Preprints
Rippe, John P., Groves Dixon, Zachary L. Fuller, Yi Liao, and Mikhail Matz. 2020. “Environmental Specialization and Cryptic Genetic Divergence in Two Massive Coral Species from the Florida Keys Reef Tract.” Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.11.17.387522.
Kelley, Emma R., Robin S. Sleith, Mikhail V. Matz, and Rachel M. Wright. 2020. “Gene Expression Associated with Disease Resistance and Long-Term Growth in a Reef-Building Coral.” Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.08.12.248286.
Kelley, Emma R., Robin S. Sleith, Mikhail V. Matz, and Rachel M. Wright. 2020. “Gene Expression Associated with Disease Resistance and Long-Term Growth in a Reef-Building Coral.” Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.08.12.248286.
Recent publications
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Dixon, Groves, and Mikhail Matz. 2021. “Benchmarking DNA Methylation Assays in a Reef-Building Coral.” Molecular Ecology Resources 21 (2): 464–77.
Davies, Sarah W., Kelsey N. Moreland, Drew C. Wham, Matt R. Kanke, and Mikhail V. Matz. 2020. “Cladocopium Community Divergence in Two Acropora Coral Hosts across Multiple Spatial Scales.” Molecular Ecology 29 (23): 4559–72.
Dixon, G, Abbott, E., and Matz, M. 2020. Meta-Analysis of the Coral Environmental Stress Response: Acropora Corals Show Opposing Responses Depending on Stress Intensity. Molecular Ecology, July. https://doi.org/10.1111/mec.15535.
Fuller, Z. L., Mocellin, V. J. L., Morris, L. A., Cantin, N., Shepherd, J., Sarre, L., Peng, J., Liao, Y., Pickrell, J., Andolfatto, P., Matz, M., Bay, L. K., & Przeworski, M. (2020). Population genetics of the coral Acropora millepora: Toward genomic prediction of bleaching. Science, 369(6501). https://doi.org/10.1126/science.aba4674
Matz, M. V., E. A. Treml, and B. C. Haller. 2020. “Estimating the Potential for Coral Adaptation to Global Warming across the Indo‐West Pacific.” Global Change Biology. DOI: 10.1111/gcb.15060
Baums, Iliana B., Andrew C. Baker, Sarah W. Davies, Andréa G. Grottoli, Carly D. Kenkel, Sheila A. Kitchen, Ilsa B. Kuffner, et al. 2019. “Considerations for Maximizing the Adaptive Potential of Restored Coral Populations in the Western Atlantic.” Ecological Applications: A Publication of the Ecological Society of America 29 (8): e01978.
Rachel M. Wright, Hanaka Mera, Carly D. Kenkel, Maria Nayfa, Line K. Bay, and Mikhail V. Matz 2019 Positive genetic associations among fitness traits support evolvability of a reef-building coral under multiple stressors. Global Change Biology, DOI: 10.1111/gcb.14764
A Ali, NG Kriefall, LE Emery, CD Kenkel, MV Matz, SW Davies. Recruit symbiosis establishment and Symbiodiniaceae composition influenced by adult corals and reef sediment. Coral Reefs 2019, 38: 405-415.
Manzello, D. P., Matz, M. V., Enochs, I. C., Valentino, L., Carlton, R. D., Kolodziej, G., Serrano, X., Towle, E. K., Jankulak, M. Role of host genetics and heat tolerant algal symbionts in sustaining populations of the endangered coral Orbicella faveolata in the Florida Keys with ocean warming. Global Change Biology 2018, https://doi.org/10.1111/gcb.14545.
Dixon, G. B., Liao, Y., Bay,L. K., and Matz, M. V. Role of gene body methylation in acclimatization and adaptation in a basal metazoan. Proc Natl Acad Sci U S A 2018, https://doi.org/10.1073/pnas.1813749115
Quigley, K. M., Strader, M.E., and Matz, M.V. Relationship between Acropora millepora juvenile fluorescence and composition of newly established Symbiodinium assemblage. PeerJ 2018, 6:e5022.
