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.

Genetic diversity of Pakistani common myna (Acridotheres tristis) revealed by RAPD-PCR

“…High degree of genetic distances among the populations was observed. These levels are comparable with the light-footed clapper rail (Rallus longirostris levipes) (Nusser et al, 1996). The highest level of Nei's genetic distance (1978) was observed between Gujranwala and Khanewal (D = 0.273, Table 3) and the owest was between Dera Gazi Khan and Khanewal (D = 0.137, Figure 2.…”

Low Genetic Diversity in the Ground Parrot (Pezoporus wallicus) Revealed by Randomly Amplified DNA Fingerprinting

“…Even many threatened or endangered avian species have higher polymorphism; such as Iberian imperial eagle (Aquila adalberti, 59.7%) (Padilla et al 2000), tufted titmouse (Parus bicolour, 45.7%) and marsh wren (Cistothorus palustris, 39.1%) (Bowditch et al 1993). Exceptions include the light-footed clapper rail (Rallus longirostris levipes) with just 1.2% using RAPD (Nusser et al 1996) and Amsterdam albatross (Diomedea amsterdamensis) with 2.1% using AFLP (Milot et al 2007). Our results on genetic diversity for the eastern ground parrot are closer to that for the clapper rail and Amsterdam albatross than for most other endangered species.…”

Analysis of genetic diversity in common loon Gavia immer using RAPD and mitochondrial RFLP techniques

“…The level of polymorphism reported here is comparable with those from other avian species surveyed with the RAPD technique. For example, the percentage of polymorphic RAPD bands for light-footed clapper rail Rallus longirostris levipes, an inhabitant of salt marshes, varied from 30 to 75% (Nusser et al 1996). Also, ≈ 40% RAPD polymorphism was detected for the marsh wren Cistothorus palustris and 46% for the tufted titmouse Parus bicolor (Bowditch et al 1994).…”