Table 2. Alignment details for the 31 gene fragments used in this study.
| M11 | This study | ||||||||
|---|---|---|---|---|---|---|---|---|---|
| Gene | Region | # sites | # taxa | # sites | # taxa | GC content | Identical sites | Matrix comp. | Mean coverage |
| A2AB | exon | 848 | 165 (4) | 603 | 290 (A) | 61.0% | 85.2% | 91.9% | 284.1 |
| ADORA3 | exon | 332 | 163 (3) | 369 | 429 (A) | 45.8% | 83.0% | 86.6% | 427.7 |
| ADRB2 | exon | 803 | 155 (5) | 846 | 218 (A) | 53.3% | 86.1% | 94.3% | 215.1 |
| APOB | exon | 2,624 | 168 (5) | 2,523 | 587 (A) | 41.8% | 35.2% | 51.7% | 334.7 |
| APP | NC | 696 | 152 (0) | 636 | 414 (M) | 37.7% | 84.1% | 94.7% | 403.6 |
| ATP7 | exon | 686 | 163 (3) | 723 | 469 (A) | 40.6% | 83.4% | 91.5% | 459.8 |
| BCHE | exon | 995 | 149 (5) | 1,020 | 309 (A) | 40.8% | 82.0% | 94.0% | 300.3 |
| BDNF | exon | 560 | 157 (5) | 612 | 508 (A) | 55.1% | 85.3% | 87.8% | 489.4 |
| BMI1 | NC | 336 | 150 (0) | 292 | 191 (O) | 33.5% | 92.4% | 98.9% | 189.9 |
| BRCA1 | exon | 3,092 | 160 (0) | 3,264 | 969 (M) | 41.7% | 36.1% | 47.0% | 538.1 |
| BRCA2 | exon | 5,045 | 163 (0) | 4,854 | 306 (O) | 34.4% | 41.8% | 52.5% | 183.3 |
| CNR1 | exon | 1,004 | 162 (5) | 1,017 | 356 (A) | 54.0% | 83.9% | 93.8% | 342.6 |
| COI | mtDNA | -- | -- | 672 | 1,686 (A) | 43.0% | 76.6% | 96.1% | 1,657.4 |
| CREM | NC | 441 | 155 (0) | 350 | 331 (O) | 44.7% | 80.7% | 95.8% | 322.5 |
| CYTB | mtDNA | -- | -- | 1,167 | 3,581 (A) | 41.5% | 65.8% | 90.4% | 3,318 |
| DMP1 | exon | 1,361 | 161 (0) | 1,503 | 415 (M) | 51.6% | 28.3% | 41.1% | 205.3 |
| EDG1 | exon | 959 | 153 (5) | 963 | 313 (A) | 56.3% | 84.1% | 95.5% | 301.8 |
| ENAM | exon | 3,899 | 162 (0) | 3,477 | 247 (O) | 44.5% | 58.2% | 68.9% | 215.5 |
| FBN1 | NC | 745 | 150 (0) | 669 | 301 (M) | 33.6% | 81.8% | 93.6% | 289.3 |
| GHR | exon | 947 | 165 (4) | 1,044 | 978 (A) | 49.1% | 58.2% | 70.1% | 794.5 |
| IRBP | exon | 1,253 | 161 (5) | 1,146 | 1,345 (A) | 59.4% | 69.5% | 85.4% | 1,231.9 |
| ND1 | mtDNA | -- | -- | 975 | 962 (A) | 40.6% | 71.0% | 94.4% | 925.5 |
| ND2 | mtDNA | -- | -- | 1,074 | 983 (A) | 37.2% | 57.7% | 86.3% | 873.3 |
| PLCB4 | NC | 350 | 156 (0) | 288 | 478 (M) | 40.1% | 75.9% | 96.2% | 469.6 |
| PNOC | exon | 320 | 144 (0) | 339 | 410 (M) | 62.5% | 79.7% | 82.7% | 403.5 |
| RAG1a | exon | 1,799 | 168 (5) | 1,050 | 639 (A) | 51.5% | 66.2% | 84.6% | 556.8 |
| RAG1b | exon | -- | -- | 1,071 | 936 (A) | 50.6% | 61.8% | 81.1% | 763.6 |
| RAG2 | exon | 446 | 163 (5) | 450 | 889 (A) | 44.1% | 86.9% | 97.5% | 879.4 |
| TTN | exon | 4,437 | 168 (5) | 4,479 | 345 (A) | 42.0% | 41.1% | 58.9% | 205.4 |
| TYR1 | exon | 428 | 151 (5) | 429 | 336 (A) | 46.9% | 85.4% | 98.8% | 334.2 |
| VWF | exon | 1,172 | 162 (3) | 1,194 | 821 (A) | 59.0% | 64.4% | 84.0% | 707.5 |
| Total concatenated | 35,603 | 164 (5) | 39,099 | 4,098 (A) | 45.3% | 13.4% | 11.9% | 1,651.2 | |
Comparison is made to the family-level phylogenetic study of Meredith and colleagues [60] (M11) for the number of aligned sites (with gaps) and mammalian taxa sampled per gene. The per-gene out-group(s) are noted in parentheses, either as the number of out-group taxa used in M11 or identifying the out-group used in gene tree building for this study. Note that RAG1a and RAG1b fragments are combined in M11. Site identity is calculated pairwise, matrix comp. is the sites-by-taxa percentage of ungapped sites, and mean coverage refers to the mean ungapped sites per matrix column (i.e., mean taxon sampling per site).
Abbreviations: A, Anolis; comp., completeness; GC, guanine-cytosine; M, Monodelphis; M11, Meredith and colleagues 2011; mtDNA, mitochondrial DNA; NC, noncoding; O, Ornithorhynchus