Cock van Oosterhout

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• 2024

  Can genetic rescue help save Arabia's last big cat?

  Al Hikmani, H., van Oosterhout, C., Birley, T., Labisko, J., Jackson, H. A., Spalton, A., Tollington, S. & Groombridge, J. J., May 2024, In: Evolutionary Applications. 17, 5, e13701.

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• Extensive immune receptor repertoire diversity in disease-resistant rice landraces

  Gladieux, P., van Oosterhout, C., Fairhead, S., Jouet, A., Ortiz, D., Ravel, S., Shrestha, R-K., Frouin, J., He, X., Zhu, Y., Morel, J-B., Huang, H., Kroj, T. & Jones, J. D. G., 9 Sep 2024, In: Current Biology. 34, 17, p. 3983-3995.e6 13 p.

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• Genomics‐informed captive breeding can reduce inbreeding depression and the genetic load in zoo populations

  Speak, S. A., Birley, T., Bortoluzzi, C., Clark, M. D., Percival-Alwyn, L., Morales, H. E. & van Oosterhout, C., Oct 2024, In: Molecular Ecology Resources. 24, 7, e13967.

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• Moderating the neutralist–selectionist debate: Exactly which propositions are we debating, and which arguments are valid?

  de Jong, M. J., van Oosterhout, C., Hoelzel, A. R. & Janke, A., Feb 2024, In: Biological Reviews. 99, 1, p. 23-55 33 p.

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• Sonification of genomic data to represent genetic load in zoo populations

  Martin, E. J., Speak, S. A., Urban, L., Morales, H. E. & van Oosterhout, C., 4 Sep 2024, (E-pub ahead of print) In: Zoo Biology.

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• The genetic basis of the kākāpō structural color polymorphism suggests balancing selection by an extinct apex predator

  Urban, L., Santure, A. W., Uddstrom, L., Digby, A., Vercoe, D., Eason, D., Crane, J., Kākāpō Recovery Team, Wylie, M. J., Davis, T., LeLec, M. F., Guhlin, J., Poulton, S., Slate, J., Alexander, A., Fuentes-Cross, P., Dearden, P. K., Gemmell, N. J., Azeem, F., Weyland, M., & 3 othersSchwefel, H. G. L., van Oosterhout, C. & Morales, H. E., 10 Sep 2024, In: PLoS Biology. 22, 9, e3002755.

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• The genome sequence of the Mauritius kestrel, Falco punctatus (Temminck, 1821)

  Morales, H. E., Norris, K., Henshaw, S., Tatayah, V., Ruhomaun, K., van Oosterhout, C., Groombridge, J. J. & Gilbert, M. T. P., 13 Jun 2024, In: Wellcome Open Research. 9, p. 312 312.

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• The genome sequence of the Mauritius parakeet, Alexandrinus eques (formerly Psittacula eques) (A. Newton & E. Newton, 1876)

  Morales, H. E., Groombridge, J. J., Tollington, S., Henshaw, S., Tatayah, V., Ruhomaun, K., van Oosterhout, C. & Gilbert, M. T. P., 16 Jul 2024, In: Wellcome Open Research. 9, 378.

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• The genome sequence of the Pink Pigeon, Nesoenas mayeri (Prévost, 1843)

  Morales, H. E., van Oosterhout, C., Whitford, H., Tatayah, V., Ruhomaun, K., Groombridge, J. J. & Gilbert, M. T. P., 24 Jun 2024, In: Wellcome Open Research. 9

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• The impact of habitat loss and population fragmentation on genomic erosion

  Pinto, A. V., Hansson, B., Patramanis, I., Morales, H. E. & van Oosterhout, C., Feb 2024, In: Conservation Genetics. 25, p. 49-57

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• What mandrills leave behind: using fecal samples to characterize the major histocompatibility complex in a threatened primate

  Weber, A., Lighten, J., van Oosterhout, C., Guibinga Mickala, A., Ntie, S., Mickala, P., Lehmann, D., Abernethy, K. & Anthony, N., Apr 2024, In: Conservation Genetics. 25, 2, p. 533-549 17 p.

