Publications

Here is a list of our publications. Please follow the links to obtain the pdf files.  Current or former group members who performed the research are highlighted in bold.  To see a collection of popular press articles and media coverage resulting from our research please see here.

≤2006    2007    2008    2009    2010    2011    2012    2013    2014  2015  2016    2017   2018   2019  2020


 


Highlights

Peart, C.R., Tusso, S., Pophaly, S.D., Botero-Castro, F., Wu, C.-C., Aurioles-Gamboa, D., Baird, A.B., Bickham, J.W., Forcada, J., Galimberti, F., Gemmell, N.J., Hoffman, J.I., Kovacs, K.M., Kunnasranta, M., Lydersen, C., Nyman, T., Rosa de Olivera, L., Orr, A.J., Sanvito, S., Valtonen, M., Shafer, A.B.A., Wolf, J.B.W. (2020) Determinants of genetic variation across eco-evolutionary scales in pinnipeds.  Nature Ecology and Evolution, 4: 1095–1104.  Doi: doi.org/10.1038/s41559-020-1215-5 pdf Supplementary information pdf

Clark, M.S, Villota Nieva, L., Hoffman, J.I., Davies, A.J., Trivedi, U.H., Turner, F., Ashton, G.V. & Peck, L.S. (2019) No long-term acclimation in Antarctic encrusting species: vulnerabilities in a warmer world.  Nature Communications, 10: 3383.  Doi: 10.1038/s41467-019-11348-w pdf

Stoffel, M.A., Humble, E., Paijmans, A.J., Acevedo-Whitehouse, K., Chilvers, B.L, Dickerson, B., Galimberti, F., Gemmell, N., Goldsworthy, S.D., Nichols, H.J., Krüger, O., Negro, S., Osborne, A., Pastor, T., Robertson, B.C., Sanvito, S., Schultz, J., Shafer, A.B.A., Wolf, J.B.W. & Hoffman, J.I. (2018) Demography and genetic diversity across pinnipeds are shaped by human exploitation, ecology and life-history.  Nature Communications, 9: 4836.  Doi: 10.1038/s41467-018-06695-z pdf Supplementary information pdf

Eberhart-Phillips, L.J., Carmona-Isunza, M.C., Vincze, O., Zefania, S., Miller, T.E.X., Küpper, C., Székely, T.*, Hoffman, J.I.* & Krüger, O.*  (2018) Demographic causes of adult sex ratio variation and their consequences for parental cooperation.  Nature Communications, 9: 1651.  Doi: 10.1038/s41467-018-03833-5 pdf Supplementary information pdf * Joint senior authors

Eberhart-Phillips, L.J., Küpper, C., Miller, T.E., Cruz-López, M., Maher, K., dos Remedios, N., Stoffel, M.A., Hoffman, J.I.*, Krüger, O.* & Székely, T.*  (2017) Sex-specific early survival drives adult sex ratio bias in snowy plovers and impacts mating system and population growth.  Proceedings of the National Academy of Sciences of the United States of America, 114: E5474-E5481.  Doi: 10.1073/pnas.1620043114   pdf Supplementary Information pdf R code pdf * Joint senior authors

Stoffel, M., Caspers, B.A., Forcada, J., Giannakara, A., Baier, M.C., Eberhart-Phillips, L.J., Müller, C. & Hoffman, J.I. (2015) Chemical fingerprints encode mother-offspring similarity, colony membership, relatedness and genetic quality in fur seals. Proceedings of the National Academy of Sciences of the United States of America, 112: E5005-E5012. Doi:10.1073/pnas.1506076112 pdf Supplementary Information pdf R code pdf Journal cover pdf Commentary articles in PNAS pdf and JEB pdf

Forcada, J. & Hoffman, J.I. (2014) Climate change selects for heterozygosity in a declining fur seal population. Nature, 511: 462-465. Doi: 10.1038/nature13542 pdf Supplementary information pdf Journal cover pdf Editorial pdf News and views pdf

Hoffman, J.I., Simpson, F., David, P., Rijks, J.M., Kuiken, T., Thorne, M.A.S., Lacey, R.C. & Dasmahapatra, K.K.  (2014) High-throughput sequencing reveals inbreeding depression in a natural population. Proceedings of the National Academy of Sciences of the United States of America, 111: 3775-3780. Doi: 10.1073/pnas.1318945111 pdf Supplementary information pdf Journal cover pdf
Access the recommendation on F1000Prime

Hoffman, J.I., Forcada, J., Trathan, P.N. & Amos, W. (2007) Female fur seals show active choice for males that are heterozygous and unrelated. Nature, 445: 912–914. doi: 10.1038/nature05558 pdf Supplementary information pdf

2020

123) Wells, D.A. Cant, M.A., Hoffman, J.I.* & Nichols, H.J.* (in press).  Inbreeding depresses altruism in a cooperative society.  Ecology Letters. Joint senior authors

122) Clark, M.S., Peck, L.S., Harper, E.M., Arivalagan, J., Backeljau, T., Berland, S., Cardoso, J.C.R., Caurcel, C., Chapelle, G., De Noia, M., Dupont, S., Gharbi, K., Hoffman, J.I., Last, K., Marie, A., Melzner, F., Michalek, K., Morris, J., Power, D.M., Ramesh, K., Saunders, S., Sillampää, K., Slight, V., Stewart-Sinclair, P., Sundell, K., Telesca, L., Vendrami, D., Ventura, A., Wilding, T., Yarra, T., Harper, E.M. (in press).  Deciphering mollusc shell production.  Biological Reviews.

