Laboratory of Aquatic Ecology, Evolution and Conservation
Charles Deberiotstraat 32 - box 2439
fax: +32163 24575
Ecological and environmental genomics
I am a molecular ecologist, with expertise in aquatic and terrestrial ecosystems. My research interest is to understand how natural populations adapt and evolve in changing environments. I pursued this interest focusing on different ecosystems and studying both classic genetic model species (fruit fly) as well as non-model species (water flea, butterfly, beetles, marine plants and unicellular algae). I often worked at the interface of ecology, evolution and genetics, refining my expertise in ecological genetics and genomics.
In the past, I focused on the study of genetic diversity combined with spatial explicit analysis of demographic processes, which is essential for a mechanistic understanding of the genetic processes underlying population dynamics. Complementary to this line of research I have always taken into account an evolutionary perspective.
My current research is embedded in an European network program (EEFG EUROCORE project STRESSFLEA) of which I am the coordinator and two national programs on functional and ecological genomics of biological archives (G061411N and G046810N). The EUROCORE program has as main goal the understanding of the genetic processes underpinning adaptation of natural populations to environmental changes, using the waterflea Daphnia magna as model system. My contribution to this program is the identification of the genomics underpinning of adaptation to multiple environmental stressors occurring in the natural landscape. To meet this challenge I applied, for the first time, genomics to resurrected Daphnia specimens (Orsini et al, 2012a Molecular Ecology). I studied spatial dynamics of Daphnia magna across a complex landscape of shallow ponds identifying adaptive responses to a suite of environmental stressors (e.g. parasites, land-use changes, fish predation), and validated these findings in time, using sediment cores with known history for specific stressors, and in experimental evolution trials. In a follow up of this study, I focused on the link between genomic and environmental variation identifying correlates between several biotic and abiotic variables naturally occurring in the landscape and patterns of neutral and adaptive genetic variation in the waterflea (Orsini et al 2013 Molecular Ecology). The environmental association analysis, combined with the analysis of markers with different mutation rates, allowed the identification of demographic and selective processes likely driving population genomic structure in the ecological model system Daphnia.
My future research interest is in forecasting population genomics of adaptation to environmental stress. Applying high-throughput genomics to species with well-studied ecologies is opening new avenues for the study of adaptive responses in the wild. A remaining challenge is to extend those inquiries beyond descriptive measures of patterns of genetic variation to reconstruct the evolutionary processes that contribute to present-day population genomic structure in the wild. My long term objective is to meet this challenge by combining population genomics of natural populations in space and time with phenotypic, ecological and environmental information.
I will be pursuing this new line of research at the University of Bimringham Edgbaston campus, UK, where I am appointed as lecturer staring from June 2013.
-March 1999-MSc Environmental Sciences, Istituto Universitario Navale, Naples, Italy. Master defended with the highest distinction
- February 2003-PhD in Biology University of Messina - Stazione Zoologica “A. Dohrn”; Naples, Italy
since 01/06/2013: lecturer (tenure) School of Biosciences, University of Birmingham Edgbaston, UK.
01/10/2012-31/05/2013: postdoctoral fellowship National research funding (FWO G061411N), Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Belgium.
01/09/2011-30/09/2012: visiting scholar at the Center of Genomics and Bioinformatics, Indiana University, Bloomington, US. National research funding (FWO V442111N)
01/05/2008-31/08/2011: postdoctoral fellowship National research funding (PDO-08-00274) Laboratory of Aquatic Ecology, Evolution and Conservation, University of Leuven, Belgium.
01/04/2006-31/03/2008: postdoctoral fellowship awarded by the Finnish Cultural Foundation, Department of Biological and Environmental Sciences, Metapopulation Research Group, University of Helsinki.
01/04/2004-31/03/2006: postdoctoral fellowship Finnish Centre of Excellence, Department of Biological and Environmental Sciences, Metapopulation Research Group, University of Helsinki.
01/03/ 2003-31/03/2004: postdoctoral fellowship EU Research Training Network grant (HPRN-CT-2002-00266), Institute of Animal Breeding and Genetics, University of Veterinary Medicine Wien.
Awarded grants and fellowships
Student and travel awards
- Student award granted by the Xth International Conference on Harmful Algae, 21-25 October, 2002, St. Pete Beach, Florida USA.
- Chancellor Travel Grant awarded by the University of Helsinki for the international conference Evolution 2006, 23-27 June 2006, New York, USA.
- Chancellor Travel Grant awarded by the University of Helsinki for the international conference SMBE08, 5-8 June 2008, Barcelona, Spain.
- FWO travel grant and contribution from the American Genetic Association for the conference "Conservation Genomics, American Genetic Association annual symposium", 26-28 July, 2010, Hilo, Hawaii (C 17-18/2).
- FWO travel grant for meetings abroad awarded by the Research Foundation Flanders (FWO), Brussels, Belgium. SETAC conference, North America 31st Annual Meeting in Portland, Oregon, 7-11 November 2010.
Fellowships awarded to Luisa Orsini
- Postdoctoral position awarded for the academic year 2006-2007 by the Finnish Cultural Foundation (Suomen Kulttuurirahasto), Helsinki, 27.02.2006.
- Postdoctoral position awarded for the academic year 2007-2008 by the Finnish Cultural Foundation (Suomen Kulttuurirahasto), Helsinki, 27.02.2007.
- Postdoctoral position awarder for the period 01.10.2008-30.09.2011 by the Research Foundation Flanders (FWO), Brussels, Belgium (PDO-08-00274)
- Visiting scholar fellowship awarded for the period September 2011-September 2012 by the research Foundation Flanders (FWO) for a research visit at the Center of Genomics and Bioinformatics, Indiana University Bloomington, US (V442111N).
- Daphnia Genomics Consortium Conference organized in Leuven, Belgium the 26-30 March, 2010 funded by the European Science Foundation (ESF), the Research Foundation Flanders (FWO), the University of Leuven, the University of Antwerp, the University of Ghent, and BioSCENTer Leuven.
- Networking activity awarded by the ESF EEFG EUROCORE for the symposium on Evolutionary Ecological Genomics organized by Luisa Orsini and Christophe Eizaguirre at the European Society of Evolutionary Biology (ESEB) conference in Tuebingen, Germany, 20-25 August, 2011.
- Networking activity awarded by the ESF EEFG EUROCORE for the VII Symposium on Eco-Evolutionary Dynamics organized by Luisa Orsini, Jelena Pantel, Filip Volckaert and Luc De Meester in Leuven, Belgium, 5-7 February 2013.
Research grants- projects in which I am PI or co-PI
- ESF EUROCORES Programme EuroEEFG (Ecological and Evolutionary Functional Genomics, Grant 09-EEFG-FP-040) approved by the ESF and funded by the national research councils. The project is titled: "How to Live in a Mosaic of Stressors – an ecological genomics approach on the water flea Daphnia (STRESSFLEA)". PIs: Prof Luc De Meester, Dr Luisa Orsini (project coordinator), Prof Ellen Decaestecker. This project was approved by the ESF but was nationally supported by a separate research grant of the Research Foundation Flanders (FWO) - see #2.
- Research project on functional genomics awarded for the period 01/01/2011-31/12/2014 by the Research Foundation Flanders (FWO), Brussels, Belgium (G061411N). The project is titled: "How to live in a mosaic of stressors – an ecological genomics approach on the water flea Daphnia". PIs: Prof Luc De Meester, Dr Luisa Orsini, Prof Ellen Decaestecker.
- Research project on Paleogenomics awarded for the period 1/1/2010-31/12/2013 by the Research Foundation Flanders (FWO), Brussels, Belgium (G046810N). The project is titled: "Evolutionary paleogenomics of Daphnia: reconstructing evolutionary responses to environmental change in wild populations". PIs: Prof Luc De Meester, Dr Luisa Orsini, Dr Joachim Mergeay.
February 2010-April 2010- "Finding the genetic response to climate change using ancient DNA: genome scans in Daphnia magna" (University of Leuven. Student: Lotte Mathe)
October 2008-November 2008- "Gene flow in natural population of Daphnia magna: the effect of connectivity on genetic diversity". (University of Leuven. Student: Inez Goris)
November 2001-november 2002-“Autoecology and life strategy in species of the genus Pseudo-nitzschia (Bacillariophyceae) in the Gulf of Naples”. (Master Degree in Environmental Science, Istituto Universitario Navale, Italy. Student: Alberto Amato).
