Overview

    The program is released as an add-on to the free statistical program R and is currently available for Linux, Mac-OS and Windows. It includes a fully clickable user interface requiring no particular knowledge of R.

Installation

    As of version 4.0.9, Geneland is distributed on github. Instructions for installation can be found on the Geneland repository. on github See manual (below) for details.

Manual


Reference papers

    G. Guillot, S. Renaud, R. Ledevin, J. Michaux, J. Claude A Unifying Model for the Analysis of Phenotypic, Genetic and Geographic Data. Systematic Biology, 61(5) 897-911, 2012.
    B. Guedj and G. Guillot Estimating the location and shape of hybrid zones Molecular Ecology Resources 11(6), 1119-1123, 2011.
    G. Guillot and F. Santos Using AFLP markers and the Geneland program for the inference of population genetic structure. Molecular Ecology Resources, 10(6), 1082-1084, 2010.
    G. Guillot and F. Santos A computer program to simulate multilocus genotype data with spatially auto-correlated allele frequencies. Molecular Ecology Resources, 9(4), 1112-1120, 2009.
    G. Guillot. Inference of structure in subdivided populations at low levels of genetic differentiation. The correlated allele frequencies model revisited. Bioinformatics, 24:2222-2228, 2008.
    G. Guillot, F. Santos and A. Estoup. Analysing georeferenced population genetics data with Geneland:  a new algorithm to deal with null alleles and a friendly graphical user interface. Bioinformatics, 24(11):1406-1407, 2008.
    G. Guillot, Mortier, F., Estoup, A. Geneland: A program for landscape genetics. Molecular Ecology Notes, 5, 712-715, 2005.
    G. Guillot, Estoup, A., Mortier, F. Cosson, J.F. A spatial statistical model for landscape genetics. Genetics, 170, 1261-1280, 2005.

Related method papers

    Violle, C., Reich, P. B., Pacala, S. W., Enquist, B. J., & Kattge, J. (2014). The emergence and promise of functional biogeography. Proceedings of the National Academy of Sciences, 201415442.
    Guillot G. and F. Rousset Dismantling the Mantel tests. To appear in Methods in Ecology and Evolution.
    Blair C, Weigel DE, Balazik M, Keeley AT, Walker FM, Landguth E, Cushman S, Murphy M, Waits L, Balkenhol N.. A simulation-based evaluation of methods for inferring linear barriers to gene flow, Mol. Ecol. Resour. 2012
    Remais J.V., Xiao N., Akullian A., Qiu D., Blair D. Genetic Assignment Methods for Gaining Insight into the Management of Infectious Disease by Understanding Pathogen, Vector, and Host Movement. PLoS Pathogens 7(4): e1002013.
    G. Guillot, R. Leblois, A. Coulon, A. Frantz Statistical methods in spatial genetics. Molecular Ecology, to appear.
    G. Guillot On the inference of spatial structure from population genetics data using the Tess program. Bioinformatics 2009.
    M. Hansen and J. Hemmer-Hansen Landscape genetics goes to sea. Journal of Biology 6:6 2007.
    L. Excoffier and G. Heckel Computer programs for population genetics data analysis: a survival guide. Nature Reviews Genetics 7, 745-758, October 2006.

Selected applications

    Westengen O.T., et al. Ethnolinguistic structuring of sorghum genetic diversity in Africa and the role of local seed systems. Proceedings of the National Academy of Sciences. (2014)
    Rieux A., T. Lenormand, J. Carlier, L. de Lapeyre de Bellair, V. Ravign? Using neutral cline decay to estimate contemporary dispersal: a generic tool and its application to a major crop pathogen 2013
    M. Del?tre, McKey D.B., Hodkinson T.R. Marriage exchanges, seed exchanges, and the dynamics of manioc diversity. PNAS 2011 108 (45) 18249-18254;
    Machol?n M, Baird SJ, Dufkov? P, Munclinger P, B?mov? BV, Pi?lek J. Assessing multilocus introgression patterns: a case study on the mouse X chromosome in central Europe. Evolution, 65(5), 1428-1446, 2011.
    Beadell, JS; Hyseni, C; Abila, PP; Azabo, R; Enyaru, JCK; Ouma, JO; Mohammed, YO; Okedi, LM; Aksoy, S; Caccone, A. Phylogeography and Population Structure of Glossina fuscipes fuscipes in Uganda: Implications for Control of Tsetse, PLoS Neglected Tropical Diseases web site, 2010
    J. A. Galarza,  J. Carreras-Carbonell,  E.Macpherson,  M.Pascual,  S. Roques,  G.F. Turner and C. Ricod . The influence of oceanographic fronts and early-life-history traits on connectivity among littoral fish species. PNAS, 106(5), 1473-1478, 2009.
    L. Joseph, G. Dolman, S. donnellan, K. M. Saint, M. L. Berg, A.T. Bennet. Where and when does a ring start and end? Testing the ring-species hypothesis in a species complex of Australian parrots. Proc. Roy. Soc. B, 275: 2431-2440, 2008.
    Coulon A., Fitzpatrick J.W., Bowman R., Stith B.M., Makarewich C.A., Stenzler L.M. and Lovette I.J. Congruent population structure inferred from dispersal behaviour and intensive genetic surveys of the threatened Florida Scrub-Jay (Aphelocoma coerulescens). Molecular Ecology, 17 1685-1701, 2008.
    U. Hannelius, E. Salmela, T. Lappalainen, G. Guillot, C.M.  Lindgren,  U. von D?beln, P. Lahermo, P. and J. Kere . Population substructure in Finland and Sweden revealed by a small number of unlinked autosomal SNPs. BMC Genetics, 9:54, 2008.
    B.N.Sacks, D.L. Bannasch, B.B. Chomel and H.B. Ernest Coyotes Demonstrate How Habitat Specialization by Individuals of a Generalist Generalist Species Can Diversify Populations in a Heterogeneous Ecoregion. Molecular Biology and Evolution 25(7):1384-1394, 2008.
    M. Fontaine, S. Baird, et al. Rise of oceanographic barriers in continuous populations of a cetacean: the genetic structure of harbour porpoises in Old World waters. BMC Biology, 2007.doi:10.1186/1741-7007-5-30
    A. Coulon, G. Guillot G., Cosson J.-F., Angibault J.M.A. Aulagnier S., Cargnelutti B., Galan M., Hewison A.J.M. Genetic structure is influenced by lansdcape features. Empirical evidence from a roe deer population. Molecular Ecology, 15 1669-1679, 2006.

Contact:

    b i o s t a t i s t i c s @ i-pri.org