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Deciphering the major trends of molecular and morphological evolution in the Amoebozoa

Grant number: 13/04585-3
Support type:Research Grants - Young Investigators Grants
Duration: December 01, 2013 - November 30, 2018
Field of knowledge:Biological Sciences - Zoology
Principal Investigator:Daniel José Galafasse Lahr
Grantee:Daniel José Galafasse Lahr
Home Institution: Instituto de Biociências (IB). Universidade de São Paulo (USP). São Paulo , SP, Brazil
Associated grant(s):15/50327-1 - Understanding microbial responses to environmental stress: integrated molecular and palaeocological approaches using testate Amoebae, AP.R
Associated scholarship(s):15/02689-1 - Experiments on competitive exclusion, BP.IC
13/25729-3 - Temporal morphological variation of natural and clonal testate amoeba (Arcella vulgaris and Arcella gibbosa) lineages, BP.IC

Abstract

The present project seeks to characterize amoebozoan diversity in Brazil, integrating aspects of traditional protistology with cutting-edge molecular techniques. Amoebae will be isolated from freshwater and marine environments in order to capture diversity in a comprehensive manner. Collected organisms will be subjected to two main study strategies: 1) unculturable organisms will be photo-documented and single-cell genome amplified, while; 2) culturable organisms will be grown monoxenically in order to generate large quantities of DNA as well as cDNA for transcriptome piro-sequencing using the 454 Titanium platform. Many of the isolated organisms will likely be new or little known species. These will be individually described along with detailed morphological studies using electronic microscopy, and their phylogenetic position will be assessed based on multigene reconstructions, on at least 4 genes (SSU-rDNA, actin, alpha and beta tubulin). Other organisms will have 8-10 genetic markers characterized and used in comprehensive phylogenetic reconstructions with emphasis on the basal relationships of Amoebozoa. The 10-12 organisms which will have the transcriptome comprehensively sequenced will be used in studies illuminating the patterns of evolution by gene duplication in Amoebozoa, with special emphasis on the actin gene family. Finally, photographic, videographic and molecular data generated during the project will be disseminated by publication in highly recognized international journals, and made available to the lay public by the creation and deposition of curated data in publicly available websites. (AU)

Articles published in Agência FAPESP Newsletter about the research grant
Amoebae diversified at least 750 million years ago, far earlier than expected 
New species of amoeba is named after a character in <i>The Lord of the Rings</i> 
Articles published in other midia outlets (1 total):
Amoeba diversified at least 750 million years ago, far earlier than expected 