Barfield, S. J., Aglyamova, G. V, Bay, L. K. & Matz, M. V. Contrasting effects of Symbiodinium identity on coral host transcriptional profiles across latitudes. Mol. Ecol. 2018. doi:10.1111/mec.14774
Cleves PA, Strader ME, Bay LK, Pringle JR, Matz M V. CRISPR/Cas9-mediated genome editing in a reef-building coral. Proc Natl Acad Sci U S A 2018; 201722151.
Matz M V., Treml EA, Aglyamova G V., Bay LK. Potential and limits for rapid genetic adaptation to warming in a Great Barrier Reef coral. PLOS Genet 2018;14: e1007220.
Matz. M. V. Fantastic beasts and how to sequence them: ecological genomics for obscure model organisms. Trends Genet 2018 34: 121-132.
Strader, M.E, Aglyamova, G.V., Matz, M.V. Molecular characterization of larval development from fertilization to metamorphosis in a reef-building coral. BMC Genomics 2018, 19:17
Torda, G., Donelson, J. M., Aranda, M., Barshis, D. J., Bay, L., Berumen, M. L., et al. Rapid adaptive responses to climate change in corals. Nature Climate Change 2017, 7: 627–636.
Pollock, F. J., Katz, S. M., van de Water J. A. J. M., Davies, S. W., Hein, M., Torda, G., Matz, M. V. et al. Coral larvae for restoration and research: a large-scale method for rearing Acropora millepora larvae, inducing settlement, and establishing symbiosis. PeerJ 2017;5: e3732.
Wright, R. M., Kenkel, C. D., Dunn, C. E., Shilling, E. N., Bay, L. K. and Matz, M. V. Intraspecific differences in molecular stress responses and coral pathobiome contribute to mortality under bacterial challenge in Acropora millepora. Scientific Reports 2017, 7:2610.
Davies, S. W., Strader, M. E., Kool, J. T., Kenkel, C. D. and Matz, M. V. Modeled differences of coral life-history traits influence the refugium potential of a remote Caribbean reef. Coral Reefs 2017, doi:10.1007/s00338-017-1583-8.
Oldach, M. J., Workentine, M., Matz, M. V., Fan, T. Y. and Vize, P. D. Transcriptome dynamics over a lunar month in a broadcast spawning acroporid coral. Molecular Ecology 2017, 26:2514-2526.
Kenkel, C. D. and Matz, M. V. Gene expression plasticity as a mechanism of coral adaptation to a variable environment. Nature Ecology & Evolution 2016, 1: 0014. doi:10.1038/s41559-016-0014.
Dixon, G., Bay, L. K., Matz, M. V. Evolutionary consequences of DNA methylation in a basal metazoan. Mol. Biol. Evol. 2016, 33: 2285-2293. doi:10.1093/molbev/msw100.
Strader ME, Aglyamova G V, Matz M V. Red fluorescence in coral larvae is associated with a diapause-like state. Mol. Ecol. 2016, 25:559–569.
Barfield, S., Aglyamova , G.V., Matz, M. V. Evolutionary origins of germline segregation in Metazoa: evidence for a germ stem cell lineage in the coral Orbicella faveolata (Cnidaria, Anthozoa). Proc. Roy. Soc. B 2016, 283: 20152128.
Kenkel, C. D., Almanza, A. T. and Matz, M. V. Fine-scale environmental specialization of reef-building corals might be limiting reef recovery in the Florida Keys. Ecology 2015, 96:3197-3212.
Strader, M. E., Davies, S. W., and Matz, M. V. Differential responses of coral larvae to the colour of ambient light guide them to suitable settlement microhabitat. Roy. Soc. Opensci. 2015, 2:150358.
Davies, S. W., Scarpino, S. V., Pongwarin, T., Scott, J. and Matz, M. V. Estimating trait heritability in highly fecund species. Genes Genomes Genetics (G3) 2015, 2639-2645.
Dixon, G. B., Davies, S. W., Aglyamova, G. V., Meyer, E., Bay, L. K. and Matz, M. V. Genomic determinants of coral heat tolerance across latitudes. Science 2015, 348:1460-1462.