November 2005-November 2009: “Molecular and morphological systematic of dung beetles from Madagascar”. (University of Helsinki. Student: Helena Wirta-Koivulehto).
October 2009-ongoing: "Evolutionary paleogenomics in Daphnia magna: finding genomic adaptive responses to climate change" (University of Leuven. Student: Aurora Geerts)
January 2010-ongoing:"Adaptive response of the seagrass Posidonia oceanica to environmental gradients: a genome scan approach". (Stazione Zologica A. Dohrn, Napoli, Italy Student: Daniela D’Esposito)
October 2010-ongoing: "A pipeline for candidate gene locus identification in the waterflea Daphnia magna- development and validation" (University of Leuven. Student: Katina Spanier)
1) Editorial activities: subject editor and guest editor of Molecular Ecology . 2) Reviewer activities: reviewer for Molecular Ecology, Heredity, Functional Ecology, Marine Ecology Progress Series, Journal of Evolutionary Biology, Genetica and others. 3) Project coordination: coordinator of the ESF EUROCORES Programme EuroEEFG project STRESSFLEA. This project involves 10 partners, 7 partners from European university and three are associated partners from UK and US; 4) Judge in PhD juries. 5) International scientific events organized: a) Daphnia Genomics Consortium Conference 2010 Leuven, Belgium, the 26-30 March, 2010; b) Evolutionary Ecological Genomics symposium at the European Society of Evolutionary Biology Conference (ESEB), Tuebingen, Germany the 20-25 August, 2011. c) Jamboree on RNA data analysis Bloomington, IN, US, 21-25 May, 2012; d) co-organizer of the 7th Symposium on Eco-Evolutionary dynamics Leuven the 5-7th of February 2013; e) co-organizer of the EEFG Conference: Frontiers in ecological and evolutionary genomics, The Nederland, 26-30 May, 2013.
International journals (with SCI impact factor 2012)
1. Orsini L. Schwenk K., De Meester L. Colbourne J.K. Pfrender M. & Weider L. J The evolutionary time machine: forecasting how populations can adapt to changing environments using dormant propagules. Trends in ecology and evolution (Invited opinion paper) In press (SCI: 15.7)
2. D' Esposito D. Orsini L. & Procaccini G. Development of 51 novel EST-linked microsatellites in the threatened seagrass Posidonia oceanica (Posidoniaceae). In press Molecular Ecology Resources. (SCI:3.1)
3. Orsini L. Andrew R. & Eizaguirre C. Evolutionary ecological genomics. Molecular Ecology. (editorial piece for the special issue on Evolutionary Ecological Genomics, eds Orsini, L., Andrew, R. and Eizaguirre, C.) 22: 527-531 (SCI 5.5)
4. Orsini L. Mergeay J. Vanoverbeke J. & De Meester L. The role of selection in driving landscape genomic structure of the waterflea Daphnia magna. Molecular Ecology (Invited contribution to the special issue on Evolutionary Ecological Genomics) 22: 583-601 (SCI 5.5)
5.Orsini L. Spanier K. I. & De Meester L. (2012) Genomic signature of natural and anthropogenic stress in wild populations of the waterflea Daphnia magna: validation in space, time and experimental evolution. Molecular Ecology 21: 2160–2175 (SCI 5.5).
This paper was highlighted in the perspectives of Molecular Ecology with the following commentary: Pfrender, M.E. "Triangulating the genetic basis of adaptation to multifarious selection" (2012)
6. De Meester L. Van Doorsaler W. Geerts A. Orsini L. & Stoks R. (2011) Thermal genetic adaptation in the water flea Daphnia and its impact - an evolving metacommunity approach. Integrative and Comparative Biology (invited contribution for a special volume on “Integrated analysis of thermal adaptation”). 51: 703–718 (SCI 2.6)
7. Orsini L. Jansen M. Souche E. Geldof S. & De Meester L. (2011) Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna. BMC Genomics. 12: 309 (SCI:4.2)
This paper has been listed in the F1000 Biology for its innovative approach. It was commented by Van Straalen, N. M. http://f1000.com/12991956.
