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Evolutionary Genetics
Introduction
The 'Evolutionary Genetics' research group at the Cavanilles Institute
for Biodiversity and Evolutionary Biology is devoted to the study of
biological evolution, from species to molecules. Our conceptual tools
are derived mainly from population and evolutionary genetics and we use
techniques from classical genetic analysis up to molecular biology, including
genomics and bioinformatics. This research program has enabled a wide
range of collaborations with groups from many different centers. Our
group includes 8 staff researchers, 4 postdoctoral associates, 15 Ph.D.
students, and 4 technicians.
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Representative Projects
- Evolutionary genomics of endosymbiotic bacteria
Beneficial associations between insects and intracellular bacteria are common in nature. These bacterial species are often referred as primary or secondary endosymbionts depending of their role (essential or not) on insect growth and development. Obligate endosymbionts are exclusively vertically transmitted from the mother to the offspring of their respective insect hosts and, during the adaptative process to intracellular life, these bacteria suffer drastic changes in their genomes.
Our goal is to explain the nature of the processes that allow the symbiotic integration of these bacteria in their host insect. We analyze the rhythm, the mode and the consequences of the process of genome reduction that has lead to several of these species to present some of the smallest bacterial genomes known to date. In recent years we have sequenced and analyzed the complete genomes of two Buchnera aphidicola strains (endosymbionts of galling aphid Baizongia pistaceae and cedar aphids, respectively) and Blochmannia floridanus (endosymbionts of carpenter ants). At present we are working on the genomes of two flavobacteria that are primary endosymbionts of the coackroaches Blattela germànica i Blatta orientalis, the primary endosymbiont of rice weevil (SOPE) and a second endosymbiont present in the cedar aphid (Serratia symbiotica BCc).
Our analyses on these reduced genomes have been the start point to a new project focused on the theoretical study of the composition and evolution of hypothetical minimal genomes for autotrophic and heterotrophic bacteria, as well as the properties of the metabolic networks deduced from their genome content
- Molecular epidemiology of infectious diseases
Most emerging and epidemic infectious diseases are caused by viruses and bacteria, many of which evolve at such a fast rate that changes in the nucleotide sequence of several genome regions can be observed within weeks or months at the population-scale level. The application of modern sequencing technology and the use of population genetics and molecular systematic tools are expanding the traditional field of epidemiology. We use this blended approach in a variety of settings, from the investigation of disease outbreaks to the ellucidation of evolutionary patterns in viruses and other pathogenic organisms
- Experimental evolution
RNA viruses are exceptional models for investigating evolution in the lab. Their high mutation rate, short generation time and large population sizes enable the observation of evolutionary phenomena to proceed in 'real' time. Under appropriate experimental conditions they are being used to test many different tenets of evolutionary theory. We have mainly worked with the vesicular stomatitis virus to measure changes in viral replication capability (fitness) and citopathogenicity during its experimental evolution in the laboratory. We have also used directed mutagenesis or RT-PCR to study the effects of nucleotide substitutions on the virus. We have recently started to use Escherichia coli phages as experimental models. We have several RNA and DNA bacteriophages with varying genome length (from 3.5 to 150 kb) to study the influence of different basic genome properties (length, complexity, mutation rate, robustness,...) on the evolutionary process.
- Genetic studies of aphids: Taxonomy and reproductive polyphenism
Aphids are a monophyletic group within Hemiptera and include more than 4000 species. Systematics and taxonomy of the group are controversial, with several alternative proposals. Our research group seeks to establish a global phylogeny for Aphididae through the analysis of gene sequences from the nuclear, mitochondrial and bacterial endosymbionts genomes. We intend to disentangle the evolutionary relationships among the different subfamilies and within the taxonomic levels of lower rank, apart from resolving specific taxonomy problems.
Aphids reproduce by cyclic parthenogenesis (with several parthenogenetic generations followed by a single sexual generation per year). In nature, the reproduction cycle is mainly controlled by the length of photoperiod and temperature, but the molecular bases of how the photoperiodic signal is translated into one or other reproduction mode (parthonogenesis vs sexuality) are completely unknown. We are interested in identifying the genes and routes implicated in the mode of reproduction and also in the characterization and analysis of the expresion of those genes.
