Haghani, Amin, Caesar Z. Li, Todd R. Robeck, Joshua Zhang, Ake T. Lu, Julia Ablaeva, Victoria A. Acosta-Rodríguez, et al. (2023) ‘DNA Methylation Networks Underlying Mammalian Traits’. Science 381 (6658): eabq5693. https://doi.org/10.1126/science.abq5693.

Lu, A. T., Z. Fei, A. Haghani, T. R. Robeck, J. A. Zoller, C. Z. Li, R. Lowe, et al. (2023). ‘Universal DNA Methylation Age across Mammalian Tissues’. Nature Aging, August.

Hearn, J., & Little, T. J. (2022) Daphnia magna egg piRNA cluster expression profiles change as mothers age. BMC Genomics 23 article 429. DOI: https://doi.org/10.1186/s12864-022-08660-z

Fields, P. D., McTaggart, S., Reisser, C. M. O., Haag, C., Palmer, W. H., Little, T. J., Ebert, D., & Obbard, D. J. (2022). Population-Genomic Analysis Identifies a Low Rate of Global Adaptive Fixation in the Proteins of the Cyclical Parthenogen Daphnia magna. Molecular Biology and Evolution, 39(3), https://doi.org/10.1093/molbev/msac048

Hearn, J., Plenderleith, F. and T. J. Little (2021) DNA methylation differs extensively between strains of the same geographical origin and changes with age in Daphnia magna. Epigenetics and Chromatin 14: article 4. https://doi.org/10.1186/s13072-020-00379-z

Winner of the American Society of Naturalists Presidential Award (best paper published in 2021): Clark, J., McNally, L., and Little, T.J (2021) Pathogen Dynamics Across the Diversity of Ageing. American Naturalist 197: https://doi.org/10.1086/712380

Little, T. J. et al.
Methylation-Based Age Estimation in a Wild Mouse. BioRixv, 2020.07.16.203687 (2020).

Hearn, J., Clark, J., Wilson, P. J. & Little, T. J.
Daphnia magna modifies its gene expression extensively in response to caloric restriction revealing a novel effect on haemoglobin isoform preference. Molecular Ecology 29: 3261-3276 https://doi.org/10.1111/mec.15557 (2020).

Hearn, J., Pearson, M., Blaxter, M., Wilson, P., and Little, T.J. (2019).
Genome-wide Methylation is modified Under Caloric Restriction in Daphnia magna. BMC Genomics 20:197

Hearn, J, Wang-Ngai Chow, F., Barton, H., Tung, M., Wilson, P., Blaxter, M., Buck, A., and T.J. Little. (2108) Daphnia magna microRNAs respond to nutritional stress and aging but are not transgenerational. Molecular Ecology
DOI: 10.1111/mec.14525

Clark, J., Garbutt, J.S., McNally
, L and Tom J. Little (2017) Disease Spread in Age Structured Populations with Maternal Age Effects. Ecology Letters 20: 445-451

Garbutt, J. S. and T. J. Little (2017) Bigger is better: changes in body size explain a maternal effect of food on offspring disease resistance. Ecology and Evolution 7: 1403–1409.

Little, T.J., and Colegrave, N. (2016). Caging and Uncaging Genetics. Plos Biology, PLoS Biol 14(7): e1002525. doi:10.1371/journal.pbio.1002525

Orsini, L., Gilbert, D., Podicheti, R., Jansen, M., Brown, J.B., Solari, O.S., Spanier, K.I., Colbourne, J.K., Rush, D., Decaestecker, E., Asselman, J., De Schamphelaere, K.A.C., Ebert, D., Haag, C.R., Kvist, J., Laforsch, C., Petrusek, A., Beckerman, A.P., Little, T.J., Chaturvedi, A., Pfrender, M.E., De Meester, L., and Frilander, M.J. (2016).
Daphnia magna transcriptome by RNA-Seq across 12 environmental stressors. Scientific data 3, 160030.

McTaggart, S.J., Cezard, T., Garbutt, J.S., Wilson, P.J., and Little, T.J. (2015).
Transcriptome profiling during a natural host-parasite interaction. Bmc Genomics 16, 643.

Garbutt, J.S., Little, T.J., and Hoyle, A. (2015).
Maternal effects on offspring consumption can stabilize fluctuating predator-prey systems. Proceedings of the Royal Society B-Biological Sciences 282 DOI: 10.1098/rspb.2015.2173.

