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.
≤2016 2017 2018 2019 2020 2021 2022 2023 2024 2025 2026
Highlights
Chen, R.S., Soulsbury, C., van Oers, K. & Hoffman, J.I. (2025) Early-life viability selection targets deleterious mutations in exons. Current Biology, 35: 5908–5914. Doi: 10.1016/j.cub.2025.10.043 
Supplementary information Journal cover
Chen, R.S., Soulsbury, C., Hench, K., van Oers, K. & Hoffman, J.I. (2025) Predicted deleterious mutations reveal the genetic architecture of male reproductive success in a lekking bird. Nature Ecology and Evolution, 9: 1924–1937. Doi: 10.1038/s41559-025-02802-8 Supplementary information
Hoffman, J.I., Vendrami, D.L.J., Hench, K., Chen, R., Stoffel, M.A., Kardos, M., Amos, W., Kalinowski, J., Rickert, D., Köhrer, K., Wachmeister, T., Goebel, M.E., Bonin, C., Gulland, F.M.D. & Dasmahapatra, K.K. (2024) Genomic and fitness consequences of a near-extinction event in the northern elephant seal. Nature Ecology and Evolution, 8: 2309–2324. Doi: 10.1038/s41559-024-02533-2 Supplementary information Journal cover
Clark, M.S.*, Hoffman, J.I.*, Peck, L.S.*, Bargelloni, L., Gande, D., Havermans, C, Meyer B., Patarnello, T., Phillips, T., Stoof-Leichsenring, K.R., Vendrami, D.L.J., Beck, A., Collins, G., Friedrich, M.W., Halanych, K.M., Masello, J.F., Nagel, R., Norén, K., Printzen, C., Ruiz, M.B., Wohlrab, S., Becker, B., Dumack, K., Ghaderiardakani, F., Glaser, K., Heesch, S., Held, C., John, U., Karsten, U., Kempf, S., Lucassen, M., Paijmans, A.J., Schimani, K., Wallberg, A., Wunder, L.C. & Mock, T.* (2023) Multi-omics for studying and understanding polar life. Nature Communications, 14: 7451. Doi: 10.1038/s41467-023-43209-y * Joint corresponding authors
Bergeron, L.A., Besenbacher, S., Zheng, J., Li, P., Bertelsen, M.F., Quintard, B., Hoffman, J.I., Li, Z., St. Leger, J., Shao, C., Stiller, J., Gilbert, M.T.P., Schierup, M.H. & Zhang, G. (2023) Evolution of the germline mutation rate across vertebrates. Nature, 615: 285–291. Doi: 10.1038/s41586-023-05752-y Recommended by Faculty Opinions and featured in Trends in Genetics spotlight article:
Schwarz, J.F.L., DeRango, E.J., Zenth, F., Kalberer, S., Hoffman, J.I., Mews, S. Piedrahita, P., Trillmich, F., Páez-Rosas, D., Thiboult, A. & Krüger, O. (2022) A stable foraging polymorphism buffers Galapagos sea lions against environmental change. Current Biology, 32: 1623–1628. Doi: 10.1016/j.cub.2022.02.007
Vendrami, D.L.J., Peck, L.S., Clark, M.S., Eldon, B., Meredith, M. & Hoffman, J.I. (2021) Sweepstake reproductive success and collective dispersal produce chaotic genetic patchiness in a broadcast spawner. Science Advances, 7: eabj4713. Doi: 10.1126/sciadv.abj4713 Supplementary information
Marshall, H.H., Johnstone, R.A., Thompson, F.J., Nichols, H.J., Wells, D., Hoffman, J.I., Kalema-Zikusoka, G., Sanderson, J.L., Vitikainen, E.I.K., Blount, J.D. & Cant, M.A. (2021) A veil of ignorance can promote fairness in a mammal society. Nature Communications, 12: 3717. Doi: 10.1038/s41467-021-23910-6 Supplementary information
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 Supplementary information
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
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 Supplementary information
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 Supplementary information * 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 Supplementary Information R code * 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 Supplementary Information R code Journal cover Commentary articles in PNAS and JEB
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 Supplementary information Journal cover Editorial News and views
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 Supplementary information Journal cover 
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 Supplementary information
2026
180) Van Benthem, K.J., Nagel, R., Beckmann, L.M., Hoffman, J.I. & Wittmann, M.J. (accepted). Can the marginal male hypothesis explain spatial density variation in pinnipeds? Scientific Reports.
179) Chen, R.S., Sepers, B., van Oers, K. & Hoffman, J.I. (accepted). The interplay between epigenetic mechanisms and deleterious mutations: implications for fitness, evolution and conservation. Philosophical Transactions of the Royal Society B Biological Sciences Special Issue “Ecological epigenetics at the intersection of behaviour and life history variation”.
178) Nicholl, M.H., Schubert, N., Alstrup, A.K.O., Höner, F., Nielsen, O.L., Höner, F., Hoffman J.I., Caspers, B.A., Spittau, B., Nichols, H.J., Winternitz, J.C. (in press). Histological analysis of the anal gland, an undescribed scent gland in banded mongooses, with implications for chemical communication. Journal of Zoology.
