Proteomic analysis of the Aggregation Factor from the sponge Clathria (Microciona) prolifera suggests an ancient protein domain toolkit for allorecognition in animals
Ruperti, F, Dzieclatkowska, M, Pankey, SM, Asensio, CS, Anselmetti, D, Fernandez-Busquets, X, and SA Nichols (2024)
BioRxiv
HCR-fluorescent in situ hybridization (HCR-FISH) of gemmule hatched freshwater sponges
SA Nichols (2023)
Protocols.io dx.doi.org/10.17504/protocols.io.5jyl8jwkdg2w/v1
Growing freshwater sponges from gemmules in the laboratory
SA Nichols (2023)
Protocols.io dx.doi.org/10.17504/protocols.io.x54v9dkj4g3e/v1
Fixation and staining of Ephydatia muelleri for fluorescence microscopy
SA Nichols (2023)
Protocols.io dx.doi.org/10.17504/protocols.io.j8nlkwnx6l5r/v1
MRTF specifies a muscle-like contractile module in Porifera
Colgren, J and SA Nichols (2022)
Nature Communications 13, article 4134, https://doi.org/10.1038/s41467-022-31756-9
Tracing the evolutionary origin of desmosomes
Green, KJ, Roth-Carter, Q, Niessen, CM and SA Nichols (2020)
Current Biology, https://doi.org/10.1016/j.cub.2020.03/047
Diverse cell junctions with unique molecular composition in tissues of a sponge (Porifera)
Mitchell, J and SA Nichols (2019)
EvoDevo 10, article 26
https://rdcu.be/b9jE3
The significance of sponges for comparative studies of developmental evolution
Colgren, J and SA Nichols (2019)
WIREs Developmental Biology e359, https://doi.org/10.1002/wdev.359
Evolution as a guide for experimental cell biology
Colgren, J and SA Nichols (2019)
PLoS Genetics
15(2): e1007937. https://doi.org/10.1371/journal.pgen.1007937
Analysis of a vinculin homolog in a sponge (phylum Porifera) reveals that vertebrate-like cell adhesions emerged early in animal evolution.
Miller, PW, Pokutta, S, Mitchell, JM, Chodaparambil, JV, Clarke, DN, Nelson, WJ, Weis, WI and SA Nichols (2018)
Journal of Biological Chemistry
http://www.jbc.org/content/293/30/11674
Evidence of adhesion and signaling roles for β-catenin in the sponge Ephydatia muelleri.
Schippers, KJ and SA Nichols (2018)
Molecular Biology and Evolution
https://doi.org/10.1093/molbev/msy033
Transcriptome sequencing and delimitation of sympatric Oscarella species (O. carmela and O. pearsei sp. nov) from California, USA.
Ereskovsky, A, Richter, DJ, Lavrov, DV, Schippers, KJ and SA Nichols (2017)
PlosONE at https://doi.org/10.1371/journal.pone.0183002
Conserved expression of vertebrate microvillar gene homologs in choanocytes of freshwater sponges
Pena, FJ, Alie, A, Richter, DJ, Wang, L, Funayama, N, and SA Nichols (2016)
EvoDevo 7:13 DOI: 10.1186/s13227-016-0050-x
What is an animal?
Nichols, SA. (2016)
In Klinman, R.M. (ed.), Encyclopedia of Evolutionary Biology. vol. 1, pp. 84-92. Oxford: Academic Press.
Deep, dark secrets of melatonin in animal evolution
Schippers, KJ and SA Nichols (2014)
Cell. 159:9-10
The identification of microRNAs in calcisponges: independent evolution of microRNAs in basal metazoans.
Robinson, JM, Sperling, EA, Bergum, B, Adamski, M, Nichols, SA, Adamska, M, and Peterson, KJ. (2013)
JEZ Part B: Molecular and Developmental Evolution. 320(3):84-93.
Origin of metazoan cadherin diversity and the antiquity of the classical cadherin/β-catenin complex.
Nichols, SA, Roberts, BW, Richter, DJ, Fairclough, SR and N King. (2012)
Proceedings of the National Academy of Sciences USA. 109(32):13046-13051.
Faculty Opinions Recommended
Cell differentiation and morphogenesis in the colony forming choanoflagellate Salpingoeca rosetta.
Dayel, MJ, Alegado, RA, Fairclough, SR, Levin, TC, Nichols, SA, McDonald, K and N King. (2011)
Developmental Biology. 357(1):73-82.
Epithelia and integration in sponges.
Leys, SP, Nichols, SA & EDM Adams. (2009)
Integrative and Comparative Biology. 49(2):167-177.
Genomic, phylogenetic and cell biological insights into metazoan origins.
Nichols, SA, Dayel, MJ & N King. (2009) MJ Telford & DTJ Littlewood (Eds.)
In: Animal evolution: genes, genomes, fossils and trees. Oxford University Press.
