The Brown Lab

Social and Evolutionary Protistology

Our lab is broadly interested in the evolution of sociality in microbes. We are developing model systems to look at the commonalities among the greatest examples of convergent evolution known to date. We have discovered that a great diversity of single celled eukaryotic microbes (AKA protists) are capable of working with one another to form a complex body made of thousands of individual cells. This is one of the simplest and most striking examples of emergent behavior. In many cases, this behavior is sacrificial where some of the cells that become part of the multicellular body die for the “greater good” of their kin. To examine the commonalities amongst the various social protists, we are taking a multi-pronged approach using comparative genomics and developmental transcriptomics to elucidate the genetic basis of sociality.

Our lab is also interested in examining the deep evolution of eukaryotic lineages. We are using novel approaches in phylogenomics to examine how the various major groups of eukaryotes evolved over the course of the last ~2 billion years. We are currently focused on the evolutionary histories of amoeboid organisms.


News


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Publications
^undergrad trainee, +grad trainee

Under Review or Revision
Geisen S, Mitchell EAD, Wilkinson DM, Adl S, Bonkowski M, Brown MW, Fiore-Donno AM, Heger TJ, Jassey VEJ, Krashevska V, Lahr DJG, Marcisz K, Mulot M, Payne R, Singer D, Anderson OR, Charman DJ, Ekelund F, Griffiths BS, Rønn R, Smirnov A, Bass D, Belbahri L, Berney C, Blandenier Q, Chatzinotas A, Clarholm M, Dunthorn M, Feest A, Fernandez-Parra LD, Foissner W, Fournier B, Gentekaki E, Hajek M, Helder J, Jousset A, Koller R, Kumar S, La Terza A, Lamentowicz M, Mazei Y, Santos SS, Seppey CVW, Spiegel FW, Walochnik J, Winding A, Lara E. Under Review. Soil protistology rebooted: 66 fundamental questions to start with. The ISEM Journal.

Tice AK+,
Shadwick LL, Fiore-Donno AM, Geisen S, Kang S+, Spiegel FW, Wilkinson K, Bonkowski M, Dumack K, Lahr DJG, Voelcker E, Clauß S, Zhang J, Brown MW. Under Revision. Expansion of the Acanthamoebidae (Centramoebida, Amoebozoa). Biology Direct.

2016
Hofstatter P, Tice AK+, Kang S+, Brown MW*, Lahr DJG*. 2016, In press. Evolution of bacterial recombinase A (recA) in eukaryotes explained by addition of genomic data of key microbial lineages. Proceedings of the Royal Society B: Biological Sciences. *Both last authors are corresponding.

Gawryluk RMR, Kamikawa R, Stairs CW, Silberman JD,
Brown MW, Roger AJ. 2016, In press. The earliest stages of mitochondrial adaptation to low oxygen revealed in a novel rhizarian. Current Biology.

Tice AK+
, Brown MW, Altig R. 2016. Hyla chrysoscelis (Cope’s gray treefrog), H. avivoca (bird-voiced treefrog), and H. cinerea (green treefrog). Interactions of protozoans and algae with frog eggs and tadpoles. Herpetological Review 47(3): 438-439.

Shadwick LL,
Brown MW, Tice AK+, Spiegel FW. 2016, In press. A new amoeba with protosteloid fruiting: Luapeleamoeba hula n. g. n. sp. Acta Protozoologica. 55(3): XXX-XXX.

Harding T,
Brown MW, Simpson AGB, Roger AJ. 2016, In press. Osmoadaptative strategy and its molecular signature in obligately halophilic heterotrophic protists. Genome Biology and Evolution. DOI: 10.1093/gbe/evw152.

Hamann E, Gruber-Vodicka H, Kleiner M, Tegetmeyer HE, Riedel D, Littmann S, Chen J, Milucka J, Viehweger B, Becker KW, Dong X, Stairs CW, Hinrichs K,
Brown MW, Roger AJ, Strous M. 2016. Environmental Breviatea harbour mutualistic Arcobacter epibionts. Nature. 534: 254-258.

Noguchi F, Tanifuji G,
Brown MW, Fujikura K, Takishita K. 2016. Complex evolution of two types of cardiolipin synthase in the eukaryotic lineage Stramenopiles. Molecular Phylogenetics and Evolution. 101: 133-141.

Walthall AC^, Tice AK+
, Brown MW. 2016. A new species of Flamella (Amoebozoa, Variosea, Gracilipodida) isolated from a freshwater pool in southern Mississippi, USA. Acta Protozoologica. 55(2): 111-117.

