基因组时代的物种形成研究

doi:10.16288/j.yczz.24-218

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Hereditas(Beijing) ›› 2025, Vol. 47 ›› Issue (1): 71-100.doi: 10.16288/j.yczz.24-218

• Review • Previous Articles Next Articles

Speciation studies in the genomic era

Zefu Wang¹(), Jianquan Liu²()

1. State Key Laboratory of Tree Genetics and Breeding, Co-Innovation Center for Sustainable Forestry in Southern China, College of Ecology and Environment, Nanjing Forestry University, Nanjing 210037, China
2. State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, College of Ecology, Lanzhou University, Lanzhou 730000, China

Received:2024-07-30 Revised:2024-09-12 Online:2025-01-20 Published:2024-10-28
Contact: Jianquan Liu E-mail:wangzefu@njfu.edu.cn;liujq@lzu.edu.cn
Supported by:
National Natural Science Foundation of China(32301411);National Natural Science Foundation of China(31590821);National Natural Science Foundation of China(91731301);Natural Science Foundation of Jiangsu Province(BK20230394)

Abstract

Abstract:

Since Darwin’s era, speciation has been one of the most central issues in evolutionary biology studies. Understanding the processes of species origin is crucial in deepening our understanding of the formation of species biodiversity, which is essential for their protections. However, speciation research has been challenging due to the rather complex evolutionary histories of many extant species. In recent years, with the continuous advancements in genomic sequencing techniques, significant advances have been achieved in the field of speciation researches. In this review, we overview speciation study advances, especially in the concepts and latest developments in research methods for studying speciation in the genomic era, encompassing the major research aspects: species delimitation, bifurcating speciation, hybrid speciation, polyploid speciation, reproductive isolation genes and speciation genes. Furthermore, we discuss the limitations of these studies and methods. Finally, we provide the outlook on the future challenges and directions in speciation researches.

Key words: speciation, genomics, research methods, research advances, future perspectives

Zefu Wang, Jianquan Liu. Speciation studies in the genomic era[J]. Hereditas(Beijing), 2025, 47(1): 71-100.

