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

References

• Li YH. Weeds of China. In: Weeds of seed plants. 1st ed. Vol. 2. Beijing: China Agriculture Press; 1998. p. 1–10.
   Google Scholar
• Baskin JM, Baskin CC. Ecology of germination and flowering in the weedy winter annual grass Bromus japonicus. J Range Manage. 1981;34(5):369–372. doi: 10.2307/3897906.
   Google Scholar
• Li Q, Tan JN, Li W, et al. Effects of environmental factors on seed germination and emergence of Japanese brome (Bromus japonicus). Weed Sci. 2015;63(3):641–646. doi: 10.1614/WS-D-14-00131.1.
   Web of Science ®Google Scholar
• Li Q, Du L, Yuan GH, et al. Density effect and economic threshold of Japanese brome (Bromus japonicus Houtt.) in wheat. Chilean J Agric Res. 2016;76(4):441–447. doi: 10.4067/S0718-58392016000400007.
   Web of Science ®Google Scholar
• Li Q, Yu J, Guo W, et al. Target-site basis for resistance to flucarbazonesodium in Japanese brome (Bromus japonicus Houtt.) in China. Chil j Agric Res. 2022;82(3):493–501. doi: 10.4067/S0718-58392022000300493.
   Web of Science ®Google Scholar
• Fisher RA. The genetical theory of natural selection. Oxford, UK: Clarendon Press; 1930. p. 291.
   Google Scholar
• Dodet M, Petit RJ, Gasquez J. Local spread of the invasive Cyperus esculentus (cyperaceae) inferred using ­molecular genetic markers. Weed Res. 2008;48(1):19–27. doi: 10.1111/j.1365-3180.2008.00606.x.
   Web of Science ®Google Scholar
• Fontana LC, Agostinetto D, Langaro AC, et al. Genetic diversity among crabgrass weed ecotypes (Digitria spp.) occurring in field crops in Rio Grande Do Sul, Brazil. Aust J Crop Sci. 2015;9:931–939.
   Google Scholar
• Grimsby JL, Tsirelson D, Gammon MA, et al. Genetic diversity and clonal vs. sexual reproduction in Fallopia spp. (Polygonaceae). Am J Bot. 2007;94(6):957–964. doi: 10.3732/ajb.94.6.957.
   PubMed Web of Science ®Google Scholar
• Hosseini M, Yassaie M, Rashed-Mohassel MH, et al. Genetic diversity of Iranian wild barley (Hordeum spontaneum Koch.) populations. J Crop Sci Biotechnol. 2022;25(3):301–311. doi: 10.1007/s12892-021-00132-2.
   Google Scholar
• Yu H, Yang J, Cui H, et al. Distribution, genetic diversity and population structure of Aegilops tauschii coss. In major wheat-growing regions in China. Agriculture. 2021;11(4):311. doi: 10.3390/agriculture11040311.
   Google Scholar
• Abdelkrim J, Pascal M, Samadi S. Establishing causes of eradication failure based on genetics: case study of ship rat eradication in ste. Anne archipelago. Conserv Biol. 2007;21(3):719–730. doi: 10.1111/j.1523-1739.2007.00696.x.
   PubMed Web of Science ®Google Scholar
• Li J, Wei S, Huang Z, et al. Genetic diversity and population structure in Solanum nigrum based on single-nucleotide polymorphism (SNP) markers. Agronomy. 2023;13(3):832. doi: 10.3390/agronomy13030832.
   Google Scholar
• Ward SM, Gaskin JF, Wilson LM. Ecological genetics of plant invasion: what do we know? Invasive Plant Sci Manag. 2008;1(1):98–109. doi: 10.1614/IPSM-07-022.1.
   Web of Science ®Google Scholar
• Ash GJ, Cother EJ, Tarleton J. Variation in lanceleaved waterplantain (Alisma lanceolatum) in southeastern Australia. Weed Sci. 2004;52(3):413–417. doi: 10.1614/WS-03-063R1.
   Web of Science ®Google Scholar
• Leon RG, Laat R. Population and quantitative genetic analyses of life-history trait adaptations in Amaranthus palmeri S. Watson. Weed Res. 2021;61(5):342–349. doi: 10.1111/wre.12492.
   Web of Science ®Google Scholar
• Du L, Gao X, Qu C, et al. Identification of purple nutsedge (Cyperus rotundus L.) ecotypes and the effect of environmental factors on tuber sprouting in China. Weed Res. 2022;62(5):360–371. doi: 10.1111/wre.12551.
   Web of Science ®Google Scholar
• Yang J, Tang L, Guan YL, et al. Genetic diversity of an alien invasive plant Mexican sunflower (Tithonia diversifolia) in China. Weed Sci. 2012;60(4):552–557. doi: 10.1614/WS-D-11-00175.1.
