Mitochondrial DNA variable number tandem repeats (VNTRs): utility and problems in molecular ecology

Abstract

Analysis of mitochondrial (mt)DNA size polymorphism in the form of variable number tandem repeats (mtVNTRs) has become an increasingly popular methodology for addressing questions in molecular ecology. When detected by PCR, mtVNTR analysis can provide a sensitive, rapid, and cost-effective measure of genetic variability that may be exploited in studies of population differentiation and biogeography. Despite the emergence of this approach, there has been little critical evaluation of its success or utility as a practical tool. In this review, we identify problematic methodological, theoretical and interpretive factors that can influence the utility of mtVNTR analysis. The reliability of the procedure is considered in terms of both detection of alleles and scoring of intra-individual allele frequencies. While many of the potential technical problems of the technique do not raise serious practical concerns, this rapid and sensitive methodology is seriously compromised by the difficulty of reliably assessing allele frequencies, of assaying only germline tissue, and in our ignorance of the mechanisms generating mtVNTR diversity. Thus, although there is a considerable potential for mtVNTR pilot studies to assess genetic diversity, the utility of the technique to resolve broader questions in molecular ecology should be treated cautiously until such a time as the system is better understood.

The population history of the deep-sea demersal fish Bothrocara hollandi in the Japan Sea revealed by tandem repeat units in the mitochondrial non-coding region

“…Various non-coding regions have been reported from fish mitochondrial DNAs: tandem repeats (Lunt et al 1998), duplication of CR (Lee et al 2001), intergenic spacers (Shields & Gust 1995, Bakke et al 1999, and tRNA pseudogenes (Mabuchi et al 2004). Exact alignment among nucleotide sequences of non-coding regions is rather difficult due to the limited length and high frequency of insertions, deletions, and duplications; nevertheless, it can enable us to reconstruct the population history in great detail.…”

Structure and Evolution of the Mitochondrial DNA Complete Control Region in the Lizard Lacerta dugesii (Lacertidae, Sauria)

“…The presence of tandem repeats near the 3 0 end of the CR is not uncommon in vertebrates, although their putative function and origin are unknown. Repeats of variable number and length have been found 3 in various organisms, but not always localized in the same domains (Moritz and Brown 1986;Lunt et al 1998;Savolainen et al 2000): turtles (Zardoya and Meyer 1998;Kumazawa and Nishida 1999), bears (Matsuhashi et al 1999), snakes and skinks (Kumazawa et al 1998;Kumazawa and Nishida 1999), and iguanas (Janke et al 2001). The several types of repeats found in L. dugesii do not follow the general pattern described by Hoelzel et al (1994) and Savolainen et al (2000) for vertebrates in general.…”

Diversidad y estructura genética de artibeus jamaicensis (chiroptera: phyllostomidae) en Chiapas, México

“…Esto podría deberse al tamaño del muestreo (34 individuos), el cual es pequeño comparado con otros estudios (de 49 a 193 individuos; Carstens et al 2004;Fleming et al 2009;Ruíz et al 2013;Del Real-Monroy et al 2014), y a la ubicación de las redes de colecta en sitios con disponibilidad de alimentos. Además, el D-loop tiene una alta tasa de evolución, de sustitución y polimorfismo (Lunt et al 1998), que promueve altos valores de diversidad genética.…”