Tice AK+
, Silberman JD, Walthall AC^, Le KND, Spiegel FW, Brown MW. 2016. Sorodiplophrys stercorea: another novel lineage of sorocarpic multicellularity. Journal of Eukaryotic Microbiology. DOI: 10.1111/jeu.12311

Bass D, Silberman JD,
Brown MW, Pearce RA, Tice AK+, Jousset A, Geisen S, Hartikainen H. 2016. Coprophilic amoebae and flagellates, including Guttulinopsis, Rosculus and Helkesimastix, characterise a divergent and diverse rhizarian radiation and contribute to a large diversity of faecal-associated protists. Environmental Microbiology. 18(5): 1604-1619.

Pánek T, Zadrobílková E, Walker G,
Brown MW, Gentekaki E, Hroudová M, Kang S+, Roger AJ, Tice AK+, Vlček C, Čepička I. 2016. First multigene analysis of Archamoebae (Amoebozoa: Conosa) robustly reveals its phylogeny and shows that Entamoebidae represents a deep lineage of the group. Molecular Phylogenetics and Evolution. 98: 41–51.

Brown LR, Gunnell SM, Cassella A, Keller LE, Scherkenbach LA, Mann B,
Brown MW, Rosch JW, Tuomanen EI, Thornton JA. 2016. AdcAII of Streptococcus pneumoniae affects pneumococcal invasiveness. PLoS ONE. 11(1): e0146785.

2015
Sharpe SC, Eme L, Brown MW, Roger AJ. 2015. Timing the origins of multicellular eukaryotes through phylogenomics and relaxed molecular clock analyses*. In Nedelcu, Ruiz-Trillo (Eds.) Evolutionary transitions to multicellular life: Principles and mechanisms. Springer, New York. pp. 3-29. ISBN 978-94-017-9641-5. DOI: 10.1007/978-94-017-9642-2_1. *peer-reviewed.

2014
Maguire F, Henriquez FL, Leonard G, Dacks JB, Brown MW, Richards TA. 2014. Complex patterns of gene fission in the eukaryotic folate biosynthesis pathway. Genome Biology and Evolution 6(10): 2709–2720.

Watson PM^
, Sorrell SC^, Brown MW. 2014. Ptolemeba n. gen., a novel genus of hartmannellid amoebae (Tubulinea, Amoebozoa); with an emphasis on the taxonomy of Saccamoeba. Journal of Eukaryotic Microbiology 61(6): 611–619.

Eme L, Sharpe SC,
Brown MW, Roger AJ. 2014. On the age of eukaryotes: Evaluating evidence from fossils and molecular clocks. Cold Spring Harbor Perspectives in Biology 6:a016139. Part of Cold Spring Harbor Perspectives on The Origin and Evolution of Eukaryotes. Keeling, Koonin (Eds.).

Stairs CW, Eme L,
Brown MW, Mutsaers C, Susko E, Dellaire G, Soanes DM, van der Giezen M, Roger AJ. 2014. A SUF Fe-S cluster biogenesis system in the mitochondrion-related organelles of the microaerophilic protist Pygsuia. Current Biology 24: 1176–1186.

Tanifuji G, Onodera N,
Brown MW, Curtis BA, Roger AJ, Wong GK, Melkonian M, Archibald JM. 2014. Nucleomorph and plastid genome sequences of the chlorarachniophyte Lotharella oceanica: convergent reductive evolution and frequent recombination in nucleomorph-bearing algae. BMC Genomics 15: 374.

Kudryavtsev A,
Brown MW, Tice A, Spiegel FW, Pawlowski J, Anderson OR. 2014. A revision of the order Pellitida Smirnov et al., 2011 (Amoebozoa, Discosea) based on ultrastructural and molecular evidence, with description of Endostelium crystalliferumn. sp. Protist 165(2): 208-229.

Suga H, Torruella G, Burger G,
Brown MW, Ruiz-Trillo I. 2014. Earliest holozoan expansion of phosphotyrosine signaling. Molecular Biology and Evolution 31(3): 517-528.

Kamikawa R, Kolisko M, Nishimura Y, Yabuki A,
Brown MW, Ishikawa SA, Ishida K, Roger AJ, Hashimoto T, Inagaki Y. 2014. Gene-content evolution in discobid mitochondria deduced from the phylogenetic position and complete mitochondrial genome of Tsukubamonas globosa. Genome Biology and Evolution 6(2): 306–315.

2013
Brown MW, Sharpe SC, Silberman JD, Heiss A, Lang BF, Simpson AGB, Roger AJ. 2013. Phylogenomics demonstrates that breviate flagellates are related to opisthokonts. Proceedings of the Royal Society B: Biological Sciences 280: 20131755.

