USFWS
Genetic Monitoring for Managers
Alaska

 

Types of GEM

We separate genetic monitoring into two categories:

Category I includes the use of diagnostic molecular markers for traditional population monitoring, such as abundance or distribution, through the identification of individuals, populations, and species.
Category II includes the use of genetic markers to monitor population genetic parameters, such as genetic variation or effective population size.
Category III addresses questions of evolutionary potential, such as adaptive genes and effects of harvest on population genetics.

Noninvasive genetic studies: The majority of noninvasive genetics studies have used DNA as a diagnostic marker (Category I) to acquire information about difficult-to-study species. For instance, we can determine species identification, sex, and individual identification from a hair sample using diagnostic molecular genetic tools. In this context, noninvasive genetic sampling has been used to address questions of occupancy, abundance, and geographic range, and when these metrics are collected over time, for genetic monitoring purposes (Schwartz et al. 2007). Bellemain et al. (2005), for example, collected brown bear (Ursus arctos) feces throughout south-central Sweden over two consecutive years. Using individual identification information from diagnostic DNA markers, along with four approaches to estimating abundance (two rarefaction indices, a Lincoln-Peterson estimate, and a closed capture model in program MARK), the authors were able to arrive at estimates of abundance for each sex per year.

Noninvasive genetic samples can also be used in a population genetic framework (Category II). Population genetics is the study of the distribution and frequency of genes. In this context, noninvasive genetic sampling has been used to investigate effective population size, gene flow, mating systems, genetic diversity, and relationships between populations of many species (Schwartz et al. 1998; Manel et al. 2003; Miller et al. 2003; Wisely et al. 2004; Schwartz et al. 2004; Leonard et al. 2005). Specifically, noninvasive genetic sampling has provided new means for collecting population genetic samples from species that are otherwise difficult to study. Cushman et al. (2006), for instance, used DNA from noninvasive hair snares, coupled with population and landscape genetic analyses, to determine the effects of roads, forest cover, slope, and elevation on black bear (Ursus americanus) movement.

Category I. Monitoring based on the use of genetic information (molecular tags, diagnostic markers) to identify individuals and sex (1a) and species or other taxonomic groups (2a). Molecular markers can be diagnostic for the taxon of interest, and probabilistic analyses based on gene frequencies are not required. Applications include:

Category Ia. Identifying individuals and sex

• Abundance estimation (population size) or minimum number known alive .......
• Vital rates, such as gender-specific apparent survival .....................................
• Population growth rates (trend, lambda) ........................................................
• Fate of reintroduced animals, reproductive output .........................................

Category Ib. Identifying species and other taxonomic groups

• Hybridization ...............................................................................................
• Geographical range, site occupancy (presence-absence) ...............................
• Presence, prevalence, transmission of pathogens, parasites, and invasive species.. ....................................................................................................... details ; examples
• Trade in wildlife and fisheries products ...................................................... details ; examples

Category II. Monitoring population genetic parameters, including using allele frequencies and assignment methods to assign individuals statistically to populations (including species). Monitoring population genetic metrics can provide insights into demographic and evolutionary processes in natural and captive populations that are difficult or impossible to obtain using traditional methods (e.g. temporal dynamics of a seed bank [Barrett et al. 2005]). In many cases, this type of monitoring can evaluate population characteristics (e.g. effective population size, Ne, or connectivity) from time periods that precede initiation of the monitoring program, as technical advances provide increasingly reliable DNA recovery from archived material (e.g. museum skins, fish scales or trophy collections). This enables 'retrospective monitoring' to assess historical conditions (Pertoldi et al. 2005, Poulsen et al. 2006). Applications include monitoring:

• Genetic variation (heterozygosity, allelic diversity, allele frequency) ...............
• Population mixtures (proportion of individuals originating from genetically
...differentiated breeding groups) ....................................................................
• Effective population size (Ne) ......................................................................
• Population structure and migration (gene flow) .............................................

Category III. Addresses questions of evolutionary potential, such as adaptive genes and effects of harvest on population genetics. (Allendorf et al. 2008)


The diagram below shows a framework for categorizing genetic monitoring efforts (click on diagram to view full size). The categories are guidelines to help direct discussions and spur research on genetic monitoring, rather than being necessarily mutually exclusive. (From Schwartz et al 2007)