2025
177) Chen, R.S., Soulsbury, C., van Oers, K. & Hoffman, J.I. Early-life viability selection targets deleterious mutations in exons. Current Biology, 35: 5908–5914. Doi: 10.1016/j.cub.2025.10.043 Supplementary information Journal cover
176) Bonin, Vendrami, D.L.J., Goebel, M.E., Kienle, S.S., Hoffman, J.I. & Krause, D. Population genomics reveals trans-generational haul-out site fidelity in leopard seals. Scientific Reports, 15: 41627. Doi: 10.1038/s41598-025-25641-w
175) Schubert, N., Nichols, H.J., Mwanguhya, F., Businge, R., Kyambulima, S., Mwesige, K., Hoffman, J.I., Cant, M.A., Winternitz, J.C. Sex-dependent influence of major histocompatibility complex diversity on fitness in a social mammal. Molecular Ecology, 34: e70058. Doi: 10.1111/mec.70058 Supplementary information
174) Chen, R.S., Soulsbury, C., Hench, K., van Oers, K. & Hoffman, J.I. Predicted deleterious mutations reveal the genetic architecture of male reproductive success in a lekking bird. Nature Ecology and Evolution, 9: 1924–1937. Doi: 10.1038/s41559-025-02802-8 Supplementary information
173) Chen, R.S., Rizvi, T., Berthelsen, A.L., Paijmans, A.J., Maune, A.L., Caspers, B., Sepers, B., Damas-Moreira, I., Schnülle, A.I., Könker, J., Hoffman, J.I., de Lima, J., Tebbe, J., Gladow, K.-P., de Vries, L., Gilles, M., Schubert, N., Chakarov, N., Korsten, P., Botsidou, P., Kraus, S., Salazar, S., Stöhr, S., Jockusch, W., Maraci, Ö. How can we make scientific events more inclusive? Insights from Q&A sessions and surveys from an international conference. Ecology and Evolution, 15: e71588. Doi: 10.1002/ece3.71588
172) Botsidou, P., Schloter, M., Maraci, Ö., Gschwendtner, S., Nagel, R., Forcada, J. & Hoffman, J.I. Skin but not gut microbial communities in Antarctic fur seals vary with social density. Frontiers in Microbiology, 16: 1603500. Doi: 10.3389/fmicb.2025.1603500
171) Berthelsen, A.L., Paijmans, A.J., Forcada, J. & Hoffman, J.I. Sustainability in the laboratory: evaluating the reusability of microtiter plates for PCR and fragment detection. Royal Society Open Science, 12: 242226. Doi: 10.1098/rsos.242226 R code
170) Canitz, J., Kienle, S.S., van der Linde, K., Borras-Chavez, R., Sperou, E., Leahy, A., Rivera, S., Autenrieth, M., Hoffman, J.I., Bonin, C.A. Reference genome of the leopard seal (Hydrurga leptonyx), a Southern Ocean apex predator. Frontiers in Genetics, 16: 1561273. Doi: 10.3389/fgene.2025.1561273
169) Brejon Lamartinière, E., Tremble, K., Dentinger, B. & Hoffman, J.I. A haplotype-resolved chromosomal reference genome for the porcini mushroom Boletus edulis. G3: Genes | Genomes | Genetics, 15: jkaf069. Doi: 10.1093/g3journal/jkaf069
168) Chen, Y.-C., Vendrami, D.L.J., Huber, M.L., Handel, L.E.Y., Cooney, C.R., Hoffman, J.I. & Gossmann, T.I. Diverse evolutionary trajectories of mitocoding DNA in mammalian and avian nuclear genomes. Genome Research, 35: 1313–1324. Doi: 10.1101/gr.279428.124
167) Nichols, H.J., Caspers, B.A., Arbuckle, K., Bennett, N.C. & Hoffman, J.I. Volatile odours reflect breeding status but not social group membership in captive Damaraland mole-rats. Animal Behaviour special issue “Chemical Communication and Behaviour”, 222: 123015. Doi: 10.1016/j.anbehav.2024.10.029
2024
166) Pereira, H., Chakarov, N.†, Caspers, B.A., Gilles, M., Jones, W., Mijoro, T., Zefania, Székely, T.†, Krüger, O.†, & Hoffman, J.I.† The gut microbiota of three avian species living in sympatry. BMC Ecology and Evolution, 24: 144. Doi: 10.1186/s12862-024-02329-9 † Joint senior authors.
165) Hoffman, J.I., Vendrami, D.L.J., Hench, K., Chen, R., Stoffel, M.A., Kardos, M., Amos, W., Kalinowski, J., Rickert, D., Köhrer, K., Wachmeister, T., Goebel, M.E., Bonin, C., Gulland, F.M.D. & Dasmahapatra, K.K. Genomic and fitness consequences of a near-extinction event in the northern elephant seal. Nature Ecology and Evolution, 8: 2309–2324. Doi: 10.1038/s41559-024-02533-2 Supplementary information Journal cover
164) Pereira, H., Hoffman, J.I.†, Krüger, O.†, Czirják, G., Rinaud, T., Ottensmann, M., Gladow, K.-P., Caspers, B., Maraci, Ö., Kaiser, S. & Chakarov, N.† The gut microbiome-immune-brain axis in a wild vertebrate: dynamic interactions and health impacts. Frontiers in Microbiology, 15: 1413976. Doi: 10.3389/fmicb.2024.1413976 † Joint senior authors.