Jennie S. Garbutt, Anna J.P. O'Donghue, Seanna J. McTaggart, Philip J. Wilson and Tom J. Little (2014)
The development of pathogen resistance in Daphnia
magna: implications for disease spread in age-structured populations
. J Exp Biol
217: 3929-3934

Jennie S. Garbutt , Philip J. Wilson and Tom J. Little (2014)
Maternal food quantity affects offspring feeding rate in Daphnia magna. Biology letters: 10, DOI: 10.1098/rsbl.2014.0356

Schoebel, Corine N.; Auld, Stuart K. J. R.; Spaak, Piet; and Tom J. Little (2014)
Effects of Juvenile Host Density and Food Availability on Adult Immune Response, Parasite Resistance and Virulence in a Daphnia-Parasite System. Plos One: 9 DOI: 10.1371/journal.pone.0094569

Garbutt, J., S.; Scholefield, J.A., Vale, P.F. and T.J. Little (2014)
Elevated maternal temperature enhances offspring disease resistance in Daphnia magna. Functional Ecology: 28: 424-431

Beckerman, A and T.J. Little. 2013.
A shared mechanism of defense against predators and parasites: chitin regulation and its implications for life-history theory. Ecology and Evolution 3: 5119-5126

Vale, P.F. and T.J. Little (2013) Host nutrition alters the variance in transmission potential. Biology Letters. DOI: 10.1098/rsbl.2012.1145

Auld, S.K.J, Wilson, P.J. and T.J. Little (2013)
Rapid change in parasite infection traits over the course of an epidemic in a wild host-parasite population. Oikos 123: 232-238

King, K, Auld, S.K.J.R., Wilson, P.J., James, J. and T.J. Little. 2013.
The bacterial parasite Pasteuria ramosa is not killed if it fails to infect: implications for coevolution. Ecology and Evolution 3: 197-203

McTaggart, S. J., Wilson, P.J. and T.J. Little (2012)
Daphnia magna shows reduced infection upon secondary exposure to a pathogen. Biology Letters in press

Vale, P.F. and T.J. Little (2012) Fecundity compensation and tolerance to a sterilizing pathogen in Daphnia. Journal of Evolutionary Biology. DOI: 10.1111/j.1420-9101.2012.02579.x

Auld, SKJR, Edel, KH and T.J. Little (2012)
The cellular immune response of Daphnia magna under host-parasite genetic variation and variation in initial dose. Evolution 66:3287-3293

McTaggart, S. J., Obbard, D.J., Conlon, C., and T.J. Little (2012) Immune genes undergo more adaptive evolution than non-immune genes in Daphnia pulex. BMC Evolutionary Biology 12: 63.

Little, T.J. Allen, J.E. Babayan, S.A., Matthews, K.R and N. Colegrave. (2012).
Harnessing evolutionary biology to combat infectious disease. Nature Medicine 18: 217-220

Auld, S., Graham, A.L. Wilson, P.J. and T.J. Little. (2012) Elevated haemocyte number is associated with infection and low fitness potential in wild Daphnia magna. Functional Ecology 26, 434-440

Stjernman, M and T.J Little. (2011)
Genetic variation for maternal effects on parasite resistance. Journal of Evolutionary Biology 24: 2357-2363

Smith, PH., Mwangi, J.M., Afrane, Y.A., Yan, G., Obbard, D.J., Ranford-Cartwright, L.C. and T.J. Little. 2011
Alternative Splicing of the Anopheles gambiae Dscam Gene in Diverse Plasmodium falciparum Infections. Malaria Journal 10:156

Decaestecker, E., Labbé, P., Ellegaard, K., Allen, J. E., and T.J. Little. 2011.
Candidate immune gene expression in the ecological functional genomics model Daphnia. Developmental and Comparative Immunology 35:1068-1077

Vale, P.F. Alex Best, A., Boots, M. and T.J. Little. 2011.
Epidemiological, evolutionary and coevolutionary implications of context-dependent parasitism. American Naturalist. 177, 510-21

Allen, D.E. and T.J. Little. 2011.
Identifying energy constraints to parasite resistance. Journal of Evolutionary Biology 24:224-229.

Obbard, D.J., Jiggins, F.M., Bradshaw, N.J. and TJ. Little. 2011. Recent and recurrent selective sweeps of the antiviral RNAi gene Argonaute-2 in three species of Drosophila. Molecular Biology and Evolution 28: 1043-1056

Labbé, P., Vale, P, and T.J Little. 2011. Successfully resisting a pathogen is rarely costly in Daphnia magna. BMC Evolutionary Biology 10: 355

A.L., Shuker, D.M., Pollitt, L., Auld, S., Wilson, A. and T.J. Little. 2011. Fitness consequences of immune responses: strengthening the empirical framework for ecoimmunology. Functional Ecology 25: 5-17.

