Billions of basepairs of recently expanded, repetitive sequences are eliminated from the somatic genome during copepod development

Table 2 Results of relative frequency comparisons of repeat superfamilies in the somatic and germline genomes of M. edax

Repeat superfamily	H₀ : f_g = f_s(P-value)	Dominant	${\hat{f}}_{g} : {\hat{f}}_{s}$ (Ratio)	Threshold λ(95%)	Threshold λ(99%)
DNA-Chapaev	0.653	Neither	0.671	NA	NA
DNA-Ginger1	5.11e-5	Somatic	0.0419	< 0.0857	< 0.113
DNA-Harbinger	8.66e-7	Somatic	0.0894	< 0.116	< 0.144
DNA-hAT	<< 1e-16	Germline	1.888	> 1.886	> 1.885
DNA-Kolobok	0.010	Somatic	0.0839	< 0.232	< 0.426
DNA-MuDR	<< 1e-16	Germline	4.66	> 4.56	> 4.48
DNA-Polinton	0.105	Neither	0.484	NA	NA
DNA-Sola	1.04e-5	Somatic	0.194	< 0.233	< 0.269
LINE-CR1	<< 1e-16	Somatic	0.119	< 0.1195	< 0.1200
LINE-L1	<< 1e-16	Germline	2.827	> 2.826	> 2.826
LINE-MINIME_DN	<< 1e-16	Somatic	0.166	< 0.169	< 0.170
LINE-Penelope	0.033	Somatic	0.168	< 0.535	NA
LTR-BEL	0.264	Neither	1.19	NA	NA
LTR-Copia	0.139	Neither	0.707	NA	NA
LTR-DIRS	3.52e-6	Somatic	0.0335	< 0.0639	< 0.0840
LTR-ERV1	<< 1e-16	Somatic	0.147	< 0.148	< 0.149
LTR-ERV3	0.072	Neither	0.252	NA	NA
LTR-Gypsy	<< 1e-16	Somatic	0.5324	< 0.5325	< 0.5325
LTR-Pao	0.042	Germline	1.05	> 1.01	NA

The first data column gives the P-value based on a x² approximation for rejecting the null hypothesis of equal relative frequencies in the two genomes. The second column identifies which genome has a statistically significant higher relative frequency (α = 0.05) The third column gives the ratio of the observed relative frequencies in the experiment. The fourth and fifth columns give 95% and 99% confidence bounds on the ratio, respectively, for a one-sided test.

ISSN: 1471-2164