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

Craig RJ, Suh A, Wang M, Ellegren H.

Mol Ecol. 2018 Jan;27(2):476-492. doi: 10.1111/mec.14462. Epub 2018 Jan 9.


Genomic consequences of intensive inbreeding in an isolated wolf population.

Kardos M, Åkesson M, Fountain T, Flagstad Ø, Liberg O, Olason P, Sand H, Wabakken P, Wikenros C, Ellegren H.

Nat Ecol Evol. 2018 Jan;2(1):124-131. doi: 10.1038/s41559-017-0375-4. Epub 2017 Nov 20.


Parallelism in genomic landscapes of differentiation, conserved genomic features and the role of linked selection.

Ellegren H, Wolf JBW.

J Evol Biol. 2017 Aug;30(8):1516-1518. doi: 10.1111/jeb.13113. No abstract available.


Insights into the genetic architecture of morphological traits in two passerine bird species.

Silva CNS, McFarlane SE, Hagen IJ, Rönnegård L, Billing AM, Kvalnes T, Kemppainen P, Rønning B, Ringsby TH, Sæther BE, Qvarnström A, Ellegren H, Jensen H, Husby A.

Heredity (Edinb). 2017 Sep;119(3):197-205. doi: 10.1038/hdy.2017.29. Epub 2017 Jun 14.


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

Kawakami T, Mugal CF, Suh A, Nater A, Burri R, Smeds L, Ellegren H.

Mol Ecol. 2017 Aug;26(16):4158-4172. doi: 10.1111/mec.14197. Epub 2017 Jul 5.


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

Vijay N, Weissensteiner M, Burri R, Kawakami T, Ellegren H, Wolf JBW.

Mol Ecol. 2017 Aug;26(16):4284-4295. doi: 10.1111/mec.14195. Epub 2017 Jun 27.


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

Wang M, Uebbing S, Ellegren H.

Genome Biol Evol. 2017 May 1;9(5):1266-1279. doi: 10.1093/gbe/evx080.


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

Dutoit L, Vijay N, Mugal CF, Bossu CM, Burri R, Wolf J, Ellegren H.

Proc Biol Sci. 2017 Feb 22;284(1849). pii: 20162756. doi: 10.1098/rspb.2016.2756.


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

Kardos M, Qvarnström A, Ellegren H.

Genetics. 2017 Mar;205(3):1319-1334. doi: 10.1534/genetics.116.198861. Epub 2017 Jan 18.


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

Knief U, Schielzeth H, Backström N, Hemmrich-Stanisak G, Wittig M, Franke A, Griffith SC, Ellegren H, Kempenaers B, Forstmeier W.

Mol Ecol. 2017 Mar;26(5):1285-1305. doi: 10.1111/mec.14009. Epub 2017 Feb 6.


Genomics advances the study of inbreeding depression in the wild.

Kardos M, Taylor HR, Ellegren H, Luikart G, Allendorf FW.

Evol Appl. 2016 Oct 23;9(10):1205-1218. eCollection 2016 Dec. Review.


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

Wolf JB, Ellegren H.

Nat Rev Genet. 2017 Feb;18(2):87-100. doi: 10.1038/nrg.2016.133. Epub 2016 Nov 14. Review.


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

Dutoit L, Burri R, Nater A, Mugal CF, Ellegren H.

Mol Ecol Resour. 2017 Jul;17(4):586-597. doi: 10.1111/1755-0998.12602. Epub 2016 Nov 14.


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

Rönnegård L, McFarlane SE, Husby A, Kawakami T, Ellegren H, Qvarnström A.

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


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

Smeds L, Qvarnström A, Ellegren H.

Genome Res. 2016 Sep;26(9):1211-8. doi: 10.1101/gr.204669.116. Epub 2016 Jul 13.


Determinants of genetic diversity.

Ellegren H, Galtier N.

Nat Rev Genet. 2016 Jul;17(7):422-33. doi: 10.1038/nrg.2016.58. Epub 2016 Jun 6. Review.


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

Smeds L, Mugal CF, Qvarnström A, Ellegren H.

