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Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes.

Thybert D, Roller M, Navarro FCP, Fiddes I, Streeter I, Feig C, Martin-Galvez D, Kolmogorov M, Janoušek V, Akanni W, Aken B, Aldridge S, Chakrapani V, Chow W, Clarke L, Cummins C, Doran A, Dunn M, Goodstadt L, Howe K, Howell M, Josselin AA, Karn RC, Laukaitis CM, Jingtao L, Martin F, Muffato M, Nachtweide S, Quail MA, Sisu C, Stanke M, Stefflova K, Van Oosterhout C, Veyrunes F, Ward B, Yang F, Yazdanifar G, Zadissa A, Adams DJ, Brazma A, Gerstein M, Paten B, Pham S, Keane TM, Odom DT, Flicek P.

Genome Res. 2018 Apr;28(4):448-459. doi: 10.1101/gr.234096.117. Epub 2018 Mar 21.


Immunogenetic novelty confers a selective advantage in host-pathogen coevolution.

Phillips KP, Cable J, Mohammed RS, Herdegen-Radwan M, Raubic J, Przesmycka KJ, van Oosterhout C, Radwan J.

Proc Natl Acad Sci U S A. 2018 Feb 13;115(7):1552-1557. doi: 10.1073/pnas.1708597115. Epub 2018 Jan 16.


Evolutionary genetics of immunological supertypes reveals two faces of the Red Queen.

Lighten J, Papadopulos AST, Mohammed RS, Ward BJ, G Paterson I, Baillie L, Bradbury IR, Hendry AP, Bentzen P, van Oosterhout C.

Nat Commun. 2017 Nov 3;8(1):1294. doi: 10.1038/s41467-017-01183-2.


Building a locally diploid genome and transcriptome of the diatom Fragilariopsis cylindrus.

Paajanen P, Strauss J, van Oosterhout C, McMullan M, Clark MD, Mock T.

Sci Data. 2017 Oct 10;4:170149. doi: 10.1038/sdata.2017.149.


Biocontrol of common carp in Australia poses risks to biosecurity.

Lighten J, van Oosterhout C.

Nat Ecol Evol. 2017 Feb 21;1(3):87. doi: 10.1038/s41559-017-0087. No abstract available.


Immigrant reproductive dysfunction facilitates ecological speciation.

Svensson O, Gräns J, Celander MC, Havenhand J, Leder EH, Lindström K, Schöld S, van Oosterhout C, Kvarnemo C.

Evolution. 2017 Oct;71(10):2510-2521. doi: 10.1111/evo.13323. Epub 2017 Sep 20.


The effects of historical fragmentation on major histocompatibility complex class II β and microsatellite variation in the Aegean island reptile, Podarcis erhardii.

Santonastaso T, Lighten J, van Oosterhout C, Jones KL, Foufopoulos J, Anthony NM.

Ecol Evol. 2017 May 18;7(13):4568-4581. doi: 10.1002/ece3.3022. eCollection 2017 Jul.


Erratum to: Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species.

Mathers TC, Chen Y, Kaithakottil G, Legeai F, Mugford ST, Baa-Puyoulet P, Bretaudeau A, Clavijo B, Colella S, Collin O, Dalmay T, Derrien T, Feng H, Gabaldón T, Jordan A, Julca I, Kettles GJ, Kowitwanich K, Lavenier D, Lenzi P, Lopez-Gomollon S, Loska D, Mapleson D, Maumus F, Moxon S, Price DR, Sugio A, van Munster M, Uzest M, Waite D, Jander G, Tagu D, Wilson AC, van Oosterhout C, Swarbreck D, Hogenhout SA.

Genome Biol. 2017 Apr 4;18(1):63. doi: 10.1186/s13059-017-1202-6. No abstract available.


Toll-like receptor variation in the bottlenecked population of the Seychelles warbler: computer simulations see the 'ghost of selection past' and quantify the 'drift debt'.

Gilroy DL, Phillips KP, Richardson DS, van Oosterhout C.

J Evol Biol. 2017 Jul;30(7):1276-1287. doi: 10.1111/jeb.13077. Epub 2017 May 15.


The genetics of mate preferences in hybrids between two young and sympatric Lake Victoria cichlid species.

Svensson O, Woodhouse K, van Oosterhout C, Smith A, Turner GF, Seehausen O.

Proc Biol Sci. 2017 Feb 22;284(1849). pii: 20162332. doi: 10.1098/rspb.2016.2332.


Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species.

