细胞核质互作形成的生态与进化过程分析
|
摘要
细胞核质互作是形成真核生物细胞的必经步骤,细胞核质基因组在遗传方式、突变率、倍数、重组、有效群体数等方面存在根本差异,这些差异必然与生态和进化过程互作,影响和参与维持核质基因组的协同进化.本文从生态与进化过程深度阐述了形成核质互作的理论和实际研究进展,包括核质基因连锁不平衡的进化理论、核质互作效应检测、核质互作的分子证据、核质基因渐渗与遗传谱系的差异、核质不亲和与物种形成等.理论和实际结果显示,基本进化动力(突变、选择、漂变及迁移)可不同程度地改变核质互作效应.今后研究重点就是基于核质全基因组序列筛选核质互作位点,分析位点的遗传进化属性,揭示核质互作形成的分子机制;理论上解析与核质根本差异都有互作的交配系统的角色,分析交配系统怎样影响群体核质不亲和及其导致的物种形成过程.
Cytonuclear interaction is an essential step in originating an eukaryotic cell. There are fundamental differences between cytoplasimic and nuclear genomes in the mode of inheritance, mutation rate, ploidy, gene recombination, and effective population size. These differences inevitably interact with ecological and evolutionary processes, and are involved in maintaining cytonuclear interactions and their coevolution. Here we review in depth the theories of cytonuclear interactions and the empirical research progress from the perspective of ecology and evolutionary processes, including the evolutionary theory of cytonuclear linkage disequilibrium, methods for detecting cytonuclear interaction, molecular evidence of cytonuclear interactions, and the discordance in cytonuclear introgression and in phylogenetic trees among species, cytonuclear incompatibility, and speciation. Theoretical studies and empirical evidence show that the basic evolutionary forces(mutation, selection, drift and migration) can change cytonuclear interactions to different extents. Future studies would concentrate on(i) screening loci of cytonuclear interactions at the genome level, testing the evolutionary attributes of significant loci, and analyzing molecular mechanisms of cytonuclear interactions;(ii) addressing the role of mating system that interacts with the fundamental differences between cytoplasmic and nuclear genomes, analyzing how mating system affects cytonuclear incompatibility at the population level and the consequence of leading to speciation.
Cytonuclear interaction is an essential step in originating an eukaryotic cell. There are fundamental differences between cytoplasimic and nuclear genomes in the mode of inheritance, mutation rate, ploidy, gene recombination, and effective population size. These differences inevitably interact with ecological and evolutionary processes, and are involved in maintaining cytonuclear interactions and their coevolution. Here we review in depth the theories of cytonuclear interactions and the empirical research progress from the perspective of ecology and evolutionary processes, including the evolutionary theory of cytonuclear linkage disequilibrium, methods for detecting cytonuclear interaction, molecular evidence of cytonuclear interactions, and the discordance in cytonuclear introgression and in phylogenetic trees among species, cytonuclear incompatibility, and speciation. Theoretical studies and empirical evidence show that the basic evolutionary forces(mutation, selection, drift and migration) can change cytonuclear interactions to different extents. Future studies would concentrate on(i) screening loci of cytonuclear interactions at the genome level, testing the evolutionary attributes of significant loci, and analyzing molecular mechanisms of cytonuclear interactions;(ii) addressing the role of mating system that interacts with the fundamental differences between cytoplasmic and nuclear genomes, analyzing how mating system affects cytonuclear incompatibility at the population level and the consequence of leading to speciation.