PLoS Genet. 2016 May 24;12(5):e1006044. doi: 10.1371/journal.pgen.1006044. eCollection 2016 May.


Noninvasive genetic sampling reveals intrasex territoriality in wolverines.

Bischof R, Gregersen ER, Brøseth H, Ellegren H, Flagstad Ø.

Ecol Evol. 2016 Feb 9;6(5):1527-36. doi: 10.1002/ece3.1983. eCollection 2016 Mar.


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

Figuet E, Nabholz B, Bonneau M, Mas Carrio E, Nadachowska-Brzyska K, Ellegren H, Galtier N.

Mol Biol Evol. 2016 Jun;33(6):1517-27. doi: 10.1093/molbev/msw033. Epub 2016 Mar 4.


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

Uebbing S, Künstner A, Mäkinen H, Backström N, Bolivar P, Burri R, Dutoit L, Mugal CF, Nater A, Aken B, Flicek P, Martin FJ, Searle SM, Ellegren H.

Mol Ecol. 2016 May;25(9):2015-28. doi: 10.1111/mec.13596. Epub 2016 Apr 2.


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

Nadachowska-Brzyska K, Burri R, Smeds L, Ellegren H.

Mol Ecol. 2016 Mar;25(5):1058-72. doi: 10.1111/mec.13540. Epub 2016 Feb 15.


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

Kardos M, Husby A, McFarlane SE, Qvarnström A, Ellegren H.

Mol Ecol Resour. 2016 May;16(3):727-41. doi: 10.1111/1755-0998.12498. Epub 2015 Dec 24.


Recombination Rate Variation Modulates Gene Sequence Evolution Mainly via GC-Biased Gene Conversion, Not Hill-Robertson Interference, in an Avian System.

Bolívar P, Mugal CF, Nater A, Ellegren H.

Mol Biol Evol. 2016 Jan;33(1):216-27. doi: 10.1093/molbev/msv214. Epub 2015 Oct 6.


Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers.

Burri R, Nater A, Kawakami T, Mugal CF, Olason PI, Smeds L, Suh A, Dutoit L, Bureš S, Garamszegi LZ, Hogner S, Moreno J, Qvarnström A, Ružić M, Sæther SA, Sætre GP, Török J, Ellegren H.

Genome Res. 2015 Nov;25(11):1656-65. doi: 10.1101/gr.196485.115. Epub 2015 Sep 9.


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

Suh A, Smeds L, Ellegren H.

PLoS Biol. 2015 Aug 18;13(8):e1002224. doi: 10.1371/journal.pbio.1002224. eCollection 2015 Aug.


Third Report on Chicken Genes and Chromosomes 2015.

Schmid M, Smith J, Burt DW, Aken BL, Antin PB, Archibald AL, Ashwell C, Blackshear PJ, Boschiero C, Brown CT, Burgess SC, Cheng HH, Chow W, Coble DJ, Cooksey A, Crooijmans RP, Damas J, Davis RV, de Koning DJ, Delany ME, Derrien T, Desta TT, Dunn IC, Dunn M, Ellegren H, Eöry L, Erb I, Farré M, Fasold M, Fleming D, Flicek P, Fowler KE, Frésard L, Froman DP, Garceau V, Gardner PP, Gheyas AA, Griffin DK, Groenen MA, Haaf T, Hanotte O, Hart A, Häsler J, Hedges SB, Hertel J, Howe K, Hubbard A, Hume DA, Kaiser P, Kedra D, Kemp SJ, Klopp C, Kniel KE, Kuo R, Lagarrigue S, Lamont SJ, Larkin DM, Lawal RA, Markland SM, McCarthy F, McCormack HA, McPherson MC, Motegi A, Muljo SA, Münsterberg A, Nag R, Nanda I, Neuberger M, Nitsche A, Notredame C, Noyes H, O'Connor R, O'Hare EA, Oler AJ, Ommeh SC, Pais H, Persia M, Pitel F, Preeyanon L, Prieto Barja P, Pritchett EM, Rhoads DD, Robinson CM, Romanov MN, Rothschild M, Roux PF, Schmidt CJ, Schneider AS, Schwartz MG, Searle SM, Skinner MA, Smith CA, Stadler PF, Steeves TE, Steinlein C, Sun L, Takata M, Ulitsky I, Wang Q, Wang Y, Warren WC, Wood JM, Wragg D, Zhou H.