Biological characterization of Haliclona (?gellius) sp.: sponge and associated microorganisms.
Sipkema, D, Holmes, B, Nichols, SA & H Blanch. (2009)
Microbial Ecology. (DOI: 10.1007/s00248-009-9534-8).
The genome of the choanoflagellate Monosiga brevicollis and the origins of metazoan multicellularity.
King, N, Westbrook, MJ, et al. (2008)
Nature. 451(7180):783-8.
Analysis of evolutionary, biogeographical and taxonomic patterns of nucleotide composition in demosponge rRNA.
Erpenbeck, D, Cleary, DFR, Voigt, O, Nichols, SA, Degnan, BM, Hooper, JNA & G Wörheide. (2007)
Journal of the Marine Biological Association of the U.K. 87(6):1607-1614.
Phylogenetic analyses under secondary structure-specific substitution models outperform traditional approaches – case studies with diploblast LSU.
Erpenbeck, D, Nichols SA, Voigt, O, Dohrmann, M, Degnan, B & JNA Hooper. (2007)
Journal of Molecular Evolution. 64(5):543-557.
Evolution of sensory structures in basal metazoa.
Jacobs, DK, Nakanishi, N, Yuan, D, Camara, A., Nichols, SA & V Hartenstein. (2007)
Integrative and Comparative Biology. 47(5):712-23.
On the phylogenetic relationships of hadromerid and poecilosclerid sponges.
Kober, K & SA Nichols. (2007)
Journal of the Marine Biological Association of the U.K. 87:1585-98.
Early evolution of animal cell signaling and adhesion genes.
Nichols, SA, Dirks, W, Pearse, JS & N King. (2006)
Proceedings of the National Academy of Sciences U.S.A. 103(33):12451-12456.
Faculty Opinions Recommended
A molecular phylogeny and historical biogeography of the marine sponge genus Placospongia (phylum Porifera) indicate low dispersal capabilities and widespread crypsis.
Nichols, SA & PAG Barnes. (2005)
Journal of Experimental Marine Biology and Ecology. 323:1-15.
An evaluation of support for order-level monophyly and interrelationships within the class Demospongiae using partial data from the large subunit rDNA and cytochrome oxidase subunit I.
Nichols, SA. (2005)
Molecular Phylogenetics and Evolution. 34:81-96
Intragenomic variation of the rDNA internal transcribed spacers in sponges (Phylum Porifera): implications for phylogenetic studies.
Wörheide, G, Nichols, SA & J Goldberg. (2004)
Molecular Phylogenetics and Evolution. 33:816-830.
Ruperti, F, Dzieclatkowska, M, Pankey, SM, Asensio, CS, Anselmetti, D, Fernandez-Busquets, X, and SA Nichols (2024)
BioRxiv
HCR-fluorescent in situ hybridization (HCR-FISH) of gemmule hatched freshwater sponges
SA Nichols (2023)
Protocols.io dx.doi.org/10.17504/protocols.io.5jyl8jwkdg2w/v1
Growing freshwater sponges from gemmules in the laboratory
SA Nichols (2023)
Protocols.io dx.doi.org/10.17504/protocols.io.x54v9dkj4g3e/v1
Fixation and staining of Ephydatia muelleri for fluorescence microscopy
SA Nichols (2023)
Protocols.io dx.doi.org/10.17504/protocols.io.j8nlkwnx6l5r/v1
MRTF specifies a muscle-like contractile module in Porifera
Colgren, J and SA Nichols (2022)
Nature Communications 13, article 4134, https://doi.org/10.1038/s41467-022-31756-9
Tracing the evolutionary origin of desmosomes
Green, KJ, Roth-Carter, Q, Niessen, CM and SA Nichols (2020)
Current Biology, https://doi.org/10.1016/j.cub.2020.03/047
Diverse cell junctions with unique molecular composition in tissues of a sponge (Porifera)
Mitchell, J and SA Nichols (2019)
EvoDevo 10, article 26
https://rdcu.be/b9jE3
The significance of sponges for comparative studies of developmental evolution
Colgren, J and SA Nichols (2019)
WIREs Developmental Biology e359, https://doi.org/10.1002/wdev.359
Evolution as a guide for experimental cell biology
Colgren, J and SA Nichols (2019)
PLoS Genetics
15(2): e1007937. https://doi.org/10.1371/journal.pgen.1007937
Analysis of a vinculin homolog in a sponge (phylum Porifera) reveals that vertebrate-like cell adhesions emerged early in animal evolution.
Miller, PW, Pokutta, S, Mitchell, JM, Chodaparambil, JV, Clarke, DN, Nelson, WJ, Weis, WI and SA Nichols (2018)
Journal of Biological Chemistry
http://www.jbc.org/content/293/30/11674
Evidence of adhesion and signaling roles for β-catenin in the sponge Ephydatia muelleri.
