Research interests
There are three lines of research in my lab:
Genetics and evolution of mtDNA
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Mitochondria have been extensively studied as cellular compartments and as functional units, and their DNA has additionally been studied as molecular marker. However, the evolutionary dynamics of mitochondria remain poorly investigated. Apart from the symbiosis theory, which explains the origin of mitochondria and is supported by multiple lines of evidence, fundamental questions regarding the evolution of mitochondria and of mtDNA have been theoretically approached but remain poorly explored at the experimental level. Such questions are "why is mtDNA uniparentally transmitted?", "why is there an elevated mutation rate in animal mtDNA but a reduced mutation rate in plant mtDNA compared to the nuclear DNA?", "why animal mtDNA has an alternative genetic code compared to the nucleus whereas in plant mtDNA the genetic code is the universal?", "how can proteins encoded by two extremely different genetic backgrounds (i.e. the mitochondrial and the nuclear DNA) collaborate within the Oxidative Phosphorylation (OXPHOS) complexes in mitochondria?", "how can mtDNA survive the accumulation of deleterious mutations, from which all non-recombining genetic elements suffer?".
In the lab, we are working on mtDNA recombination, on the inheritance of mtDNA, on mtDNA heteroplasmy, and on the mito-nuclear co-evolution. |
Evolution of
languages |
According to Darwin languages and species evolve in a "curiously parallel way ". This means that derived languages spring from common ancestral languages, they have diversity within their populations and divergence between them. In other words, languages, like species and microbial communities are evolvable systems: they consist of populations of replicable individuals (idiolects). During replication individuals inherit characteristics to the next generation. Therefore, there are successive generations in time. Evolvable systems evolve under four basic processes: generation of de novo variation, random drift, selection and migration. In collaboration with linguists we are working on two directions. First, we would like to develop a theoretical framework to find parallels of concepts and processes between language and organismal evolution. Second, we use methods inspired by evolutionary biology (e.g. phylogenetics) and we develop new ones, which we apply in linguistic data (mainly morphosyntactic ones) to ask specific questions and testing hypotheses concerning the evolution of languages.
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Microbial community structure |
Microbes are one of the most unexplored parts of the Tree of Life. Yet, they are extremely diverse, both taxonomically and functionally. Massive sequencing techniques allowed the detection and the study of unculturable microbes, and opened a window in a previously undetectable world. Which factors determine the community structure of microbes? We are addressing this question in the lab by investigating the relative role of selection (environmental filtering) versus randomness (historical effects) in the microbial community structure. We are also interested in the comparison of the ecology of microbes with the ecology of fauna. |
List of selected publications
mtDNA
- M-E Parakatselaki C-T. Zhu , D. Rand, and E. D. Ladoukakis (2022). NUMTs Can Imitate Biparental Transmission of mtDNA-A Case in Drosophila melanogaster. Genes (Basel). 13(6):1023 (doi: 10.3390/genes13061023).
- E. D. Ladoukakis, D. Michelioudakis and E. Anagnostopoulou (2022) Toward an evolutionary framework for language variation and change. BioEssays (published online https://doi.org/10.1002/bies.202100216).
- A. Gogas, G. P. Laliotis, E. Ladoukakis and V. Trachana (2021) Chemical composition and antioxidant profile of snails (Cornu aspersum aspersum) fed diets with different protein sources under intensive rearing conditions J. Anim. Feed Sci. 30(4):391–398
- M-E Parakatselaki and E. D. Ladoukakis (2021) mtDNA Heteroplasmy: Origin, Detection, Significance, and Evolutionary Consequences. Life 11:633 (https://doi.org/10.3390/life11070633)
- E-S Polovina, M-E Parakatselaki and E. D. Ladoukakis (2020) Paternal leakage of mitochondrial DNA and maternal inheritance of heteroplasmy in Drosophila hybrids. Sci. Rep. 10: 2599.
- E-S Polovina, E. Kourkouni, C. S. Tsigenopoulos, P. Sanchez-Jerez and E. D. Ladoukakis (2020) Genetic structuring in farmed and wild Gilthead seabream and European seabass in the Mediterranean Sea: implementations for detection of escapees. Aquat. Living Resour. 33:7
- Ladoukakis ED. and Zouros E. (2017) Evolution and inheritance of animal mitochondrial DNA: rules and exceptions J of Biol Res (Thessal) 24:2.
- S. Fodelianakis, A. Moustakas, N. Papageorgiou, O. Manoli, I . Tsikopoulou, G. Michoud, D. Daffonchio, I . Karakassis, E. D. Ladoukakis (2016) Modified niche optima and breadths explain the historical contingency of bacterial community responses to eutrophication in coastal sediments. Mol. Ecol. 26(7):2006-2018.
- Annie Machordom, Rafael Araujo, Carlos Toledo, Eleftherios Zouros and Emmanuel D. Ladoukakis (2015) Female-dependent transmission of paternal mtDNA is a shared feature of bivalve species with doubly uniparental inheritance (DUI) of mitochondrial DNA J. Zool. System. Evol. Res. 53(3):200-204.
- Maria Eleni Parakatselaki, Carlos Saavedra and Emmanuel D. Ladoukakis (2015) Searching for doubly uniparental inheritance of mtDNA in the apple snail Pomacea diffusa. Mitochondrial DNA. 28:1-3.
