Publications | The Brown Lab

The Brown Lab


^undergrad trainee, +grad trainee, `postdoc trainee
@=Peer-Reviewed, $=editorial review, ~=not reviewed or pre-print

Under Review or Submitted
None Currently

64. Tice AK+*, Žihala D*, Pánek T`*, Jones RE+", Salomaki E", Nenarokov S, Burki F, Eliáš M, Eme L, Roger AJ, Rokas A, Shen X, Strassert JFH, Kolísko M, Brown MW. 2021.PhyloFisher: A phylogenomic package for resolving eukaryotic relationships. PloS Biology. doi: https://10.1371/journal.pbio.3001365 @ Data Files : * & " =Contributed equally

Rodriguez-Caro F, Fenner J, Bhardwaj S, Cole J, Benson JC, Colombara AM, Papa R, Brown MW, Martin A, Range RC, Counterman BA. In Press, 2021. Novel doublesex duplication associated with sexually dimorphic development of dogface butterfly wings. Molecular Biology and Evolution. doi: @

62. Kang S+*, Tice AK+*, Stairs CW, Lahr DJG, Jones RE+, Brown MW. 2021. The integrin-mediated adhesive complex in the ancestor of animals, fungi, and amoebae. Current Biology. @ Preprint bioRivx 10.1101/2020.04.29.069435. *=Contributed equally (first). @

Porfírio-Sousa A, Tice AK+, Brown MW, Lahr DJG. 2021. Phylogenetic reconstruction and evolution of the Rab GTPase gene family in Amoebozoa. Small GTPases. 10.1080/21541248.2021.1903794 @

60. Salomaki E, Eme L, Brown MW, Kolisko M. 2020. Releasing uncurated datasets is essential for reproducible phylogenomics. Nature Ecology and Evolution. *editorial review only, not peer-reviewed. $

59. Lawal HM, Schilde C, Kin K, Brown MW, James J, Prescott AR, Schaap P. 2020. Cold climate adaptation is a plausible cause for evolution of multicellular sporulation in Dictyostelia. Scientific Reports. 10: 8797 @

58. Brown MW, Tice AK. 2020. A genetic toolbox for marine protists. Nature Methods. 17: 469–470. doi: *editorial review only, not peer-reviewed. $

57. Burki F, Roger AJ, Brown MW, Simpson AGB. 2020. The new tree of eukaryotes. Trends in Ecology and Evolution (TREE). 35: 43-55. doi: @

Yubuki N, Lopez-Garcia P, Reboul G, Brown MW, Pollet N, Moreira D. 2020. Ancient Adaptive Lateral Gene Transfers in the Symbiotic Opalina - Blastocystis Stramenopile Lineage. Molecular Biology and Evolution. 37: 651–659. doi: @

Onsbring H*, Tice AK+*, Barton BT, Brown MW”, Ettema TJG”. 2020. An efficient single-cell transcriptomics workflow for microbial eukaryotes benchmarked on Giardia intestinalis cells. BMC Genomics. 21: 448. [4.053]@ Preprint bioRxiv 10.1101/782235v1. DOI: *&”=Contributed equally (first and last). @

54. Brown MW. 2019. Effective and efficient cytoskeleton (actin and microtubules) fluorescence staining of adherent eukaryotic cells. doi: not peer-reviewed ~

53. Lahr DJG, Kosakyana A, Lara E, Mitchell EAD, Morais L, Porfirio-Sousa AL, Ribeiro GM, Tice AK+, Pánek T`, Kang S+, Brown MW. 2019. Phylogenomics and ancestral morphological reconstruction of testate amoebae demonstrate high diversity of microbial eukaryotes in the Neoproterozoic. Current Biology. 29(6): 911-1003.e3. @

Porter SM, Reidman LA. 2019. Evolution: Ancient Fossilized Amoebae Find Their Home in the Tree. Current Biology. 29 (6): PR212-R215.
Brown MW, Lahr DJG. 2019. ‘Micro snails’ we scraped from sidewalk cracks help unlock details of ancient earth’s biological evolution. The Conversation. February 28, 2019. *editorial review only, not peer-reviewed. $

