USFWS
Genetic Monitoring for Managers
Alaska

 

Considerations, Cautions, and Caveats

There are many cautions that need to be heeded before conducting a molecular genetic study. A frequent mistake made by many researchers is to assume that simply sending noninvasive samples to a laboratory will yield answers to all questions of interest. It is not unusual for someone to send samples to a laboratory and to expect a report without ever having posed a question or explicitly described the desired data. It is even more common for wildlife researchers to underestimate the effort required to conduct an analysis for a given project; after all, on television, human forensic samples are analyzed between commercials. For instance, most biologists are aware that molecular markers can determine parentage (to estimate the relative abundance of offspring in a sample), yet it is frequently assumed that this is a trivial exercise. Often, numerous molecular markers are required to provide adequate power for assigning paternity and maternity simultaneously-sometimes more than are readily available or affordable. By comparison, determining paternity given known maternity (or other information acquired in the field) is far less intensive. Thus, combining field data with genetic data can save analysis time and money. Similar caveats hold true for a suite of other questions, including those related to estimating absolute abundance and distribution.

Here we review some practical issues associated with genetic monitoring and offer some guidance on how to be successful despite the many logistical and analytical challenges. Some of this material is covered in ohter sections of this website (e.g., sample preservation, data management); however, this section provides a directional overview of potential problems beginning with sample collection and working through various analyses.

I. Defining your objective:

* Do you have a clear idea of exactly what you want to achieve? Properly defining your objective is the single most important step in successfully designing and executing any research or monitoring project.

II. Project design:

* Will the proposed sampling methodology provide appropriate data for the study's objectives? Don't assume that published methods will meet your objectives. more information

* Have you determined the appropriate marker type? Different markers answer different questions. more information

* Have I taken advantage of all available information and expertise? Go beyond the literature! Directly contact experts for added insight and to avoid pitfalls. more information

* Will the sampling design adequately represent the full population of interest? Inadequate sampling can bias results, reduce precision, and limit inferences.

III. In the field:

* Will the data you collect support your objectives? Don't waste time collecting data you will not use. Be sure to collect everything you need; you may not get another chance.

* Are you confident that your data will be accurate? Missing, incorrect, or illegible data cannot be used.

* Is training adequate? The quality of your data will be only as good as the skill level of those collecting it.

* Have you ensured the quality and security of your data and samples? Lost samples or corrupted data can undermine your hard work.

IV. Preservation and archiving:

* Are samples properly stored to minimize DNA degradation? Degraded samples result in low genotyping success rates and increased error rates.

* Are you maximizing the information that can be derived from your samples? Your choice of preservation method can facilitate or impede future analyses.

* Have you made plans for long-term storage? Think beyond the life of your project.

V. In the laboratory:

* Which loci and how many loci do you need? A pilot study might be needed to optimize your marker selection. more information

* Have you minimized genotyping error? Modern methods can reduce error rates to levels that do not bias results.

* How do you identify a reliable lab? Not all labs are created equal. Do your homework.

VI. Results:

* Are your analytical methods appropriate given your sampling methods and objectives? It's never too early to consult with experts in genetics and statistics. Seek recommendations from colleagues for geneticists and statisticians that deal with the type of genetic data you have. Experts may be identified in journal publications related to your study or in unpublished reports.

VII. Interpretation?

* Results often require interpretation to be useful to managers. For example, are differences between Fst values significant, either statistically or, more importantly, biologically? Don't hesitate to seek help in understanding the significance of your results.