Genetic analysis of populations of threatened snake species using RAPD markers

Abstract

Snakes are a particularly threatened vertebrate taxon, with distributions of many species and populations becoming increasingly fragmented. At present, little is known about the degree of genetic differentiation that exists between isolated populations even though such information may be critical to their survival and conservation. As an example of how recently developed RAPD genetic markers can be used in conservation genetics, we present preliminary results from a study which used these DNA‐based markers to assess population divergence in two threatened Canadian snakes, the black rat snake (Elaphe o. obsoleta) and the eastern massasauga rattlesnake (Sistrurus c. catenatus). We present information on the levels of variation and reliability of amplification for fragments generated from five primers. We then use a recently developed analytical technique to estimate levels of nucleotide diversity within populations and sequence divergence between populations. Our results show that intrapopulation levels of divergence as estimated by the methods of Clark & Lanigan (Molecular Biology and Evolution 1993, 10, 1096–1111) approximate those found for mtDNA in vertebrates and that diversity between snake populations is small and non‐significant when tested using randomization procedures. Thus, our study provides an example of how RAPDs can be applied to conservation genetic studies of vertebrates and suggest that the snake populations we examined have only recently become isolated and maybe considered genetically equivalent from a conservation perspective, although this conclusion needs to be confirmed with other DNA‐based markers.

Population genetics of the mangrove salt marsh snake, Nerodia clarkii compressicauda, in a linear, fragmented habitat

“…It should be noted, however, that the small number of loci we used may limit the interpretation of our results. Previous population genetic studies of snakes using allozymes, randomly amplified polymorphic DNA (RAPDs), or mtDNA loci generally revealed little to no variation among intraspecific populations (e.g., Sattler and Guttman 1976;Gartside et al 1977;Lawson 1987;Dessauer et al 1987;Rose and Selcer 1989;Gibbs et al 1994; Thompson and Crother 1998). A growing number of microsatellite studies, however, have indicated comparable levels of diversity and differentiation as detected here (Table 3).…”

Limited genetic diversity and high differentiation among the remnant adder (Vipera berus) populations in the Swiss and French Jura Mountains

“…However, the timber rattlesnake (Crotalus horridus) displayed a high level of phylopatry, with genetic distances between hibernacula being larger and significant in 50% of the comparisons (Villarreal et al 1996). Within the massasauga rattlesnake (Sistrurus c. catenatus), microsatellites markers revealed a huge differentiation between populations (Gibbs et al 1997), whereas RAPD analyses did not show any structure between the same populations (Gibbs et al 1994; see also Gibbs et al 1997 for the comparison). Also based on RAPD, Jäggi et al (2000) demonstrated a low genetic differentiation within asp viper (V. aspis) populations in the Jura Mountains.…”

FluoMEP: A new genotyping method combining the advantages of randomly amplified polymorphic DNA and amplified fragment length polymorphism

“…[4,5]), and identification of differences among strains, subspecies, or species (see e.g., ref. [6][7][8]). The methods used for such purposes include randomly amplified polymorphic DNA (RAPD) [9]; arbitrarily primed PCR (AP-PCR) [10]; DNA amplification fingerprinting (DAF) [11]; multiple arbitrary amplicon profiling (MAAP) [12]; amplified fragment length polymorphism (AFLP) [13]; representational difference analysis (RDA) [14,15]; and suppressive subtractive hybridization (SSH) [16,17].…”