Figures/Tables 6

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References 177

[1]	Coyne JA, Orr HA. Speciation. Sunderland: Sinauer Associates, Inc. 2004.
[2]	Xie P. The Aufhebung and Breakthrough of the Theories on the Origin and Evolution of Life:Life in Philosophy and Philosophy in Life Sciences. Beijing: Science Press, 2014.
	谢平. 生命的起源-演化理论之扬弃与革新:哲学中的生命, 生命中的哲学. 北京: 科学出版社, 2014.
[3]	Darwin CR. On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. London: John Murray, 1859.
[4]	Dobzhansky T. Genetics and the Origin of Species. New York: Columbia University Press, 1937.
[5]	Sanger F, Coulson AR. A rapid method for determining sequences in DNA by primed synthesis with DNA polymerase. J Mol Biol, 1975, 94(3): 441-448. doi: 10.1016/0022-2836(75)90213-2 pmid: 1100841
[6]	Zhang DX. Why is it so difficult to reach a consensus in species concept? Biodiversity Sci, 2016, 24(9): 1009-1003.
	张德兴. 为什么在物种概念上难以达成共识? 生物多样性, 2016, 24(9): 1009-1013. doi: 10.17520/biods.2016223
[7]	Xie P. A brief review on the historical changes in the concept of species. Biodiversity Sci, 2016, 24(9): 1014-1019.
	谢平. 浅析物种概念的演变历史. 生物多样性, 2016, 24(9): 1014-1019. doi: 10.17520/biods.2016243
[8]	Hong DY. Biodiversity pursuits need a scientific and operative species concept. Biodiversity Sci, 2016, 24(9): 979-999.
	洪德元. 生物多样性事业需要科学、可操作的物种概念. 生物多样性, 2016, 24(9): 979-999. doi: 10.17520/biods.2016203
[9]	Liu JQ. “The integrative species concept” and “species on the speciation way”. Biodiversity Sci, 2016, 24(9): 1004-1008.
	刘建全. “整合物种概念”和“分化路上的物种”. 生物多样性, 2016, 24(9): 1004-1008. doi: 10.17520/biods.2016222
[10]	Kennedy D, Norman C. What don’t we know? Science, 2005, 309(5731): 75. pmid: 15994521
[11]	Mayr E. Systematics and the Origin of Species. New York: Columbia University Press, 1942.
[12]	Futuyma D, Kirkpatrick M. Evolution (5th Edition). Sunderland: Sinauer Associates, 2022.
[13]	Darwin CR. The Variation of Animals and Plants under Domestication. London: John Murray, 1868.
[14]	Linnaeus C. Systema Naturae Per Regna Tria Naturae, Secundum Classes, Ordines, Genera, Species, Cum Characteribus, Differentiis, Synonymis, Locis. Tomus I, eds. Stockholm: Laurentius Salvius, 1758.
[15]	Vaughan DA, Morishima H, Kadowaki K. Diversity in the Oryza genus. Curr Opin Plant Biol, 2003, 6(2): 139-146. doi: 10.1016/s1369-5266(03)00009-8 pmid: 12667870
[16]	Gu ZL, Gong JY, Zhu Z, Li Z, Feng Q, Wang CS, Zhao Y, Zhan QL, Zhou CC, Wang AH, Huang T, Zhang L, Tian QL, Fan DL, Lu YQ, Zhao Q, Huang XH, Yang SH, Han B. Structure and function of rice hybrid genomes reveal genetic basis and optimal performance of heterosis. Nat Genet, 2023, 55(10): 1745-1756. doi: 10.1038/s41588-023-01495-8 pmid: 37679493
[17]	Jing CY, Zhang FM, Wang XH, Wang MX, Zhou L, Cai Z, Han JD, Geng MF, Yu WH, Jiao ZH, Huang L, Liu R, Zheng XM, Meng QL, Ren NN, Zhang HX, Du YS, Wang X, Qiang CG, Zou XH, Gaut BS, Ge S. Multiple domestications of Asian rice. Nat Plants, 2023, 9(8): 1221-1235.
[18]	Mayr E. Animal Species and Evolution. Cambridge: Harvard University Press, 1963.
[19]	Baack E, Melo MC, Rieseberg LH, Ortiz-Barrientos D. The origins of reproductive isolation in plants. New Phytol, 2015, 207(4): 968-984. doi: 10.1111/nph.13424 pmid: 25944305
[20]	Turelli M, Barton NH, Coyne JA. Theory and speciation. Trends Ecol Evol, 2001, 16(7): 330-343. doi: 10.1016/s0169-5347(01)02177-2 pmid: 11403865
[21]	Kaul MLH. Male Sterility in Higher Plants. Berlin: Springer Science & Business Media, 1988.
[22]	Schnable PS, Wise RP. The molecular basis of cytoplasmic male sterility and fertility restoration. Trends Plant Sci, 1998, 3(5): 175-180.
[23]	Wang ZF, Jiang YZ, Bi H, Lu ZQ, Ma YZ, Yang XY, Chen NN, Tian B, Liu BB, Mao XX, Ma T, DiFazio SP, Hu QJ, Abbott RJ, Liu JQ. Hybrid speciation via inheritance of alternate alleles of parental isolating genes. Mol Plant, 2021, 14(2): 208-222. doi: 10.1016/j.molp.2020.11.008 pmid: 33220509
[24]	Owens GL. From common gardens to candidate genes: an elegant case of homoploid hybrid speciation. Mol Plant, 2021, 14(2): 200-201. doi: 10.1016/j.molp.2020.11.020 pmid: 33271335
[25]	Ting CT, Tsaur SC, Wu CI. The phylogeny of closely related species as revealed by the genealogy of a speciation gene, Odysseus. Proc Natl Acad Sci USA, 2000, 97(10): 5313-5316. doi: 10.1073/pnas.090541597 pmid: 10779562
[26]	Ting CT, Tsaur SC, Wu ML, Wu CI. A rapidly evolving homeobox at the site of a hybrid sterility gene. Science, 1998, 282(5393): 1501-1504. pmid: 9822383
[27]	Liang M, Chen WJ, LaFountain AM, Liu YL, Peng FE, Xia R, Bradshaw HD, Yuan YW. Taxon-specific, phased siRNAs underlie a speciation locus in monkeyflowers. Science, 2023, 379(6632): 576-582. doi: 10.1126/science.adf1323 pmid: 36758083
[28]	Wang CL, Yu XW, Wang J, Zhao ZG, Wan JM. Genetic and molecular mechanisms of reproductive isolation in the utilization of heterosis for breeding hybrid rice. J Genet Genomics, 2024, 51(6): 583-593. doi: 10.1016/j.jgg.2024.01.007 pmid: 38325701
[29]	Chen JJ, Ding JH, Ouyang YD, Du HY, Yang JY, Cheng K, Zhao J, Qiu SQ, Zhang XL, Yao JL, Liu KD, Wang L, Xu CG, Li XH, Xue YB, Xia M, Ji Q, Lu JF, Xu ML, Zhang QF. A triallelic system of S5 is a major regulator of the reproductive barrier and compatibility of indica-japonica hybrids in rice. Proc Natl Acad Sci USA, 2008, 105(32): 11436-11441.
[30]	Yang JY, Zhao XB, Cheng K, Du HY, Ouyang YD, Chen JJ, Qiu SQ, Huang JY, Jiang YH, Jiang LW, Ding JH, Wang J, Xu CG, Li XH, Zhang QF. A killer-protector system regulates both hybrid sterility and segregation distortion in rice. Science, 2012, 337(6100): 1336-1340. doi: 10.1126/science.1223702 pmid: 22984070
[31]	Yu Y, Zhao ZG, Shi YR, Tian H, Liu LL, Bian XF, Xu Y, Zheng XM, Gan L, Shen YM, Wang CL, Yu XW, Wang CM, Zhang X, Guo XP, Wang JL, Ikehashi H, Jiang L, Wan JM. Hybrid sterility in rice (Oryza sativa L.) involves the tetratricopeptide repeat domain containing protein. Genetics, 2016, 203(3): 1439-1451.
[32]	Kubo T, Takashi T, Ashikari M, Yoshimura A, Kurata N. Two tightly linked genes at the hsa1 locus cause both F₁ and F₂ hybrid sterility in rice. Mol Plant, 2016, 9(2): 221-232.