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• When birds of a feather flock together: Severe genomic erosion and the implications for genetic rescue in an endangered island passerine

  Cavill, E. L., Morales, H. E., Sun, X., Westbury, M. V., van Oosterhout, C., Accouche, W., Zora, A., Schulze, M. J., Shah, N., Adam, P. A., Brooke, M. D. L., Sweet, P., Gopalakrishnan, S. & Gilbert, M. T. P., Jul 2024, In: Evolutionary Applications. 17, 7, e13739.

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• 2023

  Genetic load and adaptive potential of a recovered avian species that narrowly avoided extinction

  Femerling, G., van Oosterhout, C., Feng, S., Bristol, R. M., Zhang, G., Groombridge, J., Gilbert, M. T. P. & Morales, H. E., Dec 2023, In: Molecular Biology and Evolution. 40, 12, msad256.

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  7 Citations (SciVal)

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• Hybridisation has shaped a recent radiation of grass-feeding aphids

  Mathers, T. C., Wouters, R. H. M., Mugford, S. T., Biello, R., van Oosterhout, C. & Hogenhout, S. A., 13 Jul 2023, In: BMC Biology. 21, 157.

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• Incipient parallel evolution of SARS-CoV-2 Deltacron variant in South Brazil

  Sant’Anna, F. H., Finger Andreis, T., Salvato, R. S., Muterle Varela, A. P., Comerlato, J., Gregianini, T. S., Barcellos, R. B., de Souza Godinho, F. M., Resende, P. C., da Luz Wallau, G., y Castro, T. R., Casarin, B. C., de Almeida Vieira, A., Schwarzbold, A. V., de Arruda Trindade, P., Tumioto Giannini, G. L., Freese, L., Bristot, G., Brasil, C. S., de Oliveira Rocha, B., & 4 othersMartins, P. B., de Oliveira, F. H., van Oosterhout, C. & Wendland, E., Feb 2023, In: Vaccines. 11, 2, 212.

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• Means, motive and opportunity for biological invasions: Genetic introgression in a fungal pathogen

  Rogério, F., van Oosterhout, C., Ciampi-Guillardi, M., Correr, F. H., Hosaka, G. K., Cros-Arteil, S., Rodrigues Alves Margarido, G., Massola Júnior, N. S. & Gladieux, P., May 2023, In: Molecular Ecology. 32, 10, p. 2428-2442 15 p.

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• Recent genetic exchanges and admixture shape the genome and population structure of the zoonotic pathogen Cryptosporidium parvum

  Corsi, G. I., Tichkule, S., Sannella, A. R., Vatta, P., Asnicar, F., Segata, N., Jex, A. R., van Oosterhout, C. & Cacciò, S. M., May 2023, In: Molecular Ecology. 32, 10, p. 2633-2645 13 p.

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• 2022

  Diversity, prevalence, and expression of cyanase genes (cynS) in planktonic marine microorganisms

  Mao, X., Chen, J., van Oosterhout, C., Zhang, H., Liu, G., Zhuang, Y. & Mock, T., Feb 2022, In: The ISME Journal. 16, 2, p. 602–605 4 p.

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  17 Citations (Scopus)

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• Genome evolution of a nonparasitic secondary heterotroph, the diatom Nitzschia putrida

  Kamikawa, R., Mochizuki, T., Sakamoto, M., Tanizawa, Y., Nakayama, T., Onuma, R., Cenci, U., Moog, D., Speak, S., Sarkozi, K., Toseland, A., van Oosterhout, C., Oyama, K., Kato, M., Kume, K., Kayama, M., Azuma, T., Ishii, K., Miyashita, H., Henrissat, B., & 9 othersLombard, V., Win, J., Kamoun, S., Kashiyama, Y., Mayama, S., Miyagishima, S., Tanifuji, G., Mock, T. & Nakamura, Y., 29 Apr 2022, In: Science Advances. 8, 17, eabi5075.

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• Genomic erosion in a demographically recovered bird species during conservation rescue

  Jackson, H. A., Percival-Alwyn, L., Ryan, C., Albeshr, M. F., Venturi, L., Morales, H. E., Mathers, T. C., Cocker, J., Speak, S. A., Accinelli, G. G., Barker, T., Heavens, D., Willman, F., Dawson, D., Ward, L., Tatayah, V., Zuël, N., Young, R., Concannon, L., Whitford, H., & 12 othersClavijo, B., Bunbury, N., Tyler, K. M., Ruhomaun, K., Grace, M. K., Bruford, M. W., Jones, C. G., Tollington, S., Bell, D. J., Groombridge, J. J., Clark, M. & Van Oosterhout, C., Aug 2022, In: Conservation Biology. 36, 4, e13918.

