Metazoa Phylogenomics
Comparative genomic studies must be anchored in a phylogenetic tree. Yet many key aspects in the evolutionary relationships within and between animal groups remain elusive. Resolving the Tree of Life has been prioritized as one of the 125 most important unsolved scientific questions by Science, and the advent of phylogenomics has aided in resolving many contentious aspects in animal phylogeny. In the lab, we explore how phylogenomic inference can be improved by considering the effects of orthology inference, hidden paralogy and gene duplication.
Because all genomes are evolutionarily related, closely or distantly, the key to making sense of them lies in comparative genomics. By identifying the conserved or divergent aspects among genomes and transcriptomes, one can hope to elucidate the genes that are associated with essential housekeeping functions, or with innovation or adaptation. By using a phylogenomic spyglass, we can infer the evolutionary dynamics of animal genes to understand how (by speciation or duplication), when (in which node) and how often (how many copies) each gene in each genome was gained, duplicated or lost. In the lab, we will explore how the gene repertoire evolved in certain animal lineages to adapt to new environments, such as in the case of terrestrialization events or life in caves. We´re particularly interested in understanding how gene duplication reshapes animal genomes, and interrogating its role as the potential driver of convergent evolution.
Web page: Metazoa Phylogenomics Lab
Rojo I, Escudero N, Fernández R, Fernández-Álvarez FÁ. 2024. First record of the alien land flatworm Marionfyfea adventor (Platyhelminthes: Geoplanidae) in the Iberian Peninsula. Zootaxa, 5397(2):291-294. DOI:10.11646/zootaxa.5397.2.10
Pujal D, Escudero J, Cabrera P, Bos L, Vargas-Chávez C, Fernández R, Bellés X, Maestro JL. 2024. Functional redundancy of the three insulin receptors of cockroaches. Insect Biochemistry and Molecular Biology, 172(July):104161. DOI:10.1016/j.ibmb.2024.104161
Barrios-Núñez I, Martínez-Redondo GI, Medina-Burgos P, Cases I, Fernández R, Rojas AM. 2024. Decoding functional proteome information in model organisms using protein language models. NAR Genomics and Bioinformatics, 6(3):1-25. DOI:10.1093/nargab/lqae078
Balart-García P, Bradford TM, Beasley-Hall PG, Polak S, Cooper SJB, Fernández R. 2024. Highly dynamic evolution of the chemosensory system driven by gene gain and loss across subterranean beetles. Molecular Phylogenetics and Evolution, 194(February):108027. DOI:10.1016/j.ympev.2024.108027
Alfonso P, Butković A, Fernández R, Riesgo A, Elena SF. 2024. Unveiling the hidden viromes across the animal tree of life: insights from a taxonomic classification pipeline applied to invertebrates of 31 metazoan phyla. mSystems, 9(5). DOI:10.1128/msystems.00124-24
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Martínez‐Redondo GI, Simón Guerrero C, Aristide L, Balart‐García P, Tonzo V, Fernández R. 2023. Parallel duplication and loss of aquaporin‐coding genes during the ‘out of the sea’ transition as potential key drivers of animal terrestrialization. Molecular Ecology, 32(8): 2022-2040. DOI:10.1111/mec.16854.