8. Jansen B. Geldof S. De Meester L. & Orsini L. (2011) Isolation and characterization of microsatellite markers in the waterflea Daphnia magna. Molecular Ecology Resources. 11: 418-421 (SCI:3.1)
9. Orsini L. Decaestecker E. De Meester L. Pfrender. M. E. & Colbourne J.K. (2010) Genomics in the ecological arena. Biology Letters (SCI:3.8)
10. Wirta H. Viljanen H. Orsini L. Montreuil O. & Hanski I. (2010) Three parallel radiations of Canthonini dung beetles in Madagascar. Molecular Phylogenetics and Evolution. 57:710-727 (SCI:3.9)
11. Orsini L. Wheat W. C., Haag R.C., Kvist J. Frilander J. M. & Hanski I. (2009). Fitness differences associated with Pgi SNP genotypes in the Glanville fritillary butterfly (Melitaea cinxia). Journal of Evolutionary Biology 22: 367–375 (SCI:3.6)
12. Orsini L. Corander J. Alasentie A. & Hanski I (2008). Genetic structure in a butterfly metapopulation correlates better with past than present demographic structure. Molecular Ecology 217: 2629-2642 (SCI:6.5)
13. Wirta H. Orsini L. & Hanski I. (2008). An old adaptive radiation of forest dung beetles in Madagascar. Molecular Phylogenetic and Evolution 47: 1076-1089. (SCI:3.9)
14. Orsini L. Pajunen M. Hanski I. & Savilahti H. (2007). SNP discovery by mismatch targeting of Mu transposition. Nucleic Acids Research 35 (6) e44. (SCI: 7.8)
This paper was in the research highlights of Nature 2007, vol 4(4) doi:10.1038/nmeth0407-299
15. Orsini L. Koivulehto H. & Hanski I. (2007) Molecular Evolution and Radiation of Dung Beetles in Madagascar. Cladistics 23: 145-168. (SCI: 6.7).
16. Mirol P.M. Schäfer M.A. Orsini L. Routtu J. Schlötterer C. Hoikkala A. & Butlin R.K. (2007). Phylogeographic patterns in Drosophila montana. Molecular Ecology 16: 1085-1097. (SCI: 5.5)
17. Schäfer M.A. Orsini L. McAllister B.F. & Schlötterer C. (2006). Patterns of microsatellite variation trough a transition zone of a chromosomal cline in Drosophila americana. Heredity 97: 291-295. (SCI: 4.6)
18. Amato A. Orsini L. D´Alelio D. & Montresor M. (2005) Life cycle, size reduction patterns and ultrastructure of the pennate planktonic diatom Pseudonitzschia delicatissima (Bacillariophyceae). Journal of Phycology 41: 542-556. (SCI: 2.2)
19. Cerino F. Orsini L. Sarno D. Dell'Aversano C. Tartaglione L. & Zingone A. (2005). The alternation of different morphotypes in the seasonal cycle of the toxic diatom Pseudonitzschia galaxiae. Harmful Algae 4: 33-48. (SCI: 4.3)
20. Orsini L. & Schlötterer C. (2004). Isolation and characterization of microsatellites in Drosophila montana and their cross species amplification in D. virilis. Molecular Ecology Notes 4: 412-414. (SCI: 3.1)
21. Orsini L. Huttunen S. & Schlötterer C. (2004) A multilocus microsatellite phylogeny of the Drosophila virilis group. Heredity 93: 161-165. (SCI: 4.6)
22. Orsini L. Procaccini G. Sarno D. & Montresor M. (2004) Multiple rDNA ITS types within the diatom Pseudonitzschia delicatissima (Bacillariophyceae) and their relative abundance across a spring bloom in the Gulf of Naples. Marine Ecology Progress Series 271:87-98. (SCI: 2.5)
23. Montresor M. Lovejoy C. Orsini L., Procaccini G. & Roy S. (2003) Bipolar distribution of the cystforming dinoflagellate Polarella glacialis. Polar Biology 26: 186-194.(SCI:1.69)
24. Procaccini G. Ruggiero M.V. & Orsini L. (2002) Genetic structure and distribution of microsatellite diversity in Posidonia oceanica over the whole Mediterranean basin. Bulletin of Marine Science 71:1291-1297 (SCI: 1.4)
25. Orsini, L. Sarno D. Procaccini G. Poletti R. Dahlmann J. & Montresor M. (2002) Toxic Pseudonitzschia multistriata (Bacillariophyceae) from the Gulf of Naples: morphology, toxin analysis and phylogenetic relationships with other Pseudonitzschia species. European Journal of Phycology, 37: 247-257. (SCI: 1.9)
26. Procaccini G. Orsini L. Ruggiero M.V.& Scardi M. (2001) Spatial patterns of genetic diversity in Posidonia oceanica, an endemic Mediterranean seagrass. Molecular Ecology, 10: 1413-1421. (SCI: 5.5)
Book chapters with peer review
1. Amato A. & Orsini L. (2009) The eco-genomics of phytoplankton: an outlook on the future. In: Kersey W. T. and Munger S. P. (Eds.), Marine Phytoplankton. NOVA Publisher ISBN: 978-1-60741-087-4.
