Molecular markers

humpback whale

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Background

DNA

Molecular genetic analyses are commonly used to study dispersal and population connectivity in animals. Innovative use of genetic data, particularly in combination with other approaches, has provided new insights on movement from local to global scales. Topics of interest include sex-biased dispersal patterns, natal site fidelity and dispersal trends, long-distance dispersal, movement or gene flow between populations, and identification of migration pathways.

In the past, investigations have not always yielded the most definitive results because it was difficult to identify enough markers capable of differentiating populations. However, recent development of fast-throughput sequencing has revolutionized our ability to identify hundreds of thousands of variable microsatellites and other types of genetic markers (see Lerner and Fleischer 2010). Thus, the sky is the limit with this technology.

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Tracking populations throughout the annual cycle

Birds and other flying animals that readily disperse hundreds or thousands of miles to new breeding areas often have panmictic populations that do not show any evidence of genetic differences. This can make it difficult to use molecular markers to track populations throughout the annual cycle. There are three potential solutions to this problem:

  • Instead of randomly selecting variable low-quality markers from a small resource group to screen populations, we can selectively choose markers from a large pool to better optimize our resolution and ability to differentiate populations (as in Haig et al. 1997). This approach can provide genetic markers capable of high resolution at the population level, which can be used to monitor movements of different populations throughout the year.
  • Combine molecular genetic analyses with results from stable isotopes. Molecular markers tend to be better at differentiating east-west patterns while isotopes are better at discerning north-south patterns. Together they can be a powerful tool in tracking animal movements and understanding migratory connectivity. See Clegg et al. (2003) and Kelly et al. (2005) for more details.
  • Use a surrogate for the species of interest. Population-specific markers for a parasite or other organism that accompanies an animal in its movements can be molecularly sampled. Bensch and Akesson (2003) demonstrated this approach by sampling parasites found on Willow Warblers from various populations. They illustrated that the parasite’s DNA yielded a more refined understanding of the host species movement patterns than the host’s DNA itself.

Although analyses of high-dispersal species may have a number of challenges, it is important to recognize that many widely dispersing species have populations that are readily identifiable with molecular markers. Most noteworthy are those where geneticists have used this attribute to track illegal possession of marine mammal meat (see Baker et al. 2008, 2010).

The strongest connectivity studies are carried out using a variety of approaches. Often a molecular component would be useful but a scientist is not set up to carry out the analyses in their own lab. Fortunately, many labs routinely carry out molecular analyses of population connectivity and are happy to discuss partnerships. Working with service labs requires forming a scientific partnership.

Edited by Susan Haig, USGS Forest and Rangeland Ecosystem Science Center, susan_haig@usgs.gov.

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References

  1. Baker, C.S., D.J. Steel, Y. Choi, H. Lee, K.S. Kim, S.K. Choi, Y. Ma, C. Hambleton, L. Psihoyos, R.L. Brownell et al. 2010. Genetic evidence of illegal trade in protected whales links Japan with the US and South Korea. Biology letters.
  2. Baker, C.S. 2008. A truer measure of the market: the molecular ecology of fisheries and wildlife trade. Molecular Ecology 17:3985-3998.
  3. Beadell, J, Y. Chan and R. Fleischer. 2009. The role of ancient DNA in conservation biology. Pages 202-224 in: Population Genetics for Animal Conservation. (eds G. Bertorelle, M. W. Bruford, H. C. Hauffe, A. Rizzoli and C. Vernesi), Cambridge University Press.
  4. Bensch, S., and S. Akesson. 2003. Temporal and spatial variation in Hematozoans in Scandinavian Willow Warblers. Journal of Parasitology 88: 388-391.
  5. Braunisch, V., G. Segelbacher, and A. H. Hirzel. 2010. Modeling functional landscape connectivity from genetic population structure: a new spatially explicit approach. Molecular Ecology 19:3664-3678.
  6. Broquet, T., and E. J. Petit. 2009. Molecular estimation of dispersal for ecology and population genetics. Annual Review of Ecology Evolution and Systematics 40:193-216.
  7. Broquet, T., J. Yearsley, A.H. Hirzel, J. Goudet, and N. Perrin. 2009. Inferring recent migration rates from individual genotypes. Molecular Ecology 18:1048-1060.
  8. Clegg, S. M., J. F. Kelly, M. Kimura, and T. B. Smith. 2003. Combining genetic markers and stable isotopes to reveal population connectivity and migration patterns in a Neotropical migrant, Wilson’s Warbler (Wilsonia pusilla). Molecular Ecology 12:819-830.
  9. Excoffier, L. and G. Heckel. 2006. Computer programs for population genetics data analysis: a survival guide. Nature Genetics 7: 745-758.
  10. Fallon, S. M., R. C. Fleischer, and G. R. Graves. 2006. Malarial parasites as geographical markers in migratory birds? Biology Letters 2:213-216.
  11. Haig, S.M., W. Bronaugh, R. Crowhurst, J. D’Elia, C. Eagles-Smith, C. Epps, B. Knaus, M.P. Miller, M. Moses, S. Oyler-McCance, W.D. Robinson, and B. Sidlauskas. Perspectives in ornithology: avian conservation genomics. Auk (April 2011).
  12. Haig, S.M., C.L. Gratto-Trevor, T.D. Mullins, and M.A. Colwell. 1997. Population identification of western hemisphere shorebirds throughout the annual cycle. Molecular Ecology 6: 413-427.
  13. Hoelzel, A. R. 2010. Looking backward to look forwards: conservation genetics in a changing world. Conservation Genetics 11:655-660.
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  15. Kelly, J. F., K. C. Ruegg, and T. B. Smith. 2005. Combining isotopic and genetic markers to identify breeding origins of migrant birds. Ecological Applications 15:1487-1494.
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  22. Pulido, F. and P. Berthold. 2010. Current selection for lower migratory activity will drive the evolution of residency in a migratory bird population. Proceedings of the National Academy of Sciences, published on April 5, 2010 (doi/10.1073/pnas.0910361107).
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