引文
1 Brown J R, Doolittle W F. Archaea and the prokaryote-to-eukaryote transition. Microbiol Mol Rev, 1997, 61:456–502
2 Archibald J M, Keeling P J. Recycled plastids:A “green movement” in eukaryotic evolution. Trends Genets, 2002, 18:577–584
3 Dyall S D, Brown M T, Johnson P J. Ancient invasions:From endosymbionts to organelles. Science, 2004, 304:253–257
4 Rand D M, Haney R A, Fry A J. Cytonuclear coevolution:The genomics of cooperation. Trends Ecol Evol, 2004, 19:645–653
5 Chou J Y, Leu J Y. Speciation through cytonuclear incompatibility:Insights from yeast and implications for higher eukaryotes. Bioessays, 2010,32 :401–411
6 Burton R S, Pereira R J, Barreto F S. Cytonuclear genomic interactions and hybrid breakdown. Annu Rev Ecol Evol Syst, 2013, 44:281–302
7 Sloan D B. Using plants to elucidate the mechanisms of cytonuclear co-evolution. New Phytol, 2015, 205:1040–1046
8 Arnold J. Cytonuclear disequilibria in hybrid zones. Annu Rev Ecol Syst, 1993, 24:521–553
9 Scribner K T, Page K S, Bartron M L. Hybridization in freshwater fishes:A review of case studies and cytonuclear methods of biological inference. Rev Fish Biol Fisheries, 2001, 10:293–323
10 Caruso C M, Case A L, Bailey M F. The evolutionary ecology of cytonuclear interactions in angiosperms. Trends Plant Sci, 2012, 17:638–643
11 Datta S, Fu Y X, Arnold J. Dynamics and equilibrium behavior of cytonuclear disequilibria under genetic drift, mutation, and migration. Theor Populat Biol, 1996, 50:298–324
12 Wade M J, Goodnight C J. Cyto-nuclear epistasis:Two-locus random genetic drift in hermaphroditic and dioecious species. Evolution, 2006, 60:643 –659
13 Overath R D, Asmussen M A. The cytonuclear effects of facultative apomixis. Theor Populat Biol, 2000, 58:107–121
14 Asmussen MA, Schnabel A. Comparative effects of pollen and seed migration on the cytonuclear structure of plant populations. I. Maternal cytoplasmic inheritance. Genetics, 1991, 148:639–654
15 Arnold J, Asmussen M A, Avise J C. An epistatic mating system model can produce permanent cytonuclear disequilibria in a hybrid zone. Proc Natl Acad Sci USA, 1988, 85:1893–1896
16 Asmussen M A, Arnold J, Avise J. The effects of assortative mating and migration on cytonuclear associations in hybrid zones. Genetics, 1989,122 :923–934
17 Cruzan M B, Arnold M L. Consequences of cytonuclear epistasis and assortative mating for the genetic structure of hybrid populations. Heredity,1999, 82:36–45
18 Cellino M L, Arnold J. The effects of cytoplasmic male sterility on cytonuclear disequilibria in hybrid zones. Genetica, 1993, 88:37–50
19 Babcock CS, Asmussen MA. Effects of differential selection in the sexes on cytonuclear dynamics:Life stages with sex differences. Genetics,1998, 149:2063–2077
20 Liu R, Asmussen M A. Cytonuclear dynamics in selfing populations under selection. Theor Populat Biol, 2007, 71:445–453
21 Hu X S, Li B. Seed and pollen flow and cline discordance among genes with different modes of inheritance. Heredity, 2002, 88:212–217
22 Hu X S. Barriers to the spread of neutral alleles in the cytonuclear system. Evolution, 2008, 62:2260–2278
23 Hu X S. In the cytonuclear system. Theor Populat Biol, 2010, 77:105–118
24 Hu X S. Mating system and the critical migration rate for swamping selection. Genet Res, 2011, 93:233–254
25 Latta RG, Linhart YB, Mitton JB. Cytonuclear disequilibrium and genetic drift in a natural population of Ponderosa pine. Genetics, 2001,158:843 –885
26 Lu B R, Hui X, Xiao Y, et al. Evolutionary theory of hybridization-introgression:its implication in environmental risk assessment and research of transgene escape(in Chinese). Biodiversity Sci, 2009, 17:362–377[卢宝荣,夏辉,杨箫,等.杂交-渐渗进化理论在转基因逃逸及其环境风险评价和研究中的意义.生物多样性, 2009, 17:362–377]
27 Oleksyk T K, Smith M W, O’Brien S J. Genome-wide scans for footprints of natural selection. Phil Trans R Soc B, 2010, 365:185–205
28 Hu X S. Evolution of zygotic linkage disequilibrium in a finite local population. PLoS ONE, 2013, 8:e80538