2. Orsini L. Acunto S. Piazzi L. & Procaccini G. (2001). Sexual reproduction and recruitment in Posidonia oceanica (L.) Delile, a genetic diversity study. In: Faranda, F.M. Guglielmo L. and Spezie G. (Eds.), Mediterranean Ecosystem: Structures and Processes. Springer-Verlag , Berlin Heidelberg. Cap. 50: 385-389.
Non SCI journals
1. Ruggiero M.V. Orsini L. & Procaccini G. (2001). Depth related genetic structure in populations of endemic and introduced seagrass species: Posidonia oceanica and Halophila stipulacea. Biologia Marina Mediterranea, 8: 110.
2. Procaccini G. Orsini L. & Ruggiero M.V. (2000) Genetic structure and distribution of microsatellite diversity in Posidonia oceanica. Biologia Marina Mediterranea, 7 (2): 115-118.
3. D'Esposito D. Dattolo E. Badalamenti F. Orsini L. & Procaccini G. (2012) Comparative analysis of genetic diversity of Posidonia oceanica along a depth gradient using neutral and selective/non neutral microsatellite markers, Biologia Marina Mediterranea 19 (1): 45-48.
Participation to international conferences: I attended 35 international conferences presenting 23 talks and 12 posters. I attended six additional conferences and workshops without giving a presentation.
Invited lectures: 1) University of Cologne, Germany 31May-1 June, 2011; 2) EAWAG, Switzerland 14 April 2011 3) University of Sheffield, UK 31 March 2011; 4) University of Parma, Italy 19 May, 2010; 5) Stazione Zoologica Anton Dohrn, Napoli, Italy, PhD course in Population genetics and Phylogeny in Marine systems, 5 -8 October, 2010.
Orsini L., Schwenk K., De Meester L., Colbourne J., Pfrender M., Weider L. 2013. The evolutionary time machine: using dormant propagules to forecast how populations can adapt to changing environments. Trends in Ecology & Evolution. vol.28 (5) , pp. 274-282
Orsini L., Mergeay J., Vanoverbeke J., De Meester L. 2013. The role of selection in driving landscape genomic structure of the waterflea Daphnia magna. Molecular Ecology. vol.22 , pp. 583-601
Agostini C., Agudelo P., Ba K., Barber P., Bisol P., Brouat C., Burgess T., Calves I., Avila M., Chow S., Cordes L., Da Silva D., Dalecky A., De Meester L., Doadrio I., Dobigny G., Duplantier J., Evison S., Ford R., Fresneau D., Galetti P., Gauthier P., Geldof S., Granjon L., Guerin F., Hardy G., Escobar C., Hima K., Hu J., Huang L., Humeau L., Jansen B., Jaquemet S., Jiang Z., Jung S., Kim B., Kim C., Kim J., Lai C., Laroche J., Lavergne E., Lawton-Rauh A., Le Corre M., Leach M., Lee J., Leo A., Lichtenzveig J., Lin L., Linde C., Liu S., Marino I., McKeown N., Nohara K., Oh M., Okamoto H., Oliver R., Angel M., Ornelas-Garcia C., Orsini L., Alfonso H., Othman A., Papetti C., Patarnello T., Pedraza-Lara C., Piller K., Poteaux C., Requier J., Roziana M., Semba Y., Sembene M., Shah R., Shahril A., Shao A., Shaw P., Song L., Ferreira R., Su Y., Suzuki N., Tatard C., Taylor K., Taylor P., Thiam M., Valbuena R., Wang H., Yang B., Yuan Q., Zajonz U., Zane L., Zhu L., Zhuang Z., Zulaiha A. 2011. Permanent Genetic Resources added to Molecular Ecology Resources Database 1 October 2010-30 November 2010. Molecular Ecology Resources. vol.11 (2) , pp. 418-421
