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

Greenspoon, P. B., & Spencer, H. G. (2021). Avoiding extinction under nonlinear environmental change: Models of evolutionary rescue with plasticity. Biology Letters, 17(12), 20210459. doi: 10.1098/rsbl.2021.0459

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

Spencer, H. G., Pleasants, A. B., Gluckman, P. D., & Wake, G. C. (2022). A model of optimal timing for a predictive adaptive response. Journal of Developmental Origins of Health & Disease, 13, 101-107. doi: 10.1017/s2040174420001361

Spencer, H. G., Willan, R. C., Mariottini, P., & Salvi, D. (2022). Taxonomic consistency and nomenclatural rules within oysters: Comment on Li et al. (2021). Molecular Phylogenetics & Evolution. Advance online publication. doi: 10.1016/j.ympev.2022.107437

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

Journal - Research Other

Lockton, K. G., & Spencer, H. G. (2021). Phylogeography of the intertidal marine bivalve Lasaea hinemoa (Mollusca: Bivalvia) in New Zealand. Molluscan Research, 41(3), 191-203. doi: 10.1080/13235818.2021.1966163

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

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

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. (2021). [Review of the book Biology and evolution of the mollusca]. Molluscan Research, 41(1), 80-82. doi: 10.1080/13235818.2020.1859344

Journal - Research Other

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

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

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

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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

Journal - Research Article

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