163) Hench, K., Vendrami, D.L.J., Forcada, J. & Hoffman, J.I. Refinement of the Antarctic fur seal (Arctocephalus gazella) reference genome increases continuity and completeness. G3: Genes | Genomes | Genetics, 14: jkae179. Doi: 10.1093/g3journal/jkae179 Supplementary information
162) Mattmüller, R., Thomisch, K., Hoffman, J.I. & van Opzeeland, I. Characterizing polar ocean soundscapes using ecoacoustic intensity and diversity metrics. Royal Society Open Science, 11: 231917. Doi: 10.1098/rsos.231917 Supplementary information
161) Brejon Lamartinière, E., Tremble, K.S., Dasmahapatra, K.K., Dentinger, B. & Hoffman, J.I. Runs of homozygosity reveal contrasting histories of inbreeding across global lineages of the edible porcini mushroom, Boletus edulis. Molecular Ecology, 33: e17470. Doi: 10.1111/mec.17470 Supplementary information
160) Nagel, R., Pohle, K., Jordán, L., Tuponja, I., Stainfield, C., Toscani, C., Fox-Clarke, C., Costantini, D., Czirják, G.A.†, Forcada, J.† & Hoffman, J.I.† Life-history stage influences immune investment and oxidative stress in response to environmental heterogeneity. Communications Biology, 7: 788. Doi: 10.1038/s42003-024-06499-6 † Joint senior authors.
159) Paijmans, A.J., Berthelsen, A.L., Christaller, F., Kröcker, N., Forcada, J. & Hoffman, J.I. Little evidence of inbreeding depression for birth mass, survival and growth in Antarctic fur seal pups. Scientific Reports, 14: 12610. Doi: 10.1038/s41598-024-62290-x R code Supplementary information
158) Pereira, H., Chakarov, N.†, Hoffman, J.I.†, Rinaud, T., Ottensmann, M., Gladow, K., Busche, T., Caspers, B., Maraci, Ö. & Krüger, O.† Early-life factors shaping the gut microbiota of Common buzzard nestlings. Animal microbiome, 6:27. Doi: 10.1186/s42523-024-00313-8 † Joint senior authors.
157) Tebbe, J., Havenstein, K., Forcada, J., Tiedemann, R., Caspers, B.A.† & Hoffman, J.I.† (2024). No evidence for a role of MHC class II genotype in the chemical encoding of heterozygosity and relatedness in Antarctic fur seals. Proceedings of the Royal Society, Series B, 291: 20232519. Doi: 10.1098/rspb.2023.2519 † Joint senior authors.
2023
156) Clark, M.S.*, Hoffman, J.I.*, Peck, L.S.*, Bargelloni, L., Gande, D., Havermans, C, Meyer B., Patarnello, T., Phillips, T., Stoof-Leichsenring, K.R., Vendrami, D.L.J., Beck, A., Collins, G., Friedrich, M.W., Halanych, K.M., Masello, J.F., Nagel, R., Norén, K., Printzen, C., Ruiz, M.B., Wohlrab, S., Becker, B., Dumack, K., Ghaderiardakani, F., Glaser, K., Heesch, S., Held, C., John, U., Karsten, U., Kempf, S., Lucassen, M., Paijmans, A.J., Schimani, K., Wallberg, A., Wunder, L.C. & Mock, T.* Multi-omics for studying and understanding polar life. Nature Communications, 14: 7451. Doi: 10.1038/s41467-023-43209-y * Joint corresponding authors
155) Forcada, J., Hoffman, J.I., Gimenez, O., Staniland, I.J., Bucktrout, P. & Wood, A.G. Ninety years of change, from commercial extinction to recovery, range expansion and decline for Antarctic fur seals at South Georgia. Global Change Biology, 29: 6867–6887. Doi: 10.1111/gcb.16947 Journal cover
154) Graiff, A., Braun, M., Driemel, A., Ebbing, J., Grossart, H.-P., Harder, T., Hoffman, J.I., Koch, B., Leese, F., Piontek, J., Scheinert, M., Quillfeldt, P., Zimmermann, J. & Karsten, U. Big data in polar sciences – current status, deficiencies and future perspective. Polarforschung, 91: 45–57. Doi: 10.5194/polf-91-45-2023
153) Hoffman, J.I. & Vendrami, D.L.J. Population genetics of Mya arenaria. In: The Soft-shell Clam Mya arenaria: Biology, Fisheries, and Mariculture, Chapter 5, pp. 89–102. American Fisheries Society. Doi: 10.47886/9781934874745.ch4
152) Bender, A.N., Krause, D.J., Goebel, M.E., Hoffman, J.I., Lewallen, E.A. & Bonin, C.A. Genetic diversity and demographic history of the leopard seal: a Southern Ocean top predator. PLoS ONE, 18: e0284640. Doi: 10.1371/journal.pone.0284640