Kenkel, C. D., Setta, S. P., and Matz, M. V. Heritable differences in fitness-related traits among populations of the mustard hill coral, Porites astreoides. Heredity 2015, DOI: HDY.2015.52.
Wright, R. M., Aglyamova, G. V., Meyer, E. and Matz, M. V. Gene expression associated with white syndromes in a reef-building coral, Acropora hyacinthus. BMC Genomics 2015, 16: 371.
Davies, S.W., Treml, E.A., Kenkel, C.D, and Matz, M.V. Exploring the role of Micronesian islands in the maintenance of coral genetic diversity in the Pacific Ocean. Mol Ecol 2015, 24: 70-82.
Dixon, G. B., Bay, L. K., Matz, M. V. Bimodal signatures of germline methylation are linked with gene expression plasticity in the coral Acropora millepora. BMC Genomics 2014, 15:1109.
Puritz, J. B., Matz, M. V., Toonen, R. J., Weber, J. N., Bolnick, D.I. and Bird, C.E. Demystifying the RAD fad. Mol Ecol 2014, 23: 5937-5942.
Green. E.A., Davies, S.W., Matz. M.V., M Medina, M. Quantifying cryptic Symbiodinium diversity within Orbicella faveolata and Orbicella franksi at the Flower Garden Banks, Gulf of Mexico. PeerJ 2014, 2:e386.
Quigley, K.M., Davies, S.W., Kenkel, C.D., Willis, B.L., Matz, M.V., Bay, L.K. Deep-sequencing method for quantifying background abundances of Symbiodinium types: exploring the rare Symbiodinium biosphere in reef-building corals. PLoS ONE 2014, 9:e94297.
Davies, S.W., Meyer, E., Guermond, S.M., Matz, M.V. A cross-ocean comparison of responses to settlement cues in reef-building corals. PeerJ 2014, 2:e333.
Kenkel, C. D., Sheridan, C., Leal, M. C., Bhagooli, R., Castillo, K. D., Kurata, N., McGinty, E., Goulet, T. L. and Matz, M. V. Diagnostic gene expression biomarkers of coral thermal stress. Mol Ecol Res 2014, 14:667-678.
Matz, M. V., Wright, R. M., and Scott, J. G. No control genes required: Bayesian analysis of qRT-PCR data. PLoS ONE 2013, 8(8): e71448.
Kenkel, C. D., Goodbody-Gringley, G. , Caillaud, D., Davies, S. W., Bartels, E., and Matz, M. V. Evidence for a host role in thermotolerance divergence between populations of the mustard hill coral (Porites astreoides) from different reef environments. Mol Ecol 2013, 22: 4335-4348.
Kenkel, C. D., Meyer, E., and Matz, M. V. Gene expression under chronic heat stress in populations of the mustard hill coral (Porites astreoides) from different thermal environments. Mol Ecol 2013, 22:4322-4334.
Wang, S., Meyer, E., McKay, J.K., and Matz, M.V. 2b-RAD: a simple and flexible method for whole-genome genotyping. Nature Methods 2012, 9: 808-810.
Meyer, E., Aglyamova, G. A., and Matz, M. V. Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-Seq procedure. Mol. Ecol. 2011, 17: 3599-3616.
Kenkel, C. D., Traylor, M. R., Wiedenmann, J., Salih, A., and Matz, M. V. Fluorescence of coral larvae predicts their settlement response to crustose coralline algae and reflects stress. Proc. Roy. Soc. B 2011, 278: 2691-2697, doi:10.1098/rspb.2010.2344
Wang, S., Zhang, L., Meyer, E. and Matz, M.V. Construction of a high-resolution genetic linkage map and comparative genome analysis for a reef-building coral Acropora millepora. Genome Biology 2009, 10:R126
Meyer, E., Davies, S., Wang, S., Willis, B. L., Abrego, D., Juenger, T. and Matz, M. V. Genetic variation in responses to settlement cue and elevated temperature in a reef-building coral Acropora millepora. Mar. Ecol. Prog Ser. 2009, 392:81-92.
