Sesquicentennial Distinguished Professor Hamish Spencer, Our People, Department of Zoology, University of Otago, New Zealand

Population-Genetic Models for Genomically Imprinted Loci
Genomic imprinting describes the unequal expression of paternally and maternally inherited genes in mammals. We are interested in the population-level consequences of this form of non-Mendelian expression.
Evolutionary Origin of Genomic Imprinting
There have been several hypotheses proposed for the evolution of the unequal expression of paternally and maternally inherited genes in mammals. We are interested in examining these hypotheses rigorously, using novel mathematical models.
Phylogeography of Molluscs
Molluscs often provide ideal models to investigate questions in phylogeography, including questions about the importance of dispersal. New Zealand (and the South Pacific in general) has a diverse terrestrial and marine molluscan fauna that has already provided such model systems. We are interested in using novel DNA data sets in phylogeographic investigations.
Testing the Power to Detect Neutral Polymorphisms
Many of the statistical tests of the neutral hypothesis of evolution do not detect non-neutral systems easily. This project involves examining the power of a number of these tests for polymorphisms constructed by mutation and selection.
Frequency-Dependent Selection and Genetic Variation
In theory, frequency-dependent selection can maintain large numbers of alleles in a population. We are interested in quantifying this ability and seeing if, in fact, this form of selection might be responsible for the standing variation observed in natural populations.
Evolutionary Genetics of Parental Effects
It is becoming increasingly clear that parents pass on more than just their genes to the offspring. For example, experiments with a species of weedy cress have shown that non-genetic factors inherited from grandparents can even alter the genetic constitution of individual plants. This project will construct mathematical models that show how various parental effects can have long-term evolutionary implications.

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Current & Recent Projects

Sea Mollusc

Natural selection and the maintenance of genetic and epigenetic variation
Population-genetic models of selection at genomically imprinted loci
Phylogenies of pelicans, shags, cormorants and their relatives (with Dr Martyn Kennedy and Dr Nic Rawlence)
Models of the evolution of genomic imprinting (with Prof Andrew Clark)
Phylogeny of molluscan genera in the gastropod families Trochidae and Calliostomatidae (with Dr Kirsten Donald and Dr Bruce Marshall)
Phylogeny of Australasian nudibranchs (with Dr Martyn Kennedy, Dr Richard Willan and Prof Steve Smith)
Evolution and phylogeography of Australasian intertidal communities, especially those associated with the Bull Kelp Durvillaea (with Prof Jon Waters)
Population genetic models with spatial structure (with Dr Peter Whigham and Dr Grant Dick)
Modelling the Developmental Origins paradigm (with Prof Peter Gluckman)
Phylogeny and biogeography of New Zealand landsnails (with Dr Martyn Kennedy and Dr Fred Brook)
History of eugenics in New Zealand (with Assoc Prof John Stenhouse and Prof Diane Paul)

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Recent and Current Postdocs and Students

Philip Greenspoon, Postdoctoral Fellow, Epigenetics and Evolutionary Theory
Rebecca Cumming, PhD, Evolutionary Biogeography and Patterns of Dispersal in the Intertidal Slug Onchidella
Gert-Jan Jeunen, PhD, Evaluating Environmental DNA (eDNA) Metabarcoding as a Method for Monitoring Biodiversity in Marine Ecosystems
Katherine Lockton, MSc, Genetics of Lasaea in New Zealand
Bryce Peebles, PhD, Chiton Skeletal Genesis: Mechanics and Effects of Acidification
Gertje Petersen, PhD, The Role of Molecular Genetic Variation and Population Structure in the Genetic Improvement of the Honeybee
Kerry Walton, PhD, Ancient DNA Methods and Museum Biological Specimens
Scott Davidson, PhD, An Experimental Test of the Robustness of Sensitivity Analysis
Tim Byrne, PhD, Development and Comparison of Approaches to the Genetic Improvement of Sheep
Kirsten Donald, Postdoctoral Fellow, The Co-evolution of Topshells and Trematodes (supported by the Allan Wilson Centre for Molecular Ecology and Evolution)
Crid Fraser, PhD, Phylogeography of Bull Kelp, Durvillaea spp.
Jemma Geoghegan, PhD, Mathematical Population Epigenetics (supported by the National Research Centre for Growth and Development)
Martyn Kennedy, Postdoctoral Fellow, The Behaviour and Phylogeny of the Pelecaniformes (supported by the Allan Wilson Centre for Molecular Ecology and Evolution)
Anna Santure, PhD, Quantitative Genetic Models Incorporating Genomic Imprinting
Renate Sponer, PhD, Molecular Evolution in the Cosmopolitan, Brooding Brittle Star
Bastiaan Star, PhD, Population Structure and Genetic Variability
Rick Stoffels, Postdoctoral Fellow, Population-genetic Theory of Frequency-dependent Selection (supported by the Marsden Fund )
Meredith Trotter, PhD, Frequency-dependent Selection and the Maintenance of Genetic Variation
Anton Weisstein, Postdoctoral Fellow, Population-genetic Models of the Evolution of Genomic Imprinting (supported by the Marsden Fund)
David Winter, PhD, Phylogeography of Pacific Landsnails (See also David's blog) (supported by the Allan Wilson Centre for Molecular Ecology and Evolution)
Alexey Yanchukov, Postdoctoral Fellow, Modelling the Evolutionary Genetics of Parental Effects (supported by the Marsden Fund )