- Metagenomics of the human gut
Several factors (age, diet, diseases) influence microbial diversity in the gut. Different molecular techniques, such as 16S rDNA analysis, provide information on the gut microbiota and allow the analysis of its influence on several pathologies and their use as diagnostic tools. The metagenomic approach, combined with the analysis of biodiversity in different conditions, provides insight on the activities of a given sample and can lead us to model the relationships in a microbial community, thus helping to understand the structure and evolution of these communites.
Our project is aimed at sequencing the microbial metagenome of the gut from Chron disease affected pateints to identify genes related with pathogenicity, interaction with the host, antibiotic resistance, etc. We also pretend to analyze the variation in their expression in response to different environmental conditions through DNA microarray analysis to better understand the origin of different gastrointestinal pathologies.
- Phylogenomics
The increasing availablility of complete genome sequences of many organisms, but most notably bacteria, is allowing the investigation of evolutionary processes at a genome-wide scale. We are interested not only in deriving the evolutionary history of the genes comprising the genome of a species (its phylome) but also in ascertaining the role of horizontal gene transfer, duplication, recombination, and selection, among other relevant factors shaping the final composition of bacterial genomes.
- Bioinformatics
Biological data, mainly from gene and genome sequences, are produced at a fast pace in many research groups and ours is no exception. Although there are many available computational tools, we are continuously implementing, tailoring and developing new tools to help us interpret and analyze the sequence data we produce. Hence, bioinformatics plays a central role in the research activities of our group.
- Statistical methods in metagenomics and evolutionary molecular epidemiology
We investigate statistical methods to address questions arising in the context of these two quite new scientific disciplines. Datasets are usually large and often present complex internal structures that should be taken into account in the statistical analyses in order to provide more reliable results. To this end, we are exploring the use of multivariate statistical techniques and Bayesian methods.
- Conservation genetics of plant and animal endemic species
One of the main goals of evolutionary biology is to catalogue, document and, naturally, preserve biodiversity at all organization levels (genes, populations, species, ecosystems). We have developed and used a range of molecular techniques to obtain estimates of genetic variation in populations of endangered plants and animals. This information has been used to establish more efficient conservation strategies for these species.
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Recent Publications
2008
- Bargues, M.D.; Klisiowicz, D.R.; González-Candelas, F.; Ramsey, J.M.; Monroy, C.; Ponce, C-; Salazar-Schettino, P.M.; Panzera, F.; Abad-Franch, F.; Sousa, O.E.; Schofield, C.J.; Dujardin, J.P.; Guhl, F.; Mas-Coma, S. 2008. Phylogeography and genetic variation of Triatoma dimidiata, the main Chagas disease vector in Central America, and its position within the genus Triatoma. PLoS Neglected Tropical Diseases 2(5): e233. doi:10.1371/journal.pntd.0000233.
- Bracho, M.A.; Saludes, V.; Martro, E.; Bargallo, A.; González-Candelas, F.; Ausina, V. 2008. Complete genome of a European hepatitis C virus subtype 1g isolate: phylogenetic and genetic analyses. Virology Journal 5: 72.
- Carrillo, F.Y.E.; Sanjuán, R.; Moya,A.; Cuevas,J.M. (2008) Enhanced adaptation of vesicular stomatitis virus in cells infected with vaccinia virus. Infection, Genetics and Evolution 8(5): 614-620.
- Comas, I.; González-Candelas, F.; Zúñiga, M. 2008. Unravelling the evolutionary history of the phosphoryl-transfer chain of the phosphoenolpyruvate:phosphotransferase system by phylogenetic analyses and genome context. BMC Evolutionary Biology 8:147.
- Cortés, T.; Tagu, D.; Simon, JC.; Moya, A.; Martínez-Torres, D. 2008. Sex versus parthenogenesis: A transcriptomic approach of photoperiod response in the model aphid Acyrthosiphon pisum (Hemiptera: Aphididae). Gene 408(1-2):146-56.