Benítez-Álvarez L, Leria L, Fernández R, Mateos E, El Ouanighi Y, Bennas N, El Alami M, Yacoubi-Khebiza M, Ayt Ougougdal H, Riutort M. 2023. Phylotranscriptomics interrogation uncovers a complex evolutionary history for the planarian genus Dugesia (Platyhelminthes, Tricladida) in the Western Mediterranean. Molecular Phylogenetics and Evolution, 178:107649. DOI:10.1016/j.ympev.2022.107649
Balart-García P, Aristide L, Bradford TM, Beasley-Hall PG, Polak S, Cooper SJB, Fernández R. 2023. Parallel and convergent genomic changes underlie independent subterranean colonization across beetles. Nature Communications, 14(1):3842. DOI:10.1038/s41467-023-39603-1
Benítez-Álvarez L, Leria L, Fernández R, Mateos E, El Ouanighi Y, Bennas N, El Alami M, Yacoubi-Khebiza M, Ayt Ougougdal H, Riutort M. 2022. Phylotranscriptomics interrogation uncovers a complex evolutionary history for the planarian genus Dugesia (Platyhelminthes, Tricladida) in the Western Mediterranean. Molecular Phylogenetics and Evolution, 178 (107649). DOI:10.1016/j.ympev.2022.107649
Phillips HRP, Bach EM, Bartz MLC, Bennett JM, Beugnon R, Briones MJI, Brown GG, Ferlian O, Gongalsky KB, Guerra CA, König-Ries B, Krebs JJ, Orgiazzi A, Ramirez KS, Russell DJ, Schwarz B, Wall DH, Brose U, Decaëns T, Lavelle P, Loreau M, Mathieu J, Mulder C, van der Putten WH, Rillig MC, Thakur MP, de Vries FT, Wardle DA, Ammer C, Ammer S, Arai M, Ayuke FO, Baker GH, Baretta D, Barkusky D, Beauséjour R, Bedano JC, Birkhofer K, Blanchart E, Blossey B, Bolger T, Bradley RL, Brossard M, Burtis JC, Capowiez Y, Cavagnaro TR, Choi A, Clause J, Cluzeau D, Coors A, Crotty FV, Crumsey JM, Dávalos A, Cosín DJD, Dobson AM, Domínguez A, Duhour AE, van Eekeren N, Emmerling C, Falco LB, Fernández R, Fonte SJ, Fragoso C, Franco ALC, Fusilero A, Geraskina AP, Gholami S, González G, Gundale MJ, López MG, Hackenberger BK, Hackenberger DK, Hernández LM, Hirth JR, Hishi T, Holdsworth AR, Holmstrup M, Hopfensperger KN, Lwanga EH, Huhta V, Hurisso TT, Iannone BV 3rd, Iordache M, Irmler U, Ivask M, Jesús JB, Johnson-Maynard JL, Joschko M, Kaneko N, Kanianska R, Keith AM, Kernecker ML, Koné AW, Kooch Y, Kukkonen ST, Lalthanzara H, Lammel DR, Lebedev IM, Le Cadre E, Lincoln NK, López-Hernández D, Loss SR, Marichal R, Matula R, Minamiya Y, Moos JH, Moreno G, Morón-Ríos A, Motohiro H, Muys B, Neirynck J, Norgrove L, Novo M, Nuutinen V, Nuzzo V, Mujeeb Rahman P, Pansu J, Paudel S, Pérès G, Pérez-Camacho L, Ponge JF, Prietzel J, Rapoport IB, Rashid MI, Rebollo S, Rodríguez MÁ, Roth AM, Rousseau GX, Rozen A, Sayad E, van Schaik L, Scharenbroch B, Schirrmann M, Schmidt O, Schröder B, Seeber J, Shashkov MP, Singh J, Smith SM, Steinwandter M, Szlavecz K, Talavera JA, Trigo D, Tsukamoto J, Uribe-López S, de Valença AW, Virto I, Wackett AA, Warren MW, Webster ER, Wehr NH, Whalen JK, Wironen MB, Wolters V, Wu P, Zenkova IV, Zhang W, Cameron EK, Eisenhauer N. 2021. Global data on earthworm abundance, biomass, diversity and corresponding environmental properties. Scientific Data, 8(1):1-12. DOI:10.1038/s41597-021-00912-z
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Balart‐García P, Cieslak A, Escuer P, Rozas J, Ribera I, Fernández R. 2021. Smelling in the dark: Phylogenomic insights into the chemosensory system of a subterranean beetle. Molecular Ecology, 30(11):2573-2590. DOI: 10.1111/mec.15921