121) Humble, E., Paijmans, A., Forcada, J. & Hoffman, J.I.  A new 85k SNP array reveals inbreeding and cryptic relatedness in an Antarctic fur seal breeding colony.  G3: Genes | Genomes | Genetics, 10: 2787–2799.  Doi: 10.1534/g3.120.401268 pdf Supplementary information pdf

120) Hoffman, J.I., Nagel, R., Litzke, V., Wells, D.A. & Amos, W.  Genetic analysis of Boletus edulis suggests that intra-specific competition may reduce local genetic diversity as a woodland ages.  Royal Society Open Science, 7: 200419.  Doi: 10.1098/rsos.200419 pdf R code pdf

119) Peart, C.R., Tusso, S., Pophaly, S.D., Botero-Castro, F., Wu, C.-C., Aurioles-Gamboa, D., Baird, A.B., Bickham, J.W., Forcada, J., Galimberti, F., Gemmell, N.J., Hoffman, J.I., Kovacs, K.M., Kunnasranta, M., Lydersen, C., Nyman, T., Rosa de Olivera, L., Orr, A.J., Sanvito, S., Valtonen, M., Shafer, A.B.A., Wolf, J.B.W. Determinants of genetic variation across eco-evolutionary scales in pinnipeds.  Nature Ecology and Evolution, 4: 1095–1104.  Doi: 10.1038/s41559-020-1215-5 pdf Supplementary information pdf

118) Shah, A., Hoffman, J.I. & Schielzeth, H. (in press).  Comparative analysis of genomic repeat content in gomphocerine grasshoppers reveals expansion of satellite DNA and helitrons in species with unusually large genomes.  Genome Biology and Evolution.

117) Vendrami, D.L.J., De Noia, M., Telesca, L. & Hoffman, J.I. (in press).  Population genomic insights into introgression and its consequences for genome-wide heterozygosity in the Mytilus species complex across Europe.   Evolutionary Applications.

116) Stoffel, M., Acevedo-Whitehouse, K.*, Morales-Durán, N., Grosser, S., Chakarov, N., Krüger, O., Nichols, H.J., Elorriaga-Verplancken, F.R. & Hoffman, J.I.*  Early sexual dimorphism in the developing gut microbiome of northern elephant seals.  Molecular Ecology, 29: 2109-2122.  Doi: 10.1111/mec.15385 pdf Supplementary information pdf News and views article in Molecular Ecology pdfJoint senior authors

115) Paijmans, A.J., Stoffel, M.A., Bester, M.N., Cleary, A., De Bruyn, P.J.N., Forcada, J., Goebel, M.E., Goldsworthy, S.D., Guinet, C., Kovaks, K.M., Lowther, A. & Hoffman, J.I.  The genetic legacy of extreme exploitation in a polar vertebrate.  Scientific Reports, 10: 5089. Doi: 10.1038/s41598-020-61560-8 pdf Supplementary Information pdf

114) De Noia, M.*, Telesca, L.*, Vendrami, D.L.J.*, Gokalp, H.K., Charrier, G., Harper, E.M. & Hoffman, J.I.  Population genetic structure is unrelated to shell shape, microstructure and organic content in European populations of the soft-shell clam Mya arenariaGenes special issue “Genetic diversity in marine populations”, 11: 298.  Doi: 10.3390/genes11030298 pdf  * Joint first authors

2019

113) Clark, M.S, Villota Nieva, L., Hoffman, J.I., Davies, A.J., Trivedi, U.H., Turner, F., Ashton, G.V. & Peck, L.S. No long-term acclimation in Antarctic encrusting species: vulnerabilities in a warmer world.  Nature Communications, 10: 3383.  Doi: 10.1038/s41467-019-11348-w pdf

112) Cleary, A.C., Bester, M., Forcada, J., Goebel, M., Goldsworthy, S., Guinet, C., Hoffman, J.I., Kovaks, K.M., Lyderson, C. & Lowther, A.D.  Prey differences drive local genetic adaptation in Antarctic fur seals.  Marine Ecology Progress Series, 628: 195-209.  Doi: 10.3354/meps13108 pdf

111) Groβer, S., Sauer, J., Paijmans, A., Caspers, B.A., Forcada, J., Wolf, J.B.W.* & Hoffman, J.I.*  Fur seal microbiota are shaped by the social and physical environment, show mother-offspring similarities and are associated with host genetic quality.  Molecular Ecology, 28: 2409-2422.   Doi: 10.1111/mec.15070 pdf Supplementary Information pdf R code pdf Journal cover pdf * Joint senior authors

110) Nagel, R., Forcada, J. & Hoffman, J.I. The complete mitochondrial genome of the Antarctic fur seal (Arctocephalus gazella).  Mitochondrial DNA Part B, 4: 2936-2937.  Doi: 10.1080/23802359.2019.1662751 pdf

109) Litzke, V., Ottensmann, M., Heitzmann, L., Forcada, J. & Hoffman, J.I.   Heterozygosity at neutral and immune loci is not associated with neonatal mortality due to microbial infection in Antarctic fur seals.  Ecology and Evolution, 9: 7985-7996.  Doi: 10.1002/ece3.53170 pdf R code pdf

108) Vendrami, D.L.J., Forcada, J. & Hoffman, J.I.  Experimental validation of in silico predicted RAD locus frequencies using genomic resources and short read data from a marine mammal.  BMC Genomics, 20: 72. Doi: 10.1186/s12864-019-5440-8 pdf

107) Vendrami, D.L.J., De Noia, M., Telesca, L., Handal, W., Charrier, G., Boudry, P., Eberhart-Philips, L. & Hoffman, J.I.  RAD sequencing sheds new light on the genetic structure and local adaptation of European scallops and resolves their demographic histories.  Scientific Reports, 9: 7455.  Doi: 10.1038/s41598-019-43939-4 pdf

106) Shah, A.Hoffman, J.I., Kalinowski, J. & Schielzeth, H.  Transcriptome assembly for a colour-polymorphic grasshopper (Gomphocerus sibiricus) with a very large genome size.  BMC Genomics, 20: 370.  Doi: 10.1186/s12864-019-5756-4 pdf