- Cuevas, J. M.; Torres-Puente, M.; Jiménez-Hernández, N.; Bracho, M. A.; García-Robles, I.; Carnicer, F.; Olmo, J. D.; Ortega, E.; Moya, A.; González-Candelas, F. 2008. Refined analysis of genetic variability parameters in hepatitis C virus and the ability to predict antiviral treatment response. Journal of Viral Hepatitis. Online Early, May 12, 2008. doi:10.1111/j.1365-2893.2008.00991.x.
- Cuevas, J.M.; Torres-Puente, M.; Jiménez-Hernández, N.; Bracho, M.A.; García-Robles, I.; Wrobel, B.; Carnicer,F.; del Olmo, F.; Ortega,E.; Moya,A.; González-Candelas,F. (2008) Genetic variability of Hepatitis C Virus before and after combined therapy of interferon plus ri bavirin. PLoSONE 3(8): e3058. doi:10.1371/journal.pone.0003058.
- D'Auria, G.; Jimenez, N.; Peris-Bondia, N.; Pelaz, C.; Latorre, A.; Moya, A. 2008. Virulence factor rtx in Legionella pneumophila, evidence suggesting it is a modular multifunctional protein. BMC Genomics 9:14.
- Gil, R.; Belda, E.; Gosalbes, M.J.; Delaye, L.; Vallier, A.; Vincent-Monégat, C.; Heddi, A.; Silva, F.J.; Moya, A.; Latorre, A. 2008. Massive presence of insertion sequences in the genome of SOPE, the primary endosymbiont of the rice weevil Sitophilus oryzae. Int Microbiol 11(1): 41-48.
- Gómez-Baldó, L.; Latorre, A.; Serra, Ll.; Mestres, F. 2008. Molecular variation in the Odh gene in Chilean natural populations of Drosophila subobscura. Hereditas 145: 154-162.
- Gosalbes, M.J.; Lamelas, A.; Moya, A.; Latorre, A. 2008. The striking case of tryptophan provision in the cedar aphid Cinara cedri. Journal of Bacteriology 190(17): 6026-6029.
- Lamelas, A.;Pérez-Brocal,V.; Gómez-Valero, L.; Gosalbes, M.J.; Moya, A.; Latorre, A. 2008. Evolution of the Secondary Symbiont "Candidatus Serratia symbiotica" in Aphid Species of the Subfamily Lachninae. Appl. Environ. Microbiol. 74: 4236-4240.
- Llorens,C.; Futami,R.; Bezemer,Daniela; Moya,A. 2008. The Gypsy Database (GyDB) of mobile genetic elements. Nucleic Acids Research 36: D38-D46.
- Moya, A.; Peretó, J.; Gil, R.; Latorre, A. 2008. Learning how to live together: Genomic insights into prokaryote-animal symbioses. Nat. Rev. Genet. 9(3): 218-229.
- Novais, A.; Cantón, R.; Coque, T.M.; Moya, A.; Baquero, F.; Galán, J.C..2008. Mutational events in ESBL-cefotaximases of the CTX-M-1 cluster involved in ceftazidime resistance. Antimicrob. Agents Chemother. published ahead of print on 28 April 2008, doi:10.1128/AAC.01658-07
- Sanjuán, R.; Nebot, M.R. (2008) A network model for the correlation between epistasis and genomic complexity. PLoS ONE 3(7): e2663. doi:10.1371/journal.pone.0002663.
- Sentandreu, V.; Jiménez-Hernández, N; Torres-Puente, M.; Bracho, M.A.; Valero, A.; Gosalbes, M.J.; Ortega, E.; Moya, A.; González-Candelas, F. (2008) Evidence of Recombination in Intrapatient Populations of Hepatitis C Virus. PLoS ONE 3(9): e3239. doi:10.1371/journal.pone.0003239.
- Tagu, D.; Klingler, J.P.; Moya, A.; Simon, J.-C. 2008. Early progress in aphid genomics and consequences for plant-aphid interactions studies. Molecular Plant-Microbe Interactions 21(6): 701-708.
- Tamames, J.; Moya, A. 2008. Estimating the extent of horizontal gene transfer in metagenomic sequences. BMC Genomics 9: 136.
