Table 2 Results of the evolutionary model fitted for the evolutionary rates of SCC, SCC_RY, SCC_SW, SCC_KM, PR_K1, S1_K1, CpG, UUG. Each rate metric was regressed against time with RRphylo function search.trend to test for Temporal trends in the metric values, either computing the rate regression of the metric against time as is (p.real) and ranking the real data slope against a family of 100 randomly generated slopes obtained simulating the brownian motion model of evolution. In addition, we fitted the brownian motion model of evolution by either ignoring (BM) or admitting (BMT) the existence of a trend (term ‘trend’) in the rate metric over time. BM is compared to BMT by means of a likelihood ratio test, whose P.value is reported in the table (LRT_p).
search.trend | Brownian motion with and without trend | trend suggested by both search.trend and BMT | ||||||
|---|---|---|---|---|---|---|---|---|
GENOME TRAIT | slope | p.real | p.random | AIC.BM | AIC.BMT | trend | LRT_p | |
SCC | 5.81 | 0.94 | 0.01 | −12997.511 | −13101.695 | −545.243 | << 0.001 | decrease |
SCC_RY | 552.85 | 0.00 | 1.00 | −14177.235 | −14470.451 | −684.446 | << 0.001 | |
SCC_SW | −530.06 | 0.00 | 0.01 | −14772.989 | −14790.022 | −317.441 | << 0.001 | decrease |
SCC_KM | 185.70 | 0.01 | 0.27 | −14006.345 | −14128.078 | −561.388 | << 0.001 | |
PR_K1 | 2153.57 | 0.00 | 1.00 | −11850.513 | −11933.035 | 1000 | << 0.001 | increase |
S1_K1 | 1056.07 | 0.00 | 1.00 | −13319.047 | −13423.167 | −548.197 | << 0.001 | |
CpG | 653.81 | 0.00 | 1.00 | 6014.193 | 5869.966 | 1000 | << 0.001 | increase |
UUG | 354.39 | 0.00 | 1.00 | 4929.028 | 4891.79 | −407.604 | << 0.001 | |