105) Vendrami, D.L.J., Houston, R.D., Gharbi, K., Telesca, L., Gutierrez, A., Gurney-Smith, H., Hasegawa, N., Boudry, P. & Hoffman, J.I.  Detailed insights into pan-European population structure and inbreeding in wild and hatchery Pacific oyster (Crassostrea gigas) populations revealed by genome-wide SNP data.  Evolutionary Applications, 12: 519-534.  Doi: 10.1111/eva.12736 pdf

2018

104) Stoffel, M.A., Humble, E., Paijmans, A.J., Acevedo-Whitehouse, K., Chilvers, B.L, Dickerson, B., Galimberti, F., Gemmell, N., Goldsworthy, S.D., Nichols, H.J., Krüger, O., Negro, S., Osborne, A., Pastor, T., Robertson, B.C., Sanvito, S., Schultz, J., Shafer, A.B.A., Wolf, J.B.W. & Hoffman, J.I. Demography and genetic diversity across pinnipeds are shaped by human exploitation, ecology and life-history.  Nature Communications, 9: 4836.  Doi: 10.1038/s41467-018-06695-z pdf Supplementary information pdf

103) Hoffman, J.I., Bauer, E., Paijmans, A.P., Humble, E., Beckmann, L.M., Kubetschek, C., Christaller, F., Kröcker, N., Fuchs, B., Moreras, A., Shihlomule, Y., Bester, M.N., Cleary, A.C., De Bruyn, P.J.N., Forcada, J., Goebel, M.E., Goldsworthy, S.D., Guinet, C., Hoelzel, A.R., Lydersen, C., Kovaks, K.M., Lowther, A.  A global cline in a colour polymorphism suggests a limited contribution of gene flow towards the recovery of a heavily exploited marine mammal.  Royal Society Open Science, 5: 181227.  Doi: 10.1098/rsos.181227. 2 pdf  R code pdf

102) Humble, E., Dasmahapatra, K.K., Martinez-Barrio, A., Gregorio, I., Forcada, J., Polikeit, A-C., Goldsworthy, S.D., Goebel, M.E., Kalinowski, J., Wolf, J.B.W. & Hoffman, J.I.   RAD sequencing and a hybrid Antarctic fur seal genome assembly reveal rapidly decaying linkage disequilibrium, global population structure and evidence for inbreeding.  G3: Genes | Genomes | Genetics, 8: 2709-2722.  Doi: 10.1534/g3.118.200171  pdf Supplementary Information pdf Journal cover pdf  Featured article pdf

101) Ottensmann, M.*, Stoffel, M.*, Nichols, H.J. & Hoffman, J.I.  GCalignR: An R package for aligning Gas-Chromatography data for ecological and evolutionary studies.  PloS One, 13: e0198311.  Doi: 10.1371/journal.pone.0198311 pdf R code pdf  * Joint first authors

100) Wells, D., Cant, M.A., Nichols, H.J.* & Hoffman, J.I.*  A high quality pedigree and genetic markers both reveal inbreeding depression for quality but not survival in a cooperative mammal.  Molecular Ecology, 27: 2271-2288.  Doi: 10.1111/mec.14570 pdf Supplementary Information pdf * Joint senior authors

99) Soulsbury, C.D., Lipponen, A., Wood, K., Mein, C.A., Hoffman, J.I.* & Lebigre, C. Age and quality-dependent DNA methylation correlates with sexual trait expression in a wild bird.  Ecology and Evolution, 8: 6547-6557.  Doi: 10.1002/ece3.4132 pdf * Corresponding author

98) Klimova, A., Ortega-Rubio, A,. Vendrami, D.L.J. & Hoffman, J.I.  Genotyping by sequencing reveals contrasting patterns of population structure, ecologically mediated divergence and long-distance dispersal in North American palms.  Ecology and Evolution, 8: 5873-5890.  Doi: 10.1002/ece3.4125 pdf

97) Clark, M.S., Thorne, M.A.S., King, M., Hipperson, H., Hoffman, J.I. & Peck L.S. Life in the intertidal: cellular responses, methylation and epigenetics.  Functional Ecology, 32: 1982-1994.  Doi: 10.1111/1365-2435.13077 pdf Spotlight article in Functional Ecology pdf

96) Eberhart-Phillips, L.J., Carmona-Isunza, M.C., Vincze, O., Zefania, S., Miller, T.E.X., Küpper, C., Székely, T.*, Hoffman, J.I.* & Krüger, O.*  Demographic causes of adult sex ratio variation and their consequences for parental cooperation.  Nature Communications, 9: 1651.  Doi: 10.1038/s41467-018-03833-5 pdf Supplementary information pdf * Joint senior authors

2017

95) Eberhart-Phillips, L.J., Küpper, C., Miller, T.E., Cruz-López, M., Maher, K., dos Remedios, N., Stoffel, M.A., Hoffman, J.I.*, Krüger, O.* & Székely, T.*  Sex-specific early survival drives adult sex ratio bias in snowy plovers and impacts mating system and population growth.  Proceedings of the National Academy of Sciences of the United States of America, 114: E5474-E5481.  Doi: 10.1073/pnas.1620043114   pdf Supplementary Information pdf R code pdf * Joint senior authors

94) Krause, E.T., Krüger, O. & Hoffman, J.I.  The influence of inherited plumage colour morph on morphometric traits and breeding investment in zebra finches (Taeniopygia guttata).  PLoS ONE, 12: e0188582. Doi: 10.1371/journal.pone.0188582 pdf

93) Klimova, A., Hoffman, J.I.*, Guttierez-Rivera, J., Leon de la Luz, J. & Ortega-Rubio, A. Molecular genetic analysis of two relict desert palm genera, Washingtonia and Brahea, from Baja California and Guadalupe Island.  Ecology and Evolution, 7: 4919-4935.  Doi: 10.1002/ece3.3036   pdf * Corresponding author