29 Hu X S, Yeh F C. Assessing postzygotic isolation using zygotic disequilibria in natural hybrid zones. PLoS ONE, 2014, 9:e100568
30 Datta S. Estimation of selection parameters using multi-generation cytonuclear data. Bio J, 2001, 43:219–233
31 Dean R, Arnold J. Cytonuclear disequilibria in hybrid zones using RAPD markers. Evolution, 1996, 50:1702–1705
32 Basten CJ, Asmussen MA. The exact test for cytonuclear disequilibria. Genetics, 1997, 146:1165–1171
33 Hu XS, Kong FL. A study on the genetic models of combining ability and heterosis of endosperm traits(in Chinese). Acta Agricul Uni Pekinensis, 1992, 18:153–160[胡新生,孔繁玲.胚乳性状配合力模型和杂种优势模型研究.北京农业大学学报, 1992, 18:153–160]
34 Tang Z X, Wang X F, Hu Z Q, et al. Genetic dissection of cytonuclear epistasis in line crosses. Genetics, 2007, 177:669–672
35 Tang Z X, Hu Z Q, Yang Z F, et al. Framework for dissection of complex cytonuclear epistasis by a two-dimensional genome scan. Chin Sci Bull,2012, 57:2675–2680
36 He T, Sa J, Zhong P S, et al. Statistical dissection of cyto-nuclear epistasis subject to genomic imprinting in line crosses. PLoS ONE, 2014, 9:e91702
37 Zeng ZB. Precision mapping of quantitative trait loci. Genetics, 1994, 136:1457–1468
38 Barnard-Kubow K B, McCoy M A, Galloway L F. Biparental chloroplast inheritance leads to rescue from cytonuclear incompatibility. New Phytol, 2017, 213:1466–1476
39 Weir BS. Genetic Data Analysis II. Sunderland:Sinauer Associates, 1996
40 Neiman M, Taylor D R. The causes of mutation accumulation in mitochondrial genomes. Proc R Soc B-Biol Sci, 2009, 276:1201–1209
41 Sloan D B, Triant D A, Wu M, et al. Cytonuclear interactions and relaxed selection accelerate sequence evolution in organelle ribosomes. Mol Biol Evol, 2013, 31:673–682
42 Pett W, Lavrov D V. Cytonuclear interactions in the evolution of animal mitochondrial tRNA metabolism. Genome Biol Evol, 2015, 7:2089–2101
43 Blier P U, Dufresne F, Burton R S. Natural selection and the evolution of mtDNA-encoded peptides:evidence for intergenomic co-adaptation.Trends Genets, 2001, 17:400–406
44 Sehrish T, Symonds V V, Soltis D E, et al. Cytonuclear coordination is not immediate upon allopolyploid formation in Tragopogon miscellus(Asteraceae)allopolyploids. PLoS ONE, 2015, 10:e0144339
45 Wang C G, Chang C T, Gu Y, et al. Cytoplasmic male sterility in plant(in Chinese). Chin J Cell Biol, 2005, 27:525–529[王春国,常彩涛,古瑜,等.植物细胞质雄性不育.中国细胞生物学杂志, 2005, 27:525–529]
46 Li P, Li XH, Zhang F, et al. Studies of cytoplasmic-nuclear interaction in CMS system(in Chinese). Shandong Agr Sci, 2008, 6:36–40[李鹏,李新华,张锋,等.细胞质雄性不育系统中的核质互作研究进展.山东农业科学, 2008, 6:36–40]
47 Fishman L, Willis J H. A cytonuclear incompatibility causes anther sterility in Mimulus hybrids. Evolution, 2006, 60:1372–1381
48 Horn R, Gupta K J, Colombo N. Mitochondrion role in molecular basis of cytoplasmic male sterility. Mitochondrion, 2014, 19:198–205
49 McCauley D E, Olson M S. Do recent findings in plant mitochondrial molecular and population genetics have implications for the study of gynodioecy and cytonuclear conflict? Evolution, 2008, 62:1013–1025
50 Chen L, Liu Y G. Male sterility and fertility restoration in crops. Annu Rev Plant Biol, 2014, 65:579–606
51 Kitazaki K, Arakawa T, Matsunaga M, et al. Post-translational mechanisms are associated with fertility restoration of cytoplasmic male sterility in sugar beet(Beta vulgaris). Plant J, 2015, 83:290–299
52 Chen Z, Zhao N, Li S, et al. Plant mitochondrial genome evolution and cytoplasmic male sterility. Critical Rev Plant Sci, 2017, 36:55–69
53 Bohra A, Jha U C, Adhimoolam P, et al. Cytoplasmic male sterility(CMS)in hybrid breeding in field crops. Plant Cell Rep, 2016, 35:967–993
54 Etterson J R, Keller S R, Galloway L F. Epistatic and cytonuclear interactions govern outbreeding depression in the autotetraploid Campanulastrum americanum. Evolution, 2007, 61:2671–2683
55 Ellison C K, Burton R S. Genotype-dependent variation of mitochondrial transcriptional profiles in interpopulation hybrids. Proc Natl Acad Sci USA, 2008, 105:15831–15836
