Publications de Sylvie Stucki | EPFL Graph Search

Multiple genomic solutions for local adaptation in two closely related species (sheep and goats) facing the same climatic constraints

Stéphane Joost, Sylvie Stucki, Kevin Leempoel

The question of how local adaptation takes place remains a fundamental question in evolutionary biology. The variation of allele frequencies in genes under selection over environmental gradients remains mainly theoretical and its empirical assessment would ...

2023

Rapid identification and interpretation of gene‐environment associations using the new R.SamBada landscape genomics pipeline

Stéphane Joost, Oliver Michele Selmoni, Estelle Rochat, Sylvie Stucki, Kevin Leempoel, Elia Vajana, Solange Catherine Gaillard

Samβada is a genome‐environment association (GEA) software, designed to search for signatures of local adaptation. However, pre‐ and post‐processing of data can be labour‐intensive, preventing wider uptake of the method. We have now developed R.SamBada, an ...

2019

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

Stéphane Joost, Sylvie Stucki, Pierre Taberlet, Solange Catherine Gaillard

With the increasing availability of both molecular and topo-climatic data, the main challenges facing landscape genomics — i.e. the combination of landscape ecology with population genomics — include processing large numbers of models and distinguishing be ...

Wiley-Blackwell2017

High performance computation of landscape genomic models integrating local indices of spatial association

Stéphane Joost, Sylvie Stucki, Pierre Taberlet

Motivation: The increasing availability of high-throughput datasets requires powerful methods to support the detection of signatures of selection in landscape genomics. Results: We present an integrated approach to study signatures of local adaptation, pro ...

2014

Adaptations to Climate-Mediated Selective Pressures in Sheep

Stéphane Joost, Sylvie Stucki

Following domestication, sheep (Ovis aries) have become essential farmed animals across the world through adaptation to a diverse range of environments and varied production systems. Climate-mediated selective pressure has shaped phenotypic variation and h ...

Oxford Univ Press2014

Développement d'outils de géo-calcul haute performance pour l'identification de régions du génome potentiellement soumises à la sélection naturelle : analyse spatiale de la diversité de panels de polymorphismes nucléotidiques à haute densité (800k) chez Bos taurus et B. indicus en Ouganda

Sylvie Stucki

EPFL2014

SamBada in Uganda: landscape genomics study of traditional cattle breeds with a large SNP dataset

Stéphane Joost, Sylvie Stucki

Since its introduction, landscape genomics has developed quickly with the increasing availability of both molecular and topo-climatic data. Current challenges involve processing large numbers of models and disentangling selection from demography. Several m ...

2013

Uncovering the genetic basis of adaptive change: on the intersection of landscape genomics and theoretical population genetics

Stéphane Joost, Jeffrey David Jensen, Séverine Vuilleumier Varisco, Sylvie Stucki, Kevin Leempoel, Ivo Widmer

A workshop recently held at the École Polytechnique Fédérale de Lausanne (EPFL, Switzerland) was dedicated to understanding the genetic basis of adaptive change, taking stock of the different approaches developed in theoretical population genetics and land ...

Wiley-Blackwell2013

Geocomputational approaches for the analysis of Next-Generation Sequencing (NGS) and multi-scale data in landscape genomics

Stéphane Joost, Sylvie Stucki, Kevin Leempoel

The application of geocomputation to the field of landscape genomics (Manel et al. 2010) permits to carry out demanding computational tasks that recently emerged because of the advent of large Next-Generation Sequencing data. When investigating the genetic ...

Swiss Academy of Sciences2013

Utilization of the Scythe C++ open source library for statistical geocomputation in livestock landscape genomics

Stéphane Joost, Sylvie Stucki

Understanding genetic basis of adaptation is of key importance, especially to insure food supply for present and future populations. Cultivated plants and livestock animals are subjected to high selection pressure due to climate change, increasing food nee ...

Lulu.com2012