Table 2.
Genes Identified as Putatively under Positive Selection.
| HGCN Symbol | Foreground Branch | (1) SWAMP q-Value | (1) SWAMP P-Value | (2) Gblocks q-Value | (2) Gblocks P-Value | Gene Name |
|---|---|---|---|---|---|---|
| BEND7 a | S. sea otter | 2.36E-02 | 5.68E-06 | 1.80E-03 | 2.74E-06 | BEN domain containing 7 |
| MAST2 | S. sea otter | 1.00E+00 | 4.32E-02 | 7.14E-03 | 2.53E-05 | Microtubule-associated serine/threonine kinase 2 |
| RELN | S. sea otter | x | x | 1.30E-02 | 6.02E-05 | Reelin |
| FAM111A | S. sea otter | x | x | 1.91E-02 | 9.85E-05 | Family with sequence similarity 111, member A |
| SLC18A3 | S. sea otter | 1.00E+00 | 1.00E+00 | 2.83E-02 | 1.69E-04 | Solute carrier family 18 (vesicular monoamine), member 3 |
| CEP350 | S. sea otter | 1.00E+00 | 3.98E-03 | 2.90E-02 | 1.76E-04 | Centrosomal protein 350 |
| SWAP70 | S. sea otter | 3.75E-01 | 2.33E-04 | 3.73E-02 | 2.40E-04 | SWA-70 protein |
| SLC7A4 | S. sea otter | 3.42E-01 | 1.92E-04 | 4.02E-02 | 2.66E-04 | Solute carrier family 7 (cationic amino acid transporter, y+ system), member 4 |
| ZNF200 | S. sea otter | 1.00E+00 | 3.46E-03 | 4.55E-02 | 3.11E-04 | Zinc finger protein 200 |
| ISG20 | S. sea otter | 1.00E+00 | 6.85E-02 | 6.15E-02 | 4.49E-04 | Interferon-stimulated protein |
| PGR | S. sea otter | x | x | 7.04E-02 | 5.27E-04 | Progesterone receptor |
| TPGS1 | S. sea otter | x | x | 7.88E-02 | 6.14E-04 | Tubulin polyglutamylase complex subunit 1 |
| HADHA | S. sea otter | 6.26E-01 | 4.81E-04 | 7.90E-02 | 6.25E-04 | Hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/enoyl-Coenzyme A hydratase (trifunctional protein), alpha subunit |
| SLAMF7 | S. sea otter | 1.00E+00 | 8.75E-03 | 9.76E-02 | 8.20E-04 | SLAM family member 7 |
| PRSS35 | Giant otter | x | x | 4.31E-02 | 2.91E-04 | Protease, serine 35 |
| WBP1 | Giant otter | 4.07E-01 | 2.64E-04 | 7.90E-02 | 6.25E-04 | WW domain-binding protein 1 |
| SIK2 | Ottersb | 4.97E-01 | 3.52E-04 | 7.60E-02 | 5.83E-04 | Salt inducible kinase 2 |
| IQCD | Otters | 1.00E+00 | 1.33E-03 | 8.56E-02 | 6.93E-04 | IQ motif containing D |
Note.—Eighteen genes under positive selection were detected using the branch-site test (Yang 2007) on the branches leading to the southern sea otter, giant otter, and the ancestral otter internal branch. Two different alignment filtering schemes were used: (1) GUIDANCE2 (Sela et al. 2015) plus sliding window filtering (SWAMP; Harrison et al. 2014); or (2) GUIDANCE2 plus conserved block filtering (Gblocks; Castresana 2000). Genes with q ≤ 0.1 under either filtering scheme are shown. Additional details on these genes available in supplementary table S4D, Supplementary Material online. SWAMP: p and q-values based on codeml run on gene alignments filtered first using GUIDANCE2 then stringent SWAMP sliding window masking, with columns of the alignments containing any gaps removed. Genes with length <120 bp after filtering were excluded. Gblocks: p and q-values based from PAML’s codeml run on gene alignments filtered first using GUIDANCE2 then moderately stringent Gblocks conserved block selection filtering, with columns of the alignment with >50% of the sequences containing a gap removed. Genes with length <120 bp after filtering were excluded. “x” denotes a gene that was excluded under one of the filtering schemes if its length postfiltering was <120 bp.
BEND7 is the only gene with q-value ≤ 0.1 under both Gblocks and SWAMP filtering schemes.
The branch leading to both otter lineages.