52. Fiore-Donno AM, Tice AK+, Brown MW. 2019. A Non-Flagellated Member of the Myxogastria and Expansion of the Echinosteliida. Journal of Eukaryotic Microbiology. 66: 538-544. doi: @

51. Schuler GA+, Brown MW. 2019. Description of Armaparvus languidus n. gen. n. sp. confirms ultrastructural unity of Cutosea (Amoebozoa, Evosea). Journal of Eukaryotic Microbiology. 66: 158-166. doi: @

50. Adl SM, Bass D, Lane CE, Lukeš J, Schoch CL Smirnov A, Agatha S, Berney C, Brown MW, Burki F, Cárdenas P, Čepička I, Chistyakova L, del Campo J, Dunthorn M, Edvardsen B, Eglit Y, Guillou L, Hampl V, Heiss AA Hoppenrath M, James TY, Karpov S, Kim E, Kolisko M, Kudryavtsev A, Lahr DJG, Lara E, Le Gall L, Lynn DH, Mann DG, Massana R, Mitchell EAD, Morrow C, Park JS, Pawlowski JW, Powell MJ, Richter DJ, Rueckert S, Shadwick L, Shimano S, Simpson AGB, Spiegel FW, Torruella G, Youssef N, Zlatogursky V, Zhang Q. 2019. Revisions to the classification, nomenclature, and diversity of eukaryotes. Journal of Eukaryotic Microbiology. 66: 4-119. doi: @


49. Hofstatter PG, Brown MW, Lahr DJG. 2018. Comparative genomics supports sex and meiosis in diverse Amoebozoa. Genome Biology and Evolution. 10: 3118–3128. doi: @

48. del Campo J, Kolisko M, Boscaro V, Santoferrara L, Massana R, Guillou L, Simpson AGB, Berney C, de Vargas C, Kaye J, Bender S, Brown MW, Keeling P, Wegener Parfrey L. 2018. EukRef: phylogenetic curation of ribosomal RNA to enhance understanding of eukaryotic diversity and distribution. PLoS Biology. doi: PrePrint bioRxiv 278085; doi: @

47. Schuler GA+, Tice AK+, Pearce RA, Foreman E^, Stone J, Gammill S, Willson JD, Reading C, Silberman JD, Brown MW. 2018. Phylogeny and classification of novel diversity in Sainouroidea (Cercozoa, Rhizaria) sheds light on a highly diverse and divergent clade. Protist. 169: 853–874. @

46. Heiss AA, Kolisko M, Ekelund F, Brown MW, Roger AJ, Simpson AGB. 2018. Combined morphological and phylogenomic re-examination of malawimonads, a critical taxon for inferring the evolutionary history of eukaryotes. Royal Society Open Science. 5: 171707. @

45. Brown MW, Heiss AA, Kamikawa R, Inagaki Y, Yabuki A, Tice AK+, Shiratori T, Ishida K, Hashimoto T, Simpson AGB, Roger AJ. 2018. Phylogenomics places orphan protistan lineages in a novel eukaryotic super-group. Genome Biology and Evolution. 10: 427-433. PrePrint bioRxiv 227884; doi: SUPPLEMENTAL FILE - Single gene alignments and trees (Brown_etal.2017.CRuMS.tgz) @

44. Leonard G, Labarre A, Milner D, Monier A, Soanes D, Wideman JG, Maguire F, Stevens S, Sain D, Grau-Bove X, Sebe-Pedros A, Stajich JE, Paszkiewicz K, Brown MW, Hall N, Wickstead B, Richards TA. 2018. Comparative genomic analysis of the ‘psuedofungus’ Hyphochytrium catenoides. Open Biology. 8: 170184. @

43. Kang S+, Tice AK+, Spiegel FW, Silberman JD, Pánek T, Čepička I, Kostka M, Kosakyan A, Alcântara DM, Roger AJ, Shadwick LL, Smirnov A, Kudryavstev A, Lahr DJG, Brown MW. 2017. Between a pod and a hard test: the deep evolution of amoebae. Molecular Biology and Evolution. 34: 2258-2270. SUPPLEMENTAL FILE - Single gene alignments and trees (Kang_etal.2017.tgz) @