   Web of Science ®Google Scholar
• Reboud X, Zeyl C. Organelle inheritance in plants. Heredity. 1994;72(2):132–140. doi: 10.1038/hdy.1994.19.
   Google Scholar
• Chen Q, Chen C, Wang B, et al. Complete chloroplast ­genomes of 11 Sabia samples: genomic features, comparative analysis, and phylogenetic relationship. Front Plant Sci. 2022;13:1052920. doi: 10.3389/fpls.2022.1052920.
   PubMed Web of Science ®Google Scholar
• Gaynor ML, Fu CN, Gao LM, et al. Biogeography and ecological niche evolution in diapensiaceae inferred from phylogenetic analysis. J Syt Evol. 2020;58(5):646–662. doi: 10.1111/jse.12646.
   Web of Science ®Google Scholar
• Liu Y, Lin L, Yang D, et al. Comparative phylogenetic analysis of oolong tea (Phoenix dancong tea) using complete chloroplast genome sequences. Heliyon. 2022;8(12):e12557. doi: 10.1016/j.heliyon.2022.e12557.
   PubMed Web of Science ®Google Scholar
• Lu X, Chen L, Chen YP, et al. Molecular phylogeography and conservation genetics of Sladenia celastrifolia­inferred from chloroplast DNA sequence variation. J Syt Evol. 2014;52(4):458–465. doi: 10.1111/jse.12057.
   Web of Science ®Google Scholar
• Yeh FC, Yang RC, Boyle TB, et al. 1997) POPGENE, the user-friendly shareware for population genetic analysis. In: Molecular biology and biotechnology centre. Canada: University of Alberta.
   Google Scholar
• Lewontin RC. The apportionment of human diversity. Evol Biol. 1972;6:381–394.
   Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• Wright S. Evolution in mendelian populations. Genetics. 1931;16(2):97–159. doi: 10.1093/genetics/16.2.97.
   PubMedGoogle Scholar
• Excoffier L, Laval G, Schneider S. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinform. 2005;1:47–50.
   PubMed Web of Science ®Google Scholar
• Rohlf FJ. NTSYS-pc. Numerical taxonomy and multivariate analysis system. Version 2.0. Setauket (NY): Exeter Software; 1998.
   Google Scholar
• McCune B, Mefford MJ. PC-ORD 5.0. Multivariate analysis of ecological data. Gleneden Beach, Oregon: MjM Software Design; 2006.
   Google Scholar
• Thompson JD, Gibson TJ, Plewniak F, et al. The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997;25(24):4876–4882. doi: 10.1093/nar/25.24.4876.
   PubMed Web of Science ®Google Scholar
• Rozas J, Sánchez-DelBarrio JC, Messeguer X, et al. DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics. 2003;19(18):2496–2497. doi: 10.1093/bioinformatics/btg359.
   PubMed Web of Science ®Google Scholar
• Pons O, Petit RJ. Measuring and testing genetic differentiation with ordered versus unordered alleles. Genetics. 1996;144(3):1237–1245. doi: 10.1093/genetics/144.3.1237.
   PubMed Web of Science ®Google Scholar
• Swofford DL. PAUP∗: phylogenetic analysis using parsimony (∗ and other methods), version 4.0 b10. Sunderland: Sinauer Associates.
   Google Scholar
• Bandelt HJ, Forster P, Röhl A. Median-joining networks for inferring intraspecific phylogenies. Mol Biol Evol. 1999;16(1):37–48. doi: 10.1093/oxfordjournals.molbev.a026036.
   PubMed Web of Science ®Google Scholar
• Fu YX, Li WH. Statistical tests of neutrality of mutations. Genetics. 1993;133(3):693–709. doi: 10.1093/genetics/133.3.693.
   PubMed Web of Science ®Google Scholar
• Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics. 1989;123(3):585–595. doi: 10.1093/genetics/123.3.585.
   PubMed Web of Science ®Google Scholar
• Wang NG, He XY, Miehe G, et al. Phylogeography of the Qinghai-Tibet Plateau endemic alpine herb Pomatosace filicula (primulaceae). J Syt Evol. 2014;52(3):289–302. doi: 10.1111/jse.12089.
   Web of Science ®Google Scholar
• Mangolin CA, Junior RSO, Machado MFPS. Genetic diversity in weed. In: Alvarez-Fernandez, R, editor. Herbicides—environmental impact studies and management ­approaches. Rijeka, Croatia: InTech; 2012. P. 223–248.
   Google Scholar
• Ådahl EMMA, Lundberg PER, Jonzén N. From climate change to population change: the need to consider ­annual life cycles. Glob Change Biol. 2006;12(9):1627–1633. doi: 10.1111/j.1365-2486.2006.01196.x.