- Torres-Puente, M.; Cuevas, J.N.; Jiménez-Hernández, N.; Bracho, M.A.; García-Robles, I.; Wróbel, B.;Carnicer, F.; del Olmo, F.; Ortega, E.; Moya, A.; González-Candelas, F. 2008. Using evolutionary tools to refine the new hypervariable region 3 within the envelope 2 protein of hepatitis C virus. Infection, Genetics and Evolution 8(1): 74-82.
- Torres-Puente, M.; Cuevas, J.N.; Jiménez-Hernández, N.; Bracho, M.A.; García-Robles, I.; Wrobel, B.; Carnicer, F.; del Olmo, F.; Ortega, E.; Moya, A.; González-Candelas, F. 2008. Genetic variability in hepatitis C virus and its role in antiviral treatment response. The Journal of Viral Hepatitis 15: 188-199.
- Torres-Puente, M.; Cuevas, J.N.; Jiménez-Hernández, N.; Bracho, M.A.; García-Robles, I.; Carnicer, F.; del Olmo, F.; Ortega, E.; Moya, A.; González-Candelas, F. 2007. Hepatitis C virus and the controversial role of the interferon sensitivity determining region in the response to interferon treatment. The Journal of Medical Virology 80(2): 247-253.
2007
- Amadoz, A.; González-Candelas, F. 2007. epiPATH: an information system for the storage and management of molecular epidemiology data from infectious pathogens. BMC Infectious Diseases 7:32.
- Carrillo, F.Y.; Sanjuán, R.; Moya, A.; Cuevas, J.M. 2007. The effect of co- and superinfection on the adaptive dynamics of vesicular stomatitis virus. Infection, Genetics and Evolution, 7(1): 69-73.
- Comas, I.; Moya, A.; González-Candelas, F. 2007. From phylogenetics to phylogenomics: the evolutionary relationships of insect endosymbiotic gamma-Proteobacteria as a test case. Systematic Biology 56(1): 1-16.
- Comas, I.; Moya, A.; González-Candelas, F. 2007. Phylogenetic signal and functional categories in Proteobacteria genomes. BMC Evolutionary Biology 7 (Suppl. 1): S7 (8 February 2007)
- Coscollá, M.; González-Candelas, F. 2007. Population structure and recombination in environmental isolates of Legionella pneumophila. Environmental Microbiology 9(3): 643-656.
- Furió, V.; Moya, A.; Sanjuán, R. 2007. The cost of replication fidelity in human immunodeficiency virus 1. Proc. R. Soc. B 274: 225-230.
- Gabaldón,T.; Peretó, J.; Montero, F.; Gil, R.; Latorre, A.; Moya, A. 2007. Structural analyses of a hypothetical minimal metabolism. Phil. Trans. Royal Soc. B. 362 (1486): 1751-1762.
- Garcia-Martinez, J.; González-Candelas, F.; Perez-Ortin, J. 2007. Common gene expression strategies revealed by genome-wide analysis in yeast. Genome Biology 8:R222.
- Gómez-Valero, L; Silva, F.J.; Simon, J.C.; Latorre, A. 2007. Genome reduction of the aphid endosymbiont Buchnera aphidicola in a recent evolutionary time scale. Gene 389(1): 87-95.
- Gómez-Valero, L.; Rocha, E.P.; Latorre, A.; Silva, F.J. 2007. Reconstructing the ancestor of Mycobacterium leprae: the dynamics of gene loss and genome reduction. Genome Research 17: 1178-1185.
- Jiménez-Hernández, N.; Torres-Puente, M.; Bracho, M. A.; García-Robles, I.; Ortega, E.; del Olmo, J.;Carnicer, F. González-Candelas, F.; Moya, A. 2007. Epidemic dynamics of two coexisting hepatitis C virus subtypes. Journal of General Virology 88(1): 123-133.
- Jimenez-Hernandez N, Sentandreu V, Castro JA, Torres-Puente M, Bracho A, Garcia-Robles I, Ortega E, Del Olmo J, Carnicer F, Gonzalez-Candelas F, Moya A. 2007. Effect of antiviral treatment and host susceptibility on positive selection in hepatitis C virus (HCV). Virus Res. 2007 Nov 1;
- López-Labrador,F.X.; Dove,Lorna; Hui,Chee Kin; Phung,Yume; Kim,Michael; Berenguer,Marina; Wright,Teresa L. 2007. Trends for genetic variation of Hepatitis C Virus quasispecies in Human Immunodeficiency virus-1 coinfected patients. Virus Research 130 (1-2): 285-291.
