pied flycatcher and the collared flycatcher as judged by gene-based comparative genetic maps.

Mol Ecol 2010 Aug 28;19(16):3394-405. Epub 2010 Jul 28.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, Sweden.

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http://doi.wiley.com/10.1111/j.1365-294X.2010.04742.x
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August 2010

A high-density scan of the Z chromosome in Ficedula flycatchers reveals candidate loci for diversifying selection.

Evolution 2010 Dec;64(12):3461-75

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.

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December 2010

Obtaining mtDNA genomes from next-generation transcriptome sequencing: a case study on the basal Passerida (Aves: Passeriformes) phylogeny.

Mol Phylogenet Evol 2010 Oct 25;57(1):466-70. Epub 2010 Jun 25.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.

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http://dx.doi.org/10.1016/j.ympev.2010.06.009DOI Listing
October 2010

Molecular evolution of genes in avian genomes.

Genome Biol 2010 23;11(6):R68. Epub 2010 Jun 23.

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, Uppsala, S-752 36, Sweden.

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http://dx.doi.org/10.1186/gb-2010-11-6-r68DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2911116PMC
November 2010

Trisomy and triploidy are sources of embryo mortality in the zebra finch.

Proc Biol Sci 2010 Sep 5;277(1694):2655-60. Epub 2010 May 5.

Department of Behavioural Ecology and Evolutionary Genetics, Max Planck Institute for Ornithology, Eberhard-Gwinner Strasse, 82319 Seewiesen, Germany.

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http://dx.doi.org/10.1098/rspb.2010.0394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2982043PMC
September 2010

Speciation in Ficedula flycatchers.

Philos Trans R Soc Lond B Biol Sci 2010 Jun;365(1547):1841-52

Animal Ecology/Department of Ecology and Evolution, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden.

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http://rstb.royalsocietypublishing.org/cgi/doi/10.1098/rstb.
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http://dx.doi.org/10.1098/rstb.2009.0306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2871891PMC
June 2010

Evolutionary stasis: the stable chromosomes of birds.

Authors:
Hans Ellegren

Trends Ecol Evol 2010 May 1;25(5):283-91. Epub 2010 Apr 1.

Department of Evolutionary Biology, Evolutionary Biology Centre, Norbyvägen 18D, SE-75236 Uppsala, Sweden.

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https://linkinghub.elsevier.com/retrieve/pii/S01695347090037
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http://dx.doi.org/10.1016/j.tree.2009.12.004DOI Listing
May 2010

The genome of a songbird.

Nature 2010 Apr;464(7289):757-62

The Genome Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature08819DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3187626PMC
April 2010

Ontogenetic complexity of sexual dimorphism and sex-specific selection.

Mol Biol Evol 2010 Jul 8;27(7):1570-8. Epub 2010 Feb 8.

Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, United Kingdom.

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http://dx.doi.org/10.1093/molbev/msq042DOI Listing
July 2010

Ancient DNA reveals traces of Iberian Neolithic and Bronze Age lineages in modern Iberian horses.

Mol Ecol 2010 Jan 25;19(1):64-78. Epub 2009 Nov 25.

Centro UCM-ISCIII de Investigación sobre Evolución y Comportamiento Humanos, 28029-Madrid, Spain.

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http://dx.doi.org/10.1111/j.1365-294X.2009.04430.xDOI Listing
January 2010

Faster-Z evolution is predominantly due to genetic drift.

Mol Biol Evol 2010 Mar 18;27(3):661-70. Epub 2009 Nov 18.

Department of Zoology, Edward Grey Institute, University of Oxford, Oxford, United Kingdom.

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https://academic.oup.com/mbe/article-lookup/doi/10.1093/molb
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http://dx.doi.org/10.1093/molbev/msp282DOI Listing
March 2010

Sex determination: two copies for one cock.

Authors:
Hans Ellegren

Curr Biol 2009 Oct;19(19):R909-10

Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.

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https://linkinghub.elsevier.com/retrieve/pii/S09609822090163
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http://dx.doi.org/10.1016/j.cub.2009.09.001DOI Listing
October 2009

The different levels of genetic diversity in sex chromosomes and autosomes.

Authors:
Hans Ellegren

Trends Genet 2009 Jun 27;25(6):278-84. Epub 2009 May 27.

Department of Evolutionary Biology, Evolutionary Biology Centre, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.

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http://dx.doi.org/10.1016/j.tig.2009.04.005DOI Listing
June 2009

Is genetic diversity really higher in large populations?

Authors:
Hans Ellegren

J Biol 2009 21;8(4):41. Epub 2009 Apr 21.

Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, SE-752 36 Uppsala, Sweden.

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http://dx.doi.org/10.1186/jbiol135DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688907PMC
July 2009

Are sex-biased genes more dispensable?

Biol Lett 2009 Jun 14;5(3):409-12. Epub 2009 Jan 14.

Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.

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http://dx.doi.org/10.1098/rsbl.2008.0732DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2679909PMC
June 2009