92) Maher, K., Eberhart-Phillips, L.J., Kosztolányi, A., Carmona-Isunza, M.C., Cruz-López, M., Zefania, S., St Claire, J., Alrashidi, M., Weston, M.A., Serrano-Meneses, M.A., Krüger, O., Hoffman, J.I., Székely, T., Burke, T., Küpper, C.  High fidelity: Genetic mating systems of seven Charadrius plovers reveals low rates of extra-pair fertilisations.  Journal of Avian Biology, 48: 910-920. Doi: 10.1111/jav.01263 pdf  Journal cover pdf

91) Martínez-de la Puente, J. Eberhart-Phillips, L.J., Carmona, C., Zefania, S., Navarro, M.J., Hoffman, J.I., Kruger, O., Székely, T. & Figuerola, J. Extremely low Plasmodium prevalence in wild plovers and coursers from Cape Verde and Madagascar.  Malaria Journal, 16: 243.  Doi: 10.1186/s12936-017-1892-y   pdf

90) Vendrami, D.L.J., Telesca, L., Schweyen, H., Weiss, M., Fawcett, K., Lehmann, K., Clark, M.S., Leese, F., McMinn, C., Moore, H. & Hoffman, J.I.  RAD sequencing resolves fine-scale population structure in a benthic invertebrate: implications for understanding phenotypic plasticity.  Royal Society Open Science, 4: 160548.  Doi: 10.1098/rsos.160548   pdf

89) Krüger, O., Korsten, P. & Hoffman, J.I. The rise of behavioural genetics and the transition to behavioural genomics and beyond. American Psychological Association Handbook of Comparative Psychology, Chapter 18: 365-379. ISBN: 978-1-4338-2348-0   pdf

88) Baxter, S., Hoffman, J.I., Tregenza, T., Wedell, N. & Hosken, D.J. EB Ford revisited: assessing the long-term stability of wing-spot patterns and the population genetic structure of meadow brown butterflies from the Isles of Scilly. Heredity, 118: 322-329.  Doi: 10.1038/hdy.2016.94   pdf

2016

87) Humble, E., Forcada, J. & Hoffman, J.I.   Transcriptomic SNP discovery for custom genotyping arrays: influence of the type of sequence data, SNP calling method and genotyping technology on the probability of validation success.  BMC Research Notes, 9: 418. Doi: 10.1186/s13104-016-2209-x pdf

86) Hoffman, J.I., Kowalski, G.J., Klimova, A., Staniland, I.J., Eberhart-Phillips, L.J., Trillmich, F.T. & Baylis, A.M.M.  Population structure and historical demography of South American sea lions provide insights into the catastrophic decline of a marine mammal population.  Royal Society Open Science, 3 : 160291. Doi: 10.1098/rsos.160291 pdf

85) Peters, L., Humble, E., Kröcker, N., Fuchs, B., Forcada, J. & Hoffman, J.I.  Born blonde: a recessive loss of function mutation in the melanocortin 1 receptor is associated with cream coat colouration in Antarctic fur seals.  Ecology and Evolution,  6: 5705-5717. Doi: 10.1002/ece3.2290 pdf

84) Mueller, A.K., Chakarov, N., Krüger, O. & Hoffman, J.I.  Long-term effective population size dynamics of an intensively monitored vertebrate population.  Heredity, 117: 290–299. Doi: 10.1002/ece3.2290 pdf

83) Hoffman, J.I.  Archive computer code with raw data.  Nature, 534: 326.  Doi: 10.1038/534326d pdf

82) Fietz, K., Galatius, A., Teilmann, J., Dietz, R., Frie, A.K., Klimova, A., Palsbøll, P.J., Jensen, L.F., Graves, J.A., Hoffman, J.I. & Olsen, M.T.  Shift of grey seal subspecies boundaries in response to climate, culling and conservation.  Molecular Ecology, 25: 4097–4112.  Doi: 10.1111/mec.13748 pdf Journal cover pdf

81) Shah, A., Schielzeth, H., Albersmeier, A., Kalinowski, J. & Hoffman, J.I.  High throughput sequencing and graph-based cluster analysis facilitate microsatellite development from a complex genome.  Ecology and Evolution, 6: 5718–5727.  Doi: 10.1002/ece3.2305 pdf

80) Stoffel, M.A., Esser, M., Kardos, M., Humble, E., Nichols, H.J., David, P. & Hoffman, J.I.  InbreedR: An R package for the analysis of inbreeding based on genetic markers.  Methods in Ecology and Evolution, 7: 1331–1339.  Doi: 10.1111/2041-210X.12588 pdf Supplementary Information pdf

79) Baylis, A.M.M., Kowalski, G., Voigt, C., Orben, R.A., Staniland, I.J. & Hoffman, J.I.   Pup vibrissae stable isotopes reveal geographic differences in adult female southern sea lion habitat use during gestation.  PLoS ONE, 11: e0157394.  Doi: 10.1371/journal.pone.0157394 pdf

78) Vendrami, D.L.J., Shah, A., Telesca, L. & Hoffman, J.I. Mining the transcriptomes of four commercially important shellfish species for single nucleotide polymorphisms associated with biomineralisation genes.  Marine Genomics Special Issue “Cells to Shells”, 27: 17-23.  Doi: 10.1016/j.margen.2015.12.009 pdf

77) Humble, E., Martinez-Barrio, A., Forcada, J., Trathan, P.N., Thorne, M.A.S., Wolf, J.B.W.* & Hoffman, J.I.* A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them.  Molecular Ecology Resources, 16: 909-921. Doi: 10.1111/1755-0998.12502 pdf * Joint senior authors

