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Dr Matthew Spencer

Contact

M.Spencer@liverpool.ac.uk

+44 (0)151 795 4399

Publications

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2024

Interspecific competition between ants and African honeybees (<scp><i>Apis mellifera scutellata</i></scp>) may undermine the effectiveness of elephant beehive–deterrents in Africa

Thornley, R., Cook, R., Spencer, M., Parr, C. L., & Henley, M. (n.d.). Interspecific competition between ants and African honeybees (<scp><i>Apis mellifera scutellata</i></scp>) may undermine the effectiveness of elephant beehive–deterrents in Africa. Conservation Science and Practice. doi:10.1111/csp2.13041

DOI
10.1111/csp2.13041
Journal article

2023

2021

2020

Effects of human land use and temperature on community dynamics in European forests

Milligan, G., Bradshaw, R., Clancy, D., Zychaluk, K., & Spencer, M. (2020). Effects of human land use and temperature on community dynamics in European forests. Quaternary Science Reviews: the international multidisciplinary research and review journal, 247. doi:10.1016/j.quascirev.2020.106458

DOI
10.1016/j.quascirev.2020.106458
Journal article

2019

2018

2017

2016

Among-site variability in the stochastic dynamics of East African coral reefs

Allen, K. A., Bruno, J. F., Chong, F., Clancy, D., McClanahan, T. R., Spencer, M., & Zychaluk, K. (2017). Among-site variability in the stochastic dynamics of East African coral reefs. PEERJ, 5. doi:10.7717/peerj.3290

Journal article

2015

2013

Dynamic species distribution models from categorical survey data

Mieszkowska, N., Milligan, G., Burrows, M. T., Freckleton, R., & Spencer, M. (2013). Dynamic species distribution models from categorical survey data. JOURNAL OF ANIMAL ECOLOGY, 82(6), 1215-1226. doi:10.1111/1365-2656.12100

DOI
10.1111/1365-2656.12100
Journal article

Thoroughbred racehorse mitochondrial DNA demonstrates closer than expected links between maternal genetic history and pedigree records

Bower, M. A., Whitten, M., Nisbet, R. E. R., Spencer, M., Dominy, K. M., Murphy, A. M., . . . Binns, M. (2013). Thoroughbred racehorse mitochondrial DNA demonstrates closer than expected links between maternal genetic history and pedigree records. Journal of Animal Breeding and Genetics, 130, 227-235.

Journal article

2012

Region-wide changes in marine ecosystem dynamics: state-space models to distinguish trends from step changes

Spencer, M., Mieszkowska, N., Robinson, L. A., Simpson, S. D., Burrows, M. T., Birchenough, S. N. R., . . . Frid, C. L. J. (2012). Region-wide changes in marine ecosystem dynamics: state-space models to distinguish trends from step changes. GLOBAL CHANGE BIOLOGY, 18(4), 1270-1281. doi:10.1111/j.1365-2486.2011.02620.x

DOI
10.1111/j.1365-2486.2011.02620.x
Journal article

Patterns and processes in abundance-body size relationships for marine benthic invertebrates.

Yamanaka, T., White, P. C. L., Spencer, M., & Raffaelli, D. (2012). Patterns and processes in abundance-body size relationships for marine benthic invertebrates.. The Journal of animal ecology, 81(2), 463-471. doi:10.1111/j.1365-2656.2011.01921.x

DOI
10.1111/j.1365-2656.2011.01921.x
Journal article

Data-driven models for regional coral-reef dynamics

Zychaluk, K., Bruno, J. F., Clancy, D., McClanahan, T. R., & Spencer, M. (2012). Data-driven models for regional coral-reef dynamics. ECOLOGY LETTERS, 15(2), 151-158. doi:10.1111/j.1461-0248.2011.01720.x

DOI
10.1111/j.1461-0248.2011.01720.x
Journal article

Modelling evolutionarily stable strategies in oviposition site selection, with varying risks of predation and intraspecific competition.

