Present address: University of Rome, "La Sapienza"
P.le A. Moro, 5
Research work, on-going projects and future interests
As a Ph.D student I began to study phylogeny and phylogeography of widespread springtail species with molecular markers to describe their relationships and population structure, and to evaluate the use of this organisms as a model to infer phylogeographic pattern. In recent years there has been increasing attention of the scientific community toward the remarkable diversity, evolutionary complexity, and conservation importance of the flora and fauna in the Mediterranean region, with emphasis on the three major peninsular refugia. With the collaboration of Dr Brent C. Emerson from the University of East Anglia (UEA), UK, I investigated the phylogeographic structure of six very common species of Lepidocyrtus (Collembola) in the North-Western Mediterranean basin. The study revealed an astonishing degree of geographic structure, with numerous deeply divergent genetic lineages, originating between 5 and 15 Mya, with no apparent gene flow among populations, even across close geographic distances. Taking a conservative but robust calibration approach, I revealed a remarkably ancient origin for the group, with long-term persistence of individual lineages over fine geographic scale. This study reveals long-term ecological stability within the region, thus raising new questions on the origin of the southern European fauna. In addition to this, our study highlighted the great phylogeographic utility of Collembola as a model group to reconstruct phylogeographic history within temperate forest regions at very fine geographic scales.
During my PhD I obtained a fellowship at the Smithsonian Tropical Research Institute (STRI) where I initiated a project to investigate and quantify the biodiversity of Panamanian springtails, a group for which virtually no prior data existed. This region, very important from an evolutionary point of view, was the key element in the closure of the Central American Seaway, profoundly affecting gene flow between populations of marine and land species. During my research fellowship at STRI, I sampled more than one hundred species, most of them new to science, all across the country. After my PhD I continued my collaboration with Dr Emerson from UEA and Prof. Pietro P. Fanciulli from the University of Siena. With the use of data from publicly available databases and new sequencing data, we quantified the evolutionary diversity and spatial organisation of Collembola, chosen as a representative of the tree canopy and soil mesofauna and, more importantly, as a compelling evidence of a paradox for its tremendous cryptic diversity and very low taxonomical richness.
During my first postdoctoral fellowship, I was part of SelMol, a national project funded by the Italian Ministry of Agriculture. The aim of SELMOL was the improvement of selective strategies in animal husbandry through molecular genetic methodology using high throughput genotyping of SNPs. My main task was the discovery and characterization of copy number variants (CNVs) within the complete genome of Bos taurus. CNVs are described as segments of DNA (>1kb) that are repeated and polymorphic for repeat number. They represent a major source of genetic variation within mammals, and probably within all animals. They occupy about 5–12% of the human genome and greatly influence phenotypic traits and disease susceptibility, such as in HIV infection, autoimmunity and autism. Using the 54K SNP signal intensities of Illumina bovineSNP50 BeadChip, I characterized the level and patterns of copy number variation among bovine animals to assess the CNV landscape over thousands of individuals.
Over the last two years, as a postdoctoral fellow at the “Sapienza”, University of Rome, I have greatly improved my knowledge of next-generation sequencing methodologies, mainly with the use of the Illumina system, quantifying and characterizing (discovering new transcripts and isoforms) the transcriptome (mRNA-seq and miRNA-seq) of a neonatal cancer, the Medulloblastoma, in collaboration with Prof. Gulino's group in “Sapienza”, University of Rome. Additionally, I also initiated a study on the complex dynamic of mRNA-microRNA interaction, through the identification of competing endogenous RNAs (ceRNA), a class of poly-A+ RNAs that should interfere with coding RNAs and microRNAs, regulating the microRNA action on transcripts.
This research experience with state of the art technology have been very important as it has given me the essential background to address cutting edge questions in evolutionary biology such as phylogeography, phylogenetics and molecular evolution at the scale of genomes.
12/2011 Postoctoral Fellow at department of Physics, University of Rome "La Sapienza": “Application of Next Generation Sequencing for the study of RNA expression”. Advisors: Prof. Anna Tramontano, Dr. Giovanni Chillemi
12/2010-11/2011 Fellowship at CASPUR, Inter University Consortium for Supercomputing Applications: “Application of Next Generation Sequencing for the study of RNA expression”. Advisors: Prof. Anna Tramontano, Dr. Giovanni Chillemi
10/2010 Short course on the use of the Illumina Next Generation Sequencing an Bioinformatics tools at IGA – Institute for Applied Genomics Udine, Italy. Adviser Dr. Federica Cattonaro.
