comparative phylogeography; multiple-gene approach; mutualisms; ultra-high-throughput-sequencing technologies; reduction of genomic complexity; restriction-site associated tags genotyping; phylogeography; multi-loci; orthology/paralogy; gene phasing
Gugerli F Alvarez N Tinner W (2013), A deep dig - hindsight on Holocene plant composition from ancient environmental DNA., in Molecular Ecology
, 22, 3433-3436.
Delplancke M* Alvarez N* Benoit L Espíndola A Joly HI Neuenschwander S Arrigo N (2013), Evolutionary history of almond trees domestication in the Mediterranean basin, in Molecular Ecology
, 22, 1092-1104.
. Bothwell H Bisbing S Crawford L Therkildsen NO Alvarez N Holderegger R Manel S (2013), Identifying genetic signatures of selection in a non-model species, alpine gentian (Gentiana nivalis L.), using a landscape genetic approach, in Conservation Genetics
, 14, 467-481.
Pellissier L Litsios G Guisan A Alvarez N (2013), Molecular substitution rate increases in myrmecophilous lycaenid butterflies (Lepidoptera)., in Zoologica Scripta
, 41, 651-658.
Triponez Yann, Triponez Yann, Arrigo Nils, Arrigo Nils, Pellissier Loïc, Schatz Bertrand, Alvarez Nadir (2013), Morphological, ecological and genetic aspects associated with endemism in the Fly Orchid group, in Molecular Ecology
, 22(5), 1431-1446.
Triponez Y Arrigo N Schatz B Pellissier L Alvarez N (2013), Morphological, ecological and genetic aspects associated with endemism in the Fly Orchid group., in Molecular Ecology
, 22, 1431-1446.
Pellissier L Alvarez N Espíndola A Pottier J Dubuis A Pradervand J-N Guisan A (2013), Phylogenetic alpha and beta diversities of butterfly communities correlate with climate in the western Swiss Alps., in Ecography
, 36, 541-550.
Buerki S Forest F Stadler T Alvarez N (2013), The abrupt climate change at the Eocene-Oligocene boundary and the emergence of South-East Asia triggered the spread of sapindaceous lineages., in Annals of Botany
, 112, 151-160.
Alvarez N Manel S Schmitt T IntraBioDiv Consortium (2012), Contrasting diffusion of Quaternary gene pools across Europe: The case of the arctic-alpine Gentiana nivalis L. (Gentianaceae)., in Flora
, 207, 408-413.
Espindola Anahi, Buerki Sven, Alvarez Nadir (2012), Ecological and historical drivers of diversification in the fly genus Chiastocheta Pokorny., in Molecular Phylogenetics and Evolution
, 63(2), 466-474.
Arrigo N Holderegger R Alvarez N (2012), From raw AFLP chromatograms to ready-to-use binary matrices using RawGeno 2.0, an user-friendly interface for automatized and semi-automatized bining and scoring of genotypes in the R environment, in Bonin A & Pompanon F (ed.), Humana Press, New York, 155-175.
Revel N., Alvarez N., Gibernau M., Espíndola A. (2012), Investigating the relationship between pollination strategies and the size-advantage model in zoophilous plants using the reproductive biology of Arum cylindraceum and other European Arum species as case studies, in Arthropod Plant Interactions
, 6, 35-44.
Pellissier L., Alvarez N., Guisan A. (2012), Pollinators as drivers of plant distribution and assemblage into communities, in Patiny S. (ed.), Cambridge University Press, Cambridge, UK, 81, 392-413.
Triponez Y., Buerki S., Borer M., Naisbit R.E., Rahier M., Alvarez N. (2011), Discordances between phylogenetic and morphological patterns in alpine leaf beetles attest to an intricate biogeographic history of lineages in postglacial Europe., in Molecular Ecology
, 20(11), 2442-2463.
Borer M., van Noort T., Arrigo N., Buerki S., Alvarez N. (2011), Does a shift in host plants trigger speciation in the Alpine leaf beetle Oreina speciosissima (Coleoptera, Chrysomelidae)?, in BMC Evolutionary Biology
, 11(310), 1-11.
Manel Stéphanie, Gugerli Felix, Thuiller Wilfried, Alvarez Nadir, Legendre Pierre, Holderegger Rolf, Gielly Ludovic, Taberlet Pierre, IntraBioDiv consortium, Broad-scale adaptive genetic variation in alpine plants is driven by temperature and precipitation, in Molecular Ecology
Borer M., Arrigo N., Buerki S., Naisbit R.E., Alvarez N., Climate oscillations and species interactions: large scale congruence but regional differences in the phylogeographic structures of an alpine plant and its monophagous insect, in Journal of Biogeography
Jay F., Manel S., Alvarez N., Durand E., Thuiller W., Holderegger R., Taberlet P., Francois O., Forecasting changes in population genetic structure of Alpine plants in response to global warming, in Molecular Ecology
Delplancke M., Alvarez N., Espíndola A., Joly H., Benoit L., Brouck E., Arrigo N., Gene flow among wild and domesticated almond species: insights from chloroplast and nuclear markers, in Evolutionary Applications
Espindola Anahi, Pellissier Loïc, Hordijk Wim, Maiorano Luigi, Guisan Antoine, Alvarez Nadir, Predicting present and future intra-specific genetic structure through niche hindcasting across 24 millennia, in Ecology Letters
Boucher F., Thuiller W., Roquet C., Douzet R., Aubert S., Alvarez N., Lavergne S., Reconstructing the origin of high-alpine niches and cushion life form in the genus Androsace s.l. (Primulaceae), in Evolution
Evolutionary processes usually take place in a dynamic geographical context. As a consequence, patterns of genetic variation are typically strongly structured in space and time. Thanks to the recent development of multiple types of molecular markers, genetic information has been analyzed in numerous organisms in order to unravel phylogeographic patterns and to disentangle processes occurring at small evolutionary scales. In the last two decades, the spatial relationships of lineage genealogies have been widely analyzed to deduce the evolutionary history of populations and species. However, the field of phylogeography is now facing another major change with the advent of next-generation sequencing technology, which allows combining the advantages of gene-sequencing and DNA fingerprinting in order to obtain reproducible sequences in thousands of anonymous nuclear markers. In this project, we use this new technology in a phylogeographic framework and build a pipeline to use the millions of output sequences to explore the spatial structuring of the mosaic genome in non-model species. One of the keystones of the current proposal is genome complexity reduction, which allows to obtain an accurate sub-sampling of the genome, proportional to the genome size specific to each species. This reduction serves as a basis for further large-scale sequencing, which requires the development of new bioinformatic tools to facilitate the management of large datasets and to construct a database in which all orthologous fragments are categorized and aligned. Phasing of paternally- and maternally-inherited alleles is performed using a parcimonious approach. Application of the coalescence theory will further permit to accurately determine the processes that mould the genomes of our studied species (in particular, the European globeflower, Trollius europaeus) and more specifically, to distinguish patterns resulting from incomplete lineage sorting of ancestral polymorphisms and patterns resulting from gene flow and further recombination.