56 Ellison C K, Burton R S. Cytonuclear conflict in interpopulation hybrids:The role of RNA polymerase in mtDNA transcription and replication. J Evol Biol, 2010, 23:528–538
57 Roux F, Mary-Huard T, Barillot E, et al. Cytonuclear interactions affect adaptive traits of the annual plant Arabidopsis thaliana in the field. Proc Natl Acad Sci USA, 2016, 113:3687–3692
58 Monsen K J, Honchak B M, Locke S E, et al. Cytonuclear disequilibrium in Chrysochus hybrids is not due to patterns of mate choice. J Heredity,2007, 98:325–330
59 Fields P D, McCauley D E, McAssey E V, et al. Patterns of cyto-nuclear linkage disequilibrium in Silene latifolia:Genomic heterogeneity and temporal stability. Heredity, 2014, 112:99–104
60 Gong L, Olson M, Wendel J F. Cytonuclear evolution of Rubisco in four allopolyploid lineages. Mol Biol Evol, 2014, 31:2624–2636
61 Hu Y, Wang X, Zhang X X, et al. Advancing phylogeography with chloroplast DNA markers(in Chinese). Biodiversity Sci, 2019, 27:219–234[胡颖,王茜,张新新,等.叶绿体DNA标记在谱系地理学中的应用研究进展.生物多样性, 2019, 27:219–234]
62 Renoult J P, Kjellberg F, Grout C, et al. Cyto-nuclear discordance in the phylogeny of Ficus section Galoglychia and host shifts in plantpollinator associations. BMC Evol Biol, 2009, 9:248
63 Baraket G, Ben Abdelkrim A, Mars M, et al. Cyto-nuclear discordance in the genetic relationships among Tunisian fig cultivars(Ficus carica L.):Evidence from non coding trnL–trnF and ITS regions of chloroplast and ribosomal DNAs. Sci Horticulturae, 2011, 130:203–210
64 Bruun-Lund S, Clement W L, Kjellberg F, et al. First plastid phylogenomic study reveals potential cyto-nuclear discordance in the evolutionary history of Ficus L.(Moraceae). Mol Phylogenets Evol, 2017, 109:93–104
65 Lee-Yaw J A, Grassa C J, Joly S, et al. An evaluation of alternative explanations for widespread cytonuclear discordance in annual sunflowers(Helianthus). New Phytol, 2019, 221:515–526
66 Huang D I, Hefer C A, Kolosova N, et al. Whole plastome sequencing reveals deep plastid divergence and cytonuclear discordance between closely related balsam poplars, Populus balsamifera and P. trichocarpa(Salicaceae). New Phytol, 2014, 204:693–703
67 Levsen N D, Tiffin P, Olson M S. Pleistocene speciation in the genus Populus(Salicaceae). Systatic Biol, 2012, 61:401–412
68 Freeland J R, Ciotir C, Wensink L, et al. Widespread cytonuclear discordance in narrow-leaved cattail(Typha angustifolia)does not explain the dominance of its invasive hybrid(Typha×glauca). Hydrobiologia, 2017, 792:53–65
69 Pagès M, Bazin E, Galan M, et al. Cytonuclear discordance among Southeast Asian black rats(Rattus rattus complex). Mol Ecol, 2013, 22:1019–1034
70 Mendelson T C, Simons J N. AFLPs resolve cytonuclear discordance and increase resolution among barcheek darters(Percidae:Etheostoma:Catonotus). Mol Phylogenets Evol, 2006, 41:445–453
71 Eto K, Matsui M. Cytonuclear discordance and historical demography of two brown frogs, Rana tagoi and R. sakuraii(Amphibia:Ranidae). Mol Phylogenets Evol, 2014, 79:231–239
72 Roca A L, Georgiadis N, O’Brien S J. Cytonuclear genomic dissociation in African elephant species. Nat Genet, 2005, 37:96–100
73 Pereira R J, Martínez-Solano I, Buckley D. Hybridization during altitudinal range shifts:Nuclear introgression leads to extensive cyto-nuclear discordance in the fire salamander. Mol Ecol, 2016, 25:1551–1565
74 Hunter M E, Johnson N A, Smith B J, et al. Cytonuclear discordance in the Florida Everglades invasive Burmese python(Python bivittatu s)population reveals possible hybridization with the Indian python(P. molurus). Ecol Evol, 2018, 8:9034–9047
75 Echelle A A, Hackler J C, Lack J B, et al. Conservation genetics of the alligator snapping turtle:Cytonuclear evidence of range-wide bottleneck effects and unusually pronounced geographic structure. Conserv Genet, 2010, 11:1375–1387