Brown MW+,
Silberman JD. 2013. The Non-Dictyostelid Sorocarpic Amoebae*. In Romeralo, Escalante, Baldauf (Eds.) Dictyostelids - Evolution, Genomics and Cell Biology. Springer, Heidelberg Germany. pp 219-242. ISBN 978-3-642-38487-5. DOI: 10.1007/978-3-642-38487-5_12. +Senior & Corresponding Author. *editorial review only, not peer-reviewed.

Suga H, Chen Z, de Mendoza A, Sebé-Pedrós A,
Brown MW, Kramer E, Carr M, Kerner P, Vervoort M, Sánchez-Pons N, Torruella G, Derelle R, Manning G, Lang BF, Russ C, Haas BJ, Roger AJ, Nusbaum C, Ruiz-Trillo I. 2013. The Capsaspora genome reveals a complex unicellular prehistory of animals. Nature Communications 4: 2325.

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Kamikawa R,
Brown MW, Nishimura Y, Sako Y, Heiss AA, Yubuki N, Gawryluk R, Simpson AGB, Roger AJ, Hashimoto T, Inagaki Y. 2013. Parallel re-modeling of EF-1α function: divergent EF-1α genes co-occur with EFL genes in diverse distantly related eukaryotes. BMC Evolutionary Biology 13: 131.

Harding T,
Brown MW, Plotnikov A, Selivanova E, Park JS, Gunderson JH, Baumgartner M, Silberman JD, Roger AJ, Simpson AGB. 2013. Amoeba stages in the deepest branching heteroloboseans, including Pharyngomonas: evolutionary and systematic implications. Protist 164(2): 272-286.

2012
Adl SM, Simpson AGB, Lane CE, Lukes J, Bass D, Bowser SS, Brown MW, Burki F, Dunthorn M, Hampl V, Heiss A, Hoppenrath M, Lara E, Legall L, Lynn DH, McManus H, Mitchell EAD, Mozley-Stanridge SE, Parfrey LW, Pawlowski J, Rueckert S, Shadwick LL, Schoch C, Smirnov A, Spiegel FW. 2012. The revised classification of eukaryotes. Journal of Eukaryotic Microbiology 59(5): 429–514.

Brown MW,
Kolisko M, Silberman JD, Roger AJ. 2012. Aggregative multicellularity evolved independently in the eukaryotic supergroup Rhizaria. Current Biology 22(12): 1123-1127Movie 1, Movie 2.

Brown MW
, Silberman JD, Spiegel FW. 2012. A contemporary evaluation of the acrasids (Acrasidae, Heterolobosea, Excavata). European Journal of Protistology 48(2): 103-123.

Schnittler M, Novozhilov YK, Romeralo M,
Brown MW, Spiegel FW. 2012. Fruit body-forming protists: Myxomycetes and Myxomycete-like organisms Acrasia, Eumycetozoa*. In Frey (Ed.) Engler’s Syllabus of Plant Families, 13th ed. Part 1: Blue-green Algae, Myxomycetes and Myxomycete-like Organisms, Phytoparasitic protists, Heterotrophic Heterokontobionta and Fungi. Borntraeger Science Publishers, Berlin. ISBN 978-3-443-01061-4. DOI: 10.13140/2.1.4668.9284. *editorial review only, not peer-reviewed.

2011
Brown MW, Silberman JD, Spiegel FW. 2011. “Slime molds” among the Tubulinea (Amoebozoa): Molecular systematics and taxonomy of Copromyxa. Protist 162: 277-287.

2010
Brown MW, Silberman JD, Spiegel FW. 2010. A morphologically simple species of Acrasis (Heterolobosea, Excavata), Acrasis helenhemmesae n. sp. Journal of Eukaryotic Microbiology 57(4): 346-353.

Brown MW
. 2010. Ph.D. Dissertation, University of Arkansas, Biological Sciences. Placing the Forgotten Slime Molds (Sappinia, Copromyxa, Fonticula, Acrasis, and Pocheina), using molecular phylogenetics. 258p. (Silberman JD & Spiegel FW, Co-Supervisors).

2009
Brown MW, Spiegel FW, Silberman JD. 2009. Phylogeny of the “forgotten” cellular slime mold, Fonticula alba, reveals a key evolutionary branch within Opisthokonta. Molecular Biology and Evolution 26(12): 2699-2709.

Shadwick LL, Spiegel FW, Shadwick JDL,
Brown MW, Silberman JD. 2009. Eumycetozoa = Amoebozoa?: SSUrDNA Phylogeny of Protosteloid Slime Molds and its Significance for the Supergroup Amoebozoa. PLoS ONE 4(8): e6754.

