Castresana Lab
Animal Biodiversity and Evolution Program
Institut de Biologia Evolutiva (CSIC-UPF)
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Research
Conservation Genomics
The conservation of endangered species increasingly requires the use of cutting-edge technologies for their effective management. Among them, genomic methodologies can provide highly relevant information on population structure, kinship relationships, connectivity patterns and, in general, the genetic health of individuals and populations. The Pyrenean desman 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 have obtained genomic data of this species by next-generation sequencing techniques such as ddRAD and we have also sequenced its whole genome in order to gain further insights into the genetic health of this unique species. To get samples and carry out this research we are collaborating with scientists, companies and public administrations involved in species conservation. We are also applying these genomic methodologies to other species of birds and mammals of conservation concern.


Population Genomics and Speciation
The reconstruction of species trees of closely related species and populations 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 apply these techniques, we use intronic markers as well as massive genomic information obtained by next-generation sequencing. 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 the common geographical scenario. To obtain material for these studies we are making extensive use of noninvasive samples. The rigorous characterization of speciation in these species complexes is expected to lead to a better understanding of our biological diversity.


Bioinformatics

Software developed:

  • 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



Recent Funded Research Projects

  • Genomics applied to the conservation of species in danger of extinction. Funded by: Plan Nacional I+D+I del Ministerio de Ciencia e Innovación, cofinanced with FEDER funds. Reference: PID2020-113586GB-I00. Duration: September 2021 - August 2024. PI: Jose Castresana.
  • 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
  • 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