- Olasagasti, F.; Moreno, A.; Peretó, J.; Morán, F. 2007. Energetically plausible model of a self-maintaining protocellular system. Bulletin of Mathematical Biology 69(4):1423-1445.
- Porcar, M.; Ramos, S.; Latorre, A. 2007. A simple DNA extraction method sutiable for detection of genetically modified maize. Journal of the Science of Food and Agriculture 87: 2728-2731.
- Palop-Esteban, M.; Segarra-Moragues, J.G.; González-Candelas, F. 2007. Historical and biological determinants of genetic diversity in the highly endemic triploid sea lavender Limonium dufourii (Plumbaginaceae). Molecular Ecology 16(18): 3814-3827.
- Sanjuán, R.;Cuevas, J.M.; Furió, V.; Holmes, E.C.; Moya, A. 2007. Selection for Robustness in Mutagenized RNA Viruses. PLoS Genetics 3(6): e93.
- Segarra-Moragues J.G.; Palop-Esteban M.; González-Candelas F.; Catalán P. 2007. Nunatak survival vs. tabula rasa in the Central Pyrenees: a study on the endemic plant species Borderea pyrenaica (Dioscoreaceae). Journal of Biogeography 34: 1893-1906.
- Silva, F.J.; Latorre, A.; Gómez-Valero, L.; Moya, A. 2007. Genomic changes in bacteria: From free-living to endosymbiotic life. In: Structural approaches to sequence evolution: Molecules, networks, populations. Ed: Bastolla, U., Porto, M., Roman, H.E. & Vendruscolo, M. Springer pp. 149-165.
- Tamames, J.; Moya, A.; Valencia, A. 2007. Modular organization in the reductive evolution of protein-protein interaction networks. Genome Biology 8:R94 ( 28 May 2007 )
- Tamames J, Gil R, Latorre A, Pereto J, Silva FJ, Moya A. 2007. The frontier between cell and organelle: genome analysis of Candidatus Carsonella ruddii. BMC Evol Biol. 7(1):181
- Torres-Puente, M.; Cuevas, J.N.; Jiménez-Hernández, N.; Bracho, M.A.; García-Robles, I.; Carnicer, F.; del Olmo, F.; Ortega, E.; Moya, A.; González-Candelas, F. 2007. The contribution of insertions and deletions to the variability of hepatitis C virus populations. The Journal of General Virology 88(8): 2198-2203.
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Team
STAFF:
POSTDOCTORAL RESEARCHERS:
| Position |
Name |
Telephone |
E-mail |
| Postdoctoral Researcher, CIBERESP |
Dr. Juan José Abellán |
963543826 |
juan.j.abellan uv.es |
| Postdoctoral Researcher, SNS (ISCIII-FIS) |
Dra. Alma Bracho |
963543647 |
alma.brachouv.es |
| Postdoctoral Researcher, Programa Juan de la Cierva |
Dr. José Manuel Cuevas |
963543686 |
jose.m.cuevasuv.es |
| Postdoctoral Researcher, CIBERESP |
Dr. Giuseppe D'Auria |
963543646 |
giuseppe.dauriauv.es |
| Postdoctoral Researcher, UAM (México) |
Luis Delaye |
963543825 |
luis.delayeuv.es |
| Research Technician |
Dra. María José Gosalbes |
963543647 |
maria.jose.gosalbesuv.es |
| Postdoctoral Researcher, SNS (ISCIII-FIS) |
Dr. Xavier López Labrador |
963543648 |
fco.xavier.lopezuv.es |
| Research Technician |
Dr. Alejandro Mira |
963543825 |
alejandro.mirauv.es |
| Postdoctoral Researcher, Programa Marie Curie |
Dr. Alexander Neef |
963543629 |
alexander.neefuv.es |
| Postdoctoral Researcher, Programa Ramón y Cajal |
Dr. Rafael Sanjuan |
963543629 |
rafael.sanjuanuv.es |
| Postdoctoral Researcher, SNS (ISCIII-FIS) |
Dr. Javier Tamames |
963543648 |