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• Global population genomics of two subspecies of Cryptosporidium hominis during 500 years of evolution

  Tichkule, S., Cacciò, S. M., Robinson, G., Chalmers, R. M., Mueller, I., Emery-Corbin, S. J., Eibach, D., Tyler, K. M., van Oosterhout, C. & Jex, A. R., Apr 2022, In: Molecular Biology and Evolution. 39, 4, msac056.

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  14 Citations (Scopus)

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• The role of zinc in the adaptive evolution of polar phytoplankton

  Ye, N., Han, W., Toseland, A., Wang, Y., Fan, X., Xu, D., van Oosterhout, C., Sea of Change Consortium, Grigoriev, I. V., Tagliabue, A., Zhang, J., Zhang, Y., Ma, J., Qiu, H., Li, Y., Zhang, X. & Mock, T., Jul 2022, In: Nature Ecology & Evolution. 6, 7, p. 965-978 14 p.

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• VIVID: A web application for variant interpretation and visualization in multi-dimensional analyses

  Tichkule, S., Myung, Y., Naung, M. T., Ansell, B. R. E., Guy, A. J., Srivastava, N., Mehra, S., Cacciò, S. M., Mueller, I., Barry, A. E., van Oosterhout, C., Pope, B., Ascher, D. B. & Jex, A. R., 14 Sep 2022, In: Molecular Biology and Evolution. 39, 9, msac196.

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• 2021

  A complex resistance locus in Solanum americanum recognizes a conserved Phytophthora effector

  Witek, K., Lin, X., Karki, H. S., Jupe, F., Witek, A. I., Steuernagel, B., Stam, R., Van Oosterhout, C., Fairhead, S., Heal, R., Cocker, J. M., Bhanvadia, S., Barrett, W., Wu, C-H., Adachi, H., Song, T., Kamoun, S., Vleeshouwers, V. G. A. A., Tomlinson, L., Wulff, B. B. H., & 1 othersJones, J. D. G., 11 Feb 2021, In: Nature Plants. 7, 2, p. 198-208 11 p.

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• Chromosome-scale genome assemblies of aphids reveal extensively rearranged autosomes and long-term conservation of the X chromosome

  Mathers, T., Wouters, R. H. M., Mugford, S. T., Swarbreck, D., van Oosterhout, C. & Hogenhout, S. A., 9 Mar 2021, In: Molecular Biology and Evolution. 38, 3, p. 856–875 20 p.

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• Comment on “Individual heterozygosity predicts translocation success in threatened desert tortoises”

  Hansson, B., Morales, H. E. & Van Oosterhout, C., 4 Jun 2021, In: Science. 372, 6546, eabh1105.

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• Comparative genomics revealed adaptive admixture in Cryptosporidium hominis in Africa

  Tichkule, S., Jex, A. R., Van Oosterhout, C., Sannella, A. R., Krumkamp, R., Aldrich, C., Maiga-Ascofare, O., Dekker, D., Lamshöft, M., Mbwana, J., Rakotozandrindrainy, N., Borrmann, S., Thye, T., Schuldt, K., Winter, D., Kremsner, P. G., Oppong, K., Manouana, P., Mbong, M., Gesase, S., & 11 othersMinja, D. T. R., Mueller, I., Bahlo, M., Nader, J., May, J., Rakotozandrindrain, R., Adegnika, A. A., Lusingu, J. P. A., Amuasi, J., Eibach, D. & Caccio, S. M., Jan 2021, In: Microbial Genomics. 7, 1, 000493.

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• Depletion of MHC supertype during domestication can compromise immunocompetence

  Smallbone, W., Ellison, A., Poulton, S., Oosterhout, C. & Cable, J., Feb 2021, In: Molecular Ecology. 30, 3, p. 736-746 11 p.

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• Functional immunogenetic variation, rather than local adaptation, predicts ectoparasite infection intensity in a model fish species

  Phillips, K. P., Cable, J., Mohammed, R. S., Chmielewski, S., Przesmycka, K. J., van Oosterhout, C. & Radwan, J., Nov 2021, In: Molecular Ecology. 30, 21, p. 5588-5604 17 p.