[33]	Long YM, Zhao LF, Niu BX, Su J, Wu H, Chen YL, Zhang QY, Guo JX, Zhuang CX, Mei MT, Xia JX, Wang L, Wu HB, Liu YG. Hybrid male sterility in rice controlled by interaction between divergent alleles of two adjacent genes. Proc Natl Acad Sci USA, 2008, 105(48): 18871-18876. doi: 10.1073/pnas.0810108105 pmid: 19033192
[34]	Xie YY, Xu P, Huang JL, Ma SJ, Xie XR, Tao DY, Chen LT, Liu YG. Interspecific hybrid sterility in rice is mediated by OgTPR1 at the S1 locus encoding a peptidase-like protein. Mol Plant, 2017, 10(8): 1137-1140.
[35]	Shen RX, Wang L, Liu XP, Wu J, Jin WW, Zhao XC, Xie XR, Zhu QL, Tang HW, Li Q, Chen LT, Liu YG. Genomic structural variation-mediated allelic suppression causes hybrid male sterility in rice. Nat Commun, 2017, 8(1): 1310. doi: 10.1038/s41467-017-01400-y pmid: 29101356
[36]	Wang CL, Wang J, Lu JY, Xiong YH, Zhao ZG, Yu XW, Zheng XM, Li J, Lin QB, Ren YL, Hu Y, He XD, Li C, Zeng YL, Miao R, Guo ML, Zhang BS, Zhu Y, Zhang YH, Tang WJ, Wang YL, Hao BY, Wang QM, Cheng SQ, He XJ, Yao BW, Gao JW, Zhu XF, Yu H, Wang Y, Sun Y, Zhou CL, Dong H, Ma XD, Guo XP, Liu X, Tian YL, Liu SJ, Wang CM, Cheng ZJ, Jiang L, Zhou JW, Guo HS, Jiang LW, Tao DY, Chai JJ, Zhang W, Wang HY, Wu CY, Wan JM. A natural gene drive system confers reproductive isolation in rice. Cell, 2023, 186(17): 3577-3592.e18.
[37]	Zhou PH, Wang ZJ, Zhu XC, Tang Y, Ye L, Yu HH, Li YT, Zhang NK, Liu T, Wang T, Wu YY, Cao DY, Chen Y, Li X, Zhang QL, Xiao JH, Yu SB, Zhang QF, Mi JM, Ouyang YD. A minimal genome design to maximally guarantee fertile inter-subspecific hybrid rice. Mol Plant, 2023, 16(4): 726-738.
[38]	Zhang K, Lenstra JA, Zhang S, Liu W, Liu J. Evolution and domestication of the Bovini species. Anim Genet, 2020, 51(5): 637-657. doi: 10.1111/age.12974 pmid: 32716565
[39]	Wang ZF, Jiang YZ, Yang XY, Bi H, Li JL, Mao XX, Ma YZ, Ru DF, Zhang C, Hao GQ, Wang J, Abbott RJ, Liu JQ. Molecular signatures of parallel adaptive divergence causing reproductive isolation and speciation across two genera. Innovation (Camb), 2022, 3(3): 100247.
[40]	Presgraves DC. Hitchhiking to speciation. PLoS Biol, 2013, 11(2): e1001498.
[41]	Ellegren H, Smeds L, Burri R, Olason PI, Backström N, Kawakami T, Künstner A, Mäkinen H, Nadachowska- Brzyska K, Qvarnström A, Uebbing S, Wolf JBW. The genomic landscape of species divergence in Ficedula flycatchers. Nature, 2012, 491(7426): 756-760.
[42]	Wu H, Zhang YX, Yu L. Progress on animal speciation studies. Hereditas (Beijing), 2025, 47(1): 58-70.
	吴宏, 章誉兴, 于黎. 动物物种形成研究进展. 遗传, 2025, 47(1): 58-70.
[43]	Huang Y. Molecular Phylogenetics. Beijing: Science Press, 2012.
	黄原. 分子系统发生学. 北京: 科学出版社, 2012.
[44]	Wang J, He WC, Xiang KL, Wu ZQ, Gu CH. Advances in plant phylogeny in the genome era. J Zhejiang A&F Univ, 2023, 40(1): 227-236.
	王杰, 贺文闯, 向坤莉, 武志强, 顾翠花. 基因组时代的植物系统发育研究进展. 浙江农林大学学报, 2023, 40(1): 227-236.
[45]	Liu L, Yu LL, Kubatko L, Pearl DK, Edwards SV. Coalescent methods for estimating phylogenetic trees. Mol Phylogenet Evol, 2009, 53(1): 320-328. doi: 10.1016/j.ympev.2009.05.033 pmid: 19501178
[46]	Liu L, Yu LL, Pearl DK, Edwards SV. Estimating species phylogenies using coalescence times among sequences. Syst Biol, 2009, 58(5): 468-477. doi: 10.1093/sysbio/syp031 pmid: 20525601
[47]	Chen CJ, Wu Y, Li JW, Wang X, Zeng ZH, Xu J, Liu YL, Feng JT, Chen H, He YH, Xia R. TBtools-II: A “one for all, all for one” bioinformatics platform for biological big-data mining. Mol Plant, 2023, 16(11): 1733-1742.
[48]	Zhang D, Gao FL, Jakovlić I, Zou H, Zhang J, Li WX, Wang GT. PhyloSuite: An integrated and scalable desktop platform for streamlined molecular sequence data management and evolutionary phylogenetics studies. Mol Ecol Resour, 2020, 20(1): 348-355. doi: 10.1111/1755-0998.13096 pmid: 31599058
[49]	Yu GC, Smith DK, Zhu HC, Guan Y, Lam TTY. GGTREE: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol, 2017, 8(1): 28-36.
[50]	Zhang WP, Cao L, Lin XR, Ding YM, Liang Y, Zhang DY, Pang EL, Renner SS, Bai WN. Dead-end hybridization in walnut trees revealed by large-scale genomic sequence data. Mol Biol Evol, 2022, 39(1): msab308.
[51]	Shen XX, Li YN, Hittinger CT, Chen XX, Rokas A. An investigation of irreproducibility in maximum likelihood phylogenetic inference. Nat Commun, 2020, 11(1): 6096.
[52]	Bouckaert R, Vaughan TG, Barido-Sottani J, Duchêne S, Fourment M, Gavryushkina A, Heled J, Jones G, Kühnert D, De Maio N, Matschiner M, Mendes FK, Müller NF, Ogilvie HA, du Plessis L, Popinga A, Rambaut A, Rasmussen D, Siveroni I, Suchard MA, Wu CH, Xie D, Zhang C, Stadler T, Drummond AJ. BEAST 2.5: an advanced software platform for Bayesian evolutionary analysis. PLoS Comput Biol, 2019, 15(4): e1006650.
[53]	Yang ZH. PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol, 2007, 24(8): 1586-1591. doi: 10.1093/molbev/msm088 pmid: 17483113
[54]	Sanderson MJ. r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock. Bioinformatics, 2003, 19(2): 301-302. doi: 10.1093/bioinformatics/19.2.301 pmid: 12538260
[55]	Zuckerkandl E, Pauling L. Evolutionary divergence and convergence in proteins. In: Evolving Genes and Proteins. Bryson V, Vogel HJ, eds. New York: Academic Press, 1965, 97-166.
[56]	Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics, 2000, 155(2): 945-959. doi: 10.1093/genetics/155.2.945 pmid: 10835412
[57]	Malinsky M, Matschiner M, Svardal H. Dsuite-Fast D-statistics and related admixture evidence from VCF files. Mol Ecol Resour, 2021, 21(2): 584-595. doi: 10.1111/1755-0998.13265 pmid: 33012121
[58]	Kong S, Kubatko LS. Comparative performance of popular methods for hybrid detection using genomic data. Syst Biol, 2021, 70(5): 891-907. doi: 10.1093/sysbio/syaa092 pmid: 33404632
[59]	Pfeifer B, Wittelsbürger U, Ramos-Onsins SE, Lercher MJ. PopGenome: an efficient Swiss Army knife for population genomic analyses in R. Mol Biol Evol, 2014, 31(7): 1929-1936. doi: 10.1093/molbev/msu136 pmid: 24739305
[60]	Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, 1000 Genomes Project Analysis Group. The variant call format and VCFtools. Bioinformatics, 2011, 27(15): 2156-2158. doi: 10.1093/bioinformatics/btr330 pmid: 21653522
[61]	Korunes KL, Samuk K. PIXY: unbiased estimation of nucleotide diversity and divergence in the presence of missing data. Mol Ecol Resour, 2021, 21(4): 1359-1368. doi: 10.1111/1755-0998.13326 pmid: 33453139