Meyer, E., Aglyamova, G. V., Wang, S., Buchanan-Carter, J, Abrego, D., Colbourne, J. K., Willis, B. L., and Matz, M. V. Sequencing and de novo analysis of a coral larval transcriptome using 454 GS Flx. BMC Genomics 2009, 10: 219.
Davies, Sarah W., Kelsey N. Moreland, Drew C. Wham, Matt R. Kanke, and Mikhail V. Matz. 2020. “Cladocopium Community Divergence in Two Acropora Coral Hosts across Multiple Spatial Scales.” Molecular Ecology 29 (23): 4559–72.
Dixon, G, Abbott, E., and Matz, M. 2020. Meta-Analysis of the Coral Environmental Stress Response: Acropora Corals Show Opposing Responses Depending on Stress Intensity. Molecular Ecology, July. https://doi.org/10.1111/mec.15535.
Fuller, Z. L., Mocellin, V. J. L., Morris, L. A., Cantin, N., Shepherd, J., Sarre, L., Peng, J., Liao, Y., Pickrell, J., Andolfatto, P., Matz, M., Bay, L. K., & Przeworski, M. (2020). Population genetics of the coral Acropora millepora: Toward genomic prediction of bleaching. Science, 369(6501). https://doi.org/10.1126/science.aba4674
Matz, M. V., E. A. Treml, and B. C. Haller. 2020. “Estimating the Potential for Coral Adaptation to Global Warming across the Indo‐West Pacific.” Global Change Biology. DOI: 10.1111/gcb.15060
Baums, Iliana B., Andrew C. Baker, Sarah W. Davies, Andréa G. Grottoli, Carly D. Kenkel, Sheila A. Kitchen, Ilsa B. Kuffner, et al. 2019. “Considerations for Maximizing the Adaptive Potential of Restored Coral Populations in the Western Atlantic.” Ecological Applications: A Publication of the Ecological Society of America 29 (8): e01978.
Rachel M. Wright, Hanaka Mera, Carly D. Kenkel, Maria Nayfa, Line K. Bay, and Mikhail V. Matz 2019 Positive genetic associations among fitness traits support evolvability of a reef-building coral under multiple stressors. Global Change Biology, DOI: 10.1111/gcb.14764
A Ali, NG Kriefall, LE Emery, CD Kenkel, MV Matz, SW Davies. Recruit symbiosis establishment and Symbiodiniaceae composition influenced by adult corals and reef sediment. Coral Reefs 2019, 38: 405-415.
Manzello, D. P., Matz, M. V., Enochs, I. C., Valentino, L., Carlton, R. D., Kolodziej, G., Serrano, X., Towle, E. K., Jankulak, M. Role of host genetics and heat tolerant algal symbionts in sustaining populations of the endangered coral Orbicella faveolata in the Florida Keys with ocean warming. Global Change Biology 2018, https://doi.org/10.1111/gcb.14545.
Dixon, G. B., Liao, Y., Bay,L. K., and Matz, M. V. Role of gene body methylation in acclimatization and adaptation in a basal metazoan. Proc Natl Acad Sci U S A 2018, https://doi.org/10.1073/pnas.1813749115
Quigley, K. M., Strader, M.E., and Matz, M.V. Relationship between Acropora millepora juvenile fluorescence and composition of newly established Symbiodinium assemblage. PeerJ 2018, 6:e5022.
Barfield, S. J., Aglyamova, G. V, Bay, L. K. & Matz, M. V. Contrasting effects of Symbiodinium identity on coral host transcriptional profiles across latitudes. Mol. Ecol. 2018. doi:10.1111/mec.14774
Cleves PA, Strader ME, Bay LK, Pringle JR, Matz M V. CRISPR/Cas9-mediated genome editing in a reef-building coral. Proc Natl Acad Sci U S A 2018; 201722151.
