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RAPD analysis reveals low genetic variability in the endangered light-footed clapper rail
Article first published online: 28 JUN 2008
Volume 5, Issue 4, pages 463–472, August 1996
How to Cite
NUSSER, J. A., GOTO, R. M., LEDIG, D. B., FLEISCHER, R. C. and MILLER, M. M. (1996), RAPD analysis reveals low genetic variability in the endangered light-footed clapper rail. Molecular Ecology, 5: 463–472. doi: 10.1111/j.1365-294X.1996.tb00339.x
John Nusser, Ronald Goto and Marcia Miller are interested in the application of major histocompatibility complex markers and molecular techniques in avian conservation genetics. Dave Ledig is a conservation biologist currently working to restore habitat for threatened and endangered species at Ash Meadows National Wildlife Refuge. Rob Fleischer is head of the Molecular Genetics Laboratory at the National Zoological Park, and is studying the evolutionary and conservation genetics in several vertebrate taxa.
- Issue published online: 28 JUN 2008
- Article first published online: 28 JUN 2008
- Received 4 September 1995 revised 15 January 1996
- clapper rail;
- conservation genetics;
- genetic diversity;
- Rallus longirostris levipes;
- Rallus longirostris yumanensis;
Numbers of light-footed clapper rails Rallus longirostris levipes, an endangered bird inhabiting southern California salt marshes, have substantially declined from historic levels. RAPD (randomly amplified polymorphic DNA) analysis was employed to assess the genetic variability within and among four of the largest remaining light-footed clapper rail populations. A single, larger population of the endangered Yuma clapper rail Rallus longirostris yumanensis was used for comparison.
A total of 325 RAPD primers were tested on DNA from a subset of five clapper rails composed of a single representative for each of the four light-footed clapper rail populations and a representative for the single Yuma clapper rail population. Of the 1338 amplified bands (loci) surveyed in these five representative birds, approximately 1% were polymorphic, indicating the level of differentiation across all loci is quite low. Nine primers yielding these 16 polymorphic bands were used to analyse 48 individuals from five populations. Five of these bands were polymorphic in both subspecies, six were polymorphic only within the light-footed clapper rails, and five were polymorphic only within the Yuma clapper rail samples. Considering the few bands that were polymorphic among the light-footed clapper rail populations, a surprisingly high level of population differentiation (GST=0.28) was found. This is in accord with the results of AMOVA analyses which show that a fairly high percentage of the limited variability among the rails is due to either differences between subspecies or differences between the light-footed rail populations. Because inbreeding depression is suspected and overall genetic distances between populations are low, movement of light-footed clapper rails from larger populations into smaller ones might be considered as a management strategy. Employing RAPDs as one of a series of assays is useful in revealing the population structure of genetically depauperate species.