Research lines

Evolution of lineage-specific genes

Lineage-specific genes are those exclusively found in one species or group of related species. Their study can shed light into the mechanisms of formation of new genes. Recent research in the group has shown that many lineage-specific genes are likely to have originated de novo from genomic non-coding regions. We are currently using RNA-Seq and Ribo-Seq data to further understand the mechanisms of formation of new genes.

Blevins, W.R., Ruiz-Orera, J., Messeguer, X., Blasco-Moreno, B., Villanueva-Cañas, J-L., Espinar, L., Díez, J., Carey, L.B., Albà, M.M. (2021). Uncovering de novo gene birth in yeast using deep transcriptomics. Nature Communications 12:604.

Ruiz-Orera, J., Albà, M.M. (2019). Translation of small open reading frames: roles in regulation and evolutionary innovation. Trends in Genetics 35: 186-198.

Ruiz-Orera, J., Verdaguer-Grau, P., Villanueva-Cañas, J-l., Messeguer, X., Albà, M.M. (2018). Translation of neutrally evolving peptides provides a basis for de novo gene evolution. Nature Ecology and Evolution 2:890-896.

Villanueva-Cañas, J-L. Ruiz-Orera, J., M.I., Gallo, M., Andreu, D., Albà, M.M. (2017) New genes and functional innovation in mammals. Genome Biology and Evolution 9: 1886–1900.

Ruiz-Orera, J., Hernandez-Rodriguez, J., Chiva, C., Sabidó, E., Kondova, I., Bontrop, R., Marqués-Bonet, T., Albà, M.M (2015) Origins of de novo genes in human and chimpanzee. Plos Genetics, 11 (12), pp. e1005721.

Ruiz-Orera, J., Messeguer, X., Subirana J.A., Albà M.M. (2014) Long non-coding RNAs as a source of new peptides. eLife, 3:e03523.

Toll-Riera, M., Bosch, N., Bellora, N., Castelo, R., Armengol,Ll., Estivill, X., Albà, M.M. (2009) Origin of primate orphan genes: a comparative genomics approach. Molecular Biology and Evolution, 26:603-612.

Consequences of gene duplication in protein evolution

Gene duplication is an important motor of protein functional diversification. We have investigated the changes in expression patterns of recent duplicated mammalian genes and observed that loss of expression domains is more common than gain of novel expression patterns. We have also used large gene duplicate sets to investigate how the sequences of initially redundant gene copies progressively diverge and which are the implications for protein function.

Radó-Trilla, N., Arató, K., Pegueroles, C., Raya, A., de la Luna, S.*, Albà, M.M.* (2015) Key role of amino acid repeat expansions in the functional diversification of duplicated transcription factors. Molecular Biology and Evolution, 32(9):2263-72.

Pegueroles, C., Laurie, S., Albà, M.M. (2013) Accelerated evolution after gene duplication: a time-dependent process affecting just one copy.Molecular Biology and Evolution, 30:1830-1842.

Farré, D., Albà, M.M. (2010) Heterogeneous patterns of gene expression diversification in mammalian gene duplicates. Molecular Biology and Evolution, 27:325-335.

Adaptive molecular evolution in mammals

We have developed methods to identify shifts in the evolutionary rate of genes and to measure adaptive evolution in individual genes or clusters of functionally-related genes. We have shown that selecting isoforms of similar length with our software PALO reduces the fraction of misaligned positions and false positives in tests of selection.

Abascal, F. et al. (including Villanueva-Cañas, J-L., Ruiz-Orera, J., Albà, M.M.) (2016). Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx. Genome Biology, 17: 251.

Gayà-Vidal, M., Albà, M.M. (2014) Uncovering adaptive evolution in the human lineage. BMC Genomics, 15:599.

Villanueva-Cañas, J.L., Laurie, S., Albà, M.M. (2013) Improving genome-wide scans of positive selection by using protein isoforms of similar length. Genome Biology and Evolution, 5: 457-67.

Toll-Riera, M., Laurie, S., Albà, M.M. (2011) Lineage-specific Variation in Intensity of Natural Selection in Mammals. Molecular Biology and Evolution, 28: 383-398.


During hibernation, animals lower their metabolism to survive harsh environmental periods. In collaboration with Anne Yoder’s group at Duke we have used RNA sequencing data to assemble the transcriptome of fat-tailed dwarf lemurs and subsequently performed differential gene expression analysis to identify major metabolic switches when entering or exiting from hibernation.

Faherty, S.L.*#, Villanueva-Cañas, J-L.#, Blanco, M.B., Albà, M.M.*, Yoder, A.D. (2018) Transcriptomics in the wild: hibernation physiology in free-ranging dwarf lemurs. Molecular Ecology , 273:709-722.

Faherty, S.L.#, Villanueva-Cañas, J-L.#,Klopfer, P.H., Albà, M.M., Yoder, A.D. (2016): Gene expression profiling in the hibernating primate, Cheirogaleus medius. Genome Biology and Evolution 8: 2413–2426.

Villanueva-Cañas, J-L., Faherty, S.L., Yoder, A.D., Albà, M.M. (2014). Comparative Genomics of Mammalian Hibernators Using Gene Networks. Integrative and comparative biology 54:452-462.