151) Vitikainen, E.I.K., Meniri, M., Marshall, H.H., Thompson, F.J., Businge, R., Mwanguhya, F., Kyabulima, S., Mwesige, K., Ahabonya, S., Sanderson, S.L., Kalema-Zikusoka, G., Hoffman, J.I., Wells, D., Nichols, H.J., Blount, J.D., Cant, M.A. The social formation of fitness: lifetime consequences of prenatal nutrition versus postnatal care in a wild mammal population. Philosophical Transactions of the Royal Society B Biological Sciences Special Issue “The Evolutionary Ecology of Inequality” (Eds. Smith, E.A., Codding, B. & Smith, J.), 378: 20220309. Doi: 10.1098/rstb.2022.0309
150) Hoffman, J.I., Heesch, S. & Clark, M.S. Editorial: polar genomics in a changing world. Genes special issue “Polar Genomics”, 14: 1395. Doi: 10.3390/genes14071395
149) Lawson, R.M., Hayle, M.G.B., Shechonge, A.H., Nyingi, D.W., Ford, A.G.P., Butlin, R., Hoffman, J.I., Day, J.J., Turner, G.F. & Dasmahapatra, K.K. Sympatric and allopatric Alcolapia soda lake cichlid species show similar levels of assortative mating. Frontiers in Ecology and Evolution, 11: 1150083. Doi: 10.3389/fevo.2023.1150083
148) Bergeron, L.A., Besenbacher, S., Zheng, J., Li, P., Bertelsen, M.F., Quintard, B., Hoffman, J.I., Li, Z., St. Leger, J., Shao, C., Stiller, J., Gilbert, M.T.P., Schierup, M.H. & Zhang, G. Evolution of the germline mutation rate across vertebrates. Nature, 615: 285–291. Doi: 10.1038/s41586-023-05752-y Recommended by Faculty Opinions and featured in Trends in Genetics spotlight article
147) Toro-Valdivieso, C., Jugdaohsingh, R., Powell, J., Hoffman, J.I., Forcada, J., Moore, C., & Blacklaws, B. Heavy metal contamination in pristine environments: lessons from the Juan Fernandez fur seal (Arctocephalus philippii philippii). Royal Society Open Science, 10: 2237. Doi: 10.1098/rsos.221237
146) Chen, R., Soulsbury, C., Lebigre, C., van Oers, K. & Hoffman, J.I. Effects of hunting on genetic diversity, inbreeding and dispersal in Finnish black grouse (Lyrurus tetrix). Evolutionary Applications, 16: 625-637. Doi: 10.1111/eva.13521 Supplementary information
145) Vendrami, D.L.J., Hoffman, J.I. & Wilding, C.S. Heterogeneous genomic divergence landscape in two commercially important European scallop species. Genes, 14: 14. Doi: 10.3390/genes14010014
144) Tremble, K., Hoffman, J.I. & Dentinger, B.T.M. Contrasting continental patterns of adaptive population divergence in the holarctic ectomycorrhizal fungus Boletus edulis. New Phytologist, 237: 295–309. Doi: 10.1111/nph.18521
2022
143) Tebbe, J., Ottensmann, M., Havenstein, K., Efstratiou, A., Lenz, T., Caspers, B., Forcada, J., Tiedemann, R. & Hoffman, J.I. Intronic primers uncover unexpectedly high major histocompatibility complex diversity in Antarctic fur seals. Scientific Reports, 12: 17933. Doi: 10.1038/s41598-022-21658-7 R code
142) Vendrami, D.L.J., Gossmann, T.I., Chakarov, N., Paijmans, A.J., Litzke, V., Eyre-Walker, A., Forcada, J. & Hoffman, J.I. Signatures of selection on mitonuclear integrated genes uncover hidden mitogenomic variation in fur seals. Genome Biology and Evolution, 14: evac104. Doi: doi.org/10.1093/gbe/evac104 Supplementary information
141) Klimova, A., Sánchez, S.V., Gutiérrez, R.J. & Hoffman, J.I. The genetic consequences of captive breeding, environmental change and human exploitation in the endangered peninsular pronghorn. Scientific Reports, 12: 11253. Doi: 10.1038/s41598-022-14468-4 Supplementary information
140) Nagel, R., Coleman, J., Stainfield, C., Forcada, J.* & Hoffman, J.I.* Observations of giant petrels attacking and killing Antarctic fur seal pups. Aquatic Mammals, 48(6): 509–512. Doi: 10.1578/AM.48.6.2022.509 * Joint senior authors
139) Schwarz, J.F.L., DeRango, E.J., Zenth, F., Kalberer, S., Hoffman, J.I., Mews, S. Piedrahita, P., Trillmich, F., Páez-Rosas, D., Thiboult, A. & Krüger, O. A stable foraging polymorphism buffers Galapagos sea lions against environmental change. Current Biology, 32: 1623–1628. Doi: 10.1016/j.cub.2022.02.007
138) Hoffman, J.I., Chen, R., Vendrami, D.L.J., Paijmans, A.J., Dasmahapatra, K.K. & Forcada, J. Demographic reconstruction of Antarctic fur seals supports the krill surplus hypothesis. Genes Special Issue “Polar Genomics”, 13: 541. Doi: 10.3390/genes13030541
