Table 5.
Genes used in the phylogenetic analysis of Plethodon.
| Type of locus | Locus | Length | Variable characters | Parsimony-informative characters | Best-fitting model | Partitions | Number of taxa sampled | Data source |
|---|---|---|---|---|---|---|---|---|
| Nuclear introns | GAPD | 659 | 221 | 92 | GTR + Γ | none | 48 | this study |
| ILF3 | 281 | 56 | 34 | HKY | none | 40 | this study | |
| Mlc2a | 257 | 79 | 39 | GTR + Γ | none | 55 | this study | |
| RPL12 | 463 | 159 | 90 | HKY + Γ | none | 48 | this study | |
| RHO | 224 | 57 | 43 | HKY + I | none | 62 | this study | |
| TPI | 1938 | 569 | 211 | GTR + Γ | intron/exon | 29 | [56] | |
| Nuclear exons | RAG-1 | 1467 | 358 | 248 | GTR + I + Γ | codon | 60 | [56] |
| BDNF | 707 | 67 | 29 | GTR + Γ | codon | 14 | [60] | |
| POMC | 481 | 98 | 41 | GTR + Γ | codon | 15 | [60] | |
| Mitochondrial genes | Cyt-b | 649 | 369 | 313 | GTR + I + Γ | codon | 66 | [56] |
| ND4 | 686 | 409 | 364 | GTR + I + Γ | codon | 65 | [56] | |
| ND2 | 1107 | 741 | 635 | GTR + I + Γ | codon, tRNA-TRP | 52 | [55] | |