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• Genetic variation in resistance and high fecundity impede viral biocontrol of invasive fish

  Mintram, K. S., van Oosterhout, C. & Lighten, J., Jan 2021, In: Journal of Applied Ecology. 58, 1, p. 148-157 10 p.

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• Mitotic recombination between homologous chromosomes drives genomic diversity in diatoms

  Bulankova, P., Sekulić, M., Jallet, D., Nef, C., van Oosterhout, C., Delmont, T. O., Vercauteren, I., Osuna-Cruz, C. M., Vancaester, E., Mock, T., Sabbe, K., Daboussi, F., Bowler, C., Vyverman, W., Vandepoele, K. & De Veylder, L., 9 Aug 2021, In: Current Biology. 31, 15, p. 3221-3232.e9 22 p.

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• Significance of differential allelic expression (DAE) in phenotypic plasticity and evolutionary potential of microbial eukaryotes

  Tatman, B., Mock, T., Wu, T. & van Oosterhout, C., 15 Dec 2021, In: Quantitative Biology. 9, 4, p. 400-410 11 p.

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• 2020

  An aphid RNA transcript migrates systemically within plants and is a virulence factor

  Chen, Y., Singh, A., Kaithakottil, G. G., Mathers, T. C., Gravino, M., Mugford, S. T., van Oosterhout, C., Swarbreck, D. & Hogenhout, S. A., 9 Jun 2020, In: Proceedings of the National Academy of Sciences of the United States of America. 117, 23, p. 12763-12771 9 p.

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• Giraffe translocation population viability analysis

  Lee, D. E., Fienieg, E., van Oosterhout, C., Muller, Z., Strauss, M., Carter, K. D., Scheijen, C. P. J. & Deacon, F., 2020, In: Endangered Species Research. 41, p. 245-252 8 p.

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• Parasite diversity and ecology in a model species, the guppy (Poecilia reticulata) in Trinidad

  Mohammed, R. S., King, S. D., Bentzen, P., Marcogliese, D., van Oosterhout, C. & Lighten, J., Jan 2020, In: Royal Society Open Science. 7, 1, 8 p., 191112.

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  9 Citations (Scopus)

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• 2019

  Albugo candida race diversity, ploidy and host‐associated microbes revealed using DNA sequence capture on diseased plants in the field

  Jouet, A., Saunders, D. G. O., McMullan, M., Ward, B., Furzer, O., Jupe, F., Cevik, V., Hein, I., Thilliez, G. J. A., Holub, E., van Oosterhout, C. & Jones, J. D. G., Feb 2019, In: New Phytologist. 221, 3, p. 1529-1543 15 p.

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• Evolutionary genomics of anthroponosis in Cryptosporidium

  Nader, J., Mathers, T. C., Ward, B. J., Pachebat, J., Swain, M., Robinson, G., Chalmers, R. M., Hunter, P., van Oosterhout, C. & Tyler, K., 4 Mar 2019, In: Nature Microbiology. 4, 5, p. 826–836 11 p.

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• Long-term cleaning patterns of the sharknose goby (Elacatinus evelynae)

  Dunkley, K., Ellison, A. R., Mohammed, R. S., van Oosterhout, C., Whittey, K. E., Perkins, S. E. & Cable, J., Apr 2019, In: Coral Reefs. 38, 2, p. 321–330

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• Pathogen enrichment sequencing (PenSeq) enables population genomic studies in oomycetes

  Thilliez, G. J. A., Armstrong, M. R., Lim, T-Y., Baker, K., Jouet, A., Ward, B., Van Oosterhout, C., Jones, J. D. G., Huitema, E., Birch, P. R. J. & Hein, I., Feb 2019, In: New Phytologist. 221, 3, p. 1634-1648 15 p.

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• Sex-specific changes in the aphid DNA methylation landscape

  Mathers, T. C., Mugford, S. T., Percival-Alwyn, L., Chen, Y., Kaithakottil, G., Swarbreck, D., Hogenhout, S. A. & van Oosterhout, C., Sep 2019, In: Molecular Ecology. 28, 18, p. 4228-4241

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• 2018

  Contrasting effects of acute and chronic stress on the transcriptome, epigenome, and immune response of Atlantic salmon

  Uren Webster, T. M., Rodriguez-Barreto, D., Martin, S. A. M., van Oosterhout, C., Orozco-terWengel, P., Cable, J., Hamilton, A., Garcia De Leaniz, C. & Consuegra, S., Dec 2018, In: Epigenetics. 13, 12, p. 1191-1207 17 p.