Kershenbaum, A., Spencer, M., Blaustein, L., & Cohen, J. E. (2012). Modelling evolutionarily stable strategies in oviposition site selection, with varying risks of predation and intraspecific competition.. Evolutionary Ecology, 26, 955-974.

Journal article

2011

Marine biology in time and space

Green, J. A., Paramor, O. A. L., Robinson, L. A., Spencer, M., Watts, P. C., & Frid, C. L. J. (2011). Marine biology in time and space. MARINE ECOLOGY-AN EVOLUTIONARY PERSPECTIVE, 32, V-VII. doi:10.1111/j.1439-0485.2011.00444.x

DOI
10.1111/j.1439-0485.2011.00444.x
Journal article

Empirical models of transitions between coral reef states: effects of region, protection, and environmental change

Lowe, P. K., Bruno, J. F., Selig, E. R., & Spencer, M. (2011). Empirical models of transitions between coral reef states: effects of region, protection, and environmental change. PLoS One.

Journal article

Phylogenetic substitution models for detecting heterotachy during plastid evolution.

Whelan, S., Blackburne, B. P., & Spencer, M. (2011). Phylogenetic substitution models for detecting heterotachy during plastid evolution.. Molecular biology and evolution, 28(1), 449-458. doi:10.1093/molbev/msq215

DOI
10.1093/molbev/msq215
Journal article

Temporal change in UK marine communities: trends or regime shifts?

Spencer, M., Birchenough, S. N. R., Mieszkowska, N., Robinson, L. A., Simpson, S. D., Burrows, M. T., . . . Frid, C. L. J. (2011). Temporal change in UK marine communities: trends or regime shifts?. Marine Ecology: An Evolutionary Perspective, 32, 1-15. doi:10.1111/j.1439-0485.2010.00422.x

DOI
10.1111/j.1439-0485.2010.00422.x
Journal article

Temporal change in UK marine communities: trends or regime shifts?

Spencer, M., Birchenough, S. N. R., Mieszkowska, N., Robinson, L. A., Simpson, S. D., Burrows, M. T., . . . Frid, C. L. J. (2011). Temporal change in UK marine communities: trends or regime shifts?. Marine Ecology, 32, 10-24.

Journal article

2010

A flock of sheep, goats and cattle: ancient DNA analysis reveals complexities of historical parchment manufacture

Campana, M. G., Bower, M. A., Bailey, M. J., Stock, F., O'Connell, T. C., Edwards, C. J., . . . Howe, C. J. (2010). A flock of sheep, goats and cattle: ancient DNA analysis reveals complexities of historical parchment manufacture. Journal of Archaeological Science, 37(6), 1317-1325. doi:10.1016/j.jas.2009.12.036

DOI
10.1016/j.jas.2009.12.036
Journal article

Parameterising variable assimilation efficiency in predator-prey models

Fenton, A., Spencer, M., & Montagnes, D. J. S. (2010). Parameterising variable assimilation efficiency in predator-prey models. OIKOS, 119(6), 1000-1010. doi:10.1111/j.1600-0706.2009.17875.x

DOI
10.1111/j.1600-0706.2009.17875.x
Journal article

Quantifying parameter uncertainty in a coral reef model using Metropolis-Coupled Markov Chain Monte Carlo

Clancy, D., Tanner, J. E., McWilliam, S., & Spencer, M. (2010). Quantifying parameter uncertainty in a coral reef model using Metropolis-Coupled Markov Chain Monte Carlo. ECOLOGICAL MODELLING, 221(10), 1337-1347. doi:10.1016/j.ecolmodel.2010.02.001

DOI
10.1016/j.ecolmodel.2010.02.001
Journal article

Evaluating length heteroplasmy in the human mitochondrial DNA control region.

