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 Appointments

Departmental Science Advisor, Ministry of Business, Innovation & Employment
Honorary Academic, Liggins Institute, University of Auckland
Honorary Professor, Massey University

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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 SpecimensScott 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

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

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

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

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

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

Edited Book - Research
Chapter in Book - Research
Journal - Research Article

Edited Book - Research

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Chapter in Book - Research

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

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.

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Journal - Research Article

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Fraser, C. I., Spencer, H. G., & Waters, J. M. (2012). Durvillaea poha sp. nov. (Fucales, Phaeophyceae): A buoyant southern bull-kelp species endemic to New Zealand. Phycologia, 51(2), 151-156. doi: 10.2216/11-47.1

Santure, A. W., & Spencer, H. G. (2012). Genomic imprinting leads to less selectively maintained polymorphism on X chromosomes. Genetics, 192, 1455-1464. doi: 10.1534/genetics.112.145607

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

Smith, A. M., Henderson, Z. E., Kennedy, M., King, T. M., & Spencer, H. G. (2012). Reef formation versus solitariness in two New Zealand serpulids does not involve cryptic species. Aquatic Biology, 16(1), 97-103. doi: 10.3354/ab00444

Donald, K. M., Preston, J., Williams, S. T., Reid, D. G., Winter, D., Alvarez, R., … Spencer, H. G. (2012). Phylogenetic relationships elucidate colonization patterns in the intertidal grazers Osilinus Philippi, 1847 and Phorcus Risso, 1826 (Gastropoda: Trochidae) in the northeastern Atlantic Ocean and Mediterranean Sea. Molecular Phylogenetics & Evolution, 62(1), 35-45. doi: 10.1016/j.ympev.2011.09.002

Geoghegan, J. L., & Spencer, H. G. (2012). Population-epigenetic models of selection. Theoretical Population Biology, 81(3), 232-242. doi: 10.1016/j.tpb.2011.08.001

Nikula, R., Spencer, H. G., & Waters, J. M. (2011). Comparison of population-genetic structuring in congeneric kelp- versus rock-associated snails: A test of a dispersal-by-rafting hypothesis. Ecology & Evolution, 1(2), 169-180. doi: 10.1002/ece3.16

Nikula, R., Spencer, H. G., & Waters, J. M. (2011). Evolutionary consequences of microhabitat: Population-genetic structuring in kelp- vs. rock-associated chitons. Molecular Ecology, 20, 4915-4924. doi: 10.1111/j.1365-294X.2011.05332.x

Donald, K. M., Keeney, D. B., & Spencer, H. G. (2011). Contrasting population makeup of two intertidal gastropod species that differ in dispersal opportunities. Journal of Experimental Marine Biology & Ecology, 396(2), 224-232. doi: 10.1016/j.jembe.2010.10.028

Santure, A. W., & Spencer, H. G. (2011). Quantitative genetics of genomic imprinting: A comparison of simple variance derivations, the effects of inbreeding, and response to selection. Genes Genomes Genetics, 1, 131-142. doi: 10.1534/g3.111.000042

Holland, B. R., Spencer, H. G., Worthy, T. H., & Kennedy, M. (2010). Identifying cliques of convergent characters: Concerted evolution in the cormorants and shags. Systematic Biology, 59(4), 433-445. doi: 10.1093/sysbio/syq023

Fraser, C. I., Thiel, M., Spencer, H. G., & Waters, J. M. (2010). Contemporary habitat discontinuity and historic glacial ice drive genetic divergence in Chilean kelp. BMC Evolutionary Biology, 10, 203. doi: 10.1186/1471-2148-10-203

Nikula, R., Fraser, C. I., Spencer, H. G., & Waters, J. M. (2010). Circumpolar dispersal by rafting in two subantarctic kelp-dwelling crustaceans. Marine Ecology Progress Series, 405, 221-230. doi: 10.3354/meps08523

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