[62]	Korneliussen TS, Albrechtsen A, Nielsen R. ANGSD: analysis of next generation sequencing data. BMC Bioinformatics, 2014, 15(1): 356.
[63]	Lancaster AK, Single RM, Mack SJ, Sochat V, Mariani MP, Webster GD. PyPop: a mature open-source software pipeline for population genomics. Front Immunol, 2024, 15: 1378512.
[64]	Gao F, Ming C, Hu WJ, Li HP. New software for the fast estimation of population recombination rates (FastEPRR) in the genomic era. G3 (Bethesda), 2016, 6(6): 1563-1571.
[65]	Li H, Durbin R. Inference of human population history from individual whole-genome sequences. Nature, 2011, 475(7357): 493-496
[66]	Schiffels S, Durbin R. Inferring human population size and separation history from multiple genome sequences. Nat Genet, 2014, 46(8): 919-925. doi: 10.1038/ng.3015 pmid: 24952747
[67]	Terhorst J, Kamm JA, Song YS. Robust and scalable inference of population history from hundreds of unphased whole genomes. Nat Genet, 2017, 49(2): 303-309. doi: 10.1038/ng.3748 pmid: 28024154
[68]	Cornuet JM, Santos F, Beaumont MA, Robert CP, Marin JM, Balding DJ, Guillemaud T, Estoup A. Inferring population history with DIY ABC: a user-friendly approach to approximate Bayesian computation. Bioinformatics, 2008, 24(23): 2713-2719.
[69]	Cornuet JM, Pudlo P, Veyssier J, Dehne-Garcia A, Gautier M, Leblois R, Marin JM, Estoup A. DIYABC v2.0: a software to make approximate Bayesian computation inferences about population history using single nucleotide polymorphism, DNA sequence and microsatellite data. Bioinformatics, 2014, 30(8): 1187-1189.
[70]	Excoffier L, Marchi N, Marques DA, Matthey-Doret R, Gouy A, Sousa VC. fastsimcoal2: demographic inference under complex evolutionary scenarios. Bioinformatics, 2021, 37(24): 4882-4885. doi: 10.1093/bioinformatics/btab468 pmid: 34164653
[71]	Gutenkunst RN, Hernandez RD, Williamson SH, Bustamante CD. Inferring the joint demographic history of multiple populations from multidimensional SNP frequency data. PLoS Genet, 2009, 5(10): e1000695.
[72]	Blischak PD, Sajan M, Barker MS, Gutenkunst RN. Demographic history inference and the polyploid continuum. Genetics, 2023, 224(4): iyad107.
[73]	1001 Genomes Consortium. 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell, 2016, 166(2): 481-491.
[74]	Zhao XB, Guo YF, Kang LP, Yin CB, Bi AY, Xu DX, Zhang ZL, Zhang JJ, Yang XH, Xu J, Xu S, Song XY, Zhang M, Li YW, Kear P, Wang J, Liu ZY, Fu XD, Lu F. Population genomics unravels the Holocene history of bread wheat and its relatives. Nat Plants, 2023, 9(3): 403-419. doi: 10.1038/s41477-023-01367-3 pmid: 36928772
[75]	Gronau I, Hubisz MJ, Gulko B, Danko CG, Siepel A. Bayesian inference of ancient human demography from individual genome sequences. Nat Genet, 2011, 43(10): 1031-1034. doi: 10.1038/ng.937 pmid: 21926973
[76]	Yang ZH. The BPP program for species tree estimation and species delimitation. Curr Zool, 2015, 61(5): 854-865.
[77]	Flouri T, Jiao XY, Huang J, Rannala B, Yang ZH. Efficient Bayesian inference under the multispecies coalescent with migration. Proc Natl Acad Sci USA, 2023, 120(44): e2310708120.
[78]	Wu CI. The genic view of the process of speciation. J Evol Biol, 2001, 14(6): 851-865.
[79]	Feder JL, Nosil P. The efficacy of divergence hitchhiking in generating genomic islands during ecological speciation. Evolution, 2010, 64(6): 1729-1747. doi: 10.1111/j.1558-5646.2010.00943.x pmid: 20624183
[80]	Feder JL, Egan SP, Nosil P. The genomics of speciation-with-gene-flow. Trends Genet, 2012, 28(7): 342-350. doi: 10.1016/j.tig.2012.03.009 pmid: 22520730
[81]	Noor MAF, Bennett SM. Islands of speciation or mirages in the desert? Examining the role of restricted recombination in maintaining species. Heredity (Edinb), 2009, 103(6): 439-444.
[82]	Semenov GA, Safran RJ, Smith CCR, Turbek SP, Mullen SP, Flaxman SM. Unifying theoretical and empirical perspectives on genomic differentiation. Trends Ecol Evol, 2019, 34(11): 987-995. doi: S0169-5347(19)30206-X pmid: 31400942
[83]	Ravinet M, Faria R, Butlin RK, Galindo J, Bierne N, Rafajlović M, Noor MAF, Mehlig B, Westram AM. Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow. J Evol Biol, 2017, 30(8): 1450-1477.
[84]	Han F, Lamichhaney S, Grant BR, Grant PR, Andersson L, Webster MT. Gene flow, ancient polymorphism, and ecological adaptation shape the genomic landscape of divergence among Darwin's finches. Genome Res, 2017, 27(6): 1004-1015. doi: 10.1101/gr.212522.116 pmid: 28442558
[85]	Nachman MW, Payseur BA. Recombination rate variation and speciation: theoretical predictions and empirical results from rabbits and mice. Philos Trans R Soc Lond B Biol Sci, 2012, 367(1587): 409-421.
[86]	Cruickshank TE, Hahn MW. Reanalysis suggests that genomic islands of speciation are due to reduced diversity, not reduced gene flow. Mol Ecol, 2014, 23(13): 3133-3157. doi: 10.1111/mec.12796 pmid: 24845075
[87]	Malinsky M, Challis RJ, Tyers AM, Schiffels S, Terai Y, Ngatunga BP, Miska EA, Durbin R, Genner MJ, Turner GF. Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake. Science, 2015, 350(6267): 1493-1498. doi: 10.1126/science.aac9927 pmid: 26680190
[88]	Fay JC, Wyckoff GJ, Wu CI. Positive and negative selection on the human genome. Genetics, 2001, 158(3): 1227-1234. doi: 10.1093/genetics/158.3.1227 pmid: 11454770
[89]	Sabeti PC, Schaffner SF, Fry B, Lohmueller J, Varilly P, Shamovsky O, Palma A, Mikkelsen TS, Altshuler D, Lander ES. Positive natural selection in the human lineage. Science, 2006, 312(5780): 1614-1620. doi: 10.1126/science.1124309 pmid: 16778047
[90]	Koropoulis A, Alachiotis N, Pavlidis P. Detecting positive selection in populations using genetic data. Methods Mol Biol, 2020, 2090: 87-123. doi: 10.1007/978-1-0716-0199-0_5 pmid: 31975165
[91]	Hudson RR, Kreitman M, Aguadé M. A test of neutral molecular evolution based on nucleotide data. Genetics, 1987, 116(1): 153-159. doi: 10.1093/genetics/116.1.153 pmid: 3110004
[92]	McDonald JH, Kreitman M. Adaptive protein evolution at the Adh locus in Drosophila. Nature, 1991, 351(6328): 652-654.
[93]	Chen H, Patterson N, Reich D. Population differentiation as a test for selective sweeps. Genome Res, 2010, 20(3): 393-402. doi: 10.1101/gr.100545.109 pmid: 20086244