Keywords

population-genetic theory, genomic imprinting, phylogenetics, plasticity, molluscs, epigenetics

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Publications

Whigham, P. A., & Spencer, H. G. (2021). Graph-structured populations and the Hill–Robertson effect. Royal Society Open Science, 8, 201831. doi: 10.1098/rsos.201831

González-Wevar, C. A., Segovia, N. I., Rosenfeld, S., Noll, D., Maturana, C. S., Hüne, M., … Spencer, H. G., … Poulin, E. (2021). Contrasting biogeographical patterns in Margarella (Gastropoda: Calliostomatidae: Margarellinae) across the Antarctic Polar Front. Molecular Phylogenetics & Evolution, 156, 107039. doi: 10.1016/j.ympev.2020.107039

Zuk, M., & Spencer, H. G. (2020). Killing the behavioral zombie: Genes, evolution, and why behavior Isn't special. BioScience, 70(6), 515-520. doi: 10.1093/biosci/biaa042

Kennedy, M., Seneviratne, S. S., Rawlence, N. J., Ratnayake, S., & Spencer, H. G. (2019). The phylogenetic placement of the enigmatic Indian Cormorant, Phalacrocorax fuscicollis (Phalacrocoracidae). Molecular Phylogenetics & Evolution, 130, 227-232. doi: 10.1016/j.ympev.2018.10.019

Paul, D. B., Stenhouse, J., & Spencer, H. G. (Eds.). (2018). Eugenics at the edges of empire: New Zealand, Australia, Canada and South Africa. Cham, Switzerland: Palgrave MacMillan, 320p. doi: 10.1007/978-3-319-64686-2

Whigham, P. A., & Spencer, H. G. (2021). Graph-structured populations and the Hill–Robertson effect. Royal Society Open Science, 8, 201831. doi: 10.1098/rsos.201831

Journal - Research Article

Zuk, M., & Spencer, H. G. (2020). Killing the behavioral zombie: Genes, evolution, and why behavior Isn't special. BioScience, 70(6), 515-520. doi: 10.1093/biosci/biaa042

Journal - Research Article

Edited Book - Research

Spencer, H. G., Pleasants, A. B., Gluckman, P. D., & Wake, G. C. (2021). A model of optimal timing for a predictive adaptive response. Journal of Developmental Origins of Health & Disease. Advance online publication. doi: 10.1017/s2040174420001361

Journal - Research Article

Donald, K. M., McCulloch, G. A., Dutoit, L., & Spencer, H. G. (2020). Population structure of the New Zealand whelk, Cominella glandiformis (Gastropoda: Buccinidae), suggests sporadic dispersal of a direct developer. Biological Journal of the Linnean Society, 130, 49-60. doi: 10.1093/biolinnean/blaa033

Journal - Research Article

Spencer, H. G. (2020). Beyond equilibria: The neglected role of history in ecology and evolution. Quarterly Review of Biology, 95(4), 311-321. doi: 10.1086/711803