Forster, L., Forster, P., Gurney, S. M. R., Spencer, M., Huang, C., Röhl, A., & Brinkmann, B. (2010). Evaluating length heteroplasmy in the human mitochondrial DNA control region.. International journal of legal medicine, 124(2), 133-142. doi:10.1007/s00414-009-0385-0

DOI
10.1007/s00414-009-0385-0
Journal article

Linking population, community and ecosystem ecology within mainstream ecology

Fenton, A., & Spencer, M. (2010). Linking population, community and ecosystem ecology within mainstream ecology. In D. G. Raffaelli, & C. L. J. Frid (Eds.), Ecosystem ecology: a new synthesis (pp. 19-39). Cambridge: Cambridge University Press.

Chapter

On the artefactual parastic eubacteria clan in conditioned logdet phylogenies: heterotachy and ortholog identification artefacts as explanations

Sangaralingam, A., Susko, E., Bryant, D., & Spencer, M. (2010). On the artefactual parastic eubacteria clan in conditioned logdet phylogenies: heterotachy and ortholog identification artefacts as explanations. BMC Evolutionary Biology. Retrieved from http://www.biomedcentral.com/bmcevolbiol/

Journal article

2009

A phylogenetic mixture model for gene family loss in parasitic bacteria.

Spencer, M., & Sangaralingam, A. (2009). A phylogenetic mixture model for gene family loss in parasitic bacteria.. Molecular biology and evolution, 26(8), 1901-1908. doi:10.1093/molbev/msp102

DOI
10.1093/molbev/msp102
Journal article

2008

Integron-associated gene cassettes in Halifax Harbour: assessment of a mobile gene pool in marine sediments.

Koenig, J. E., Boucher, Y., Charlebois, R. L., Nesbø, C., Zhaxybayeva, O., Bapteste, E., . . . Doolittle, W. F. (2008). Integron-associated gene cassettes in Halifax Harbour: assessment of a mobile gene pool in marine sediments.. Environmental microbiology, 10(4), 1024-1038. doi:10.1111/j.1462-2920.2007.01524.x

DOI
10.1111/j.1462-2920.2007.01524.x
Journal article

Lotka-Volterra competition models for sessile organisms.

Spencer, M., & Tanner, J. E. (2008). Lotka-Volterra competition models for sessile organisms.. Ecology, 89(4), 1134-1143. doi:10.1890/07-0941.1

DOI
10.1890/07-0941.1
Journal article

Past states of continuous-time Markov models for ecological communities.

Spencer, M. (2008). Past states of continuous-time Markov models for ecological communities.. Mathematical biosciences, 211(2), 299-313. doi:10.1016/j.mbs.2007.08.006

DOI
10.1016/j.mbs.2007.08.006
Journal article

Topological estimation biases with covarion evolution.

Wang, H. -C., Susko, E., Spencer, M., & Roger, A. J. (2008). Topological estimation biases with covarion evolution.. Journal of molecular evolution, 66(1), 50-60. doi:10.1007/s00239-007-9062-4

DOI
10.1007/s00239-007-9062-4
Journal article

2007

Multilocus characterization scheme for Shiga toxin-encoding bacteriophages

Smith, D. L., Wareing, B. M., Fogg, P. C. M., Riley, L. M., Spencer, M., Cox, M. J., . . . Allison, H. E. (2007). Multilocus characterization scheme for Shiga toxin-encoding bacteriophages. APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 73(24), 8032-8040. doi:10.1128/AEM.01278-07

DOI
10.1128/AEM.01278-07
Journal article

Conditioned genome reconstruction: how to avoid choosing the conditioning genome.

Spencer, M., Bryant, D., & Susko, E. (2007). Conditioned genome reconstruction: how to avoid choosing the conditioning genome.. Systematic biology, 56(1), 25-43. doi:10.1080/10635150601156313

DOI
10.1080/10635150601156313
Journal article

Testing for covarion-like evolution in protein sequences.

Wang, H. -C., Spencer, M., Susko, E., & Roger, A. J. (2007). Testing for covarion-like evolution in protein sequences.. Molecular biology and evolution, 24(1), 294-305. doi:10.1093/molbev/msl155

DOI
10.1093/molbev/msl155
Journal article

2006

Authenticated DNA from ancient wood remains.