[94]	Sabeti PC, Reich DE, Higgins JM, Levine HZP, Richter DJ, Schaffner SF, Gabriel SB, Platko JV, Patterson NJ, McDonald GJ, Ackerman HC, Campbell SJ, Altshuler D, Cooper R, Kwiatkowski D, Ward R, Lander ES. Detecting recent positive selection in the human genome from haplotype structure. Nature, 2002, 419(6909): 832-837.
[95]	Voight BF, Kudaravalli S, Wen XQ, Pritchard JK. A map of recent positive selection in the human genome. PLoS Biol, 2006, 4(3): e72.
[96]	Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie XH, Byrne EH, McCarroll SA, Gaudet R, Schaffner SF, Lander ES, International HapMap Consortium, Frazer KA, Ballinger DG, Cox DR, Hinds DA, Stuve LL, Gibbs RA, Belmont JW, Boudreau A, Hardenbol P, Leal SM, Pasternak S, Wheeler DA, Willis TD, Yu FL, Yang HM, Zeng CQ, Gao Y, Hu HR, Hu WT, Li CH, Lin W, Liu SQ, Pan H, Tang XL, Wang J, Wang W, Yu J, Zhang B, Zhang QR, Zhao HB, Zhao H, Zhou J, Gabriel SB, Barry R, Blumenstiel B, Camargo A, Defelice M, Faggart M, Goyette M, Gupta S, Moore J, Nguyen H, Onofrio RC, Parkin M, Roy J, Stahl E, Winchester E, Ziaugra L, Altshuler D, Shen Y, Yao ZJ, Huang W, Chu X, He YG, Jin L, Liu YF, Shen YY, Sun WW, Wang HF, Wang Y, Wang Y, Xiong XY, Xu L, Waye MMY, Tsui SKW, Xue H, Wong JTF, Galver LM, Fan JB, Gunderson K, Murray SS, Oliphant AR, Chee MS, Montpetit A, Chagnon F, Ferretti V, Leboeuf M, Olivier JF, Phillips MS, Roumy S, Sallée C, Verner A, Hudson TJ, Kwok PY, Cai DM, Koboldt DC, Miller RD, Pawlikowska L, Taillon-Miller P, Xiao M, Tsui LC, Mak W, Song YQ, Tam PKH, Nakamura Y, Kawaguchi T, Kitamoto T, Morizono T, Nagashima A, Ohnishi Y, Sekine A, Tanaka T, Tsunoda T, Deloukas P, Bird CP, Delgado M, Dermitzakis ET, Gwilliam R, Hunt S, Morrison J, Powell D, Stranger BE, Whittaker P, Bentley DR, Daly MJ, Barrett J, Chretien YR, Maller J, McCarroll S, Patterson N, Pe'er I, Price A, Purcell S, Richter DJ, Sabeti P, Saxena R, Schaffner SF, Sham PC, Varilly P, Altshuler D, Stein LD, Krishnan L, Smith AV, Tello-Ruiz MK, Thorisson GA, Chakravarti A, Chen PE, Cutler DJ, Kashuk CS, Lin S, Abecasis GR, Guan WH, Li Y, Munro HM, Steve Qin Z, Thomas DJ, McVean G, Auton A, Bottolo L, Cardin N, Eyheramendy S, Freeman C, Marchini J, Myers S, Spencer C, Stephens M, Donnelly P, Cardon LR, Clarke G, Evans DM, Morris AP, Weir BS, Tsunoda T, Johnson TA, Mullikin JC, Sherry ST, Feolo M, Skol A, Zhang HC, Zeng CQ, Zhao H, Matsuda I, Fukushima Y, Macer DR, Suda E, Rotimi CN, Adebamowo CA, Ajayi I, Aniagwu T, Marshall PA, Nkwodimmah C, Royal CDM, Leppert MF, Dixon M, Peiffer A, Qiu RZ, Kent A, Kato K, Niikawa N, Adewole IF, Knoppers BM, Foster MW, Clayton EW, Watkin J, Gibbs RA, Belmont JW, Muzny D, Nazareth L, Sodergren E, Weinstock GM, Wheeler DA, Yakub I, Gabriel SB, Onofrio RC, Richter DJ, Ziaugra L, Birren BW, Daly MJ, Altshuler D, Wilson RK, Fulton LL, Rogers J, Burton J, Carter NP, Clee CM, Griffiths M, Jones MC, McLay K, Plumb RW, Ross MT, Sims SK, Willey DL, Chen Z, Han H, Kang L, Godbout M, Wallenburg JC, L'Archevêque P, Bellemare G, Saeki K, Wang HG, An DC, Fu HB, Li Q, Wang Z, Wang RW, Holden AL, Brooks LD, McEwen JE, Guyer MS, Wang VO, Peterson JL, Shi M, Spiegel J, Sung LM, Zacharia LF, Collins FS, Kennedy K, Jamieson R, Stewart J. Genome-wide detection and characterization of positive selection in human populations, Nature, 2007, 449(7164): 913-918.
[97]	Zeng J, de Vlaming R, Wu Y, Robinson MR, Lloyd-Jones LR, Yengo L, Yap CX, Xue AL, Sidorenko J, McRae AF, Powell JE, Montgomery GW, Metspalu A, Esko T, Gibson G, Wray NR, Visscher PM, Yang J. Signatures of negative selection in the genetic architecture of human complex traits. Nat Genet, 2018, 50(5): 746-753. doi: 10.1038/s41588-018-0101-4 pmid: 29662166
[98]	Stebbins GL. Chromosomal Evolution in Higher Plants. London: AddisonWesley, 1971.
[99]	Grant V. Plant Speciation. New York: Columbia University Press, 1981.
[100]	Mallet J. Hybrid speciation. Nature, 2007, 446(7133): 279-283.
[101]	Abbott R, Albach D, Ansell S, Arntzen JW, Baird SJE, Bierne N, Boughman J, Brelsford A, Buerkle CA, Buggs R, Butlin RK, Dieckmann U, Eroukhmanoff F, Grill A, Cahan SH, Hermansen JS, Hewitt G, Hudson AG, Jiggins C, Jones J, Keller B, Marczewski T, Mallet J, Martinez-Rodriguez P, Möst M, Mullen S, Nichols R, Nolte AW, Parisod C, Pfennig K, Rice AM, Ritchie MG, Seifert B, Smadja CM, Stelkens R, Szymura JM, Väinölä R, Wolf JBW, Zinner D. Hybridization and speciation. J Evol Biol, 2013, 26(2): 229-246.
[102]	Wu SD, Wang Y, Wang ZF, Shrestha N, Liu JQ. Species divergence with gene flow and hybrid speciation on the Qinghai-Tibet Plateau. New Phytol, 2022, 234(2): 392-404. doi: 10.1111/nph.17956 pmid: 35020198
[103]	Chen ZJ. Molecular mechanisms of polyploidy and hybrid vigor. Trends Plant Sci, 2010, 15(2): 57-71. doi: 10.1016/j.tplants.2009.12.003 pmid: 20080432
[104]	Chen ZJ. Genomic and epigenetic insights into the molecular bases of heterosis. Nat Rev Genet, 2013, 14(7): 471-482. doi: 10.1038/nrg3503 pmid: 23752794
[105]	Wang ZF, Kang MH, Li JL, Zhang ZY, Wang YF, Chen CL, Yang YZ, Liu JQ. Genomic evidence for homoploid hybrid speciation between ancestors of two different genera. Nat Commun, 2022, 13(1): 1987. doi: 10.1038/s41467-022-29643-4 pmid: 35418567
[106]	Rosser N, Seixas F, Queste LM, Cama B, Mori-Pezo R, Kryvokhyzha D, Nelson M, Waite-Hudson R, Goringe M, Costa M, Elias M, Freitas AVL, Joron M, Kozak K, Lamas G, Martins ARP, McMillan WO, Ready J, Rueda-Muñoz N, Salazar C, Salazar P, Schulz S, Shirai LT, Silva-Brandão KL, Mallet J, Dasmahapatra KK. Hybrid speciation driven by multilocus introgression of ecological traits. Nature, 2024, 628(8009): 811-817.
[107]	Schumer M, Rosenthal GG, Andolfatto P. How common is homoploid hybrid speciation? Evolution, 2014, 68(6): 1553-1560. doi: 10.1111/evo.12399 pmid: 24620775
[108]	Schumer M, Rosenthal GG, Andolfatto P. What do we mean when we talk about hybrid speciation? Heredity, 2018, 120(4): 379-382. doi: 10.1038/s41437-017-0036-z pmid: 29302049
[109]	Yan X, Shi GH, Sun M, Shan SC, Chen RZ, Li RH, Wu SL, Zhou Z, Li YH, Liu ZH, Hu YH, Liu ZJ, Soltis PS, Zhang JQ, Soltis DE, Ning GG, Bao MZ. Genome evolution of the ancient hexaploid Platanus × acerifolia (London planetree). Proc Natl Acad Sci USA, 2024, 121(24): e2319679121.