07/2010 Short course on the use of the Illumina Genome Analyzer IIe at Regina Elena – Cancer Institute Rome, Italy. Adviser Dr. Maurizio Fanciulli.
07/2008-10/2010 Post-doc at the University of Tuscia, Department of Animal Production: “Research and Innovation in animal genetic improvement with molecular genetic techniques for the competitiveness of the national animal husbandry system. Advisor: Prof. Alessandro Nardone
Main task: discovery and mapping of copy number variants (CNVs) across the complete genome of Bos taurus and database creation/maintenance for genetic data analysis.
Secondary task: Role of casein biopeptides on human health.
08/2009 Workshop on Molecular Evolution at the MBL Woods Hole, USA.
12/2007-07/2008 Research assistant in Evolutionary Biology at the Department of Evolutionary Biology, University of Siena, Italy.
07/2008 Erasmus Intensive Program (IP) Graduate course on Mathematics and Biology at AgroParisTech, Paris.
2004-2007 European Graduate School in Evolutionary Biology (Ph.D.) at the University of Siena, Department of Evolutionary Biology, Italy. “Comparative phylogeography of the genus Lepidocyrtus (Hexapoda: Collembola) in the north-western Mediterranean basin and its phylogenetic implication.” Advisor: Prof. Francesco Frati.
07-2007/09-2007 Short Term Fellowship at the Smithsonian Tropical Research Institute (STRI). “Phylogeographic patterns of Lepidocyrtus (Collembola) springtails and the formation of the Isthmus of Panama”. Advisor: Dr. Donald Windsor.
01-2007/06-2007 Research assistant at the Centre for Ecology, Evolution and Conservation, University of East Anglia, Norwich UK, developing new nuclear molecular markers for phylogeographic studies. Advisor: Dr. Brent C. Emerson.
2003 Degree (M.Sc. equivalent) in Natural Sciences - University of Siena (Italy) with a thesis on “The Collembola spermatozoa winding process and its adaptive meaning”. Advisor: Prof. Romano Dallai, Prof. Pietro Paolo Fanciulli. Final grade: 110/110 Summa cum Laude.
2010-11 RNA-seq/miR-seq On Medulloblastoma for the discovery of involved genes in the Hedgehog (Hh) patched signaling pathway. In collaboration with Prof. Alberto Gulino, (Department of Experimental Medicine, University “La Sapienza”, Rome.
2008-10 High-throughput SNP genotyping and Copy Number Variants in Bos taurus
2006-10 Phylogenetic and Phylogeography.
Use of springtails as a model organisms to infer complex phylogeographic scenarios, both at fine and large geographical scales.
Use of mitochondrial and nuclear markers to infer phylogenesis and population structure of north-western species of Lepidocyrtus (Hexapoda: Collembola).
Relaxed molecular clock: calibration and use of molecular marker to date phylogenetic, colonization and vicariance events.
2003-06 Taxonomy of Collembola and other Apterygota (Soil Zoology, University of Siena Prof. P.P. Fanciulli):
Taxonomical and faunistic study of the Circeo National Park soil fauna (Italy).
Taxonomical and faunistic study across different Panamanian National Parks. (Panama).
Impact of transgenic oilseed rape and transgenic eggplant on soil arthropod assemblages. (Department of Science and Agroenvironmental Technologies, University of Bologna).
Taxonomy of Charimachilis (Hexapoda: Microcoryphia). (Department of Vegetal Biology and Ecology, Autonomous University of Barcelona, Spain).
2003-06 Ultrastructural research (laboratory of Zoology, University of Siena, Prof. R. Dallai:
Ultrastructural analyses of the secretory and sensory organs in the Trichoniscus alexandrae Caruso (Crustacea: Isopoda). (Department of Animal Biology, University of Catania).
Ultrastructural observation of Ephemeroptera spermatozoa (Department of Cell and Environmental Biology, University of Perugia).
2004 Research on the influence of exogenous estrogen on spatial memory abilities of Rattus norvegicus at the Department of Physiology, University of Siena. (Prof. Leonida Fusani).
2002-03 Intern-ship in the laboratory of Zoology, department of Evolutionary Biology, University of Siena (Supervisors: Prof. R. Dallai, Prof. P.P. Fanciulli).
2006-07 Course on Experimental Biology (Bachelor degree in Biological Sciences, University of Siena).
2005-06 Practicals in zoology (Bachelor degree in Biological Sciences, University of Siena).
2005 Co-advisor to Yuri Pistolesi at University of Siena; thesis (M.Sc. equivalent) on “Genetic variability in the Antarctic species Cryptopygus antarcticus (Willem 1901) (Collembola, Isotomidae).”
Organization of sampling trips with STRI to: Chiriquì, Comarca de Nobe Bugle, Veraguas, Herrera, Los Santos, Coclé, Panamà, Colòn, Sherman, Barro Colorado (Panama).
Organization of sampling trips with the Department of Evolutionary Biology to: Central Italy, Sardinia and Corsica islands (02/2006), Tuscan Archipelago and Southern France (04/2006).
Italian Mother language
English First Certificate of English -FCE- (University of Cambridge). At Linguistic Centre (University of Siena) (2006).
Spanish Intermediate level, spoken and written.
Portuguese Beginners course at Università Popolare Senese. (2006)
Microsoft Windows, Unix/Linux-based systems, Mac Os X.
Sequences analysis software:
Sequencer, SeaView, BioEdit, Geneious, CLC Workbench, Mesquite, CLUSTALX and W, MAFFT.
Phylogenetic analysis software.
jModeltest, PAUP*, MrBayes, BEAST package, Garli, RaxML, Tracer, Treestat.
Population genetics analysis software.
Phase, TCS, Arlequin, Structure.
R (advanced), Phyton (advanced), MySQL (advanced), Perl (intermediate level)
Next Generation Sequencing analysus software
Casava (illumina inc.), Bowtie, Tophat, Cufflinks package, Scripture, HMMsplicer, SAMtools, BAMtools, MirDeep.
Microsoft Office, Open Office, Adobe Photoshop, Acrobat, Illustrator, GenomeStudio, QuantiSNP, PennCNV.
Other activities & skills
10/2005 01/2006 Collaboration with Natural History Museum of Ferrara. “Insects. A world with six legs.” (Pictures exhibition).
Licensed Scuba diver Padi – Open Water Diver (18m deep with experience at 30m)
F. CICCONARDI, P.P. FANCIULLI, B.C. EMERSON 2012 – Collembola and the Biological Species Concept: evidence from Panama for the underestimation of global species diversity. In prep.
F. CICCONARDI, G. CHILLEMI, A. TRAMONTANO, P. AJMONE MARSAN, A. NARDONE 2013 – Massive screening of copy number population-scale variation in Bos taurus genome. BMC Genomics. in press
B.C. EMERSON, F. CICCONARDI, P.P. FANCIULLI, P.J.A. SHAW 2011 – Phylogeny, phylogeography, phylobetadiversity and the molecular analysis of biological communities. Philosophical Transactions of Royal Society B, 366: 2391-2402.
R. DALLAI, F. CICCONARDI, P.P. FANCIULLI, 2010 - Insecta Collembola. Biologia Marina Mediterranea, 17: 538-544.
F. CICCONARDI, F. NARDI, B.C. EMERSON, F. FRATI, P.P. FANCIULLI, 2010 - Evidence for deep phylogeographic divisions and long-term persistence of forest invertebrates in the north-western Mediterranean basin. Molecular Ecology, 19: 386-400.
V. VIGNOLI, N. SALOMONE, F. CICCONARDI, F. BERNINI, 2007 - The Scorpion of Montecristo. Euscorpius oglasae Di Caporiacco, 1950, stat. nov. (Scorpiones, Euscorpiidae): a paleo-endemism of the Tuscan Archipelago (central Tyrrhenian, Italy). Comptes Rendus Biologies, 330: 113-125.
B.M. LOMBARDO, P.P. FANCIULLI, R. GRASSO, F. CICCONARDI, D. CARUSO, R. DALLAI, 2006 - Fine structure of the secretory and sensory organs on the cephalon and the first pereionite of the Trichoniscus alexandrae Caruso (Crustacea, Isopoda). Tissue and Cell, 38: 99-110.
