Table 1.
Contemporary approaches for genotyping low‐quality and/or quantity DNA samples
| Reference | Platform/method | Starting material | Species | Inference |
|---|---|---|---|---|
| SNP Arrays | ||||
| Morin and Mccarthy (2007) | Ampliflour SNP genotyping | Bone | Bowhead whale (Balaena mysticetus) | Development/validation of SNP markers |
| Mesnick et al. (2011) | Ampliflour SNP and microsatellite genotyping | Skin | Sperm whale (Physeter macroephalus) | Population structure |
| Nussberger et al. (2014) | Fluidigm | Hair | European wildcat (Felis silvestris silvestris) | Validation of SNP markers and studying introgression |
| Ruegg et al. (2014) | Fluidigm | Feathers | Wilson's warbler (Cardellina pusilla) | Tracking migratory populations |
| Kraus et al. (2015) | Fluidigm | Faeces | Grey wolf (Canis lupus) | Development/validation of SNP markers |
| Norman and Spong (2015) | Fluidigm | Faeces | Brown bear (Ursus arctos) | Reconstructing pedigrees and estimating dispersal |
| Doyle et al. (2016), Katzner et al. (2016) | Fluidigm | Feathers | Golden eagle (Aquila chrysaetos) | Population structure, parentage and provenance |
| Stetz et al. (2016) | Fluidigm | Faeces | River otter (Lontra canadensis) | Development/validation of markers, population assignment |
| Spitzer et al. (2016) | Fluidigm | Faeces | Brown bear (Ursus arctos) | Pedigree and population size estimation |
| DeWoody et al., 2017; | Fluidigm | Skin | Grey whale (Eschrichtius robustus) | Individual ID and relatedness |
| von Thaden et al. (2017) | Fluidigm | Hair and faeces | European wildcat (Felis silvestris silvestris); brown bear (Ursus arctos); grey wolf (Canis lupus) | Validation and population structure analysis |
| Hoffman et al. (2012) | Illumina GoldenGate genotyping assay | Skin | Antarctic fur seal (Arctocephalus gazella) | Development/validation of markers |
| Monzón et al. (2014) | Illumina GoldenGate genotyping assay BeadXpress platform | Faeces | Coyote (Canis latrans) | Admixture and hybridization |
| Fitak et al. (2015) | MassARRAY (Sequenom) | Faeces | Pumas (Puma concolor) | Development/validation of SNP markers |
| Goossens et al. (2016) | MassARRAY (Sequenom) | Faeces | Asian elephant (Elephas maximus) | Population structure and genetic diversity, comparison of SNPs with microsatellites |
| Fabbri et al. (2012) | SNPs Pyrosequencing (Biotage), SNaPshot (ABI), Taqman (ABI) | Faeces | Grey wolf (Canis lupus) | Development/validation of markers |
| Targeted sequence capture | ||||
| Perry et al. (2010) | RNA bait capture/Illumina sequencing (Agilent's SureSelect) | Faeces | Chimpanzees (Pan troglodytes) | Validation/SNP genotyping for genetic diversity |
| Snyder‐Mackler et al. (2016) | RNA bait capture/Illumina sequencing | Faeces | Baboons (Papio papio) | Development/validation of markers, pedigree analysis |
| De Barba et al. (2017) | High‐throughput sequencing of microsatellites (Illumina MiSeq) | Faeces | Brown bear (Ursus arctos) | Development/validation of markers |
| Other examples | ||||
| Chiou and Bergey (2015) | ddRAD using FecalSeq | Faeces | Baboons (Papio papio) | Development/validation of markers |
| Russello et al. (2015) | nextRAD | Hair | American pika (Ochotona princeps) | Population structure and outlier loci analysis |