Allen, D.E. and T.J. Little. 2010. Dissecting the effect of a heterogeneous environment on the interaction between host and parasite fitness traits. Evolutionary Ecology 24:499-508.

Auld, S.K.J., and T.J. Little. 2010.
Genetic variation in the cellular response of Daphnia magna (Crustacea: Cladocera) to its bacterial parasite. Proceedings of the Royal Society B 277: 3291-329

Little, T.J. Shuker, D.M., Colegrave, N., Day, T. and A.L. Graham. 2010. The coevolution of virulence: tolerance in perspective. PLoS Pathogens 6(9): e1001006.

Vale, P. and T.J. Little. 2010.
CRISPR-mediated phage resistance and the ghost of coevolution past. Proceedings of the Royal Society B 277: 2097-2103.

McTaggart, S.J., Conlon,
C., Colbourne, J.K., Blaxter, M.L. and T.J. Little. 2009. The components of the Daphnia pulex immune system as revealed by complete genome sequencing. BMC Genomics 10: 17

Allen, D.E. and T.J. Little. 2009. The molecular landscape of host-parasite coevolution. Cold Spring Harbor Symposia on Quantitative Bilogy LXXIV.

Duncan, A.B., Hall, S. and T.J. Little. 2009. Parasitism and environmental sex determination in Daphnia. Evolutionary Ecology Research 11: 965-973

Haag, C.R., McTaggart, S.J., Anaïs Didier, A., Little, T.J. and D. Charlesworth. 2009. Nucleotide polymorphism and within-gene recombination in Daphnia magna and Daphnia pulex, two cyclical parthenogens. Genetics 182: 313-323

Labbe, P., MacTaggart, S.J. and T.J. Little. 2009. An ancient immunity gene duplication in Daphnia magna: RNA expression and sequence analysis of two Nitric Oxide Synthase genes. Developmental and Comparative Immunology 33: 1000-1010

Obbard, D.J.O., Welch, J.J. and Tom J Little. 2009. Inferring selection in the Anopheles gambiae species complex: an example from immune-related serine protease inhibitors. Malaria Journal 8:117

Vale, P. and T.J. Little. 2009.
Measuring parasite fitness under thermal variation. Heredity 103: 102-109

Labbe, P. and T.J. Little. 2009. ProPhenolOxidase in Daphnia magna: cDNA sequencing and expression in relation to resistance to parasitism. Developmental and Comparative Immunology 33: 674-680

Lazarro, B.P. and T.J. Little. 2009. Immunity in a noisy world. Philosophical Transactions of the Royal Society 364: 15-26

Obbard, D.J., Callister, D.M., Jiggins, F.M., Soares, D., Yan, G. and T.J. Little. 2008. The evolution of TEP1, an exceptionally polymorphic immunity gene in Anopheles gambiae. BMC Evolutionary Biology 8:274

Brites, D., McTaggart, S., Morris, K., Anderson, J., Thomas, K., Colson, I., Fabbro, T., Little, T.J., Ebert,, D. and L. Du Pasquier. 2008. The Dscam homologue of the crustacean Daphnia is diversified by alternative splicing like in insects. Molecular Biology and Evolution 25: 1429-1439.

Vale, P. F., Stjernman, M. and T.J. Little. 2008. Temperature dependent costs of parasitism and the maintenance of polymorphism under genotype-by-environment interactions. The Journal of Evolutionary Biology 21:1418-1427

Little, T.J., Perutz, M., Crossan, C, Palmer, M. and V. A. Braithwaite. 2008.
Male Sticklebacks Make Antibiotic Nests: A Novel Form Of Parental Protection? Journal of Fish Biology 73: 2380-2389.

Nelson, L., Anderson, S., Archibald, A., Rhind, S., Condie, A., McIntyre, N., Thompson, J., Whitelaw, B., Little, T.J. and T. Hupp. 2008. An animal model to evaluate the function and regulation of the adaptively evolving stress protein SEP53 in oesophageal bile damage responses. Cell Stress and Chaperones 13: 375-285.

