research

NYC became home in August 2001, as I enrolled in Columbia University E3B's Ecology & Evolutionary Biology PhD program and worked in Rob DeSalle's lab at AMNH. Before crossing the Atlantic, I worked on loggerhead turtle population genetics in Eleftherios Zouros' lab at the Dept. of Biology, University of Crete, and on plant sexual trait evolutionary ecology under Jacqui Shykoff's supervision at Université Paris-Sud XI. Early on I was introduced to evolutionary biology through an internship in François Catzeflis' lab by Emmanuel Douzery (Inst. des Sciences de l'Evolution de Montpellier) and classes taught by Isabelle Olivieri in Montpellier. As an undergrad summer intern, I was exposed to a variety of research fields such as molecular oncology at INSERM in Paris (Andreas Tsapis' lab), cancer biochemistry at the University of Crete Faculty of Medicine (Elias Castanas's lab), and Drosophila population genetics at the University of Barcelona (lab of Montserrat Aguadé & Julio Rozas). As an EU Marie Curie fellow, I did some work on odorant binding protein gene evolution with Julio Rozas in Barcelona, whom with I collaborate now on bacterial evolutionary genomics projects. My main research focus is on the molecular evolution of endangered species and [their] pathogens as well as phylogenomics of non-model organisms.

conservation genetics

In 2007-2011 I coordinated the AMNH's DNA Barcoding Initiative for Conservation (PI: George Amato), funded by the Alfred P. Sloan Foundation, where we characterize the genetic diversity of species of conservation concern (endangered or threatened) and involved in [illegal] trade. Cephalophus_zebra-120pxCase studies include tuna, sturgeons, sharks, bushmeat, mislabeled animal products in the New York City markets, as well as items confiscated by the authorities. We employ DNA Barcoding as well as DNA sequencing of gene regions that help elucidate relationships of recently diverged species and regional intraspecific variation. Those projects also serve as a training ground for students across a multitude of educational levels, such as high school, undergraduate, masters, and PhD.

Quantifying the genetic units among African elephants is of paramount importnace when drafting conservation and protection policies globally and at the regional and national level. We are using mitochondrial DNA and nuclear genetic markers to understand the apportionment of Loxodonta_cyclotis-240pxgenetic variation within and between Loxodonta africana (the savanna elephant) and Loxodonta cyclotis, its forest counterpart. Furthermore, we are analyzing genes that might be of potential functional significance in the divergence of elephants and mammoths using ancient DNA paleogenetics techniques and computational modeling approaches. – In collaboration with Al Roca (U Illinois) and Alex Greenwood (Inst. Zoo & Wildlife, Berlin).

plant phylogenomics

cycad-involute_vernation-240pxAlong with AMNH's Rob DeSalle (co-PI), NYU (PI: Gloria Coruzzi, co-PI: Dennis Shasha), the New York Botanical Garden (co-PI: Dennis Stevenson, Damon Little), and Cold Spring Harbor Lab (co-PIs: Rob Martienssen & Dick McCombie), we form the NSF-funded New York Plant Genomics Consortium working on various aspects of evolutionary and comparative genomics of the seed plants.

elephant & human tuberculosis

Mycobacterium tuberculosis, the causative agent of tuberculosis in humans has been believed to infect other vertebrates including elephants. Mtuberculosis_NIAIDIn collaboration with scientists from the U.S. Department of Agriculture, we have examined rapidly evolving genetic markers on the M. tuberculosis genome and found that elephant infections in captive settings in the U.S.A. are indeed of human origin. Ongoing work includes description of mycobacterial isolates from the range countries, where elephants are endangered and protected under CITES among other legal frameworks – in collaboration with Ramiro Isaza (U Florida, Veterinary Medicine). The range of genetic diversity is being examined within the spectrum of human MTB isolate diversity in collaboration with Barry Kreiswirth and Barun Mathema at the Public Health Research Institute (based at UMDNJ).

The NGO Elephant-Care-IntlElephant Care International works on the management of tuberculosis in elephants in the U.S.A. and the range countries, and I try contributing information on M. tuberculosis's evolution by participating on their Elephant TB Scientific Advisory Board.

phylogenomic patterns in bacteria

Next-generation sequencing technologies are opening the door to large-scale collection of prokaryotic genome sequence data. We are investigating genome-wide patterns of phylogenetic agreement and incongruence to understand and quantify the evolutionary heterogeneity of different genome segments and gene families in various bacterial phyla. In collaboration with Paul Planet (Columbia U Medical Center), Rick Baker, Apurva Narechania and Rob DeSalle (AMNH).

In a parallel line of research we are examining the dynamics of expansion and contraction of bacterial gene families in the light of newly established phylogenetic backgrounds based on finished genomes and novel algorithmic implementations – in collaboration with Julio Rozas (U Barcelona), funded by the Spanish Ministry of Science & Innovation.

wildlife virus surveillance and evolution

In order to better understand the ecological movement and dispersal of pathogenic viruses as well as the emergence of pathogenicity as a lifestyle, we are looking at their non- or low-pathogenic cousins. Anas_platyrhynchos_male-240px Examples include: avian influenza A virus isolated from waterfowl across the U.S.A. in different points in time – in collaboration with the U.S. Department of Agriculture; endogenous feline leukemia virus (FeLV) lineage evolution – in collaboration with Al Roca (U Illinois) and Gila Bar-Gal (Hebrew U Jerusalem); St. Louis encephalitis virus (SLEV) temporal diversification across the Americas – with Greg Baillie (now at U Cambridge) and Susan Perkins (AMNH).

paleogenetics and ancient DNA

Ancient DNA provides a unique window in Tasmanian_wolftime for the study of historical evolution of extant and also extinct species. With Simon Ho (U Sydney) we have been estimating intraspecific evolutionary rates of vertebrates using coalescent frameworks, thus informing phylogeographic studies. In collaboration with Alex Greenwood (Inst. Zoo & Wildlife, Berlin) we have been looking at the ocurrence of mtDNA insertions in the nucleus in Pleistocene mammals and the evolution of candidate genes in mammoths.

news

Gymnosperm and monocot clades from BigPlant v1.0 ML tree - Fig. 1 from PLoS Genetics paper http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1002411

publication: Seed plant phylogenomics @ PLoS Genetics.   Read more

conference: Health & Environment @ AMNH.   Read more

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