Jansen B., Geldof S., De Meester L., Orsini L. 2010. Isolation and characterization of microsatellite markers in the waterflea Daphnia magna. Molecular Ecology Resources. vol.doi: 10.1111/j.1755-0998.2010.02970.x
Orsini L., Wheat C., Haag C., Kvist J., Frilander M., Hanski I. 2009. Fitness differences associated with Pgi SNP genotypes in the Glanville fritillary butterfly (Melitaea cinxia). Journal of Evolutionary Biology. vol.22 (2) , pp. 367-375
Wirta H., Orsini L., Hanski I. 2008. An old adaptive radiation of forest dung beetles in Madagascar. Molecular phylogenetics and evolution. vol.47 (3) , pp. 1076-89
Orsini L., Koivulehto H., Hanski I. 2007. Molecular evolution and radiation of dung beetles in Madagascar. Cladistics. vol.23 (2) , pp. 145-168
Mirol P., Orsini L., Routtu J., Hoikkala A., Butlin R. 2007. Phylogeographic patterns in Drosophila montana. Molecular ecology. vol.16 (5) , pp. 1085-97
Orsini L., McAllister B. 2006. Patterns of microsatellite variation through a transition zone of a chromosomal cline in Drosophila americana. Heredity. vol.97 (4) , pp. 291-5
Amato A., Orsini L., D'Alelio D., Montresor M. 2005. Life cycle, size reduction patterns, and ultrastructure of the pennate planktonic diatom Pseudo-nitzschia delicatissima (Bacillariophyceae). Journal of phycology. vol.41 (3) , pp. 542-556
Cerino F., Orsini L., Sarno D., Dell'Aversano C., Tartaglione L., Zingone A. 2005. The alternation of different morphotypes in the seasonal cycle of the toxic diatom Pseudo-nitzschia galaxiae. Harmful algae. vol.4 (1) , pp. 33-48
Orsini L., Schlotterer C. 2004. Isolation and characterization of microsatellites in Drosophila montana and their cross-species amplification in D-virilis. Molecular ecology notes. vol.4 (3) , pp. 412-414
Orsini L., Huttunen S. 2004. A multilocus microsatellite phylogeny of the Drosophila virilis group. Heredity. vol.93 (2) , pp. 161-5
Orsini L., Procaccini G., Sarno D., Montresor M. 2004. Multiple rDNA ITS-types within the diatom Pseudo-nitzschia delicatissima (Bacillariophyceae) and their relative abundances across a spring bloom in the Gulf of Naples. Marine ecology-progress series. vol.271 , pp. 87-98
Orsini L., Acunto S., Piazzi L., Procaccini G. 2001. Sexual reproduction and recruitment in Posidonia oceanica (L.) Delile, a genetic diversity study. In Mediterranean Ecosystems: structures and processes. Faranda F., Guglielmo L., apezie G. (eds.) Springer-Verlag (Berlin Heidelberg) , pp. 385-389
Procaccini G., Ruggiero M., Orsini L. 2002. Genetic structure and distribution of microsatellite population genetic diversity in Posidonia oceanica in the Mediterranean basin. In Bulletin of marine science. vol.71 (3) Psodonia , pp. 1291-1297 , ISSN 0007-4977
Procaccini G., Orsini L., Ruggiero M. 2000. Genetic structure and distribution of microsatellite diversity in Posidonia oceanica. Biologia Marina Mediterranea