Table 1 Literature survey of empirical studies focusing on phylogeography, hybridization and speciation that used PHASE for haplotype reconstruction (see Additional file 4 for a complete list of references).
| Â | Birds | Herpetofauna | Mammals | Fish | Invertebrates | Total |
|---|---|---|---|---|---|---|
| Â | (N= 15) | (N= 12) | (N= 10) | (N= 8) | (N= 15) | (N= 60) |
PHASE threshold used | ||||||
0.95 | 3 | - | 1 | 4 | 2 | 10 |
0.90 | - | 4 | 1 | 1 | 2 | 8 |
0.75-0.80 | 4 | - | - | - | - | 4 |
0.70 | 1 | 1 | - | - | - | 2 |
0.60 | - | - | - | 2 | 3 | 5 |
Best of replicate runsa | - | 1 | - | - | 2 | 3 |
Not reported | 7 | 6 | 8 | 1 | 6 | 28 |
Unresolved genotypes | ||||||
Excluded or coded as missing | 5 | 5 | 1 | 5 | 3 | 19 |
Resolved experimentally | 2 | - | - | - | 2 | 4 |
Included despite uncertainty | 3 | - | - | - | - | 3 |
None present | 1 | 1 | - | 3 | 4 | 9 |
Not reported | 4 | 6 | 9 | - | 6 | 25 |
Experimental validation | ||||||
Cloning | 1 | 2 | - | 1 | 4 | 8 |
Allele-specific PCR | 3 | - | - | - | - | 3 |
None | 11 | 10 | 10 | 7 | 11 | 49 |
Downstream analyses | ||||||
Theta (Θ)b | 14 | 6 | 9 | 4 | 7 | 40 |
Nucleotide diversity (Î ) | 9 | 7 | 9 | 4 | 7 | 36 |
Neutrality or population growth | 7 | 6 | 4 | 6 | 5 | 28 |
Network or phylogenetic tree | 10 | 9 | 9 | 6 | 10 | 44 |