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Table 1 Likelihood analysis of the usp sequence datasets of five extant insect groups

From: Molecular adaptation and resilience of the insect’s nuclear receptor USP

Model

Drosophilidae

Diptera

Lepidoptera

Tenebrionidae

Blattaria

M1a

LnL (np)

-5649.5 (31)

-6946.6 (25)

-4376.2 (12)

-2113.5 (10)

-1945.6 (13)

ω 0 ω 1

0.02 1.00

0.03 1.00

0.03 1.00

0.01 1.00

0.00 1.00

p 0 p 1

0.98 0.02

0.98 0.02

0.95 0.05

0.99 0.01

0.99 0.01

M2a

LnL (np)

-5649.5 (33)

-6946.6 (27)

-4376.2 (14)

-2113.5 (12)

-1945.6 (15)

ω 0 ω 1 ω 2

0.02 1.00 1.00

0.03 1.00 1.00

0.03 1.00 1.00

0.01 1.00 1.00

0.00 1.00 1.24

p 0 p 1 p 2

0.98 0.01 0.01

0.98 0.01 0.01

0.95 0.03 0.02

0.99 0.01 0.00

0.99 0.01 0.00

M7

LnL (np)

-5610.8 (31)

-6859.5 (25)

-4339.9 (12)

-2112.9 (10)

-1950.0 (13)

p q

0.16 5.05

0.40 10.7

0.15 2.58

0.06 3.13

0.01 0.31

M8

LnL (np)

-5610.8 (33)

-6857.1 (27)

-4338.8 (14)

-2112.9 (12)

-1946 (15)

p q

0.16 5.05

0.43 12.9

0.16 2.85

0.06 3.13

0.02 2.09

ω s

1.00

1.00

4.46

1.00

1.00

p s

0.00

0.01

0.00

0.00

0.01

LRT (p-value)

test of positive selection

M2a vs M1a

1

1

1

1

1

M8 vs M7

1

0.08

0.32

1

0.02

  1. LnL: log likelihood. np: number of parameters. ω 0 , ω 1 , ω 2 : non-synonymous/synonymous rate ratio that characterize a negative, a neutral, and a positive selection regime, respectively (with corresponding proportions of sites p 0 , p 1 , p 2 ). p and q: shape parameters of a β function describing the distribution of non-synonymous/synonymous rate ratios. ω s : ratio affecting a p s proportion of sites under positive selection in model M8. LRT: Likelihood ratio test.