76) Meise, K., Von Englehardt, N., Forcada, J., Hoffman, J.I.  Offspring hormones reflect the maternal prenatal social environment: potential for foetal programming?  PLoS ONE, 11: e0145352.  Doi: 10.1371/journal.pone.0145352 pdf

2015

75) Pauli, M., Chakarov, N., Rupp, O., Kalinowski, J., Goessmann, A., Sorenson, M., Krüger, O. & Hoffman, J.I. De novo assembly of the dual transcriptomes of a polymorphic raptor species and its malarial parasite.  BMC Genomics, 16: 1038. Doi: 10.1186/s12864-015-2254-1 pdf

74) Stoffel, M., Caspers, B.A., Forcada, J., Giannakara, A., Baier, M.C., Eberhart-Phillips, L.J., Müller, C. & Hoffman, J.I. (2015) Chemical fingerprints encode mother-offspring similarity, colony membership, relatedness and genetic quality in fur seals. Proceedings of the National Academy of Sciences of the United States of America, 112: E5005-E5012. Doi:10.1073/pnas.1506076112 pdf Supplementary Information pdf R code pdf Journal cover pdf Commentary articles in PNAS pdf and JEB pdf

73) Lopes, F.R.V., Hoffman, J.I., Valati, V.H., Bonatto, S., Wolf, J.B.W., Trillmich, F. & Oliveira, L.R. Fine-scale matrilineal population structure in the Galápagos fur seal and its implications for conservation management. Conservation Genetics, 16: 1099-1113. Doi: 10.1007/s10592-015-072501 pdf

72) Peck, L.S., Thorne, M.A.S., Hoffman, J.I., Morley, S.A. & Clark, M.S. Variability among individuals is generated at the gene expression level. Ecology, 96: 2004-2014. Doi: 10.1890/14-0726.1 pdf

71) Eberhart-Phillips, L.J., Hoffman, J.I., Kamrad, K., Zefania, S., Székely, T. & Bruford, M.W. Contrasting genetic diversity and population structure among three sympatric Madagascan shorebirds: parallels with rarity, endemism, and dispersal. Ecology and Evolution, 5: 997-1010. Doi: 10.1002/ece3.1393 pdf

70) Chakarov, N., Linke, B., Boerner, M., Goessmann, A., Krüger, O. & Hoffman, J.I. Apparent vector-mediated parent-to-offspring transmission in an avian malaria-like parasite. Molecular Ecology, 24: 1355-1363. Doi: 10.1111/mec.13115 pdf

2014

69) Nichols, H.J., Cant, M., Hoffman, J.I. & Sanderson, J.L. Evidence for frequent incest in a cooperatively breeding mammal. Biology Letters, 23: 20140898. Doi: 10.1098/rsbl.2014.0898 pdf

68) Klimova, A., Munguia-Vega, A., Hoffman, J.I. & Culver, M. Genetic diversity and historical demography of two endangered captive pronghorn subspecies from the Sonoran Desert. Journal of Mammalogy, 95: 1263-1277. Doi: 10.1644/13-MAMM-A-321pdf

67) Klimova, A., Fietz, K., Olsen, M.T., Harwood, J., Amos, W. & Hoffman, J.I. Global population structure and demographic history of the grey seal. Molecular Ecology, 23: 3999-4017. Doi: 10.1111/mec.12850 pdf

66) Forcada, J. & Hoffman, J.I. (2014) Climate change selects for heterozygosity in a declining fur seal population. Nature, 511: 462-465. Doi: 10.1038/nature13542 pdf Supplementary information pdf Journal cover pdf Editorial pdf News and views pdf

65) Hoffman, J.I., Simpson, F., David, P., Rijks, J.M., Kuiken, T., Thorne, M.A.S., Lacey, R.C. & Dasmahapatra, K.K.  High-throughput sequencing reveals inbreeding depression in a natural population. Proceedings of the National Academy of Sciences of the United States of America, 111: 3775-3780. Doi: 10.1073/pnas.1318945111 pdf Supplementary information pdf Journal cover pdf
Access the recommendation on F1000Prime

64) Krüger, O., Wolf, J.B.W., Jonker, R.M., Hoffman, J.I. & Trillmich, F. Disentangling the contribution of sexual selection and ecology to the evolution of size dimorphism in pinnipeds. Evolution, 68: 1485–1496. Doi: 10.1111/evo.12370 pdfJournal cover pdf

63) Hoffman, J.I., Krause, E.T., Lehmann, K. & Krüger, O.   MC1R genotype and plumage colouration in the zebra finch: population structure generates artefactual associations. PLoS One, 9: e86519. Doi: 10.1371/journal.pone.0086519 pdf

62) Bonin, C.A., Goebel, M.E., Hoffman, J.I. & Burton, R.S.   High male reproductive skew in a low density Antarctic fur seal (Arctocephalus gazella) breeding colony. Behavioural Ecology, 68: 597-604. Doi: 10.1007/s00265-013-1674-7 pdf

2013

61) Székely, T., Hoffman, J.I., & Krüger, O.  Why do males care for their competitor’s offspring? Animal Behaviour, 86: e1-e2. Doi: 10.1016/j.anbehav.2013.10.004 pdf

60) Kurvers, R.H.J.M., Adamczyk, V.M.A.P., Kraus, R.H.S., Hoffman, J.I., van der Jeug, H., van Wieren, S.E., Amos, W., Prins, H.H.T. & Jonkers, R.  Contrasting context-dependence of familiarity and kinship in animal social networks. Animal Behaviour, 86: 993-1001. Doi: 10.1016/j.anbehav.2013.09.001 pdf

59) Chakarov, N., Jonker, R.M., Boerner, M., Hoffman, J.I. & Kruger, O.   Variation at phenological candidate genes correlates with timing of dispersal and plumage morph in a sedentary bird of prey. Molecular Ecology, 22: 5430-5440. Doi: 10.1111/mec.12493 pdf