Matz M V., Treml EA, Aglyamova G V., Bay LK. Potential and limits for rapid genetic adaptation to warming in a Great Barrier Reef coral. PLOS Genet 2018;14: e1007220.
Matz. M. V. Fantastic beasts and how to sequence them: ecological genomics for obscure model organisms. Trends Genet 2018 34: 121-132.
Strader, M.E, Aglyamova, G.V., Matz, M.V. Molecular characterization of larval development from fertilization to metamorphosis in a reef-building coral. BMC Genomics 2018, 19:17
Torda, G., Donelson, J. M., Aranda, M., Barshis, D. J., Bay, L., Berumen, M. L., et al. Rapid adaptive responses to climate change in corals. Nature Climate Change 2017, 7: 627–636.
Pollock, F. J., Katz, S. M., van de Water J. A. J. M., Davies, S. W., Hein, M., Torda, G., Matz, M. V. et al. Coral larvae for restoration and research: a large-scale method for rearing Acropora millepora larvae, inducing settlement, and establishing symbiosis. PeerJ 2017;5: e3732.
Wright, R. M., Kenkel, C. D., Dunn, C. E., Shilling, E. N., Bay, L. K. and Matz, M. V. Intraspecific differences in molecular stress responses and coral pathobiome contribute to mortality under bacterial challenge in Acropora millepora. Scientific Reports 2017, 7:2610.
Davies, S. W., Strader, M. E., Kool, J. T., Kenkel, C. D. and Matz, M. V. Modeled differences of coral life-history traits influence the refugium potential of a remote Caribbean reef. Coral Reefs 2017, doi:10.1007/s00338-017-1583-8.
Oldach, M. J., Workentine, M., Matz, M. V., Fan, T. Y. and Vize, P. D. Transcriptome dynamics over a lunar month in a broadcast spawning acroporid coral. Molecular Ecology 2017, 26:2514-2526.
Kenkel, C. D. and Matz, M. V. Gene expression plasticity as a mechanism of coral adaptation to a variable environment. Nature Ecology & Evolution 2016, 1: 0014. doi:10.1038/s41559-016-0014.
Dixon, G., Bay, L. K., Matz, M. V. Evolutionary consequences of DNA methylation in a basal metazoan. Mol. Biol. Evol. 2016, 33: 2285-2293. doi:10.1093/molbev/msw100.
Strader ME, Aglyamova G V, Matz M V. Red fluorescence in coral larvae is associated with a diapause-like state. Mol. Ecol. 2016, 25:559–569.
Barfield, S., Aglyamova , G.V., Matz, M. V. Evolutionary origins of germline segregation in Metazoa: evidence for a germ stem cell lineage in the coral Orbicella faveolata (Cnidaria, Anthozoa). Proc. Roy. Soc. B 2016, 283: 20152128.
Kenkel, C. D., Almanza, A. T. and Matz, M. V. Fine-scale environmental specialization of reef-building corals might be limiting reef recovery in the Florida Keys. Ecology 2015, 96:3197-3212.
Strader, M. E., Davies, S. W., and Matz, M. V. Differential responses of coral larvae to the colour of ambient light guide them to suitable settlement microhabitat. Roy. Soc. Opensci. 2015, 2:150358.
Davies, S. W., Scarpino, S. V., Pongwarin, T., Scott, J. and Matz, M. V. Estimating trait heritability in highly fecund species. Genes Genomes Genetics (G3) 2015, 2639-2645.
Dixon, G. B., Davies, S. W., Aglyamova, G. V., Meyer, E., Bay, L. K. and Matz, M. V. Genomic determinants of coral heat tolerance across latitudes. Science 2015, 348:1460-1462.
Kenkel, C. D., Setta, S. P., and Matz, M. V. Heritable differences in fitness-related traits among populations of the mustard hill coral, Porites astreoides. Heredity 2015, DOI: HDY.2015.52.
Wright, R. M., Aglyamova, G. V., Meyer, E. and Matz, M. V. Gene expression associated with white syndromes in a reef-building coral, Acropora hyacinthus. BMC Genomics 2015, 16: 371.
