Genetic diversity and phylogeography of Japanese brome (Bromus japonicus Thunb. ex Murr.) populations in China

Figures & data

Table 1. Origins and geographical characteristics of studied B. japonicus populations.

Population	Sample code	Locality	Longitude (E)	Latitude (N)	Altitude (m)
Pop 1	BJ01	Beijing Fangshan	115°58′	39°35′	41
Pop 2	SD01	Shandong Yantai	120°23′	37°37′	23
Pop 3	SD02	Shandong Qingdao	119°47′	35°56′	6
Pop 4	SD08	Shandong Weihai	121°57′	37°10	55
Pop 5	SD09	Shandong Jinan	117°31′	36°44′	51
Pop 6	SD10	Shandong Heze	115°23′	35°10′	54
Pop 7	SD21	Shandong Dezhou	117°30′	37°42′	11
Pop 8	SD23	Shandong Linyi	118°24′	35°5′	70
Pop 9	JS01	Jiangsu Suqian	118°24′	33°42′	18
Pop 10	JS02	Jiangsu Taizhou	120°4′	32°38′	1
Pop 11	HB01	Hebei Xingtai	114°40′	37°0′	46
Pop 12	HB02	Hebei Shijiazhuang	114°39′	38°1′	62
Pop 13	HB04	Hebei Cangzhou	117°7′	37°58′	13
Pop 14	HN01	Henan Xuchang	114°7′	34°5′	64
Pop 15	HN03	Henan Shangqiu	115°51′	34°31′	45
Pop 16	HN04	Henan Luoyang	112°22′	34°45′	343
Pop 17	HN06	Henan Zhumadian	114°37′	33°1′	45
Pop 18	HN08	Henan Nanyang	112°39′	32°25′	114
Pop 19	SS01	Shanxi Xianyang	108°50′	34°31′	404
Pop 20	SX01	Shanxi Linfen	111°40′	36°15′	456
Pop 21	SX02	Shanxi Jinzhong	112°20′	37°20′	766
Pop 22	SX03	Shanxi Yuncheng	110°59′	35°6′	388
Pop 23	GS01	Gansu Tianshui	105°53′	34°34′	1095
Pop 24	GS02	Gansu Longnan	105°36′	33°20′	1300

Table 2. Genetic diversity parameters among 12 ISSR markers for all 24 B. japonicus populations.

Population	N^a	Na^b	Ne^c	H^d	I^e	P^f
BJ01	8	1.0755	1.0573	0.0318	0.0459	7.55%
SD01	8	1.2358	1.1837	0.1009	0.1452	23.58%
SD02	8	1.0849	1.0578	0.0320	0.0469	8.49%
SD08	8	1.0849	1.0503	0.0289	0.0431	8.49%
SD09	8	1.1226	1.0915	0.0510	0.0740	12.26%
SD10	8	1.1132	1.0805	0.0458	0.0667	11.32%
SD21	8	1.2547	1.1634	0.0933	0.1382	25.47%
SD23	8	1.0283	1.0165	0.0095	0.0143	2.83%
JS01	8	1.0472	1.0314	0.0184	0.0272	4.72%
JS02	8	1.0566	1.0311	0.0191	0.0291	5.66%
HB01	8	1.1604	1.1100	0.0617	0.0904	16.04%
HB02	8	1.0943	1.0545	0.0324	0.0489	9.43%
HB04	8	1.2736	1.2329	0.1257	0.1784	27.36%
HN01	8	1.4717	1.3216	0.1824	0.2676	47.17%
HN03	8	1.1604	1.1161	0.0646	0.0940	16.04%
HN04	8	1.1415	1.0877	0.0508	0.0756	14.15%
HN06	8	1.4528	1.3081	0.1707	0.2495	45.28%
HN08	8	1.4057	1.2243	0.1293	0.1952	40.57%
SS01	8	1.0377	1.0152	0.0105	0.0169	3.77%
SX01	8	1.3679	1.2680	0.1496	0.2170	36.79%
SX02	8	1.3962	1.3400	0.1806	0.2560	39.62%
SX03	8	1.1698	1.1028	0.0586	0.0874	16.98%
GS01	8	1.2264	1.1788	0.0979	0.1404	22.64%
GS02	8	1.0472	1.0096	0.0078	0.0142	4.72%

^aN = number of samples; ^bNa = Observed number of alleles; ^cNe = Effective number of alleles; ^dH = Nei’s gene diversity; ^eI = Shannon’s Information index; ^fP = the percentage of polymorphic loci.

Table 3. Analysis of molecular variance (AMOVA) of B. japonicus based on ISSR.

Source of variation	d.f.	SSD	MSD	Variance components	Ratio of variance	p-value
Among populations	23	1248.526	54.284	6.334	63.72	<.001
Within populations	168	605.875	3.606	3.606	36.28	<.001

Figure 1. (a) UPGMA dendrogram of the analyzed populations generated from ISSR data and estimated according to the [26] formula. (b) Population-based cluster analysis using STRUCTURE for K = 4 based on ISSR data. Samples from east of China(cluster IV); samples from middle of China(cluster III); samples from west of China(cluster II); samples from west of China (cluster I). The distribution of the populations to different groups is indicated by color (G1: green, G2: red, G3: yellow, G4: blue).

Figure 2. Geographical distribution in China of 15 cpDNA haplotypes in B. japonicus (Pie charts shows the different haplotypes with their proportions).

Table 4. The analysis of molecular variance (AMOVA) of B. japonicus based on two chloroplast DNA sequences.

Source of variation	SSD	Variance components	Ratio of variance	p-value
Among populations	100.777	0.453	52.721	<.001
Within populations	75.896	0.406	47.279	<.001

Figure 3. Divergence dating of fifteen cpDNA haplotypes in B. japonicus based on MP coalescence analysis.

Figure 4. Haplotype network of B. japonicus (Size of the circle is the proportional to the relative frequency of the haplotypes).

Figure 5. Population-based cluster analysis using STRUCTURE for K = 3 based on cpDNA data.

Figure 6. Mismatch distribution established of B. japonicus (Thin line represents the observed mismatch distribution; the dotted line represents the expected mismatch distribution).

Nei M. Analysis of gene diversity in subdivided populations. Proc Natl Acad Sci U S A. 1973;70(12):3321–3323. doi: 10.1073/pnas.70.12.3321.

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Data availability statement

The data that support the findings of this study are available on request from the corresponding authors.