Cytogenet Genome Res. 2015;145(2):78-179. doi: 10.1159/000430927. Epub 2015 Jul 14. No abstract available.


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

Nater A, Burri R, Kawakami T, Smeds L, Ellegren H.

Syst Biol. 2015 Nov;64(6):1000-17. doi: 10.1093/sysbio/syv045. Epub 2015 Jul 17.


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

Uebbing S, Konzer A, Xu L, Backström N, Brunström B, Bergquist J, Ellegren H.

Mol Biol Evol. 2015 Oct;32(10):2716-25. doi: 10.1093/molbev/msv147. Epub 2015 Jun 24.


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

Knief U, Schielzeth H, Ellegren H, Kempenaers B, Forstmeier W.

Mol Ecol. 2015 Aug;24(15):3846-59. doi: 10.1111/mec.13281. Epub 2015 Jul 17.


Evolutionary analysis of the female-specific avian W chromosome.

Smeds L, Warmuth V, Bolivar P, Uebbing S, Burri R, Suh A, Nater A, Bureš S, Garamszegi LZ, Hogner S, Moreno J, Qvarnström A, Ružić M, Sæther SA, Sætre GP, Török J, Ellegren H.

Nat Commun. 2015 Jun 4;6:7330. doi: 10.1038/ncomms8330.


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

Nadachowska-Brzyska K, Li C, Smeds L, Zhang G, Ellegren H.

Curr Biol. 2015 May 18;25(10):1375-80. doi: 10.1016/j.cub.2015.03.047. Epub 2015 Apr 16.


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

Husby A, Kawakami T, Rönnegård L, Smeds L, Ellegren H, Qvarnström A.

Proc Biol Sci. 2015 May 7;282(1806):20150156. doi: 10.1098/rspb.2015.0156.


Phylogenomic analyses data of the avian phylogenomics project.

Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Alfaro-Núñez A, Narula N, Liu L, Burt D, Ellegren H, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G; Avian Phylogenomics Consortium.

Gigascience. 2015 Feb 12;4:4. doi: 10.1186/s13742-014-0038-1. eCollection 2015.


Two Antarctic penguin genomes reveal insights into their evolutionary history and molecular changes related to the Antarctic environment.

Li C, Zhang Y, Li J, Kong L, Hu H, Pan H, Xu L, Deng Y, Li Q, Jin L, Yu H, Chen Y, Liu B, Yang L, Liu S, Zhang Y, Lang Y, Xia J, He W, Shi Q, Subramanian S, Millar CD, Meader S, Rands CM, Fujita MK, Greenwold MJ, Castoe TA, Pollock DD, Gu W, Nam K, Ellegren H, Ho SY, Burt DW, Ponting CP, Jarvis ED, Gilbert MT, Yang H, Wang J, Lambert DM, Wang J, Zhang G.

Gigascience. 2014 Dec 12;3(1):27. doi: 10.1186/2047-217X-3-27. eCollection 2014.


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

Mugal CF, Arndt PF, Holm L, Ellegren H.

G3 (Bethesda). 2015 Jan 15;5(3):441-7. doi: 10.1534/g3.114.015545.