- Emmanouil Dokianakis and Emmanuel D. Ladoukakis (2014) Different degree of paternal mtDNA leakage between male and female progeny in interspecific Drosophila crosses. Ecology and Evolution 4(13): 2633–2641.
- Jonci N. Wolff, Emmanuel D. Ladoukakis, José A. Enríquez and Damian K. Dowling (2014) Mitonuclear interactions: evolutionary consequences over multiple biological scales. Phil. Trans. R. Soc. B 369:20130443.
- Emmanuel D. Ladoukakis, Ioannis Theologidis, George C. Rodakis and Eleftherios Zouros. (2011). Homologous recombination between highly diverged mitochondrial sequences: examples from maternally and paternally transmitted genomes. Molecular Biology and Evolution 28(6): 1847-1859.
- Tsaousis A., Martin D., Ladoukakis ED., Posada D. and E. Zouros (2005). Widespread recombination in published animal mtDNA sequences. Molecular Biology and Evolution 22:925-933.
- Ladoukakis E.D. and A. Eyre-Walker (2004). Direct evidence of recombination in human mitochondrial DNA. Heredity 93:321. Invited comments on a Science paper.
- Rokas A, E.D. Ladoukakis and E. Zouros (2003). Animal mitochondrial DNA recombination revisited. Trends in Ecology and Evolution 18: 411-417.
- Ladoukakis E.D., C. Saavedra A. Magoulas and E. Zouros. (2002). Mitochondrial DNA variation in a species with two mitochondrial genomes: the case of Mytilus galloprovincialis from the Atlantic, the Mediterranean and the Black Sea. Molecular Ecology 11: 755-769.
- Ladoukakis E.D. and E. Zouros. (2001). Recombination in Animal mitochondrial DNA: evidence from published sequences. Molecular Biology and Evolution 18: 2127-2131.
- Ladoukakis E.D. and E. Zouros. (2001). Direct evidence for homologous recombination in the mussel Mytilus galloprovincialis mitochondrial DNA. Molecular Biology and Evolution 18: 1168-1175.
Microbial community structure
- Stilianos Fodelianakis, Nafsika Papageorgiou, Ioannis Karakassis and Emmanuel D. Ladoukakis (2015). Community structure changes in sediment bacterial communities along an organic enrichment gradient associated with fish farming. Ann Microbiol 65:331-338.
- Stilianos Fodelianakis, Paraskevi Pitta, Tron Frede Thingstad, Panagiotis Kasapidis, Ioannis Karakassis and Emmanuel D. Ladoukakis (2014) Phosphate addition has minimal short-term effects on bacterioplankton community structure of the P-starved Eastern Mediterranean. Aquatic Microbial Ecology 72(2):98-106.
- Stilianos Fodelianakis, Nafsika Papageorgiou, Paraskevi Pitta, Panagiotis Kasapidis, Ioannis Karakassis and Emmanuel D. Ladoukakis (2014). The pattern of change in the abundances of specific bacterioplankton groups is consistent across different nutrient-enriched habitats in Crete. Appl. Environ. Microbiol. 80(13):3784.
Other publications
- Panagiotis F. Sarris, Emmanuel D. Ladoukakis, Nickolas J. Panopoulos and Effie V. Scoulica (2014) A phage tail-derived element with wide distribution among both prokaryotic domains: a comparative genomic and phylogenetic study. Genome Biol. Evol. 6(7):1739–1747
- Pablo Arechavala-Lopez, Damian Fernandez-Jover, Kenneth D. Black, Emmanuel Ladoukakis, Just T. Bayle-Sempere, Pablo Sanchez-Jerez and Tim Dempster (2013). Differentiating the wild or farmed origin of Mediterranean fish: a review of tools for sea bream and sea bass. Reviews in Aquaculture 4:1–21.
- Emmanuel Ladoukakis, Vini Pereira, Emile Magny, Adam Eyre-Walker and Juan Pablo Couso (2011). Hundreds of putatively functional small Open Reading Frames in Drosophila. Genome Biology 12(11):R118.
- Touraki, M., Niopas, I., Ladoukakis, E., Karagiannis, V. (2010). Efficacy of flumequine administered by bath or through medicated nauplii of Artemia fransiscana (L.) in the treatment of vibriosis in sea bass larvae. Aquaculture 306: 146-152.
- Hodgkinson A, Ladoukakis E, Eyre-Walker A. (2009). Cryptic Variation in the Human Mutation Rate. PLoS Biology 7: 226-232.
- Ladoukakis ED, Eyre-Walker A (2008). The excess of small inverted repeats in prokaryotes. Journal of Molecular Evolution 67: 291-300.
- Ladoukakis ED and A. Eyre-Walker. (2007). Sequence directed mutagenesis in eukaryotes. Journal of Molecular Evolution 64: 1-3.
- Ladoukakis E.D., Lefort F., Sotiri P., Bacu A., Kongjika E. and Roubrlakis-Angelakis K. (2005). Genetic characterization of Albanian grapevine cultivars by microsatellite markers. J Int Sci Vigne Vin 39:109-119.
- Touraki M., Ladoukakis M. and C. Prokopiou (2001). High-performance liquid chromatographic determination of oxolinic acid and flumequine in the live fish feed Artemia. Journal of Chromatography B 751: 247-256.