Mathers TC, Chen Y, Kaithakottil G, Legeai F, Mugford ST, Baa-Puyoulet P, Bretaudeau A, Clavijo B, Colella S, Collin O, Dalmay T, Derrien T, Feng H, Gabaldón T, Jordan A, Julca I, Kettles GJ, Kowitwanich K, Lavenier D, Lenzi P, Lopez-Gomollon S, Loska D, Mapleson D, Maumus F, Moxon S, Price DR, Sugio A, van Munster M, Uzest M, Waite D, Jander G, Tagu D, Wilson AC, van Oosterhout C, Swarbreck D, Hogenhout SA.

Genome Biol. 2017 Feb 13;18(1):27. doi: 10.1186/s13059-016-1145-3. Erratum in: Genome Biol. 2017 Apr 4;18(1):63.


Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus.

Mock T, Otillar RP, Strauss J, McMullan M, Paajanen P, Schmutz J, Salamov A, Sanges R, Toseland A, Ward BJ, Allen AE, Dupont CL, Frickenhaus S, Maumus F, Veluchamy A, Wu T, Barry KW, Falciatore A, Ferrante MI, Fortunato AE, Glöckner G, Gruber A, Hipkin R, Janech MG, Kroth PG, Leese F, Lindquist EA, Lyon BR, Martin J, Mayer C, Parker M, Quesneville H, Raymond JA, Uhlig C, Valas RE, Valentin KU, Worden AZ, Armbrust EV, Clark MD, Bowler C, Green BR, Moulton V, van Oosterhout C, Grigoriev IV.

Nature. 2017 Jan 26;541(7638):536-540. doi: 10.1038/nature20803. Epub 2017 Jan 16.


The effect of extrinsic mortality on genome size evolution in prokaryotes.

Bentkowski P, van Oosterhout C, Ashby B, Mock T.

ISME J. 2017 Apr;11(4):1011-1018. doi: 10.1038/ismej.2016.165. Epub 2016 Dec 6.


Adaptive phenotypic response to climate enabled by epigenetics in a K-strategy species, the fish Leucoraja ocellata (Rajidae).

Lighten J, Incarnato D, Ward BJ, van Oosterhout C, Bradbury I, Hanson M, Bentzen P.

R Soc Open Sci. 2016 Oct 26;3(10):160299. eCollection 2016 Oct.


The effects of inbreeding on disease susceptibility: Gyrodactylus turnbulli infection of guppies, Poecilia reticulata.

Smallbone W, van Oosterhout C, Cable J.

Exp Parasitol. 2016 Aug;167:32-7. doi: 10.1016/j.exppara.2016.04.018. Epub 2016 Apr 27.


Hybridization generates a hopeful monster: a hermaphroditic selfing cichlid.

Svensson O, Smith A, García-Alonso J, van Oosterhout C.

R Soc Open Sci. 2016 Mar 23;3(3):150684. doi: 10.1098/rsos.150684. eCollection 2016 Mar.


A further cost for the sicker sex? Evidence for male-biased parasite-induced vulnerability to predation.

Stephenson JF, Kinsella C, Cable J, van Oosterhout C.

Ecol Evol. 2016 Mar 14;6(8):2506-15. doi: 10.1002/ece3.2049. eCollection 2016 Apr.


Getting into hot water: sick guppies frequent warmer thermal conditions.

Mohammed RS, Reynolds M, James J, Williams C, Mohammed A, Ramsubhag A, van Oosterhout C, Cable J.

Oecologia. 2016 Jul;181(3):911-7. doi: 10.1007/s00442-016-3598-1. Epub 2016 Mar 10.


Pace of life, predators and parasites: predator-induced life-history evolution in Trinidadian guppies predicts decrease in parasite tolerance.

Stephenson JF, van Oosterhout C, Cable J.

Biol Lett. 2015 Nov;11(11). pii: 20150806. doi: 10.1098/rsbl.2015.0806.


HYBRIDCHECK: software for the rapid detection, visualization and dating of recombinant regions in genome sequence data.

Ward BJ, van Oosterhout C.

Mol Ecol Resour. 2016 Mar;16(2):534-9. doi: 10.1111/1755-0998.12469. Epub 2015 Oct 12.


A Model of Genome Size Evolution for Prokaryotes in Stable and Fluctuating Environments.

Bentkowski P, Van Oosterhout C, Mock T.

Genome Biol Evol. 2015 Aug 4;7(8):2344-51. doi: 10.1093/gbe/evv148.


Parasites of Trinidadian guppies: evidence for sex- and age-specific trait-mediated indirect effects of predators.

Stephenson JF, van Oosterhout C, Mohammed RS, Cable J.

Ecology. 2015 Feb;96(2):489-98.