Afrane, Y.A., Little, T.J., Lawson, B.W., Githeko, A.K. and G Yan. 2008. Deforestation and vectorial capacity of Anopheles gambiae Giles mosquitoes in malaria transmission, Kenya. Emerging Infectious Diseases 14: 1533-1538

Killick, S., Obbard, D., West, S.A. and T.J. Little. 2008. Breeding system variation in North American Daphnia pulex: a role for parasites? Ecological Research 23: 235-240

Little, T.J., Chadwick, W. and K. Watt. 2008.
Parasite strain variation and the evolution of virulence in a Daphnia-microparasite system. Parasitology doi:10.1017/S0031182007003939

Little, T.J., Nelson, L. and T. Hupp. 2007. Adaptive Evolution of a Stress Response Protein. PLoS One 2(10): e1003. doi:10.1371/journal.pone.0001003.

Obbard, D.J., Yan, G.Y Linton, Walton, C. and T.J. Little. 2007.
Population genetics of plasmodium resistance genes in Anopheles gambiae: no evidence for strong selection. Molecular Ecology 16: 3497-3510

Little, T.J. and S. Killick. 2007 Evidence for a cost of immunity when the crustacean Daphnia magna is exposed to the bacterial pathogen Pasteuria ramosa. Journal of Animal Ecology 76: 1202-1207

Duncan, A., and T.J. Little. 2007
Parasite-driven genetic change in a natural population of Daphnia. Evolution 61: 796–803

Little, T.J., Birch, J., Vale, P. and M. Tseng 2007
Parasite transgenerational effects on infection. Evolutionary Ecology Research 9: 459-469

Guinnee, M, Gardner, A, Howard, A, West, S.A. and T.J. Little. 2007
The causes and consequences of variation in offspring size: a case study using Daphnia. Journal of Evolutionary Biology 20: 577-587

Wedekind, C., Walker, M. and T.J. Little 2006
The separate and combined effects of MHC genotype, parasite clone, and host gender on the course of malaria in mice. BMC Genetics 7:55.

Killick. S.C., Carlsson, A.M., West, S.A. and T.J. Little. 2006. Testing the Pluralist Approach to sex: the influence of environment on synergistic interactions between mutation load and parasitism in Daphnia magna. The Journal of Evolutionary Biology 19: 1603-1611

Jensen, K.N., Little, T.J., Skorping, A. and D. Ebert. 2006.
Empirical support for an optimal virulence in a castrating parasite. PloS Biology 4 e197

Obbard, D.J., Jiggins, F.M. and T.J. Little. 2006.
Rapid Evolution of antiviral RNAi genes. Current Biology 16: 580-585.

Duncan, A., Mitchell S.E. and T.J. Little. 2006.
Parasite-mediated selection in Daphnia: the role of sex and diapause. The Journal of Evolutionary Biology 19: 1183-1189

Little, T.J., Lamza, K. and D. Ebert. 2006. Parasite-host specificity: experimental studies on the basis of parasite adaptation. Evolution 60: 31-38.

Little, T. J. 2005.
Genetic diversity and polyploidy in the cosmopolitan asexual ostracod Cypris pubera. Journal of Plankton Research 27: 1287-1293.

Little, T.J. and N. Cobbe. 2005. Molecular evolution of immune-related genes from disease-carrying mosquitoes in the genus Anopeheles. Insect Molecular Biology 14:599-605.

Little, T.J., Hultmark, D. and A.F. Read. 2005.
Invertebrate immunity and the limits of mechanistic immunology. Nature Immunology 6: 651-654.

Wedekind, C., Walker, M. and T.J. Little. 2005
The course of malaria in mice: MHC effects, but no general MHC heterozygote advantage in single-strain infections Genetics 170: 1427-130.

Chadwick, W., and T.J. Little. 2005.
A parasite-mediated life-history shift in Daphnia magna. Proceedings of the Royal Society of London B 272: 505-509.

Mitchell, S.E., Rogers, E., Little, T.J. and A.F. Read. 2005.
Host-parasite and genotype by environment interactions: Temperature modifies the potential for selection by a sterilising pathogen. Evolution 59:70-80.

Wedekind, C. and T.J. Little. 2004. The clearance of hidden cestode infection triggered by an independent activation of host defense in a teleost fish. The Journal of Parasitology 90: 1329-1331.

Little, T.J., Colbourne, J.K. and T.J. Crease. 2004.
Molecular evolution of Daphnia immunity genes: polymorphism in a Gram Negative Binding Protein and an Alpha-2-Macroglobulin. Journal of Molecular Evolution: 59:498-506.