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

Jarvis ED, Mirarab S, Aberer AJ, Li B, Houde P, Li C, Ho SY, Faircloth BC, Nabholz B, Howard JT, Suh A, Weber CC, da Fonseca RR, Li J, Zhang F, Li H, Zhou L, Narula N, Liu L, Ganapathy G, Boussau B, Bayzid MS, Zavidovych V, Subramanian S, Gabaldón T, Capella-Gutiérrez S, Huerta-Cepas J, Rekepalli B, Munch K, Schierup M, Lindow B, Warren WC, Ray D, Green RE, Bruford MW, Zhan X, Dixon A, Li S, Li N, Huang Y, Derryberry EP, Bertelsen MF, Sheldon FH, Brumfield RT, Mello CV, Lovell PV, Wirthlin M, Schneider MP, Prosdocimi F, Samaniego JA, Vargas Velazquez AM, Alfaro-Núñez A, Campos PF, Petersen B, Sicheritz-Ponten T, Pas A, Bailey T, Scofield P, Bunce M, Lambert DM, Zhou Q, Perelman P, Driskell AC, Shapiro B, Xiong Z, Zeng Y, Liu S, Li Z, Liu B, Wu K, Xiao J, Yinqi X, Zheng Q, Zhang Y, Yang H, Wang J, Smeds L, Rheindt FE, Braun M, Fjeldsa J, Orlando L, Barker FK, Jønsson KA, Johnson W, Koepfli KP, O'Brien S, Haussler D, Ryder OA, Rahbek C, Willerslev E, Graves GR, Glenn TC, McCormack J, Burt D, Ellegren H, Alström P, Edwards SV, Stamatakis A, Mindell DP, Cracraft J, Braun EL, Warnow T, Jun W, Gilbert MT, Zhang G.

Science. 2014 Dec 12;346(6215):1320-31. doi: 10.1126/science.1253451.


Early mesozoic coexistence of amniotes and hepadnaviridae.

Suh A, Weber CC, Kehlmaier C, Braun EL, Green RE, Fritz U, Ray DA, Ellegren H.

PLoS Genet. 2014 Dec 11;10(12):e1004559. doi: 10.1371/journal.pgen.1004559. eCollection 2014 Dec.


Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor.

Romanov MN, Farré M, Lithgow PE, Fowler KE, Skinner BM, O'Connor R, Fonseka G, Backström N, Matsuda Y, Nishida C, Houde P, Jarvis ED, Ellegren H, Burt DW, Larkin DM, Griffin DK.

BMC Genomics. 2014 Dec 11;15:1060. doi: 10.1186/1471-2164-15-1060.


Evidence for GC-biased gene conversion as a driver of between-lineage differences in avian base composition.

Weber CC, Boussau B, Romiguier J, Jarvis ED, Ellegren H.

Genome Biol. 2014;15(12):549.


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

Smeds L, Kawakami T, Burri R, Bolivar P, Husby A, Qvarnström A, Uebbing S, Ellegren H.

Nat Commun. 2014 Nov 7;5:5448. doi: 10.1038/ncomms6448.


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

Ekblom R, Smeds L, Ellegren H.

BMC Genomics. 2014 Jun 12;15:467. doi: 10.1186/1471-2164-15-467.


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.

Kawakami T, Smeds L, Backström N, Husby A, Qvarnström A, Mugal CF, Olason P, Ellegren H.

Mol Ecol. 2014 Aug;23(16):4035-58. doi: 10.1111/mec.12810. Epub 2014 Jun 17.


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

Kawakami T, Backström N, Burri R, Husby A, Olason P, Rice AM, Ålund M, Qvarnström A, Ellegren H.

Mol Ecol Resour. 2014 Nov;14(6):1248-60. doi: 10.1111/1755-0998.12270. Epub 2014 May 26.


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

Yazdi HP, Ellegren H.

Mol Biol Evol. 2014 Jun;31(6):1444-53. doi: 10.1093/molbev/msu101. Epub 2014 Mar 10.


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

Nadachowska-Brzyska K, Burri R, Olason PI, Kawakami T, Smeds L, Ellegren H.

PLoS Genet. 2013 Nov;9(11):e1003942. doi: 10.1371/journal.pgen.1003942. Epub 2013 Nov 7.


Genome sequencing and population genomics in non-model organisms.

Ellegren H.

Trends Ecol Evol. 2014 Jan;29(1):51-63. doi: 10.1016/j.tree.2013.09.008. Epub 2013 Oct 17. Review.


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

Uebbing S, Künstner A, Mäkinen H, Ellegren H.

Genome Biol Evol. 2013;5(8):1555-66. doi: 10.1093/gbe/evt114.

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