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 genomic data obtained by next-generation sequencing techniques, we are studying its population structure, contemporary connectivity, barriers to dispersal, kinship relationships, and inbreeding levels. We are also sequencing its whole genome in order to improve the robustness of these analyses and gain further insights into the genetic health of this unique species. 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, which also allows us to study the diet of this animal. To get samples and carry out this research we are collaborating with scientists, companies and public administrations involved in the conservation of the Pyrenean desman. The results we are obtaining have crucial implications for the conservation and management 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 obtaining 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 Development
  • 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

  • Genome sequencing of the Iberian desman for its application in studies of evolution and conservation. 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. 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. 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. 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. 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. 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
Galemys pyrenaicus: David Perez
Neomys fodiens: Saxifraga - Rudmer Zwerver