42. 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. 2017. Soil protistology rebooted: 30 fundamental questions to start with. Soil Biology and Biochemistry. 111: 94-103. @

41. Spiegel FW, Shadwick LL, Ndiritu G, Brown MW, Aguilar M, Shadwick JD. 2017. Protosteloid Amoebozoa (Protosteliida, Protosporangiida, Cavosteliida, Schizoplasmodiida, Fractoviteliida, and sporocarpic members of Vannellida, Centramoebida, and Pellitida). In Archibald, Simpson, Slamovits, Margulis, Melkonian, Chapman, Corliss (Eds.) Handbook of the Protists. Springer International Publishing. pp. 1-38. ISBN: 978-3-319-32669-6. DOI:10.1007/978-3-319-32669-6_12-1. @

40. Pánek T, Simpson AGB, Brown MW, Dexter-Dyer B. 2016. Heterolobosea. In Archibald, Simpson, Slamovits, Margulis, Melkonian, Chapman, Corliss (Eds.) Handbook of the Protists. Springer International Publishing. pp. 1-42. ISBN: 978-3-319-32669-6. DOI: 10.1007/978-3-319-32669-6_10-1. @

39. Tice AK+, Shadwick LL, Fiore-Donno AM, Geisen S, Kang S+, Schuler GA+, Spiegel FW, Wilkinson K, Bonkowski M, Dumack K, Lahr DJG, Voelcker E, Clauß S, Zhang J, Brown MW. 2016. Expansion of the molecular and morphological diversity of Acanthamoebidae (Centramoebida, Amoebozoa) and identification of a novel life cycle type within the group. Biology Direct. 11: 69. @

38. Heiss AA, Brown MW, Simpson AGB. 2016. Apusomonadida. In Archibald, Simpson, Slamovits, Margulis, Melkonian, Chapman, Corliss (Eds.) Handbook of the Protists. Springer International Publishing. pp. 1-27. ISBN: 978-3-319-32669-6. DOI: 10.1007/978-3-319-32669-6_15-1. @

37. Hofstatter P, Tice AK+, Kang S+, Brown MW*, Lahr DJG*. 2016. 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 283: 20161453. *Both last authors are corresponding. @

36. Gawryluk RMR, Kamikawa R, Stairs CW, Silberman JD, Brown MW, Roger AJ. 2016. The earliest stages of mitochondrial adaptation to low oxygen revealed in a novel rhizarian. Current Biology 26(20): 2729–2738. @

35. 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. $

34. Shadwick LL, Brown MW, Tice AK+, Spiegel FW. 2016. A new amoeba with protosteloid fruiting: Luapeleamoeba hula n. g. n. sp. Acta Protozoologica 55(3): 123-134. @

33. Harding T, Brown MW, Simpson AGB, Roger AJ. 2016. Osmoadaptative strategy and its molecular signature in obligately halophilic heterotrophic protists. Genome Biology and Evolution 8(7): 2241-2258. @

32. 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. @

31. 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. @

30. 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. @

29. 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 63(5): 623-628. @

28. 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. @

27. 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. @

26. 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. @

25. 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. @

24. 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. @

23. 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. @

22. 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.). @

21. 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.

20. 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. @

19. 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. @

18. 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. @

17. 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. @

16. 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. SUPPLEMENTAL FILE - Single gene alignments and trees (Brown_etal.2013.SingleGenes.tgz) @

15. 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. $

14. 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. @


13. 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. @

12. 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. @

11. 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. @

10. 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. @

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

8. 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. $

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

6. 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. @

5. 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).

4. 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. @

3. 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. @

2. Spiegel FW, Shadwick JD, Lindley LA, Brown MW, Nderitu G. 2007. A Beginner’s Guide to Identifying the Protostelids. not peer-reviewed. ~

1. 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.