The effects of recombination, mutation and selection on the evolution of the Rp1 resistance genes in grasses.

Jouet A, McMullan M, van Oosterhout C.

Mol Ecol. 2015 Jun;24(12):3077-92. doi: 10.1111/mec.13213. Epub 2015 Jun 5.


Evidence for suppression of immunity as a driver for genomic introgressions and host range expansion in races of Albugo candida, a generalist parasite.

McMullan M, Gardiner A, Bailey K, Kemen E, Ward BJ, Cevik V, Robert-Seilaniantz A, Schultz-Larsen T, Balmuth A, Holub E, van Oosterhout C, Jones JD.

Elife. 2015 Feb 27;4. doi: 10.7554/eLife.04550.


Evidence for cryptic speciation in directly transmitted gyrodactylid parasites of Trinidadian guppies.

Xavier R, Faria PJ, Paladini G, van Oosterhout C, Johnson M, Cable J.

PLoS One. 2015 Jan 9;10(1):e0117096. doi: 10.1371/journal.pone.0117096. eCollection 2015.


Secondary contact seeds phenotypic novelty in cichlid fishes.

Nichols P, Genner MJ, van Oosterhout C, Smith A, Parsons P, Sungani H, Swanstrom J, Joyce DA.

Proc Biol Sci. 2015 Jan 7;282(1798):20142272. doi: 10.1098/rspb.2014.2272.


Multiple FLC haplotypes defined by independent cis-regulatory variation underpin life history diversity in Arabidopsis thaliana.

Li P, Filiault D, Box MS, Kerdaffrec E, van Oosterhout C, Wilczek AM, Schmitt J, McMullan M, Bergelson J, Nordborg M, Dean C.

Genes Dev. 2014 Aug 1;28(15):1635-40. doi: 10.1101/gad.245993.114. Epub 2014 Jul 17.


Critical review of NGS analyses for de novo genotyping multigene families.

Lighten J, van Oosterhout C, Bentzen P.

Mol Ecol. 2014 Aug;23(16):3957-72. doi: 10.1111/mec.12843. Epub 2014 Jul 21. Review.


Divergent selection for opsin gene variation in guppy (Poecilia reticulata) populations of Trinidad and Tobago.

Tezuka A, Kasagi S, van Oosterhout C, McMullan M, Iwasaki WM, Kasai D, Yamamichi M, Innan H, Kawamura S, Kawata M.

Heredity (Edinb). 2014 Nov;113(5):381-9. doi: 10.1038/hdy.2014.35. Epub 2014 Apr 2.


Ultra-deep Illumina sequencing accurately identifies MHC class IIb alleles and provides evidence for copy number variation in the guppy (Poecilia reticulata).

Lighten J, van Oosterhout C, Paterson IG, McMullan M, Bentzen P.

Mol Ecol Resour. 2014 Jul;14(4):753-67. doi: 10.1111/1755-0998.12225. Epub 2014 Feb 5.


High variance in reproductive success generates a false signature of a genetic bottleneck in populations of constant size: a simulation study.

Hoban SM, Mezzavilla M, Gaggiotti OE, Benazzo A, van Oosterhout C, Bertorelle G.

BMC Bioinformatics. 2013 Oct 16;14:309. doi: 10.1186/1471-2105-14-309.


Can parasites use predators to spread between primary hosts?

Cable J, Archard GA, Mohammed RS, McMullan M, Stephenson JF, Hansen H, van Oosterhout C.

Parasitology. 2013 Aug;140(9):1138-43. doi: 10.1017/S003118201300067X. Epub 2013 May 29.


Maintenance of major histocompatibility supertype variation in selfing vertebrate is no evidence for overdominant selection.

van Oosterhout C.

Proc Biol Sci. 2013 Jan 8;280(1754):20122501. doi: 10.1098/rspb.2012.2501. Print 2013 Mar 7. No abstract available.


Interactions between males guppies facilitates the transmission of the monogenean ectoparasite Gyrodactylus turnbulli.

Richards EL, van Oosterhout C, Cable J.

Exp Parasitol. 2012 Dec;132(4):483-6. doi: 10.1016/j.exppara.2012.09.019. Epub 2012 Oct 6.


Mendelian inheritance pattern and high mutation rates of microsatellite alleles in the diatom Pseudo-nitzschia multistriata.

Tesson SV, Legrand C, van Oosterhout C, Montresor M, Kooistra WH, Procaccini G.

Protist. 2013 Jan;164(1):89-100. doi: 10.1016/j.protis.2012.07.001. Epub 2012 Aug 28.