58) Boerner, M., Hoffman, J.I., Amos, W., Chakarov, N. & Krüger, O.  No correlation between multilocus heterozygosity and fitness in the common buzzard despite heterozygote advantage for plumage colour. Journal of Evolutionary Biology, 26: 2233-2243. Doi: 10.1111/jeb.12221 pdf

57) Bonin, C.A., Goebel, M.E., Forcada, J. & Burton, R.S. & Hoffman, J.I.  Unexpected genetic differentiation between recently recolonised populations of a long lived and highly vagile marine mammal. Ecology and Evolution, 3: 3701-3712. Doi: 10.1002/ece3.732 pdf

56) Hoffman, J.I., Thorne, M.A.S., McEwing, R., Forcada, J. & Ogden, R.  Cross-amplification and validation of SNPs conserved over 44 million years between seals and dogs. PLoS ONE, 8: e68365. Doi: 10.1371/journal.pone.0068365 pdf

55) Caspers, B.A., Hoffman, J.I., Kohlmeyer, P., Krüger, O. & Kraus, T.  Olfactory imprinting as a mechanism for kin recognition in zebra finches. Animal Behaviour, 86: 85-90. Doi: 10.1016/j.anbehav.2013.04.015 pdf

54) Hoffman, J.I., Clarke, A., Clark, M.S., Fretwell, P. & Peck, L.   Hierarchical population genetic structure in a direct developing Antarctic marine invertebrate. PLoS ONE, 8: e63954. Doi: 10.1186/1471-2164-14-52 pdf

53) Hoffman, J.I., Thorne, M.A.S., Trathan, P.N. & Forcada, J.   Transcriptome of the dead: characterisation of immune genes and marker development from necropsy samples in a free-ranging marine mammal. BMC Genomics, 14: 52. Doi: 10.1186/1471-2164-14-52 pdf

52) Phillips, C.D., Hoffman, J.I., George, J.C., Suydam, R.S., Huebinger , R.M., Patton, J.C. & Bickham, J.W.   Molecular insights into the historical demography of bowhead whales: understanding the evolutionary basis of contemporary management practices. Ecology and Evolution, 3: 18-37. Doi: 10.1002/ece3.374 pdf

2012

51) Nichols, H.J., Jamie, G.A., Jordan, N., Cant, M.A. & Hoffman, J.I.   Fine-scale spatiotemporal patterns of genetic variation reflect budding dispersal coupled with strong natal philopatry in a cooperatively breeding mammal. Molecular Ecology, 21: 5348-5362. Doi: 10.1111/mec.12015 pdf

50) Harper, L., Morley, S., Hoffman, J.I., Clark, M.S. & Peck, L.   Iceberg scour and shell damage in the Antarctic bivalve Laternula elliptica. PLoS ONE, 7: e46341. Doi: 10.1371/journal.pone.0046341 pdf

49) da Assunção Soares Franco, M., Hoffman, J.I., Harwood, J. & Amos, W.  MHC genotype and near-deterministic mortality in grey seals. Nature Scientific Reports, 2: 659. Doi: 10.1038/srep00659 pdf

48) Hoffman, J.I., Tucker, R., Clark, M.S., Forcada, J., Slate, J.   Rates of assay success and genotyping error when single nucleotide polymorphism genotyping in non-model organisms: a case study in the Antarctic fur seal. Molecular Ecology Resources, 16: 861-872. Doi: 10.1111/j.1755-0998.2012.03158.x pdf

47) Hoffman, J.I., Peck, L.S., Amos, W., Clark, M.S.   Widespread amplification of Amplified Fragment Length Polymorphisms (AFLPs) in marine Antarctic animals. Polar Biology, 35: 919-929. Doi: 10.1007/s00300-011-1139-2 pdf

46) Hoffman, J.I.  Clarke, A., Clark, M.S., Fretwell, P., Linse, K. & Peck, L.  Unexpected fine-scale population structure in a broadcast-spawning Antarctic marine mollusc. PLoS ONE, 7: e32415. Doi: 10.1371/journal.pone.0032415 pdf

45) Smith, E., Hoffman, J.I., Amos, W., Green, L.E. Association of candidate microsatellite heterozygosity with footrot in domestic sheep. Livestock Science, 143: 293-299. Doi: 10.1016/j.livsci.2011.10.009 pdf

44) Hoffman, J.I. & Forcada, J. Extreme natal philopatry in female Antarctic fur seals (Arctocephalus gazella). Mammalian Biology, 77: 71-73. Doi: 10.1016/j.mambio.2011.09.002 pdf

2011

43) Hoffman, J.I., Grant, S.M., Forcada, J. & Phillips, C.D. Bayesian inference of a historical genetic bottleneck in a heavily exploited marine mammal. Molecular Ecology, 20: 3989-4008. Doi: 10.1111/j.1365-294X.2011.05248.x pdf Supplementary information pdf

42) Hoffman, J.I. & Nichols, H.J.  A novel approach for mining polymorphic microsatellite markers in silicoPLoS ONE, 6: e23283. Doi: 10.1371/journal.pone.0023283 pdf

41) Hoffman, J.I. Gene discovery in the Antarctic fur seal (Arctocephalus gazella) skin transcriptome. Molecular Ecology Resources, 11: 703-711. Doi: 10.1111/j.1755-0998.2011.02999.x pdf Journal cover pdf

40) Driscol, E., Hoffman J.I., Green, L.E. & Amos, W.  A preliminary study of genetic factors that influence susceptibility to tuberculosis in the British cattle herd. PloS ONE, 6: e18806. Doi: 10.1371/journal.pone.0018806 pdf

