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Librado Pablo

Pablo Librado

PostDoc - Laboratoire AMIS CNRS UMR 5288

Contact : plibrado@snm.ku.dk

Research Interests

My main research interest is deciphering the evolutionary mechanisms shaping the levels and patterns of genetic diversity, most especially including the role of natural selection across different phylogenetic lineages. These can be divided into four subcategories : (i) multigene family evolution and genomic architecture, including work on Drosophila and several plant species ; (ii) natural selection in coding and non-coding regions at different time scales ; (iii) exploiting ancient DNA to infer population demography, adaptation and migration ; (iv) developing new methods and implementing new bioinformatics tools, most notably including DnaSP v5.

Current/Ongoing Research

Each evolutionary process shapes to a certain extent the levels and patterns of genetic variation, yielding a footprint in our genomes. These molecular signatures are however eroded over time, which limits our resolution to infer past evolutionary events. Genomic sequences retrieved from ancient remains, such as fossils, open a window to the past, allowing to directly monitor evolutionary processes that would be otherwise undetectable in light of modern genomes. In my current research, I mostly focus on efficiently exploiting ancient DNA information to unravel one of the most important processes in recent human history : the domestication of the horse and its spread across the world. Owing to the peculiar nature of ancient DNA data, and the advent of Next-Generation Sequencing, this often entails using and implementing dedicated computational methods, including tools for the analysis of low depth-of-coverage sequences and with increased error rates due to post-mortem DNA damage.

Academic background and research experiences

· 12/2017 - present : PostDoc in the group of Prof. Ludovic Orlando, Laboratoire AMIS CNRS UMR 5288, Faculté de Médecine de Purpan, Université Paul Sabatier, Toulouse, France

· 01/2015 – 12/2017 : PostDoc in the group of Prof. Ludovic Orlando, Centre of Excelence for Geogenetics, Copenhagen, Denmark

· 09/2008 – 04/2014 : Ph.D. in the group of Prof. Julio Rozas, University of Barcelona, Spain

· 02/2007 - 08/2008 : Diploma thesis at the University of Barcelona, Spain.

· 02/2006 - 02/2007 : Diploma thesis at the University of Barcelona, Spain.

Bibliography

- LIBRADO P, Rozas J : DnaSP v5 : a software for comprehensive analysis of DNA
polymorphism data. Bioinformatics 2009, 25 (11):1451-1452.

- LIBRADO P, Vieira FG, Rozas J : BadiRate : Estimating Family Turnover Rates by Likelihood-Based Methods. Bioinformatics 2012, 28 (2) : 279-281.

- Mackay TF, ..., LIBRADO P, ..., Gibbs RA : The Drosophila melanogaster Genetic Reference Panel. Nature 2012, 482:173-178.

- Ramia M*, LIBRADO P*, Casillas S, Rozas J, Barbadilla A : PopDrowser : the Population Drosophila Browser. Bioinformatics 2012, 28 (4) : 595-596.

- Yeh S-D, ..., LIBRADO P, ..., Ranz JM : Functional evidence that a recently evolved Drosophila sperm-specific gene boosts sperm competition. Proceedings of the National Academy of Sciences 2012, 109 (6) : 2043-2048.

- LIBRADO P, Rozas J : Uncovering the functional constraints underlying the genomic
organisation of the Odorant-Binding Protein Genes. Genome Biology and Evolution 2013, 5 (11):2096-2108.

- LIBRADO P*, Vieira FG*, Sanchez-Gracia A*, Kolokotronis S-O*, Rozas J : Mycobacterial phylogenomics : An enhanced method for gene turnover analysis reveals uneven levels of gene gain and loss among species and gene families. Genome Biology and Evolution 2014, 6 (6):1454-1465.

- Denoeud F, ..., LIBRADO P, ..., Philippe Lashermes : The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science 2014, 345 (6201) : 1181-1184.

- Carretero-Paulet L, Chang T-H, LIBRADO P, Ibarra-Laclette E, Herrera-Estrella L, Rozas J, Albert VA : Genome-wide analysis of adaptive molecular evolution in the carnivorous plant Utricularia gibba. Genome Biology and Evolution 2015, 7 (2) : 444-456.