[110]	Wang DY, Xu XT, Zhang HY, Xi ZX, Abbott RJ, Fu J, Liu JQ. Abiotic niche divergence of hybrid species from their progenitors. Am Nat, 2022, 200(5): 634-645.
[111]	Li JL, Milne RI, Ru DF, Miao JB, Tao WJ, Zhang L, Xu JJ, Liu JQ, Mao KS. Allopatric divergence and hybridization within Cupressus chengiana (Cupressaceae), a threatened conifer in the northern Hengduan Mountains of western China. Mol Ecol, 2020, 29(7): 1250-1266.
[112]	Maerki D, Hoch J. Taxonomy of the cypresses of Sichuan and Gansu. Bull Cupressus Conservation Proj, 2020, 9(1): 3-12.
[113]	Hu L, Long J, Lin Y, Gu ZR, Su H, Dong XM, Lin ZZ, Xiao Q, Batbayar N, Bold B, Deutschová L, Ganusevich S, Sokolov V, Sokolov A, Patel HR, Waters PD, Graves JAM, Dixon A, Pan SK, Zhan XJ. Arctic introgression and chromatin regulation facilitated rapid Qinghai-Tibet Plateau colonization by an avian predator. Nat Commun, 2022, 13(1): 6413. doi: 10.1038/s41467-022-34138-3 pmid: 36302769
[114]	Wu H, Wang ZF, Zhang YX, Frantz L, Roos C, Irwin DM, Zhang CL, Liu XF, Wu DD, Huang S, Gu TT, Liu JQ, Yu L. Hybrid origin of a primate, the gray snub-nosed monkey. Science, 2023, 380(6648): eabl4997.
[115]	Sukumaran J, Holder MT. DendroPy: a python library for phylogenetic computing. Bioinformatics, 2010, 26(12): 1569-1571. doi: 10.1093/bioinformatics/btq228 pmid: 20421198
[116]	Moreno MA, Holder MT, Sukumaran J. DendroPy 5: a mature python library for phylogenetic computing. arXiv, 2024, 2405: 14120.
[117]	Edelman NB, Frandsen PB, Miyagi M, Clavijo B, Davey J, Dikow RB, García-Accinelli G, Van Belleghem SM, Patterson N, Neafsey DE, Challis R, Kumar S, Moreira GRP, Salazar C, Chouteau M, Counterman BA, Papa R, Blaxter M, Reed RD, Dasmahapatra KK, Kronforst M, Joron M, Jiggins CD, McMillan WO, Palma FD, Blumberg AJ, Wakeley J, Jaffe D, Mallet J. Genomic architecture and introgression shape a butterfly radiation. Science, 2019, 366(6465): 594-599. doi: 10.1126/science.aaw2090 pmid: 31672890
[118]	Ma PF, Liu YL, Guo C, Jin GH, Guo ZH, Mao L, Yang YZ, Niu LZ, Wang YJ, Clark LG, Kellogg EA, Xu ZC, Ye XY, Liu JX, Zhou MY, Luo Y, Yang Y, Soltis DE, Bennetzen JL, Soltis PS, Li DZ. Genome assemblies of 11 bamboo species highlight diversification induced by dynamic subgenome dominance. Nat Genet, 2024, 56(4): 710-720.
[119]	Du K, Ricci JMB, Lu Y, Garcia-Olazabal M, Walter RB, Warren WC, Dodge TO, Schumer M, Park H, Meyer A, Schartl M. Phylogenomic analyses of all species of swordtail fishes (genus Xiphophorus) show that hybridization preceded speciation. Nat Commun, 2024, 15(1): 6609.
[120]	Jia DR, Wang YJ, Liu TL, Wu GL, Kou YX, Cheng K, Liu JQ. Diploid hybrid origin of Hippophaë gyantsensis (Elaeagnaceae) in the western Qinghai-Tibet Plateau. Biol J Linn Soc, 2016, 117(4): 658-671.
[121]	Pool JE, Nielsen R. Inference of historical changes in migration rate from the lengths of migrant tracts. Genetics, 2009, 181(2): 711-719. doi: 10.1534/genetics.108.098095 pmid: 19087958
[122]	Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai WW, Fritz MHY, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prüfer T, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Ž, Gušic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PLF, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S. A draft sequence of the Neandertal genome. Science, 2010, 328(5979): 710-722. doi: 10.1126/science.1188021 pmid: 20448178
[123]	The Heliconius Genome Consortium. Butterfly genome reveals promiscuous exchange of mimicry adaptations among species. Nature, 2012, 487(7405): 94-98.
[124]	Martin SH, Davey JW, Jiggins CD. Evaluating the use of ABBA-BABA statistics to locate introgressed loci. Mol Biol Evol, 2015, 32(1): 244-257. doi: 10.1093/molbev/msu269 pmid: 25246699
[125]	Pease JB, Hahn MW. Detection and polarization of introgression in a five-taxon phylogeny. Syst Biol, 2015, 64(4): 651-662. doi: 10.1093/sysbio/syv023 pmid: 25888025
[126]	Pickrell JK, Pritchard JK. Inference of population splits and mixtures from genome-wide allele frequency data. PLoS Genet, 2012, 8(11): e1002967.
[127]	Than C, Ruths D, Nakhleh L. PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships. BMC Bioinformatics, 2008, 9: 322. doi: 10.1186/1471-2105-9-322 pmid: 18662388
[128]	Solís-Lemus C, Bastide P, Ané C. PhyloNetworks: a package for phylogenetic networks. Mol Biol Evol, 2017, 34(12): 3292-3298. doi: 10.1093/molbev/msx235 pmid: 28961984
[129]	Reich D, Thangaraj K, Patterson N, Price AL, Singh L. Reconstructing Indian population history. Nature, 2009, 461(7263): 489-494.
[130]	Blischak PD, Chifman J, Wolfe AD, Kubatko LS. HyDe: a python package for genome-scale hybridization detection. Syst Biol, 2018, 67(5): 821-829. doi: 10.1093/sysbio/syy023 pmid: 29562307
[131]	Dias-Alves T, Mairal J, Blum MGB. Loter: a software package to infer local ancestry for a wide range of species. Mol Biol Evol, 2018, 35(9): 2318-2326. doi: 10.1093/molbev/msy126 pmid: 29931083
[132]	Zhang BL, Chen W, Wang ZF, Pang W, Luo MT, Wang S, Shao Y, He WQ, Deng Y, Zhou L, Chen JW, Yang MM, Wu YJ, Wang L, Fernández-Bellon H, Molloy S, Meunier H, Wanert F, Kuderna L, Marques-Bonet T, Roos C, Qi XG, Li M, Liu ZJ, Schierup MH, Cooper DN, Liu JQ, Zheng YT, Zhang GJ, Wu DD. Comparative genomics reveals the hybrid origin of a macaque group. Sci Adv, 2023, 9(22): eadd3580.
[133]	Zou TT, Kuang WM, Yin TT, Frantz L, Zhang C, Liu JQ, Wu H, Yu L. Uncovering the enigmatic evolution of bears in greater depth: the hybrid origin of the Asiatic black bear. Proc Natl Acad Sci USA, 2022, 119(31): e2120307119.
[134]	Schumer M, Cui RF, Rosenthal GG, Andolfatto P. Reproductive isolation of hybrid populations driven by genetic incompatibilities. PLoS Genet, 2015, 11(3): e1005041.
[135]	Blanckaert A, Bank C. In search of the Goldilocks zone for hybrid speciation. PLoS Genet, 2018, 14(9): e1007613.
[136]	Van de Peer Y, Mizrachi E, Marchal K. The evolutionary significance of polyploidy. Nat Rev Genet, 2017, 18(7): 411-424. doi: 10.1038/nrg.2017.26 pmid: 28502977
[137]	Lichman BR, Godden GT, Buell CR. Gene and genome duplications in the evolution of chemodiversity: perspectives from studies of Lamiaceae. Curr Opin Plant Biol, 2020, 55: 74-83. doi: S1369-5266(20)30035-2 pmid: 32344371
