COMPUTER PROGRAM ARTICLE FLOCK: a method for quick mapping of admixture without source samples P. DUCHESNE and J. TURGEON De ´partement de Biologie, Universite ´ Laval, Que ´bec, QC, Canada, G1V 0A6 Abstract Identifying and estimating individual and/or population admixture is a very common objective in evolution and conservation biology. There are many situations where samples from one or many of the putatively hybridizing entities are not available or easily identified. Here we describe FLOCK, a new method especially designed to provide spatial and/or temporal admixture maps in the absence of one or several source samples. FLOCK is a non- Bayesian method and therefore differs substantially from previous clustering algorithms. Its working principle is repeated re-allocation of all collected specimens (total sample) to the k subsamples, each re-allocation being more effective than the previous one in attracting genetically similar individuals. This snowball effect, more formally referred to as a positive feedback mechanism, makes FLOCK an efficient and quick sorting process. The usage of FLOCK is illustrated with two empirical situations which have been thoroughly analysed previously with other approaches. A number of simulations were run to better assess the power of the FLOCK algorithm. Performance comparisons were made between the FLOCK and Structure algorithms. When non-negligible numbers of pure genotypes were present, the two performed equally well. However, FLOCK proved significantly more powerful in the absence of pure genotypes. Moreover, FLOCK showed more potential for fast processing. Run times were shown to increase linearly with size of total sample and with size of k, the number of reference samples from which admixture mapping is performed. Keywords: admixture analysis, iterative method, introgression, hybridization, population re-allocation Received 20 August 2008; revision accepted 8 January 2009 Introduction The concept of biological population is as central to biology as it is difficult to define. On the one hand, the multiple facets of the population concept derive from the alternative cohesive mechanism, either demographic or reproductive, that is pertinent to the question one asks and the tools one utilizes (e.g. Waples & Gaggiotti 2006). On the other hand, connectivity among groups of conspecific individuals necessarily blurs the delineation of populations. From an evolutionary standpoint, spatially discrete, demographically stable and isolated populations are relatively easy to identify because they often possess distinct genetic features. However, reproductive connectivity among distinct groups of indi- viduals is common and results in individuals having ancestry in more than one such group. These genetic exchanges may be viewed as gene flow, introgression or hybridization, or more generally, as genetic admixture. Identifying and estimating individual and/or population admixture is a very common objective in evolution and conservation biology. Hybrid zones are often revealed in studies of ancient or contemporary colonization patterns (e.g. Hewitt 2000) and they are widely used to study speciation mechanisms and selection processes (e.g. Barton & Hewitt 1985; Mavarez et al. 2006). Conservation biology also makes wide use of information about genetic admixture, for example, to evaluate the impact of supplementing wild native populations (e.g. Hansen 2002), to estimate genetic restoration potential (e.g. Hansen et al. 2006) or to analyse and monitor the spread of intentionally re-introduced populations or species (e.g. Hedrick & Fredrickson 2008; Jacobsen et al. 2008) as well as hybridizing invasive species (e.g. Boyer et al. 2008). Correspondence: Julie Turgeon, Fax: 418-656-2043, E-mail: julie.turgeon@bio.ulaval.ca Ó 2009 Blackwell Publishing Ltd Molecular Ecology Resources (2009) 9, 1333–1344 doi: 10.1111/j.1755-0998.2009.02571.x