137) Nagel, R., Kaiser, S., Stainfield, C., Toscani, C., Fox-Clarke, C., Paijmans, A.J., Costa, C., Vendrami, D.L.J., Forcada, J.* & Hoffman, J.I.* Low heritability and high phenotypic plasticity of salivary cortisol in response to environmental heterogeneity in fur seals. Ecology and Evolution, 12: e8757. Doi: 10.1002/ece3.8757 R code * Joint senior authors
136) Liu, X., Schjøtt, S.R., Granquist, S.M., Rosing-Asvid, A., Dietz, R., Teilmann, J., Galatius, A., Cammen, C., O´Corry-Crowe, G., Harding, K., Härkönen, T., Hall, A., Carroll, E.L., Kobayashi, Y., Hammill, M., Stenson, G., Frie, A.K., Lydersen, C., Kovacs, K.M., Andersen, L.W., Hoffman, J.I., Goodman, S.J., Vieira, F.G., Heller, R., Moltke, I. & Olsen, M.T. Origin and expansion of the world’s most widespread pinniped: range-wide population genomics of the harbour seal (Phoca vitulina). Molecular Ecology, 31: 1682–1699. Doi: 10.1111/mec.16365
135) Jones, W., Eberhart-Phillips, Freckleton, R., Hoffman, J.I., Krüger, O., Sandercock, B., Vincze, O., Zefania, S. & Székely, T. Exceptionally high apparent adult survival in a Malagasy plover community. Journal of Avian Biology, 1: e02911. Doi: 10.1111/jav.02911 Journal cover
134) Nichols, H.J., Fuchs, B., Paijmans, A.J., Lewis, G., Bonin, C., Goebel, M.* & Hoffman, J.I.*, Where are the beachmasters? Unexpectedly weak polygyny among southern elephant seals on a South Shetland island. Journal of Zoology, 316: 104–117. Doi: 10.1111/jzo.12936 * Joint senior authors.
2021
133) Vendrami, D.L.J., Peck, L.S., Clark, M.S., Eldon, B., Meredith, M. & Hoffman, J.I. Sweepstake reproductive success and collective dispersal produce chaotic genetic patchiness in a broadcast spawner. Science Advances, 7: eabj4713. Doi: 10.1126/sciadv.abj4713 Supplementary information
132) Cleary, A.C., Hoffman, J.I., Forcada, J., Lydersen, C., Lowther, A.D. & Kovaks, K.M. 50,000 years of ice and seals: impacts of the last glacial maximum on Antarctic fur seal populations. Ecology and Evolution,11: 14003–14011. Doi: 10.1002/ece3.8104 Supplementary information
131) Khera, M., Arbuckle, K., Hoffman, J.I., Sanderson, J.L., Cant, M. & Nichols, H. Cooperatively breeding banded mongooses do not avoid inbreeding through familiarity-based kin recognition. Behavioural Ecology and Sociobiology, 75: 135. Doi: 10.1007/s00265-021-03076-3
130) Nagel, R., Mews, S., Adam, T., Stainfield, C., Fox-Clarke, C., Toscani, C., Langrock, R., Forcada, J. & Hoffman, J.I. Movement patterns and activity levels are shaped by the neonatal environment in Antarctic fur seal pups. Scientific Reports, 11: 14323. Doi: 10.1038/s41598-021-93253-1 Supplementary information R code
129) Marshall, H.H., Johnstone, R.A., Thompson, F.J., Nichols, H.J., Wells, D., Hoffman, J.I., Kalema-Zikusoka, G., Sanderson, J.L., Vitikainen, E.I.K., Blount, J.D. & Cant, M.A. A veil of ignorance can promote fairness in a mammal society. Nature Communications, 12: 3717. Doi: 10.1038/s41467-021-23910-6 Supplementary information
128) Michalek, K., Vendrami, D.L.J, Bekaert, M., Wilson, J., Telesca, L., Green, D.H., Wilding, T.A., Last, K.S. & Hoffman, J.I. Mytilus trossulus introgression and its consequences for shell traits in longline cultivated mussels. Evolutionary Applications, 14: 1830–1843. Doi: 10.1111/eva.13245 Supplementary information
127) Peart, C.R., Williams, C., Pophaly, S.D., Johnson, J., Neely, B.A., Gulland, F., Adams, D., Ng, B.L., Cheng, W., Goebel, M.E., Fedrigo, O., Haase, B., Mountcastle, J., Fungtammasan, A., Formenti, G., Collins, J., Wood, J., Sims, Y., Torrace, J., Tracey, A., Howe, K., Rhie, A., Hoffman, J.I., Johnson, J., Jarvis, E.D., Breen, M. & Wolf, J.B.W. Hi-C scaffolded short-and long-read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution. Molecular Ecology Resources, 21: 2455– 2470. DOI: 10.1111/1755-0998.13443
126) Nagel, R., Stainfield, C., Fox-Clarke, C., Toscani, C., Forcada, J.† & Hoffman, J.I.† Evidence for an Allee effect in a declining fur seal population. Proceedings of the Royal Society, Series B, 288: 20202882. Doi: 10.1098/rspb.2020.2882 Supplementary information R code Journal cover † Joint senior authors.