Schippers, KJ and SA Nichols (2018)
Molecular Biology and Evolution
https://doi.org/10.1093/molbev/msy033
Transcriptome sequencing and delimitation of sympatric Oscarella species (O. carmela and O. pearsei sp. nov) from California, USA.
Ereskovsky, A, Richter, DJ, Lavrov, DV, Schippers, KJ and SA Nichols (2017)
PlosONE at https://doi.org/10.1371/journal.pone.0183002
Conserved expression of vertebrate microvillar gene homologs in choanocytes of freshwater sponges
Pena, FJ, Alie, A, Richter, DJ, Wang, L, Funayama, N, and SA Nichols (2016)
EvoDevo 7:13 DOI: 10.1186/s13227-016-0050-x
What is an animal?
Nichols, SA. (2016)
In Klinman, R.M. (ed.), Encyclopedia of Evolutionary Biology. vol. 1, pp. 84-92. Oxford: Academic Press.
Deep, dark secrets of melatonin in animal evolution
Schippers, KJ and SA Nichols (2014)
Cell. 159:9-10
The identification of microRNAs in calcisponges: independent evolution of microRNAs in basal metazoans.
Robinson, JM, Sperling, EA, Bergum, B, Adamski, M, Nichols, SA, Adamska, M, and Peterson, KJ. (2013)
JEZ Part B: Molecular and Developmental Evolution. 320(3):84-93.
Origin of metazoan cadherin diversity and the antiquity of the classical cadherin/β-catenin complex.
Nichols, SA, Roberts, BW, Richter, DJ, Fairclough, SR and N King. (2012)
Proceedings of the National Academy of Sciences USA. 109(32):13046-13051.
Faculty Opinions Recommended
Cell differentiation and morphogenesis in the colony forming choanoflagellate Salpingoeca rosetta.
Dayel, MJ, Alegado, RA, Fairclough, SR, Levin, TC, Nichols, SA, McDonald, K and N King. (2011)
Developmental Biology. 357(1):73-82.
Epithelia and integration in sponges.
Leys, SP, Nichols, SA & EDM Adams. (2009)
Integrative and Comparative Biology. 49(2):167-177.
Genomic, phylogenetic and cell biological insights into metazoan origins.
Nichols, SA, Dayel, MJ & N King. (2009) MJ Telford & DTJ Littlewood (Eds.)
In: Animal evolution: genes, genomes, fossils and trees. Oxford University Press.
Biological characterization of Haliclona (?gellius) sp.: sponge and associated microorganisms.
Sipkema, D, Holmes, B, Nichols, SA & H Blanch. (2009)
Microbial Ecology. (DOI: 10.1007/s00248-009-9534-8).
The genome of the choanoflagellate Monosiga brevicollis and the origins of metazoan multicellularity.
King, N, Westbrook, MJ, et al. (2008)
Nature. 451(7180):783-8.
Analysis of evolutionary, biogeographical and taxonomic patterns of nucleotide composition in demosponge rRNA.
Erpenbeck, D, Cleary, DFR, Voigt, O, Nichols, SA, Degnan, BM, Hooper, JNA & G Wörheide. (2007)
Journal of the Marine Biological Association of the U.K. 87(6):1607-1614.
Phylogenetic analyses under secondary structure-specific substitution models outperform traditional approaches – case studies with diploblast LSU.
Erpenbeck, D, Nichols SA, Voigt, O, Dohrmann, M, Degnan, B & JNA Hooper. (2007)
Journal of Molecular Evolution. 64(5):543-557.
Evolution of sensory structures in basal metazoa.
Jacobs, DK, Nakanishi, N, Yuan, D, Camara, A., Nichols, SA & V Hartenstein. (2007)
Integrative and Comparative Biology. 47(5):712-23.
On the phylogenetic relationships of hadromerid and poecilosclerid sponges.
Kober, K & SA Nichols. (2007)
Journal of the Marine Biological Association of the U.K. 87:1585-98.
Early evolution of animal cell signaling and adhesion genes.
Nichols, SA, Dirks, W, Pearse, JS & N King. (2006)
Proceedings of the National Academy of Sciences U.S.A. 103(33):12451-12456.
Faculty Opinions Recommended
A molecular phylogeny and historical biogeography of the marine sponge genus Placospongia (phylum Porifera) indicate low dispersal capabilities and widespread crypsis.
Nichols, SA & PAG Barnes. (2005)
Journal of Experimental Marine Biology and Ecology. 323:1-15.
An evaluation of support for order-level monophyly and interrelationships within the class Demospongiae using partial data from the large subunit rDNA and cytochrome oxidase subunit I.
Nichols, SA. (2005)
Molecular Phylogenetics and Evolution. 34:81-96
Intragenomic variation of the rDNA internal transcribed spacers in sponges (Phylum Porifera): implications for phylogenetic studies.
Wörheide, G, Nichols, SA & J Goldberg. (2004)
Molecular Phylogenetics and Evolution. 33:816-830.