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Jeunen, G.-J., Lamare, M. D., Knapp, M., Spencer, H. G., Taylor, H. R., Stat, M., … Gemmell, N. J. (2020). Water stratification in the marine biome restricts vertical environmental DNA (eDNA) signal dispersal. Environmental DNA, 2(1), 99-111. doi: 10.1002/edn3.49

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Kennedy, M., Seneviratne, S. S., Mendis, U. K., & Spencer, H. G. (2019). Sorting out the snakebirds: The species status, phylogeny, and biogeography of the Darters (Aves: Anhingidae). Journal of Zoological Systematics & Evolutionary Research, 57, 892-899. doi: 10.1111/jzs.12299

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González-Wevar, C. A., Hüne, M., Rosenfeld, S., Nakano, T., Saucède, T., Spencer, H., & Poulin, E. (2019). Systematic revision of Nacella (Patellogastropoda: Nacellidae) based on a complete phylogeny of the genus, with the description of a new species from the southern tip of South America. Zoological Journal of the Linnean Society, 186(2), 303-336. doi: 10.1093/zoolinnean/zly067

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Rawlence, N. J., Rayner, M. J., Lovegrove, T. G., Stoddart, D., Vermeulen, M., Easton, L. J., … Kennedy, M., Spencer, H., & Waters, J. M. (2019). Archival DNA reveals cryptic biodiversity within the Spotted Shag (Phalacrocorax punctatus) from New Zealand. Condor, 121, 1-16. doi: 10.1093/condor/duz029

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Jeunen, G.-J., Knapp, M., Spencer, H. G., Taylor, H. R., Lamare, M. D., Stat, M., … Gemmell, N. J. (2019). Species‐level biodiversity assessment using marine environmental DNA metabarcoding requires protocol optimization and standardization. Ecology & Evolution, 9, 1323-1335. doi: 10.1002/ece3.4843

Journal - Research Article

Jeunen, G.-J., Knapp, M., Spencer, H. G., Lamare, M. D., Taylor, H. R., Stat, M., … Gemmell, N. J. (2019). Environmental DNA (eDNA) metabarcoding reveals strong discrimination among diverse marine habitats connected by water movement. Molecular Ecology Resources, 19, 426-438. doi: 10.1111/1755-0998.12982

Journal - Research Article

Greenspoon, P. B., & Spencer, H. G. (2018). The evolution of epigenetically-mediated adaptive transgenerational plasticity in a subdivided population. Evolution, 72(12), 2773-2780. doi: 10.1111/evo.13619

Journal - Research Article

González-Wevar, C. A., Segovia, N. I., Rosenfeld, S., Ojeda, J., Hüne, M., Naretto, J., … Spencer, H. G., & Poulin, E. (2018). Unexpected absence of island endemics: Long-distance dispersal in higher latitude sub-Antarctic Siphonaria (Gastropoda: Euthyneura) species. Journal of Biogeography, 45(4), 874-884. doi: 10.1111/jbi.13174

Journal - Research Article

Spencer, H. G. (2018). Eugenic sterilization in New Zealand: The story of the Mental Defectives Amendment Act of 1928. In D. B. Paul, J. Stenhouse & H. G. Spencer (Eds.), Eugenics at the edges of empire: New Zealand, Australia, Canada and South Africa. (pp. 85-106). Cham, Switzerland: Palgrave MacMillan. doi: 10.1007/978-3-319-64686-2

Chapter in Book - Research

Kelly, S. T., & Spencer, H. G. (2017). Population-genetic models of sex-limited genomic imprinting. Theoretical Population Biology, 115, 35-44. doi: 10.1016/j.tpb.2017.03.004

Journal - Research Article

González-Wevar, C. A., Hüne, M., Segovia, N. I., Nakano, T., Spencer, H. G., Chown, S. L., … Poulin, E. (2017). Following the Antarctic Circumpolar Current: Patterns and processes in the biogeography of the limpet Nacella (Mollusca: Patellogastropoda) across the Southern Ocean. Journal of Biogeography, 44(4), 861-874. doi: 10.1111/jbi.12908

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Peebles, B. A., Smith, A. M., & Spencer, H. G. (2017). Valve microstructure and phylomineralogy of New Zealand chitons. Journal of Structural Biology, 197(3), 250-259. doi: 10.1016/j.jsb.2016.12.002