76 Kindler E, Arlettaz R, Heckel G. Deep phylogeographic divergence and cytonuclear discordance in the grasshopper Oedaleus decorus. Mol Phylogenets Evol, 2012, 65:695–704
77 Lindell J, Méndez-de La Cruz F R, Murphy R W. Deep biogeographical history and cytonuclear discordance in the black-tailed brush lizard(Urosaurus nigricaudus)of Baja California. Biol J Linnean Soc, 2008, 94:89–104
78 Lee-Yaw J A, Jacobs C G C, Irwin D E. Individual performance in relation to cytonuclear discordance in a northern contact zone between longtoed salamander(Ambystoma macrodactylum)lineages. Mol Ecol, 2014, 23:4590–4602
79 Oswald K J, Grady J M, Quattro J M. Cytonuclear patterns of genetic diversity and the intricate evolutionary history of the inland silverside(Menidia beryllina). J Heredity, 2009, 100:526–532
80 Beck E A, Thompson A C, Sharbrough J, et al. Gene flow between Drosophila yakuba and Drosophila santomea in subunit V of cytochrome c oxidase:A potential case of cytonuclear cointrogression. Evolution, 2015, 69:1973–1986
81 Wolf J B. Cytonuclear interactions can favor the evolution of genomic imprinting. Evolution, 2009, 63:1364–1371
82 Barnard-Kubow K B, So N, Galloway L F. Cytonuclear incompatibility contributes to the early stages of speciation. Evolution, 2016, 70:2752–2766
83 Coyne JA, Orr HA. Speciation. Sunderland:Sinauer Associates, Inc., 2004
84 Sambatti J B M, Ortiz-Barrientos D, Baack E J, et al. Ecological selection maintains cytonuclear incompatibilities in hybridizing sunflowers. Ecol Lett, 2008, 11:1082–1091
85 Hu Y C, Zhang Q, Rao G Y, et al. Occurrence of plastids in the sperm cells of Caprifoliaceae:biparental plastid inheritance in angiosperms is unilaterally derived from maternal inheritance. Plant Cell Physiol, 2008, 49:958–968
86 Hu X S. Mating system as a barrier to gene flow. Evolution, 2015, 69:1158–1177
87 Hu X S, Zhang X X, Zhou W, et al. Mating system shifts a species’ range. Evolution, 2019, 73:158–174
88 Otto S P, Marks J C. Mating systems and the evolutionary transition between haploidy and diploidy. Biol J Linnean Soc, 1996, 57:197–218
2 Archibald J M, Keeling P J. Recycled plastids:A “green movement” in eukaryotic evolution. Trends Genets, 2002, 18:577–584
3 Dyall S D, Brown M T, Johnson P J. Ancient invasions:From endosymbionts to organelles. Science, 2004, 304:253–257
4 Rand D M, Haney R A, Fry A J. Cytonuclear coevolution:The genomics of cooperation. Trends Ecol Evol, 2004, 19:645–653
5 Chou J Y, Leu J Y. Speciation through cytonuclear incompatibility:Insights from yeast and implications for higher eukaryotes. Bioessays, 2010,32 :401–411
6 Burton R S, Pereira R J, Barreto F S. Cytonuclear genomic interactions and hybrid breakdown. Annu Rev Ecol Evol Syst, 2013, 44:281–302
7 Sloan D B. Using plants to elucidate the mechanisms of cytonuclear co-evolution. New Phytol, 2015, 205:1040–1046
8 Arnold J. Cytonuclear disequilibria in hybrid zones. Annu Rev Ecol Syst, 1993, 24:521–553
9 Scribner K T, Page K S, Bartron M L. Hybridization in freshwater fishes:A review of case studies and cytonuclear methods of biological inference. Rev Fish Biol Fisheries, 2001, 10:293–323
10 Caruso C M, Case A L, Bailey M F. The evolutionary ecology of cytonuclear interactions in angiosperms. Trends Plant Sci, 2012, 17:638–643
11 Datta S, Fu Y X, Arnold J. Dynamics and equilibrium behavior of cytonuclear disequilibria under genetic drift, mutation, and migration. Theor Populat Biol, 1996, 50:298–324
12 Wade M J, Goodnight C J. Cyto-nuclear epistasis:Two-locus random genetic drift in hermaphroditic and dioecious species. Evolution, 2006, 60:643 –659
13 Overath R D, Asmussen M A. The cytonuclear effects of facultative apomixis. Theor Populat Biol, 2000, 58:107–121
14 Asmussen MA, Schnabel A. Comparative effects of pollen and seed migration on the cytonuclear structure of plant populations. I. Maternal cytoplasmic inheritance. Genetics, 1991, 148:639–654
15 Arnold J, Asmussen M A, Avise J C. An epistatic mating system model can produce permanent cytonuclear disequilibria in a hybrid zone. Proc Natl Acad Sci USA, 1988, 85:1893–1896
