TABLE 1.

Summary statistics for polymorphism in 29 URs in 13 A. thaliana accessions

				Nucleotide diversity								Indel diversity				Neutrality test statistics
UR type	Locus	Flanking genes		Sample size	No. of sites	No. of segregating sites	No. of sites with outgroup	Ratio alignable region (%)	No. of fixed differences between species	K	π	Length of alignment (including indel positions)	Total no. of indels	Average indel length within A. thaliana	Indel diversity per site, π(i)	D	H	E	Relative participation to significance of global HKA
Bi-directional URs	770	AT4G35770	AT4G35760	13	420	1	420	100	20	0.049	0.0004	458	0	0.0	0.0000	−1.149	0.318	−0.898	0.93
	570	AT4G02570	AT4G02560	13	597	2	597	100	38	0.067	0.0005	641	1	1.0	0.0002	−1.468	0.422	−1.229	1.38
	220	AT5G64210	AT5G64220	13	815	6	764	94	74	0.104	0.0011	909	2	9.0	0.0007	−1.930	0.604	−1.899	1.05
	670	AT1G19670	AT1G19680	13	778	3	298	38	37	0.136	0.0012	851	7	2.6	0.0030	−0.227	0.520	−0.585	2.33
	400	AT5G66400	AT5G66410	13	718	4	655	91	102	0.176	0.0015	790	3	4.0	0.0009	−0.626	−0.061	−0.352	3.33
	560	AT3G46560	AT3G46550	13	736	6	507	69	36	0.075	0.0016	816	4	2.8	0.0008	−1.440	0.422	−1.229	1.26
	490	AT3G09490	AT3G09480	13	338	3	338	100	36	0.116	0.0017	437	0	0.0	0.0000	−1.233	0.593	−1.290	0.68
	990	AT1G73990	AT1G73980	12	524	4	524	100	45	0.092	0.0019	567	0	0	0.0000	−0.902	0.657	−1.176	0.57
	680	AT2G42680	AT2G42670	13	710	8	452	64	54	0.131	0.0022	849	7	6.1	0.0031	−1.485	0.574	−1.780	0.67
	840	AT2G17840	AT2G17845	10	508	5	508	100	50	0.111	0.0023	1076	12	2.2	0.0039	−1.388	−2.031	1.002	0.34
	500	AT3G24500	AT3G24495	13	526	6	405	77	56	0.158	0.0027	682	2	1.0	0.0007	−0.950	−0.686	−0.022	0.49
	190	AT2G28180	AT2G28190	13	643	9	551	86	58	0.119	0.0034	751	8	11.5	0.0027	−0.944	−0.978	0.492	0.27
	940	AT5G64940	AT5G64930	13	765	12	489	64	31	0.069	0.0036	923	3	6	0.0011	−1.213	0.876	−1.610	2.38
	749	AT1G77490	AT1G77480	13	475	7	475	100	37	0.096	0.0040	576	1	1.0	0.0003	−0.559	0.750	−1.103	0.01
	120	AT5G47110	AT5G47120	13	646	18	627	97	43	0.086	0.0082	873	15	11.7	0.0039	−0.360	−1.978	1.726	4.69
	370	AT5G50370	AT5G50375	11	1040	27	367	35	33	0.096	0.0097	1309	21	6.5	0.0054	0.427	0.362	−0.905	1.78
	Average			12.6	639.9	7.6	498.6	82	46.9	0.105	0.0029	781.8	5.4	4.1	0.0017	−0.965	0.023	−0.679
	Standard deviation			0.9	174.8	6.7	122.7	22	19.6	0.034	0.0026	225.5	6.1	4.0	0.0017	0.586	0.935	1.020
Uni-directional URs	430	AT4G23430	AT4G23420	13	499	1	46	9	13	0.355	0.0003	637	1	1.0	0.0008	−1.149	na	na	1.84
	580	AT1G70580	AT1G70570	13	732	3	732	100	76	0.115	0.0011	826	2	2.5	0.0004	−0.478	−2.729	2.104	2.81
	810	AT2G42810	AT2G42820	13	890	5	687	77	63	0.099	0.0019	1062	4	6.8	0.0019	0.179	0.672	0.271	2.85
	667	AT2G26670	AT3G26640	13	1059	11	944	89	134	0.162	0.0026	1210	12	1.8	0.0030	−0.884	−0.800	0.106	1.54
	870	AT5G06870	AT5G06865	13	478	6	478	100	42	0.097	0.0038	559	3	7.3	0.0014	−0.216	0.457	−0.574	0.03
	630	AT1G27630	AT1G27620	13	760	11	638	84	102	0.185	0.0043	897	1	1.0	0.0006	−0.358	0.395	−0.520	0.92
	960	AT2G27960	AT2G27970	13	800	14	665	83	75	0.128	0.0049	1070	0	0	0.0000	−0.541	−0.149	−0.437	0.00
	470	AT5G08470	AT5G08460	13	431	8	398	92	31	0.091	0.0049	614	6	14.0	0.0020	−0.676	−1.574	1.007	0.68
	850	AT4G11850	AT4G11860	12	855	27	717	84	48	0.084	0.0081	1588	7	7.7	0.0013	−1.009	−1.642	1.110	6.94
	650	AT3G26650	AT3G26640	13	845	18	845	100	111	0.155	0.0096	1028	6	11.8	0.0027	1.665	0.193	1.174	0.01
	240	AT3G21240	AT3G21250	12	339	10	339	100	49	0.175	0.0123	383	3	1.0	0.0040	1.081	−0.173	0.981	0.13
	760	AT2G03760	AT2G03770	11	385	33	385	100	21	0.103	0.0220	450	8	4.1	0.0055	−1.154	−3.085	2.341	35.30
	410	AT3G62410	AT3G62400	13	315	36	315	100	21	0.142	0.0422	406	11	7.4	0.0100	0.641	−2.573	3.335	34.06
	Average			12.7	645.2	14.1	522.3	81	60.5	0.145	0.0091	825.4	4.9	5.1	0.0026	−0.223	−0.917	0.908
	Standard deviation			0.6	245.9	11.3	266.6	29	37.6	0.071	0.0115	360.0	3.8	4.5	0.0027	0.883	1.355	1.228
Average				12.3	627.2	10.3	509.3	81.9	51.7	0.120	0.0055	782.1	5.2	4.5	0.0021	−0.604	−0.323	0.013
Standard deviation				2.2	215.7	9.2	196.1	24.7	29.0	0.057	0.0081	297.3	4.9	4.0	0.0022	0.817	1.192	1.326

K is an estimate of per-site divergence between A. thaliana and A. lyrata (with Jukes–Cantor correction), D is Tajima's test statistic (Tajima 1989), Hn is the normalized Fay and Wu statistic (Fay and Wu 2000; Zeng et al. 2006), and E is a composite test statistic (Zeng et al. 2006). Sequences were established as described in de Meaux et al. (2005) and were deposited under accession nos. FN674063-674399. URs were defined as the UTR and the intergenic regions sensu stricto. ClustalW alignments were optimized by eye. Summary statistics of population variation and neutrality tests were performed using the software MANVa, a software for multilocus analysis of variation (http://www.ub.edu/softevol/manva/). Indel analysis was performed with DNAsp version 5, following model 4 (Librado and Rozas 2009). Summary statistics departing from neutrality are shown in bold.