- Romero-Hernández B, Tedim AP, Sánchez-Herrero JF, LIBRADO P, Rozas J, Muñoz G, Baquero F, Cantón R, del Campo R : Streptococcus gallolyticus subsp. gallolyticus from human and animal origins : genetic diversity, antimicrobial susceptibility, and characterization of a vancomycin-resistant calf isolate carrying a vanA-Tn1546-like element. Antimicrobial Agents and Chemoterapy 2015, 59 (4) : 2006-2015.

- Blanco I, ..., LIBRADO P, ..., Stenmark-Askmalm M. Assessing associations between the AURKA-HMMR-TPX2-TUBG1 functional module and breast cancer risk in BRCA1/2 mutation carriers. PLoS One 2015, 10 (4) : e0120020

- Carretero-Paulet L*, LIBRADO P*, Chang T-H, Ibarra-Laclette E, Herrera-Estrella L, Rozas J, Albert VA. High gene family turnover rates and gene space adaptation in the compact genome of the carnivorous plant Utricularia gibba. Molecular Biology and Evolution 2015, 32 (5) : 1284-1295.

- Der Sarkissian C, ..., LIBRADO P, ..., Orlando L. Evolutionary genomics and conservation of the endangered Przewalski’s horse. Current Biology 2015, 25 (19) : 2577-2583.

- Calvo-Martín JM, LIBRADO P, Aguadé M, Papaceit M, Segarra C. Adaptive selection and coevolution at the proteins of the Polycomb repressive complexes in Drosophila. Heredity 2015, 116 (2) : 213-223.

- LIBRADO P*, Der Sarkissian C*, …, Orlando L. Tracking the origins of Yakutian horses and the genetic basis for their fast adaptation to subarctic environments. Proceedings of the National Academy of Sciences 2015, 112 (50) : E6889-E6897.

- Leonardi M, LIBRADO P, Der Sarkissian C, Schubert M, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Gamba C, Willerslev E, Orlando L. Evolutionary patterns and processes : lessons from ancient DNA. Systematic Biology 2016, doi : 10.1093/sysbio/syw059.

- LIBRADO P and Rozas J. Weak polygenic selection drives the rapid adaptation of the chemosensory system : lessons from the upstream regions of the major gene families. Genome Biology and Evolution 2016 , 8 (8) : 2493-2504 .

- LIBRADO P, ..., Orlando L. The Evolutionary Origin and Genetic Makeup of Domestic
Horses. Genetics 2016, 204 (2):423-434.

- Clifton BD, LIBRADO P, ..., Ranz JM. Rapid Functional And Sequence Differentiation of a Tandemly-Repeated Species-Specific Multigene Family in Drosophila. Molecular Biology and Evolution 2016, doi : 10.1093/molbev/msw212.

- Fukushima K, ..., LIBRADO P, …, Hasebe M. The genome of the heterophyllous pitcher plant Cephalotus reveals genetic changes associated with carnivory. Nature Ecology and Evolution 2017, 1:59 .

- LIBRADO P* , Gamba C*, Gaunitz C, Sarkissian CD, Pruvost M, Albrechtsen A, Fages A, Khan N, Schubert M, Jagannathan V, et al. 2017. Ancient genomic changes associated with domestication of the horse. Science 356:442–445.

- Cruz-Dávalos DI, Llamas B, Gaunitz C, Fages A, Gamba C, Soubrier J, LIBRADO P , Seguin-Orlando A, Pruvost M, Alfarhan AH, et al. 2017. Experimental conditions improving insolution target enrichment for ancient DNA. Mol. Ecol. Resour. 17:508–522

- Rozas J, Ferrer-Mata A, Sánchez-DelBarrio JC, Guirao-Rico S, LIBRADO P , Ramos-Onsins SE, Sánchez-Gracia A. 2017. DnaSP 6 : DNA Sequence Polymorphism Analysis of Large DataSets. Mol. Biol. Evol. 34:3299–3302. [

- Gaunitz C*, Fages A*, Hanghøj K, … LIBRADO P, Outram A, Orlando L. 2018. Ancient genomes revisit the ancestry of domestic and Przewalski’s horses. Science. Accepted.

- Alberto F, Boyer F, Orozco-terWengel P, Streeter I, Servin B, de Villemereuil P, Benjelloun B., LIBRADO P, Biscarinni F, Colli L, et al. 2018. Convergent genomic signatures of domestication in sheep and goats. Nat. Commun. Accepted.

*Equal contribution

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