Microsatellites and single nucleotide polymorphisms in avian hybrid identification: a comparative case study

Abstract

The correct identification of hybrids is essential in avian hybridisation studies, but selection of the appropriate set of genetic markers for this purpose is at times complicated. Microsatellites and single nucleotide polymorphisms (SNPs) are currently the most commonly used markers in this field. We compare the efficiency of these two marker types, and their combination, in the identification of the threatened avian species, the greater spotted eagle and the lesser spotted eagle, as well as hybrids between the two species. We developed novel SNP markers from genome‐wide distributed 122 candidate introns using only sympatric samples, and tested these markers successfully in 60 sympatric and allopatric spotted eagles using Bayesian model‐based approaches. Comparatively, only one out of twelve previously described avian nuclear intron markers showed significant species‐specific allele frequency difference, thus stressing the importance of selecting the proper markers. Twenty microsatellites outperformed selected nine SNPs in species identification, but were poorer in hybrid detection, whereas the resolution power of ten microsatellites remained too low for correct assignment. A combination of SNPs and microsatellites resulted in the most efficient and accurate identification of all individuals. Our study shows that the use of various sets of markers could lead to strikingly different assignment results, hybridisation studies may have been affected by too low a resolution power of used markers, and that an appropriate set of markers is essential for successful hybrid identification.

The use of microsatellite loci for accurate hybrid detection in a recent contact zone between an endangered and a recently-arrived hummingbird

“…In addition to NewHybrids, Structure (Pritchard et al 2000) is also commonly used to detect hybrids, which differs from NewHybrids in its analytical methods, thus potentially providing conflicting results. In practice, however, the two programmes typically provide very similar results, and appropriate marker selection appears to be a lot more important than analysis method (Vähä and Primmer 2006;Gomes et al 2009;Neaves et al 2010;Väli et al 2010). We therefore only use NewHybrids here.…”

“…There appears to be no consensus in which threshold value to use and q n values used in past studies vary widely, ranging from 0.5 (e.g. Bittner et al 2010;Colliard et al 2010;Väli et al 2010) to 0.8 (e.g. Hird et al 2010).…”

“…Many molecular techniques have been developed to detect hybrids, including the use of single nucleotide polymorphisms (e.g. Chatfield et al 2010;Väli et al 2010), amplified fragment length polymorphisms (e.g. Vallender et al 2007;Sternkopf et al 2010) and restriction fragment length polymorphisms (e.g.…”

Genetic Introgression: An Integral but neglected component of speciation in birds

“…Yet even in a hybrid zone it is challenging to identify patterns of DNA sharing as introgression. A large combination of marker types may be needed to identify individuals with introgressed DNA (Väli et al 2010b). Hybrid zones are often "tension zones" in which selection acts against the neutral diffusion of alleles across species (e.g., Kvist and Rytkönen 2006;Carling and Brumfield 2008;Gay et al 2008Gay et al , 2009Irwin et al 2009a;Mettler and Spellman 2009).…”

Genetic Diversity and Its Spatial Distribution in Self-Regenerating Norway Spruce and Scots Pine Stands

“…This method has some limitations because of a questionable mutation mechanism which is not considered in most modern computer programs used in population studies [41]. The microsatellite method may be inferior compared to a single nucleotide polymorphism (SNP) analysis in hybrid detection [42], inbreeding assessment [43] or parentage and kinship analyses [44,45], but it proves to be very useful in studies that focus on small spatial scales, for applications that require good resolution and cross-species range [41,46].…”