Ebert,, D., Carius, H. J., Little, T.J. and Decaestecker, E. 2004
The evolution of virulence, host castration and gigantism in a bacteria-Daphnia system. American Naturalist 164: s19-s32.

Mitchell, S., Read, A.F. and T.J. Little. 2004.
The effect of a pathogen epidemic on the susceptibility to infection, reproductive investment and genetic structure of the cyclical parthenogen Daphnia magna. Ecology Letters7: 848-858.

Guinnee, M, West, S.A. and T.J. Little. 2004.
Testing small integer clutch-size models using Daphnia. American Naturalist 163:880-887.

Little, T.J. & A. R. Kraaijeveld. 2004.
The ecological and evolutionary implications of immunological priming in invertebrates. Trends in Ecology and Evolution 19: 58-60.

Little, T.J., O’Connor, B., Colegrave, N., Watt, K. and A.F. Read. 2003. Maternal transfer of strain-specific immunity in an invertebrate. Current Biology 13: 489-492.

Little, T.J., Carius, H.J., Sakwinska, O. and D. Ebert. 2002.
Competitiveness and life-history characteristics of Daphnia with respect to susceptibility to a parasite. The Journal of Evolutionary Biology15:796-802.

Little, T.J. 2002.
The evolutionary significance of parasitism: do parasite-driven genetic dynamics occur ex silico? The Journal of Evolutionary Biology 15: 1-9.

Little, T.J. and D. Ebert. 2001.
Temporal patterns of infectivity in a Daphnia-microparasite system. Evolution 55: 1146-1152

Carius, H-J, Little, T.J., and D. Ebert. 2001.
The potential for frequency-dependent selection and coevolution in a Daphnia-microparasite system. Evolution 55: 1136-1145

Little, T.J. and D. Ebert. 2000.
The cause of parasitic infection in natural populations of Daphnia(Crustacea: Cladocera): the role of host genetics. Proceedings of the Royal Society of London B 267:2037-2042.

Little, T.J. and D. Ebert. 2000.
Sex, linkage disequilibrium, and patterns of parasitism in natural populations of Daphnia. Heredity 85: 257-265.

Little, T.J. and D. Ebert. 1999.
Associations between parasitism and host genotype in natural populations of Daphnia (Crustacea: Cladocera). Journal of Animal Ecology 68: 134-149.

Little, T.J., DeMelo, R., Taylor, D.J. and P.D.N. Hebert. 1997. Genetic characterization of an arctic zooplankter: insights into geographic polyploidy. Proceedings of the Royal Society of London B 264: 1363-70.

Little, T.J. and P.D.N. Hebert. 1997. Clonal Diversity in high arctic ostracodes. Journal of Evolutionary Biology 10: 233-252.

Crease, T.J. and T.J. Little. 1997. Partial sequence of the mitochondrial genome of the crustacean Daphnia pulex. Current Genetics 31: 48-54.

Little, T.J. and P. D. N. Hebert. 1996. Endemism & ecological islands: the ostracodes from Jamaican bromeliads. Freshwater Biology 36: 327-337.

Little, T.J. and P.D.N. Hebert. 1994. Abundant asexuality in tropical freshwater ostracodes. Heredity 73: 549-555.

Book chapters
Little, T.J. and D. Ebert. 2004. Evolutionary dynamics of Daphnia and their microparasites in Evolutionary Aspects of Infectious Disease, Edited by K. R. Dronamraju. Cambridge University Press. (Invited)

Little, T.J. 2005. Natural variation in immune system genes and how this might impact engineering issues in Christophe Boete (editor), Malaria Control with Genetically-Modified Mosquitoes. Landes Biosciences, Rotterdam. (Invited)

Book reviews, comments, etc
Little, T.J., Colegrave, N, Sadd, B. and P. Schmid-Hempel. 2008. Studying Immunity at the whole organism level. Bioessays 30: 404-405

Little, T.J. The Evolutionary Ecology of Parasites by Robert J. Poulin. 2008. The Quarterly Review of Biology 83: 102-103. (Invited)

Carpenter J.A., Jiggins, F.M. and T.J. Little. 2008. Dialogue on defenses: Report from the workshop on “the impact of the environment on innate immunity: At the defence frontier”, 22–27 April 2007. Developmental & Comparative Immunology 32: 307-309

Little, T.J. and P.D.N. Hebert. 1996. Ancient asexuals: scandal or artefact? Trends in Ecology and Evolution 11:296

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