2007
Spiegel FW, Shadwick JD, Lindley LA, Brown MW, Nderitu G. 2007. A Beginner’s Guide to Identifying the Protostelids. http://slimemold.uark.edu/pdfs/Handbook1_3rd.pdf

Brown MW
, Spiegel FW, Silberman JD. 2007. Amoeba at Attention: Phylogenetic Affinity of Sappinia pedata. Journal of Eukaryotic Microbiology 54(6): 511-519.

Published Abstracts
Hofstatter PG, Lahr DJG, Brown MW. 2016. Primary and secondary endosymbiotic gene transfer of bacterial RecA in eukaryotes. Protistology 10(2):27

Kosakyan A,
Brown MW, Lara E, Mitchell EAD, Lahr DJG. 2016. Bridging the gap between traditional taxonomy and transcriptomics in arcellinids (Amoebozoa). Protistology 10(2):37

Tice AK, Shadwick LL, Spiegel FW, Geisen S, Fiore-Donno AM, Bonkowski M, Dumack K, Kang S,
Brown MW. 2016. Many previously incertae sedis amoebozoans find a home within the Centramoebida. Protistology 10(2):80.

Park JS, Grimm K, Zhang QQ, Harding T,
Brown MW, Simpson AGB. 2011. The deeper-level phylogeny and evolution of Heterolobosea: a major group of protists. Joint meeting of the Phycological Society of America and the International Society of Protistologists. University of Washington. Seattle, Washington, USA. Journal of Phycology 47:S32.

Brown MW
, Silberman JD, Spiegel FW. 2008. Morphological and molecular variation in three morphotypes of Acrasis. Annual Meeting of the Mycological Society of America. Penn State University, Pennsylvania, USA. Inoculum 59(4): 21.

Brown MW
, Spiegel FW 2007. Assessment of protostelid diversity in Ozark Plateau oak-hickory forests in south central USA. Annual Meeting of the Mycological Society of America. Louisiana State University. Baton Rogue, Louisiana, USA. Inoculum 59(2): 9.

Lindley LA,
Brown MW, Lawrence A, Silberman JD, Spiegel FW. 2007. Schizoplasmodium: a genus reconstituted. Annual Meeting of the Mycological Society of America. Louisiana State University, Louisiana, USA. Inoculum 59(2): 27.

Spiegel FW, Shadwick JD,
Brown MW, Hemmes DE. 2007. Protostelids of the Hawaiian Archipelago. Annual Meeting of the Mycological Society of America. Louisiana State University, Louisiana, USA. Inoculum 59(2): 38.

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Dr. Matthew W. Brown, Ph.D., Matthew Brown’s Lab, Matt Brown Lab, Assistant Professor, Department of Biological Sciences, Mississippi State University, The Brown Lab, The Brown Laboratory Keywords: Functional genomics, protistan, phylogeny, biodiversity, phylogenomics, Evo-Devo, Developmental Biology, RNAseq, Genome, Phylogenetics, Systematics, Taxonomy, Animal, Metazoa, Fungi, Opisthokonta, Amoebozoa, Rhizaria, Stramenopiles, ciliates, alveolates, Alveolata, Heterolobosea, heterolobosean, Acrasis, Pocheina, Fonticula, Guttulinopsis, Dictyostelium, Dictyostelid, Acytostelium, cellular slime mold, sorocarpic amoeba, Copromyxa, Hartmannella, protostelid, protostelioid, Nuclearia, nucleariid, Sorogena, Copromyxella, Pygsuia, Breviata, breviate, anaerobic, anoxic, mitochondria, hydrogenosome, eukaryote, emergent behavior, altruism, sorocyst, protosteloid, amoeba, ameba, amoeboid, mould, protist, stramenopiles, Tubulinea, Endostelium, animals, heterokont, heterokonta, psuedofungi, oomycetes, Opalina, opalines, proteromonas, Ancyromonas, Apusomonas, Obazoa, eukarya, PCR, qPCR, SSU, small subunit, Ptolemeba, Thecamoeba, Cercomonas, NSF, National Science Foundation, National Institutes of Health, Journal of Eukaryotic Microbiology, Acta Protozoologica, Taxonomist, Alveoli, Leshimania, Toxoplasma, Protist Laboratory, Protistology Laboratory, Microbial Eukaryote Diversity, Eukaryotic Microbiology, Euk Micro, Microbial Genetics, Microbial Genomics, 454, Next Generation Sequencing, Illumina, Roche, msstate, msu, Oktibbeha Sorodiplophrys stercorea, Cashia, Saccamoeba, Coprophilia, Coprophilis, Coprophilic, Dung amoebae, Labyrithulomycetes, Labyrithulids, molecular clocks, acrasid, Acrasoid, pochenioid, pochenid, social protist, moelcular biology and evolution, genome biology and evolution, current biology,