javier.tamamesuv.es |
| Postdoctoral Researcher |
Carmen M. González Doménech |
963543651 |
carmen.m.gonzalezuv.es |
TECHNICIANS:
| Position |
Name |
Telephone |
E-mail |
| Research Technician, SNS (ISCIII-FIS) |
Dra. Nuria Jiménez |
963543648 |
nuria.jimenezuv.es |
| Research Technician |
Dr. Miguel Pignatelli |
963543272 |
miguel.pignatelli uv.es |
| Research Technician |
Silvia Ramos |
963543646 |
silvia.ramosuv.es |
| Research Technician |
Eva Amparo Jaime Daudén |
963543882 |
eva.jaimeuv.es |
| Computers Technician |
Pascual Asensi |
963543686 |
pascual.asensiuv.es |
| Oficial de Laboratorio |
Concepción Hueso Climent |
963543772 |
concepcion.huesouv.es |
PREDOCTORAL RESEARCHERS:
| Name |
Telephone |
E-mail |
| Alicia Amadoz |
963543687 |
alicia.amadozuv.es |
| Eugeni Belda |
963543651 |
eugenio.beldauv.es |
| Francy Yolima Carrillo |
963543669 |
francy.carrillouv.es |
| Teresa Cortés |
963543646 |
teresa.cortesuv.es |
| Mireia Coscollá |
963543648 |
mireia.coscollauv.es |
| Pilar Domingo |
963543668 |
pidocaalumni.uv.es |
| Ana Durbán |
963543651 |
ana.durbanuv.es |
| Araceli Lamelas |
963543651 |
Araceli.Lamelasuv.es |
| Victoria Furió |
963543669 |
victoria.furiouv.es |
| Mª Jose López |
963543651 |
maria.jose.lopezuv.es |
| Sergio López |
963543651 |
serlomaalumni.uv.es |
| Maximiliano Martinez |
963543438 |
Maximiliano.Martinezuv.es |
| Benjamín Ortiz |
963543646 |
benjamin.ortizuv.es |
| Rafael Patiño |
963543651 |
rafael.patinouv.es |
| Ana Elena Pérez |
963543651 |
apecoalumni.uv.es |
| Francesc Peris |
963543648 |
francisco.peris-bondiauv.es |
| Pilar Domingo Calap |
963543668 |
Pilar.Domingouv.es |
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Techniques and equipment:
General laboratories:
- Laminar flow cabinet
- Autoclaves
- Incubators for microbiological cultures (controlled
temperatura)
- Spectophotometer: to determine optical density of
microbial cultures, to quantify nucleic acid
- Sonicator: to break cells and nucleic acid
- Electroporator: to transform microorganism
- Gel electrophoresis, gel imaging system
- Pulsed field electrophoresis
- Benchtop centrifuges for tubes or plates
- DNA speed-vaccium system: to dry samples
- DNA fragment analysis system (SNPs and size) based
in liquid chromatography
- Multiprobe II robotic liquid handling system
- PCR systems for tubes (24, 96) or plates
- Gradient PCR systems
- Water purification system: distillation system
- Fridges and freezers (-20ºC and -80ºC
- Controlled temperature, photoperiod, humidity chambers
- Microscope Axioskop 40 "Carl Zeiss"
- Hybridization oven, non-radioactive hybridization
- Fume hoods
Laboratory of experimental evolution and
cell culture:
- Laminar flow cabinet
- Liquid nitrogen freezer for frozen cell stock
- CO 2 incubators for cell culture
- Water bath
- Filtration system
- Inverted microscope (Axiovert 25 Zeiss
- Electronic cell counter
- Autoclave
- Water purification system: distillation system, Milli-Q
system
- Fridges and freezers (-20ºC and -80ºC). 4ºC
room
- Benchtop centrifuges for tubes or plates
- Electroporador
- PHmetro
- Fume hoods
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[Last update: 24/03/09]