16 Asmussen M A, Arnold J, Avise J. The effects of assortative mating and migration on cytonuclear associations in hybrid zones. Genetics, 1989,122 :923–934
17 Cruzan M B, Arnold M L. Consequences of cytonuclear epistasis and assortative mating for the genetic structure of hybrid populations. Heredity,1999, 82:36–45
18 Cellino M L, Arnold J. The effects of cytoplasmic male sterility on cytonuclear disequilibria in hybrid zones. Genetica, 1993, 88:37–50
19 Babcock CS, Asmussen MA. Effects of differential selection in the sexes on cytonuclear dynamics:Life stages with sex differences. Genetics,1998, 149:2063–2077
20 Liu R, Asmussen M A. Cytonuclear dynamics in selfing populations under selection. Theor Populat Biol, 2007, 71:445–453
21 Hu X S, Li B. Seed and pollen flow and cline discordance among genes with different modes of inheritance. Heredity, 2002, 88:212–217
22 Hu X S. Barriers to the spread of neutral alleles in the cytonuclear system. Evolution, 2008, 62:2260–2278
23 Hu X S. In the cytonuclear system. Theor Populat Biol, 2010, 77:105–118
24 Hu X S. Mating system and the critical migration rate for swamping selection. Genet Res, 2011, 93:233–254
25 Latta RG, Linhart YB, Mitton JB. Cytonuclear disequilibrium and genetic drift in a natural population of Ponderosa pine. Genetics, 2001,158:843 –885
26 Lu B R, Hui X, Xiao Y, et al. Evolutionary theory of hybridization-introgression:its implication in environmental risk assessment and research of transgene escape(in Chinese). Biodiversity Sci, 2009, 17:362–377[卢宝荣,夏辉,杨箫,等.杂交-渐渗进化理论在转基因逃逸及其环境风险评价和研究中的意义.生物多样性, 2009, 17:362–377]
27 Oleksyk T K, Smith M W, O’Brien S J. Genome-wide scans for footprints of natural selection. Phil Trans R Soc B, 2010, 365:185–205
28 Hu X S. Evolution of zygotic linkage disequilibrium in a finite local population. PLoS ONE, 2013, 8:e80538
29 Hu X S, Yeh F C. Assessing postzygotic isolation using zygotic disequilibria in natural hybrid zones. PLoS ONE, 2014, 9:e100568
30 Datta S. Estimation of selection parameters using multi-generation cytonuclear data. Bio J, 2001, 43:219–233
31 Dean R, Arnold J. Cytonuclear disequilibria in hybrid zones using RAPD markers. Evolution, 1996, 50:1702–1705
32 Basten CJ, Asmussen MA. The exact test for cytonuclear disequilibria. Genetics, 1997, 146:1165–1171
33 Hu XS, Kong FL. A study on the genetic models of combining ability and heterosis of endosperm traits(in Chinese). Acta Agricul Uni Pekinensis, 1992, 18:153–160[胡新生,孔繁玲.胚乳性状配合力模型和杂种优势模型研究.北京农业大学学报, 1992, 18:153–160]
34 Tang Z X, Wang X F, Hu Z Q, et al. Genetic dissection of cytonuclear epistasis in line crosses. Genetics, 2007, 177:669–672
35 Tang Z X, Hu Z Q, Yang Z F, et al. Framework for dissection of complex cytonuclear epistasis by a two-dimensional genome scan. Chin Sci Bull,2012, 57:2675–2680
36 He T, Sa J, Zhong P S, et al. Statistical dissection of cyto-nuclear epistasis subject to genomic imprinting in line crosses. PLoS ONE, 2014, 9:e91702
37 Zeng ZB. Precision mapping of quantitative trait loci. Genetics, 1994, 136:1457–1468
38 Barnard-Kubow K B, McCoy M A, Galloway L F. Biparental chloroplast inheritance leads to rescue from cytonuclear incompatibility. New Phytol, 2017, 213:1466–1476
39 Weir BS. Genetic Data Analysis II. Sunderland:Sinauer Associates, 1996
40 Neiman M, Taylor D R. The causes of mutation accumulation in mitochondrial genomes. Proc R Soc B-Biol Sci, 2009, 276:1201–1209
41 Sloan D B, Triant D A, Wu M, et al. Cytonuclear interactions and relaxed selection accelerate sequence evolution in organelle ribosomes. Mol Biol Evol, 2013, 31:673–682
42 Pett W, Lavrov D V. Cytonuclear interactions in the evolution of animal mitochondrial tRNA metabolism. Genome Biol Evol, 2015, 7:2089–2101
43 Blier P U, Dufresne F, Burton R S. Natural selection and the evolution of mtDNA-encoded peptides:evidence for intergenomic co-adaptation.Trends Genets, 2001, 17:400–406
