Castresana Lab
Animal Biodiversity and Evolution Program
Institut de Biologia Evolutiva (CSIC-UPF)
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Research
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. Using data obtained by next-generation sequencing techniques, we are studying its population structure, contemporary connectivity, barriers to dispersal, kinship relationships, inbreeding and, in short, the genetic health of this unique species. We are also sequencing the genome of the Pyrenean desman in order to obtain more detailed information about many aspects of its biology. Much of the material we use for the detection of new populations and their genetic analysis comes from the small faeces that desmans deposit on emerged rocks in the rivers. To get samples and carry out this research we are collaborating with different scientists and public 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.


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.



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



Funded Research Projects

  • Genome sequencing of the Iberian desman for its application in studies of evolution and conservation (Secuenciación del genoma del desmán ibérico para su aplicación en estudios de evolución poblacional y conservación). Funded by: Plan Nacional I+D+I del Ministerio de Economía, Industria y Competitividad, cofinanced with FEDER funds. Reference: CGL2017-84799-P. Duration: January 2018 - December 2020. PI: Jose Castresana.
  • 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