Scientific publications (16)
(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)
TREVISAN, BRUNA; ALCANTARA, DANIEL M. C.; MACHADO, DENIS JACOB; MARQUES, FERNANDO P. L.; LAHR, DANIEL J. G. Genome skimming is a low-cost and robust strategy to assemble complete mitochondrial genomes from ethanol preserved specimens in biodiversity studies. PeerJ, v. 7, SEP 13 2019. Web of Science Citations: 0.
HOFSTATTER, PAULO G.; LAHR, DANIEL J. G. All Eukaryotes Are Sexual, unless Proven Otherwise: Many So-Called Asexuals Present Meiotic Machinery and Might Be Able to Have Sex. BIOESSAYS, v. 41, n. 6 JUN 2019. Web of Science Citations: 1.
LAHR, DANIEL J. G.; KOSAKYAN, ANUSH; LAR, ENRIQUE; MITCHELL, EDWARD A. D.; MORAIS, LUANA; PORFIRIO-SOUSA, ALFREDO L.; RIBEIRO, GIULIA M.; TICE, ALEXANDER K.; PANEK, TOMAS; KANG, SEUNGHO; BROWN, MATTHEW W. Phylogenomics and Morphological Reconstruction of Arcellinida Testate Amoebae Highlight Diversity of Microbial Eukaryotes in the Neoproterozoic. Current Biology, v. 29, n. 6, p. 991+, MAR 18 2019. Web of Science Citations: 2.
DUMACK, KENNETH; KAHLICH, CHRISTOPHER; LAHR, DANIEL J. G.; BONKOWSKI, MICHAEL. Reinvestigation of Phryganella paradoxa (Arcellinida, Amoebozoa) Penard 1902. Journal of Eukaryotic Microbiology, v. 66, n. 2, p. 232-243, MAR-APR 2019. Web of Science Citations: 0.
HOFSTATTER, PAULO G.; BROWN, MATTHEWW.; LAHR, DANIEL J. G. Comparative Genomics Supports Sex and Meiosis in Diverse Amoebozoa. GENOME BIOLOGY AND EVOLUTION, v. 10, n. 11, p. 3118-3128, NOV 2018. Web of Science Citations: 3.
MACHICAO, JEANETH; FILHO, HUMBERTO A.; LAHR, DANIEL J. G.; BUCKERIDGE, MARCOS; BRUNO, ODEMIR M. Topological assessment of metabolic networks reveals evolutionary information. SCIENTIFIC REPORTS, v. 8, OCT 29 2018. Web of Science Citations: 1.
GEISEN, STEFAN; MITCHELL, EDWARD A. D.; WILKINSON, DAVID M.; ADL, SINA; BONKOWSKI, MICHAEL; BROWN, MATTHEW W.; FIORE-DONNO, ANNA MARIA; HEGER, THIERRY J.; JASSEY, VINCENT E. J.; KRASHEVSKA, VALENTYNA; LAHR, DANIEL J. G.; MARCISZ, KATARZYNA; MULOT, MATTHIEU; PAYNE, RICHARD; SINGER, DAVID; ANDERSON, O. ROGER; CHARMAN, DAN J.; EKELUND, FLEMMING; GRIFFITHS, BRYAN S.; RONN, REGIN; SMIRNOV, ALEXEY; BASS, DAVID; BELBAHRI, LASSAAD; BERNEY, CEDRIC; BLANDENIER, QUENTIN; CHATZINOTAS, ANTONIS; CLARHOLM, MARIANNE; DUNTHORN, MICAH; FEEST, ALAN; FERNANDEZ, LEONARDO D.; FOISSNER, WILHELM; FOURNIER, BERTRAND; GENTEKAKI, ELENI; HAJEK, MICHAL; HELDER, JOHANNES; JOUSSET, ALEXANDRE; KOLLER, ROBERT; KUMAR, SANTOSH; LA TERZA, ANTONIETTA; LAMENTOWICZ, MARIUSZ; MAZEI, YURI; SANTOS, SUSANA S.; SEPPEY, CHRISTOPHE V. W.; SPIEGEL, FREDERICK W.; WALOCHNIK, JULIA; WINDING, ANNE; LARA, ENRIQUE. Soil protistology rebooted: 30 fundamental questions to start with. SOIL BIOLOGY & BIOCHEMISTRY, v. 111, p. 94-103, AUG 2017. Web of Science Citations: 23.
GOMAA, FATMA; LAHR, DANIEL J. G.; TODOROV, MILCHO; LI, JINGCHUN; LARA, ENRIQUE. A contribution to the phylogeny of agglutinating Arcellinida (Amoebozoa) based on SSU rRNA gene sequences. EUROPEAN JOURNAL OF PROTISTOLOGY, v. 59, p. 99-107, JUN 2017. Web of Science Citations: 4.
MORAIS, LUANA; FAIRCHILD, THOMAS RICH; LAHR, DANIEL J. G.; RUDNITZKI, ISAAC D.; SCHOPF, J. WILLIAM; GARCIA, AMANDA K.; KUDRYAVTSEV, ANATOLIY B.; ROMERO, GUILHERME R. Carbonaceous and siliceous Neoproterozoic vase-shaped microfossils (Urucum Formation, Brazil) and the question of early protistan biomineralization. JOURNAL OF PALEONTOLOGY, v. 91, n. 3, p. 393-406, MAY 2017. Web of Science Citations: 10.
BLANDENIER, QUENTIN; LARA, ENRIQUE; MITCHELL, EDWARD A. D.; ALCANTARA, DANIEL M. C.; SIEMENSMA, FERRY J.; TODOROV, MILCHO; LAHR, DANIEL J. G. NAD9/NAD7 (mitochondrial nicotinamide adenine dinucleotide dehydrogenase gene)-A new ``Holy Grail{''} phylogenetic and DNA-barcoding marker for Arcellinida (Amoebozoa)?. EUROPEAN JOURNAL OF PROTISTOLOGY, v. 58, p. 175-186, APR 2017. Web of Science Citations: 4.
KOSAKYAN, ANUSH; LAHR, DANIEL J. G.; MULOT, MATTHIEU; MEISTERFELD, RALF; MITCHELL, EDWARD A. D.; LARA, ENRIQUE. Phylogenetic reconstruction based on COI reshuffles the taxonomy of hyalosphenid shelled (testate) amoebae and reveals the convoluted evolution of shell plate shapes. CLADISTICS, v. 32, n. 6, p. 606-623, DEC 2016. Web of Science Citations: 18.
KOSAKYAN, ANUSH; GOMAA, FATMA; LARA, ENRIQUE; LAHR, DANIEL J. G. Current and future perspectives on the systematics, taxonomy and nomenclature of testate amoebae. EUROPEAN JOURNAL OF PROTISTOLOGY, v. 55, n. B, SI, p. 105-117, SEP 2016. Web of Science Citations: 22.
FUCIKOVA, KAROLINA; LAHR, DANIEL J. G. Uncovering Cryptic Diversity in Two Amoebozoan Species Using Complete Mitochondrial Genome Sequences. Journal of Eukaryotic Microbiology, v. 63, n. 1, p. 112-122, JAN-FEB 2016. Web of Science Citations: 9.
FERES, JORDANA C.; PORFIRIO-SOUSA, ALFREDO L.; RIBEIRO, GIULIA M.; ROCHA, GUSTAVO M.; STERZA, JOSE MAURO; SOUZA, MARIA BEATRIZ G.; SOARES, CARLOS EDUARDO A.; LAHR, DANIEL J. G. Morphological and Morphometric Description of a Novel Shelled Amoeba Arcellagandalfi sp nov (Amoebozoa: Arcellinida) from Brazilian Continental Waters. ACTA PROTOZOOLOGICA, v. 55, n. 4, p. 221-229, 2016. Web of Science Citations: 0.
LAHR, DANIEL J. G.; BOSAK, TANJA; LARA, ENRIQUE; MITCHELL, EDWARD A. D. The Phanerozoic diversification of silica-cycling testate amoebae and its possible links to changes in terrestrial ecosystems. PeerJ, v. 3, SEP 8 2015. Web of Science Citations: 17.
LAHR, DANIEL J. G.; LAUGHINGHOUSE, HAYWOOD DAIL; OLIVERIO, ANGELA M.; GAO, FENG; KATZ, LAURA A. How discordant morphological and molecular evolution among microorganisms can revise our notions of biodiversity on Earth. BIOESSAYS, v. 36, n. 10, p. 950-959, OCT 2014. Web of Science Citations: 27.

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