UCP family evolution and mammalian UCP1 selection analysis
A quality-controlled analysis of UCP1, UCP2 and UCP3 family membership, followed by codon-based tests of UCP1 evolution in 12 deep-hibernating mammals and 18 non-hibernating controls.
Biological interpretation
UCP1 coding sequences are predominantly conserved by purifying selection. Across the sampled mammals, the analysis does not support a common shift in UCP1 selection pressure associated with deep hibernation, selection relaxation or intensification on deep-hibernator branches, or episodic diversifying positive selection in those branches.
The result argues against one broad explanation—widespread coding-sequence adaptation of UCP1 shared by deep hibernators—under the tested models and sampling. It directs attention toward expression regulation, tissue-specific control, protein activity, individual sites, and lineage-specific mechanisms. Those are follow-up hypotheses, not findings established by this release.
A gene-average ω below 1 indicates purifying selection on average. Different ω estimates between groups do not by themselves demonstrate positive selection, and a non-significant test does not prove biological equivalence.
Data and methods
- Resolve the UCP family. Separate UCP1, UCP2 and UCP3 representatives and assess family membership with a phylogenetic tree.
- Validate coding sequences. Require CDS length to be divisible by three, translation identity of at least 98%, and a protein-length difference of no more than two amino acids.
- Build codon alignments. Align proteins with MAFFT L-INS-i and back-translate using validated CDS. Analyze both the full alignment and an 80% occupancy alignment.
- Test selection on an independent species topology. Run PAML M0 and two-ω branch models, HyPhy RELAX, and HyPhy BUSTED.
- Assess robustness. Repeat PAML and RELAX after removing bats, sciurids, bears, or hedgehog.
| Quality-control measure | Result |
|---|---|
| UCP family representatives | 56 UCP1; 81 UCP2; 65 UCP3 |
| CDS–protein validation | 55 of 56 UCP1 representatives passed |
| Mammalian UCP1 clade | 42 sequences; UFBoot = 99 |
| Primary phenotype groups | 12 deep hibernators; 18 controls |
| Full / 80% occupancy alignments | 313 / 306 codons |
Primary and sensitivity results
| Dataset | Hibernator ω | Control ω | PAML P | RELAX K | RELAX P |
|---|---|---|---|---|---|
| Primary, 80% occupancy | 0.16666 | 0.15345 | 0.5976 | 1.0262 | 0.9384 |
| Full alignment | 0.16488 | 0.15472 | 0.6833 | 1.0769 | 0.8037 |
| Bats removed | 0.11276 | 0.13372 | 0.4606 | 1.1648 | 0.5943 |
| Sciurids removed | 0.17220 | 0.15922 | 0.6336 | 3.3071 | 0.1718 |
| Bears removed | 0.16323 | 0.15556 | 0.7598 | 1.0672 | 0.8534 |
| Hedgehog removed | 0.20292 | 0.15262 | 0.1125 | 0.8147 | 0.4169 |
All six PAML branch comparisons and all six RELAX tests were non-significant. BUSTED returned P = 0.5000 for the primary dataset.
Key output files
The complete archive additionally contains inputs, alternative alignments, model outputs, scripts and logs. SHA-256 checksums accompany the downloaded files.