Posted by: salamandercandy | July 27, 2006

How Useful are Neutral Genetic Markers in Conservation?

“Conservation genetics” is a new field that has grown rapidly, and there are now several books and a peer-reviewed journal with that exact title. Conservation geneticists use putatively neutral genetic markers, like microsatellites and mitochondrial DNA, to identify genetically distinct groups of organisms that should be conserved. “Neutral” in this case means that the genetic variation observed is not thought to make a difference to the fitness of the organisms, and therefore it is not affected by natural selection. For example, in a particular species, all of the western populations might have neutral genotypes that are quite similar to each other, but substantially distinct from the neutral genotypes of the eastern populations. Even if this east-west distinction is not apparent by looking at the phenotypes of the organisms, a conservation geneticist might recommend that the two populations be managed as distinct units, since they are different at the DNA level. The idea is that these two groups have been evolving independently of each other for a long time, and therefore they might have unique adaptations worthy of preservation, even if it’s not apparent what these adaptations are.

The problem is, a growing body of evidence suggests that patterns of variation and divergence in adaptive traits are not well reflected by neutral markers (refs 1-8). In the hypothetical species mentioned above, a small amount of gene flow between east and west would be enough to swap small numbers of alleles. This would hardly affect the divergent neutral genotypes at all, but newly introduced advantageous alleles would increase in frequency even if they were originally rare. For example, maybe all the northern ones have adaptations for cold temperatures and the southern ones are adapted to warmth. This pattern would not be reflected in the neutral markers.

Unfortunately, documenting these climate adaptations might take intensive ecological or physiological research. It’s much easier to just take some tissue samples, extract DNA, and look at neutral molecular patterns. This convenience, combined with the “coolness factor” of new technology, and the large amount of information obtainable from molecular analysis, has made neutral markers popular in conservation biology. Remember, though, we’re not really interested in conserving neutral biodiversity per se, so its only useful to the extent that it’s a proxy for adaptive biodiversity.

What, then, to do? Several sensible conservationists are pointing out that neutral markers are indeed useful, but they can’t do the job alone (refs 9-10). Data on fitness-related traits are also needed to accurately group organisms in “evolutionarily significant units.” One way to obtain those data is the old-fashioned way: in-depth research on the whole organism, not just its molecules. Another way is to identify the genetic basis for adaptive variation, and study molecular markers linked to those genes (ref 11). This is still impossible for most species, and extremely difficult in the remaining cases. But progress is being made quickly, and I wouldn’t be surprised if non-neutral markers soon begin to play a significant role in conservation.

Neutral markers have taught us a great deal, and I am certainly not suggesting that we dispense with them. But we have to be careful not to rely on them too much. There’s a lot more going on out there that they don’t tell us.


1. Gomez-Mestre, I., M. Tejedo. 2004. Contrasting patterns of quantitative and neutral genetic variation in locally adapted populations of the natterjack toad, Bufo calamita. Evolution 58:2343-2352.

2. Hedrick, P. W. 2001. Conservation genetics: where are we now? Trends in Ecology and Evolution 16:629-636.

3. Luikart, G., P. R. England, D. Tallmon, S. Jordan, P. Taberlet. 2003. The power and promise of population genomics: from genotyping to genome typing. Nature Reviews Genetics 4:981-994.

4. Lynch, M. 1996. A quantitative genetic perspective on conservation issues. Pp. 471–501 in J. C. Avise and J. L. Hamrick, eds. Conservation Genetics: Case Histories From Nature. Chapman and Hall, New York.

5. McKay, J. K., R. G. Latta. 2002. Adaptive population divergence: markers, QTL, and traits. Trends in Ecology and Evolution 17:285-291.

6. Palo, J. U., R. B. O’Hara, A. T. Laugen, A. Laurila, C. R. Primmers, J. Merilä. 2003. Latitudinal divergence of common frog (Rana temporaria) life history traits by natural selection: evidence from a comparison of molecular and quantitative genetic data. Molecular Ecology 12:1963-1978.

7. Pfrender, M. E., K. Spitze, J. Hicks, K. Morgan, L. Latta, M. Lynch. 2000. Lack of concordance between genetic diversity estimates at the molecular and quantitative-trait levels. Conservation Genetics 1:263-269.

8. Reed, D. H., R. Frankham. 2001. How closely correlated are molecular and quantitative measures of genetic variation? A meta-analysis. Evolution 55:1095-1103.

9. Crandall, K. A., O. R. P. Bininda-Emonds, G. M. Mace, R. K. Wayne. 2000. Considering evolutionary processes in conservation biology. Trends in Ecology and Evolution 15:290-295.

10. Fraser, D. J., L. Bernatchez. 2001. Adaptive evolutionary conservation: towards a unified concept for defining conservation units. Molecular Ecology 10:2741-2752.

11. van Tienderen, P. H., A. A. de Haan, C. G. van der Linden, B. Vosman. 2002. Biodiversity assessment using markers for ecologically important traits. Trends in Ecology and Evolution 17:577-582.



  1. Neutral Markers and Conservation Genetics

    I have mentioned before that at one point in my life I wanted to study conservation genetics. This field can be thought of a subdiscipline of molecular ecology — wherein researchers use molecular markers to test hypotheses regarding demography in…

  2. Intogression-1

    RPM points me to a post at Salamander Candy which discusses the usefulness of neutral markers in conservation genetics. Obviously this complements my recent posts about introgression, and in fact, my last entry was a comment on a conservation genetic…

  3. it is evil to eat salemanders

  4. That is definitely the best comment this site has ever received. As a vegetarian, I can only concur.

  5. As an update on this topic; you can look at this paper “Applications and Implications of Neutral versus Non-neutral Markers in Molecular Ecology” 2011 by H. Kirk and J. Freeland

Leave a Reply

Fill in your details below or click an icon to log in: Logo

You are commenting using your account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s


%d bloggers like this: