Table 4.
Comparison of analysis methods used to classify 19 individuals as having a possible hybrid origin. Qualitative methods included identity of mtDNA haplotype as either MOJ (G. agassizii) or SON (G. morafkai) and the presence/zygosity of locus Goag05a where the locus is typically “null” in G. agassizii, and thus, an admixed individual is expected to be homozygous at this locus. GeneClass 2 (Piry et al. 2004) was run for four different models and on datasets with and without locus Goag05 (8 total methods); proportion of methods identifying an individual as a hybrid are reported as well as whether the dominant admixture type, G. agassizii (Goag) or G. morafkai (Gomo), matches that of the maternal lineage. STRUCTURE (Pritchard et al. 2000) was used to classify individuals without prior putative population information. NewHybrids (Anderson 2008) was used to predict specific recombinant classes (F1, F2, or backcross)
| Location | Site ID | MtDNA Haplotype | Gender | Goag05a | New Hybrids | GeneClass 2 | Structure Proportion of admixture (Q) | ||
|---|---|---|---|---|---|---|---|---|---|
| GeneClass/mtDNA mismatch | Proportion of GeneClass2 hybrid detection | Gomo | Goag | ||||||
| Black Mountains | EB | MOJ_A1 | M | HOM | F2 | Yes | 7 of 8 | 0.60 | 0.40 |
| Black Mountains | EB | SON_01 | M | HET | F2 | Yes | 5 of 8 | 0.37 | 0.63 |
| Black Mountains | EB | MOJ_A1 | M | NULL | F2/Bx | No | 2 of 8 | 0.12 | 0.88 |
| Black Mountains | EB | SON_01 | F | NULL | F2/Bx | Yes | 3 of 8 | 0.15 | 0.85 |
| Black Mountains | WBM | MOJ_A01 | M | HOM | F2 | Yes | 8 of 8 | 0.50 | 0.50 |
| Black Mountains | WBM | MOJ_A01 | F | NULL | Pure_Goag | No | 2 of 8 | 0.02 | 0.98 |
| Buck Mountains | BUCK | SON_05 | M | HET | F2 | No | 4 of 8 | 0.66 | 0.34 |
| Buck Mountains | BUCK | MOJ_A01 | F | NULL | F2 | No | 6 of 8 | 0.40 | 0.60 |
| Buck Mountains | BUCK | MOJ_A01 | M | HOM | F2 | No | 2 of 8 | 0.30 | 0.70 |
| Buck Mountains | BUCK | MOJ_A01 | F | HOM | F2 | Yes | 8 of 8 | 0.54 | 0.46 |
| Hualapai Mountains | HF | SON_05 | M | HET | F2 | – | 0 of 8 | 0.71 | 0.29 |
| Hualapai Mountains | HF | SON_01 | M | HOM | F2 | No | 1 of 8 | 0.71 | 0.29 |
| Hualapai Mountains | HF | MOJ_A01 | M | HET | Gomo_Bx | Yes | 3 of 8 | 0.96 | 0.04 |
| Hualapai Mountains | HF | SON_01 | F | HET | Gomo_Bx | – | 0 of 8 | 0.90 | 0.10 |
| Hualapai Mountains | HSC | MOJ_A01 | F | HOM | F2 | Yes | 5 of 8 | 0.61 | 0.39 |
| Hualapai Mountains | HSC | SON_01 | M | HOM | F2 | No | 2 of 8 | 0.76 | 0.25 |
| Hualapai Mountains | HSC | SON_01 | F | NULL | F2 | – | 0 of 8 | 0.63 | 0.37 |
| Hualapai Mountains | HSC | SON_01 | unk. | HOM | F2 | Yes | 6 of 8 | 0.52 | 0.48 |
| Arrastra Mountains | AM | SON_01 | unk. | HOM | F2/Bx | – | 0 of 8 | 0.72 | 0.28 |