RAPD analysis reveals low genetic variability in the endangered light‐footed clapper rail

Abstract

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.

Uncloaking a cryptic, threatened rail with molecular markers: origins, connectivity and demography of a recently-discovered population

“…Another unexpected result was the similar genetic composition of the Eastern and California Black Rail subspecies (Eddleman et al 1994), a pattern that has also been observed for other rail species (Fleischer et al 1995;Nusser et al 1996). Our result is particularly striking because similarity was observed not only for mtDNA, for which the subspecies shared one haplotype, but also for several microsatellites on which most alleles were common.…”

Direct evidence for biased gene diversity estimates from dominant random amplified polymorphic DNA (RAPD) fingerprints

“…To be effective, this fragment exclusion criterion should be applied at the population level (Lynch & Milligan 1994), and not to the overall fragment frequencies (e.g. Nusser et al 1996).…”

Direct vs. Indirect Benefits of Caching by Gray Squirrels (Sciurus carolinensis)

“…Haig et al 1994;Nusser et al 1996;Antolin et al 2001), few studies to date have used RAPDs to analyze microgeographic genetic structuring (Apostol et al 1993;Masters & Forester 1995;Sinclair et al 1996). Although RAPDs are a common technique for comparing genetic differences among animal populations (e.g.…”