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Rawlence, N. J., Till, C. E., Easton, L. J., Spencer, H. G., Schuckard, R., Melville, D. S., … Waters, J. M., & Kennedy, M. (2017). Speciation, range contraction and extinction in the endemic New Zealand King Shag complex. Molecular Phylogenetics & Evolution, 115, 197-209. doi: 10.1016/j.ympev.2017.07.011

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Spencer, H. G., & Priest, N. K. (2016). The evolution of sex-specific dominance in response to sexually antagonistic selection. American Naturalist, 187(5), 658-666. doi: 10.1086/685827

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Spencer, H. G., & Mitchell, C. (2016). The selective maintenance of allelic variation under generalized dominance. Genes Genomes Genetics, 6(11), 3725-3732. doi: 10.1534/g3.116.028076

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Spencer, H. G., & Zuk, M. (2016). For host's sake: The pluses of parasite preservation [Forum]. Trends in Ecology & Evolution, 31(5), 341-343. doi: 10.1016/j.tree.2016.02.021

Journal - Research Other

Paul, D. B., & Spencer, H. G. (2016). Eugenics without eugenists? Anglo-American critiques of cousin marriages in the nineteenth and early twentieth centuries. In S. Müller-Wille & C. Brandt (Eds.), Heredity explored: Between public domain and experimental science, 1850-1930. (pp. 49-79). Cambridge, MA: MIT Press.

Chapter in Book - Research

Donald, K. M., & Spencer, H. G. (2016). Phylogeographic patterns in New Zealand and temperate Australian cantharidines (Mollusca: Gastropoda: Trochidae: Cantharidinae): Trans-Tasman divergences are ancient. Molecular Phylogenetics & Evolution, 100, 333-344. doi: 10.1016/j.ympev.2016.04.029

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Rawlence, N. J., Scofield, R. P., Spencer, H. G., Lalas, C., Easton, L. J., Tennyson, A. J. D., … Waters, J. M., & Kennedy, M. (2016). Genetic and morphological evidence for two species of Leucocarbo shag (Aves, Pelecaniformes, Phalacrocoracidae) from southern South Island of New Zealand. Zoological Journal of the Linnean Society, 177(3), 676-694. doi: 10.1111/zoj.12376

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Donald, K. M., & Spencer, H. G. (2016). Host and ecology both play a role in shaping distribution of digenean parasites of New Zealand whelks (Gastropoda: Buccinidae: Cominella). Parasitology, 143(9), 1143-1156. doi: 10.1017/S0031182016000494

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Cumming, R. A., Nikula, R., Spencer, H. G., & Waters, J. M. (2016). Trans-Tasman genetic connectivity in the intertidal air-breathing slug Onchidella nigricans. Marine Ecology Progress Series, 562, 93-100. doi: 10.3354/meps11926

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Smith, A. M., & Spencer, H. G. (2016). Skeletal mineralogy of scaphopods: An unusual uniformity. Journal of Molluscan Studies, 82(2), 344-348. doi: 10.1093/mollus/eyv061

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Donald, K. M., Winter, D. J., Ashcroft, A. L., & Spencer, H. G. (2015). Phylogeography of the whelk genus Cominella (Gastropoda: Buccinidae) suggests long-distance counter-current dispersal of a direct developer. Biological Journal of the Linnean Society, 115(2), 315-332. doi: 10.1111/bij.12529

Journal - Research Article

Spencer, H. G., & Chiew, K. X. (2015). The maintenance of single-locus polymorphism by maternal selection. Genes Genomes Genetics, 5, 963-969. doi: 10.1534/g3.115.017392

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Donald, K. M., & Spencer, H. G. (2015). New Zealand screw shells Maoricolpus roseus (Gastropoda: Turritellidae): Two species, two subspecies or a single variable species? Molluscan Research, 35(2), 123-127. doi: 10.1080/13235818.2014.977838

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Spencer, H. G., & Clark, A. G. (2014). Non-conflict theories for the evolution of genomic imprinting. Heredity, 113, 112-118. doi: 10.1038/hdy.2013.129