Liepelt, S., Sperisen, C., Deguilloux, M. -F., Petit, R. J., Kissling, R., Spencer, M., . . . Ziegenhagen, B. (2006). Authenticated DNA from ancient wood remains.. Annals of botany, 98(5), 1107-1111. doi:10.1093/aob/mcl188

DOI
10.1093/aob/mcl188
Journal article

Sensitivity analysis of Markov models for communities of competing sessile organisms.

Spencer, M. (2006). Sensitivity analysis of Markov models for communities of competing sessile organisms.. The Journal of animal ecology, 75(4), 1024-1033. doi:10.1111/j.1365-2656.2006.01124.x

DOI
10.1111/j.1365-2656.2006.01124.x
Journal article

Copying and conflation in Geoffrey Chaucer’s Treatise on the astrolabe: a stemmatic analysis using phylogenetic software

Eagleton, C., & Spencer, M. (2006). Copying and conflation in Geoffrey Chaucer’s Treatise on the astrolabe: a stemmatic analysis using phylogenetic software. Studies in History and Philosophy of Science Part A, 37(2), 237-268. doi:10.1016/j.shpsa.2005.08.020

DOI
10.1016/j.shpsa.2005.08.020
Journal article

Modelling prokaryote gene content

Spencer, M., Susko, E., & Roger, A. J. (2006). Modelling prokaryote gene content. Evolutionary Bioinformatics Online, 2, 165-186. Retrieved from http://la-press.com/cr_data/files/f_EBO-2-Spencer-et-al_192.pdf

Journal article

Optimal strategies for accurate transcription of manuscripts

Spencer, M., & Howe, C. J. (2006). Optimal strategies for accurate transcription of manuscripts. Literary and Linguistic Computing, 21, 353-362.

Journal article

2005

CONTINUOUS-TIME MARKOV MODELS FOR SPECIES INTERACTIONS

Spencer, M., & Susko, E. (2005). CONTINUOUS-TIME MARKOV MODELS FOR SPECIES INTERACTIONS. Ecology, 86(12), 3272-3278. doi:10.1890/05-0029

DOI
10.1890/05-0029
Journal article

Impact of replicate types on proteomic expression analysis.

Karp, N. A., Spencer, M., Lindsay, H., O'Dell, K., & Lilley, K. S. (2005). Impact of replicate types on proteomic expression analysis.. Journal of proteome research, 4(5), 1867-1871. doi:10.1021/pr050084g

DOI
10.1021/pr050084g
Journal article

Biases in phylogenetic estimation can be caused by random sequence segments.

Susko, E., Spencer, M., & Roger, A. J. (2005). Biases in phylogenetic estimation can be caused by random sequence segments.. Journal of molecular evolution, 61(3), 351-359. doi:10.1007/s00239-004-0352-9

DOI
10.1007/s00239-004-0352-9
Journal article

Likelihood, parsimony, and heterogeneous evolution.

Spencer, M., Susko, E., & Roger, A. J. (2005). Likelihood, parsimony, and heterogeneous evolution.. Molecular biology and evolution, 22(5), 1161-1164. doi:10.1093/molbev/msi123

DOI
10.1093/molbev/msi123
Journal article

The identification of exemplar change in the Wife of Bath's prologue using the maximum chi-squared method

Windram, H. F., Spencer, M., & Howe, C. J. (2005). The identification of exemplar change in the Wife of Bath's prologue using the maximum chi-squared method. Literary and Linguistic Computing, 20, 189-204.

Journal article

2004

CONFIDENCE INTERVALS AND HYPOTHESIS TESTING FOR BETA DIVERSITY

Kiflawi, M., & Spencer, M. (2004). CONFIDENCE INTERVALS AND HYPOTHESIS TESTING FOR BETA DIVERSITY. Ecology, 85(10), 2895-2900. doi:10.1890/03-3058

DOI
10.1890/03-3058
Journal article

Article: Collating Texts Using Progressive Multiple Alignment

Spencer, M., & Howe, C. (2004). Article: Collating Texts Using Progressive Multiple Alignment. Computers and the Humanities, 38(3), 253-270. doi:10.1007/s10579-004-8682-1

DOI
10.1007/s10579-004-8682-1
Journal article

Evolution of alternative mating tactics: conditional versus mixed strategies

Plaistow, S. J. (2004). Evolution of alternative mating tactics: conditional versus mixed strategies. Behavioral Ecology, 15(4), 534-542. doi:10.1093/beheco/arh029

DOI
10.1093/beheco/arh029
Journal article

Phylogenetics of artificial manuscripts.

