The future of parentage analysis: From microsatellites to SNPs and beyond

Abstract

Parentage analysis is a cornerstone of molecular ecology that has delivered fundamental insights into behaviour, ecology and evolution. Microsatellite markers have long been the king of parentage, their hypervariable nature conferring sufficient power to correctly assign offspring to parents. However, microsatellite markers have seen a sharp decline in use with the rise of next‐generation sequencing technologies, especially in the study of population genetics and local adaptation. The time is ripe to review the current state of parentage analysis and see how it stands to be affected by the emergence of next‐generation sequencing approaches. We find that single nucleotide polymorphisms (SNPs), the typical next‐generation sequencing marker, remain underutilized in parentage analysis but are gaining momentum, with 58 SNP‐based parentage analyses published thus far. Many of these papers, particularly the earlier ones, compare the power of SNPs and microsatellites in a parentage context. In virtually every case, SNPs are at least as powerful as microsatellite markers. As few as 100–500 SNPs are sufficient to resolve parentage completely in most situations. We also provide an overview of the analytical programs that are commonly used and compatible with SNP data. As the next‐generation parentage enterprise grows, a reliance on likelihood and Bayesian approaches, as opposed to strict exclusion, will become increasingly important. We discuss some of the caveats surrounding the use of next‐generation sequencing data for parentage analysis and conclude that the future is bright for this important realm of molecular ecology.

Last exit before the brink: Conservation genomics of the Cambodian population of the critically endangered southern river terrapin

“…Our study was not directly designed for the comparison of the power of genome‐wide neutral SNPs and microsatellites on parentage and relatedness analyses. Recent studies aimed to do so have shown that even few hundreds of genome‐wide SNPs outperform microsatellites in parentage assignment accuracy and relatedness estimation (Flanagan & Jones, ; Thrasher, Butcher, Campagna, Webster, Lovette, ), including in very small populations (Andrews et al, ).…”

A comparison of pedigree, genetic and genomic estimates of relatedness for informing pairing decisions in two critically endangered birds: Implications for conservation breeding programmes worldwide

“…With that said, there are relatively few studies to date that effectively combine existing pedigree data with genomic estimates of relatedness to inform pairing recommendations (but see Hogg et al, 2019;Ivy, Putnam, Navarro, Gurr, & Ryder, 2016). To date, these studies are largely limited to SNPs being used for parentage reconstruction (reviewed in Flanagan & Jones, 2019), where unknown or uncertain relationships are reconstructed using empirical data and software (e.g., Whalen, Gorjanc, & Hickey, 2019), and more complete pedigrees are used moving forward. Alternatively, there is an option to produce empirical estimates of relatedness for all founders or breeding individuals in conservation breeding programmes-as suggested in Ivy et al (2016) , this approach requires caution, as the calculation of pedigree-based identity by descent for subsequent generations-including kinship and gene diversity-will be affected by the addition of empirical data .…”

Estimating a Key Parameter of Mammalian Mating Systems: The Chance of Siring Success for a Mated Male

“…Studies of multiple parentage were stimulated by the advent of molecular techniques, primarily analyses of microsatellite DNA but in the future perhaps single nucleotide polymorphisms (SNPs), that allowed assessment of paternity (reviewed by ref. []). Molecular studies document the proportion of litters or clutches with multiple paternity and the number of sires that contribute to each of the broods.…”