Ecological Archives E096-194-A4
A. Coulon, J. Aben, S. C. F. Palmer, V. M. Stevens, T. Callens, D. Strubbe, L. Lens, E. Matthysen, M. Baguette, and J. M. J. Tavis. 2015. A stochastic movement simulator improves estimates of landscape connectivity. Ecology 96:2203–2213. http://dx.doi.org/10.1890/14-1690.1
Appendix D. Genotyping procedure and genotypic data quality assessment for the Cabanis’s greenbul.
DNA was extracted from blood which was collected by trapping greenbul individuals in each of the four focal patches between 1996 and 2010 using standard mist-netting procedures (see Callens et al. 2011) for details on sampling, DNA extraction and polymerase chain reactions). We used MICROCHECKER 2.2.3 (Van Oosterhout et al. 2004) to identify scoring errors. Running 10000 Monte Carlo simulations and calculating 95% confidence provided no evidence for null alleles in any of the loci under study. Deviations from Hardy–Weinberg equilibrium and linkage disequilibrium per locus were tested with GENEPOP 4.0 (Raymond and Rousset 1995, Rousset 2008). All loci were consistent with Hardy-Weinberg equilibrium (all P > 0.05 after Bonferroni correction, Rice 1989) and linkage disequilibrium was only significant between Pca3-WBSW2 (period 1) and Pfi04-Pfl54 (period 2; see below for the definition of the periods) after correction for multiple testing (Rice 1989).
Literature cited
Callens, T., P. Galbusera, E. Matthysen, E. Y. Durand, M. Githiru, J. R. Huyghe, and L. Lens. 2011. Genetic signature of population fragmentation varies with mobility in seven bird species of a fragmented Kenyan cloud forest. Molecular Ecology 20:1829–1844.
Raymond, M., and F. Rousset. 1995. GENEPOP version 1.2: population genetics sofware for exact tests and ecuminicism. Journal of Heredity 86:248–249.
Rice, W. R. 1989. Analyzing tables of statistical tests. Evolution 43:223–225.
Rousset, F. 2008. GENEPOP'007: a complete re-implementation of the GENEPOP software for Windows and Linux. Molecular Ecology Resources 8:103–106.
Van Oosterhout, C., W. F. Hutchinson, D. P. M. Wills, and P. Shipley. 2004. MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Molecular Ecology Notes 4:535–538.