With the increasing availability of both molecular and topo-climatic data, the main challenges facing landscape genomics – that is the combination of landscape ecology with population genomics – include processing large numbers of models and distinguishing between selection and demographic processes (e.g. population structure). Several methods address the latter, either by estimating a null model of population history or by simultaneously inferring environmental and demographic effects. Here we present samβada, an approach designed to study signatures of local adaptation, with special emphasis on high performance computing of large-scale genetic and environmental data sets. samβada identifies candidate loci using genotype–environment associations while also incorporating multivariate analyses to assess the effect of many environmental predictor variables. This enables the inclusion of explanatory variables representing population structure into the models to lower the occurrences of spurious genotype–environment associations. In addition, samβada calculates local indicators of spatial association for candidate loci to provide information on whether similar genotypes tend to cluster in space, which constitutes a useful indication of the possible kinship between individuals. To test the usefulness of this approach, we carried out a simulation study and analysed a data set from Ugandan cattle to detect signatures of local adaptation with samβada, bayenv, lfmm and an FSToutlier method (FDIST approach in arlequin) and compare their results. samβada – an open source software for Windows, Linux and Mac OS X available at http://lasig.epfl.ch/sambada – outperforms other approaches and better suits whole-genome sequence data processing.

Stucki, S., Orozco-Terwengel, P., Forester, B. R., Duruz, S., Colli, L., Masembe, C., Negrini, R., Landguth, E., Jones, M. R., Bruford, M. W., Taberlet, P., Joost, S., High performance computation of landscape genomic models including local indicators of spatial association, <<MOLECULAR ECOLOGY RESOURCES>>, 2017; 17 (5): 1072-1089. [doi:10.1111/1755-0998.12629] [http://hdl.handle.net/10807/124473]

High performance computation of landscape genomic models including local indicators of spatial association

Colli, L.;Negrini, R.;
2017

Abstract

With the increasing availability of both molecular and topo-climatic data, the main challenges facing landscape genomics – that is the combination of landscape ecology with population genomics – include processing large numbers of models and distinguishing between selection and demographic processes (e.g. population structure). Several methods address the latter, either by estimating a null model of population history or by simultaneously inferring environmental and demographic effects. Here we present samβada, an approach designed to study signatures of local adaptation, with special emphasis on high performance computing of large-scale genetic and environmental data sets. samβada identifies candidate loci using genotype–environment associations while also incorporating multivariate analyses to assess the effect of many environmental predictor variables. This enables the inclusion of explanatory variables representing population structure into the models to lower the occurrences of spurious genotype–environment associations. In addition, samβada calculates local indicators of spatial association for candidate loci to provide information on whether similar genotypes tend to cluster in space, which constitutes a useful indication of the possible kinship between individuals. To test the usefulness of this approach, we carried out a simulation study and analysed a data set from Ugandan cattle to detect signatures of local adaptation with samβada, bayenv, lfmm and an FSToutlier method (FDIST approach in arlequin) and compare their results. samβada – an open source software for Windows, Linux and Mac OS X available at http://lasig.epfl.ch/sambada – outperforms other approaches and better suits whole-genome sequence data processing.
Inglese
Stucki, S., Orozco-Terwengel, P., Forester, B. R., Duruz, S., Colli, L., Masembe, C., Negrini, R., Landguth, E., Jones, M. R., Bruford, M. W., Taberlet, P., Joost, S., High performance computation of landscape genomic models including local indicators of spatial association, <<MOLECULAR ECOLOGY RESOURCES>>, 2017; 17 (5): 1072-1089. [doi:10.1111/1755-0998.12629] [http://hdl.handle.net/10807/124473]
File in questo prodotto:
File Dimensione Formato  
Stucki et al (2017) - High performance computation of landscape genomic models including local indicators of spatial association.pdf

accesso aperto

Tipologia file ?: Versione Editoriale (PDF)
Licenza: Creative commons
Dimensione 831.05 kB
Formato Adobe PDF
831.05 kB Adobe PDF Visualizza/Apri

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/10807/124473
Citazioni
  • ???jsp.display-item.citation.pmc??? 42
  • Scopus 76
  • ???jsp.display-item.citation.isi??? 77
social impact