The origin of modern frogs (Neobatrachia) was accompanied by acceleration in mitochondrial and nuclear substitution rates

Irisarri, Iker; Mauro, Diego San; Abascal, Federico; Ohler, Annemarie; Vences, Miguel; Zardoya, Rafael

doi:10.1186/1471-2164-13-626

Table 2 Results from branch models that assume branch-specific changes in the selection coefficient (ω) in Neobatrachia, based on nucleotide single-gene alignments and mt and nuclear nucleotide data sets

From: The origin of modern frogs (Neobatrachia) was accompanied by acceleration in mitochondrial and nuclear substitution rates

models	null model	"Neob-stem"		"All Neob"		"All Nobleob"		"All Ranoides"
gene	Backgr	Backgr	Branch	Backgr	Branch	Backgr	Branch	Backgr	Branch
atp6	0.03086	0.03076	0.03585	0.03045	0.03126	0.03086	1.1225	0.03082	0.04203
atp8	0.1481	0.14592	1.50841	0.13361	0.16694	0.14838	0.13614	0.14683	0.35429
cob	0.03357	*0.03313*	*0.06875*	0.03302	0.0342	0.03347	0.04419	0.03353	0.0431
cox1	0.01129	*0.011*	*0.03737*	*0.00783*	*0.0144*	0.01122	0.02381	*0.01115*	*0.03898*
cox2	0.02236	0.02224	0.02642	0.02186	0.02271	0.02234	0.0236	0.02227	0.03366
cox3	0.02741	*0.02704*	*0.08793*	*0.02482*	*0.03046*	0.02727	0.03895	0.02733	0.05843
nad1	0.03005	*0.02977*	*0.05077*	*0.02823*	*0.03211*	0.03001	0.03416	0.02996	0.04253
nad2	0.02817	0.02813	0.03252	0.02803	0.02835	0.02818	0.02814	0.02814	0.03007
nad3	0.06499	0.06457	0.14425	0.06435	0.06582	0.06467	0.10545	0.06499	0.93185
nad4	0.03632	0.03622	0.0392	0.0358	0.03675	0.03626	0.04061	0.0363	0.03703
nad4L	0.04471	0.04458	0.04792	0.04662	0.04311	0.04474	0.04294	0.04468	0.04637
nad5	0.03516	0.03503	0.03793	0.03459	0.03571	0.0351	0.03749	0.03511	0.03836
nad6	0.02901	0.02895	0.03107	0.02753	0.03081	0.02897	0.03286	0.02895	0.03359
all mt genes	0.04693	*0.04632*	*0.08313*	*0.04483*	*0.04914*	*0.04673*	*0.06435*	*0.04667*	*0.07065*
bdnf	0.04595	0.04723	0.01186	0.04393	0.04979	0.04577	0.05385	0.04545	0.11214
cxcr4	0.06461	0.06454	0.06745	0.06028	0.07344	0.06588	0.03076	0.06441	0.0748
h3a	0.00476	0.00483	0.0001	0.00599	0.00283	0.005	0.0001	0.00488	0.0001
pomc	0.08214	0.0808	0.23558	0.09098	0.07043	0.08298	0.05716	*0.08548*	*0.02649*
rag1	0.05736	0.05778	0.03692	*0.05249*	*0.06532*	0.05772	0.0438	*0.05802*	*0.01704*
rag2	0.16003	0.15849	0.24864	0.16786	0.1515	0.16003	0.0001	0.1612	0.04584
rho	0.0903	0.092	0.02424	*0.07483*	*0.11389*	0.09175	0.02681	0.09226	0.04981
slc8a1	0.03996	*0.04067*	*0.0001*	*0.03588*	*0.04702*	0.0402	0.03164	0.04055	0.01522
slc8a3	0.02649	0.02684	0.0144	0.02623	0.02707	0.02664	0.01996	0.0268	0.01046
all nuc genes	0.06908	0.06922	0.06195	*0.06426*	*0.07719*	0.06976	0.04153	*0.06984*	*0.03298*

The table shows ω values estimated for the whole frog tree (null model) and values estimated for specific (Branch) and remaining background (Backgr.) branches under the four alternative models tested. Bold italics highlight results that are significantly different to the null model (LRT p < 0.05). See Additional file 3 for full details.

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