Conservation Genet Resour DOI 10.1007/s12686-011-9545-x TECHNICAL REVIEW Guidelines for collecting and maintaining archives for genetic monitoring Jennifer A. Jackson • Linda Laikre • C. Scott Baker • Katherine C. Kendall • The Genetic Monitoring Working Group Received: 20 April 2011 / Accepted: 20 September 2011 Ó Springer Science+Business Media B.V. 2011 Abstract Rapid advances in molecular genetic tech- biological diversity and ecological analysis, helping to niques and the statistical analysis of genetic data have illuminate and define cryptic and poorly understood revolutionized the way that populations of animals, plants species and populations. Many of the detected biodiversity and microorganisms can be monitored. Genetic monitoring declines, changes in distribution and hybridization events is the practice of using molecular genetic markers to track have helped to drive changes in policy and management. changes in the abundance, diversity or distribution of Because a time series of samples is necessary to detect populations, species or ecosystems over time, and to follow trends of change in genetic diversity and species compo- adaptive and non-adaptive genetic responses to changing sition, archiving is a critical component of genetic moni- external conditions. In recent years, genetic monitoring has toring. Here we discuss the collection, development, become a valuable tool in conservation management of maintenance, and use of archives for genetic monitoring. This includes an overview of the genetic markers that facilitate effective monitoring, describes how tissue and The NCEAS/NESCent Working Group on Genetic Monitoring (GeM) is chaired by F. W. Allendorf, University of Montana, USA, and DNA can be stored, and provides guidelines for proper M. K. Schwartz, USDA Forest Service, USA. The other members are: practice. C. S. Baker (Oregon State University, USA), D. P. Gregovich (University of Alaska, USA), M. M. Hansen (Aarhus University, Keywords Conservation Á Museum DNA Á Biodiversity Á Denmark), J.A. Jackson (Oregon State University, USA), K. C. Kendall (US Geological Survey, USA), L. Laikre (Stockholm Molecular markers Á Biological collections University, Sweden), K. McKelvey (USDA Forest Service, USA), M. C. Neel (University of Maryland, USA), I. Olivieri (Universite´ de Montpellier II, France), N. Ryman (Stockholm University, Sweden), Since the origins of human societies, marine and terrestrial R. Short Bull (University of Montana, USA), J.B. Stetz (University of Montana, USA), D. A. Tallmon (University of Alaska, USA), plant and animal populations have been subject to a variety C. D. Vojta (US Forest Service, USA), D. M. Waller (University of of anthropogenic environmental impacts including loss of Wisconsin, USA) and R. S. Waples (National Marine Fisheries habitat, direct exploitation and encroachment of introduced Service, USA). C. S. Baker J. A. Jackson Marine Mammal Institute and Department of Fisheries Marine Mammal Institute, Oregon State University, and Wildlife, Oregon State University, 2030 SE Marine Science 2030 SE Marine Science Drive, Newport, OR 97365, USA Drive, Newport, OR 97365, USA e-mail: [email protected] Present Address: J. A. Jackson (&) C. S. Baker British Antarctic Survey, High Cross, Madingley Road, School of Biological Sciences, University of Auckland, Cambridge CB3 0ET, UK Auckland, New Zealand e-mail: [email protected] K. C. Kendall L. Laikre US Geological Survey, Northern Rocky Mountain Science Division of Population Genetics, Department of Zoology, Center, Glacier National Park, West Glacier, MT, USA Stockholm University, 10691 Stockholm, Sweden 123 Conservation Genet Resour species (including pathogens). Impacts on biodiversity individual level, genetic identification can enable estima- include changes in species abundance and distribution and tion of population abundance and vital rates within the loss of genetic diversity (Frankham 2005; Wright et al. framework of mark-recapture models. Genetic species 2008). Methods for assessing and monitoring these types of identification can be used to monitor changes in distribu- changes are necessary to assure conservation and sustain- tion through occupancy modeling that incorporates detec- able use of our remaining biodiversity. Various molecular tion probability (MacKenzie et al. 2006). Category II genetic techniques are now becoming affordable and reli- represents the use of genetic markers to monitor changes in able approaches in this respect (Schwartz et al. 2007). population genetic parameters, e.g., amount of genetic Genetic monitoring has been defined as ‘‘quantifying variation, degree of population divergence, rate of gene temporal changes in population genetic metrics or other flow, and effective population size (Ne). We focus on the population data generated using molecular markers’’ use of both modern and historical DNA archives for (Schwartz et al. 2007). Integral to genetic monitoring is the genetic monitoring but do not discuss the use of ancient interpretation of individual and population genetic data DNA, as this has been covered elsewhere (e.g., Leonard in the context of ecological and evolutionary processes, 2008;Pa¨a¨bo et al. 2004). particularly in human impacted environments. In addition, genetic monitoring can provide valuable baseline infor- mation to evaluate population responses to future global Construction of archives environmental changes, such as global warming. Genetic monitoring can be used to monitor population processes in The ability of archival time series to detect changes elusive and cryptic species that cannot be directly counted, depends on a combination of factors, including the gener- e.g., by using DNA obtained from feces, shed hair, feath- ation time of the species of interest relative to the age of the ers, skin and scales (Proctor et al. 2005; Boulanger et al. archival data, the number and distribution of individuals 2004; Piggott et al. 2006; Prugh et al. 2005), or from hunter sampled at each time point, the preservation of material for kills, market products or incidental mortality (e.g., fisheries DNA analysis, and the genetic marker types employed to by-catch, road-kills) (Pichler and Baker 2000; Bellinger perform the analysis. The success of genetic monitoring 2003; Baker 2008). ‘‘Resurrection’’ analyses of museum- thus crucially hinges on the quality, age, and size of the collected specimens or other artifacts (e.g., Austin and genetic archive available for the species or population of Melville 2006; Kelley Thomas et al. 1990; Groombridge interest. et al. 2000) can also provide an historical baseline for comparison with current estimates of species abundance. Marker types and their utility for genetic monitoring Genetic monitoring projects require a time series of archived genetic data, either in the form of specimen tissue, Genetic monitoring schemes that estimate abundance or extracted DNA, or records of previously obtained genetic monitor population changes require variable genetic markers information (e.g., DNA sequences or genotypic data). For that allow identification of individuals or population level the purposes of genetic monitoring, DNA and tissue diversity, in order to identify changes in the abundance or archives are spatially and temporally explicit, intentional diversity of individuals or populations through time. Com- collections of individuals from the population of interest, monly used genetic marker types include mitochondrial and with multiple samples obtained from each period of col- chloroplast DNA, nuclear introns, microsatellites, single lection. In contrast, the temporal or spatial spread of tra- nucleotide polymorphisms (SNPs) and amplified fragment ditional historical archives is often sporadic or unknown. length polymorphisms. Attributes of these markers and their Although methods of genetic monitoring have received utility in molecular ecology have been discussed elsewhere considerable attention, less attention has been given to the (Sunnucks 2000; Morin et al. 2004; Selkoe and Toonen archiving of samples required to detect trends over time. 2006). Here we review the techniques available for generating and The utility of different types of molecular markers for maintaining tissue and DNA archives for genetic moni- genetic monitoring depends on the quality and quantity of toring, discuss challenges facing archivists, geneticists, and DNA available for analysis. For example, large amounts of managers, and present a series of guidelines for archiving good quality DNA are required to amplify microsatellites material in order to facilitate genetic monitoring of wild and screen for SNPs. These markers can be used to esti- plants and animals. We consider archives that span both mate population size, bottlenecks and kinship and deter- genetic monitoring categories defined by Schwartz et al. mine sex and identity (Selkoe and Toonen 2006). (2007). Category I encompasses the use of genetic markers Microsatellite loci are prone to amplification errors when as identifiers of individuals, populations and species DNA quantity or quality is low, biasing amplification for traditional population monitoring purposes. At the toward shorter fragment lengths (Taberlet et al. 1999)orto 123 Conservation Genet Resour just one allele at a locus (i.e., allelic dropout). Furthermore, genetic analyses to complement traditional taxonomic microsatellite data are often difficult to compare between approaches to species identification. Such archives are laboratories and studies when