Spencer, M., Davidson, E. A., Barbrook, A. C., & Howe, C. J. (2004). Phylogenetics of artificial manuscripts.. Journal of theoretical biology, 227(4), 503-511. doi:10.1016/j.jtbi.2003.11.022

DOI
10.1016/j.jtbi.2003.11.022
Journal article

Representing multiple pathways of textual flow in the Greek manuscripts of the Letter of James using reduced median networks

Spencer, M., Wachtel, K., & Howe, C. J. (2004). Representing multiple pathways of textual flow in the Greek manuscripts of the Letter of James using reduced median networks. Computers and the Humanities, 38, 1-14.

Journal article

2002

OVIPOSITION HABITAT SELECTION BY MOSQUITOES (CULISETA LONGIAREOLATA) AND CONSEQUENCES FOR POPULATION SIZE

Spencer, M., Blaustein, L., & Cohen, J. E. (2002). OVIPOSITION HABITAT SELECTION BY MOSQUITOES (CULISETA LONGIAREOLATA) AND CONSEQUENCES FOR POPULATION SIZE. Ecology, 83(3), 669-679. doi:10.1890/0012-9658(2002)083[0669:ohsbmc]2.0.co;2

DOI
10.1890/0012-9658(2002)083[0669:ohsbmc]2.0.co;2
Journal article

Are there fine-scale spatial patterns in community similarity among temporary freshwater pools?

Spencer, M., Schwartz, S. S., & Blaustein, L. (2002). Are there fine-scale spatial patterns in community similarity among temporary freshwater pools?. Global Ecology And Biogeography, 11(1), 71-78.

Journal article

2001

Manuscript evolution.

Howe, C. J., Barbrook, A. C., Spencer, M., Robinson, P., Bordalejo, B., & Mooney, L. R. (2001). Manuscript evolution.. Trends in genetics : TIG, 17(3), 147-152. doi:10.1016/s0168-9525(00)02210-1

DOI
10.1016/s0168-9525(00)02210-1
Journal article

Hatching fraction and timing of resting stage production in seasonal environments: effects of density dependence and uncertain season length

Spencer, M., Colegrave, N., & Schwartz, S. S. (2001). Hatching fraction and timing of resting stage production in seasonal environments: effects of density dependence and uncertain season length. Journal Of Evolutionary Biology, 14(3), 357-367.

Journal article

Hatching responses of temporary pool invertebrates to signals of environmental quality

Spencer, M., & Blaustein, L. (2001). Hatching responses of temporary pool invertebrates to signals of environmental quality. Israel Journal Of Zoology, 47(4), 397-417.

Journal article

Risk of Predation and Hatching of Resting Eggs in the Ostracod Heterocypris Incongruens

Spencer, M., & Blaustein, L. (2001). Risk of Predation and Hatching of Resting Eggs in the Ostracod Heterocypris Incongruens. Journal of Crustacean Biology, 21(3), 575-581. doi:10.1163/20021975-99990159

DOI
10.1163/20021975-99990159
Journal article

Temporal variability and ignorance in Monte Carlo contaminant bioaccumulation models:: A case study with selenium in <i>Mytilus edulis</i>

Spencer, M., Fisher, N. S., Wang, W. X., & Ferson, S. (2001). Temporal variability and ignorance in Monte Carlo contaminant bioaccumulation models:: A case study with selenium in <i>Mytilus edulis</i>. RISK ANALYSIS, 21(2), 383-394. doi:10.1111/0272-4332.212119

DOI
10.1111/0272-4332.212119
Journal article