Which genetic marker for which conservation genetics issue?

Abstract

Conservation genetics focuses on the effects of contemporary genetic structuring on long-term survival of a species. It helps wildlife managers protect biodiversity by identifying a series of conservation units, which include species, evolutionarily significant units (ESUs), management units (MUs), action units (AUs), and family nets (FNs). Although mitochondrial DNA (mtDNA) evolves 5-10 times faster than single-copy nuclear DNA (scnDNA), it records few traces of contemporary events. Thus, mtDNA can be used to resolve taxonomic uncertainties and ESUs. Variable number of tandem repeats (VNTRs) evolve 100-1000 times faster than scnDNA and provide a powerful tool for analyzing recent and contemporary events. VNTR analysis techniques include polymerase chain reaction (PCR)-based microsatellite assays and oligonucleotide probing. Size homoplasy problems in PCR-based microsatellite assays can strongly affect the inference of recent population history. The high homozygosity in endangered species is reflected in a relatively low number and level of variability in microsatellite loci. This combined with "allelic dropout" and "misprinting" errors contributes to the generation of highly biased genetic data following analyses of natural populations. Thus, in conservation genetics, microsatellites are of limited use for identifying ESUs, MUs, and AUs. In contrast to PCR-based microsatellite analysis, oligonucleotide probing avoids errors resulting from PCR amplification. It is particularly suitable for inferring recent population history and contemporary gene flow between fragmented subpopulations. Oligonucleotide fingerprinting generates individual-specific DNA banding patterns and thus provides a highly precise tool for monitoring demography of natural populations. Hence, DNA fingerprinting is powerful for distinguishing ESUs, MUs, AUs, and FNs. The use of oligonucleotide fingerprinting and fecal DNA is opening new areas for conservation genetics.

Mitochondrial DNA Data Unveil Highly Divergent Populations within the Genus Hynobius (Caudata: Hynobiidae) in South Korea

“…However, Kim et al (2007) estimated the divergence time between H. leechii and H. quelpaertensis at about 4.3 MYA based on allozyme data. This difference may result from characteristics of mtDNA, high mutation fixation and fast evolution (Wan et al, 2004).…”

Pronounced genetic differentiation of small, isolated and fragmented tilapia populations inhabiting the Magadi Soda Lake in Kenya

“…However, an earlier study by Wilson et al (2000) based on minisatellites using samples from only two lagoons of the main Lake Magadi and a subset of samples from a single location in Lake Natron reported substantial genetic differentiation between the three populations studied. The difference in the studies by Wilson et al (2000Wilson et al ( , 2004 could be attributed to the low resolution power of the markers and the limited number of samples used (Wan et al, 2004).…”

Population genetic structure of the Japanese eel Anguilla japonica: panmixia at spatial and temporal scales

“…Although mtDNA gene regions are powerful markers for resolving phylogenetic problems at the species level, these are of limited use in population genetic studies because of their limited resolving power and the presence of mitochondrial pseudogenes in the nuclear genome of many organisms (reviewed in Zhang & Hewitt 2003, Wan et al 2004. On the other hand, although studies using allozyme markers have detected spatial heterogeneity in allele frequency within the American eel (Williams et al 1973), European eel (De Ligny & Pantelouris 1973, Comparini et al 1977 and Japanese eel (Chan et al 1997), the significant clinal shift in allele frequency was putatively attributed to single-generation selection along an environmental gradient (Avise 2003).…”