[138]	Comai L. The advantages and disadvantages of being polyploid. Nat Rev Genet, 2005, 6(11): 836-846. doi: 10.1038/nrg1711 pmid: 16304599
[139]	Fang Z, Morrell PL. Domestication: polyploidy boosts domestication. Nat Plants, 2016, 2: 16116. doi: 10.1038/nplants.2016.116 pmid: 28221341
[140]	Song XM, Wei YP, Xiao D, Gong K, Sun PC, Ren YM, Yuan JQ, Wu T, Yang QH, Li XY, Nie FL, Li N, Feng SY, Pei QY, Yu T, Zhang CW, Liu TK, Wang XY, Yang JH. Brassica carinata genome characterization clarifies U’s triangle model of evolution and polyploidy in Brassica. Plant Physiol, 2021, 186(1): 388-406.
[141]	Marcussen T, Sandve SR, Heier L, Spannagl M, Pfeifer M, International Wheat Genome Sequencing Consortium, Jakobsen KS, Wulff BBH, Steuernagel B, Mayer KFX, Olsen OA. Ancient hybridizations among the ancestral genomes of bread wheat. Science, 2014, 345(6194): 1250092.
[142]	Jiao YN, Wickett NJ, Ayyampalayam S, Chanderbali AS, Landherr L, Ralph PE, Tomsho LP, Hu Y, Liang HY, Soltis PS, Soltis DE, Clifton SW, Schlarbaum SE, Schuster SC, Ma H, Leebens-Mack J, dePamphilis CW. Ancestral polyploidy in seed plants and angiosperms. Nature, 2011, 473(7345): 97-100.
[143]	Soltis PS, Soltis DE. The role of hybridization in plant speciation. Annu Rev Plant Biol, 2009, 60(1): 561-588.
[144]	Rice A, Šmarda P, Novosolov M, Drori M, Glick L, Sabath N, Meiri S, Belmaker J, Mayrose I. The global biogeography of polyploid plants. Nat Ecol Evol, 2019, 3(2): 265-273. doi: 10.1038/s41559-018-0787-9 pmid: 30697006
[145]	Wang J, Dong SY, Yang LH, Harris A, Schneider H, Kang M. Allopolyploid speciation accompanied by gene flow in a tree fern. Mol Biol Evol, 2020, 37(9): 2487-2502. doi: 10.1093/molbev/msaa097 pmid: 32302390
[146]	Li FP, Hou ZW, Xu SQ, Han DL, Li B, Hu HF, Liu JY, Cai SK, Gan ZP, Gu Y, Zhang XF, Zhou XF, Wang SK, Zhao JL, Mei Y, Zhang JS, Wang ZF, Wang JH. Haplotype-resolved genomes of octoploid species in Phyllanthaceae family reveal a critical role for polyploidization and hybridization in speciation. Plant J, 2024, 119(1): 348-363.
[147]	Hu QJ, Ma YZ, Mandáková T, Shi S, Chen CL, Sun PC, Zhang L, Feng LD, Zheng YD, Feng XQ, Yang WJ, Jiang JB, Li T, Zhou PP, Yu QS, Wan DS, Lysak MA, Xi ZX, Nevo E, Liu JQ. Genome evolution of the psammophyte Pugionium for desert adaptation and further speciation. Proc Natl Acad Sci USA, 2021, 118(42): e2025711118.
[148]	Luo X, Hu QJ, Zhou PP, Zhang D, Wang Q, Abbott RJ, Liu JQ. Chasing ghosts: allopolyploid origin of Oxyria sinensis (Polygonaceae) from its only diploid congener and an unknown ancestor. Mol Ecol, 2017, 26(11): 3037-3049.
[149]	Mu WJ, Li KX, Yang YZ, Breiman A, Lou SL, Yang J, Wu Y, Wu S, Liu JQ, Nevo E, Catalan P. Scattered differentiation of unlinked loci across the genome underlines ecological divergence of the selfing grass Brachypodium stacei. Proc Natl Acad Sci USA, 2023, 120(45): e2304848120.
[150]	Mu WJ, Li KX, Yang YZ, Breiman A, Yang J, Wu Y, Zhu MJ, Wang S, Catalan P, Nevo E, Liu JQ. Subgenomic stability of progenitor genomes during repeated allotetraploid origins of the same grass Brachypodium hybridum. Mol Biol Evol, 2023, 40(12): msad259.
[151]	Chen ZJ, Sreedasyam A, Ando A, Song QX, De Santiago LM, Hulse-Kemp AM, Ding MQ, Ye WX, Kirkbride RC, Jenkins J, Plott C, Lovell J, Lin YM, Vaughn R, Liu B, Simpson S, Scheffler BE, Wen L, Saski CA, Grover CE, Hu GJ, Conover JL, Carlson JW, Shu SQ, Boston LB, Williams M, Peterson DG, McGee K, Jones DC, Wendel JF, Stelly DM, Grimwood J, Schmutz J. Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement. Nat Genet, 2020, 52(5): 525-533.
[152]	Kang L, Qian LW, Zheng M, Chen LY, Chen H, Yang L, You L, Yang B, Yan ML, Gu YG, Wang TY, Schiessl SV, An H, Blischak P, Liu XJ, Lu HF, Zhang DW, Rao Y, Jia DH, Zhou DG, Xiao HG, Wang YG, Xiong XH, Mason AS, Chris Pires J, Snowdon RJ, Hua W, Liu ZS. Genomic insights into the origin, domestication and diversification of Brassica juncea. Nat Genet, 2021, 53(9): 1392-1402. doi: 10.1038/s41588-021-00922-y pmid: 34493868
[153]	Sun PC, Jiao BB, Yang YZ, Shan LX, Li T, Li XN, Xi ZX, Wang XY, Liu JQ. WGDI: a user-friendly toolkit for evolutionary analyses of whole-genome duplications and ancestral karyotypes. Mol Plant, 2022, 15(12): 1841-1851.
[154]	Sun PC, Lu ZQ, Wang ZY, Wang S, Zhao KX, Mei D, Yang J, Yang YZ, Renner SS, Liu JQ. Subgenome-aware analyses reveal the genomic consequences of ancient allopolyploid hybridizations throughout the cotton family. Proc Natl Acad Sci USA, 2024, 121(15): e2313921121.
[155]	Wang XW, Wang HZ, Wang J, Sun RF, Wu J, Liu SY, Bai YQ, Mun JH, Bancroft I, Cheng F, Huang SW, Li XX, Hua W, Wang JY, Wang XY, Freeling M, Pires JC, Paterson AH, Chalhoub B, Wang B, Hayward A, Sharpe AG, Park BS, Weisshaar B, Liu BH, Li B, Liu B, Tong CB, Song C, Duran C, Peng CF, Geng CY, Koh C, Lin CY, Edwards D, Mu DS, Shen D, Soumpourou E, Li F, Fraser F, Conant G, Lassalle G, King GJ, Bonnema G, Tang HB, Wang HP, Belcram H, Zhou HL, Hirakawa H, Abe H, Guo H, Wang H, Jin HZ, Parkin IAP, Batley J, Kim JS, Just J, Li JW, Xu JH, Deng J, Kim JA, Li JP, Yu JY, Meng JL, Wang JP, Min JM, Poulain J, Wang J, Hatakeyama K, Wu K, Wang L, Fang L, Trick M, Links MG, Zhao MX, Jin MN, Ramchiary N, Drou N, Berkman PJ, Cai QL, Huang QF, Li RQ, Tabata S, Cheng SF, Zhang S, Zhang SJ, Huang SM, Sato S, Sun SL, Kwon SJ, Choi SR, Lee TH, Fan W, Zhao X, Tan X, Xu X, Wang Y, Qiu Y, Yin Y, Li YR, Du YC, Liao YC, Lim Y, Narusaka Y, Wang YP, Wang ZY, Li ZY, Wang ZW, Xiong ZY, Zhang ZH, The Brassica rapa Genome Sequencing Project Consortium. The genome of the mesopolyploid crop species Brassica rapa. Nat Genet, 2011, 43(10): 1035-1039.
[156]	Liu SY, Liu YM, Yang XH, Tong CB, Edwards D, Parkin IAP, Zhao MX, Ma JX, Yu JY, Huang SM, Wang XY, Wang JY, Lu K, Fang ZY, Bancroft I, Yang TJ, Hu Q, Wang XF, Yue Z, Li HJ, Yang LF, Wu J, Zhou Q, Wang WX, King GJ, Pires JC, Lu CX, Wu ZY, Sampath P, Wang Z, Guo H, Pan SK, Yang LM, Min JM, Zhang D, Jin DC, Li WS, Belcram H, Tu JX, Guan M, Qi CK, Du DZ, Li JN, Jiang LC, Batley J, Sharpe AG, Park BS, Ruperao P, Cheng F, Waminal NE, Huang Y, Dong CH, Wang L, Li JP, Hu ZY, Zhuang M, Huang Y, Huang JY, Shi JQ, Mei DS, Liu J, Lee TH, Wang JP, Jin HZ, Li ZY, Li X, Zhang JF, Xiao L, Zhou YM, Liu ZS, Liu XQ, Qin R, Tang X, Liu WB, Wang YP, Zhang YY, Lee J, Kim HH, Denoeud F, Xu X, Liang XM, Hua W, Wang XW, Wang J, Chalhoub B, Paterson AH. The Brassica oleracea genome reveals the asymmetrical evolution of polyploid genomes. Nat Commun, 2014, 5(1): 3930.