125) Wells, D.A., Cant, M.A., Thompson, F.J., Marshall, H.H., Vitikainen, E.I.K., Hoffman, J.I.* & Nichols, H.J.* Extra-group paternity varies with proxies of relatedness in a social mammal with high inbreeding risk. Behavioural Ecology, 32(1): 94–104. Doi:10.1093/beheco/araa105 * Joint senior authors
2020
124) Tebbe, J., Humble, E., Stoffel, M.A., Forcada, J., Müller, C., Caspers, B.A. & Hoffman, J.I. Chemical patterns of colony membership and mother-offspring similarity in Antarctic fur seals are reproducible. PeerJ, 8: e10131. Doi: 10.7717/peerj.10131 R code
123) Wells, D.A. Cant, M.A., Hoffman, J.I.* & Nichols, H.J.* Inbreeding depresses altruism in a cooperative society. Ecology Letters, 23:1460-1467. Doi: 10.1111/ele.13578 Supplementary information Journal cover * 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. Deciphering mollusc shell production: the roles of genetic mechanisms through to ecology, aquaculture and biomimetics. Biological Reviews, 95: 1812–1837. Doi: 10.1111/brv.12640
121) Humble, E., Paijmans, A.J., 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 Supplementary information
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 Supplementary Information R code
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 Supplementary information
118) Shah, A., Hoffman, J.I. & Schielzeth, H. 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, 12: 1180–1193. Doi: 10.1093/gbe/evaa119
117) Vendrami, D.L.J., De Noia, M., Telesca, L. & Hoffman, J.I. Genome-wide insights into introgression and its consequences for genome-wide heterozygosity in the Mytilus species complex across Europe. Evolutionary Applications, 13: 2130-2142. Doi: 10.1111/eva12974
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 Supplementary information News and views article in Molecular Ecology * Joint 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 Supplementary Information
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 arenaria. Genes special issue “Genetic diversity in marine populations”, 11: 298. Doi: 10.3390/genes11030298 * 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
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
111) Grosser, S., Sauer, J., Paijmans, A.J., 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 Supplementary Information R code Journal cover * 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
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 R code
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
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
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
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
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 Supplementary information
103) Hoffman, J.I., Bauer, E., Paijmans, A.J., 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 R code
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 Supplementary Information Journal cover Featured article
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 R code * 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 Supplementary Information * 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 * 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
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 Spotlight article in Functional Ecology
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 Supplementary information * 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 Supplementary Information R code * 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
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 * 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 Journal cover
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
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
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
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
2016 and previous
87) Humble, E., Forcada, J. &Hoffman, J.I. (2016) 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
86) Hoffman, J.I., Kowalski, G.J., Klimova, A., Staniland, I.J., Eberhart-Phillips, L.J., Trillmich, F.T. & Baylis, A.M.M. (2016) 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
85) Peters, L., Humble, E., Kröcker, N., Fuchs, B., Forcada, J. &Hoffman, J.I. (2016) 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
84) Mueller, A.K., Chakarov, N., Krüger, O. & Hoffman, J.I. (2016) Long-term effective population size dynamics of an intensively monitored vertebrate population. Heredity, 117: 290–299. Doi: 10.1002/ece3.2290
83) Hoffman, J.I. (2016) Archive computer code with raw data. Nature, 534: 326. Doi: 10.1038/534326d
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. (2016) Shift of grey seal subspecies boundaries in response to climate, culling and conservation. Molecular Ecology, 25: 4097–4112. Doi: 10.1111/mec.13748 Journal cover
81) Shah, A., Schielzeth, H., Albersmeier, A., Kalinowski, J. & Hoffman, J.I. (2016) 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
80) Stoffel, M.A., Esser, M., Kardos, M., Humble, E., Nichols, H.J., David, P. & Hoffman, J.I. (2016) 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 Supplementary Information
79) Baylis, A.M.M., Kowalski, G., Voigt, C., Orben, R.A., Staniland, I.J. & Hoffman, J.I. (2016) 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
78) Vendrami, D.L.J., Shah, A., Telesca, L. &Hoffman, J.I. (2016) 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