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Herman, J. J., Spencer, H. G., Donohue, K., & Sultan, S. E. (2014). How stable 'should' epigenetic modifications be? Insights from adaptive plasticity and bet hedging. Evolution, 68(3), 632-643. doi: 10.1111/evo.12324

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Kennedy, M., & Spencer, H. G. (2014). Classification of the cormorants of the world. Molecular Phylogenetics & Evolution, 79, 249-257. doi: 10.1016/j.ympev.2014.06.020

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Rawlence, N. J., Till, C. E., Scofield, R. P., Tennyson, A. J. D., Collins, C. J., Lalas, C., … Matisoo-Smith, E., Waters, J. M., Spencer, H. G., & Kennedy, M. (2014). Strong phylogeographic structure in a sedentary seabird, the Stewart Island Shag (Leucocarbo chalconotus). PLoS ONE, 9(3), e90769. doi: 10.1371/journal.pone.0090769

Journal - Research Article

Cumming, R. A., Nikula, R., Spencer, H. G., & Waters, J. M. (2014). Transoceanic genetic similarities of kelp-associated sea slug populations: Long-distance dispersal via rafting? Journal of Biogeography, 41, 2357-2370. doi: 10.1111/jbi.12376

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Geoghegan, J. L., & Spencer, H. G. (2013). Exploring epiallele stability in a population-epigenetic model. Theoretical Population Biology, 83, 136-144. doi: 10.1016/j.tpb.2012.09.001

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Paul, D. B., Stenhouse, J., & Spencer, H. G. (2013). The two faces of Robert FitzRoy, captain of HMS Beagle and governor of New Zealand. Quarterly Review of Biology, 88(3), 219-225. doi: 10.1086/671485

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Trotter, M. V., & Spencer, H. G. (2013). Models of frequency-dependent selection with mutation from parental alleles. Genetics, 195(1), 231-242. doi: 10.1534/genetics.113.152496

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Star, B., & Spencer, H. G. (2013). Effects of genetic drift and gene flow on the selective maintenance of genetic variation. Genetics, 194, 235-244. doi: 10.1534/genetics.113.149781

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Geoghegan, J. L., & Spencer, H. G. (2013). The evolutionary potential of paramutation: A population-epigenetic model. Theoretical Population Biology, 88, 9-19. doi: 10.1016/j.tpb.2013.05.003

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Geoghegan, J. L., & Spencer, H. G. (2013). The adaptive invasion of epialleles in a heterogeneous environment. Theoretical Population Biology, 88, 1-8. doi: 10.1016/j.tpb.2013.05.001

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Nikula, R., Spencer, H. G., & Waters, J. M. (2013). Passive rafting is a powerful driver of transoceanic gene flow. Biology Letters, 9(1), 20120821. doi: 10.1098/rsbl.2012.0821

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Marshall, B. A., & Spencer, H. G. (2013). Comments on some taxonomic changes affecting marine Bivalvia of the New Zealand region recently introduced in Huber's Compendium of bivalves, with some additional taxonomic changes. Molluscan Research, 33(1), 40-49. doi: 10.1080/13235818.2012.754147

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Waters, J. M., Trewick, S. A., Paterson, A. M., Spencer, H. G., Kennedy, M., Craw, D., Burridge, C. P., & Wallis, G. P. (2013). Biogeography off the tracks. Systematic Biology, 62(3), 494-498. doi: 10.1093/sysbio/syt013

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Kennedy, M., Taylor, S. A., Nádvorník, P., & Spencer, H. G. (2013). The phylogenetic relationships of the extant pelicans inferred from DNA sequence data. Molecular Phylogenetics & Evolution, 66(1), 215-222. doi: 10.1016/j.ympev.2012.09.034

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Fraser, C. I., Zuccarello, G. C., Spencer, H. G., Salvatore, L. C., Garcia, G. R., & Waters, J. M. (2013). Genetic affinities between trans-oceanic populations of non-buoyant macroalgae in the high latitudes of the Southern Hemisphere. PLoS ONE, 8(7), e69138. doi: 10.1371/journal.pone.0069138

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Nakagawa, S., Lagisz, M., Hector, K. L., & Spencer, H. G. (2012). Comparative and meta-analytic insights into life extension via dietary restriction. Aging Cell, 11(3), 401-409. doi: 10.1111/j.1474-9726.2012.00798.x

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