Estimates of genetic differentiation measured by F(ST) do not necessarily require large sample sizes when using many SNP markers.

Willing EM, Dreyer C, van Oosterhout C.

PLoS One. 2012;7(8):e42649. doi: 10.1371/journal.pone.0042649. Epub 2012 Aug 14.


Inference of selection based on temporal genetic differentiation in the study of highly polymorphic multigene families.

McMullan M, van Oosterhout C.

PLoS One. 2012;7(8):e42119. doi: 10.1371/journal.pone.0042119. Epub 2012 Aug 10.


Parasites pitched against nature: Pitch Lake water protects guppies (Poecilia reticulata) from microbial and gyrodactylid infections.

Schelkle B, Mohammed RS, Coogan MP, McMullan M, Gillingham EL, VAN Oosterhout C, Cable J.

Parasitology. 2012 Nov;139(13):1772-9. doi: 10.1017/S0031182012001059. Epub 2012 Jul 26.


Mixed infections and hybridisation in monogenean parasites.

Schelkle B, Faria PJ, Johnson MB, van Oosterhout C, Cable J.

PLoS One. 2012;7(7):e39506. doi: 10.1371/journal.pone.0039506. Epub 2012 Jul 11.


Cryptic MHC polymorphism revealed but not explained by selection on the class IIb peptide-binding region.

Llaurens V, McMullan M, van Oosterhout C.

Mol Biol Evol. 2012 Jun;29(6):1631-44. doi: 10.1093/molbev/mss012. Epub 2012 Jan 18.


Gene conversion rapidly generates major histocompatibility complex diversity in recently founded bird populations.

Spurgin LG, van Oosterhout C, Illera JC, Bridgett S, Gharbi K, Emerson BC, Richardson DS.

Mol Ecol. 2011 Dec;20(24):5213-25. doi: 10.1111/j.1365-294X.2011.05367.x. Epub 2011 Nov 22.


Parasite transmission in social interacting hosts: monogenean epidemics in guppies.

Johnson MB, Lafferty KD, van Oosterhout C, Cable J.

PLoS One. 2011;6(8):e22634. doi: 10.1371/journal.pone.0022634. Epub 2011 Aug 29.


Segregation of species-specific male attractiveness in f(2) hybrid lake Malawi cichlid fish.

Svensson O, Egger B, Gricar B, Woodhouse K, van Oosterhout C, Salzburger W, Seehausen O, Turner GF.

Int J Evol Biol. 2011;2011:426179. doi: 10.4061/2011/426179. Epub 2011 Apr 6.


Invasive cyprinid fish in Europe originate from the single introduction of an admixed source population followed by a complex pattern of spread.

Simon A, Britton R, Gozlan R, van Oosterhout C, Volckaert FA, Hänfling B.

PLoS One. 2011;6(6):e18560. doi: 10.1371/journal.pone.0018560. Epub 2011 Jun 3.


Rapid loss of MHC class II variation in a bottlenecked population is explained by drift and loss of copy number variation.

Eimes JA, Bollmer JL, Whittingham LA, Johnson JA, VAN Oosterhout C, Dunn PO.

J Evol Biol. 2011 Sep;24(9):1847-56. doi: 10.1111/j.1420-9101.2011.02311.x. Epub 2011 May 23.


The MC1R gene in the guppy (Poecilia reticulata): Genotypic and phenotypic polymorphisms.

Tezuka A, Yamamoto H, Yokoyama J, van Oosterhout C, Kawata M.

BMC Res Notes. 2011 Feb 4;4:31. doi: 10.1186/1756-0500-4-31.


Sex-specific differences in shoaling affect parasite transmission in guppies.

Richards EL, van Oosterhout C, Cable J.

PLoS One. 2010 Oct 11;5(10):e13285. doi: 10.1371/journal.pone.0013285.


Genome-wide single nucleotide polymorphisms reveal population history and adaptive divergence in wild guppies.

Willing EM, Bentzen P, van Oosterhout C, Hoffmann M, Cable J, Breden F, Weigel D, Dreyer C.

Mol Ecol. 2010 Mar;19(5):968-84. doi: 10.1111/j.1365-294X.2010.04528.x. Epub 2010 Feb 8.


Elevated mtDNA diversity in introduced populations of Cynotilapia afra (Günther 1894) in Lake Malawi National Park is evidence for multiple source populations and hybridization.

Zidana H, Turner GF, Van Oosterhout C, Hänfling B.

Mol Ecol. 2009 Nov;18(21):4380-9. doi: 10.1111/j.1365-294X.2009.04362.x. Epub 2009 Sep 28.


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