77) Humble, E., Martinez-Barrio, A., Forcada, J., Trathan, P.N., Thorne, M.A.S., Wolf, J.B.W.* & Hoffman, J.I.* (2016) 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 * Joint senior authors
76) Meise, K., Von Englehardt, N., Forcada, J., Hoffman, J.I. (2016) Offspring hormones reflect the maternal prenatal social environment: potential for foetal programming? PLoS ONE, 11: e0145352. Doi: 10.1371/journal.pone.0145352
75) Pauli, M., Chakarov, N., Rupp, O., Kalinowski, J., Goessmann, A., Sorenson, M., Krüger, O. & Hoffman, J.I. (2015) 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
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 Supplementary Information R code Journal cover Commentary articles in PNAS and JEB
73) Lopes, F.R.V., Hoffman, J.I., Valati, V.H., Bonatto, S., Wolf, J.B.W., Trillmich, F. & Oliveira, L.R. (2015) 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
72) Peck, L.S., Thorne, M.A.S., Hoffman, J.I., Morley, S.A. & Clark, M.S. (2015) Variability among individuals is generated at the gene expression level. Ecology, 96: 2004-2014. Doi: 10.1890/14-0726.1
71) Eberhart-Phillips, L.J., Hoffman, J.I., Kamrad, K., Zefania, S., Székely, T. & Bruford, M.W. (2015) 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
70) Chakarov, N., Linke, B., Boerner, M., Goessmann, A., Krüger, O. & Hoffman, J.I. (2015) Apparent vector-mediated parent-to-offspring transmission in an avian malaria-like parasite. Molecular Ecology, 24: 1355-1363. Doi: 10.1111/mec.13115
69) Nichols, H.J., Cant, M., Hoffman, J.I. & Sanderson, J.L. (2014) Evidence for frequent incest in a cooperatively breeding mammal. Biology Letters, 23: 20140898. Doi: 10.1098/rsbl.2014.0898
68) Klimova, A., Munguia-Vega, A., Hoffman, J.I. & Culver, M. (2014) 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-321
67) Klimova, A., Fietz, K., Olsen, M.T., Harwood, J., Amos, W. & Hoffman, J.I. (2014) Global population structure and demographic history of the grey seal. Molecular Ecology, 23: 3999-4017. Doi: 10.1111/mec.12850
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 Supplementary information Journal cover Editorial News and views
65) 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 Supplementary information Journal cover
64) Krüger, O., Wolf, J.B.W., Jonker, R.M., Hoffman, J.I. & Trillmich, F. (2014) 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 Journal cover
63) Hoffman, J.I., Krause, E.T., Lehmann, K. & Krüger, O. (2014) MC1R genotype and plumage colouration in the zebra finch: population structure generates artefactual associations. PLoS One, 9: e86519. Doi: 10.1371/journal.pone.0086519
62) Bonin, C.A., Goebel, M.E., Hoffman, J.I. & Burton, R.S. (2014) 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
61) Székely, T., Hoffman, J.I., & Krüger, O. (2013) Why do males care for their competitor’s offspring? Animal Behaviour, 86: e1-e2. Doi: 10.1016/j.anbehav.2013.10.004
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. (2013) Contrasting context-dependence of familiarity and kinship in animal social networks. Animal Behaviour, 86: 993-1001. Doi: 10.1016/j.anbehav.2013.09.001
59) Chakarov, N., Jonker, R.M., Boerner, M., Hoffman, J.I. & Kruger, O. (2013) 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
58) Boerner, M., Hoffman, J.I., Amos, W., Chakarov, N. & Krüger, O. (2013) 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
57) Bonin, C.A., Goebel, M.E., Forcada, J. & Burton, R.S. & Hoffman, J.I. (2013) 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
56) Hoffman, J.I., Thorne, M.A.S., McEwing, R., Forcada, J. & Ogden, R. (2013) 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
55) Caspers, B.A., Hoffman, J.I., Kohlmeyer, P., Krüger, O. & Kraus, T. (2013) Olfactory imprinting as a mechanism for kin recognition in zebra finches. Animal Behaviour, 86: 85-90. Doi: 10.1016/j.anbehav.2013.04.015
54) Hoffman, J.I., Clarke, A., Clark, M.S., Fretwell, P. & Peck, L. (2013) Hierarchical population genetic structure in a direct developing Antarctic marine invertebrate. PLoS ONE, 8: e63954. Doi: 10.1186/1471-2164-14-52
53) Hoffman, J.I., Thorne, M.A.S., Trathan, P.N. & Forcada, J. (2013) 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
52) Phillips, C.D., Hoffman, J.I., George, J.C., Suydam, R.S., Huebinger , R.M., Patton, J.C. & Bickham, J.W. (2012) 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
51) Nichols, H.J., Jamie, G.A., Jordan, N., Cant, M.A. & Hoffman, J.I. (2012) 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
50) Harper, L., Morley, S., Hoffman, J.I., Clark, M.S. & Peck, L. (2012) Iceberg scour and shell damage in the Antarctic bivalve Laternula elliptica. PLoS ONE, 7: e46341. Doi: 10.1371/journal.pone.0046341
49) da Assunção Soares Franco, M., Hoffman, J.I., Harwood, J. & Amos, W. (2012) MHC genotype and near-deterministic mortality in grey seals. Nature Scientific Reports, 2: 659. Doi: 10.1038/srep00659
48) Hoffman, J.I., Tucker, R., Clark, M.S., Forcada, J., Slate, J. (2012) 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
47) Hoffman, J.I., Peck, L.S., Amos, W., Clark, M.S. (2012) Widespread amplification of Amplified Fragment Length Polymorphisms (AFLPs) in marine Antarctic animals. Polar Biology, 35: 919-929. Doi: 10.1007/s00300-011-1139-2
46) Hoffman, J.I. Clarke, A., Clark, M.S., Fretwell, P., Linse, K. & Peck, L. (2012) Unexpected fine-scale population structure in a broadcast-spawning Antarctic marine mollusc. PLoS ONE, 7: e32415. Doi: 10.1371/journal.pone.0032415