Davies, S.W., Treml, E.A., Kenkel, C.D, and Matz, M.V. Exploring the role of Micronesian islands in the maintenance of coral genetic diversity in the Pacific Ocean. Mol Ecol 2015, 24: 70-82.
Dixon, G. B., Bay, L. K., Matz, M. V. Bimodal signatures of germline methylation are linked with gene expression plasticity in the coral Acropora millepora. BMC Genomics 2014, 15:1109.
Puritz, J. B., Matz, M. V., Toonen, R. J., Weber, J. N., Bolnick, D.I. and Bird, C.E. Demystifying the RAD fad. Mol Ecol 2014, 23: 5937-5942.
Green. E.A., Davies, S.W., Matz. M.V., M Medina, M. Quantifying cryptic Symbiodinium diversity within Orbicella faveolata and Orbicella franksi at the Flower Garden Banks, Gulf of Mexico. PeerJ 2014, 2:e386.
Quigley, K.M., Davies, S.W., Kenkel, C.D., Willis, B.L., Matz, M.V., Bay, L.K. Deep-sequencing method for quantifying background abundances of Symbiodinium types: exploring the rare Symbiodinium biosphere in reef-building corals. PLoS ONE 2014, 9:e94297.
Davies, S.W., Meyer, E., Guermond, S.M., Matz, M.V. A cross-ocean comparison of responses to settlement cues in reef-building corals. PeerJ 2014, 2:e333.
Kenkel, C. D., Sheridan, C., Leal, M. C., Bhagooli, R., Castillo, K. D., Kurata, N., McGinty, E., Goulet, T. L. and Matz, M. V. Diagnostic gene expression biomarkers of coral thermal stress. Mol Ecol Res 2014, 14:667-678.
Matz, M. V., Wright, R. M., and Scott, J. G. No control genes required: Bayesian analysis of qRT-PCR data. PLoS ONE 2013, 8(8): e71448.
Kenkel, C. D., Goodbody-Gringley, G. , Caillaud, D., Davies, S. W., Bartels, E., and Matz, M. V. Evidence for a host role in thermotolerance divergence between populations of the mustard hill coral (Porites astreoides) from different reef environments. Mol Ecol 2013, 22: 4335-4348.
Kenkel, C. D., Meyer, E., and Matz, M. V. Gene expression under chronic heat stress in populations of the mustard hill coral (Porites astreoides) from different thermal environments. Mol Ecol 2013, 22:4322-4334.
Wang, S., Meyer, E., McKay, J.K., and Matz, M.V. 2b-RAD: a simple and flexible method for whole-genome genotyping. Nature Methods 2012, 9: 808-810.
Meyer, E., Aglyamova, G. A., and Matz, M. V. Profiling gene expression responses of coral larvae (Acropora millepora) to elevated temperature and settlement inducers using a novel RNA-Seq procedure. Mol. Ecol. 2011, 17: 3599-3616.
Kenkel, C. D., Traylor, M. R., Wiedenmann, J., Salih, A., and Matz, M. V. Fluorescence of coral larvae predicts their settlement response to crustose coralline algae and reflects stress. Proc. Roy. Soc. B 2011, 278: 2691-2697, doi:10.1098/rspb.2010.2344
Wang, S., Zhang, L., Meyer, E. and Matz, M.V. Construction of a high-resolution genetic linkage map and comparative genome analysis for a reef-building coral Acropora millepora. Genome Biology 2009, 10:R126
Meyer, E., Davies, S., Wang, S., Willis, B. L., Abrego, D., Juenger, T. and Matz, M. V. Genetic variation in responses to settlement cue and elevated temperature in a reef-building coral Acropora millepora. Mar. Ecol. Prog Ser. 2009, 392:81-92.
Meyer, E., Aglyamova, G. V., Wang, S., Buchanan-Carter, J, Abrego, D., Colbourne, J. K., Willis, B. L., and Matz, M. V. Sequencing and de novo analysis of a coral larval transcriptome using 454 GS Flx. BMC Genomics 2009, 10: 219.