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• Immunogenetic novelty confers a selective advantage in host–pathogen coevolution

  Phillips, K. P., Cable, J., Mohammed, R. S., Herdegen-Radwan, M., Raubic, J., Przesmycka, K. J., van Oosterhout, C. & Radwan, J., Feb 2018, In: Proceedings of the National Academy of Sciences of the United States of America (PNAS). 115, 7, p. 1552-1557 6 p.

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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, F. C. P., 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., & 26 othersHowell, M., Josselin, A-A., Karn, R. C., Laukaitis, C. M., Jingtao, L., Martin, F., Muffato, M., Nachtweide, S., Quail, M. A., Sisu, C., Stanke, M., Stefflova, K., van Oosterhout, C., Veyrunes, F., Ward, B., Yang, F., Yazdanifar, G., Zadissa, A., Adams, D. J., Brazma, A., Gerstein, M., Paten, B., Pham, S., Keane, T. M., Odom, D. T. & Flicek, P., Apr 2018, In: Genome Research. 28, 4, p. 448-459 12 p.

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• 2017

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

  Paajanen, P., Strauss, J., van Oosterhout, C., McMullan, M., Clark, M. D. & Mock, T., 10 Oct 2017, In: Scientific Data. 4, 170149.

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

  Lighten, J., Papadopulos, A. S. T., Mohammed, R. S., Ward, B. J., Paterson, I., Baillie, L., Bradbury, I. R., Hendry, A. P., Bentzen, P. & van Oosterhout, C., 3 Nov 2017, In: Nature Communications. 8, 1294.

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• Evolutionary genomics of a cold-adapted diatom: Fragilariopsis cylindrus

  Mock, T., Otillar, R. P., Strauss, J., McMullan, M., Paajanen, P., Schmutz, J., Salamov, A., Sanges, R., Toseland, A., Ward, B. J., Allen, A. E., Dupont, C. L., Frickenhaus, S., Maumus, F., Veluchamy, A., Wu, T., Barry, K. W., Falciatore, A., Ferrante, M. I., Fortunato, A. E., & 24 othersGlöckner, G., Gruber, A., Hipkin, R., Janech, M. G., Kroth, P. G., Leese, F., Lindquist, E. A., Lyon, B. R., Martin, J., Mayer, C., Parker, M., Quesneville, H., Raymond, J. A., Uhlig, C., Valas, R. E., Valentin, K. U., Worden, A. Z., Armbrust, E. V., Clark, M. D., Bowler, C., Green, B. R., Moulton, V., van Oosterhout, C. & Grigoriev, I. V., 26 Jan 2017, In: Nature. 541, p. 536–540 5 p.

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• Immigrant reproductive dysfunction facilitates ecological speciation

  Svensson, O., Gräns, J., Celander, M. C., Havenhand, J., Leder, E. H., Lindström, K., Schöld, S., van Oosterhout, C. & Kvarnemo, C., Oct 2017, In: Evolution. 71, 10, p. 2510–2521 12 p.

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

  Mathers, T. C., Chen, Y., Kaithakottil, G., Legeai, F., Mugford, S. T., Baa-Puyoulet, P., Bretaudeau, A., Clavijo, B., Colella, S., Collin, O., Dalmay, T., Derrien, T., Feng, H., Gabaldón, T., Jordan, A., Julca, I., Kettles, G. J., Kowitwanich, K., Lavenier, D., Lenzi, P., & 16 othersLopez-Gomollon, S., Loska, D., Mapleson, D., Maumus, F., Moxon, S., Price, D. R. G., Sugio, A., van Munster, M., Uzest, M., Waite, D., Jander, G., Tagu, D., Wilson, A. C. C., van Oosterhout, C., Swarbreck, D. & Hogenhout, S. A., 13 Feb 2017, In: Genome Biology. 18, 27.

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

  Bentkowski, P., van Oosterhout, C., Ashby, B. & Mock, T., Apr 2017, In: The ISME Journal. 11, 4, p. 1011–1018 8 p.

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• 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, K. L., Foufopoulos, J. & Anthony, N. M., Jul 2017, In: Ecology and Evolution. 7, 13, p. 4568–4581

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