44 Sehrish T, Symonds V V, Soltis D E, et al. Cytonuclear coordination is not immediate upon allopolyploid formation in Tragopogon miscellus(Asteraceae)allopolyploids. PLoS ONE, 2015, 10:e0144339
45 Wang C G, Chang C T, Gu Y, et al. Cytoplasmic male sterility in plant(in Chinese). Chin J Cell Biol, 2005, 27:525–529[王春国,常彩涛,古瑜,等.植物细胞质雄性不育.中国细胞生物学杂志, 2005, 27:525–529]
46 Li P, Li XH, Zhang F, et al. Studies of cytoplasmic-nuclear interaction in CMS system(in Chinese). Shandong Agr Sci, 2008, 6:36–40[李鹏,李新华,张锋,等.细胞质雄性不育系统中的核质互作研究进展.山东农业科学, 2008, 6:36–40]
47 Fishman L, Willis J H. A cytonuclear incompatibility causes anther sterility in Mimulus hybrids. Evolution, 2006, 60:1372–1381
48 Horn R, Gupta K J, Colombo N. Mitochondrion role in molecular basis of cytoplasmic male sterility. Mitochondrion, 2014, 19:198–205
49 McCauley D E, Olson M S. Do recent findings in plant mitochondrial molecular and population genetics have implications for the study of gynodioecy and cytonuclear conflict? Evolution, 2008, 62:1013–1025
50 Chen L, Liu Y G. Male sterility and fertility restoration in crops. Annu Rev Plant Biol, 2014, 65:579–606
51 Kitazaki K, Arakawa T, Matsunaga M, et al. Post-translational mechanisms are associated with fertility restoration of cytoplasmic male sterility in sugar beet(Beta vulgaris). Plant J, 2015, 83:290–299
52 Chen Z, Zhao N, Li S, et al. Plant mitochondrial genome evolution and cytoplasmic male sterility. Critical Rev Plant Sci, 2017, 36:55–69
53 Bohra A, Jha U C, Adhimoolam P, et al. Cytoplasmic male sterility(CMS)in hybrid breeding in field crops. Plant Cell Rep, 2016, 35:967–993
54 Etterson J R, Keller S R, Galloway L F. Epistatic and cytonuclear interactions govern outbreeding depression in the autotetraploid Campanulastrum americanum. Evolution, 2007, 61:2671–2683
55 Ellison C K, Burton R S. Genotype-dependent variation of mitochondrial transcriptional profiles in interpopulation hybrids. Proc Natl Acad Sci USA, 2008, 105:15831–15836
56 Ellison C K, Burton R S. Cytonuclear conflict in interpopulation hybrids:The role of RNA polymerase in mtDNA transcription and replication. J Evol Biol, 2010, 23:528–538
57 Roux F, Mary-Huard T, Barillot E, et al. Cytonuclear interactions affect adaptive traits of the annual plant Arabidopsis thaliana in the field. Proc Natl Acad Sci USA, 2016, 113:3687–3692
58 Monsen K J, Honchak B M, Locke S E, et al. Cytonuclear disequilibrium in Chrysochus hybrids is not due to patterns of mate choice. J Heredity,2007, 98:325–330
59 Fields P D, McCauley D E, McAssey E V, et al. Patterns of cyto-nuclear linkage disequilibrium in Silene latifolia:Genomic heterogeneity and temporal stability. Heredity, 2014, 112:99–104
60 Gong L, Olson M, Wendel J F. Cytonuclear evolution of Rubisco in four allopolyploid lineages. Mol Biol Evol, 2014, 31:2624–2636
61 Hu Y, Wang X, Zhang X X, et al. Advancing phylogeography with chloroplast DNA markers(in Chinese). Biodiversity Sci, 2019, 27:219–234[胡颖,王茜,张新新,等.叶绿体DNA标记在谱系地理学中的应用研究进展.生物多样性, 2019, 27:219–234]
62 Renoult J P, Kjellberg F, Grout C, et al. Cyto-nuclear discordance in the phylogeny of Ficus section Galoglychia and host shifts in plantpollinator associations. BMC Evol Biol, 2009, 9:248
63 Baraket G, Ben Abdelkrim A, Mars M, et al. Cyto-nuclear discordance in the genetic relationships among Tunisian fig cultivars(Ficus carica L.):Evidence from non coding trnL–trnF and ITS regions of chloroplast and ribosomal DNAs. Sci Horticulturae, 2011, 130:203–210
64 Bruun-Lund S, Clement W L, Kjellberg F, et al. First plastid phylogenomic study reveals potential cyto-nuclear discordance in the evolutionary history of Ficus L.(Moraceae). Mol Phylogenets Evol, 2017, 109:93–104
65 Lee-Yaw J A, Grassa C J, Joly S, et al. An evaluation of alternative explanations for widespread cytonuclear discordance in annual sunflowers(Helianthus). New Phytol, 2019, 221:515–526
