Genetic tagging: contemporary molecular ecology

BiologicalJournal ofthe Linnean Sock9 (1999), 68: 3-22. With 4 figures Article ID: bijl. 1999.0327, a~ailableonline at http://w.idealibrary.com. on IDE kL@ h Molecular genetics in animal ecology. Edited by II A. Racy, P 3. Bacon, 3. E: Dallas and S. B. Piertny 0 Genetic tagging: contemporary molecular ecology Unit of Evolutionaly Genetics, Department of Molecular Biology, Free Universip of Brussels, CP 244 Boulevard du Tiomphe, B-1050 Brussels, Belgium; and School of Biologzcal Sciences, Universip of Wales Bangor, Deiniol Road, Bangor, Gwynedd LL57 2UW Population genetic analyses have been highly successful in deciphering inter- and intraspecific evolutionary relationships, levels of gene flow, genetic divergence and effective population sizes. Parameters estimated by traditional population genetic analyses are evolutionary averages and thus not necessarily relevant for contemporary ecological or conservation issues. Molecular data can, however, also provide insight into contemporary patterns of divergence, population size and gene flow when a sufficient number of variable loci are analysed to focus subsequent data analyses on individuals rather than populations. Genetic tagging of individuals is an example of such individual-based approaches and recent studies have shown it to be a viable alternative to traditional tagging methods. Owing to the ubiquitous presence of hyper-variable DNA sequences in eukaryote genomes it is in pl;nc$le possible to tag any eukaryote species and the required DNA can be obtained indirectly from substrates such as faeces, sloughed skin and hair. The purpose of this paper is to present the concept of genetic tagging and to further advocate the extension of individual-based genetic analyses beyond the identification of individuals to other kinds of relationships, such as parent-offspring relations, which more fully exploit the genetic nature of the data. 0 1999 The Linnean Society of London Keywords:-microsatellite genetics - Cetaceae. ~ individual identification - parent-offspring detection population CONTENTS Introduction . . . . . . . . . . . . . . . . . . . . . . Genetic tagging of individuals . . . . . . . . . . . . . . . . Genetic and conventional tagging techniques . . . . . . . . . Different methods for genetic individual identification . . . . . . . Genetic tagging of North Atlantic humpback whales . . . . . . . Indirect sampling of black and brown bears for genetic tagging . . . Identification of parent-offspring relations . . . . . . . . . . . . Obscure gene flow between pilot whale pods . . . . . . . . . Identification of parent-offspring relations . . . . . . . . . . . How many loci are necessary for reliable detection of parent-offspring relations? . . . . . . . . . . . . . . . . . . . . Inferring contemporary population structure from parent-offspring relations Conclusions . . . . . . . . . . . . . . . . . . . . . . Acknowledgements . . . . . . . . . . . . . . . . . . . References . . . . . . . . . . . . . . . . . . . . . . 4 5 5 9 10 11 12 13 13 14 18 18 19 19 * Correspondence to University of Wales Bangor. Email: 0024-4066/99/090003+20 $30.00 3 0 1999 The Linnean Society of London PER J. PALSBBLL* 1’. ,J. I’AI,SBOT,L -1- INTRODUCTION 0.3 I X X -0.3 I 500 X X x I 1000 Generations (in units of me) x X X I 1500 Figure 1. The rate of divergence between two equal size populations expressed as Rs,. Coalescence simulations were carried out under a single-step mutation model as described by Hudson (1990) and employed in Palsball (1999). For each data point 1000 coalescence simulations were conducted with $ample sizes of 50 diploid individuals, 4 4 p = 10 (where 4 is the effective population size and p the number of mutations per generation) and six loci. The degee of divergence was estimated as R,, as definrd by Slatkin (1995). The lower (+) and upper ( X ) 95% confidence limit wrre calculated from thr \ ariance. (0) Mean value of R\T. Estimation of genetic divergence and gene flow among sub-populations and effective population sizes is central to molecular ecology. Such parameters are typically estimated from one or several loci either from haplotype counts only (e.g.Weir & Cockerham, 1984) or from haplotype divergence and haplotype frequencies (e.g. Hudson et al., 1992). Population divergence, gene flow and effective population size estimated in this manner are evolutionary averages, which may not equal the contemporary values of these parameters. The divergence between haplotype sequences and frequencies among populations are generated by mutation and genetic drift, each slow processes from a human perspective, and significant lcvels of genetic divergence among sub-populations are usually only obtained after many generations (Fig. 1) even for rapid evolving loci, such as microsatellites. In contrast, the objectives of ecological and conservation-related research are usually to obtain contemporary estimates; by relying on traditional evolutionary approaches these may fail to detect, for instance, recent population divergence, or recent changes in gene flow and effective population size. Hence, contemporary estimates of migration, abundance and structure have usually been obtained by studying individuals, each identified by some sort of tag (e.g. Seber, 1982). Individual animals can also be identified from genetic data, e.g. by the composite genotype at multiple polymorphic VNTR (variable number of tandem repeats) loci (Jeffreys, 1985). Such a genetic ‘tag’ is in principle similar to conventional tags and enables tracking of individuals in a ‘real-time mode’, i.e. on a temporal and spatial scale relevant to ecological and conservation issues (e.g. Palsball et al., 1997; Taberlet et al., 1997). Genetic tagging based upon the composite genotype at multiple microsatellite loci (VNTR loci with 1-5 nucleotide long repeats) is in principle GENETIC TAGGIKG 7 GENETIC TAGGING OF INDIVIDUALS Genetic and conventional taging techniques A cornerstone in ecological research is the ability to identify and track the movements of individuals (e.g. Hammond et al., 1990). Identification of individual animals in their natural environment relies either on man-made tags (e.g. Kaye, 1960), variations in natural markings (Pennycuick, 1978) or genetic markers (e.g. Palsboll et al., 1997; Taberlet et al., 1997). Ideally, any individual identification technique should possess several basic characteristics, such as: (1) (2) (3) Universal applicability. Tagging conducted remotely and preferably non-invasively. No significant loss of tags over time. applicable to all eukaryotic organisms, as microsatellites appear to be a general feature of the eukaryotic genome (Tautz & Renz, 1984). The critical parameter for the feasibility of genetic tagging is the degree of polymorphism within a population, which in turn is the product of the effective population size and mutation rate. For example, populations with a sm (...truncated)