39) Amos W., Driscoll, E. & Hoffman, J.I. Candidate genes versus genomewide associations: which are better for detecting genetic susceptibility to infectious disease? Proceedings of the Royal Society, Series B, 278: 1183–1188. Doi: 10.1098/rspb.2010.1920 pdf

38) Hoffman, J.I., Clarke, A., Linse, K. & Peck, L. Effects of brooding and broadcasting reproductive modes on the population genetic structure of two Antarctic gastropod molluscs. Marine Biology, 158: 287–296. Doi: 10.1007/s00227-010-1558-6 pdf

37) Hoffman, J.I., Clarke, A.C., Linse, K. & Peck, L. Strong population genetic structure in a broadcast-spawning Antarctic marine invertebrate. Journal of Heredity, 102: 55–66. Doi: 10.1093/jhered/esq094 pdf

36) Cammen, K, Hoffman, J.I., Knapp, L.A., Harwood, J. & Amos, W. (2011). Geographic variation of the major histocompatibility complex in Eastern Atlantic grey seals (Halichoerus grypus). Molecular Ecology, 20: 740–752. Doi: 10.1111/j.1365-294X.2010.04975.x pdf

2010

35) Hoffman, J.I., Hanson, N., Forcada, J., Trathan, P.N. & Amos, W. Getting long in the tooth: a strong positive correlation between canine size and heterozygosity in the Antarctic fur seal Arctocephalus gazella. Journal of Heredity, 101: 527–538. Doi: 10.1093/jhered/esq04 pdf Journal cover pdf

34) Hoffman, J.I., Forcada, J. & Amos, W. Exploring the mechanisms underlying a heterozygosity-fitness correlation for canine size in the Antarctic fur seal Arctocephalus gazella. Journal of Heredity, 101: 539–552. Doi:10.1093/jhered/esq046 pdf

33) Hoffman, J.I., Peck L.S., Hillyard, G., Zieritz, A. & Clark, M.S. No evidence for genetic differentiation between Antarctic limpet Nacella concinna morphotypes. Marine Biology, 157: 765–778. Doi: 10.1007/s00227-009-1360-5 pdf

32) Hoffman, J.I., Munro, K., Amos, W. & Kilner, R.M. High rates of infidelity in the grey fantail Rhipidura albiscapa suggest that testis size may be a better correlate of extra-pair paternity than sexual dimorphism. Ibis, 152: 378–385. Doi: 10.1111/j.1474-919x.2009.01007.x pdf

31) Zieritz, A., Hoffman, J.I., Amos, W. & Aldridge D.C. Phenotypic plasticity and genetic isolation-by-distance in the freshwater mussel Unio pictorum (Mollusca: Unionoida). Evolutionary Ecology, 24: 923–938. Doi: 10.1007/s10682-009-9350-0 pdf

30) Amos, W. & Hoffman, J.I. Evidence that two main bottleneck events shaped modern human genetic diversity. Proceedings of the Royal Society, Series B, 277: 131–137. Doi: 10.1098/rspb.2009.1473 pdf

29) Dasmahapatra, K.K., Elias, M., Hill, R.I., Hoffman, J.I. & Mallet, J. Mitochondrial DNA barcoding detects some species that are real, and some that are not. Molecular Ecology Resources, 10: 264–273. Doi: 10.1111/j.1755-0998.2009.02763.x pdf

28) Skidmore, R., Leach, C., Hoffman, J.I., Amos, W. & Aldridge, D. Conservation Genetics of the Endangered Depressed River Mussel, Pseudanodonta complanata, using Amplified Fragment Length Polymorphism (AFLP) Markers. Aquatic Conservation: Marine and Freshwater Ecosystems, 20: 560–567. Doi: 10.1002/aqc.1131 pdf

27) Brammah, M., Hoffman J.I., Amos, W. & Davies N. Genetic divergence between and within two subspecies of Laudakia stellio on islands in the Greek Cyclades. The Herpetological Journal, 20: 91–98 pdf

2009

26) Hoffman, J.I., Dasmahapatra, K.K., Amos, W., Phillips, C.D., Gelatt, T.S. & Bickham, J.W. Contrasting patterns of genetic diversity at three different genetic markers in a marine mammal metapopulation. Molecular Ecology, 18: 2961–2978. Doi: 10.1111/j.1365-294X.2009.04246.x pdf

25) Hoffman, J.I. & Forcada, J. Genetic analysis of twinning in Antarctic fur seals (Arctocephalus gazella). Journal of Mammalogy, 90: 621–628. Doi: 10.1644/08-MAMM-A-264R1.1 pdf

24) Hoffman, J.I. A panel of new microsatellite loci for genetic studies of Antarctic fur seals and other otariid species. Conservation Genetics, 10: 989–992. Doi: 10.1007/s10592-008-9669-z pdf

23) Dasmahapatra, K.K., Hoffman, J.I. & mos, W. (2009). Pinniped phylogenetic relationships inferred using AFLP markers. Heredity, 103: 168–177. Doi: 10.1038/hdy.2009.25 pdf

22) Oliveira, L., Meyer, D., Hoffman, J.I., Majluf, P. & Morgante, J.S. Evidence of a genetic bottleneck in an El Nino affected population of South American fur seals, Arctocephalus australis. Journal of the Marine Biological Association of the United Kingdom, 89: 1717–1725. Doi: 10.1017/S0025315409000162 pdf

21) Parkes, K.A., Amos, W., Moore, N.W., Hoffman, J.I. & Moore, J. Population structure and speciation in the dragonfly Sympetrum striolatum / nigrescens: an analysis using AFLP markers. European Journal of Entomology, 106: 179–184 pdf

20) Temple, H.J., Hoffman, J.I. & Amos, W. Group structure, mating system and extra-group paternity in the cooperatively breeding White-breasted Thrasher Ramphocinclus brachyurus. Ibis, 151: 99–112. Doi: 10.1111/j.1474-919X.2008.00867.x pdf