Rispe C, Legeai F, Nabity PD, Fernández R, Arora AK, Baa-Puyoulet P, Banfill CR, Bao L, Barberà M, Bouallègue M, Bretaudeau A, Brisson JA, Calevro F, Capy P, Catrice O, Chertemps T, Couture C, Delière L, Douglas AE, Dufault-Thompson K, Escuer P, Feng H, Forneck A, Gabaldón T, Guigó R, Hilliou F, Hinojosa-Alvarez S, Hsiao YM, Hudaverdian S, Jacquin-Joly E, James EB, Johnston S, Joubard B, Le Goff G, Le Trionnaire G, Librado P, Liu S, Lombaert E, Lu HL, Maïbèche M, Makni M, Marcet-Houben M, Martínez-Torres D, Meslin C, Montagné N, Moran NA, Papura D, Parisot N, Rahbé Y, Lopes MR, Ripoll-Cladellas A, Robin S, Roques C, Roux P, Rozas J, Sánchez-Gracia A, Sánchez-Herrero JF, Santesmasses D, Scatoni I, Serre RF, Tang M, Tian W, Umina PA, van Munster M, Vincent-Monégat C, Wemmer J, Wilson ACC, Zhang Y, Zhao C, Zhao J, Zhao S, Zhou X, Delmotte F, Tagu D. 2020. The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest. BMC Biology, 18(1):90. DOI:10.1186/s12915-020-00820-5
Marchán DF, Novo M, Sánchez N, Domínguez J, Díaz Cosín DJ, Fernández R. 2020. Local adaptation fuels cryptic speciation in terrestrial annelids. Molecular Phylogenetics and Evolution, 146:106767. DOI:10.1016/j.ympev.2020.106767
Fernández R, Marcet-Houben M, Legeai F, Richard G, Robin S, Wucher V, Pegueroles C, Gabaldón T, Tagu D. 2020. Selection following Gene Duplication Shapes Recent Genome Evolution in the Pea Aphid Acyrthosiphon pisum. Molecular Biology and Evolution, 37(9):2601–2615. DOI: 10.1093/molbev/msaa110
Fernández R, Gabaldón T. 2020. Gene gain and loss across the metazoan tree of life. Nature Ecology & Evolution, 4(4):524–533. DOI: 10.1038/s41559-019-1069-x
Fernández D, Fernández R, Domínguez J, Díaz Cosín DJ, Novo M. 2020. Genome-informed integrative taxonomic description of three cryptic species in the earthworm genus Carpetania (Oligochaeta, Hormogastridae). Systematics and Biodiversity, 18(3):203–215. DOI: 10.1080/14772000.2020.1730474
Phillips HRP, Guerra CA, Bartz MLC, Briones MJI, Brown G, Crowther TW, Ferlian O, Gongalsky KB, van den Hoogen J, Krebs J, Orgiazzi A, Routh D, Schwarz B, Bach EM, Bennett J, Brose U, Decaëns T, König-Ries B, Loreau M, Mathieu J, Mulder C, van der Putten WH, Ramirez KS, Rillig MC, Russell D, Rutgers M, Thakur MP, de Vries FT, Wall DH, Wardle DA, Arai M, Ayuke FO, Baker GH, Beauséjour R, Bedano JC, Birkhofer K, Blanchart E, Blossey B, Bolger T, Bradley RL, Callaham MA, Capowiez Y, Caulfield ME, Choi A, Crotty FV, Dávalos A, Cosin DJD, Dominguez A, Duhour AE, van Eekeren N, Emmerling C, Falco LB, Fernández R, Fonte SJ, Fragoso C, Franco ALC, Fugère M, Fusilero AT, Gholami S, Gundale MJ, López MG, Hackenberger DK, Hernández LM, Hishi T, Holdsworth AR, Holmstrup M, Hopfensperger KN, Lwanga EH, Huhta V, Hurisso TT, Iannone BV 3rd, Iordache M, Joschko M, Kaneko N, Kanianska R, Keith AM, Kelly CA, Kernecker ML, Klaminder J, Koné AW, Kooch Y, Kukkonen ST, Lalthanzara H, Lammel DR, Lebedev IM, Li Y, Lidon JBJ, Lincoln NK, Loss SR, Marichal R, Matula R, Moos JH, Moreno G, Morón-Ríos A, Muys B, Neirynck J, Norgrove L, Novo M, Nuutinen V, Nuzzo V, Rahman P M, Pansu J, Paudel S, Pérès G, Pérez-Camacho L, Piñeiro R, Ponge JF, Rashid MI, Rebollo S, Rodeiro-Iglesias J, Rodríguez MÁ, Roth AM, Rousseau GX, Rozen A, Sayad E, van Schaik L, Scharenbroch BC, Schirrmann M, Schmidt O, Schröder B, Seeber J, Shashkov MP, Singh J, Smith SM, Steinwandter M, Talavera JA, Trigo D, Tsukamoto J, de Valença AW, Vanek SJ, Virto I, Wackett AA, Warren MW, Wehr NH, Whalen JK, Wironen MB, Wolters V, Zenkova IV, Zhang W, Cameron EK, Eisenhauer N. 2019. Global distribution of earthworm diversity. Science, 366(6464):480-485. DOI:10.1126/science.aax4851