[157]	Schnable JC, Springer NM, Freeling M. Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. Proc Natl Acad Sci USA, 2011, 108(10): 4069-4074.
[158]	Cheng F, Wu J, Cai X, Liang JL, Freeling M, Wang XW. Gene retention, fractionation and subgenome differences in polyploid plants. Nat Plants, 2018, 4(5): 258-268. doi: 10.1038/s41477-018-0136-7 pmid: 29725103
[159]	Li ZJ, Zhang YY, Ding CH, Chen Y, Wang HY, Zhang JY, Ying SB, Wang MY, Zhang RZ, Liu JJ, Xie YL, Tang TF, Diao HS, Ye LH, Zhuang YL, Teng W, Zhang B, Huang L, Tong YP, Zhang WL, Li GY, Benhamed M, Dong ZC, Gou JY, Zhang YJ. LHP1-mediated epigenetic buffering of subgenome diversity and defense responses confers genome plasticity and adaptability in allopolyploid wheat. Nat Commun, 2023, 14(1): 7538. doi: 10.1038/s41467-023-43178-2 pmid: 37985755
[160]	Song QX, Zhang TZ, Stelly DM, Chen ZJ. Epigenomic and functional analyses reveal roles of epialleles in the loss of photoperiod sensitivity during domestication of allotetraploid cottons. Genome Biol, 2017, 18(1): 99. doi: 10.1186/s13059-017-1229-8 pmid: 28558752
[161]	Luo J, Chai J, Wen YL, Tao M, Lin GL, Liu XC, Ren L, Chen ZY, Wu SG, Li SN, Wang YD, Qin QB, Wang S, Gao Y, Huang F, Wang L, Ai C, Wang XB, Li LW, Ye CX, Yang HM, Luo M, Chen J, Hu H, Yuan LJ, Zhong L, Wang J, Xu J, Du ZL, Ma ZS, Murphy RW, Meyer A, Gui JF, Xu P, Ruan J, Chen ZJ, Liu SJ, Lu XM, Zhang YP. From asymmetrical to balanced genomic diversification during rediploidization: subgenomic evolution in allotetraploid fish. Sci Adv, 2020, 6(22): eaaz7677.
[162]	Li LF, Liu B. The roles of epigenetic variation in plant hybridization and polyploidization. Biodiversity Sci, 2017, 25(6): 600-607.
	李霖锋, 刘宝. 表观遗传变异在植物杂交与多倍化过程中的作用. 生物多样性, 2017, 25(6): 600-607. doi: 10.17520/biods.2017028
[163]	Li ZH, Lu X, Gao Y, Liu SJ, Tao M, Xiao H, Qiao YQ, Zhang YP, Luo J. Polyploidization and epigenetics. Chin Sci Bull, 2011, 56(3): 245-252.
[164]	Yant L, Hollister JD, Wright KM, Arnold BJ, Higgins JD, Franklin FCH, Bomblies K. Meiotic adaptation to genome duplication in Arabidopsis arenosa. Curr Biol, 2013, 23(21): 2151-2156.
[165]	Chat J, Chalak L, Petit RJ. Strict paternal inheritance of chloroplast DNA and maternal inheritance of mitochondrial DNA in intraspecific crosses of kiwifruit. Theor Appl Genet, 1999, 99: 314-322.
[166]	Cipriani G, Testolin R, Morgante M. Paternal inheritance of plastids in interspecific hybrids of the genus Actinidia revealed by PCR-amplification of chloroplast DNA fragments. Mol Gen Genet, 1995, 247: 693-697.
[167]	Liu YF, Li DW, Zhang Q, Song C, Zhong CH, Zhang XD, Wang Y, Yao XH, Wang ZP, Zeng SH, Wang Y, Guo YT, Wang SB, Li XW, Li L, Liu CY, McCann HC, He WM, Niu Y, Chen M, Du LW, Gong JJ, Datson PM, Hilario E, Huang HW. Rapid radiations of both kiwifruit hybrid lineages and their parents shed light on a two-layer mode of species diversification. New Phytol, 2017, 215(2): 877-890. doi: 10.1111/nph.14607 pmid: 28543189
[168]	Cheng HY, Concepcion GT, Feng XW, Zhang HW, Li H. Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm. Nat Methods, 2021, 18(2): 170-175.
[169]	Zhang XT, Zhang SC, Zhao Q, Ming R, Tang HB. Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data. Nat Plants, 2019, 5(8): 833-845. doi: 10.1038/s41477-019-0487-8 pmid: 31383970
[170]	Zeng XF, Yi ZL, Zhang XT, Du YH, Li Y, Zhou ZQ, Chen SJ, Zhao HJ, Yang S, Wang YB, Chen GA. Chromosome-level scaffolding of haplotype-resolved assemblies using Hi-C data without reference genomes. Nat Plants, 2024, 10(8): 1184-1200. doi: 10.1038/s41477-024-01755-3 pmid: 39103456
[171]	Jiang ZJ, Peng ZX, Wei ZY, Sun JH, Luo YJ, Bie LZ, Zhang GQ, Wang Y. A deep learning-based method enables the automatic and accurate assembly of chromosome-level genomes. Nucleic Acids Res, 2024, 17: gkae789.
[172]	Rautiainen M, Nurk S, Walenz BP, Logsdon GA, Porubsky D, Rhie A, Eichler EE, Phillippy AM, Koren S. Telomere-to-telomere assembly of diploid chromosomes with Verkko. Nat Biotechnol, 2023, 41(10): 1474-1482. doi: 10.1038/s41587-023-01662-6 pmid: 36797493
[173]	Chen HT, Zeng Y, Yang YZ, Huang LL, Tang BL, Zhang H, Hao F, Liu W, Li YH, Liu YB, Zhang XS, Zhang R, Zhang YS, Li YX, Wang K, He H, Wang ZK, Fan GY, Yang H, Bao AK, Shang ZH, Chen JH, Wang W, Qiu Q. Allele-aware chromosome-level genome assembly and efficient transgene-free genome editing for the autotetraploid cultivated alfalfa. Nat Commun, 2020, 11(1): 2494. doi: 10.1038/s41467-020-16338-x pmid: 32427850
[174]	Zhang Q, Qi YY, Pan HR, Tang HB, Wang G, Hua XT, Wang YJ, Lin LY, Li Z, Li YH, Yu F, Yu ZH, Huang YJ, Wang TY, Ma PP, Dou MJ, Sun ZY, Wang YB, Wang HB, Zhang XT, Yao W, Wang YT, Liu XL, Wang MJ, Wang JP, Deng ZH, Xu JS, Yang QH, Liu ZJ, Chen BS, Zhang MQ, Ming R, Zhang JS. Genomic insights into the recent chromosome reduction of autopolyploid sugarcane Saccharum spontaneum. Nat Genet, 2022, 54(6): 885-896. doi: 10.1038/s41588-022-01084-1 pmid: 35654976
[175]	Bao ZG, Li CH, Li GC, Wang P, Peng Z, Cheng L, Li HB, Zhang ZY, Li YY, Huang W, Ye MW, Dong DF, Cheng ZK, VanderZaag P, Jacobsen E, Bachem CWB, Dong SM, Zhang CZ, Huang SW, Zhou Q. Genome architecture and tetrasomic inheritance of autotetraploid potato. Mol Plant, 2022, 15(7): 1211-1226. doi: 10.1016/j.molp.2022.06.009 pmid: 35733345
[176]	Qiu Q, Wang LZ, Wang K, Yang YZ, Ma T, Wang ZF, Zhang X, Ni ZQ, Hou FJ, Long RJ, Abbott R, Lenstra J, Liu JQ. Yak whole-genome resequencing reveals domestication signatures and prehistoric population expansions. Nat Commun, 2015, 6(1): 10283.
[177]	Liu XF, Liu WY, Lenstra JA, Zheng ZY, Wu XY, Yang J, Li BW, Yang YZ, Qiu Q, Liu HY, Li KX, Liang CN, Guo X, Ma XM, Abbott RJ, Kang MH, Yan P, Liu JQ. Evolutionary origin of genomic structural variations in domestic yaks. Nat Commun, 2023, 14(1): 5617.

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