2008

19) Hoffman, J.I., Dasmahapatra, K.K. & Nichols, H.J. Ten novel polymorphic dinucleotide microsatellite loci cloned from the Antarctic fur seal Arctocephalus gazella. Molecular Ecology Resources, 8: 459–461. doi: 10.1111/j.1471-8286.2007.01993.x pdf

18) Oliveira, L., Hoffman, J.I., Hingst-Zaher, E., Majluf, P., Muelbert, M.M.C., Amos, W. & Morgante, J.S. Morphological and genetic evidence for two Evolutionary Significant Units (ESUs) in the South American fur seal Arctocephalus australis. Conservation Genetics, 9: 1451–1466. Doi: 10.1007/s10592-007-9473-1 pdf

17) Rijks, J.M., Hoffman, J.I., Kuiken, T., Osterhaus, A.D.M.E. & Amos, W. Heterozygosity and lungworm burden in harbour seals (Phoca vitulina). Heredity, 100: 587-593. Doi: 10.1038/hdy.2008.18 pdf

2007

16) Hoffman, J.I., Forcada, J., Trathan, P.N. & Amos, W. Female fur seals show active choice for males that are heterozygous and unrelated. Nature, 445: 912–914. doi: 10.1038/nature05558 pdf Supplementary information pdf

15) Hoffman, J.I., Wolf, J.B.W. & Steinfartz, S. Ten novel dinucleotide microsatellite loci cloned from the Galapagos sea lion (Zalophus californianus wollebaeki) are polymorphic in other pinniped species. Molecular Ecology Notes, 7: 103–105. doi: 10.1111/j.1471-8286.2006.01544.x pdf

14) Amos, W., Hoffman, J.I., Frodsham, A., Zhang, L., Best, S. & Hill, A.V.S. Automated binning of microsatellite alleles: problems and solutions. Molecular Ecology Notes, 7: 10–14. doi: 10.1111/j.1471-8286.2006.01560.x pdf

2006

13) Hoffman, J.I., Trathan, P.N. & Amos, W. Genetic tagging reveals extreme site fidelity in territorial male Antarctic fur seals Arctocephalus gazella. Molecular Ecology, 15: 3841–3847. doi: 10.1111/j.1365-294X.2006.03053.x pdf

12) Hoffman, J.I., Matson, C., Amos, W. Loughlin, T.R. & Bickham, J.W. Deep genetic subdivision within a continuously distributed and highly vagile marine mammal, the Steller’s sea lion Eumetopias jubatus. Molecular Ecology, 15: 2821–2832. doi: 10.1111/j.1365-294X.2006.02991.x pdf

11) Hoffman, J.I., Forcada, J. & Amos, W. No relationship between microsatellite variation and neonatal fitness in Antarctic fur seals Arctocephalus gazella. Molecular Ecology, 15: 1995-2005. doi: 10.1111/j.1365-294X.2006.02894.x0 pdf

10) Temple, H.J., Hoffman, J.I. & Amos, W. Dispersal, philopatry and inter-group relatedness: fine-scale genetic structure in the white-breasted thrasher Ramphocinclus brachyurus. Molecular Ecology, 15: 3449–3458. doi:10.1111/j.1365-294X.2006.03006.x pdf

9) Jin, L., Temple, H. J., Hoffman, J.I., Tan, S. & Amos, W. Polymorphic microsatellite DNA markers for the White-breasted Thrasher, Ramphocinclus brachyurus. Molecular Ecology Notes, 6: 862–864. doi: 10.1111/j.1471-8286.2006.01375.x pdf

8) Jin, L., Munro, K., Tan, S. Hoffman, J.I. & Amos, W. Polymorphic microsatellite DNA markers for the grey fantail, Rhipidura albiscapa. Molecular Ecology Notes, 6: 75–76. doi: 10.1111/j.1471-8286.2005.01143.x pdf

≤2005

7) Hoffman, J.I. & Amos, W. (2005) Microsatellite genotyping errors: detection approaches, common sources and consequences for paternal exclusion. Molecular Ecology, 14: 599–612. doi: 10.1111/j.1365-294X.2004.02419.x pdf

6) Hoffman, J.I. & Amos, W. (2005) Does kin selection influence fostering behaviour in Antarctic fur seals (Arctocephalus gazella)? Proceedings of the Royal Society, Series B, 272: 2017–2022. doi: 10.1098/rspb.2005.31760 pdf

5) Hoffman, J.I., Boyd, I.L.B. & Amos, W. (2004) Exploring the relationship between parental relatedness and male reproductive success in the Antarctic fur seal Arctocephalus gazella. Evolution, 58(9): 2087–2099 pdf

4) Hoffman, J.I., Boyd, I.L.B. & Amos, W. (2003) Male reproductive strategy and the importance of maternal status in the Antarctic fur seal Arctocephalus gazella. Evolution, 57(8): 1917–1930 pdf

3) Webster, J.P., Hoffman, J.I. & Berdoy, M. (2003) Parasite resistance and mate choice–battle of the genders in a simultaneous hermaphrodite. Proceedings of the Royal Society, Series B, 270: 1481–1485 pdf

2) Webster, J.P., Davies, C., Hoffman, J.I. & Woolhouse, M.E.J. (2001) Population genetics of the schistosome intermediate host Biomphalaria pfeifferi in the Zimbabwean highveld: implications for co-evolutionary theory. Annals of Tropical Medicine and Parasitology, 95: 203–214
pdf

1) Hoffman, J.I., Webster, J.P., Ndamba, J. & Woolhouse, M.E.J. (1998) Extensive genetic variation revealed within Biomphalaria pfeifferi from one river system in the Zimbabwean highveld. Annals of Tropical Medicine and Parasitology, 92: 693–698 pdf