Castresana Lab
Animal Biodiversity and Evolution Program
Institut de Biologia Evolutiva (CSIC-UPF)
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Population Genomics and Speciation
The reconstruction of species trees of closely related species based on multiple genomic markers and coalescent theory can help to estimate speciation times, study gene flow, delimit species and, in general, better understand the speciation process. To be able to effectively use these techniques in mammals, we have developed a large set of intronic markers. In addition, we are generating massive genomic information using next-generation sequencing techniques. We are sequencing these markers in several groups of small mammals such as Neomys, Sorex and Arvicola, which we use as models to understand population divergence and speciation in a comparative perspective, with the Iberian Peninsula as common geographical scenario. To obtain material for these studies we are making extensive use of noninvasive samples such as skulls obtained from owl pellets. The rigorous characterization of speciation in these species complexes is expected to lead to a better understanding of our biological diversity.

Conservation Genomics
The Pyrenean desman (Galemys pyrenaicus) is a small semi-aquatic mammal endemic to the northern half of the Iberian Peninsula and is endangered in a large part of its distribution range. We are currently studying several aspects of the evolutionary history of this unique species using large amounts of sequence data and SNPs obtained by next-generation sequencing techniques. We are also analyzing postglacial and contemporary dispersal patterns, as well as connectivity problems between populations, using highly innovative approaches. Much of the material we use for genetic analysis comes from the small faeces that desmans deposit on emerged rocks in the rivers, whose use for genetic studies was pioneered by our group. To get additional samples and carry out this research we are collaborating with different scientists and administrations involved in the conservation of the Pyrenean desman. The results we are obtaining are of high scientific relevance at the same time that have crucial implications for the conservation of this species.

  • GetCrosses: Simulation of offspring genotypes from a SNPs file for their use in relatedness analysis
  • Ktreedist: Calculation of the minimum branch length distance (K tree score) between phylogenetic trees
  • Gblocks: Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis

Funded Research Projects

  • Studies of genomic divergence and contact zones of populations of small mammals in the Iberian Peninsula using next-generation sequencing techniques (Estudios de divergencia genómica y zonas de contacto de poblaciones de micromamíferos de la Península Ibérica mediante técnicas de secuenciación de alto rendimiento). Funded by: Plan Nacional I+D+I del Ministerio de Economía y Competitividad, cofinanced with FEDER funds. Reference: CGL2014-53968-P. Duration: January 2015 - December 2017. PI: Jose Castresana.
  • Reconstruction of species trees with genomic markers and its application to the study of mammalian speciation (Reconstrucción de árboles de especies mediante marcadores genómicos y su aplicación al estudio de la especiación de mamíferos). Funded by: Plan Nacional I+D+I del Ministerio de Ciencia e Innovación, cofinanced with FEDER funds. Reference: CGL2011-22640. Duration: January 2012 - June 2015. PI: Jose Castresana.
  • Phylogeny and speciation of mammals studied with multiple nuclear markers (Filogenia y especiación de mamíferos estudiadas con múltiples marcadores nucleares). Funded by: Plan Nacional I+D+I del Ministerio de Ciencia e Innovación, cofinanced with FEDER funds. Reference: CGL2008-00434. Duration: January 2009 - December 2011. PI: Jose Castresana.
  • Large-scale phylogenetic analysis of mammals and birds to study their patterns and rates of diversification (Análisis filogenéticos a gran escala de mamíferos y aves para estudiar sus patrones y tasas de diversificación). Funded by: Plan Nacional I+D+I del Ministerio de Educación y Ciencia, cofinanced with FEDER funds. Reference: CGL2005-01341. Duration: January 2006 - December 2008. PI: Jose Castresana
  • Phylogenomics: the quality of sequence alignments. Funded by: Fundación BBVA. Duration: February 2004 - February 2006. PI: Jose Castresana
  • Variability of the mutation rate in the mammalian genome (Variabilidad de la velocidad de mutación en el genoma de mamíferos). Funded by: Plan Nacional I+D+I del Ministerio de Ciencia y Tecnología, cofinanced with FEDER funds. Reference: BIO2002-04426-C02-02. Duration: January 2003 - December 2005. PI: Jose Castresana
Picture credits
Neomys fodiens: Rudmer Zwerver
Galemys pyrenaicus: David Perez