G. BURGIO, F. RAMILLI, P. P. FANCIULLI, F. FRATI, M. MIGLIORINI, F. CICCONARDI, M. FIORE, F. CELLINI, 2005 - Studio dell'artropodofauna del terreno su colza Bt, melanzana Bt e relative linee isogeniche. Volume: Studio dell'impatto derivante dal rilascio deliberato nell'ambiente di piante geneticamente modificate (PGM) sulle popolazioni di artropodi e altri invertebrati negli ecosistemi agricoli interessati. Ministero dell'Ambiente e della Tutela del Territorio Eds: Tipolitografia Negri s.r.l. Bologna, Italia. 7-30.
Contributions to scientific meetings
2010 F. CICCONARDI, F. NARDI, B.C. EEMERSON, F. FRATI, P.P. FANCIULLI – Deep phylogeographic divisions and long-term persistence of Lepidocyrtus (Collembola: Entomobryidae) in the North-Western Mediterranean basin. VIIIth International seminar on Apterygota, Siena, Italy, 13th-15th September 2010. (Oral presentation).
2009 M. DI GIOVANNI, C. MARCHITELLI, F. CICCONARDI, U. BERNABUCCI, A. NARDONE – Comparison of ACE inhibitor effect in cow, buffalo and goat milk by in silico and in vitro digestion of caseins. Proceedings of the ASPA, 18th Congress, Palermo, Italy, 9-12 June 2009.
2008 F. CICCONARDI, F. NARDI, B.C. EMERSON, F. FRATI, P.P. FANCIULLI – Comparative phylogeography of the genus Lepidocyrtus (Hexapoda: Collembola) in the north-western Mediterranean basin. Annual Meeting of the Society of Molecular Biology and Evolution (SMBE), Barcelona, Spain, 5-8 June 2008.
2006 R. DALLAI, Z.V. ZIZZARI, F. CICCONARDI, P.P. FANCIULLI - Ulteriori osservazioni sulla riproduzione dei Collemboli. Atti del 67th Congresso Nazionale Unione Zoologica Italiana, Naples, Italy, 12-15 Settembre 2006.
V. VIGNOLI, N. SALOMONE, F. CICCONARDI, F. BERNINI - Euscorpius carpathicus oglasae Di Caporiacco, 1950 (Scorpiones, Euscorpiidae): an interesting scorpion endemism from Montecristo Island (central Tyrrhenian, Italy). 23rd European Colloquium of Arachnology, Sitges, Barcelona, Spain, 4-8 September 2006.
F. CICCONARDI – Phylogeography of the Tuscan Archipelago (Italy). XII European Meeting of PhD. Students in Evolutionary Biology, St. Andrews, Scotland, 4th-8th September 2006. (Oral presentation).
R. DALLAI, Z.V. ZIZZARI, F. CICCONARDI, P.P. FANCIULLI – Further observations on Collembola reproduction. VIIth International seminar on Apterygota, Texel, Netherlands, 27th-30th August 2006.
C. BACH DE ROCA, P.P. FANCIULLI, F. CICCONARDI, M. GARJU-RICART, R. MOLERO BALTANÀS – Description of the male of Charimachilis wahrmani Wygodzinsky, 1959 (Insecta: Microcoryphia). VIIth International seminar on Apterygota, Texel, Netherlands, 27th-30th August 2006.
C. BACH DE ROCA, P.P. FANCIULLI, F. CICCONARDI, M. GARJU-RICART, R. MOLERO BALTANÀS – Description of a new species of Charimachilis Wygodzinsky, 1939 from Turkey (Insecta: Microcoryphia). VIIth International seminar on Apterygota, Texel, Netherlands, 27th-30th August 2006.
2003 E. GAINO, P.P. FANCIULLI, F. CICCONARDI, E. PACCAGNINI, C. MENCARELLI, P. LUPETTI, D. MERCATI, F. GIUSTI, R. DALLAI – Osservazioni ultrastrutturali sullo spermatozoo degli Ephemeroptera (Insecta). Atti del 64th Congresso Nazionale Unione Zoologica Italiana, Varese, Italy, 21-25 Settembre 2003.