45) Smith, E., Hoffman, J.I., Amos, W., Green, L.E. (2012) Association of candidate microsatellite heterozygosity with footrot in domestic sheep. Livestock Science, 143: 293-299. Doi: 10.1016/j.livsci.2011.10.009
44) Hoffman, J.I. & Forcada, J. (2012) Extreme natal philopatry in female Antarctic fur seals (Arctocephalus gazella). Mammalian Biology, 77: 71-73. Doi: 10.1016/j.mambio.2011.09.002
43) Hoffman, J.I., Grant, S.M., Forcada, J. & Phillips, C.D. (2011) 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 Supplementary information
42) Hoffman, J.I. & Nichols, H.J. (2011) A novel approach for mining polymorphic microsatellite markers in silico. PLoS ONE, 6: e23283. Doi: 10.1371/journal.pone.0023283
41) Hoffman, J.I. (2011) 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 Journal cover
40) Driscol, E., Hoffman J.I., Green, L.E. & Amos, W. (2011) 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
39) Amos W., Driscoll, E. & Hoffman, J.I. (2011) 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
38) Hoffman, J.I., Clarke, A., Linse, K. & Peck, L. (2011) 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
37) Hoffman, J.I., Clarke, A.C., Linse, K. & Peck, L. (2011) Strong population genetic structure in a broadcast-spawning Antarctic marine invertebrate. Journal of Heredity, 102: 55–66. Doi: 10.1093/jhered/esq094
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
35) Hoffman, J.I., Hanson, N., Forcada, J., Trathan, P.N. & Amos, W. (2010) 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 Journal cover
34) Hoffman, J.I., Forcada, J. & Amos, W. (2010) 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
33) Hoffman, J.I., Peck L.S., Hillyard, G., Zieritz, A. & Clark, M.S. (2010) No evidence for genetic differentiation between Antarctic limpet Nacella concinna morphotypes. Marine Biology, 157: 765–778. Doi: 10.1007/s00227-009-1360-5
32) Hoffman, J.I., Munro, K., Amos, W. & Kilner, R.M. (2010) 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
31) Zieritz, A., Hoffman, J.I., Amos, W. & Aldridge D.C. (2010) 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
30) Amos, W. & Hoffman, J.I. (2010) 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
29) Dasmahapatra, K.K., Elias, M., Hill, R.I., Hoffman, J.I. & Mallet, J. (2010) 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
28) Skidmore, R., Leach, C., Hoffman, J.I., Amos, W. & Aldridge, D. (2010) 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
27) Brammah, M., Hoffman J.I., Amos, W. & Davies N. (2010) Genetic divergence between and within two subspecies of Laudakia stellio on islands in the Greek Cyclades. The Herpetological Journal, 20: 91–98
26) Hoffman, J.I., Dasmahapatra, K.K., Amos, W., Phillips, C.D., Gelatt, T.S. & Bickham, J.W. (2009) 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
25) Hoffman, J.I. & Forcada, J. (2009) Genetic analysis of twinning in Antarctic fur seals (Arctocephalus gazella). Journal of Mammalogy, 90: 621–628. Doi: 10.1644/08-MAMM-A-264R1.1
24) Hoffman, J.I. (2009) 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
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
22) Oliveira, L., Meyer, D., Hoffman, J.I., Majluf, P. & Morgante, J.S. (2009) 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
21) Parkes, K.A., Amos, W., Moore, N.W., Hoffman, J.I. & Moore, J. (2009) Population structure and speciation in the dragonfly Sympetrum striolatum / nigrescens: an analysis using AFLP markers. European Journal of Entomology, 106: 179–184
20) Temple, H.J., Hoffman, J.I. & Amos, W. (2009) 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
19) Hoffman, J.I., Dasmahapatra, K.K. & Nichols, H.J. (2008) 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
18) Oliveira, L., Hoffman, J.I., Hingst-Zaher, E., Majluf, P., Muelbert, M.M.C., Amos, W. & Morgante, J.S. (2008) 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
17) Rijks, J.M., Hoffman, J.I., Kuiken, T., Osterhaus, A.D.M.E. & Amos, W. (2008) Heterozygosity and lungworm burden in harbour seals (Phoca vitulina). Heredity, 100: 587-593. Doi: 10.1038/hdy.2008.18
16) 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 Supplementary information
15) Hoffman, J.I., Wolf, J.B.W. & Steinfartz, S. (2007) 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
14) Amos, W., Hoffman, J.I., Frodsham, A., Zhang, L., Best, S. & Hill, A.V.S. (2007) Automated binning of microsatellite alleles: problems and solutions. Molecular Ecology Notes, 7: 10–14. doi: 10.1111/j.1471-8286.2006.01560.x
13) Hoffman, J.I., Trathan, P.N. & Amos, W. (2006) 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
12) Hoffman, J.I., Matson, C., Amos, W. Loughlin, T.R. & Bickham, J.W. (2006) 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
11) Hoffman, J.I., Forcada, J. & Amos, W. (2006) 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
10) Temple, H.J., Hoffman, J.I. & Amos, W. (2006) 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
9) Jin, L., Temple, H. J., Hoffman, J.I., Tan, S. & Amos, W. (2006) 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
8) Jin, L., Munro, K., Tan, S. Hoffman, J.I. & Amos, W. (2006) 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
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
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
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
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
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
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
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
The Hoffman Lab 