   Web of Science ®Google Scholar
• Excoffier L, Smouse PE, Quattro JM. Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics. 1992;131(2):479–491. doi: 10.1093/genetics/131.2.479.
   PubMed Web of Science ®Google Scholar
• O’Hanlon PC, Peakall R, Briese DT (2000) A review of new PCR-based genetic markers and their utility to weed ecology. Weed Res. 40: 239–254 doi: 10.1046/j.1365-3180.2000.00191.x.
   Web of Science ®Google Scholar
• Wright S. 1984) Evolution and the genetics of populations. Variability within and among natural populations. vol. 4. Chicago: University of Chicago Press; p. 590.
   Google Scholar
• Franklin IR. Conservation biology: an evolutionary-eecological perspective. In: Soule ME, Wilcox BA, editors. Evolutionary change in small populations. vol. 4. Massachusetts: Sinauer Associates; 1930. p. 135–150.
   Google Scholar
• Kočiš Tubić N, Djan M, Veličković N, et al. Microsatellite DNA variation within and among invasive populations of Ambrosia artemisiifolia from the southern Pannonian Plain. Weed Res. 2015;55(3):268–277. doi: 10.1111/wre.12139.
   Web of Science ®Google Scholar
• Linhart YB, Grant MC. Evolutionary significance of local genetic differentiation in plants. Annu Rev Ecol Syst. 1996;27(1):237–277. doi: 10.1146/annurev.ecolsys.27.1.237.
   Google Scholar
• Wang XR, Szmidt AE. Molecular markers in population genetics of Forest trees. Scand J Res. 2001;16(3):199–220. doi: 10.1080/02827580118146.
   Google Scholar
• Comes HP, Kadereit JW. The effect of quaternary climatic changes on plant distribution and evolution. Trends Plant Sci. 1998;3(11):432–438. doi: 10.1016/S1360-1385(98)01327-2.
   Web of Science ®Google Scholar
• Parsons JB, Newbury HT, Jackson MT, et al. Contrasting genetic diversity relationships are revealed in rice (Oryza sativa L.) using different marker types. Mol Breed. 1997;3(2):115–125. doi: 10.1023/A:1009635721319.
   Web of Science ®Google Scholar
• Slatkin M. Gene flow in natural populations. Ann Rev Ecol Syst. 1985;16(1):393–430. doi: 10.1146/annurev.ecolsys.16.1.393.
   Google Scholar
• Schaal BA, Hayworth DA, Olsen KM, et al. Phylogeographic studies in plants: problems and prospects. Mol Ecol. 1998;7(4):465–474. doi: 10.1046/j.1365-294x.1998.00318.x.
   Web of Science ®Google Scholar
• Novaes RML, Filho JPDL, Ribeiro RA, et al. Phylogeography of Plathymenia reticulata (leguminosae) reveals patterns of recent range expansion towards northeastern Brazil and Southern cerrados in Eastern tropical South America. Mol Ecol. 2010;19(5):985–998. doi: 10.1111/j.1365-294X.2010.04530.x.
   PubMed Web of Science ®Google Scholar
• Yang FS, Li YF, Ding X, et al. Extensive population ­expansion of Pedicularis longiflora (Orobanchaceae) on the Qinghai-Tibetan Plateau and its correlation with the quaternary climate change. Mol Ecol. 2008;17(23):5135–5145. doi: 10.1111/j.1365-294X.2008.03976.x.
   PubMed Web of Science ®Google Scholar
• Burdon JJ, Brown AHD. Population genetics of Echium plantagineum, a target weed for biological control. Aust Jnl of Bio Sci. 1986;39(4):369–378. doi: 10.1071/BI9860369.
   Google Scholar
• Jasieniuk M, Maxwell BD. Plant diversity: new insights from molecular biology and genomics technologies. Weed Sci. 2001;49(2):257–265. doi: 10.1614/0043-1745(2001)049[0257:PDNIFM]2.0.CO;2.
   Web of Science ®Google Scholar
• Nissen SJ, Masters RA, Lee DJ, et al. DNA-based marker systems to determine genetic diversity of weedy species and their application to biocontrol. Weed Sci. 1995;43(3):504–513. doi: 10.1017/S0043174500081546.
   Web of Science ®Google Scholar
• Mengistu LW, Messersmith CG. Genetic diversity of Kochia. Weed Sci. 2002;50(4):498–503. doi: 10.1614/0043-1745(2002)050[0498:GDOK]2.0.CO;2.
   Web of Science ®Google Scholar
• Tan JN, Li Q, Bai S, et al. Potential distribution of Bromus japonicus in both China and the rest of the world as predicted by MaxEnt. Chin Agric Sci Bull. 2016;32:49–54.
   Google Scholar