66 Huang D I, Hefer C A, Kolosova N, et al. Whole plastome sequencing reveals deep plastid divergence and cytonuclear discordance between closely related balsam poplars, Populus balsamifera and P. trichocarpa(Salicaceae). New Phytol, 2014, 204:693–703
67 Levsen N D, Tiffin P, Olson M S. Pleistocene speciation in the genus Populus(Salicaceae). Systatic Biol, 2012, 61:401–412
68 Freeland J R, Ciotir C, Wensink L, et al. Widespread cytonuclear discordance in narrow-leaved cattail(Typha angustifolia)does not explain the dominance of its invasive hybrid(Typha×glauca). Hydrobiologia, 2017, 792:53–65
69 Pagès M, Bazin E, Galan M, et al. Cytonuclear discordance among Southeast Asian black rats(Rattus rattus complex). Mol Ecol, 2013, 22:1019–1034
70 Mendelson T C, Simons J N. AFLPs resolve cytonuclear discordance and increase resolution among barcheek darters(Percidae:Etheostoma:Catonotus). Mol Phylogenets Evol, 2006, 41:445–453
71 Eto K, Matsui M. Cytonuclear discordance and historical demography of two brown frogs, Rana tagoi and R. sakuraii(Amphibia:Ranidae). Mol Phylogenets Evol, 2014, 79:231–239
72 Roca A L, Georgiadis N, O’Brien S J. Cytonuclear genomic dissociation in African elephant species. Nat Genet, 2005, 37:96–100
73 Pereira R J, Martínez-Solano I, Buckley D. Hybridization during altitudinal range shifts:Nuclear introgression leads to extensive cyto-nuclear discordance in the fire salamander. Mol Ecol, 2016, 25:1551–1565
74 Hunter M E, Johnson N A, Smith B J, et al. Cytonuclear discordance in the Florida Everglades invasive Burmese python(Python bivittatu s)population reveals possible hybridization with the Indian python(P. molurus). Ecol Evol, 2018, 8:9034–9047
75 Echelle A A, Hackler J C, Lack J B, et al. Conservation genetics of the alligator snapping turtle:Cytonuclear evidence of range-wide bottleneck effects and unusually pronounced geographic structure. Conserv Genet, 2010, 11:1375–1387
76 Kindler E, Arlettaz R, Heckel G. Deep phylogeographic divergence and cytonuclear discordance in the grasshopper Oedaleus decorus. Mol Phylogenets Evol, 2012, 65:695–704
77 Lindell J, Méndez-de La Cruz F R, Murphy R W. Deep biogeographical history and cytonuclear discordance in the black-tailed brush lizard(Urosaurus nigricaudus)of Baja California. Biol J Linnean Soc, 2008, 94:89–104
78 Lee-Yaw J A, Jacobs C G C, Irwin D E. Individual performance in relation to cytonuclear discordance in a northern contact zone between longtoed salamander(Ambystoma macrodactylum)lineages. Mol Ecol, 2014, 23:4590–4602
79 Oswald K J, Grady J M, Quattro J M. Cytonuclear patterns of genetic diversity and the intricate evolutionary history of the inland silverside(Menidia beryllina). J Heredity, 2009, 100:526–532
80 Beck E A, Thompson A C, Sharbrough J, et al. Gene flow between Drosophila yakuba and Drosophila santomea in subunit V of cytochrome c oxidase:A potential case of cytonuclear cointrogression. Evolution, 2015, 69:1973–1986
81 Wolf J B. Cytonuclear interactions can favor the evolution of genomic imprinting. Evolution, 2009, 63:1364–1371
82 Barnard-Kubow K B, So N, Galloway L F. Cytonuclear incompatibility contributes to the early stages of speciation. Evolution, 2016, 70:2752–2766
83 Coyne JA, Orr HA. Speciation. Sunderland:Sinauer Associates, Inc., 2004
84 Sambatti J B M, Ortiz-Barrientos D, Baack E J, et al. Ecological selection maintains cytonuclear incompatibilities in hybridizing sunflowers. Ecol Lett, 2008, 11:1082–1091
85 Hu Y C, Zhang Q, Rao G Y, et al. Occurrence of plastids in the sperm cells of Caprifoliaceae:biparental plastid inheritance in angiosperms is unilaterally derived from maternal inheritance. Plant Cell Physiol, 2008, 49:958–968
86 Hu X S. Mating system as a barrier to gene flow. Evolution, 2015, 69:1158–1177
87 Hu X S, Zhang X X, Zhou W, et al. Mating system shifts a species’ range. Evolution, 2019, 73:158–174
88 Otto S P, Marks J C. Mating systems and the evolutionary transition between haploidy and diploidy. Biol J Linnean Soc, 1996, 57:197–218